title: 1001703005_G7

description: mRNA + vRNA


title: 1001703005_G9

status: Public on Feb 25 2020

type: SRA

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

description: mRNA + vRNA

library_source: transcriptomic

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

molecule: total RNA

organism: Homo sapiens

source_name: U87 cells

extract_protocol:
no extraction
viscRNA-Seq
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

treatment_protocol: Infection with VEEV TC-83

tag: moi

tag: hours post infection

tag: plate

tag: well


title: 1001703005_G5

description: mRNA + vRNA


title: 1001703005_H4

description: mRNA + vRNA


title: 1001703005_G6

description: mRNA + vRNA


title: 1001703005_G4

description: mRNA + vRNA


title: 1001703005_H3

description: mRNA + vRNA


title: 1001703005_H24

description: mRNA + vRNA


title: 1001703005_H23

description: mRNA + vRNA


title: 1001703005_G3

description: mRNA + vRNA


title: 1001703005_G24

description: mRNA + vRNA


title: 1001703005_G23

description: mRNA + vRNA


title: 1001703005_G22

description: mRNA + vRNA


title: 1001703005_G18

description: mRNA + vRNA


title: 1001703005_G2

description: mRNA + vRNA


title: 1001703005_G20

description: mRNA + vRNA


title: 1001703005_G21

description: mRNA + vRNA


title: 1001703005_G19

description: mRNA + vRNA


title: 1001703005_H11

description: mRNA + vRNA


title: 1001703005_G16

description: mRNA + vRNA


title: 1001703005_G15

description: mRNA + vRNA


title: 1001703005_G11

description: mRNA + vRNA


title: 1001703005_G13

description: mRNA + vRNA


title: 1001703005_G12

description: mRNA + vRNA


title: 1001703005_G10

description: mRNA + vRNA


title: 1001703005_G1

description: mRNA + vRNA


title: 1001703005_F9

description: mRNA + vRNA


title: 1001703005_F8

description: mRNA + vRNA


title: 1001703005_F5

description: mRNA + vRNA


title: 1001703005_F24

description: mRNA + vRNA


title: 1001703005_F6

description: mRNA + vRNA


title: 1001703005_F3

description: mRNA + vRNA


title: 1001703005_F7

description: mRNA + vRNA


title: 1001703005_F22

description: mRNA + vRNA


title: 1001703005_F23

description: mRNA + vRNA


title: 1001703005_F20

description: mRNA + vRNA


title: 1001703005_F2

description: mRNA + vRNA


title: 1001703005_F19

description: mRNA + vRNA


title: 1001703005_F21

description: mRNA + vRNA


title: 1001703005_F18

description: mRNA + vRNA


title: 1001703005_F17

description: mRNA + vRNA


title: 1001703005_F14

description: mRNA + vRNA


title: 1001703005_G17

description: mRNA + vRNA


title: 1001703005_F16

description: mRNA + vRNA


title: 1001703005_F15

description: mRNA + vRNA


title: 1001703005_F13

description: mRNA + vRNA


title: 1001703005_G14

description: mRNA + vRNA


title: 1001703005_F12

description: mRNA + vRNA


title: 1001703005_F1

description: mRNA + vRNA


title: 1001703005_F4

description: mRNA + vRNA


title: 1001703005_E9

description: mRNA + vRNA


title: 1001703005_E6

description: mRNA + vRNA


title: 1001703005_E8

description: mRNA + vRNA


title: 1001703005_E7

description: mRNA + vRNA


title: 1001703005_E24

description: mRNA + vRNA


title: 1001703005_E4

description: mRNA + vRNA


title: 1001703005_E3

description: mRNA + vRNA


title: 1001703005_E21

description: mRNA + vRNA


title: 1001703005_E2

description: mRNA + vRNA


title: 1001703005_E22

description: mRNA + vRNA


title: 1001703005_E20

description: mRNA + vRNA


title: 1001703005_E5

description: mRNA + vRNA


title: 1001703005_E19

description: mRNA + vRNA


title: 1001703005_E15

description: mRNA + vRNA


title: 1001703005_E17

description: mRNA + vRNA


title: 1001703005_E11

description: mRNA + vRNA


title: 1001703005_E13

description: mRNA + vRNA


title: 1001703005_E18

description: mRNA + vRNA


title: 1001703005_E16

description: mRNA + vRNA


title: 1001703005_E14

description: mRNA + vRNA


title: 1001703005_F11

description: mRNA + vRNA


title: 1001703005_E10

description: mRNA + vRNA


title: 1001703005_E12

description: mRNA + vRNA


title: 1001703005_E1

description: mRNA + vRNA


title: 1001703005_F10

description: mRNA + vRNA


title: 1001703005_D9

description: mRNA + vRNA


title: 1001703005_D8

description: mRNA + vRNA


title: 1001703005_D6

description: mRNA + vRNA


title: 1001703005_E23

description: mRNA + vRNA


title: 1001703005_D7

description: mRNA + vRNA


title: 1001703005_D4

description: mRNA + vRNA


title: 1001703005_D24

description: mRNA + vRNA


title: 1001703005_D3

description: mRNA + vRNA


title: 1001703005_D22

description: mRNA + vRNA


title: 1001703005_D23

description: mRNA + vRNA


title: 1001703005_D5

description: mRNA + vRNA


title: 1001703005_D20

description: mRNA + vRNA


title: 1001703005_D21

description: mRNA + vRNA


title: 1001703005_D19

description: mRNA + vRNA


title: 1001703005_D2

description: mRNA + vRNA


title: 1001703005_D17

description: mRNA + vRNA


title: 1001703005_D16

description: mRNA + vRNA


title: 1001703005_D18

description: mRNA + vRNA


title: 1001703005_D15

description: mRNA + vRNA


title: 1001703005_D13

description: mRNA + vRNA


title: 1001703005_D14

description: mRNA + vRNA


title: 1001703005_D1

description: mRNA + vRNA


title: 1001703005_C9

description: mRNA + vRNA


title: 1001703005_D10

description: mRNA + vRNA


title: 1001703005_D12

description: mRNA + vRNA


title: 1001703005_C8

description: mRNA + vRNA


title: 1001703005_D11

description: mRNA + vRNA


title: 1001703005_C5

description: mRNA + vRNA


title: 1001703005_C7

description: mRNA + vRNA


title: 1001703005_C6

description: mRNA + vRNA


title: 1001703005_C24

description: mRNA + vRNA


title: 1001703005_C3

description: mRNA + vRNA


title: 1001703005_C23

description: mRNA + vRNA


title: 1001703005_C22

description: mRNA + vRNA


title: 1001703005_C20

description: mRNA + vRNA


title: 1001703005_C19

description: mRNA + vRNA


title: 1001703005_C2

description: mRNA + vRNA


title: 1001703005_C14

description: mRNA + vRNA


title: 1001703005_C15

description: mRNA + vRNA


title: 1001703005_C17

description: mRNA + vRNA


title: 1001703005_C18

description: mRNA + vRNA


title: 1001703005_C13

description: mRNA + vRNA


title: 1001703005_C16

description: mRNA + vRNA


title: 1001703005_C12

description: mRNA + vRNA


title: 1001703005_C10

description: mRNA + vRNA


title: 1001703005_C1

description: mRNA + vRNA


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description: mRNA + vRNA


title: 1001703005_C4

description: mRNA + vRNA


title: 1001703005_C11

description: mRNA + vRNA


title: 1001703005_B7

description: mRNA + vRNA


title: 1001703005_B6

description: mRNA + vRNA


title: 1001703005_B5

description: mRNA + vRNA


title: 1001703005_B3

description: mRNA + vRNA


title: 1001703005_B4

description: mRNA + vRNA


title: 1001703005_B8

description: mRNA + vRNA


title: 1001703005_B24

description: mRNA + vRNA


title: 1001703005_B22

description: mRNA + vRNA


title: 1001703005_C21

description: mRNA + vRNA


title: 1001703005_B20

description: mRNA + vRNA


title: 1001703005_B23

description: mRNA + vRNA


title: 1001703005_B21

description: mRNA + vRNA


title: 1001703005_B2

description: mRNA + vRNA


title: 1001703005_B19

description: mRNA + vRNA


title: 1001703005_B17

description: mRNA + vRNA


title: 1001703005_B18

description: mRNA + vRNA


title: 1001703005_B16

description: mRNA + vRNA


title: 1001703005_B15

description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


title: 1001703005_B14

description: mRNA + vRNA


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description: mRNA + vRNA


title: 1001703005_A8

description: mRNA + vRNA


title: 1001703005_A6

description: mRNA + vRNA


title: 1001703005_A23

description: mRNA + vRNA


title: 1001703005_A24

description: mRNA + vRNA


title: 1001703005_A3

description: mRNA + vRNA


title: 1001703005_A21

description: mRNA + vRNA


title: 1001703005_A22

description: mRNA + vRNA


title: 1001703005_A2

description: mRNA + vRNA


title: 1001703005_A19

description: mRNA + vRNA


title: 1001703005_A4

description: mRNA + vRNA


title: 1001703005_A15

description: mRNA + vRNA


title: 1001703005_A17

description: mRNA + vRNA


title: 1001703005_A14

description: mRNA + vRNA


title: 1001703005_A13

description: mRNA + vRNA


title: 1001703005_B11

description: mRNA + vRNA


title: 1001703005_A11

description: mRNA + vRNA


title: 1001703005_A16

description: mRNA + vRNA


title: 1001703003_P8

description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


title: 1001703005_A5

description: mRNA + vRNA


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description: mRNA + vRNA


title: 1001703003_P5

description: mRNA + vRNA


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description: mRNA + vRNA


title: 1001703003_P23

description: mRNA + vRNA


title: 1001703005_A20

description: mRNA + vRNA


title: 1001703003_P21

description: mRNA + vRNA


title: 1001703003_P22

description: mRNA + vRNA


title: 1001703003_P20

description: mRNA + vRNA


title: 1001703003_P2

description: mRNA + vRNA


title: 1001703005_A12

description: mRNA + vRNA


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description: mRNA + vRNA


title: 1001703003_P17

description: mRNA + vRNA


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description: mRNA + vRNA


title: 1001703003_P16

description: mRNA + vRNA


title: 1001703003_P18

description: mRNA + vRNA


title: 1001703003_P15

description: mRNA + vRNA


title: 1001703003_P11

description: mRNA + vRNA


title: 1001703003_P14

description: mRNA + vRNA


title: 1001703003_O9

description: mRNA + vRNA


title: 1001703003_O8

description: mRNA + vRNA


title: 1001703003_P12

description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


title: 1001703003_P10

description: mRNA + vRNA


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description: mRNA + vRNA


title: 1001703003_O5

description: mRNA + vRNA


title: 1001703003_O4

description: mRNA + vRNA


title: 1001703003_O3

description: mRNA + vRNA


title: 1001703003_O20

description: mRNA + vRNA


title: 1001703003_O2

description: mRNA + vRNA


title: 1001703003_O23

description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


title: 1001703003_P1

description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


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description: mRNA + vRNA


title: 1001703003_F3

description: mRNA + vRNA


title: 1001703003_F24

description: mRNA + vRNA


title: 1001703003_F18

description: mRNA + vRNA


title: 1001703003_F2

description: mRNA + vRNA


title: 1001703003_F20

description: mRNA + vRNA


title: 1001703003_F21

description: mRNA + vRNA


title: 1001703003_F22

description: mRNA + vRNA


title: 1001703003_F19

description: mRNA + vRNA


title: 1001703003_F17

description: mRNA + vRNA


title: 1001703003_F15

description: mRNA + vRNA


title: 1001703003_F16

description: mRNA + vRNA


title: 1001703003_F12

description: mRNA + vRNA


title: 1001703003_F13

description: mRNA + vRNA


title: 1001703003_F11

description: mRNA + vRNA


title: 1001703003_F1

description: mRNA + vRNA


title: 1001703003_F10

description: mRNA + vRNA


title: 1001703003_E9

description: mRNA + vRNA


title: 1001703003_E7

description: mRNA + vRNA


title: 1001703003_E6

description: mRNA + vRNA


title: 1001703003_E5

description: mRNA + vRNA


title: 1001703003_E4

description: mRNA + vRNA


title: 1001703003_E3

description: mRNA + vRNA


title: 1001703003_E22

description: mRNA + vRNA


title: 1001703003_E24

description: mRNA + vRNA


title: 1001703003_E23

description: mRNA + vRNA


title: 1001703003_E21

description: mRNA + vRNA


title: 1001703003_E20

description: mRNA + vRNA


title: 1001703003_E2

description: mRNA + vRNA


title: 1001703003_E14

description: mRNA + vRNA


title: 1001703003_E13

description: mRNA + vRNA


title: 1001703003_E16

description: mRNA + vRNA


title: 1001703003_E18

description: mRNA + vRNA


title: 1001703003_E15

description: mRNA + vRNA


title: 1001703003_E17

description: mRNA + vRNA


title: 1001703003_E19

description: mRNA + vRNA


title: 1001703003_F14

description: mRNA + vRNA


title: 1001703003_E11

description: mRNA + vRNA


title: 1001703003_E12

description: mRNA + vRNA


title: 1001703003_E8

description: mRNA + vRNA


title: 1001703003_D8

description: mRNA + vRNA


title: 1001703003_E1

description: mRNA + vRNA


title: 1001703003_D7

description: mRNA + vRNA


title: 1001703003_D9

description: mRNA + vRNA


title: 1001703003_D6

description: mRNA + vRNA


title: 1001703003_E10

description: mRNA + vRNA


title: 1001703003_D5

description: mRNA + vRNA


title: 1001703003_D4

description: mRNA + vRNA


title: 1001703003_D24

description: mRNA + vRNA


title: 1001703003_D21

description: mRNA + vRNA


title: 1001703003_D22

description: mRNA + vRNA


title: 1001703003_D23

description: mRNA + vRNA


title: 1001703003_D3

description: mRNA + vRNA


title: 1001703003_D20

description: mRNA + vRNA


title: 1001703003_D18

description: mRNA + vRNA


title: 1001703003_G14

description: mRNA + vRNA


title: 1001703003_D16

description: mRNA + vRNA


title: 1001703003_D14

description: mRNA + vRNA


title: 1001703003_D10

description: mRNA + vRNA


title: 1001703003_D1

description: mRNA + vRNA


title: 1001703003_D17

description: mRNA + vRNA


title: 1001703003_D11

description: mRNA + vRNA


title: 1001703003_D13

description: mRNA + vRNA


title: 1001703003_C9

description: mRNA + vRNA


title: 1001703003_C8

description: mRNA + vRNA


title: 1001703003_C6

description: mRNA + vRNA


title: 1001703003_C3

description: mRNA + vRNA


title: 1001703003_C4

description: mRNA + vRNA


title: 1001703003_C5

description: mRNA + vRNA


title: 1001703003_C23

description: mRNA + vRNA


title: 1001703003_C24

description: mRNA + vRNA


title: 1001703003_C22

description: mRNA + vRNA


title: 1001703003_C20

description: mRNA + vRNA


title: 1001703003_C19

description: mRNA + vRNA


title: 1001703003_D2

description: mRNA + vRNA


title: 1001703003_C18

description: mRNA + vRNA


title: 1001703003_D19

description: mRNA + vRNA


title: 1001703003_C15

description: mRNA + vRNA


title: 1001703003_C17

description: mRNA + vRNA


title: 1001703003_D15

description: mRNA + vRNA


title: 1001703003_D12

description: mRNA + vRNA


title: 1001703003_C11

description: mRNA + vRNA


title: 1001703003_C13

description: mRNA + vRNA


title: 1001703003_C14

description: mRNA + vRNA


title: 1001703003_C10

description: mRNA + vRNA


title: 1001703003_C1

description: mRNA + vRNA


title: 1001703003_C12

description: mRNA + vRNA


title: 1001703003_C7

description: mRNA + vRNA


title: 1001703003_B5

description: mRNA + vRNA


title: 1001703003_B7

description: mRNA + vRNA


title: 1001703003_B4

description: mRNA + vRNA


title: 1001703003_B9

description: mRNA + vRNA


title: 1001703003_B3

description: mRNA + vRNA


title: 1001703003_B6

description: mRNA + vRNA


title: 1001703003_B8

description: mRNA + vRNA


title: 1001703003_B24

description: mRNA + vRNA


title: 1001703003_C21

description: mRNA + vRNA


title: 1001703003_B22

description: mRNA + vRNA


title: 1001703003_C2

description: mRNA + vRNA


title: 1001703003_C16

description: mRNA + vRNA


title: 1001703003_B19

description: mRNA + vRNA


title: 1001703003_B18

description: mRNA + vRNA


title: 1001703003_B20

description: mRNA + vRNA


title: 1001703003_B2

description: mRNA + vRNA


title: 1001703003_B16

description: mRNA + vRNA


title: 1001703003_B17

description: mRNA + vRNA


title: 1001703003_B15

description: mRNA + vRNA


title: 1001703003_B1

description: mRNA + vRNA


title: 1001703003_B10

description: mRNA + vRNA


title: 1001703003_B13

description: mRNA + vRNA


title: 1001703003_B12

description: mRNA + vRNA


title: 1001703003_A7

description: mRNA + vRNA


title: 1001703003_A8

description: mRNA + vRNA


title: 1001703003_A5

description: mRNA + vRNA


title: 1001703003_B14

description: mRNA + vRNA


title: 1001703003_B23

description: mRNA + vRNA


title: 1001703003_A9

description: mRNA + vRNA


title: 1001703003_B11

description: mRNA + vRNA


title: 1001703003_A21

description: mRNA + vRNA


title: 1001703003_A4

description: mRNA + vRNA


title: 1001703003_A6

description: mRNA + vRNA


title: 1001703003_A3

description: mRNA + vRNA


title: 1001703003_B21

description: mRNA + vRNA


title: 1001703003_A22

description: mRNA + vRNA


title: 1001703003_A23

description: mRNA + vRNA


title: 1001703003_A24

description: mRNA + vRNA


title: 1001703003_A16

description: mRNA + vRNA


title: 1001703003_A18

description: mRNA + vRNA


title: 1001703003_A19

description: mRNA + vRNA


title: 1001703003_A15

description: mRNA + vRNA


title: 1001703003_A14

description: mRNA + vRNA


title: 1001703003_A2

description: mRNA + vRNA


title: 1001703003_A13

description: mRNA + vRNA


title: 1001703003_A17

description: mRNA + vRNA


title: 1001703003_A12

description: mRNA + vRNA


title: 1001703003_A10

description: mRNA + vRNA


title: 1001703001_P9

description: mRNA + vRNA


title: 1001703001_P8

description: mRNA + vRNA


title: 1001703001_P7

description: mRNA + vRNA


title: 1001703001_P22

description: mRNA + vRNA


title: 1001703001_P4

description: mRNA + vRNA


title: 1001703001_P5

description: mRNA + vRNA


title: 1001703001_P3

description: mRNA + vRNA


title: 1001703001_P24

description: mRNA + vRNA


title: 1001703001_P16

description: mRNA + vRNA


title: 1001703001_P18

description: mRNA + vRNA


title: 1001703001_P21

description: mRNA + vRNA


title: 1001703001_P23

description: mRNA + vRNA


title: 1001703001_P20

description: mRNA + vRNA


title: 1001703001_P19

description: mRNA + vRNA


title: 1001703003_A20

description: mRNA + vRNA


title: 1001703001_P6

description: mRNA + vRNA


title: 1001703001_P14

description: mRNA + vRNA


title: 1001703001_P13

description: mRNA + vRNA


title: 1001703001_P12

description: mRNA + vRNA


title: 1001703001_P2

description: mRNA + vRNA


title: 1001703001_P15

description: mRNA + vRNA


title: 1001703001_P10

description: mRNA + vRNA


title: 1001703001_P11

description: mRNA + vRNA


title: 1001703003_A11

description: mRNA + vRNA


title: 1001703003_A1

description: mRNA + vRNA


title: 1001703001_P1

description: mRNA + vRNA


title: 1001703001_O9

description: mRNA + vRNA


title: 1001703001_O8

description: mRNA + vRNA


title: 1001703001_O6

description: mRNA + vRNA


title: 1001703001_O4

description: mRNA + vRNA


title: 1001703001_O3

description: mRNA + vRNA


title: 1001703001_P17

description: mRNA + vRNA


title: 1001703001_O7

description: mRNA + vRNA


title: 1001703001_O5

description: mRNA + vRNA


title: 1001703001_O22

description: mRNA + vRNA


title: 1001703001_O24

description: mRNA + vRNA


title: 1001703001_O21

description: mRNA + vRNA


title: 1001703001_O23

description: mRNA + vRNA


title: 1001703001_O17

description: mRNA + vRNA


title: 1001703001_O19

description: mRNA + vRNA


title: 1001703001_O2

description: mRNA + vRNA


title: 1001703001_O18

description: mRNA + vRNA


title: 1001703001_O20

description: mRNA + vRNA


title: 1001703001_O16

description: mRNA + vRNA


title: 1001703001_O13

description: mRNA + vRNA


title: 1001703003_K13

description: mRNA + vRNA


title: 1001703001_O11

description: mRNA + vRNA


title: 1001703001_O14

description: mRNA + vRNA


title: 1001703001_O15

description: mRNA + vRNA


title: 1001703001_N7

description: mRNA + vRNA


title: 1001703001_O1

description: mRNA + vRNA


title: 1001703001_O10

description: mRNA + vRNA


title: 1001703001_O12

description: mRNA + vRNA


title: 1001703001_N4

description: mRNA + vRNA


title: 1001703001_N8

description: mRNA + vRNA


title: 1001703001_N9

description: mRNA + vRNA


title: 1001703001_N6

description: mRNA + vRNA


title: 1001703001_N5

description: mRNA + vRNA


title: 1001703001_N24

description: mRNA + vRNA


title: 1001703001_N22

description: mRNA + vRNA


title: 1001703001_N23

description: mRNA + vRNA


title: 1001703001_N21

description: mRNA + vRNA


title: 1001703001_N2

description: mRNA + vRNA


title: 1001703001_N19

description: mRNA + vRNA


title: 1001703001_N3

description: mRNA + vRNA


title: 1001703001_N17

description: mRNA + vRNA


title: 1001703001_N15

description: mRNA + vRNA


title: 1001703001_N13

description: mRNA + vRNA


title: 1001703001_N20

description: mRNA + vRNA


title: 1001703001_N14

description: mRNA + vRNA


title: 1001703001_N12

description: mRNA + vRNA


title: 1001703001_N1

description: mRNA + vRNA


title: 1001703001_N11

description: mRNA + vRNA


title: GW_TGFB_APC_TP53_rep2-batch5

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

library_source: genomic

data_processing:
library strategy: DNA amplicon seq
Demultiplexing using CLC Genomics Workbench
Create readcount sgRNA tables using MAGeCK

molecule: genomic DNA

source_name: APC/TP53-KO Human Intestinal Organoids

growth_protocol: Culture medium of Human Intestinal Organoids contained Advanced DMEM/F12 supplemented with 10 mM HEPES, 1x Glutamax, 1% Penicillin/Streptomycin, 1x N2, 1x B27, 1.25 mM N-acetylcysteine, 50% WNT3A-conditioned medium (CM), 20% RSPO1-CM 20%, 10% NOGGIN-CM (all CM produced in-house), 10 mM Nicotinamide, 50 ng/ml human EGF, 10 nM Gastrin, 0.5 µM TGFß type I receptor inhibitor A83-01 and 10 µM p38-inhibitor SB202190

extract_protocol:
Viagen Direct PCR Mix
Libraries were prepared by PCR amplification of integrated sgRNAs from gDNA. Barcoded primers were used for high throughput analysis of organoid clones. The Illumina TruSeq Nano DNA library prep was used for subquented blunt-ended ligation of sequencing adaptors.

treatment_protocol: For selection, organoids were cultured without A83-01 and in 10 ng/ml recombinant TGFB1

tag: genotype

value: APC-KO TP53-KO

tag: tissue

value: Human small intestine

tag: cell type

value: organoids

tag: library

value: genome-wide

tag: extraction

value: single-organoid-gdna-extraction


title: 1001703001_N10

description: mRNA + vRNA


title: 1001703001_M9

description: mRNA + vRNA


title: 1001703001_M6

description: mRNA + vRNA


title: 1001703001_M8

description: mRNA + vRNA


title: GW_TGFB_APC_TP53_rep2-batch3


title: GW_TGFB_APC_TP53_rep2-batch2


title: 1001703001_M4

description: mRNA + vRNA


title: 1001703001_M3

description: mRNA + vRNA


title: GW_TGFB_APC_TP53_rep2-batch1


title: 1001703001_M23

description: mRNA + vRNA


title: 1001703001_M24

description: mRNA + vRNA


title: GW_WNT

source_name: WT Human Intestinal Organoids

value: WT


title: 1001703001_N18

description: mRNA + vRNA


title: GW_TGFB_APC_rep2-batch4

source_name: APC-KO Human Intestinal Organoids

value: APC-KO


title: 1001703001_M21

description: mRNA + vRNA


title: 1001703001_N16

description: mRNA + vRNA


title: 1001703001_M22

description: mRNA + vRNA


title: GW_TGFB_APC_rep2-batch5


title: GW_TGFB_APC_rep2-batch3


title: 1001703001_M20

description: mRNA + vRNA


title: 1001703001_M2

description: mRNA + vRNA


title: 1001703001_M7

description: mRNA + vRNA


title: 1001703001_M5

description: mRNA + vRNA


title: GW_TGFB_APC_rep2-batch1


title: GW_TGFB_APC_TP53_rep2-batch4


title: 1001703001_M18

description: mRNA + vRNA


title: 1001703001_M19

description: mRNA + vRNA


title: GW_TGFB_APC_rep1-batch4+GW_TGFB_APC_TP53_rep1

source_name: APC-KO and APC/TP53-KO Human Intestinal Organoids

value: APC-KO and APC-KO TP53-KO


title: GW_TGFB_APC_rep1-batch3


title: 1001703001_M17

description: mRNA + vRNA


title: GW_TGFB_APC_rep1-batch2


title: GW_TGFB_APC_rep1-batch1


title: GW_TGFB_WT_rep2-batch5


title: 1001703001_M14

description: mRNA + vRNA


title: GW_TGFB_WT_rep2-batch4


title: GW_TGFB_WT_rep1-batch2


title: 1001703001_M11

description: mRNA + vRNA


title: 1001703001_M12

description: mRNA + vRNA


title: GW_TGFB_WT_rep2-batch2


title: GW_TGFB_WT_rep2-batch3


title: 1001703001_M13

description: mRNA + vRNA


title: GW_TGFB_APC_rep2-batch2


title: GW_TGFB_WT_rep2-batch1


title: 1001703001_M10

description: mRNA + vRNA


title: 1001703001_M1

description: mRNA + vRNA


title: 1001703001_L7

description: mRNA + vRNA


title: TSG_WNT_treatment_rep3

description:
processed data file:
tsg_wnt_gene_summary.txt

extract_protocol:
Phenol Extraction and Isopropanol Precipitaiton
Libraries were prepared by PCR amplification of integrated sgRNAs from gDNA. Barcoded primers were used for high throughput analysis of organoid clones. The Illumina TruSeq Nano DNA library prep was used for subquented blunt-ended ligation of sequencing adaptors.

value: TSG-sub-library

tag: data processing

value: Test genes for enrichment and depletion using MAGeCK

value: bulk-gdna-extraction


title: 1001703001_L9

description: mRNA + vRNA


title: TSG_WNT_treatment_rep2


title: 1001703001_L6

description: mRNA + vRNA


title: 1001703001_L8

description: mRNA + vRNA


title: TSG_WNT_treatment_rep1


title: TSG_WNT_ctrl

description:
processed data file:
tsg_wnt_gene_summary.txt,


title: 1001703001_L4

description: mRNA + vRNA


title: 1001703001_M15

description: mRNA + vRNA


title: 1001703001_M16

description: mRNA + vRNA


title: 1001703001_L3

description: mRNA + vRNA


title: Ad18

city: kashiwa

first: Eri

last: Sugiyama

address: 6-5-1 kashiwanoha

department: Division of Cancer Immunology

country: Japan

institute: National Cancer Center

data_processing:
Sequence data were evaluated with GeneData Expressionist for Genomic Profiling (version 9.1.4a).
Read-mapping was performed with Hg19 as the reference genome and TopHat (version 2.0.14), followed by transcriptome reconstruction and expression quantification into FPKM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM and count values for each sample.

source_name: lung adenocarcinoma

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung adenocarcinoma

tag: age

tag: Sex

value: M

tag: smoking status

value: Never

tag: brinkman index

tag: clinical stage

value: IIIA

tag: egfr mutation


title: Ad19

value: Past


title: Ad17

value: IA


title: 1001703001_L24

description: mRNA + vRNA


title: 1001703001_L23

description: mRNA + vRNA


title: Ad16


title: GW_TGFB_WT_rep1-batch1


title: Ad13

value: F


title: 1001703001_L22

description: mRNA + vRNA


title: Ad15

value: IV


title: 1001703001_L21

description: mRNA + vRNA


title: 1001703001_L20

description: mRNA + vRNA


title: 1001703001_L2

description: mRNA + vRNA


title: 1001703001_L5

description: mRNA + vRNA


title: Ad10

value: Current

value: IB


title: Ad12

value: mt


title: Ad9

value: IIB

value: WT


title: Ad8


title: 1001703001_L16

description: mRNA + vRNA


title: 1001703001_L17

description: mRNA + vRNA


title: 1001703001_L15

description: mRNA + vRNA


title: 1001703001_L18

description: mRNA + vRNA


title: Ad7


title: Ad6


title: 1001703001_L13

description: mRNA + vRNA


title: Ad3


title: Ad4


title: 1001703001_L12

description: mRNA + vRNA


title: Ad14


title: Ad5


title: 1001703001_L11

description: mRNA + vRNA


title: 1001703001_L14

description: mRNA + vRNA


title: 1001703001_L10

description: mRNA + vRNA


title: Ad2

value: IIA


title: 1001703001_K9

description: mRNA + vRNA


title: 32-0018b

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

country: USA

institute: Fred Hutch Cancer Research Center

description: lower extremity muscle biopsy accessible by needle

data_processing:
Filtered unqualified raw reads whose filter flag is tagged with "Y".
Trimmed Illumina universal adapters by Trimmomatic-0.32.
Mapped processed reads to genome built hg38 by Taphat-2.1.0/Bowtie2-2.2.6.
Counedt reads to the features collected from GENCODE v24 and the Bioconductor funciton GenomicAlignments::summarizedOverlap() and "iInersectionStrick" mode were used.
All the scripts and codes for analysis were depostied in our github repos (https://github.com/Fredhutch/Rwellstone_FSHD_muscle_biopsy) and explained in our gitbook (https://fredhutch.github.io/Rwellstone_FSHD_muscle_biopsy).
Genome_build: hg38
Supplementary_files_format_and_content: year2.dds.rda stored a DESeq2's DESeqDataSet instance including controls and one-year follow-up RNA-seq gene counts matrix along with all MRI/histopathology signals as column data.    year2_column_data.csv stored MRI signals, histopathology signals, phenotype data and marker scores.
year2_column_data.csv.gz: sample phenotype metedata, follow-up visit sample only
year2_genecounts.csv.gz: gene counts for the follow-up visit
year2_normalized_genecounts.csv.gz: normalized gene counts for the follow-up visit
year2_TPM.csv.gz: TPM gene matrix for initial the follow-up visit
year2.dds.rda: DESeqDataSet instance storing gene features, gene counts and phenotype metadata, follow-up visit only

source_name: muscle biopsy

growth_protocol: Muscle biopsy samples extracted from 27 FSHD subjects, and on 8 control quadriceps muscle biopsies from unaffected individuals.

extract_protocol:
Total RNA was extracted from whole cells using NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's instructions.
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).  RNA-seq libraries were pooled (14-plex) and clustered onto two flow cell lanes.

value: muscle

tag: batch

value: VII

tag: disease state

value: FSHD

tag: visit

value: II

tag: sizefactor

tag: inflammation

value: Mild

value: Normal

tag: fibrosis


title: Ad11

tag: tissue

value: lung adenocarcinoma

value: M

value: IIIA


title: Ad1

value: Past


title: 1001703001_L1

description: mRNA + vRNA

tag: moi

tag: hours post infection

tag: plate

tag: well


title: 1001703001_L19

description: mRNA + vRNA


title: 32-0017b

value: Severe

value: Moderate


title: 1001703001_K7

description: mRNA + vRNA


title: 1001703001_K8

description: mRNA + vRNA


title: 32-0016b


title: 32-0015b


title: 32-0013b

value: VI


title: 1001703001_K5

description: mRNA + vRNA


title: 1001703001_K6

description: mRNA + vRNA


title: 32-0014b


title: 1001703001_K4

description: mRNA + vRNA


title: 1001703001_K3

description: mRNA + vRNA


title: 32-0012b


title: 1001703001_K24

description: mRNA + vRNA


title: 32-0009b


title: 1001703001_K23

description: mRNA + vRNA


title: 32-0010b


title: 1001703001_K22

description: mRNA + vRNA


title: 1001703001_K21

description: mRNA + vRNA


title: 32-0005b


title: 1001703001_K20

description: mRNA + vRNA


title: 32-0002b


title: 32-0007b


title: 1001703001_K2

description: mRNA + vRNA


title: 1001703001_K19

description: mRNA + vRNA


title: 1001703001_K18

description: mRNA + vRNA


title: 01-0036b


title: 01-0037b


title: 01-0034b


title: 1001703001_K17

description: mRNA + vRNA


title: 01-0035b


title: 1001703001_K16

description: mRNA + vRNA


title: 1001703001_K14

description: mRNA + vRNA


title: 01-0029b


title: 01-0030b


title: 1001703001_K15

description: mRNA + vRNA


title: 1001703001_K13

description: mRNA + vRNA


title: 01-0033b


title: 1001703001_K12

description: mRNA + vRNA


title: 1001703001_K10

description: mRNA + vRNA


title: 1001703001_K11

description: mRNA + vRNA


title: 01-0027b


title: 01-0025b


title: 1001703001_J9

description: mRNA + vRNA


title: 01-0026b


title: 01-0023b


title: 1001703001_J8

description: mRNA + vRNA


title: 01-0022b


title: 1001703001_J7

description: mRNA + vRNA


title: 01-0045_control

value: III

value: Control

value: I


title: 1001703001_J4

description: mRNA + vRNA


title: 32-0006b


title: 01-0049_control

value: IV


title: 1001703001_J6

description: mRNA + vRNA


title: 1001703001_J5

description: mRNA + vRNA


title: 01-0046_control

value: muscle


title: 1001703001_J3

description: mRNA + vRNA


title: 1001703001_J21

description: mRNA + vRNA


title: 01-0028b


title: 1001703001_J24

description: mRNA + vRNA


title: 1001703001_J23

description: mRNA + vRNA


title: 01-0044_control


title: TB_14: TB patient 14

city: Newark

first: Padmini

last: Salgame

state: NJ

address: 185 South Orange Ave

department: Medicine

institute: Rutgers New Jersey Medical School

data_processing:
Sequence Quality control: FastQC_v0.11.5 (default)
Alignment: Rsubread-1.8.2 (indels = 5, unique = TRUE)
Gene Filtering: rowSums(matrix) > 5
Normalization: DEseq2 1.14.1 (RLE method)
Genome_build: hg19
Supplementary_files_format_and_content: Excel file matrix of normalized expression counts with genes in rows and samples in columns

molecule: polyA RNA

source_name: Tuberculosis patient 14

extract_protocol:
TRIzol Reagent (Invitrogen, ThermoFisher Scientific, MA, USA)
Strand-specific cDNA libraries prepared based on low-input Illumina TruSeq RNA Sample Preparation protocol

tag: gender

value: Male

tag: age

value: PBMC


title: 1001703001_K1

description: mRNA + vRNA


title: 01-0042_control


title: 1001703001_J22

description: mRNA + vRNA


title: 01-0024b

value: FSHD

value: II


title: 01-0043_control


title: 01-0041_control


title: 1001703001_J19

description: mRNA + vRNA


title: TB_13: TB patient 13

source_name: Tuberculosis patient 13


title: 01-0048_control


title: TB_8: TB patient 8

source_name: Tuberculosis patient 8


title: TB_9: TB patient 9

source_name: Tuberculosis patient 9


title: 1001703001_J16

description: mRNA + vRNA


title: 1001703001_J18

description: mRNA + vRNA


title: TB_7: TB patient 7

source_name: Tuberculosis patient 7


title: TB_12: TB patient 12

source_name: Tuberculosis patient 12

value: female


title: TB_10: TB patient 10

source_name: Tuberculosis patient 10


title: 1001703001_J2

description: mRNA + vRNA


title: 1001703001_J20

description: mRNA + vRNA


title: 1001703001_J14

description: mRNA + vRNA


title: 1001703001_J12

description: mRNA + vRNA


title: 1001703001_J10

description: mRNA + vRNA


title: TB_6: TB patient 6

source_name: Tuberculosis patient 6


title: 1001703001_J17

description: mRNA + vRNA


title: 1001703001_I9

description: mRNA + vRNA


title: 1001703001_J13

description: mRNA + vRNA


title: NP_21: Non-progressor 21

source_name: Non-progressor 21


title: TB_5: TB patient 5

source_name: Tuberculosis patient 5


title: TB_3: TB patient 3

source_name: Tuberculosis patient 3


title: 1001703001_J11

description: mRNA + vRNA

source_name: U87 cells


title: TB_1: TB patient 1

source_name: Tuberculosis patient 1


title: TB_2: TB patient 2

source_name: Tuberculosis patient 2


title: 1001703001_I5

description: mRNA + vRNA


title: NP_20: Non-progressor 20

source_name: Non-progressor 20


title: 1001703001_J15

description: mRNA + vRNA


title: NP_19: Non-progressor 19

source_name: Non-progressor 19


title: NP_17: Non-progressor 17

source_name: Non-progressor 17


title: 1001703001_I6

description: mRNA + vRNA


title: NP_16: Non-progressor 16

source_name: Non-progressor 16


title: TB_11: TB patient 11

source_name: Tuberculosis patient 11


title: NP_18: Non-progressor 18

source_name: Non-progressor 18


title: TB_4: TB patient 4

source_name: Tuberculosis patient 4


title: 1001703001_I4

description: mRNA + vRNA


title: 1001703001_I8

description: mRNA + vRNA


title: NP_14: Non-progressor 14

source_name: Non-progressor 14


title: 1001703001_J1

description: mRNA + vRNA


title: 1001703001_I7

description: mRNA + vRNA


title: 1001703001_I24

description: mRNA + vRNA


title: 1001703001_I3

description: mRNA + vRNA


title: 1001703001_I22

description: mRNA + vRNA


title: 1001703001_I23

description: mRNA + vRNA


title: 1001703001_I21

description: mRNA + vRNA


title: 1001703001_I20

description: mRNA + vRNA


title: NP_10: Non-progressor 10

source_name: Non-progressor 10


title: 1001703001_I2

description: mRNA + vRNA


title: NP_12: Non-progressor 12

source_name: Non-progressor 12


title: 1001703001_I19

description: mRNA + vRNA


title: NP_9: Non-progressor 9

source_name: Non-progressor 9


title: 1001703001_I18

description: mRNA + vRNA


title: NP_8: Non-progressor 8

source_name: Non-progressor 8


title: NP_6: Non-progressor 6

source_name: Non-progressor 6


title: NP_15: Non-progressor 15

source_name: Non-progressor 15


title: 1001703001_I17

description: mRNA + vRNA

source_name: U87 cells


title: NP_5: Non-progressor 5

source_name: Non-progressor 5


title: 1001703001_I16

description: mRNA + vRNA


title: NP_7: Non-progressor 7

source_name: Non-progressor 7


title: 1001703001_I15

description: mRNA + vRNA


title: 1001703001_I13

description: mRNA + vRNA


title: NP_3: Non-progressor 3

source_name: Non-progressor 3


title: NP_11: Non-progressor 11

source_name: Non-progressor 11


title: NP_13: Non-progressor 13

source_name: Non-progressor 13


title: NP_2: Non-progressor 2

source_name: Non-progressor 2


title: 1001703001_I11

description: mRNA + vRNA


title: 1001703001_I14

description: mRNA + vRNA


title: P_16: Progressor 16

source_name: Progressor 16


title: 1001703001_I10

description: mRNA + vRNA


title: 1001703001_I12

description: mRNA + vRNA


title: 1001703001_I1

description: mRNA + vRNA


title: P_14: Progressor 14

source_name: Progressor 14


title: 1001703001_H9

description: mRNA + vRNA


title: P_15: Progressor 15

source_name: Progressor 15


title: 1001703001_H8

description: mRNA + vRNA


title: NP_1: Non-progressor 1

source_name: Non-progressor 1


title: P_12: Progressor 12

source_name: Progressor 12


title: P_11: Progressor 11

source_name: Progressor 11


title: 1001703001_H7

description: mRNA + vRNA


title: P_13: Progressor 13

source_name: Progressor 13


title: P_9: Progressor 9

source_name: Progressor 9


title: P_10: Progressor 10

source_name: Progressor 10


title: 1001703001_H3

description: mRNA + vRNA


title: NP_4: Non-progressor 4

source_name: Non-progressor 4


title: 1001703001_H4

description: mRNA + vRNA

source_name: U87 cells


title: 1001703001_H5

description: mRNA + vRNA


title: P_6: Progressor 6

source_name: Progressor 6


title: 1001703001_H24

description: mRNA + vRNA


title: 1001703001_H21

description: mRNA + vRNA


title: P_5: Progressor 5

source_name: Progressor 5


title: P_4: Progressor 4

source_name: Progressor 4


title: P_3: Progressor 3

source_name: Progressor 3


title: 1001703001_H23

description: mRNA + vRNA


title: P_8: Progressor 8

source_name: Progressor 8


title: 1001703001_H2

description: mRNA + vRNA


title: P_1: Progressor 1

source_name: Progressor 1


title: 1001703001_H18

description: mRNA + vRNA


title: 1001703001_H22

description: mRNA + vRNA


title: tgfb_control

city: Aurora

first: Timothy

last: McKinsey

state: CO

department: Division of Cardiology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Sequenced reads were aligned to RN6 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: rn6
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format, called peaks in bed format

organism: Rattus norvegicus

source_name: adult rat ventricular fibroblasts

growth_protocol: Adult rat ventricular fibroblasts (ARVFs) were isolated from female Sprague Dawley rats using enzymatic digestion (1 mg/ml collagenase type II; Worthington Biochemical Corporation) followed by gentle centrifugation for collection of cells, as previously described 55. Cells were maintained in DMEM/F12 media supplemented with 20% FBS, 1 % antibiotics-L glutamine and 1 mmol/L ascorbic acid. ARVFs were then passaged once to P1 (passage 1) or twice to P2 (passage 2), and plated appropriately for downstream assays. Equilibration of cells in low serum medium (0.1% FBS) was carried out prior to all treatments.

extract_protocol:
Anti-BRD4 (301-985, Bethyl Laboratories) and anti-RNA Pol II (39097, Active Motif) Chromatin Immunoprecipitation was performed as previously described 33. Five independent 10-cm plates of ARVFs were combined per immunoprecipitation.
Libraries were prepared using the Rubicon TruPLEX Tag-seq kit and submitted to the UC Denver Genomics and Microarray core facility for sequencing (HiSeq2000).

treatment_protocol: Cells were treated with the following agents (DMSO as vehicle; 0.1% final concentration): recombinant TGF-β1 (10ng/mL; Novoprotein), JQ1 (500nM; synthesized in-house)

tag: cell line

value: ARVF

tag: strain

value: Sprague Dawley

tag: antibody

tag: treatment


title: veh_control


title: 1001703001_H17

description: mRNA + vRNA


title: pol2_veh

value: anti-RNA Pol II (39097, Active Motif)

value: DMSO as vehicle


title: 1001703001_H6

description: mRNA + vRNA


title: 1001703001_H16

description: mRNA + vRNA


title: 1001703001_H19

description: mRNA + vRNA


title: 1001703001_H15

description: mRNA + vRNA


title: P_7: Progressor 7

source_name: Progressor 7


title: 1001703001_H14

description: mRNA + vRNA


title: pol2_tgfb

value: GF-β1 (10ng/mL; Novoprotein)


title: 1001703001_H12

description: mRNA + vRNA


title: 1001703001_H13

description: mRNA + vRNA


title: 1001703001_H20

description: mRNA + vRNA


title: 1001703001_H11

description: mRNA + vRNA


title: P_2: Progressor 2

source_name: Progressor 2


title: 1001703001_H10

description: mRNA + vRNA


title: brd4_tgfb

value: Anti-BRD4 (301-985, Bethyl Laboratories)


title: 1001703001_H1

description: mRNA + vRNA


title: brd4_veh


title: 1001703001_G8

description: mRNA + vRNA


title: 1001703001_G9

description: mRNA + vRNA


title: RNA-seq analysis of 2h VV-iPDL1/GM-infected MC38 cells

city: los angeles

first: Guan

last: Wang

state: ca

address: 1450 biggy st, NRT7509

institute: University of southern california

data_processing:
 Total RNA is enriched by oligo (dT) magnetic beads (rRNA removed)
RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific. The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification qPCR method. To sequence the libraries on the Illumina HiSeq 4000 instrument, the barcoded libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified in situ, and subsequently sequenced for 150 cycles for both ends on Illumina HiSeq instrument
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Sequence quality was examined using the FastQC software. The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt [2]  ) were aligned to reference genome using Hisat2 software. The transcript abundances for each sample was estimated with StringTie [4]  , and the FPKM [8]  value for gene and transcript level were calculated with R package Ballgown
The differentially expressed genes and transcripts were filtered using R package Ballgown. The novel genes and transcripts were predicted from assembled results by comparing to the reference annotation using StringTie and Ballgown, then use CPAT [10]  to assess the coding potential of those sequences. Then use rMATS [11]  to detecting alternative splicing events and plots. Principle Component Analysis (PCA) and correlation analysis were based on gene expression level, Hierarchical Clustering, Gene Ontology, Pathway analysis, Gene Ontology, Pathway analysis, scatter plots and volcano plots were performed with the differentially expressed genes in R, Python or shell environment for statistical computing and graphics
Genome_build: based on uninfected cell genome
Supplementary_files_format_and_content: fastq raw data files and all different expressed genes and transcripts in xlsx.

organism: Mus musculus

source_name: MC38 cells

growth_protocol: MC38 cells were cultured in DMEM media supplemented with 10%FBS in tissue treated dish or flask in 37ºC, 5% CO2 incubator

extract_protocol:
Cell lysates were processed to extract total RNA using Rneasy Plus Mini Kit (Qiagen).
RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina). The libraries were sequenced on a HiSeq 4000 instrument using 2x150bp pair-end sequencing (Arraystar Inc, Rockville, MD).

treatment_protocol: MC38 cells were infected with VV-iPDL1/GM at MOI of 2. At different indicated time points, cells were collected for total RNA extraction.

tag: cell type

value: colon adenocarcinoma cells

tag: passage


title: RNA-seq analysis of uninfected MC38 cells

source_name: colon adenocarcinoma cells


title: RNA-seq analysis of 16h VV-iPDL1/GM-infected MC38 cells


title: RNA-seq analysis of 8h VV-iPDL1/GM-infected MC38 cells


title: 1001703001_G6

description: mRNA + vRNA


title: AAVHLF5

first: Lukas

last: Rambousek

address: Winterthurerstrasse 161

institute: University of Zurich

description:
HLF AAV-HLF
543

data_processing:
Reads were quality-checked with FastQC. Reads at least 20 bases long, and an overall average phred quality score greater than 10 were aligned to the reference genome and transcriptome (FASTA and GTF files, respectively, downloaded from Ensembl) with STAR v2.5.1 with default settings for single end reads.
Distribution of the reads across genomic isoform expression was quantified using the R package GenomicRanges from Bioconductor Version 3.0. Differentially expressed genes were identified using the R package edgeR  from Bioconductor Version 3.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file, differential gene expression analysis (ENSEMBL, baseMean, log2fold change, stat, pvalue, padj, symbol, gene name)

source_name: dorsal hippocampus

extract_protocol:
Brain tissue samples were homogenized (Qiagen TissueLyser) and whole cell RNA extracted using NucleoSpin-RNA II kit (Macherey-Nagel)
Illumina TruSeq RNA Stranded, PolyA

treatment_protocol: AAV-EGFP and AAV-HLF vectors were injected at a final titer of 1.1 x 1.2 x 10^12 vg/ml, 280 µl into dorsal hippocmapus (-1.8 AP, +1.6 ML, +1.9 DV). After 14 days of expression, animals were sacrificed.

value: dorsal hippocampus

tag: genotype

value: HLF AAV-HLF


title: AAVHLF4

description:
HLF AAV-HLF
514


title: AAVHLF6

description:
HLF AAV-HLF
544


title: RNA-seq analysis of 4h VV-iPDL1/GM-infected MC38 cells


title: 1001703001_G7

description: mRNA + vRNA


title: RNA-seq analysis of 24h VV-iPDL1/GM-infected MC38 cells


title: 1001703001_G5

description: mRNA + vRNA


title: 1001703001_G4

description: mRNA + vRNA


title: AAVHLF7

description:
HLF AAV-HLF
545


title: 1001703001_G3

description: mRNA + vRNA


title: AAVHLF2

description:
HLF AAV-HLF
511


title: AAVHLF1

description:
HLF AAV-HLF
370


title: AAVHLF3

description:
HLF AAV-HLF
512


title: 1001703001_G24

description: mRNA + vRNA


title: 1001703001_G23

description: mRNA + vRNA


title: CONTROL7

description:
control AAV-EGFP
542

value: control AAV-EGFP


title: 1001703001_G22

description: mRNA + vRNA


title: 1001703001_G21

description: mRNA + vRNA


title: CONTROL5

description:
control AAV-EGFP
540


title: CONTROL4

description:
control AAV-EGFP
504


title: 1001703001_G20

description: mRNA + vRNA


title: 1001703001_G2

description: mRNA + vRNA


title: CONTROL3

description:
control AAV-EGFP
503


title: 1001703001_G18

description: mRNA + vRNA


title: cardiac fibroblasts_Sham/Vehicle_4B

description: Barcode: ATCACG

data_processing:
Read trimming: Trim Galore! (v.0.3.7)
alignment: STAR (v.2.5.2a)
expression: raw counts were loaded into R and genes with a median of <1 mapped read per million were removed before differential expression analysis with edgeR
Genome_build: Mm10 - UCSC annotations (July 2016)
Supplementary_files_format_and_content: Raw counts
Supplementary_files_format_and_content: DE analysis: Excel spreadsheets with tab 1=list of DE genes and tab 2=DE table

source_name: cardiac fibroblasts_Sham/Vehicle

extract_protocol:
Cardiac fibroblast isolation followed immediately by RNA isolation using the DirectZol Miniprep kit
Libraries were constructed using the NEB Next Ultra Directional Library prep kit following rRNA depletion

treatment_protocol: Mice were subjected to TAC or sham surgery and treated with JQ1 or vehicle

value: sham surgery

tag: agent

value: Vehicle

value: cardiac fibroblasts


title: 1001703001_G16

description: mRNA + vRNA


title: 1001703001_G15

description: mRNA + vRNA


title: 1001703001_G19

description: mRNA + vRNA


title: CONTROL6

description:
control AAV-EGFP
541


title: 1001703001_G17

description: mRNA + vRNA


title: CONTROL2

description:
control AAV-EGFP
502


title: 1001703001_G11

description: mRNA + vRNA


title: 1001703001_G14

description: mRNA + vRNA


title: cardiac fibroblasts_TAC/JQ1_21B

description: Barcode: ACTTGA

source_name: cardiac fibroblasts_TAC/JQ1

value: TAC


title: cardiac fibroblasts_TAC/JQ1_20B

description: Barcode: CAGATC


title: 1001703001_G10

description: mRNA + vRNA


title: 1001703001_G1

description: mRNA + vRNA


title: 1001703001_F9

description: mRNA + vRNA


title: 1001703001_F8

description: mRNA + vRNA


title: cardiac fibroblasts_TAC/JQ1_19A

description: Barcode: ACTTGA


title: cardiac fibroblasts_TAC/Vehicle_13A

description: Barcode: GCCAAT

source_name: cardiac fibroblasts_TAC/Vehicle


title: cardiac fibroblasts_Sham/Vehicle_1A

description: Barcode: ATCACG


title: cardiac fibroblasts_TAC/Vehicle_12A

description: Barcode: ACAGTG


title: 1001703001_G13

description: mRNA + vRNA


title: CONTROL1

description:
control AAV-EGFP
500


title: cardiac fibroblasts_Sham/Vehicle_5B

description: Barcode: CGATGT


title: VgControl-3LW-Wing-antiHA-ChIP-Rep2

city: Chapel Hill

first: Spencer

middle: L

last: Nystrom

state: NC

address: 250 Bell Tower Drive

department: Curriculum in Genetics and Molecular Biology

institute: UNC-Chapel Hill

description:
VgControl-3LW-Wing-antiHA-ChIP-Rep2
VgControl-3LW-Wing-ChIP_2Reps_POOLED_zNorm.bw

data_processing:
FAIREseq – Fastq files from technical replicates were combined before alignment
FAIREseq – Sequenced reads were mapped ot the dm3 whole genome using bowtie2 v2.2.8, using seed 123
FAIREseq – the resulting bam file was indexed and sorted using samtools v1.3.1, and all reads with a mapq score less than 5 were removed setting -bq 5
FAIREseq – the resulting bam file was indexed and sorted using samtools v1.3.1
FAIREseq – PCR duplicates were marked in the resulting sorted, indexed sam file using Picard v2.2.4 MarkDuplicates
FAIREseq – PCR duplicates were removed with samtools v1.3.1 by removing all reads marked with the PCR duplicates bit flag (samtools view -bF 0x400)
FAIREseq – The resulting bam file was indexed and further filtered to include only reads mapping to chr2L, chr2R, chr3L, chr3R, chr4, and chrX (no Y, U, or heterochromatic regions)
FAIREseq – the resulting bam file was indexed and converted to a bed file with bedtools v2.25.0
FAIREseq – bigwigs normalized to reads per genomic content (RPGC) were generated from the resulting bedfile using Deeptools v2.24.0 bamCoverage setting: --normalizeTo1x 121400000 –binSize 10 -e 125 –outFileFormat bedgraph
FAIREseq – bigwigs were Z-normalized using standard deviations and means for each chromosome arm
ChIPseq – Fastq files from technical replicates were combined before alignment
ChIPseq – Sequenced reads were mapped ot the dm3 whole genome using bowtie2 v2.2.8, using seed 123
ChIPseq – the resulting bam file was indexed and sorted using samtools v1.3.1, and all reads with a mapq score less than 5 were removed setting -bq 5
ChIPseq – the resulting bam file was indexed and sorted using samtools v1.3.1
ChIPseq – PCR duplicates were marked in the resulting sorted, indexed sam file using Picard v2.2.4 MarkDuplicates
ChIPseq – PCR duplicates were removed with samtools v1.3.1 by removing all reads marked with the PCR duplicates bit flag (samtools view -bF 0x400)
ChIPseq – The resulting bam file was indexed and further filtered to include only reads mapping to chr2L, chr2R, chr3L, chr3R, chr4, and chrX (no Y, U, or heterochromatic regions)
ChIPseq – the resulting bam file was indexed and converted to a bed file with bedtools v2.25.0
ChIPseq – bigwigs normalized to reads per genomic content (RPGC) were generated from the resulting bedfile using Deeptools v2.24.0 bamCoverage setting: --normalizeTo1x 121400000 –binSize 10 -e 125 –outFileFormat bedgraph
ChIPseq – bigwigs were Z-normalized using standard deviations and means for each chromosome arm
ChIPseq – peak calls were generated for individual replicates using MACS2 (v 2015-06-03) setting -g dm, --nomodel, --extsize 125, --seed 123. For E93gfstf-24h-Wing-ChIP the ControlGenomicDNA_q5_sorted_dupsRemoved_noYUHet.bed was used as background.  For E93GOF-3LW-Wing-ChIP, pooled data from the VgControl-3LW-Wing-ChIP was used as background.
ChIPseq – union peak list was generated by keeping all peaks which overlap between experimental replicates, then merging the resulting lists. Peaks annotated as “ectopic” are found only inside E93GOF-3LW-Wing, peaks labeled “orphan” are unique to E93-24hAPF-Wing, while “entopic” peaks are shared between both conditions.
ChIPseq – Summits from the resulting union ChIP peak list were recomputed from aligned reads from pooled replicates using FunChip (setting d = 125) (v1.0.0) Summits from entopic and orphan sites were computed from wild-type late E93 ChIP-seq, while summits from ectopic sites were computed from precocious E93 ChIP.
ChIPseq – Chromatin accessibility differences within precocious E93 ChIP peaks were identified by counting FAIRE-seq reads within the union set of E93 ChIP peaks using featureCounts (setting allowMultioverlap = T) from Rsubread and testing for differential accessibility with DESeq2 using an adjusted p value < 0.05 and an absolute log2FoldChange > 1. Concordance of precocious chromatin accessibility changes with wild-type chromatin accessibility changes was determined using DESeq2, using an adjusted p value < 0.05.
FAIREseq – Clustering of chromatin accessibility changes within ChIP peaks during wild-type development was performed by computing cpm normalized counts for each FAIRE-seq replicate using DESeq2. Mean cpm counts were computed for each timepoint and converted to fraction of maximum accessibility score by dividing mean cpm counts by the maximum cpm value over time. Peaks were clustered by similarities in their accessibility profile over time using the R function kmeans(k -= 8, nstart = 25, iter.max = 15) after setting the random seed to 1230412 (chosen using a random number generator).
FAIREseq – Clustering of chromatin accessibility changes within ChIP peaks during wild-type development was performed by computing cpm normalized counts for each FAIRE-seq replicate using DESeq2. Mean cpm counts were computed for each timepoint and converted to fraction of maximum accessibility score by dividing mean cpm counts by the maximum cpm value over time. Peaks were clustered by similarities in their accessibility profile over time using the R function kmeans(k -= 8, nstart = 25, iter.max = 15) after setting the random seed to 1230412 (chosen using a random number generator).
Genome_build: dm3
Supplementary_files_format_and_content: FAIREseq – Z-normalized bigwig files generated from the pooled datasets
Supplementary_files_format_and_content: ChIPseq – narrowPeak files containing output from MACS2 peak calls
Supplementary_files_format_and_content: ChIPseq – Z-normalized bigwig files generated from the pooled datasets
Supplementary_files_format_and_content: FAIREseq – Z-normalized bigwig files generated from individual replicates for wild-type timecourse
Supplementary_files_format_and_content: ChIPseq – union peak list used for analysis in csv format (coordinates are bed-format, ie 0 indexed)
Supplementary_files_format_and_content: ChIPseq – csv file containing the fraction of maximum FAIRE-seq signal within ChIP peaks along with their assigned cluster values
Supplementary_files_format_and_content: FAIREseq – csv file containing the fraction of maximum FAIRE-seq signal within ChIP peaks along with their assigned cluster values

organism: Drosophila melanogaster

source_name: 3LW wing imaginal discs

extract_protocol:
200+ Wings were manually dissected from 3LW male and female larvae lacking the UAS-E93-3xHA transgene. Wings were fixed in batches of 20 in 4% paraformaldehyde, 50mM HEPES, 100mM NaCl, 1mM EDTA, 0.5mM EGTA for 20-minutes at room temperature, followed by quenching with 125mM glycine in 1x PBS, 0.01% Triton. Fixed wings were Dounce homogenized in 10mM HEPES, 10mM EDTA, 0.5mM EGTA, 0.25% Triton, 1mM PMSF. Nuclei were pelleted at 4,500xg for 20-minutes, and re-suspended in 10mM HEPES, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.01% Triton, 1mM PMSF. After nutating at 4C for 10-minutes, nuclei were pelleted again and re-suspended in 140mM NaCl, 10mM HEPES, 1mM EDTA, 0.5mM EGTA, 1mM PMSF, 0.1% SDS, followed by sonication on ice with a Branson Sonifier until average chromatin fragment size was 200bp. The soluble chromatin fraction was used for ChIP. Briefly, extracts were pre-cleared with protein-A dynabeads for 2 hours at 4C, and cleared extracts were incubated with 5 µg of Rabbit anti-HA (Abcam, ab9110) overnight at 4C. Bead pulldown was performed for 3-hours the following day. Antibody-bead complexes were washed successively, and then eluted with 1% SDS, 250mM NaCl, 10mM Tris, 1mM EDTA. Samples were treated with RNase A and proteinase K, heated overnight at 65C to reverse crosslinks, and purified DNA was recovered by phenol-chloroform/ethanol precipitation.
Rubicon Thruplex DNA-seq kit

value: wing

tag: developmental stage

value: yw;vg-GAL4, UAS-flp, tub>STOP>GAL4, UAS-GFP/+;Gal80ts/+

tag: protocol

value: ChIP-seq

tag: biological replicate number

tag: chip antibody


title: VgControl-3LW-Wing-antiHA-ChIP-Rep1

description:
VgControl-3LW-Wing-antiHA-ChIP-Rep1
VgControl-3LW-Wing-ChIP_2Reps_POOLED_zNorm.bw

tag: tissue


title: 1001703001_F7

description: mRNA + vRNA

source_name: U87 cells

tag: moi

tag: hours post infection

tag: plate


title: cardiac fibroblasts_Sham/Vehicle_2A

description: Barcode: CGATGT


title: cardiac fibroblasts_TAC/Vehicle_14B

description: Barcode: ACAGTG


title: 1001703001_G12

description: mRNA + vRNA

tag: well


title: 1001703001_F6

description: mRNA + vRNA


title: E93GOF-3LW-Wing-antiHA-ChIP-Rep2

description:
E93GOF-3LW-Wing-antiHA-ChIP-Rep2
E93GOF-3LW-Wing-ChIP_2Reps_POOLED_zNorm.bw
union_chip_peaks_annotated.csv
chip_peaks_fraction_max_FAIRE.csv

extract_protocol:
200+ Wings were manually dissected from 3LW male and female UAS-E93-3xHA larvae. Wings were fixed in batches of 20 in 4% paraformaldehyde, 50mM HEPES, 100mM NaCl, 1mM EDTA, 0.5mM EGTA for 20-minutes at room temperature, followed by quenching with 125mM glycine in 1x PBS, 0.01% Triton. Fixed wings were Dounce homogenized in 10mM HEPES, 10mM EDTA, 0.5mM EGTA, 0.25% Triton, 1mM PMSF. Nuclei were pelleted at 4,500xg for 20-minutes, and re-suspended in 10mM HEPES, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.01% Triton, 1mM PMSF. After nutating at 4C for 10-minutes, nuclei were pelleted again and re-suspended in 140mM NaCl, 10mM HEPES, 1mM EDTA, 0.5mM EGTA, 1mM PMSF, 0.1% SDS, followed by sonication on ice with a Branson Sonifier until average chromatin fragment size was 200bp. The soluble chromatin fraction was used for ChIP. Briefly, extracts were pre-cleared with protein-A dynabeads for 2 hours at 4C, and cleared extracts were incubated with 5 µg of Rabbit anti-HA (Abcam, ab9110) overnight at 4C. Bead pulldown was performed for 3-hours the following day. Antibody-bead complexes were washed successively, and then eluted with 1% SDS, 250mM NaCl, 10mM Tris, 1mM EDTA. Samples were treated with RNase A and proteinase K, heated overnight at 65C to reverse crosslinks, and purified DNA was recovered by phenol-chloroform/ethanol precipitation.
Rubicon Thruplex DNA-seq kit

value: yw;vg-GAL4, UAS-flp, tub>STOP>GAL4, UAS-GFP/+;Gal80ts/UAS-3xHA-E93


title: 1001703001_F5

description: mRNA + vRNA


title: 1001703001_F24

description: mRNA + vRNA


title: E93gfstf-24APF-Wing-ChIP-Rep1_re-analyzed

description:
E93gfstf-24APF-Wing-ChIP-Rep1
E93gfstf-24APF-Wing-ChIP_2Reps_POOLED_zNorm.bw
union_chip_peaks_annotated.csv
chip_peaks_fraction_max_FAIRE.csv
GSM2583768

source_name: 24hAPF wings

extract_protocol:
700+ Wings were manually dissected from 24hAPF male and female E93 protein trap flies. Wings were fixed in batches of 20 in 4% paraformaldehyde, 50mM HEPES, 100mM NaCl, 1mM EDTA, 0.5mM EGTA for 20-minutes at room temperature, followed by quenching with 125mM glycine in 1x PBS, 0.01% Triton. Fixed wings were Dounce homogenized in 10mM HEPES, 10mM EDTA, 0.5mM EGTA, 0.25% Triton, 1mM PMSF. Nuclei were pelleted at 4,500xg for 20-minutes, and re-suspended in 10mM HEPES, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.01% Triton, 1mM PMSF. After nutating at 4C for 10-minutes, nuclei were pelleted again and re-suspended in 140mM NaCl, 10mM HEPES, 1mM EDTA, 0.5mM EGTA, 1mM PMSF, 0.1% SDS, followed by sonication on ice with a Branson Sonifier until average chromatin fragment size was 200bp. The soluble chromatin fraction was used for ChIP. Briefly, extracts were pre-cleared with protein-A dynabeads for 2 hours at 4C, and cleared extracts were incubated with 5µg of rabbit anti-GFP antibody (Abcam cat# ab290) overnight at 4C. Bead pulldown was performed for 3-hours the following day. Antibody-bead complexes were washed successively, and then eluted with 1% SDS, 250mM NaCl, 10mM Tris, 1mM EDTA. Samples were treated with RNase A and proteinase K, heated overnight at 65C to reverse crosslinks, and purified DNA was recovered by phenol-chloroform/ethanol precipitation.
Rubicon Thruplex DNA-seq kit

value: yw/+; + ; Mi{MIC}Eip93F/+


title: E93GOF-3LW-Wing-antiHA-ChIP-Rep1

description:
E93GOF-3LW-Wing-antiHA-ChIP-Rep1
E93GOF-3LW-Wing-ChIP_2Reps_POOLED_zNorm.bw
union_chip_peaks_annotated.csv
chip_peaks_fraction_max_FAIRE.csv


title: 1001703001_F3

description: mRNA + vRNA


title: 1001703001_F23

description: mRNA + vRNA


title: E93GOF-3LW-Wing-FAIRE-Rep1_resequenced

description:
E93GOF-3LW-Wing-FAIRE-Rep1_resequenced
E93GOF-3LW-Wing-FAIRE_2Reps_POOLED_zNorm.bw
resequencing of library from GSM4212619

extract_protocol:
A minimum of 40 wings were dissected from staged female flies in 1x PBS and transferred to ice for subsequent processing. 6 rounds of bead beating (1 minute beating, 2 minutes resting) were performed on dissected tissue. Lysate was sonicated with a Branson sonifier to a fragment size range of 500 bp – 2kb. Soluble chromatin fraction was isolated by centrifugation at 15,000 RCF x 5’ at 4C. Soluble chromatin fraction was phenol-chloroform extracted. Isolated FAIRE-enriched DNA was used for library prep.
Rubicon Thruplex DNA-seq kit

value: FAIRE-seq


title: E93gfstf-24APF-Wing-ChIP-Rep2_re-analyzed

description:
E93gfstf-24APF-Wing-ChIP-Rep2
E93gfstf-24APF-Wing-ChIP_2Reps_POOLED_zNorm.bw
union_chip_peaks_annotated.csv
chip_peaks_fraction_max_FAIRE.csv
GSM2583769


title: 1001703001_F4

description: mRNA + vRNA


title: E93GOF-3LW-Wing-FAIRE-Rep2

description:
E93GOF-3LW-Wing-FAIRE-Rep2
E93GOF-3LW-Wing-FAIRE_2Reps_POOLED_zNorm.bw


title: 1001703001_F22

description: mRNA + vRNA


title: E93-44hAPF-FAIRE-Rep2_re-analyzed

description:
E93-44hAPF-FAIRE-Rep2
E93mut-44APF-Wing-FAIRE_2Reps_POOLED_zNorm.bw
GSM2583767

source_name: 44hAPF wings


title: 1001703001_F21

description: mRNA + vRNA


title: 1001703001_F20

description: mRNA + vRNA


title: 1001703001_F19

description: mRNA + vRNA


title: 1001703001_F2

description: mRNA + vRNA


title: 1001703001_F18

description: mRNA + vRNA


title: E93-44hAPF-FAIRE-Rep1_re-analyzed

description:
E93-44hAPF-FAIRE-Rep1
E93mut-44APF-Wing-FAIRE_2Reps_POOLED_zNorm.bw
GSM2583766


title: E93-3LW-FAIRE-Rep1_re-analyzed

description:
E93-3LW-FAIRE-Rep1
E93mut-3LW-Wing-FAIRE_2Reps_POOLED_zNorm.bw
GSM2583762


title: E93-3LW-FAIRE-Rep2_re-analyzed

description:
E93-3LW-FAIRE-Rep2
E93mut-3LW-Wing-FAIRE_2Reps_POOLED_zNorm.bw
GSM2583763


title: 1001703001_F17

description: mRNA + vRNA


title: E93-24hAPF-FAIRE-Rep1_re-analyzed

description:
E93-24hAPF-FAIRE-Rep1
E93mut-24APF-Wing-FAIRE_2Reps_POOLED_zNorm.bw
GSM2583764


title: WT-44hAPF-FAIRE-Rep3_re-analyzed

description:
WT-44hAPF-FAIRE-Rep3
OR-44APF-Wing-FAIRE_3Reps_POOLED_zNorm.bw
chip_peaks_fraction_max_FAIRE.csv
GSM3833344

value: Wild-type


title: WT-44hAPF-FAIRE-Rep2_re-analyzed

description:
WT-44hAPF-FAIRE-Rep2
OR-44APF-Wing-FAIRE_3Reps_POOLED_zNorm.bw
chip_peaks_fraction_max_FAIRE.csv
GSM3833343


title: 1001703001_F12

description: mRNA + vRNA


title: 1001703001_F15

description: mRNA + vRNA


title: WT-44hAPF-FAIRE-Rep1_re-analyzed

description:
WT-44hAPF-FAIRE-Rep1
OR-44APF-Wing-FAIRE_3Reps_POOLED_zNorm.bw
chip_peaks_fraction_max_FAIRE.csv
GSM3833342


title: WT-36hAPF-FAIRE-Rep2_re-analyzed

description:
WT-36hAPF-FAIRE-Rep2
chip_peaks_fraction_max_FAIRE.csv
GSM3833340

source_name: 36hAPF wings


title: 1001703001_F14

description: mRNA + vRNA


title: 1001703001_F13

description: mRNA + vRNA


title: 1001703001_F10

description: mRNA + vRNA


title: WT-36hAPF-FAIRE-Rep3_re-analyzed

description:
WT-36hAPF-FAIRE-Rep3
chip_peaks_fraction_max_FAIRE.csv
GSM3833341


title: 1001703001_E9

description: mRNA + vRNA


title: WT-24hAPF-FAIRE-Rep3_re-analyzed

description:
WT-24hAPF-FAIRE-Rep3
OR-24APF-Wing-FAIRE_3Reps_POOLED_zNorm.bw
chip_peaks_fraction_max_FAIRE.csv
GSM3833338


title: WT-24hAPF-FAIRE-Rep2_re-analyzed

description:
WT-24hAPF-FAIRE-Rep2
OR-24APF-Wing-FAIRE_3Reps_POOLED_zNorm.bw
chip_peaks_fraction_max_FAIRE.csv
GSM3833337


title: WT-24hAPF-FAIRE-Rep1_re-analyzed

description:
WT-24hAPF-FAIRE-Rep1
OR-24APF-Wing-FAIRE_3Reps_POOLED_zNorm.bw
chip_peaks_fraction_max_FAIRE.csv
GSM3833336


title: E93-24hAPF-FAIRE-Rep2_re-analyzed

description:
E93-24hAPF-FAIRE-Rep2
E93mut-24APF-Wing-FAIRE_2Reps_POOLED_zNorm.bw
GSM2583765


title: 1001703001_F16

description: mRNA + vRNA


title: WT-36hAPF-FAIRE-Rep1_re-analyzed

description:
WT-36hAPF-FAIRE-Rep1
chip_peaks_fraction_max_FAIRE.csv
GSM3833339


title: WT-18hAPF-FAIRE-Rep4_re-sequenced

description:
WT-18hAPF-FAIRE-Rep4_resequenced
chip_peaks_fraction_max_FAIRE.csv
resequencing of library from GSM4212602

source_name: 18hAPF wings


title: 1001703001_E6

description: mRNA + vRNA


title: WT-18hAPF-FAIRE-Rep4

description:
WT-18hAPF-FAIRE-Rep4
chip_peaks_fraction_max_FAIRE.csv


title: 1001703001_E7

description: mRNA + vRNA


title: WT-18hAPF-FAIRE-Rep3_re-sequenced

description:
WT-18hAPF-FAIRE-Rep3_resequenced
chip_peaks_fraction_max_FAIRE.csv
resequencing of library from GSM3833335


title: WT-18hAPF-FAIRE-Rep3_re-analyzed

description:
WT-18hAPF-FAIRE-Rep3
chip_peaks_fraction_max_FAIRE.csv
GSM3833335


title: 1001703001_E5

description: mRNA + vRNA


title: 1001703001_E3

description: mRNA + vRNA


title: 1001703001_F11

description: mRNA + vRNA


title: WT-18hAPF-FAIRE-Rep1_re-analyzed

description:
WT-18hAPF-FAIRE-Rep1
chip_peaks_fraction_max_FAIRE.csv
GSM3833333


title: 1001703001_E24

description: mRNA + vRNA


title: 1001703001_F1

description: mRNA + vRNA


title: E93GOF-3LW-Wing-FAIRE-Rep1

description:
E93GOF-3LW-Wing-FAIRE-Rep1
E93GOF-3LW-Wing-FAIRE_2Reps_POOLED_zNorm.bw


title: WT-6hAPF-FAIRE-Rep2_re-sequenced

description:
WT-6hAPF-FAIRE-Rep2_resequenced
chip_peaks_fraction_max_FAIRE.csv
resequencing of library from GSM4212596

source_name: 6hAPF wings


title: WT-6hAPF-FAIRE-Rep1_re-sequenced

description:
WT-6hAPF-FAIRE-Rep1_resequenced
chip_peaks_fraction_max_FAIRE.csv
resequencing of library from GSM3833332


title: 1001703001_E22

description: mRNA + vRNA


title: 1001703001_E8

description: mRNA + vRNA


title: 1001703001_E21

description: mRNA + vRNA


title: WT-6hAPF-FAIRE-Rep1_re-analyzed

description:
WT-6hAPF-FAIRE-Rep1
chip_peaks_fraction_max_FAIRE.csv
GSM3833332


title: WT-6hAPF-FAIRE-Rep2

description:
WT-6hAPF-FAIRE-Rep2
chip_peaks_fraction_max_FAIRE.csv


title: WT-3LW-FAIRE-Rep3_re-sequenced

description:
WT-3LW-FAIRE-Rep3_resequenced
OR-3LW-Wing-FAIRE_3Reps_POOLED_zNorm.bw
chip_peaks_fraction_max_FAIRE.csv
resequencing of library from GSM3833329


title: WT-3LW-FAIRE-Rep3_re-analyzed

description:
WT-3LW-FAIRE-Rep3
OR-3LW-Wing-FAIRE_3Reps_POOLED_zNorm.bw
chip_peaks_fraction_max_FAIRE.csv
GSM3833329


title: 1001703001_E2

description: mRNA + vRNA


title: 1001703001_E19

description: mRNA + vRNA


title: WT-3LW-FAIRE-Rep2_re-analyzed

description:
WT-3LW-FAIRE-Rep2
OR-3LW-Wing-FAIRE_3Reps_POOLED_zNorm.bw
chip_peaks_fraction_max_FAIRE.csv
GSM3833328


title: 1001703001_E17

description: mRNA + vRNA


title: 1001703001_E18

description: mRNA + vRNA


title: WT-3LW-FAIRE-Rep1_re-analyzed

description:
WT-3LW-FAIRE-Rep1
OR-3LW-Wing-FAIRE_3Reps_POOLED_zNorm.bw
chip_peaks_fraction_max_FAIRE.csv
GSM3833327


title: 1001703001_E16

description: mRNA + vRNA


title: 1001703001_E15

description: mRNA + vRNA


title: 1001703001_E20

description: mRNA + vRNA


title: 1001703001_E4

description: mRNA + vRNA


title: 1001703001_E14

description: mRNA + vRNA


title: 1001703001_E12

description: mRNA + vRNA


title: 1001703001_E23

description: mRNA + vRNA


title: 1001703001_E13

description: mRNA + vRNA


title: SMARCA4_24h_rep2

data_processing:
Reads were quality-checked with FastQC. Sequencing adapters were removed with Trimmomatic and reads were hard-trimmed by 5 bases at the 3’-end (Bolger et al., 2014)
Successively, reads at least 20 bases long, and with an overall average phred quality score greater than 10 were aligned to the reference genome and transcriptome of Homo Sapiens (FASTA and GTF files, respectively, downloaded from GRCh38) with STAR v2.5.1  with default settings for single end reads (Dobin et al., 2013)
Distribution of the reads across genomic isoform expression was quantified using the R package GenomicRanges  from Bioconductor Version 3.0 (Lawrence et al., 2013). Differentially expressed genes (DE) were identified using the R package edgeR  from Bioconductor Version 3.0 (Robinson et al., 2010).
A gene is marked as DE if it possesses the following characteristics: 1) at least 10 counts in at least half of the samples in one group, 2) p < 0.05. and 3) log2 ratio >= 1.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: SMARCA4_24h_human intestinal organoids

extract_protocol:
Qiagen RNEasy
For RNA extraction, 8 x 20 µl Matrigel droplets with organoids were harvested and organoid pellets were lysed in RLT buffer. RNA was isolated using the RNeasy Kit (Qiagen) according to the manufacturer’s instructions. The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies) and a Bioanalyzer 2100 (Agilent). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. The TruSeq RNA Sample Prep Kit v2 (Illumina) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were poly-A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences). The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq PE Cluster Kit HS4000 or TruSeq SR Cluster Kit HS4000 (Illumina) was used for cluster generation using 10 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the Illumina HiSeq2000 single end 100 bp using the TruSeq SBS Kit HS4000 (Illumina, Inc, California, USA).

treatment_protocol: For TGF-pathway activation, organoids were cultured without A83-01 and in 10 ng/ml recombinant TGFB1

value: organoids

value: Human small intestine

value: APC-KO, SMARCA4-KO


title: SMARCA4_0h_rep2

source_name: SMARCA4_0h_human intestinal organoids


title: SMARCA4_0h_rep3


title: SMARCA4_0h_rep1


title: 1001703001_E10

description: mRNA + vRNA


title: SMARCA4_24h_rep1


title: SMARCA4_24h_rep3


title: 1001703001_E11

description: mRNA + vRNA


title: ARID1A_24h_rep3

source_name: ARID1A_24h_human intestinal organoids

value: APC-KO, ARID1A-KO


title: Zebrafish Wt brain, 8 days post fertilization

city: Esch-sur-Alzette

first: Kamil

last: Grzyb

email: kamilgen@gmail.com, kamil.grzyb@uni.lu

address: 2, avenue de l'Université

country: Luxembourg

institute: University of Luxembourg - LCSB

data_processing:
R1 contains the cell barcode (1-12 bp) and UMI (13-20 bp). R2 contains the cDNA sequence.
Bcl2fastq ver 2.0 was used for the base calling
Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation (Macosko et al; 2015), the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner - with default parameters
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include raw counts

organism: Danio rerio

source_name: Wt brain, 8 days post fertilization

growth_protocol: as described in Tiraboschi et al., EPI-00649-2019

extract_protocol:
Single cell RNA seq using Dropseq - 3' bead based enrichment technique, using SMART synthesis (Macosko et al, 2015 doi: 10.1016/j.cell.2015.05.002)
Libraries were prepared according to Drop-seq methods (Macosko et al, 2015 doi: 10.1016/j.cell.2015.05.002). After cDNA tagmenation, PCR amplification was performed using Illumina primers (N701,N702, A501). The purified cDNA fragments of ~600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.

value: brain

value: WT

tag: age

value: 8 day post fertilization


title: 1001703001_D9

description: mRNA + vRNA


title: Zebrafish Mut(scn1Lab) brain, 8 days post fertilization


title: 1001703001_E1

description: mRNA + vRNA


title: 1001703001_D7

description: mRNA + vRNA


title: 1001703001_D8

description: mRNA + vRNA


title: Zebrafish Mut(scn1Lab) brain, 5 days post fertilization

value: 5 day post fertilization


title: 1001703001_D6

description: mRNA + vRNA


title: ARID1A_24h_rep1


title: Zebrafish Wt brain, 5 days post fertilization

source_name: Wt brain, 5 days post fertilization


title: 1001703001_D5

description: mRNA + vRNA


title: ARID1A_0h_rep3

source_name: ARID1A_0h_human intestinal organoids


title: 1001703001_D4

description: mRNA + vRNA


title: 1001703001_D3

description: mRNA + vRNA


title: 1001703001_D24

description: mRNA + vRNA


title: LoVo which co-cultured with LV-NC fibroblasts rep2

city: shanghai

first: Hui

last: Zhao

state: China

address: 600 YiShan Road, Shanghai 200233, People's Republic of China.

country: China

institute: Shanghai Jiao Tong University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: LoVo cell

extract_protocol:
LoVo cells flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 24 hours of co-culture ( LoVo cell  which co-cultured with LV-GALC HFL1 fibroblasts cells and LoVo cell which co-cultured with LV-NC HFL1 fibroblasts cells using Transwell chamber), the Transwell chamber was discarded and RNA was extracted from co-cultured LoVo cells  for RNA-seq analysis.

tag: time point

value: co-cultrued 24h

value: LV-NC HFL1


title: LoVo which co-cultured with LV-NC fibroblasts rep3


title: ARID1A_0h_rep2


title: WT-18hAPF-FAIRE-Rep2_re-analyzed

description:
WT-18hAPF-FAIRE-Rep2
chip_peaks_fraction_max_FAIRE.csv
GSM3833334

value: wing

tag: strain


title: LoVo which co-cultured with LV-NC fibroblasts rep1


title: ARID1A_0h_rep1


title: 1001703001_D22

description: mRNA + vRNA

extract_protocol:
no extraction
viscRNA-Seq
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq


title: ARID1A_24h_rep2


title: 1001703001_D20

description: mRNA + vRNA


title: 1001703001_D21

description: mRNA + vRNA


title: 1001703001_D23

description: mRNA + vRNA


title: 1001703001_D2

description: mRNA + vRNA


title: LoVo which co-cultured with LV-GALC fibroblasts rep2

value: LV-GALC HFL1


title: 1001703001_D19

description: mRNA + vRNA


title: APC_24h_rep2

source_name: APC_24h_human intestinal organoids

value: APC-KO


title: 1001703001_D18

description: mRNA + vRNA


title: LoVo which co-cultured with LV-GALC fibroblasts rep1


title: LoVo which co-cultured with LV-GALC fibroblasts rep3


title: 1001703001_D17

description: mRNA + vRNA


title: APC_24h_rep1


title: 1001703001_D16

description: mRNA + vRNA


title: 1001703001_D15

description: mRNA + vRNA


title: APC_0h_rep3

source_name: APC_0h_human intestinal organoids


title: 1001703001_D14

description: mRNA + vRNA


title: APC_0h_rep2


title: 1001703001_D13

description: mRNA + vRNA


title: HIF1α-Arsenic-ChIPSeq

city: Detroit

first: Fei

last: Chen

state: Michigan

address: 4417 Second Ave APT 119

department: Department of Pharmaceutical Sciences

institute: wayne state university

data_processing:
The 75-nt sequence reads were performed by using Illumina NextSeq 500 platform.
The reads were mapped to the genome hg19 using the BWA algorithm with default settings.
The 75-nt reads were expanded to 200 nt fragments at their 3'-end by Active Motif software. The whole genome was seperated into number of bins in every 32 nt, and the number of fragments in each bin were identified as fragment densities.
The peaks were called by MACS (version 2.1.0).
Spike-in Adjustment was used for normalization.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file is the processed data showing the signal maps.

source_name: Bronchial epithelial cells

growth_protocol: The human bronchial epithelial cell line BEAS-2B were purchased from the American Type Culture Collection(ATCC). The cells were cultured in DMEM medium with 5% fetal bovine serum,1% penicillin-streptomycin and 1% L-Glutamine, and maintained in humidified incubator at 37℃ with 5% CO2.

extract_protocol:
Ten million control and arsenic treated BEAS-2B cells were fixed and subjected to immunoprecipitation using ChIP-grade antibodies against Nrf2 and HIF1α. ChIP and input/control DNA were prepared for sequencing using Illumina NextSeq 500.
Libraries were generated using Next Gen DNA library kit

treatment_protocol: Day1, change to serum-free medium to starve the cells overnight. Day2, treat cells with or without Aresinic (1 μM) for 6 hrs before collecting samples.

value: lung, bronchus

tag: cell line

value: HIF1α (Abcam cat#ab2185)

tag: treatment

value: arsenic


title: Input DNA-Seq


title: 1001703001_D12

description: mRNA + vRNA


title: APC_24h_rep3

tag: cell type


title: 1001703001_D11

description: mRNA + vRNA


title: APC_0h_rep1

tag: genotype


title: 1001703001_D10

description: mRNA + vRNA


title: Nrf2-Arsenic-ChIPSeq

value: Nrf2 (Santa Cruz cat#sc-13032)


title: 1001703001_C9

description: mRNA + vRNA


title: 1001703001_C8

description: mRNA + vRNA


title: HIF1α-Control-ChIPSeq

value: control


title: Nrf2-Control-ChIPSeq


title: 1001703001_C7

description: mRNA + vRNA


title: 1001703001_C6

description: mRNA + vRNA


title: 1001703001_C4

description: mRNA + vRNA


title: 1001703001_C3

description: mRNA + vRNA


title: CTRL_KO_rep2

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

country: Germany

institute: Heidelberg University

description: RiboMethSeq

data_processing:
Library strategy: RiboMethSeq
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina NextSeq500
Adapter sequences were removed using trim-galore with a minimum length of 15 nt,
Reads were mapped using Bowtie2 to a reference sequence file containing rDNA sequences of U18, U28 and U5.8S
For each position the number of 5’-read ends was counted.
2’O-methyation was calculated as scoreC based on 5’-end frequencies as described before by Birkedal et al., 2015
Genome_build: Annotation of modification sites as well as rRNA sequence was downloaded from https://www-snorna.biotoul.fr
Supplementary_files_format_and_content: RiboMethSeq_read_count.txt contains counts of 5’-read end positions: subunit TAB pos TAB sample_counts. RiboMethSeq_scoreC.txt contains calculated scoreC for annotated modification sites: subunit TAB pos TAB annoation TAB sample_scoreC

extract_protocol: 100 ng total RNA was fragmented by alkaline hydrolysis at 95°C for 12 min. to achieve a fragment length of about 30 nucleotides. Libraries were prepared using the NEBNext® Small RNA library prep kit.

value: CTRL KO


title: SMARCA4_TREAT_atacseq_REP2

data_processing:
Raw sequencing reads were filtered for low-quality after adapter removal and aligned on GRCh38 using Bowtie2  with default mapping parameters
PCR duplicates were removed using Picard. The mapped reads of all replicates were merged for each condition prior to peak calling. Peaks were called on each sample using MACS2 with “--nomodel --shift -100 --extsize 200”, to obtain a consensus peak set for each sample. The peak set was used to build a count matrix using the aligned reads for all samples and their replicates.
Differential peaks between sample groups were identified using edgeR. For this, the count matrix was filtered for peaks with low coverage across all samples based on minimum read count of 10 for each sample. The remaining counts were normalized using the total library size as well as edgeR’s TMM derived normalization factors.
Between two sample groups, only regions with a log fold change above > 0.5 and an FDR value < 0.05 were considered as differentially accessible for further analysis. The peaks were annotated using HOMER
Genome_build: GRCh38

extract_protocol:
Lysis buffer
For ATAC-Seq with hSI organoids, organoids were dissociated into single cells and 50,000 cells were lysed in 50 µl cold Lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After centrifugation at 500 g for 10 min at 4˚C, cells were resuspended in 1X transposition mix (Illumina; 25 µl Tagment DNA Buffer, 2.5 µl Tagment DNA Enzyme, 22.5 µl ddH2O) and incubated for 30 min at 37˚C on a shaker at 300 rpm. Immediately after the transposition reaction, DNA was purified using the QIAgen MinElute PCR Purification Kit according to the manufacturer’s instructions. Library was amplified with Nextera Sequencing primers in NEBNext Q5 Hot Start HiFi 2X PCR master mix for 5 cycles. To remove large DNA fragments, the PCR reaction was incubated with 0.55X AMPure XP beads (Beckman Coulter) and the unbound supernatant was subsequently purified with QIAgen MinElute coloumns. Again, DNA was amplified with Nextera Sequencing primers in NEBNext Q5 Hot Start HiFi 2X PCR master mix for 9 cycles. Finally, to remove primers and small DNA fragments, PCR reaction was bead-purified with 1.8X AMPure XP beads.

value: organoids

value: Human small intestine

value: APC-KO, SMARCA4-KO


title: SMARCA4_CTRL_atacseq_REP2


title: ARID1A_TREAT_atacseq_REP2

value: APC-KO, ARID1A-KO


title: SMARCA4_CTRL_atacseq_REP1


title: ARID1A_TREAT_atacseq_REP1


title: 1001703001_C23

description: mRNA + vRNA


title: CTRL_KO_rep1

description: RiboMethSeq


title: CTRL_KO_rep3

description: RiboMethSeq


title: 1001703001_C24

description: mRNA + vRNA


title: 1001703001_C22

description: mRNA + vRNA


title: SNORD42A_KO_rep3

description: RiboMethSeq

value: SNORD42A KO


title: 1001703001_C21

description: mRNA + vRNA


title: SNORD42A_KO_rep2

description: RiboMethSeq


title: ARID1A_CTRL_atacseq_REP2


title: 1001703001_C20

description: mRNA + vRNA


title: 1001703001_D1

description: mRNA + vRNA


title: 1001703001_C2

description: mRNA + vRNA


title: 1001703001_C5

description: mRNA + vRNA


title: SMARCA4_TREAT_atacseq_REP1


title: SNORD42A_KO_rep1

description: RiboMethSeq


title: APC_TREAT_atacseq_REP2


title: ARID1A_CTRL_atacseq_REP1


title: Pol HLCs rep2

first: Viet Loan

last: Dao Thi

address: Im Neuenheimer Feld 344

department: University Hospital Heidelberg

institute: Center for Integrative Infectious Disease Research (CIID)

description: hepatocyte_polarization_system_counts_and_DE.csv

data_processing:
Sequencing reads were trimmed for low-quality/adapter sequence and mapped to the reference genome using Tophat2 (version 2.0.12; Bowtie version 2.2.7) with first strand library type, no novel junctions, and otherwise default options.
Mapped reads were counted using featureCounts (from subread version 1.4.6) with default options.
Statistical analysis was performed using a count-based workflow with the edgeR Bioconductor package (version 3.12.1). Briefly, gene counts were normalized to counts per million (CPM) and genes with less than 10-15 mapped reads were filtered out. Transcriptome composition bias between samples was eliminated using edgeR’s default trimmed mean of M-values (TMM) normalization. Differential expression analyses were performed using edgeR’s quantile-adjusted conditional maximum likelihood (qCML) method.
Genome_build: GRCh37
Supplementary_files_format_and_content: csv file with Abundance measurements and diff express

source_name: Hepatocyte-like cells (HLCs)_polarized

growth_protocol: 2x10e5 cells/cm of hESC were differentiated to definitive endoderm (DE) by harvesting them with gentle cell dissociation reagent (Stemcell Technologies) and plating onto Matrigel-coated culture dishes (Corning) in mTeSR1 medium  (Stemcell  Technologies).  The next day, DE differentiation was initiated by using the STEMdiff Definitive Endoderm Kit (Stemcell Technologies). To induce hepatic differentiation, definitive endoderm cells were harvested using Accutase (Innovative Cell Technologies), re-seeded in Matrigel-coated transwells and cultured in the presence of medium A (basolateralmedium  [BM]: CTS KnockOut DMEM/F12, 10% KnockOut Serum Replacement, 0.5% GlutaMAX supplement, and 0.5% non-essential amino acids all from ThermoFisher Scientific, supplemented with 100ng/ml hepatocyte growth factor [HGF]), 1% DMSO) for eight days followed by incubation in medium B (BM, 100ng/ml HGF, 1% DMSO,40ng/ml dexamethasone) for three more days. Cells were further matured in Hepatocyte Culture Medium (HCM, Lonza) supplemented with 20ng/ml oncostatin-M for five to seven days.

extract_protocol:
Total RNA was prepared from biological duplicate samples using the RNeasy mini Kit (Qiagen).
Sequencing libraries were constructed from approximately 100ng of total RNA using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina).

value: hESC-derived HLCs


title: 1001703001_C17

description: mRNA + vRNA

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

source_name: U87 cells


title: 1001703001_C16

description: mRNA + vRNA


title: APC_TREAT_atacseq_REP1


title: Pol HLCs rep1


title: 1001703001_C14

description: mRNA + vRNA


title: 1001703001_C13

description: mRNA + vRNA


title: Non-pol HLCs rep2


title: Non-pol HLCs rep1


title: 1001703001_C11

description: mRNA + vRNA


title: 1001703001_C12

description: mRNA + vRNA


title: 1001703001_C10

description: mRNA + vRNA


title: 1001703001_C19

description: mRNA + vRNA