title: 50d_ensheathing_glia_P2_J4

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_J3

status: Public on May 31 2021

type: SRA

city: Houston

first: Hongjie

last: Li

state: TX

address: one Baylor Plaza

country: USA

institute: Baylor College of Medicine

description:
single_cell
in house

library_source: transcriptomic

data_processing:
alignment (STAR 2.4.2a, ENCODE standard options, except --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --  outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04)
gene count (HTSeq-count 0.7.1, default options, except -m intersection-strict)
Genome_build: Dmel r6.10
Supplementary_files_format_and_content: adata_aging_glia.h5ad

molecule: polyA RNA

organism: Drosophila melanogaster

extract_protocol:
Smart-seq2
full-length cDNA

tag: genotype

value: GMR56F03-Gal4, GFP

tag: cell type

value: glia

tag: number of cells

tag: orn type


title: 50d_ensheathing_glia_P2_J2

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I5

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I9

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_J10

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_J21

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_J23

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I7

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_J17

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_J1

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_J18

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_J20

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I2

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_J11

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_J13

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_J16

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I3

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I20

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I6

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I24

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I21

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I1

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I4

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I19

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I18

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I23

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I16

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I15

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I22

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I17

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H9

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I10

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H8

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I14

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I8

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I13

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I12

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H2

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H22

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H6

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_I11

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H23

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H5

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H3

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H20

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H1

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H24

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H18

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H14

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H19

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H17

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H4

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H21

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H7

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H10

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G9

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H15

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H13

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G6

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H12

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G8

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G2

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G7

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G5

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G23

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G22

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G20

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G4

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G15

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G21

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G24

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G16

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G10

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G18

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G17

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G3

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F3

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G14

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G12

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F22

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F24

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F9

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G11

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G1

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H11

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F6

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F7

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G13

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F18

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F4

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F2

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F15

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F14

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F23

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F16

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F20

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F1

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E5

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E4

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E9

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E8

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F5

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F13

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F17

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E7

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_G19

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E24

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F21

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F11

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E22

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F10

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F8

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F12

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E20

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E19

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E21

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E16

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E23

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E18

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_F19

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E3

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E2

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E6

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E17

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E15

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E1

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E14

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E13

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E11

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E12

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_E10

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D9

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D8

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D4

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D6

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D24

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D3

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D5

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D21

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D22

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D23

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D17

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D18

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D14

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D13

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D15

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D11

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D7

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D12

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D1

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D10

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C7

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C6

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C8

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C5

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C4

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D16

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D2

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C9

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C2

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C24

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C23

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D20

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_D19

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C21

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C20

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C1

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C19

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C18

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C17

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C3

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C16

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C14

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C15

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C12

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C11

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C13

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B8

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B6

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B9

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B7

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C22

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B3

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B4

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B2

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B23

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B24

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B22

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B1

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B20

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B18

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B17

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B16

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B15

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B14

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_C10

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B12

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B13

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B11

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A9

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B5

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B10

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A5

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A4

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A6

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A7

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A2

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A24

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A20

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B19

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A21

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A23

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A1

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_B21

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A22

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_H16

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A8

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A3

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A10

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A11

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A18

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A15

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A17

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P7

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A19

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P9

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A16

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A12

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A13

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P6

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P8

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P4

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P5

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P3

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P24

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P2

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P23

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P21

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P19

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P20

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P22

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P18

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P1

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P16

description:
single_cell
in house


title: 50d_ensheathing_glia_P2_A14

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P17

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_O3

description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_O7

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P10

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_O5

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_P11

description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_O9

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_O4

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_O17

description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_O14

description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_O10

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_O13

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_N9

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_O6

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_N8

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_N6

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_N3

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_N4

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_N24

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_N7

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_N22

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_O15

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_N21

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_N13

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_N12

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_M8

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_M21

description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_M24

description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_M5

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_M22

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_M17

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_M16

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_M4

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_L9

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_L6

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_M2

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_M10

description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_M1

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_L5

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_L4

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_L2

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_M20

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_L12

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_K7

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_L13

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_L10

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_L11

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_K3

description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_L22

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_K21

description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_K20

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_K16

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_K17

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_K15

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_J4

description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_J20

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_J3

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_J2

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_J21

description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_J24

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_J16

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_I2

description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_I3

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_I4

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_I14

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_I19

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_H9

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_I9

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_H7

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_H8

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_H5

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_H2

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_H23

description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_H22

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_I7

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_H19

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_H3

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


title: 50d_ensheathing_glia_P1_G5

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_G6

description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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description:
single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


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single_cell
in house


title: 50d_ensheathing_glia_P1_E15

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_E18

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_E19

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_E17

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_E22

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_E12

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_E13

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_E6

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_E14

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D9

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D8

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_E11

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_E5

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_E10

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_E23

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D6

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D4

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D3

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D23

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D2

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D22

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D24

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D21

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_F10

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D5

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_H24

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D1

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D18

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D20

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D15

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D14

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D7

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D13

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D17

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C9

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C7

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C8

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D11

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C5

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D12

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C3

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C2

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C22

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C23

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C1

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D19

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C21

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C20

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C17

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D16

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C4

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C18

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C16

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C15

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_D10

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C19

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C10

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C12

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B9

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C14

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B8

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C13

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B3

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B6

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B5

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B4

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B7

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B24

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C24

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B23

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B22

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B20

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B21

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B1

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B19

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B17

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B16

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B13

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B18

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_C11

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B11

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B15

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B14

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A9

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A8

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B12

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B2

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A6

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A3

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A4

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A22

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A21

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A23

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A2

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A20

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A1

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A19

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A24

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A13

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A15

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A12

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A17

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A14

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A18

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A16

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_B10

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A10

description:
single_cell
in house


title: 50d_ensheathing_glia_P1_A5

description:
single_cell
in house


title: adult3

city: New York

first: Maija

last: Slaidina

state: NY

address: 540 1st ave

department: Skirball Institute

institute: New York University School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: dm6
Supplementary_files_format_and_content: raw seq files and gene-barcode matrices.
Supplementary_files_format_and_content: Seurat_objects.RData: Seurat objects.

molecule: total RNA

source_name: ovary

growth_protocol: Flies were raised on medium containing yeast, molasses and cornmeal, and kept at 25 oC. Adult females were fattened on yeast for 24-48 hours prior to dissections.

extract_protocol:
For each sample, 30-40 pairs of adult ovaries were dissected one by one in ice-cold DPBS, no calcium, no magnesium (Thermo Fisher Scientific #14190136). Abdomens were removed using forceps and parts of intestine and abdominal cuticle were removed. Using forceps and a dissection needle, we cut off the anterior tip of the ovary and transferred to a new well. Method B: For dissociation, anterior tips of ovaries we transferred to a 1.5 ml tube and were incubated in dissociation solution (0.25 mg/ml Type I Collagenase, 0.4 mg/ml elastase (Worthington Biochemical #LS002290) in Cell Dissociation Buffer (Thermo Fisher Scientific #13151014)) for 30 minutes with gentle rotation. The suspension was vigorously pipetted every 5 minutes during the dissociation to enhance the dissociation efficiency. Enzymatic dissociation was stopped by adding Schneider cell culture media with fetal bovine serum (S-FBS). Starting from this step, all plastic materials – pipet tips, tubes, filters – were coated with S-FBS. Cell suspension was filtered through a 70-micron filter (Miltenyi Biotec #130-095-823), and 30 micron filter (Miltenyi Biotec #130-041-407). Cell suspension was centrifuged for 5 minutes at 3500 rcf at 40C. Cells were resuspended in 0.04% ultrapure BSA (Thermo Fisher Scientific #AM2616) in DBPS.
10x Genomics Chromimum v3 kit

treatment_protocol: Samples 3, 4, 5 were generated using the Method B and 10x Genomics kit v3. All three samples were processed in parallel on the same day.

value: w; His2AV:GFP/+

tag: Sex

value: female

tag: age

value: 2-3 days

tag: tissue

value: anterior part of the ovary

tag: sample preparation protocol

value: protocol B


title: 50d_ensheathing_glia_P1_A7

description:
single_cell
in house


title: adult5


title: adult4


title: plus CdH1 mRNA

city: Beijing

first: Hong

middle: Yu

last: Zhang

address: Qinglongqiao Street

department: Research Institute of Forestry

country: China

institute: Chinese Academy of Forestry

description:
plus CdH1
mRNA

data_processing:
Raw reads were obtained using Illumina’s Pipeline (Version 1.5) following sequencing image analysis and base-calling
Potentially cleaved transcripts were identified by CleaveLand (version 3.0).
The high-quality reads were mapped to the genome sequence of P. trichocarpa using Tophat package (version 2.1.1)
The FPKMs were calculated using a protocol from Pertea et al. Nature Biotechnology, 2015
Genome_build: version 3.0
Supplementary_files_format_and_content: Tab-defined each excel files include FPKMs for each samples

organism: Populus deltoides

source_name: Leaf

growth_protocol: Stem cuttings of Populus deltoides were rooted and planted in plastic pots and irrigated with 50 mL modified Hoagland nutritional solution in the evening of every other day. After 8 weeks, 72 plants with similar height and growth performance were selected and cultivated in hydroponics using modified Hoagland nutritional solution which was refreshed every 2 days.

extract_protocol:
Total RNA was extracted in the leaves of poplars using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure with minor modifications. The quantity and purity (RIN number >7.0) of the extracted RNA were analyzed by Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and RNA 6000 Nano LabChip Kit (Agilent, CA, USA). Afterwards, the extracted RNA samples were treated with total RNA purification kit (TRK1001, LC Science, Houston, TX) to eliminate genomic DNA contamination.
For mRNA sequencing, the purified total RNA from each sample was reverse-transcribed to create the cDNA library according to the protocol of the RNA-sequencing sample preparation kit (Illumina, San Diego, USA). For small RNA sequencing, the extracted RNA was used to construct a small RNA library using TruSeq Small RNA Prep Kits (RS-200, Illumina, CA, USA). For degradome sequencing, equal amounts of the 9 RNA samples from poplar leaves treated with either 0 or 50 µM CdCl2 were mixed to form a pooled sample. About 150 ng of RNA with poly(A) was annealed and captured with biotinylated random primers. Then, the RNAs containing 5’-monophosphates were ligated to 5’ adaptor and transcribed to cDNAs
Total mRNA sequencing was performed on an Illumina Hiseq2000/2500 sequencer (Illumina, CA, USA).The single-end sequencing was performed on an Illumina Hiseq2500 sequencer (Illumina, CA, USA) at the LC Science (Hangzhou, China) following the vendor’s recommended protocol for  small RNA sequenceing and degradome sequencing.

treatment_protocol: After treated with 0 (low, L), 100 (middle, M), or 1500 (high, H) µM SO42- for 12 days, the plants were exposed to either 0 (-Cd) or 50 (+Cd) μM CdCl2 together with the S treatments for 21 additional days.

tag: strain

value: monilifera (Aiton) Eckenw

tag: developmental stage

tag: culture

value: sand culture + hydroponics


title: plus CdH3 mRNA

description:
plus CdH3
mRNA


title: adult2

extract_protocol:
For each sample, 30-40 pairs of adult ovaries were dissected one by one in ice-cold DPBS, no calcium, no magnesium (Thermo Fisher Scientific #14190136). Abdomens were removed using forceps and parts of intestine and abdominal cuticle were removed. Using forceps and a dissection needle, we cut off the anterior tip of the ovary and transferred to a new well. Method A: For dissociation, anterior tips of ovaries were incubated in dissociation solution (0.5% Type I Collagenase (Thermo Fisher Scientific #17018029), 1% Trypsin 1:250 (Thermo Fisher Scientific #27250018) in DPBS) for 15 minutes with gentle rotation. The suspension was vigorously pipetted multiple times during the dissociation to enhance the dissociation efficiency. Enzymatic dissociation was stopped by adding Schneider cell culture media (Fisher # 21720-001) with 10% fetal bovine serum (Invitrogen #10082-147) (S-FBS). Starting from this step, all plastic materials – pipet tips, tubes, filters – were coated with S-FBS. Cell suspension was filtered through a custom-made ~40-micron cell strainer. The strainer was built by securing nylon mesh (Component Supply #U-CMN-40) in a cap of a 0.2 ml PCR tube and cutting the bottom of the tube and the cap (Slaidina et al. 2020). Upon filtering, dissociated cells were purified by fluorescence activated cell sorting (FACS) using a 100-micron nozzle on Sony SY3200 Cell Sorter. Cell suspension was centrifuged for 5 minutes at 250 rcf at RT, and resuspended in S-FBS.
10x Genomics Chromimum v2 kit

treatment_protocol: Samples 1, 2 were generated using the Method A and 10xGenomics kit v2. They were processed on two independent days.

value: protocol A


title: plus CdL2 mRNA

description:
plus CdL2
mRNA


title: plus CdL1 mRNA

description:
plus CdL1
mRNA


title: plus CdH2 mRNA

description:
plus CdH2
mRNA


title: plus CdM2 mRNA

description:
plus CdM2
mRNA


title: plus CdM1 mRNA

description:
plus CdM1
mRNA


title: plus CdM3 mRNA

description:
plus CdM3
mRNA


title: plus CdL3 mRNA

description:
plus CdL3
mRNA


title: minus CdH2 mRNA

description:
minus CdH2
mRNA


title: minus CdH1 mRNA

description:
minus CdH1
mRNA


title: 50d_ensheathing_glia_P1_A11

description:
single_cell
in house


title: minus CdM1 mRNA

description:
minus CdM1
mRNA


title: minus CdL1 mRNA

description:
minus CdL1
mRNA


title: minus CdL3 mRNA

description:
minus CdL3
mRNA


title: minus CdM3 mRNA

description:
minus CdM3
mRNA


title: minus CdL2 mRNA

description:
minus CdL2
mRNA


title: Rag1-/-; Sal/Alt rep2

city: Denver

first: Rafeul

last: Alam

state: Colorado

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

library_source: genomic

data_processing:
(ATAC) in Rag-/- (illumina high-seq) samples  ATAC-seq reads were trimmed of adapters and poor sequence by skewer-0.2.2 (Jiang et al., 2014) and then quality control was assessed with fastqc-0.11.5 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Bam files were generated by mapping to the mm10 mouse genome with Bowtie2-2.3.2 (Langmead and Salzberg, 2012) with max fragment length set to    –X 2000. The resulting Bam files are filtered for ChrM, PCR duplicates and the ATAC-seq Blacklist from Encode (https://www.encode.org/files/ENCFF299EZH/@@download/ENCFF299EZH.bed.gz) using picardtools-2.12.1 (http://broadinstitute.github.io/picard/) and samtools1.5 (Li et al., 2009). Peaks were called for each sample using MACS-2.1.1 (Zhang et al., 2008) with -B --SPMR --nomodel --nolambda --call-summits options. A bed file of peak summits +/-200bp was generated using bedtools2-2.26.0 (Quinlan and Hall, 2010) slopbed tool and using bedops-2.4.14 (Neph et al., 2012) merged across samples to create a common reference peak list. A count table of the number of fragments intersecting each reference peak was then generated with Bedtools2 multiBamCov tool for each sample and imported into R-3.4.2 where differential peak calling was performed using EdgeR-3.20.9 (Robinson et al., 2010). Significant differential peaks were determined as those with relative peak fragment counts between different exposed ILC2 groups differing by >2 fold and padj<0.05. Peaks were annotated by Homer-4.8 (http://homer.ucsd.edu/homer/index.html) annotatePeaks.pl with nearest gene and genomic location.  Homer (findMotifsGenome.pl) was used to determine enriched motifs in the defined peaks of each data-set. Peaks were visualized with the genome using the Integrated Genome Viewer IGV-2.3.97.
(ATAC) in WT (illumina nova-seq) samples same as above but trimmed to 50bp
Genome_build: (ATAC) assembly: mm10
Supplementary_files_format_and_content: (ATAC) tab delimited raw counts file
(RNA-Seq) We trimmed and culled raw demultiplexed cDNA reads in FASTQ files using Cutadapt, trimming poly A tails and 5’ and 3’ ends with q < 20 and removing any reads shorter than 25 base pairs. We then aligned trimmed reads to the GRCm38 mouse genome with GSNAP, setting “max-mismatches=0.05” and accounting for both known Ensembl splice sites and SNPs.
(RNA-Seq) We quantified gene expression using HTSeq with “stranded=yes”, “mode=intersection-nonempty”, and “t=gene” and then summed the number of unique molecular identifiers (UMIs) for each gene across runs for each cell to obtain a UMI count matrix that we used for all downstream analysis.
Genome_build: (RNA-Seq) assembly: GRCm38
Supplementary_files_format_and_content: (RNA-Seq) "expressionMatrix" text files contain expression count tables that include all samples in the original fastq files. All sample names include the sequencing barcode (after the underscore)

molecule: genomic DNA

organism: Mus musculus

source_name: Lung

growth_protocol: After flow sorting cells were kept in RPMI1640@ 37°C in 5% CO2 incubator

extract_protocol:
50,000 viable cells were resuspended in 50ul lysis buffer (0.01% Digitonin, 0.1% NP-40, 0.1% Tween-20, 10mM Tris-HCl pH=7.4,10mM NaCl and 3mM MgCl2.) and incubated on ice for 3min. Lysis buffer was washed out by adding 1mL Resuspending buffer (0.1% Tween-20, 10mM Tris-HCl pH=7.4,10mM NaCl and 3mM MgCl2.) and invert tubes for 3 times. Nuclei were centrifuged at 500 x g for 10 min at 4˚C. All supernatant was carefully aspirated. Transposase reaction was performed by Nextera DNA Library Preparation kit from Illumina (San Diego, CA, USA.) Transposed DNA was isolated by MiniElute PCR Purification Kit from Qiagen(Valencia, CA, USA).
Libraries were made by PCR. Real-time PCR was performed to determine PCR cycle number by calculating one-third of maximum fluorescent intensity. Primers are listed on Buenrostro et al. (2013) and synthesized by Integrated DNA technologies (Coralville, IA, USA) All libraries were sequenced using 2x50 bps reads on Hiseq 2500 from Illumina (San Diego, CA, USA.)

tag: treatment

value: Saline (Sal) sensitized and Alt challenged

value: Lung ILCs:Flow sorted CD45+NK1.1-CD25+ICOS+ cells


title: Rag1-/-; Sal/Alt rep3


title: Rag1-/-; Sal/- rep2

value: Saline (Sal) sensitized and no recall challenge


title: scRNA-seq for alternaria challenge experiment

value: 1A:Wk6 before Alternaria (Alt) recall challenge;  1B:Wk7 after recall;  2A:Saline, Wk6 before recall;  2B:Saline, Wk7 ater recall


title: Rag1-/-; Sal/- rep3


title: Rag1-/-; Sal/- rep1


title: Rag1-/-; Alt/Alt rep3

value: Alternaria (Alt) sensitized and Alt challenged


title: minus CdM2 mRNA

description:
minus CdM2
mRNA


title: Rag1-/-; Alt/Alt rep2


title: minus CdH3 mRNA

description:
minus CdH3
mRNA


title: Rag1-/-; Alt/Alt rep1


title: Rag1-/-; Alt/- rep2

value: Alternaria (Alt) sensitized and no recall challenge


title: Rag1-/-; Alt/- rep1


title: ILC2_1

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
Illumina Casava was used for basecalling.
All libraries have been assessed for sufficient read quality (Phred score > 30) and potential contamination using the FastQC program. Identified adapter contamination has been removed using the programs trim_galore and cutadapt. Trimmed reads with a remaining length <30 nucleotides were discarded.
Resulting libraries were aligned to the mouse reference genome (GRCm38) using the RNA-seq aligner STAR with default parametrization. Reads aligned to annotated genes were quantified with the HTseq-count program using gene annotations from Ensembl release 81. The determined read counts served as input to DESeq2 for pairwise detection and quantification of differential gene expression. For DESeq2 parametrization we used a beta prior and disabled the Cook distance cutoff filtering.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: *.tab files: CSV format with raw read counts per gene; *.rpkm files: CSV format with RPKM normalized read counts per gene; DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes

source_name: Innate lymphoid cells 2 (1)

extract_protocol:
Lymph nodes were removed and meshed through a sieve. RNA was prepared from ILC subpopulations sorted by FACS. RNA was transcribed into cDNA and subjected to library preparation.
The cDNA and sequencing library was generated by using the SMART Seq v4 Ultra Low Input RNA Kit (Takara Bio) and the Nextera XT DNA Library Prep Kit, respectively.

value: Innate lymphoid cells

value: lymph node

tag: marker


title: ILC3_3

source_name: Innate lymphoid cells 3 (3)


title: ILC1_3

source_name: Innate lymphoid cells 1 (3)


title: LTi_3

source_name: Lymphoid tissue inducer cells (3)


title: LTi_1

source_name: Lymphoid tissue inducer cells (1)


title: LTi_2

source_name: Lymphoid tissue inducer cells (2)


title: ILC2_3

source_name: Innate lymphoid cells 2 (3)


title: ILC3_1

source_name: Innate lymphoid cells 3 (1)


title: FFD_2_6

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps University Marburg

data_processing:
de-multiplexed fastq files were tested with FastQC. Over-represented sequences and adapters were trimmed with the Qiagen CLC Workbench Software v. 10.0.1.
Reads were mapped with the Qiagen CLC Workbench Software v. 10.0.1., using the GRCm38 mouse reference genome using default mapping parameters
Mapped total reads were analysed with the R package DeSeq2 v. 1.22.2 in R version 3.5.1, and the contrast FFD (fiber free diet) vs. CD (conventional diet) was calculated
The DeSeq2 output, namely the contrast FFD (fiber free diet) vs. CD (conventional diet), is provided as excel file processed_results.xlsx
Genome_build: GRCm38
Supplementary_files_format_and_content: processed_results.xlsx, DeSeq2 contrast of FFD vs. CD

source_name: colonic epithelium

extract_protocol:
Epithelial cells were obtained from the colon and total RNA was isolated with the RNeasy Plus Micro Kit (Quiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice received CD or FFD for four weeks and were then treated with dextran sulphate sodium in the drinking water for five days.

value: RAG1 KO

value: colonic epithelium

tag: diet

value: FFD, without cellulose


title: FFD_2_5


title: FFD_2_4


title: ILC2_2

source_name: Innate lymphoid cells 2 (2)


title: ILC3_2

source_name: Innate lymphoid cells 3 (2)


title: ILC1_2

source_name: Innate lymphoid cells 1 (2)


title: FFD_2_3


title: Rag1-/-; Sal/Alt rep1


title: ILC1_1

source_name: Innate lymphoid cells 1 (1)


title: FFD_2_2


title: CD_1_5

value: CD, with cellulose


title: CD_1_2


title: DMV neuron nucleus 213

city: Charlottesville

first: John

middle: N

last: Campbell

state: VA

address: 485 MCCORMICK RD, GILMER HALL ROOM 229 PO BOX 400328

department: Biology

institute: University of Virginia

data_processing:
sequencing reads were demultiplexed using bcl2fastq and aligned to the GRCm38 mouse genome assembly using STAR (Dobin et al., 2013)
sequencing replicates were pooled and PCR duplicates and low-quality reads were removed by Picard (https://broadinstitute.github.io/picard).
Filtered reads were assigned to the annotated transcriptome and quantiﬁed using Drop-seq tools (https://github.com/broadinstitute/Drop-seq), allowing for intronic alignments.
Normalization and differential expression analysis were performed using EdgeR (Robinson et al., 2010).
For differential gene expression analysis, we only tested genes that were detected in at least two samples with log2CPM ≥ 2. Genes were considered signiﬁcant if they passed a fold change (FC) cutoff of log2FC ≥1 and a false discovery rate (FDR) cutoff of FDR ≤ 0.05.
Nuclei were clustered in Seurat v3 (Stuart, et al. 2019); nuclei with less than 1000 unique genes expressed or with more than 10% mitochondrial content were filtered out.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: nuclear RNA

source_name: dorsal motor nucleus of the vagus

extract_protocol:
The following morning, the RNAlater-preserved tissue samples were processed into single-nuclei suspensions according to the sNuc-Seq as previously described (Todd et al., 2020). Briefly, the pooled DMV tissue samples were dounce homogenized (Wheaton tissue grinders, catalog # 357538) and separated by density gradient centrifugation. Each pellet was then re-suspended in 0.5 ml sNuc-Seq resuspension buffer and filtered through a 20 μm mesh (Miltenyi Biotec pre-separation filters, catalog # 130-101-812) to remove clumped nuclei and larger debris. Nuclei were counterstained with two drops of NucBlue Live ReadyProbes Reagent (ThermoFisher Scientific catalog # R37605) per ml of nuclei. Nuclei were sorted by MoFlo Astrios EQ cell sorter (Harvard Bauer core facility), gating for NucBlue+/mCherry+ singlets and distributing them individually to wells of 96-well plates containing 5 μl per well of nuclei capture buffer (1% beta-mercaptoethanol in Qiagen Buffer TCL; catalog # 1031576). Each plate was loaded with single nuclei, one per well. Loaded plates were centrifuged for 5 min at 2,500 xg and 4degC to ensure nuclei reached the capture buffer and frozen at -80degC for up to 8 weeks until use.
Sample plates were transferred to an RNA-dedicated PCR cabinet, thawed quickly, and immediately purified with RNA-Clean XP (Beckman Coulter, catalog # A63987; 2.5:1 ratio of RNA-Clean XP to sample volume), eluting in 4μl Smart-seq2 buffer (2 μl Smart-seq2 cell lysis buffer, 1 μl 100 μM oligo-dT primer, and 1 μl 10 mM dNTP mix). cDNA was then generated and amplified as described in the Smart-Seq2 protocol, except that 22 PCR cycles were used for the amplification step. After the PCR step, 10 μl of each sample was transferred to new 96-well plates for subsequent processing. Amplified cDNA was purified with two rounds of SPRIselect (Beckman Coulter, catalog # B23318; 0.8:1 ratio of SPRIselect to sample volume), eluting in ultrapure water. cDNA concentration was measured by Qubit fluorometry in a microplate format, each well containing 2 μl of cDNA sample and 98 μl of Qubit working solution (ThermoFisher Scientific, catalog # Q32854). Qubit readings were collected with a fluorescence microplate reader (Molecular Devices SpectraMax M5; Harvard Medical School ICCB-Longwood core facility) and used to calculate DNA concentrations by comparing each sample’s Qubit reading to standards in a 50% dilution series (n=8 standards; range, 0.25 ng/μl to 0.01 ng/μl plus a negative control, 0.0 ng/μl). cDNA samples were then diluted to 0.15 ng/ μl with ultrapure water and processed into sequencing libraries with sample-specific Nextera indices and the Nextera DNA Sample Prep Kit and Nextera XT Index Kit v2 sets A-D (Illumina, catalog #s FC-131-1096, FC-131- 2001, FC-131-2002, FC-131-2003, FC-131-2004, respectively). Nextera XT was used at 1/4 reaction volumes but otherwise according to manufacturer’s instructions. Sequencing libraries were purified with two rounds of SPRIselect (0.8:1 ratio of SPRIselect to sample volume) and eluted in a single volume of ultrapure water. Library pool concentration was measured by Qubit according to the manufacturer’s instructions, sized using Agilent BioAnalyzer high sensitivity kit, and then diluted with ultrapure water to a size-corrected concentration of 2 nM. The diluted library pool was denatured and further diluted to 2 pM loading concentration according to Illumina NextSeq recommendations, then sequenced with a NextSeq 500 v2 75cycle sequencing kit (Illumina, catalog # FC-404-2005).
Smart-Seq2

treatment_protocol: 10 week old Chat-IRES-Cre male mice received a 100nL stereotaxic injection of AAV9-DIO-H2b-mCherry into their dorsal motor nucleus of the vagus (DMV).  Sixteen days later, they were removed from their home cage and rapidly decapitated in order to minimize stress related changes in gene expression. Brains were extracted quickly, chilled briefly in ice cold DMEM/F12 media, and then sectioned coronally at 1 mm intervals in a chilled stainless-steel brain matrix. The brain sections containing and neighboring the SCN were collected in ice-cold RNAlater (Qiagen catalog # 76106). Each section was imaged by a fluorescence stereoscope (Zeiss Discovery V8) in order to visualize fluorescently labeled cells in the DMV for dissection. Dissected tissue was pooled and placed into ice-cold RNAlater overnight in the dark at 4degC.

value: dorsal motor nucleus of the vagus

value: neuron


title: CD_1_1


title: DMV neuron nucleus 214


title: FFD_2_1


title: CD_1_3


title: DMV neuron nucleus 212


title: DMV neuron nucleus 211


title: DMV neuron nucleus 210


title: DMV neuron nucleus 209


title: DMV neuron nucleus 207


title: DMV neuron nucleus 205


title: DMV neuron nucleus 206


title: DMV neuron nucleus 204


title: DMV neuron nucleus 202


title: DMV neuron nucleus 208


title: DMV neuron nucleus 203


title: DMV neuron nucleus 200


title: DMV neuron nucleus 198


title: DMV neuron nucleus 195


title: DMV neuron nucleus 196


title: DMV neuron nucleus 199


title: DMV neuron nucleus 201


title: DMV neuron nucleus 191


title: DMV neuron nucleus 193


title: DMV neuron nucleus 192


title: CD_1_4


title: DMV neuron nucleus 190


title: DMV neuron nucleus 197


title: DMV neuron nucleus 189


title: DMV neuron nucleus 188


title: DMV neuron nucleus 187


title: DMV neuron nucleus 185


title: DMV neuron nucleus 182


title: DMV neuron nucleus 183


title: DMV neuron nucleus 181


title: DMV neuron nucleus 180


title: DMV neuron nucleus 186


title: DMV neuron nucleus 179


title: DMV neuron nucleus 174


title: DMV neuron nucleus 173


title: DMV neuron nucleus 178


title: DMV neuron nucleus 172


title: DMV neuron nucleus 175


title: DMV neuron nucleus 177


title: DMV neuron nucleus 176


title: DMV neuron nucleus 171


title: DMV neuron nucleus 166


title: DMV neuron nucleus 167


title: DMV neuron nucleus 168


title: DMV neuron nucleus 184


title: DMV neuron nucleus 161


title: DMV neuron nucleus 165


title: DMV neuron nucleus 163


title: DMV neuron nucleus 162


title: DMV neuron nucleus 159


title: DMV neuron nucleus 158


title: DMV neuron nucleus 157


title: DMV neuron nucleus 155


title: DMV neuron nucleus 153


title: DMV neuron nucleus 154


title: DMV neuron nucleus 152


title: DMV neuron nucleus 164


title: DMV neuron nucleus 156


title: DMV neuron nucleus 170


title: DMV neuron nucleus 144


title: DMV neuron nucleus 146


title: DMV neuron nucleus 142


title: DMV neuron nucleus 148


title: DMV neuron nucleus 160


title: DMV neuron nucleus 145


title: DMV neuron nucleus 140


title: DMV neuron nucleus 139


title: DMV neuron nucleus 136


title: DMV neuron nucleus 138


title: DMV neuron nucleus 137


title: DMV neuron nucleus 134


title: DMV neuron nucleus 141


title: DMV neuron nucleus 133


title: DMV neuron nucleus 135


title: DMV neuron nucleus 132


title: DMV neuron nucleus 150


title: DMV neuron nucleus 131


title: DMV neuron nucleus 130


title: DMV neuron nucleus 128


title: DMV neuron nucleus 169


title: DMV neuron nucleus 127


title: DMV neuron nucleus 149


title: DMV neuron nucleus 151


title: DMV neuron nucleus 125


title: DMV neuron nucleus 143


title: DMV neuron nucleus 126


title: DMV neuron nucleus 124


title: DMV neuron nucleus 123


title: DMV neuron nucleus 122


title: DMV neuron nucleus 116


title: DMV neuron nucleus 120


title: DMV neuron nucleus 118


title: DMV neuron nucleus 119


title: DMV neuron nucleus 121


title: DMV neuron nucleus 115


title: DMV neuron nucleus 112


title: DMV neuron nucleus 114


title: DMV neuron nucleus 111


title: DMV neuron nucleus 113


title: DMV neuron nucleus 110


title: DMV neuron nucleus 109


title: DMV neuron nucleus 108


title: DMV neuron nucleus 129


title: DMV neuron nucleus 107


title: DMV neuron nucleus 104


title: DMV neuron nucleus 105


title: DMV neuron nucleus 106


title: DMV neuron nucleus 103


title: DMV neuron nucleus 102


title: DMV neuron nucleus 117


title: DMV neuron nucleus 100


title: DMV neuron nucleus 101


title: DMV neuron nucleus 147


title: DMV neuron nucleus 97


title: DMV neuron nucleus 99


title: DMV neuron nucleus 98


title: DMV neuron nucleus 96


title: DMV neuron nucleus 95


title: DMV neuron nucleus 93


title: DMV neuron nucleus 90


title: DMV neuron nucleus 88


title: DMV neuron nucleus 91


title: DMV neuron nucleus 87


title: DMV neuron nucleus 92


title: DMV neuron nucleus 85


title: DMV neuron nucleus 86


title: DMV neuron nucleus 82


title: DMV neuron nucleus 84


title: DMV neuron nucleus 81


title: DMV neuron nucleus 80


title: DMV neuron nucleus 79


title: DMV neuron nucleus 78


title: DMV neuron nucleus 94


title: DMV neuron nucleus 77


title: DMV neuron nucleus 76


title: DMV neuron nucleus 75


title: DMV neuron nucleus 74


title: DMV neuron nucleus 89


title: DMV neuron nucleus 67


title: DMV neuron nucleus 72


title: DMV neuron nucleus 66


title: DMV neuron nucleus 73


title: DMV neuron nucleus 71


title: DMV neuron nucleus 69


title: DMV neuron nucleus 65


title: DMV neuron nucleus 83


title: DMV neuron nucleus 63


title: DMV neuron nucleus 60


title: DMV neuron nucleus 59


title: DMV neuron nucleus 62


title: DMV neuron nucleus 57


title: DMV neuron nucleus 56


title: DMV neuron nucleus 70


title: DMV neuron nucleus 68


title: DMV neuron nucleus 52


title: DMV neuron nucleus 53


title: DMV neuron nucleus 51


title: DMV neuron nucleus 55


title: DMV neuron nucleus 49


title: DMV neuron nucleus 64


title: DMV neuron nucleus 61


title: DMV neuron nucleus 40


title: DMV neuron nucleus 45


title: DMV neuron nucleus 46


title: DMV neuron nucleus 48


title: DMV neuron nucleus 35


title: DMV neuron nucleus 42


title: DMV neuron nucleus 39


title: DMV neuron nucleus 44


title: DMV neuron nucleus 54


title: DMV neuron nucleus 36


title: DMV neuron nucleus 43


title: DMV neuron nucleus 47


title: DMV neuron nucleus 31


title: DMV neuron nucleus 50


title: DMV neuron nucleus 29


title: DMV neuron nucleus 28


title: DMV neuron nucleus 27


title: DMV neuron nucleus 41


title: DMV neuron nucleus 58


title: DMV neuron nucleus 34


title: DMV neuron nucleus 37


title: DMV neuron nucleus 32


title: DMV neuron nucleus 33


title: DMV neuron nucleus 21


title: DMV neuron nucleus 30


title: DMV neuron nucleus 16


title: DMV neuron nucleus 25


title: DMV neuron nucleus 24


title: DMV neuron nucleus 14


title: DMV neuron nucleus 22


title: DMV neuron nucleus 26


title: DMV neuron nucleus 10


title: DMV neuron nucleus 20


title: DMV neuron nucleus 38


title: DMV neuron nucleus 5


title: DMV neuron nucleus 9


title: DMV neuron nucleus 23


title: DMV neuron nucleus 19


title: DMV neuron nucleus 17


title: DMV neuron nucleus 15


title: DMV neuron nucleus 1


title: DMV neuron nucleus 12


title: PCGF1_ERT2-Cre_Pcgf1Control_EB_rep2

city: Tsurumi-ku,Yokohama

first: Hiroki

last: Sugishita

state: Kanagawa

address: 1-7-22, Suehiro-cho

department: IMS

country: Japan

institute: RIKEN

description:
ERT2-Cre;Pcgf1f/f
PCGF1_ERT2-Cre_Pcgf1Control_EB.bw

data_processing:
Sequencing was performed with 75 bp single-end read by NextSeq500 (run by Kazusa DNA Research Institute) or 50bp single-end read by HiSeq1500 (run in RIKEN-IMS NGS facility).
The data were mapped onto UCSC-mm9 from illumina igenome. Generated sam format file combine to bam format file using samtools view (version 1.3.1). Then, PCR duplicate and multiple aligned reads are removed.
For bigwig generation, bam format files were processed by deeptools bamCoverage. The data of CpG island and TSS are derived from UCSC mm9.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: EB

growth_protocol: Embryonic stem cells (ESCs) were cultured with LIF (1U: Laboratory made), SU5402 (Altair corporation), PD184352 (Altair corporation) and CHIR99021 (Altair corporation) on MEF. For Embryoid Body (EB) formation, ESCs were cultured without LIF, SU5402, PD184352, CHIR99021 for 2 days on low attach culture dish. For epiblast stem cell (EpiSC) establishment, Embryoid Body (day2) are dispersed. And the cells were cultured on MEF with ActivinA (Peprotech), bFGF (Wako) and IWP-2 (Wako) on MEF in F12 medium (Gibco) 1%KSR (Gibco).

extract_protocol:
10^6-10^7 cells were cross-linking by 1% formaldehyde for 10 min at room temperature. Cross-linked cells were washed once with PBS, added swelling buffer (0.1% NP-40, 1 mM DTT in PBS) and chilled on ice for 10 minutes. After centrifuge, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1mM EDTA, 140 mM NaCl, 1%Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), and then were sonicated by using a BioRuptor sonicator (Diagenode). After sonication, DNA concentration is measured with Qubit 1x dsDNA HS Assay Kit (Thermo, cat. Q33230). On the other hand, protein A/G beads were prepared as washed twice with beads blocking buffer and suspended with beads blocking buffer with approximately 5 µg of antibody and incubated at 4ºC for more than 2 hours. Then, antibody attached beads were washed twice with beads blocking buffer and the chromatin samples were added to those antibody-attached-beads. After overnight incubation at 4ºC, chromatin samples bound beads were washed with RIPA for 6 times, RIPA high salt buffer(10 mM Tris-HCl pH8.0, 1mM EDTA, 500 mM NaCl, 1%Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) twice, LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) twice and TE twice. The chromatins were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1 % SDS) overnight at 65ºC and treated with RNase for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA samples were purified and used for further ChIP-qPCR or ChIP-seq.
ChIP-seq libraries were prepared by using NEBNext Ultra II FS DNA prep kit (NEB E7805) following manufacturer’s instruction.

tag: tamoxifen treatment

value: without 4-OHT

value: embryoid body

tag: antibody

value: PCGF1 (Laboratory made)

tag: replicate


title: PCGF1_ERT2-Cre_Pcgf1Control_EB_rep1

tag: genotype


title: DMV neuron nucleus 13

tag: cell type


title: DMV neuron nucleus 11


title: DMV neuron nucleus 8


title: DMV neuron nucleus 7


title: DMV neuron nucleus 6


title: DMV neuron nucleus 4


title: PLAC_seq_230238_H3K4me3_rep2

city: Lund

first: Mikael

last: Sigvardsson

address: Sölvegatan 19

country: Sweden

institute: Lund University

description: 230238_H3K4me3_FitHiChIP.interactions_FitHiC_Q0.05_MergeNearContacts.bed

data_processing:
Library strategy: PLAC-Seq
ATAC data was mapped to mm10 using Bowtie2 (Langmead & Salzberg, 2012; Langmead et al., 2009) with standard settings. Tag directories with reads mapped to the mitochondrial chromosome filtered out and UCSC BedGraph files normalized to 10M total mapped reads were created using the HOMER platform (Heinz et al, 2010) (makeTagDirectory, makeUCSCfile). BedGraph files were up-loaded to the UCSC-genome browser (Kent et al, 2002) for visualization. Abundance of ATAC-tags on defined peak positions was analyzed in HOMER using the annotatePeaks.pl command with normalization to 10M mapped reads. When used for differential binding analysis, annotatePeaks.pl command with the -noadj option was used followed by processing with edgeR. Reads from OMNI-ATAC data were trimmed using TrimGalore and mapped to mm10 (Gencode build GRCm38.p5) with Bowtie2 (v. 2.3.5) (Langmead & Salzberg, 2012). PCR duplicates were removed with Picard MarkDuplicates (v. 2.21.4) and files were further filtered for mapq score of 10 using Samtools (v. 1.9). BigWig files from the mapq score 10 filtered bam file was generated using bamCoverage (v.3.3.1) from the deepTools suite (Ramirez et al, 2016). Peak calling from the mapq10 filtered bam file was performed using the Kundaje lab ATAC-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL792NWO/) with MACS2 and IDR (irreproducible discovery rate) threshhold set to 0.05 and 0.1, respectively. Samtools was used to remove mitochondrial reads prior to peak calling. From the processed duplicate, the Optimal peak set was used for downstream analysis. Aditionally, Tag directories with reads mapped to the mitochondrial chromosome filtered out were created using the HOMER platform (v. 4.10; 4.11) (Heinz et al., 2010).
ChIP-seq: Reads were aligned to mouse reference genome mm10 using Bowtie2 (Langmead et al., 2009). If not indicated, further analyzes were performed using the HOMER package (Heinz et al., 2010). ChIP-peaks/regions from single samples ChIPs were identified using findPeaks.pl with the –style factor parameter for TF-peaks and –style histone for histone ChIPs. Identified peaks were normalized to input controls. When duplicate or more ChIPs  were  available, transcription factor peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”. Transcription factor peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package (Li QB, 2011) (Karmel A. 2015. homer-idr: Second pass updated) according to (https://sites.google.com/site/anshulkundaje/projects/idr). Motif enrichment analysis was performed with the findMotifsGenome.pl command of the HOMER package. Overlapping peaks between samples were identified using mergePeaks.pl (default parameters). Tag density plots and heat maps were created with annotatePeaks.pl (–hist or –hist & -ghist respectively), normalizing data to 10 million mapped reads per experiment, and visualized using Excel or by hierarchical clustering in Cluster3 (de Hoon et al, 2004) followed by Java Treeview (Saldanha, 2004). UCSC genome browser was used for visualization of BedGraph files (Kent et al., 2002). To create Violin-plots, peak positions were annotated using annotatePeaks.pl normalizing data to 10 million mapped reads per experiment. Prior to log transformation a small number was added to all normalized read values and Log2 values were exported to Prism for visualization and statistics.  For H3K27me3 ChIP, reads were trimmed with Trim-galore in paired-end mode (Babraham Bioinformatics) and mapped to the mm10 genome (Gencode version GRCm38) with Bowtie2 (2.3.5) (Langmead & Salzberg, 2012). Bam-files were generated using Samtools v.1.9 (Li et al, 2009) and PCR duplicates were removed with Picard MarkDuplicates (2.21.4) followed by a filtration of read för MAPQ-score ³ 10 using Samtools. BigWig files from the MAPQ-score filtered bam files were generated using bamCoverage (v.3.3.1) from the deepTools suite (Ramirez et al., 2016). Tag directories as above and genomic regions enriched for H3K27me3 signal were identified using findPeaks.pl (Heinz et al., 2010) with the –style histone parameter and normalized to their respective inputs.
Cut and Run Reads were trimmed with Trim-galore in paired-end mode (Babraham Bioinformatics) and mapped to the mm10 genome (Gencode version GRCm38) with Bowtie2 (2.3.5) (Langmead & Salzberg, 2012). Bam-files were generated using Samtools v.1.9 (Li et al., 2009) and PCR duplicates were removed with Picard MarkDuplicates (2.21.4) followed by a filtration of read för MAPQ-score ³ 10 using Samtools. Peaks were called from the filtered bam-file using MACS2 callpeak (Zhang et al, 2008) with default settings, using the Normal IgG as the control. Subsequently, the bam-files were used to generate HOMER Tag directories with makeTagDirectory (Heinz et al., 2010) .
PLAC-seq: To maximize interaction calling, fastq-files containing both read 1 and read 2 with their counter parts from the replicates were combined for a total of 460M (230-238)  Trim Galore trimmed paired-end reads per sample. Reads were trimmed in pair-end mode with Trim Galore (0.6.4)(--paired --fastqc --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 3 --three_prime_clip_R2 3) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed paired fastq reads were preprocessed through the HiC-Pro pipeline (v2.11.1) (Servant et al, 2015), using Bowtie2 (2.3.5) (Langmead & Salzberg, 2012; Langmead et al, 2009) for alignment against mm10 (GRCm38) reference genome, assigning mapped reads to a mm10 MboI restriction map followed by removal of PCR duplicates with Picard tools MarkDuplicates (2.21.4) (https://broadinstitute.github.io/picard/) and subsequently the generation of a list of valid interaction read pairs. Single-end sequenced fastq files from the 230-238 H3K4me3 ChIP-seq were used as inputs for the generation of interaction anchor points. Bias corrected significant interactions (FDR ≤ 0.05) between anchor points and other anchor points/non-anchor-points  (peak-to-all) were identified for the 230-238 H3K4me3 PLAC-sequence data with the FitHiChIP pipeline (v. 6.0) (Bhattacharyya et al, 2019) using the HiC-Pro valid pairs and identified ChIP-anchors as input files with following settings: GCSize (size of the window upstream and downstream the restriction site used to calculate the GC content)=200, MappSize (size of the window upstream and downstream the restriction site used to calculate the mappability)=500, BINSIZE (Size of the bins in bases, for detecting the interactions)=5000, LowDistThr (Lower distance threshold of interaction between two segments)=10000, UppDistThr (Upper distance threshold of interaction between two segments)=3000000, BiasCorrection with Coverage specific bias. FitHiChIP was used to merge adjacent loops. Interactions were uploaded and visualized on the WashU EpiGenome. Interaction anchor points were annotated against mm10 with a custom bash script utilizing the HOMER annotation database (annotatePeaks.pl). Annotated interactions files were further processed in R as follows: We defined anchor-points spanning one bin size (5 kb) surrounding TSS as a TSS-annotated bin. Interactions lacking a TSS in either anchor-point or interactions containing a TSS in both anchor-points were filtered out. After this filtration step 40179 (57.5%) TSS-distal interactions remained. The distally located anchor-points were subsequently assigned to their connected TSS. Since our PLAC-seq analysis is limited to a 5 kb resolution, we used a 10 kb cutoff (distance from TSS to the middle of a 5 kb bin) for identification of distal interactions. Contrasting this, ATAC-peaks located within a 7.5 kb window from the TSS were proximity annotated to the closest gene.
Genome_build: mm10
Supplementary_files_format_and_content: txt-files describing ChIP-and-ATAC-seq data anno

source_name: 230-238 murine Progenitor B celline

growth_protocol: Fetal liver cells were purified from wild-type, Ebf1 deficient, E2A deficient or Pax5 deficient fetuses, and expanded on OP9 stromal cells in Opti-MEM supplemented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol, 10ng/ml KIT ligand, 10ng/ml Fms-like tyrosine kinase 3 ligand, and 10ng/ml Interleukin-7. Murine pre-B cell line, 230-238 cells were maintained in RPMI1640 supplimented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, and 50μM β-mercaptoethanol. Infection: Retronectin coated 24-well plates were pre-inkubated with 500ul viral supernatant. Cells were harvested,  resuspended 500ul media and added to 500μl of virus supernatant. Polybrene was added to supernatant at concentration of 0.5μg/ml. Spin-infection was performed at 1800xg, for 90min at 32°C.

extract_protocol:
ATAC-seq: Cells were washed in ice cold PBS prior to Assay for Transposase Accessible Chromatin (ATAC-seq) as described in (Buenrostro et al, 2013) or for 230-238 cells as described in (Corces et al, 2017). Cells for transcriptions factor ChIP were fixed at RT in 1 mg/ml DSG (ThermoFisher Scientific) in PBS for 30 min followed by additional 10 min after addition of formaldehyde up to 1%. Cells for histone modification ChIP were fixed in 1% formaldehyde for 10 min at RT. The reactions were quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed in PBS. Nuclei were isolated by 10 min incubation in Nuclei Isolation buffer (50 mM Tris-pH 8.0, 60 mM KCl, 0.5% NP40) + protease inhibitor cocktail (PIC) (Roche) on ice. Pelleted nuclei were dissolved in Lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8)) + PIC and sonicated on a Bioruptor (Diagenode). Sonication was followed by pelleting of debris and the supernatant was transferred to new tube and chromatin was diluted 5X in Dilution Buffer (1% Triton, 2mM EDTA, 150 mM NaCl, 20 mM Tris-HCl (pH 8) + PIC) for transcription factor ChIP and in HBSS (Lonza, Verviersa, Belgium) +PIC and 2X RIPA buffer (20 mM Tris–HCl, pH 7.5, 2 mM EDTA, 2% Triton X-100, 0.1% SDS, 0.2% Sodiumdeoxycholate, 200 mM NaCl + PIC) for histone modification ChIPs. Cut&Run was performed similar to (Skene et al, 2018) with minor changes using one million FL Wt or Ebf1-/- cells per sample and 2 ug of the following antibodies: rabbit polyclonal aH3K27ac (Abcam, ab4729, Lot GR3231937-1), and polyclonal Normal Rabbit IgG (Millipore 12-370, Lot 3109265). PLAC-seq was carried out similar to previously reported (Okuyama et al, 2019) with minor modifications. Cells that had been cross-linked with 1% formaldehyde for 5 min (Covaris sonication) or 10 min (Bioruptor sonication) were thawed on ice for 5 min, re-suspended in ice cold lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP-40, 1x Roche protease inhibitors – 11697498001 (PIC), and subsequently processed for PLAC-seq.
ChIP-Seq: Libraries were constructed using Illumina Truseq Nano DNA library preparation kit or by addition of Bioo-scientiffic Nextflex barcodes following standard procedures. Libraries were run on the Illumina NexSeq500. Cut&Run libraries for sequencing was essentially prepared as previously descried for ChIP-sequencing (Okuyama et al., 2019) with two modifications: 1) Prior to adapter ligation all purification steps were carried out using Zymo Research ChIP DNA Clean and Concentrator to not lose fragments smaller than 100 nt and 2) size-selection with Ampure XP beads was performed after adapter ligation with a targeted mean fragment size of 150-300 bp. Libraries were paired-end sequenced on an Illumina Nextseq 500 (read-length: 2 × 38 bp).   ATAC-seq library preparation was as described in (Buenrostro et al, 2013) or for 230-238 cells as described in (Corces et al, 2017).   PLAC-seq was carried out similar to previously reported (Okuyama et al, 2019) with minor modifications. NEXTflex DNA barcode ligation  (BIOO scientific) was performed using the Fast-link ligation kit (Epicenter, LK0750H). PLAC-seq libraries were subject to 2X 75 cycles of paired-end sequencing on a NextSeq500.

treatment_protocol:
Cultured in RPMI1640 + UltraGlutamine +10% FBS, 20mM HEPES, 50ug/ml Gentamicin and 50uM β-ME.
FL-Ebf1-KO cells transduced with pMiG-Ebf1-ER constructs were treated with 1mM of Tamoxifen (4OHT) for indicated times prior to processing by ATAC-seq.

tag: strain background

value: cell line

tag: genotype / variation

value: Abelson transformed Progenitor B cell-line

tag: chip (antibody)

value: Rabbit anti H3K4-Me3 polyclonal (Millipore, 07-473)


title: DMV neuron nucleus 2


title: PCGF1_ERT2-Cre_Pcgf1Control_ES_rep2

description:
ERT2-Cre;Pcgf1f/f
PCGF1_ERT2-Cre_Pcgf1Control_ES.bw

source_name: ES

value: embryonic stem cell


title: PLAC_seq_230238_H3K4me3_rep1


title: DMV neuron nucleus 3


title: DMV neuron nucleus 18


title: CutNRun_seq_FL_Ebf1KO_a_H3K27Ac

description:
Annotate-WT_EKO_histone_ChIP_andH3K27Ac_CnR_on_ATAC-peaks_WT-enriched-genes-OpenWTandEKO-NOT-Promoter.txt
Annotate-WT_EKO_histone_ChIP_andH3K27Ac_CnR_on_ATAC-peaks_WT-enriched-genes-OpenWTandEKO-Promoter.txt
Annotate-WT_EKO_histone_ChIP_andH3K27Ac_CnR_on_ATAC-peaks_WT-enriched-genes-OpenWTnotEKO-NOT-Promoter.txt
Annotate-WT_EKO_histone_ChIP_andH3K27Ac_CnR_on_ATAC-peaks_WT-enriched-genes-OpenWTnotEKO-Promoter.txt

data_processing:
Library strategy: CUT&RUN
ATAC data was mapped to mm10 using Bowtie2 (Langmead & Salzberg, 2012; Langmead et al., 2009) with standard settings. Tag directories with reads mapped to the mitochondrial chromosome filtered out and UCSC BedGraph files normalized to 10M total mapped reads were created using the HOMER platform (Heinz et al, 2010) (makeTagDirectory, makeUCSCfile). BedGraph files were up-loaded to the UCSC-genome browser (Kent et al, 2002) for visualization. Abundance of ATAC-tags on defined peak positions was analyzed in HOMER using the annotatePeaks.pl command with normalization to 10M mapped reads. When used for differential binding analysis, annotatePeaks.pl command with the -noadj option was used followed by processing with edgeR. Reads from OMNI-ATAC data were trimmed using TrimGalore and mapped to mm10 (Gencode build GRCm38.p5) with Bowtie2 (v. 2.3.5) (Langmead & Salzberg, 2012). PCR duplicates were removed with Picard MarkDuplicates (v. 2.21.4) and files were further filtered for mapq score of 10 using Samtools (v. 1.9). BigWig files from the mapq score 10 filtered bam file was generated using bamCoverage (v.3.3.1) from the deepTools suite (Ramirez et al, 2016). Peak calling from the mapq10 filtered bam file was performed using the Kundaje lab ATAC-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL792NWO/) with MACS2 and IDR (irreproducible discovery rate) threshhold set to 0.05 and 0.1, respectively. Samtools was used to remove mitochondrial reads prior to peak calling. From the processed duplicate, the Optimal peak set was used for downstream analysis. Aditionally, Tag directories with reads mapped to the mitochondrial chromosome filtered out were created using the HOMER platform (v. 4.10; 4.11) (Heinz et al., 2010).
ChIP-seq: Reads were aligned to mouse reference genome mm10 using Bowtie2 (Langmead et al., 2009). If not indicated, further analyzes were performed using the HOMER package (Heinz et al., 2010). ChIP-peaks/regions from single samples ChIPs were identified using findPeaks.pl with the –style factor parameter for TF-peaks and –style histone for histone ChIPs. Identified peaks were normalized to input controls. When duplicate or more ChIPs  were  available, transcription factor peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”. Transcription factor peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package (Li QB, 2011) (Karmel A. 2015. homer-idr: Second pass updated) according to (https://sites.google.com/site/anshulkundaje/projects/idr). Motif enrichment analysis was performed with the findMotifsGenome.pl command of the HOMER package. Overlapping peaks between samples were identified using mergePeaks.pl (default parameters). Tag density plots and heat maps were created with annotatePeaks.pl (–hist or –hist & -ghist respectively), normalizing data to 10 million mapped reads per experiment, and visualized using Excel or by hierarchical clustering in Cluster3 (de Hoon et al, 2004) followed by Java Treeview (Saldanha, 2004). UCSC genome browser was used for visualization of BedGraph files (Kent et al., 2002). To create Violin-plots, peak positions were annotated using annotatePeaks.pl normalizing data to 10 million mapped reads per experiment. Prior to log transformation a small number was added to all normalized read values and Log2 values were exported to Prism for visualization and statistics.  For H3K27me3 ChIP, reads were trimmed with Trim-galore in paired-end mode (Babraham Bioinformatics) and mapped to the mm10 genome (Gencode version GRCm38) with Bowtie2 (2.3.5) (Langmead & Salzberg, 2012). Bam-files were generated using Samtools v.1.9 (Li et al, 2009) and PCR duplicates were removed with Picard MarkDuplicates (2.21.4) followed by a filtration of read för MAPQ-score ³ 10 using Samtools. BigWig files from the MAPQ-score filtered bam files were generated using bamCoverage (v.3.3.1) from the deepTools suite (Ramirez et al., 2016). Tag directories as above and genomic regions enriched for H3K27me3 signal were identified using findPeaks.pl (Heinz et al., 2010) with the –style histone parameter and normalized to their respective inputs.
Cut and Run Reads were trimmed with Trim-galore in paired-end mode (Babraham Bioinformatics) and mapped to the mm10 genome (Gencode version GRCm38) with Bowtie2 (2.3.5) (Langmead & Salzberg, 2012). Bam-files were generated using Samtools v.1.9 (Li et al., 2009) and PCR duplicates were removed with Picard MarkDuplicates (2.21.4) followed by a filtration of read för MAPQ-score ³ 10 using Samtools. Peaks were called from the filtered bam-file using MACS2 callpeak (Zhang et al, 2008) with default settings, using the Normal IgG as the control. Subsequently, the bam-files were used to generate HOMER Tag directories with makeTagDirectory (Heinz et al., 2010) .
PLAC-seq: To maximize interaction calling, fastq-files containing both read 1 and read 2 with their counter parts from the replicates were combined for a total of 460M (230-238)  Trim Galore trimmed paired-end reads per sample. Reads were trimmed in pair-end mode with Trim Galore (0.6.4)(--paired --fastqc --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 3 --three_prime_clip_R2 3) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed paired fastq reads were preprocessed through the HiC-Pro pipeline (v2.11.1) (Servant et al, 2015), using Bowtie2 (2.3.5) (Langmead & Salzberg, 2012; Langmead et al, 2009) for alignment against mm10 (GRCm38) reference genome, assigning mapped reads to a mm10 MboI restriction map followed by removal of PCR duplicates with Picard tools MarkDuplicates (2.21.4) (https://broadinstitute.github.io/picard/) and subsequently the generation of a list of valid interaction read pairs. Single-end sequenced fastq files from the 230-238 H3K4me3 ChIP-seq were used as inputs for the generation of interaction anchor points. Bias corrected significant interactions (FDR ≤ 0.05) between anchor points and other anchor points/non-anchor-points  (peak-to-all) were identified for the 230-238 H3K4me3 PLAC-sequence data with the FitHiChIP pipeline (v. 6.0) (Bhattacharyya et al, 2019) using the HiC-Pro valid pairs and identified ChIP-anchors as input files with following settings: GCSize (size of the window upstream and downstream the restriction site used to calculate the GC content)=200, MappSize (size of the window upstream and downstream the restriction site used to calculate the mappability)=500, BINSIZE (Size of the bins in bases, for detecting the interactions)=5000, LowDistThr (Lower distance threshold of interaction between two segments)=10000, UppDistThr (Upper distance threshold of interaction between two segments)=3000000, BiasCorrection with Coverage specific bias. FitHiChIP was used to merge adjacent loops. Interactions were uploaded and visualized on the WashU EpiGenome. Interaction anchor points were annotated against mm10 with a custom bash script utilizing the HOMER annotation database (annotatePeaks.pl). Annotated interactions files were further processed in R as follows: We defined anchor-points spanning one bin size (5 kb) surrounding TSS as a TSS-annotated bin. Interactions lacking a TSS in either anchor-point or interactions containing a TSS in both anchor-points were filtered out. After this filtration step 40179 (57.5%) TSS-distal interactions remained. The distally located anchor-points were subsequently assigned to their connected TSS. Since our PLAC-seq analysis is limited to a 5 kb resolution, we used a 10 kb cutoff (distance from TSS to the middle of a 5 kb bin) for identification of distal interactions. Contrasting this, ATAC-peaks located within a 7.5 kb window from the TSS were proximity annotated to the closest gene.
Genome_build: mm10
Supplementary_files_format_and_content: txt-files describing ChIP-and-ATAC-seq data annot

source_name: Ebf1-KO Fetal liver

treatment_protocol:
Cultured in Optimem +10% FBS, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol FL, KL, IL7 on OP9
FL-Ebf1-KO cells transduced with pMiG-Ebf1-ER constructs were treated with 1mM of Tamoxifen (4OHT) for indicated times prior to processing by ATAC-seq.

value: ProB

value: Rabbit anti H3K27ac polyclonal IgG [ab4729, Abcam]