title: heart_127s_A21


title: heart_127s_A17

status: Public on Sep 26 2022

type: SRA

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic single cell

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the mouse reference genome (GRCm38 / mm10) using TapHat2, Bowtie1 or Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the sample-plates were combined into one expression matrix file
counts data was processed and analyzed using SingleCellExperiment, pagoda2 and monocle packages in R-software
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

molecule: total RNA

organism: Mus musculus

source_name: male mouse

extract_protocol:
FACS into 384well plate of single cells from dissociation of mouse heart in Miltenyi's skeletal muscle dissociation kit (supplemented with collagenase IV-S).
RNA libraries were prepared using standard Smart-Seq2 protocol

tag: tissue

value: heart

tag: strain

tag: age

value: 8-30 weeks

tag: description


title: heart_127s_A20


title: heart_127s_A2


title: heart_127s_A19


title: heart_127s_A6


title: heart_127s_A18


title: heart_127s_G16


title: heart_127s_A13


title: heart_127s_A16


title: heart_127s_B12


title: heart_127s_A14


title: heart_127s_A15


title: heart_127s_A11


title: heart_126s_P9


title: heart_127s_A1


title: heart_127s_A10


title: heart_126s_P7


title: heart_127s_A12


title: heart_126s_P8


title: heart_126s_P3


title: heart_126s_P5


title: heart_126s_P4


title: heart_126s_P20


title: heart_126s_P22


title: heart_126s_P2


title: heart_126s_P6


title: heart_126s_P17


title: heart_126s_P16


title: heart_126s_P15


title: heart_126s_P12


title: heart_126s_P13


title: heart_126s_P1


title: heart_126s_P14


title: heart_126s_P11


title: heart_126s_P21


title: heart_126s_P18


title: heart_126s_O12


title: heart_126s_O14


title: heart_126s_O13


title: heart_126s_O7


title: heart_126s_O3


title: heart_126s_O6


title: heart_126s_O15


title: heart_126s_O22


title: heart_126s_O2


title: heart_126s_O20


title: heart_126s_O24


title: heart_126s_O21


title: heart_126s_O9


title: heart_126s_O4


title: heart_126s_O17


title: heart_126s_O8


title: heart_126s_O11


title: heart_126s_O5


title: heart_126s_O18


title: heart_126s_O19


title: heart_126s_O16


title: heart_126s_O23


title: heart_126s_O10


title: heart_126s_N4


title: heart_126s_O1


title: heart_126s_N8


title: heart_126s_N9


title: heart_126s_N5


title: heart_126s_N6


title: heart_126s_N7


title: heart_126s_N22


title: heart_126s_N19


title: heart_126s_N3


title: heart_126s_N20


title: heart_126s_N18


title: heart_126s_N23


title: heart_126s_N16


title: heart_126s_N14


title: heart_126s_N2


title: heart_126s_N21


title: heart_126s_N13


title: heart_126s_N10


title: heart_126s_N11


title: heart_126s_N1


title: heart_126s_N12


title: heart_126s_M8


title: heart_126s_N15


title: heart_126s_N24


title: heart_126s_M9


title: heart_126s_M7


title: heart_126s_M6


title: heart_126s_M23


title: heart_126s_M3


title: heart_126s_M22


title: heart_126s_N17


title: heart_126s_M24


title: heart_126s_M5


title: heart_126s_M4


title: heart_126s_M20


title: heart_126s_M21


title: heart_126s_M2


title: heart_126s_M18


title: heart_126s_M19


title: heart_126s_M15


title: heart_126s_M17


title: heart_126s_M10


title: heart_126s_M11


title: heart_126s_M16


title: heart_126s_L7


title: heart_126s_M12


title: heart_126s_L6


title: heart_126s_L4


title: heart_126s_M1


title: heart_126s_L3


title: heart_126s_L9


title: heart_126s_L5


title: heart_126s_L8


title: heart_126s_M14


title: heart_126s_M13


title: heart_126s_L23


title: heart_126s_L21


title: heart_126s_L19


title: heart_126s_L2


title: heart_126s_L18


title: heart_126s_L20


title: heart_126s_L17


title: heart_126s_L16


title: heart_126s_L14


title: heart_126s_L15


title: heart_126s_L13


title: heart_126s_L10


title: heart_126s_L1


title: heart_126s_L24


title: heart_126s_L11


title: heart_126s_K7


title: heart_126s_K9


title: heart_126s_K6


title: heart_126s_K8


title: heart_126s_K20


title: heart_126s_K21


title: heart_126s_K5


title: heart_126s_K23


title: heart_126s_K22


title: heart_126s_K18


title: heart_126s_K2


title: heart_126s_K3


title: heart_126s_L12


title: heart_126s_K19


title: heart_126s_K13


title: heart_126s_K11


title: heart_126s_K15


title: heart_126s_K1


title: heart_126s_K24


title: heart_126s_K17


title: heart_126s_J9


title: heart_126s_K4


title: heart_126s_J8


title: heart_126s_K10


title: heart_126s_J7


title: heart_126s_J6


title: heart_126s_J24


title: heart_126s_K14


title: heart_126s_J3


title: heart_126s_J4


title: heart_126s_J23


title: heart_126s_J2


title: heart_126s_J22


title: heart_126s_J19


title: heart_126s_J16


title: heart_126s_J18


title: heart_126s_K12


title: heart_126s_J21


title: heart_126s_J15


title: heart_126s_J17


title: heart_126s_J1


title: heart_126s_J5


title: heart_126s_I7


title: heart_126s_J20


title: heart_126s_J14


title: heart_126s_J12


title: heart_126s_J11


title: heart_126s_I6


title: heart_126s_I24


title: heart_126s_I8


title: heart_126s_I4


title: heart_126s_I20


title: heart_126s_I3


title: heart_126s_K16


title: heart_126s_I22


title: heart_126s_I23


title: heart_126s_J10


title: heart_126s_I21


title: heart_126s_I17


title: heart_126s_I9


title: heart_126s_I15


title: heart_126s_I11


title: heart_126s_I19


title: heart_126s_I12


title: heart_126s_J13


title: heart_126s_I13


title: heart_126s_I16


title: heart_126s_I10


title: heart_126s_I1


title: heart_126s_I14


title: heart_126s_H9


title: heart_126s_H8


title: heart_126s_H7


title: heart_126s_H6


title: heart_126s_H3


title: heart_126s_H5


title: heart_126s_I2


title: heart_126s_I18


title: heart_126s_H23


title: heart_126s_H24


title: heart_126s_H22


title: heart_126s_H20


title: heart_126s_H17


title: heart_126s_H2


title: heart_126s_H18


title: heart_126s_H16


title: heart_126s_H4


title: heart_126s_H15


title: heart_126s_H10


title: heart_126s_H1


title: heart_126s_H11


title: heart_126s_G7


title: heart_126s_G8


title: heart_126s_H14


title: heart_126s_G5


title: heart_126s_G9


title: heart_126s_G4


title: heart_126s_G3


title: heart_126s_H21


title: heart_126s_G24


title: heart_126s_H19


title: heart_126s_G6


title: heart_126s_G20


title: heart_126s_G22


title: heart_126s_G23


title: heart_126s_G2


title: heart_126s_G21


title: heart_126s_G19


title: heart_126s_H12


title: heart_126s_G18


title: heart_126s_G17


title: heart_126s_H13


title: heart_126s_G15


title: heart_126s_G11


title: heart_126s_G14


title: heart_126s_G13


title: heart_126s_G12


title: heart_126s_F8


title: heart_126s_G1


title: heart_126s_F9


title: heart_126s_F7


title: heart_126s_F6


title: heart_126s_F5


title: heart_126s_F24


title: heart_126s_F23


title: heart_126s_F20


title: heart_126s_F3


title: heart_126s_F2


title: heart_126s_F22


title: heart_126s_F12


title: heart_126s_F13


title: heart_126s_F16


title: heart_126s_G16


title: heart_126s_F4


title: heart_126s_F11


title: heart_126s_F15


title: heart_126s_F19


title: heart_126s_F10


title: heart_126s_E8


title: heart_126s_F18


title: heart_126s_E9


title: heart_126s_E3


title: heart_126s_E24


title: heart_126s_E4


title: heart_126s_E5


title: heart_126s_E23


title: heart_126s_E7


title: heart_126s_F1


title: heart_126s_E2


title: heart_126s_E22


title: heart_126s_E19


title: heart_126s_E20


title: heart_126s_E18


title: heart_126s_E17


title: heart_126s_E14


title: heart_126s_E16


title: heart_126s_E11


title: heart_126s_E12


title: heart_126s_D9


title: heart_126s_E10


title: heart_126s_D5


title: heart_126s_E13


title: heart_126s_E1


title: heart_126s_D7


title: heart_126s_D6


title: heart_126s_D4


title: heart_126s_E21


title: heart_126s_D3


title: heart_126s_D24


title: heart_126s_D2


title: heart_126s_D21


title: heart_126s_D22


title: heart_126s_E15


title: heart_126s_D19


title: heart_126s_D18


title: heart_126s_D20


title: heart_126s_D15


title: heart_126s_D14


title: heart_126s_D17


title: heart_126s_D8


title: heart_126s_D16


title: heart_126s_D12


title: heart_126s_D11


title: heart_126s_C9


title: heart_126s_D10


title: heart_126s_C4


title: heart_126s_C6


title: heart_126s_D23


title: heart_126s_C8


title: heart_126s_C20


title: heart_126s_C21


title: heart_126s_C3


title: heart_126s_C23


title: heart_126s_C24


title: heart_126s_C22


title: heart_126s_C2


title: heart_126s_C17


title: heart_126s_D13


title: heart_126s_C19


title: heart_126s_D1


title: heart_126s_C12


title: heart_126s_C16


title: heart_126s_C15


title: heart_126s_C13


title: heart_126s_C18


title: heart_126s_C14


title: heart_126s_B9


title: heart_126s_B8


title: heart_126s_C1


title: heart_126s_B6


title: heart_126s_B7


title: heart_126s_C11


title: heart_126s_B4


title: heart_126s_B24


title: heart_126s_B20


title: heart_126s_B2


title: heart_126s_B22


title: heart_126s_B5


title: heart_126s_B17


title: heart_126s_B18


title: heart_126s_B21


title: heart_126s_B19


title: heart_126s_B16


title: heart_126s_B12


title: heart_126s_B15


title: heart_126s_B13


title: heart_126s_B14


title: heart_126s_B10


title: heart_126s_B3


title: heart_126s_A8


title: heart_126s_B1


title: heart_126s_B23


title: heart_126s_A6


title: heart_126s_A5


title: heart_126s_A7


title: heart_126s_A9


title: heart_126s_A4


title: heart_126s_A24


title: heart_126s_A23


title: heart_126s_A3


title: heart_126s_A22


title: heart_126s_A20


title: heart_126s_A2


title: heart_126s_A19


title: heart_126s_A16


title: heart_126s_A18


title: heart_126s_A13


title: heart_126s_A17


title: heart_126s_A15


title: heart_126s_A14


title: heart_126s_A12


title: heart_126s_A11


title: heart_126s_A10


title: colon_686s_D8

library_source: transcriptomic

value: colon

value: PDGFRbGFP


title: colon_686s_D7


title: heart_126s_A21


title: colon_686s_D4


title: colon_686s_D6


title: colon_686s_D5


title: colon_686s_D22


title: colon_686s_D21


title: colon_686s_D2


title: colon_686s_D24


title: colon_686s_D18


title: colon_686s_D20


title: colon_686s_D17


title: colon_686s_D16


title: colon_686s_D15


title: colon_686s_D23


title: colon_686s_D13


title: colon_686s_D19


title: colon_686s_D14


title: colon_686s_D10


title: colon_686s_D1


title: colon_686s_C9


title: colon_686s_C7


title: colon_686s_C8


title: colon_686s_C5


title: colon_686s_C6


title: colon_686s_D9


title: colon_686s_C3


title: colon_686s_C4


title: colon_686s_C24


title: colon_686s_C23


title: colon_686s_C22


title: colon_686s_C21


title: colon_686s_C16


title: colon_686s_C20


title: colon_686s_C12


title: colon_686s_C13


title: colon_686s_C15


title: colon_686s_C14


title: colon_686s_B9


title: colon_686s_C1


title: colon_686s_C2


title: colon_686s_C18


title: colon_686s_B7


title: colon_686s_B8


title: colon_686s_C10


title: colon_686s_B4


title: colon_686s_B5


title: colon_686s_B6


title: colon_686s_B24


title: colon_686s_B23


title: colon_686s_B22


title: colon_686s_B21


title: colon_686s_B18


title: colon_686s_B15


title: colon_686s_B16


title: colon_686s_C11


title: colon_686s_B14


title: colon_686s_B13


title: colon_686s_B10


title: colon_686s_B12


title: colon_686s_A24


title: colon_686s_A7


title: colon_686s_A5


title: colon_686s_A22


title: colon_686s_B11


title: colon_686s_B2


title: colon_686s_A21


title: colon_686s_A23


title: colon_686s_A15


title: colon_686s_B17


title: colon_686s_A12


title: colon_686s_A16


title: colon_686s_B1


title: colon_686s_A1


title: colon_686s_A18


title: colon_685s_P2


title: colon_686s_A20


title: colon_686s_A13


title: colon_685s_P5


title: colon_686s_A10


title: colon_686s_D12


title: colon_685s_M14


title: colon_685s_M11


title: colon_685s_N15


title: colon_685s_P1


title: colon_685s_O10


title: colon_685s_N16


title: colon_685s_O22


title: colon_685s_N22


title: colon_685s_N6


title: colon_685s_O5


title: colon_685s_P15


title: colon_685s_O13


title: colon_685s_N9


title: colon_685s_M9


title: colon_685s_P18


title: colon_685s_O4


title: colon_685s_O16


title: colon_685s_M15


title: colon_685s_M21


title: colon_685s_M24


title: colon_685s_N3


title: colon_685s_O2


title: colon_685s_P13


title: colon_685s_O12


title: colon_685s_N12


title: colon_685s_P10


title: colon_685s_N23


title: colon_685s_M10


title: colon_685s_M1


title: colon_685s_L16


title: colon_685s_P4


title: colon_685s_P9


title: colon_685s_C8


title: colon_685s_C3


title: colon_685s_D8


title: colon_685s_D21


title: colon_685s_C9


title: colon_685s_D14


title: colon_685s_D3


title: colon_685s_D17


title: colon_685s_D19


title: colon_685s_C6


title: colon_685s_D24


title: colon_685s_D6


title: colon_685s_D7


title: colon_685s_D5


title: colon_685s_D11


title: colon_685s_D10


title: colon_685s_D2


title: colon_685s_C7


title: colon_685s_D9


title: colon_685s_D18


title: colon_685s_D13


title: colon_685s_D22


title: colon_685s_D16


title: colon_685s_D12


title: colon_685s_C5


title: colon_685s_D4


title: colon_685s_D15


title: colon_685s_D1


title: colon_685s_C4


title: colon_685s_C2


title: colon_685s_C18


title: colon_685s_C21


title: colon_685s_C19


title: colon_686s_A2


title: colon_685s_C23


title: colon_685s_C17


title: colon_685s_B7


title: colon_685s_B8


title: colon_685s_C22


title: colon_685s_B4


title: colon_685s_C11


title: colon_685s_C14


title: colon_685s_C16


title: colon_685s_C12


title: colon_685s_C13


title: colon_685s_B9


title: colon_685s_C24


title: colon_685s_B6


title: colon_685s_B18


title: colon_685s_C20


title: colon_685s_C1


title: colon_685s_C15


title: colon_685s_C10


title: colon_685s_B2


title: colon_685s_B22


title: colon_685s_B23


title: colon_685s_B20


title: colon_685s_B21


title: colon_685s_B24


title: colon_685s_B12


title: colon_685s_B17


title: colon_685s_B14


title: colon_685s_B11


title: colon_685s_A2


title: colon_685s_A7


title: colon_685s_A22


title: colon_685s_A19


title: colon_685s_A23


title: colon_685s_A3


title: colon_685s_A24


title: colon_685s_A20


title: colon_685s_B10


title: colon_685s_A5


title: colon_685s_A12


title: colon_685s_A13


title: colon_685s_A14


title: colon_685s_A16


title: colon_685s_B1


title: colon_685s_A6


title: colon_685s_A4


title: colon_685s_A9


title: colon_685s_A15


title: colon_685s_A18


title: colon_685s_A10


title: colon_685s_A1


title: colon_685s_A17


title: colon_682s_P3


title: colon_682s_J12


title: colon_682s_J20


title: colon_682s_I9


title: colon_682s_I15


title: colon_682s_F23


title: colon_682s_G24


title: colon_516s_P2


title: colon_516s_P22


title: colon_516s_P7


title: colon_516s_P5


title: colon_516s_P3


title: colon_682s_D18


title: colon_516s_O19


title: colon_516s_O4


title: colon_516s_O17


title: colon_516s_P19


title: colon_516s_N7


title: colon_516s_N21


title: colon_516s_N9


title: colon_516s_N22


title: colon_516s_O21


title: colon_516s_M3


title: colon_516s_N16


title: colon_516s_N13


title: colon_516s_N19


title: colon_516s_M22


title: colon_516s_N12


title: colon_516s_M21


title: colon_516s_M14


title: colon_516s_M12


title: colon_516s_L6


title: colon_516s_P1


title: colon_516s_L5


title: colon_516s_L11


title: colon_516s_L22


title: colon_516s_K8


title: colon_516s_J2


title: colon_516s_J24


title: colon_516s_I2


title: colon_516s_K16


title: colon_516s_I8


title: colon_516s_D23


title: colon_516s_I7


title: colon_516s_D22


title: colon_516s_D20


title: colon_516s_D7


title: colon_516s_D24


title: colon_516s_D9


title: colon_516s_E9


title: colon_516s_D6


title: colon_516s_G16


title: colon_516s_D8


title: colon_516s_L19


title: colon_516s_D5


title: colon_516s_D2


title: colon_516s_I12


title: colon_516s_D21


title: colon_516s_D17


title: colon_516s_K7


title: colon_516s_J4


title: colon_516s_D11


title: colon_516s_D3


title: colon_516s_C7


title: colon_516s_C6


title: colon_516s_D4


title: colon_516s_D1


title: colon_516s_D10


title: colon_516s_C8


title: colon_516s_B7


title: colon_516s_C10


title: colon_516s_C22


title: colon_516s_B8


title: colon_516s_C18


title: colon_516s_C4


title: colon_516s_B23


title: colon_516s_C3


title: colon_516s_C1


title: colon_516s_C19


title: colon_516s_B5


title: colon_516s_C5


title: colon_516s_B4


title: colon_516s_C16


title: colon_516s_B24


title: colon_516s_C23


title: colon_516s_B3


title: colon_516s_C11


title: colon_516s_C2


title: colon_516s_C24


title: colon_516s_B6


title: colon_516s_C21


title: colon_516s_C12


title: colon_516s_B22


title: colon_516s_B2


title: colon_516s_B19


title: colon_516s_B17


title: colon_516s_B18


title: colon_516s_B21


title: colon_516s_B20


title: colon_516s_B16


title: colon_516s_B12


title: colon_516s_A5


title: colon_516s_B14


title: colon_516s_B1


title: colon_516s_A3


title: colon_516s_A21


title: colon_516s_B10


title: colon_516s_A22


title: colon_516s_B11


title: colon_516s_B15


title: colon_516s_A8


title: colon_516s_A23


title: colon_516s_A24


title: colon_516s_A6


title: colon_516s_A18


title: colon_513s_G7


title: colon_516s_A19


title: colon_516s_A11


title: colon_516s_A16


title: colon_513s_E23


title: colon_516s_A17


title: colon_513s_M7


title: colon_516s_A12


title: colon_516s_A1


title: colon_513s_I20


title: colon_513s_J6


title: colon_516s_A15


title: colon_516s_A10


title: colon_516s_A2


title: colon_506s_P4

source_name: female mouse


title: colon_506s_P22


title: colon_506s_P5


title: colon_506s_P8


title: colon_506s_P3


title: colon_506s_P6


title: colon_506s_P9


title: colon_506s_P7


title: colon_506s_P2


title: colon_506s_P17


title: colon_506s_P20


title: colon_506s_P18


title: colon_506s_P16


title: colon_506s_P21


title: colon_506s_P15


title: colon_506s_O7


title: colon_506s_P10


title: colon_506s_O6


title: colon_506s_P12


title: colon_506s_P1


title: colon_506s_O3


title: colon_506s_P14


title: colon_506s_P11


title: colon_506s_O8


title: colon_506s_O4


title: colon_506s_O2


title: colon_506s_O13


title: colon_506s_O14


title: colon_506s_O24


title: colon_506s_O20


title: colon_506s_O22


title: colon_506s_O23


title: colon_516s_A7


title: colon_506s_O18


title: colon_506s_O10


title: colon_506s_O11


title: colon_506s_O12


title: colon_506s_O16


title: colon_506s_O15


title: colon_506s_O1


title: colon_506s_N6


title: colon_506s_P13


title: colon_506s_O5


title: colon_506s_N7


title: colon_506s_N5


title: colon_506s_N24


title: colon_506s_N23


title: colon_506s_N20


title: colon_506s_N21


title: colon_506s_N19


title: colon_506s_N18


title: colon_506s_N2


title: colon_506s_N17


title: colon_506s_N1


title: colon_506s_N16


title: colon_506s_N14


title: colon_506s_M7


title: colon_506s_N11


title: colon_506s_N13


title: colon_506s_N12


title: colon_506s_M8


title: colon_506s_M6


title: colon_506s_M3


title: colon_506s_M23


title: colon_506s_M22


title: colon_506s_M24


title: colon_506s_M21


title: colon_506s_M17


title: colon_506s_M5


title: colon_506s_M16


title: colon_506s_M19


title: colon_506s_N22


title: colon_506s_M15


title: colon_506s_N15


title: colon_506s_M14


title: colon_506s_M13


title: colon_506s_M10


title: colon_506s_M1


title: colon_506s_L9


title: colon_506s_L6


title: colon_506s_L8


title: colon_506s_M2


title: colon_506s_L23


title: colon_506s_L24


title: colon_506s_L21


title: colon_506s_L4


title: colon_506s_L22


title: colon_506s_L20


title: colon_506s_L2


title: colon_506s_L19


title: colon_506s_L17


title: colon_506s_M11


title: colon_506s_L16


title: colon_506s_L14


title: colon_506s_K24


title: colon_506s_K5


title: colon_506s_K6


title: colon_506s_L12


title: colon_506s_K3


title: colon_506s_L13


title: colon_506s_K4


title: colon_506s_L15


title: colon_506s_K9


title: colon_506s_K23


title: colon_506s_K21


title: colon_506s_K22


title: colon_506s_K15


title: colon_506s_K16


title: colon_506s_K14


title: colon_506s_K11


title: colon_506s_K12


title: colon_506s_K1


title: colon_506s_J5


title: colon_506s_J4


title: colon_506s_K18


title: colon_506s_K2


title: colon_506s_K20


title: colon_506s_J8


title: colon_506s_J24


title: colon_506s_J6


title: colon_506s_J3


title: colon_506s_J16


title: colon_506s_J20


title: colon_506s_J19


title: colon_506s_K17


title: colon_506s_J22


title: colon_506s_J18


title: colon_506s_J2


title: colon_506s_J21


title: colon_506s_J23


title: colon_506s_J15


title: colon_506s_J12


title: colon_506s_J13


title: colon_506s_J11


title: colon_506s_J9


title: colon_506s_K13


title: colon_506s_J10


title: colon_506s_J17


title: colon_506s_I8


title: colon_506s_I5


title: colon_506s_I3


title: colon_506s_I24


title: colon_506s_I23


title: colon_506s_I22


title: colon_506s_I19


title: colon_506s_I2


title: colon_506s_I20


title: colon_506s_I9


title: colon_506s_I18


title: colon_506s_I16


title: colon_506s_I14


title: colon_506s_I21


title: colon_506s_I13


title: colon_506s_J1


title: colon_506s_I10


title: colon_506s_I12


title: colon_506s_I11


title: colon_506s_I1


title: colon_506s_H6


title: colon_506s_I7


title: colon_506s_H7


title: colon_506s_H24


title: colon_506s_H3


title: colon_506s_H21


title: colon_506s_I17


title: colon_506s_H23


title: colon_506s_H20


title: colon_506s_I15


title: colon_506s_H22


title: colon_506s_H8


title: colon_506s_H2


title: colon_506s_H19


title: colon_506s_H18


title: colon_506s_H17


title: colon_506s_H9


title: colon_506s_H16


title: colon_506s_H4


title: colon_506s_H13


title: colon_506s_H1


title: colon_506s_H11


title: colon_506s_G7


title: colon_506s_G5


title: colon_506s_G8


title: colon_506s_G3


title: colon_506s_G24


title: colon_506s_G23


title: colon_506s_G22


title: colon_506s_G21


title: colon_506s_G20


title: colon_506s_G2


title: colon_506s_G19


title: colon_506s_G18


title: colon_506s_G17


title: colon_506s_G15


title: colon_506s_G16


title: colon_506s_H15


title: colon_506s_G14


title: colon_506s_G9


title: colon_506s_G10


title: colon_506s_J14


title: colon_506s_G13


title: colon_506s_F7


title: colon_506s_F9


title: colon_506s_G12


title: colon_506s_F5


title: colon_506s_F6


title: colon_506s_F24


title: colon_506s_F23


title: colon_506s_F21


title: colon_506s_F20


title: colon_506s_F2


title: colon_506s_F3


title: colon_506s_F4


title: colon_506s_F22


title: colon_506s_F17


title: colon_506s_F18


title: colon_506s_F15


title: colon_506s_F14


title: colon_506s_F16


title: colon_506s_F13


title: colon_506s_F12


title: colon_506s_F10


title: colon_506s_G1


title: colon_506s_F1


title: colon_506s_E4


title: colon_506s_E5


title: colon_506s_E3


title: colon_506s_E9


title: colon_506s_E20


title: colon_506s_E8


title: colon_506s_E23


title: colon_506s_E24


title: colon_506s_E18


title: colon_506s_E2


title: colon_506s_E22


title: colon_506s_E16


title: colon_506s_E15


title: colon_506s_E12


title: colon_506s_E14


title: colon_506s_E10


title: colon_506s_E1


title: colon_506s_E11


title: colon_506s_D9


title: colon_506s_E13


title: colon_506s_D8


title: colon_506s_D6


title: colon_506s_D24


title: colon_506s_D4


title: colon_506s_D21


title: colon_506s_D22


title: colon_506s_D20


title: colon_506s_D7


title: colon_506s_D19


title: colon_506s_D17


title: colon_506s_D18


title: colon_506s_E17


title: colon_506s_D2


title: colon_506s_D13


title: colon_506s_D16


title: colon_506s_D14


title: colon_506s_C9


title: colon_506s_D1


title: colon_506s_D12


title: colon_506s_D11


title: colon_506s_C7


title: colon_506s_C6


title: colon_506s_C8


title: colon_506s_C5


title: colon_506s_C22


title: colon_506s_C24


title: colon_506s_C23


title: colon_506s_C21


title: colon_506s_D15


title: colon_506s_C20


title: colon_506s_C19


title: colon_506s_D10


title: colon_506s_C2


title: colon_506s_C18


title: colon_506s_C15


title: colon_506s_C17


title: colon_506s_C11


title: colon_506s_C14


title: colon_506s_C12


title: colon_506s_C10


title: colon_506s_C1


title: colon_506s_B9


title: colon_506s_B6


title: colon_506s_B5


title: colon_506s_C4


title: colon_506s_B4


title: colon_506s_B7


title: colon_506s_C3


title: colon_506s_B3


title: colon_506s_B23


title: colon_506s_B24


title: colon_506s_B22


title: colon_506s_C16


title: colon_506s_B21


title: colon_506s_B20


title: colon_506s_B19


title: colon_506s_B17


title: colon_506s_B18


title: colon_506s_B8


title: colon_506s_B15


title: colon_506s_B16


title: colon_506s_B14


title: colon_506s_B13


title: colon_506s_B12


title: colon_506s_B11


title: colon_506s_A9


title: colon_506s_B1


title: colon_506s_A24


title: colon_506s_A21


title: colon_506s_A8


title: colon_506s_A19


title: colon_506s_A16


title: colon_504s_P6


title: colon_506s_A14


title: colon_506s_A6


title: colon_504s_P8


title: colon_506s_B2


title: colon_504s_P9


title: colon_504s_P22


title: colon_504s_P5


title: colon_504s_P4


title: colon_504s_P3


title: colon_504s_P2


title: colon_504s_P21


title: colon_504s_P18


title: colon_504s_P20


title: colon_504s_P15


title: colon_504s_P16


title: colon_504s_P14


title: colon_504s_P19


title: colon_504s_P12


title: colon_504s_P13


title: colon_504s_P17


title: colon_504s_P11


title: colon_506s_B10


title: colon_504s_O11


title: colon_504s_O7


title: colon_504s_P1


title: colon_504s_O6


title: colon_504s_O20


title: colon_504s_O13


title: colon_504s_O19


title: colon_504s_O22


title: colon_504s_O16


title: colon_504s_O3


title: colon_504s_O5


title: colon_504s_O9


title: colon_504s_N4


title: colon_504s_O17


title: colon_504s_O18


title: colon_504s_O15


title: colon_504s_O12


title: colon_504s_P10


title: colon_504s_N8


title: colon_504s_O21


title: colon_504s_O14


title: colon_504s_O8


title: colon_504s_N9


title: colon_504s_O24


title: colon_504s_N5


title: colon_504s_O23


title: colon_504s_O10


title: colon_504s_O2


title: colon_504s_O4


title: colon_504s_O1


title: colon_504s_N15


title: colon_504s_N2


title: colon_504s_N18


title: colon_504s_N14


title: colon_504s_N21


title: colon_504s_N3


title: colon_504s_N13


title: colon_504s_N22


title: colon_504s_N16


title: colon_504s_N23


title: colon_504s_N24


title: colon_504s_N17


title: colon_504s_N20


title: colon_504s_N19


title: colon_504s_N1


title: colon_504s_M11


title: colon_504s_M9


title: colon_504s_M22


title: colon_504s_N12


title: colon_504s_M24


title: colon_504s_M20


title: colon_504s_M18


title: colon_504s_M15


title: colon_504s_M16


title: colon_504s_M3


title: colon_504s_M4


title: colon_504s_M1


title: colon_504s_L9


title: colon_504s_M13


title: colon_504s_M6


title: colon_504s_L8


title: colon_504s_M19


title: colon_504s_M17


title: colon_504s_M12


title: colon_504s_M10


title: colon_504s_M5


title: colon_504s_N10


title: colon_504s_M2


title: colon_504s_M8


title: colon_504s_N11


title: colon_504s_M7


title: colon_504s_M23


title: colon_504s_M21


title: colon_504s_M14


title: colon_504s_L7


title: colon_504s_L6


title: colon_504s_L5


title: colon_504s_L4


title: colon_504s_L22


title: colon_504s_L3


title: colon_504s_L15


title: colon_504s_L20


title: colon_504s_L18


title: colon_504s_L17


title: colon_504s_L14


title: colon_504s_L16


title: colon_504s_L2


title: colon_504s_L19


title: colon_504s_K9


title: colon_504s_K8


title: colon_504s_K22


title: colon_504s_L12


title: colon_504s_K4


title: colon_504s_K23


title: colon_504s_L13


title: colon_504s_L1


title: colon_504s_K3


title: colon_504s_K20


title: colon_504s_L10


title: colon_504s_K6


title: colon_504s_K5


title: colon_504s_L11


title: colon_504s_K21


title: colon_504s_K7


title: colon_504s_K19


title: colon_504s_K18


title: colon_504s_K16


title: colon_504s_K17


title: colon_504s_K10


title: colon_504s_K13


title: colon_504s_K11


title: colon_504s_K12


title: colon_504s_K14


title: colon_504s_K1


title: colon_504s_J8


title: colon_504s_J9


title: colon_504s_K2


title: colon_504s_J6


title: colon_504s_J5


title: colon_504s_J24


title: colon_504s_J4


title: colon_504s_J21


title: colon_504s_J17


title: colon_504s_J19


title: colon_504s_J3


title: colon_504s_K15


title: colon_504s_J16


title: colon_504s_J2


title: colon_504s_J20


title: colon_504s_J22


title: colon_504s_J14


title: colon_504s_J11


title: colon_504s_J15


title: colon_504s_J12


title: colon_504s_J13


title: colon_504s_J10


title: colon_504s_I6


title: colon_504s_I8


title: colon_504s_J1


title: colon_504s_I3


title: colon_504s_I4


title: colon_504s_I9


title: colon_504s_I7


title: colon_504s_I24


title: colon_504s_J18


title: colon_504s_I23


title: colon_504s_I22


title: colon_504s_I20


title: colon_504s_I2


title: colon_504s_I18


title: colon_504s_I19


title: colon_504s_I17


title: colon_504s_I5


title: colon_504s_I12


title: colon_504s_I13


title: colon_504s_I16


title: colon_504s_I15


title: colon_504s_H9


title: colon_504s_I1


title: colon_504s_I14


title: colon_504s_H8


title: colon_504s_H7


title: colon_504s_H3


title: colon_504s_H5


title: colon_504s_H22


title: colon_504s_H20


title: colon_504s_H24


title: colon_504s_H23


title: colon_504s_H19


title: colon_504s_H2


title: colon_504s_H18


title: colon_504s_I21


title: colon_504s_H17


title: colon_504s_H16


title: colon_504s_H15


title: colon_504s_H14


title: colon_504s_I10


title: colon_504s_H6


title: colon_504s_H11


title: colon_504s_H13


title: colon_504s_H10


title: colon_504s_H21


title: colon_504s_G5


title: colon_504s_H1


title: colon_504s_G9


title: colon_504s_G6


title: colon_504s_G7


title: colon_504s_G4


title: colon_504s_G3


title: colon_504s_G24


title: colon_504s_G23


title: colon_504s_G22


title: colon_504s_G21


title: colon_504s_G19


title: colon_504s_G20


title: colon_504s_H12


title: colon_504s_G14


title: colon_504s_G15


title: colon_504s_G18


title: colon_504s_G16


title: colon_504s_G12


title: colon_504s_G13


title: colon_504s_G2


title: colon_504s_G8


title: colon_504s_G1


title: colon_504s_G10


title: colon_504s_F9


title: colon_504s_F7


title: colon_504s_F8


title: colon_504s_F6


title: colon_504s_G17


title: colon_504s_F4


title: colon_504s_F5


title: colon_504s_F23


title: colon_504s_F22


title: colon_504s_F21


title: colon_504s_F24


title: colon_504s_F2


title: colon_504s_F18


title: colon_504s_F17


title: colon_504s_F16


title: colon_504s_F19


title: colon_504s_F3


title: colon_504s_F15


title: colon_504s_F13


title: colon_504s_F11


title: colon_504s_F12


title: colon_504s_F1


title: colon_504s_F10


title: colon_504s_F14


title: colon_504s_E9


title: colon_504s_E6


title: colon_504s_E24


title: colon_504s_E5


title: colon_504s_E8


title: colon_504s_E7


title: colon_504s_E4


title: colon_504s_E3


title: colon_504s_E23


title: colon_504s_E21


title: colon_504s_E20


title: colon_504s_E19


title: colon_504s_E2


title: colon_504s_E18


title: colon_504s_E15


title: colon_504s_E16


title: colon_504s_E14


title: colon_504s_E11


title: colon_504s_E12


title: colon_504s_E13


title: colon_504s_E1


title: colon_504s_D7


title: colon_504s_E10


title: colon_504s_F20


title: colon_504s_D5


title: colon_504s_D9


title: colon_504s_E22


title: colon_504s_D6


title: colon_504s_D4


title: colon_504s_D23


title: colon_504s_D20


title: colon_504s_D3


title: colon_504s_E17


title: colon_504s_D22


title: colon_504s_D19


title: colon_504s_D18


title: colon_504s_D21


title: colon_504s_D17


title: colon_504s_D16


title: colon_504s_D8


title: colon_504s_D15


title: colon_504s_D12


title: colon_504s_D13


title: colon_504s_D2


title: colon_504s_D10


title: colon_504s_D11


title: colon_504s_C5


title: colon_504s_C6


title: colon_504s_C4


title: colon_504s_C3


title: colon_504s_C7


title: colon_504s_C24


title: colon_504s_C20


title: colon_504s_C18


title: colon_504s_C2


title: colon_504s_C22


title: colon_504s_C21


title: colon_504s_C19


title: colon_504s_C16


title: colon_504s_C17


title: colon_504s_D14


title: colon_504s_C13


title: colon_504s_C15


title: colon_504s_C11


title: colon_504s_C23


title: colon_504s_C14


title: colon_504s_C10


title: colon_504s_C8


title: colon_504s_C1


title: colon_504s_D1


title: colon_504s_B7


title: colon_504s_B5


title: colon_504s_B9


title: colon_504s_B4


title: colon_504s_B3


title: colon_504s_B8


title: colon_504s_B21


title: colon_504s_B22


title: colon_504s_B23


title: colon_504s_B24


title: colon_504s_C12


title: colon_504s_B20


title: colon_504s_B18


title: colon_504s_B16


title: colon_504s_B19


title: colon_504s_B15


title: colon_504s_B17


title: colon_504s_B10


title: colon_504s_A9


title: colon_504s_B14


title: colon_504s_B1


title: colon_504s_B2


title: colon_504s_A6


title: colon_504s_A7


title: colon_504s_B12


title: colon_504s_A5


title: colon_504s_B11


title: colon_504s_B13


title: colon_504s_A23


title: colon_504s_A20


title: colon_504s_A2


title: colon_504s_A16


title: colon_504s_A3


title: colon_504s_A10


title: colon_504s_A14


title: colon_504s_A11


title: colon_502s_P9


title: colon_502s_P7


title: colon_502s_P22


title: colon_502s_P4


title: colon_502s_P2


title: colon_502s_P3


title: colon_504s_A21


title: colon_502s_P6


title: colon_502s_P5


title: colon_504s_G11


title: colon_502s_O6


title: colon_502s_P14


title: colon_502s_P17


title: colon_502s_O7


title: colon_502s_P18


title: colon_502s_P19


title: colon_502s_P20


title: colon_502s_O24


title: colon_502s_O9


title: colon_502s_O23


title: colon_502s_P10


title: colon_502s_P12


title: colon_502s_O22


title: colon_504s_A19


title: colon_502s_O2


title: colon_502s_O4


title: colon_504s_A1


title: colon_502s_O19


title: colon_502s_O18


title: colon_502s_O3


title: colon_502s_O17


title: colon_502s_O16


title: colon_502s_O13


title: colon_502s_O10


title: colon_502s_O15


title: colon_502s_O11


title: colon_502s_O1


title: colon_502s_O20


title: colon_502s_O12


title: colon_502s_N8


title: colon_502s_N7


title: colon_502s_N1


title: colon_502s_N12


title: colon_502s_N6


title: colon_502s_N3


title: colon_502s_N20


title: colon_502s_N22


title: colon_502s_M5


title: colon_502s_M7


title: colon_502s_N23


title: colon_502s_M8


title: colon_502s_N2


title: colon_502s_M4


title: colon_502s_M3


title: colon_502s_N18


title: colon_502s_M24


title: colon_502s_N19


title: colon_502s_N24


title: colon_502s_M23


title: colon_502s_M6


title: colon_502s_M20


title: colon_502s_M19


title: colon_502s_M2


title: colon_502s_M21


title: colon_502s_M18


title: colon_502s_M16


title: colon_502s_M15


title: colon_502s_M10


title: colon_502s_M12


title: colon_502s_M1


title: colon_502s_L6


title: colon_502s_L7


title: colon_502s_L3


title: colon_502s_L8


title: colon_502s_L24


title: colon_502s_L22


title: colon_502s_L23


title: colon_502s_L4


title: colon_502s_L21


title: colon_502s_L5


title: colon_502s_L2


title: colon_502s_M22


title: colon_502s_L19


title: colon_502s_L18


title: colon_502s_L20


title: colon_502s_L14


title: colon_502s_L16


title: colon_502s_L13


title: colon_502s_L17


title: colon_502s_L9


title: colon_502s_L12


title: colon_502s_L1


title: colon_502s_L11


title: colon_502s_K8


title: colon_502s_K7


title: colon_502s_K9


title: colon_502s_K6


title: colon_502s_K5


title: colon_502s_K3


title: colon_502s_K18


title: colon_502s_K13


title: colon_502s_K24


title: colon_502s_K22


title: colon_502s_K10


title: colon_502s_J9


title: colon_502s_K2


title: colon_502s_K17


title: colon_502s_K12


title: colon_502s_J8


title: colon_502s_L10


title: colon_502s_J6


title: colon_502s_J7


title: colon_502s_K16


title: colon_502s_J3


title: colon_502s_J5


title: colon_502s_J4


title: colon_502s_J24


title: colon_502s_J23


title: colon_502s_J20


title: colon_502s_K19


title: colon_502s_J2


title: colon_502s_J18


title: colon_502s_K1


title: colon_502s_J17


title: colon_502s_J14


title: colon_502s_J16


title: colon_502s_J13


title: colon_502s_I9


title: colon_502s_J12


title: colon_502s_J10


title: colon_502s_I7


title: colon_502s_I5


title: colon_502s_I4


title: colon_502s_I6


title: colon_502s_I8


title: colon_502s_I22


title: colon_502s_I20


title: colon_502s_I23


title: colon_502s_I3


title: colon_502s_I19


title: colon_502s_I17


title: colon_502s_J19


title: colon_502s_I21


title: colon_502s_I2


title: colon_502s_I16


title: colon_502s_I18


title: colon_502s_I14


title: Nicotiana_benthamiana_leaf wt_rep4

city: Ljubljana

first: Mojca

last: Juteršek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

data_processing:
FastQC quality control
CLC Genomics Workbench 21.0.5 mapping to the genome with 'RNA-Seq analysis' tool (parameters: Mismatch cost 2, Insertion cost 3, Deletion cost 3, Length fraction 0.9, Similarity fraction 0.9, Global alignment No, Auto-detect paired distances Yes, Strand specific Both, Maximum number of hits for a read 10, Count paired reads as two No, Expression value Total counts) and export of 'Expression Browser' count table
R with package edgeR, filtering out not expressed genes and TMM normalization
R with package limma, voom transformation, linear model fit, adj.p.val calculation (BH correction) with eBayes function, DE table export
Genome_build: Nicotiana benthamiana genome V3.5, downloaded from https://www.nbenth.com/ on 15.12.2021.
Supplementary_files_format_and_content: tab-delimited text file with total counts for all samples
Supplementary_files_format_and_content: spreadsheet with logFC values and adjusted P-values for all contrasted lines

molecule: polyA RNA

organism: Nicotiana benthamiana

source_name: Nicotiana benthamiana leaf

growth_protocol:
Transgenic SxP seeds were placed in a germination medium (MS with vitamins 4
9 g L-1, sucrose 30 g L-1, Phytoagar 9 g L-1, pH = 5:7) supplemented with 100mgL-1 kanamycin for positive transgene selection
Control WT plants were obtained similarly by placing seeds in a non-selective germination medium
WT and kanamycin-resistant seedlings were transferred to the greenhouse a week after germination, where they were grown at 24 : 20°C (light : darkness) with a 16 : 8 h light : darkness photoperiod

extract_protocol:
total RNA isolation and cleanup
Illumina TrueSeq RNA-Seq strand-specific library prep

value: leaf

tag: genotype


title: Nicotiana_benthamiana_leaf wt_rep2


title: colon_502s_I24


title: colon_502s_I1


title: colon_502s_H8


title: Nicotiana_benthamiana_leaf wt_rep1


title: SxPv1.2_HighProducer_line_4_3_rep3

source_name: transgenic Nicotiana benthamiana leaf


title: colon_502s_I10


title: SxPv1.2_HighProducer_line_4_3_rep2


title: colon_502s_H7


title: SxPv1.2_HighProducer_line_4_3_rep1


title: colon_502s_H5


title: SxPv1.2_HighProducer_line_4_1_rep4


title: colon_502s_I13


title: colon_502s_H21


title: colon_502s_I12


title: SxPv1.2_HighProducer_line_4_1_rep2


title: SxPv1.2_HighProducer_line_4_3_rep4


title: colon_502s_H22


title: SxPv1.2_HighProducer_line_4_1_rep3


title: colon_502s_H19


title: Nicotiana_benthamiana_leaf wt_rep3


title: Nicotiana_benthamiana_wt_rep3

data_processing:
FastQC quality control
CLC Genomics Workbench 12.0.3 mapping to the genome with 'RNA-Seq analysis' tool (parameters: Mismatch cost 2, Insertion cost 3, Deletion cost 3, Length fraction 0.9, Similarity fraction 0.9, Global alignment No, Auto-detect paired distances Yes, Strand specific Reverse, Maximum number of hits for a read 10, Count paired reads as two No, Expression value Total counts) and export of 'Expression Browser' count table
R with package edgeR, filtering genes with raw counts below 50 in more than 3 samples
R with package edgeR, TMM normalization
R with package limma, voom transformation, linear model fit, adj.p.val calculation (BH correction) with eBayes function, DE table export
Genome_build: Nicotiana benthamiana genome V3.5, downloaded from https://www.nbenth.com/ on 15.12.2021.
Supplementary_files_format_and_content: tab-delimited text file with total counts for all samples
Supplementary_files_format_and_content: spreadsheet with logFC values and adjusted P-values for all contrasted lines

growth_protocol: Transgenic SxP seeds were placed in a germination medium (MS with vitamins 4.9 g L-1, sucrose 30 g L-1, Phytoagar 9 g L-1, pH = 5:7) supplemented with 100mgL-1 kanamycin for positive transgene selection. Control WT plants were obtained similarly by placing seeds in a non-selective germination medium. WT and kanamycin-resistant seedlings were transferred to the greenhouse a week after germination, where they were grown at 24 : 20°C (light : darkness) with a 16 : 8 h light : darkness photoperiod.

tag: pheromone production

value: no producer


title: SxPv1.2_HighProducer_line_4_1_rep1


title: colon_502s_H2


title: Nicotiana_benthamiana_wt_rep4


title: colon_502s_H23


title: colon_502s_H18


title: Nicotiana_benthamiana_wt_rep2


title: colon_502s_H20


title: colon_502s_H16


title: colon_502s_H4


title: colon_502s_H12


title: Nicotiana_benthamiana_wt_rep1


title: colon_502s_H10


title: SxPv1.0_LowProducer_line_5_2_5_rep3

value: low producer


title: colon_502s_H1


title: SxPv1.0_LowProducer_line_5_2_5_rep2


title: colon_502s_G8


title: SxPv1.0_LowProducer_line_5_2_5_rep1


title: colon_502s_G7


title: SxPv1.0_HighProducer_line_5_2_4_rep4

value: high producer


title: colon_502s_G4


title: SxPv1.0_HighProducer_line_5_2_4_rep3


title: colon_502s_G24


title: SxPv1.0_HighProducer_line_5_2_4_rep2


title: SxPv1.0_LowProducer_line_5_2_5_rep4


title: SxPv1.0_HighProducer_line_5_2_4_rep1


title: SxPv1.0_HighProducer_line_5_1_7_rep4


title: colon_502s_G2


title: colon_502s_G21


title: colon_502s_G22


title: SxPv1.0_HighProducer_line_5_1_7_rep2


title: colon_502s_G19


title: SxPv1.0_HighProducer_line_5_1_7_rep3


title: colon_502s_G20


title: SxPv1.0_LowProducer_line_5_1_10_rep4


title: colon_502s_G13


title: SxPv1.0_HighProducer_line_5_1_7_rep1


title: SxPv1.0_LowProducer_line_5_1_10_rep1


title: SxPv1.0_LowProducer_line_5_1_10_rep3


title: colon_502s_F8


title: colon_502s_G1


title: colon_502s_G23


title: colon_502s_F6


title: colon_502s_F4


title: colon_502s_F3


title: colon_502s_F22


title: Xylose_1

city: Heidelberg

first: Ed

last: Hurt

address: Im Neuenheimer Feld 328

country: Germany

institute: BZH

data_processing:
Mapping was done with Tophat2, using ‘-i 40 -I 5000’ parameters based on C.t. gene characteristics
DESeq2 object was created from the mapped samples with summarizeOverlaps from the GenomicAlignments package, using the corresponding .gtf file as the gene source
Count table output from DESeq2 object is used as the count table for the ‘processed data’.
Assembly: Ensembl release 28
Supplementary files format and content: Tab separated text file with gene Ids and one column for each sample

organism: Thermochaetoides thermophila

source_name: whole cell extract

growth_protocol: Chaetomium thermophilum wildtype cells were grown in complete cultivation medium (CCM) at 50°C and subsequently exposed to a minimal medium for 48h for carbon depletion.

extract_protocol:
Total RNA was isolated from C. thermphilum cultures using the SV total RNA extraction kit from Promega according to the manufacturers instructions
Sequencing libraries were prepared using NEBNext Ultra II Directional RNA Preparation Kit with NEBNext PolyA selection Module, and NEBNext Multiplex Oligos according to the manufacturers instructions.
Illumina NextSeq 500, single-end

treatment_protocol: C. thermophilum wildtype cells were exposed for further 6h to 1% (w/v) D-glucose or 1% (w/v) D-xylose medium as well as to minimal medium without sugar treatment for three biological replicates, each.

value: whole cell extract

value: wildtype

tag: treatment

value: xylose induction

tag: time


title: Xylose_3


title: Xylose_2


title: Glucose_3

value: glucose induction


title: SxPv1.0_LowProducer_line_5_1_10_rep2


title: colon_502s_F21


title: Reference_3

value: carbon depletion


title: Glucose_1


title: colon_502s_F18


title: colon_502s_E9


title: colon_502s_F10


title: Glucose_2


title: colon_502s_F2


title: Reference_1


title: colon_502s_E3


title: Reference_2


title: colon_502s_E24


title: colon_502s_E23


title: colon_502s_E5


title: spores,incubated with exosomes,biol rep 2

city: Guangzhou

first: chunxiao

last: yin

state: Guangdong

address: Xingke Road

department: Agriculture and Biotechnology Research Center

country: China

institute: South China Botanical Garden, Chinese Academy of Sciences

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: penicillium italicum genome
Supplementary files format and content: txt,tab delimited text files include FPKM and count value  for each Sample

organism: Penicillium italicum

source_name: spores

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: spores

value: incubated with exosomes


title: colon_502s_E22


title: spores,biol rep 3

value: incubated


title: spores,biol rep 2


title: colon_502s_E21


title: spores,incubated with exosomes,biol rep 1


title: spores,incubated with exosomes,biol rep 3


title: colon_502s_E20


title: colon_502s_E1


title: colon_502s_E12


title: spores,biol rep 1


title: colon_502s_D5


title: colon_502s_E14


title: colon_502s_D3


title: colon_502s_D4


title: colon_502s_D24


title: colon_502s_D23


title: colon_502s_D21


title: colon_502s_D18


title: colon_502s_D1


title: colon_502s_E19


title: colon_502s_C5


title: colon_502s_C3


title: colon_502s_C6


title: colon_502s_C20


title: colon_502s_C1


title: colon_502s_C19


title: colon_502s_C24


title: colon_502s_C23


title: colon_502s_C22


title: colon_502s_C21


title: colon_502s_C2


title: colon_502s_C13


title: colon_502s_C4


title: colon_502s_D20


title: colon_502s_B22


title: colon_502s_B6


title: colon_502s_B23


title: colon_502s_B21


title: colon_502s_D19


title: colon_502s_D2


title: colon_502s_C18


title: colon_502s_B5


title: colon_502s_B18


title: colon_502s_B24


title: colon_502s_B1


title: colon_502s_B19


title: colon_502s_B20


title: colon_502s_B4


title: colon_502s_A2


title: colon_502s_A3


title: colon_502s_A21


title: colon_502s_A4


title: colon_502s_A22


title: colon_502s_A24


title: colon_502s_A23


title: colon_439s_O7


title: colon_439s_O16


title: colon_439s_P4


title: colon_502s_A18


title: colon_439s_P6


title: colon_439s_O13


title: colon_439s_P17


title: colon_439s_P16


title: colon_439s_P5


title: colon_439s_O24


title: colon_439s_P3


title: colon_439s_O18


title: colon_502s_A1


title: colon_439s_P10


title: colon_439s_P1


title: colon_439s_O22


title: colon_439s_O21


title: colon_439s_O19


title: colon_439s_O15


title: colon_439s_O12


title: colon_439s_P12


title: colon_439s_O17


title: colon_439s_O2


title: colon_439s_O5


title: colon_439s_P9


title: colon_439s_P11


title: colon_439s_O20


title: colon_439s_P7


title: colon_502s_A19


title: colon_439s_O8


title: colon_439s_O11


title: colon_439s_N22


title: colon_439s_N23


title: colon_439s_N3


title: colon_439s_N4


title: colon_439s_N2


title: colon_439s_N18


title: colon_439s_N13


title: colon_439s_O1


title: colon_439s_N19


title: colon_439s_N21


title: colon_439s_N17


title: colon_439s_N14


title: colon_439s_N15


title: colon_439s_N7


title: colon_439s_N16


title: colon_439s_N5


title: colon_439s_M8


title: colon_439s_M16


title: colon_439s_M19


title: colon_439s_M15


title: colon_439s_M3


title: colon_439s_N1


title: colon_439s_M18


title: colon_439s_M23


title: colon_439s_M6


title: colon_439s_N12


title: colon_439s_M7


title: colon_439s_M21


title: colon_439s_M22


title: colon_439s_M13


title: colon_439s_M14


title: colon_439s_M1


title: colon_439s_M12


title: colon_439s_M11


title: colon_1075s_N15


title: colon_1075s_N22


title: colon_1075s_N21


title: colon_1075s_N16


title: colon_1075s_O14


title: colon_1075s_O16


title: colon_1075s_O2


title: colon_1075s_O5


title: colon_1075s_O18


title: colon_1075s_M22


title: colon_439s_C21


title: colon_1075s_N13


title: colon_1075s_O11


title: colon_1075s_O1


title: colon_1075s_M24


title: colon_1075s_N14


title: colon_1075s_M23


title: colon_1075s_O8


title: colon_1075s_P5


title: colon_1075s_N20


title: colon_1075s_M15


title: colon_1075s_M21


title: colon_1075s_M17


title: colon_1075s_M20


title: colon_1075s_M14


title: colon_1075s_M18


title: colon_1075s_M19


title: colon_1075s_M13


title: colon_1075s_M16


title: colon_075s_P12


title: colon_075s_D7


title: colon_075s_G21


title: colon_075s_G8


title: colon_075s_D5


title: colon_075s_K9


title: colon_075s_D6


title: colon_075s_O7


title: colon_075s_L24


title: colon_075s_N3


title: colon_075s_O11


title: colon_075s_D8


title: colon_075s_D9


title: colon_075s_L5


title: colon_075s_C22


title: colon_075s_C24


title: colon_075s_C8


title: colon_075s_D16


title: colon_075s_C6


title: colon_075s_D19


title: colon_075s_C4


title: colon_075s_D10


title: colon_075s_C23


title: colon_075s_C3


title: colon_075s_D22


title: colon_075s_D21


title: colon_075s_D23


title: colon_075s_D12


title: colon_075s_D13


title: colon_075s_D14


title: colon_075s_D2


title: colon_075s_C9


title: colon_075s_D11


title: colon_075s_D3


title: colon_075s_D18


title: colon_075s_D15


title: colon_075s_D17


title: colon_075s_B3


title: colon_075s_C2


title: colon_075s_C18


title: colon_075s_C13


title: colon_075s_B22


title: colon_075s_C19


title: colon_075s_B21


title: colon_075s_B14


title: colon_075s_B16


title: colon_075s_B19


title: colon_075s_C11


title: colon_075s_B17


title: colon_075s_B24


title: colon_075s_B18


title: colon_075s_B15


title: colon_075s_C10


title: colon_075s_B5


title: colon_075s_B9


title: colon_075s_B7


title: colon_075s_C15


title: colon_075s_C21


title: colon_075s_B2


title: colon_075s_B1


title: colon_075s_A8


title: colon_075s_B10


title: colon_075s_B11


title: colon_075s_C1


title: colon_075s_B13


title: colon_075s_B12


title: colon_075s_C16


title: colon_075s_A5


title: colon_075s_A14


title: colon_075s_A4


title: colon_075s_A22


title: colon_075s_A16


title: colon_075s_A2


title: colon_075s_A7


title: colon_073s_O5


title: colon_073s_N21


title: colon_075s_A12


title: colon_075s_A1


title: colon_075s_A17


title: colon_075s_A23


title: colon_075s_A6


title: colon_075s_A15


title: colon_073s_O22


title: colon_073s_D23


title: colon_073s_L24


title: colon_073s_M18


title: colon_073s_L17


title: colon_073s_G7


title: colon_053s_P22


title: colon_053s_P5


title: colon_053s_O5


title: colon_073s_B7


title: colon_053s_P19


title: colon_053s_P6


title: colon_053s_P21


title: colon_053s_P4


title: colon_053s_P20


title: colon_053s_O7


title: colon_053s_O3


title: colon_053s_O8


title: colon_053s_P12


title: colon_053s_P11


title: colon_053s_P8


title: colon_053s_O4


title: colon_053s_P14


title: colon_053s_P9


title: colon_053s_P10


title: colon_053s_P2


title: colon_053s_P1


title: colon_053s_O9


title: colon_053s_O6


title: colon_053s_O24


title: colon_053s_O23


title: colon_053s_P17


title: colon_053s_P16


title: colon_053s_P15


title: colon_053s_P3


title: colon_053s_P13


title: colon_053s_O20


title: colon_053s_O21


title: colon_053s_O22


title: colon_053s_O18


title: colon_053s_O15


title: colon_053s_O19


title: colon_053s_O16


title: colon_053s_O2


title: colon_053s_O17


title: colon_053s_N10


title: colon_053s_N15


title: colon_053s_N12


title: colon_053s_N20


title: colon_053s_N13


title: colon_053s_O11


title: colon_053s_N11


title: colon_053s_N14


title: colon_053s_N1


title: colon_053s_N6


title: colon_053s_N16


title: colon_053s_N7


title: colon_053s_N17


title: colon_053s_N8


title: colon_053s_N3


title: colon_053s_N19


title: colon_053s_N5


title: colon_053s_O14


title: colon_053s_O1


title: colon_053s_N4


title: colon_053s_O13


title: colon_053s_O10


title: colon_053s_N23


title: colon_053s_N18


title: colon_053s_N21


title: colon_053s_N22


title: colon_053s_N9


title: colon_053s_N2


title: colon_053s_O12


title: colon_053s_N24


title: colon_053s_M5


title: colon_053s_M4


title: colon_053s_M3


title: colon_053s_M6


title: colon_053s_M2


title: colon_053s_M9


title: colon_053s_M22


title: colon_053s_M21


title: colon_053s_M7


title: colon_053s_M23


title: colon_053s_L6


title: colon_053s_L5


title: colon_053s_M24


title: colon_053s_M18


title: colon_053s_L8


title: colon_053s_M12


title: colon_053s_M13


title: colon_053s_M15


title: colon_053s_M17


title: colon_053s_M1


title: colon_053s_M20


title: colon_053s_M8


title: colon_053s_L7


title: colon_053s_L4


title: colon_053s_M19


title: colon_053s_M14


title: colon_053s_L3


title: colon_053s_M11


title: colon_053s_L9


title: colon_053s_M16


title: colon_053s_L18


title: colon_053s_L17


title: colon_053s_L20


title: colon_053s_L2


title: colon_053s_L16


title: colon_053s_L11


title: colon_053s_K24


title: colon_053s_L13


title: colon_053s_L10


title: colon_053s_K19


title: colon_053s_K20


title: colon_053s_K8


title: colon_053s_K9


title: colon_053s_K3


title: colon_053s_K2


title: colon_053s_L1


title: colon_053s_K16


title: colon_053s_K14


title: colon_053s_K17


title: colon_053s_K7


title: colon_053s_K18


title: colon_053s_K15


title: colon_053s_L23


title: colon_053s_L24


title: colon_053s_K5


title: colon_053s_L19


title: colon_053s_K23


title: colon_053s_K13


title: colon_053s_K12


title: colon_053s_K4


title: colon_053s_K10


title: colon_053s_J8


title: colon_053s_K1


title: colon_053s_J7


title: colon_053s_J5


title: colon_053s_J22


title: colon_053s_J20


title: colon_053s_J3


title: colon_053s_J2


title: colon_053s_J4


title: colon_053s_J17


title: colon_053s_J19


title: colon_053s_J21


title: colon_053s_J14


title: colon_053s_J18


title: colon_053s_J12


title: colon_053s_J13


title: colon_053s_I24


title: colon_053s_I4


title: colon_053s_I6


title: colon_053s_I5


title: colon_053s_I3


title: colon_053s_I23


title: colon_053s_I8


title: colon_053s_J1


title: colon_053s_J11


title: colon_053s_J16


title: colon_053s_J15


title: colon_053s_K11


title: colon_053s_I22


title: colon_053s_I20


title: colon_053s_I21


title: colon_053s_I18


title: colon_053s_I2


title: colon_053s_I17


title: colon_053s_I16


title: colon_053s_I1


title: colon_053s_I15


title: colon_053s_H9


title: colon_053s_I11


title: colon_053s_I13


title: colon_053s_H8


title: colon_053s_H3


title: colon_053s_H5


title: colon_053s_H6


title: colon_053s_H7


title: colon_053s_H4


title: colon_053s_H24


title: colon_053s_H21


title: colon_053s_H2


title: colon_053s_H23


title: colon_053s_H16


title: colon_053s_H19


title: colon_053s_H13


title: colon_053s_H14


title: colon_053s_H10


title: colon_053s_H11


title: colon_053s_H17


title: aorta_912s_O21

value: aorta

value: 10 weeks


title: aorta_912s_O17


title: aorta_912s_P06


title: aorta_912s_P04


title: aorta_912s_O16


title: aorta_912s_P05


title: aorta_912s_P09


title: aorta_912s_O22


title: aorta_912s_P11


title: aorta_912s_P20


title: aorta_912s_P17


title: aorta_912s_P19


title: aorta_912s_O14


title: aorta_912s_P10


title: aorta_912s_P21


title: aorta_912s_O20


title: aorta_912s_P03


title: aorta_912s_O12


title: aorta_912s_P18


title: aorta_912s_P07


title: aorta_912s_O19


title: aorta_912s_P14


title: aorta_912s_O15


title: aorta_912s_P15


title: aorta_912s_O18


title: aorta_912s_P01


title: aorta_912s_O13


title: aorta_912s_O11


title: aorta_912s_P16


title: aorta_912s_O23


title: aorta_912s_O07


title: aorta_912s_O10


title: aorta_912s_O09


title: aorta_912s_N20


title: aorta_912s_N23


title: aorta_912s_N22


title: aorta_912s_O05


title: aorta_912s_O06


title: aorta_912s_N21


title: aorta_912s_N24


title: aorta_912s_N15


title: aorta_912s_N18


title: aorta_912s_N16


title: aorta_912s_N14


title: aorta_912s_N12


title: aorta_912s_N05


title: aorta_912s_N04


title: aorta_912s_N07


title: aorta_912s_N13


title: aorta_912s_N02


title: aorta_912s_N11


title: aorta_912s_N01


title: aorta_912s_N10


title: aorta_912s_N03


title: aorta_912s_N09


title: aorta_912s_N06


title: aorta_912s_O02


title: aorta_912s_M24


title: aorta_912s_N17


title: aorta_912s_M22


title: aorta_912s_M20


title: aorta_912s_M23


title: aorta_912s_M19


title: aorta_912s_M17


title: aorta_912s_M16


title: aorta_912s_M13


title: aorta_912s_M07


title: aorta_912s_M09


title: aorta_912s_M05


title: aorta_912s_M14


title: aorta_912s_M04


title: aorta_912s_M10


title: aorta_912s_L22


title: aorta_912s_L20


title: aorta_912s_L17


title: aorta_912s_L15


title: aorta_912s_L16


title: aorta_912s_L23


title: aorta_912s_M03


title: aorta_912s_L14


title: aorta_912s_M15


title: aorta_912s_M06


title: aorta_912s_L13


title: aorta_912s_M01


title: aorta_912s_M02


title: aorta_912s_L24


title: aorta_912s_L11


title: aorta_912s_L10


title: aorta_912s_L12


title: aorta_912s_L07


title: aorta_912s_M11


title: aorta_912s_L18


title: aorta_912s_L09


title: aorta_912s_L05


title: aorta_912s_L04


title: aorta_912s_L02


title: aorta_912s_L03


title: aorta_912s_K24


title: aorta_912s_K23


title: aorta_912s_L01


title: aorta_912s_K20


title: aorta_912s_K17


title: aorta_912s_K18


title: aorta_912s_K22


title: aorta_912s_K19


title: aorta_912s_K16


title: aorta_912s_K14


title: aorta_912s_K11


title: aorta_912s_K12


title: aorta_912s_K21


title: aorta_912s_K10


title: aorta_912s_K09


title: aorta_912s_K15


title: aorta_912s_K07


title: SLE51-post Bcell

type: RNA

city: Kyoto

first: Kenji

last: Okuma

state: Kyoto

address: 53, Shogoin Kawara-cho, Sakyo-ku, Medical Innovation Center

country: Japan

institute: Astellas Pharma Inc.

hyb_protocol: Labeled samples were hybridized to microarray G4110B Human 1A Microarray (V2) for 17hr, 65 deg C.

scan_protocol: Gene expression pixel intensities were extracted by scanning the microarrays with an Agilent Scanner.

data_processing: Data processing and trimming were performed with GeneSpring ver. 12.6.1.

organism: Homo sapiens

source_name: peripheral blood

label_protocol: Total RNA from a human sample were amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit and labeled with Cy3 respectively according to manufacturer’s protocol.

extract_protocol: Total RNA was extracted using RNAqueous Micro Kit (Thermo Fisher Scientific/Ambion, USA) with RNase-Free DNase Set (Qiagen). RNA Integrity Number (RIN) value was measured using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). RNA samples with RIN ≥7.0 were used.

treatment_protocol: Fresh peripheral blood from SLE patients and healthy volunteers was collected and T, B, monocyte, mDC, pDC, naiveB, memoryB and PBMC were isolated at spontaneous state.

tag: diagnosis

value: SLE

tag: cell type

value: Bcell

tag: date measured

tag: Sex

value: F

tag: sex (1 vs 2)

tag: antidna(ria)antibody titer（u/ml：<6）

tag: renal disorder (0

tag: neurologic disorder (0

value: Negative, 1:Positive):0

tag: pre / post

value: post

tag: untreat / treat

value: treat


title: SLE71-post Bcell


title: HC33 Bcell

value: Healthy control


title: HC31 Bcell


title: aorta_912s_K06

tag: tissue

tag: strain


title: SLE51-pre Bcell

tag: age

value: pre

value: untreat


title: HC34 Bcell


title: HC32 Bcell


title: aorta_912s_K01

tag: description


title: SLE29 Bcell

value: Negative, 1:Positive):1


title: aorta_912s_K03


title: aorta_912s_K02


title: aorta_912s_J24


title: aorta_912s_J23


title: aorta_912s_K04


title: SLE24 Bcell


title: aorta_912s_J22


title: aorta_912s_J21


title: SLE27 Bcell

value: M


title: SLE1 Bcell


title: HC30 Bcell


title: HC28 Bcell


title: HC29 Bcell


title: aorta_912s_J19


title: HC27 Bcell


title: aorta_912s_J18


title: aorta_912s_J17


title: aorta_912s_J16


title: aorta_912s_J14


title: SLE71-pre Bcell


title: SLE18 PBMC

value: PBMC


title: SLE43-post PBMC


title: SLE25 PBMC


title: aorta_912s_J12


title: HC33 PBMC


title: SLE39 PBMC


title: aorta_912s_J11


title: HC31 PBMC


title: HC32 PBMC


title: SLE51-post PBMC


title: SLE47-post PBMC


title: aorta_912s_J15


title: aorta_912s_I24


title: aorta_912s_I23


title: SLE38 PBMC


title: aorta_912s_I20


title: aorta_912s_I22


title: aorta_912s_I21


title: aorta_912s_I16


title: aorta_912s_I13


title: aorta_912s_J13


title: SLE64-pre PBMC


title: HC12 PBMC


title: aorta_912s_I15


title: HC29 PBMC


title: aorta_912s_I11


title: aorta_912s_H24


title: aorta_912s_I12


title: aorta_912s_I19


title: HC30 PBMC


title: SLE18 memory B

value: memory B


title: HC36 memory B


title: aorta_912s_H22


title: HC28 PBMC


title: SLE43 memory B


title: SLE16 memory B


title: HC35 memory B


title: aorta_912s_H19


title: SLE25 memory B


title: aorta_912s_H20


title: HC34 memory B


title: aorta_912s_H23


title: aorta_912s_H16


title: aorta_912s_H15


title: aorta_912s_H13


title: aorta_912s_H12


title: SLE39 memory B


title: SLE47-post memory B


title: SLE47-pre memory B


title: HC33 memory B


title: HC31 memory B


title: aorta_912s_H11


title: aorta_912s_H10


title: HC30 memory B


title: aorta_912s_H09


title: SLE37 memory B


title: SLE38 memory B


title: aorta_912s_H07


title: aorta_912s_H17


title: SLE51-post memory B


title: HC27 PBMC


title: SLE29 memory B


title: aorta_912s_H04


title: HC28 memory B


title: aorta_912s_H06


title: aorta_912s_H03


title: aorta_912s_H02


title: aorta_912s_H01


title: aorta_912s_G21


title: aorta_912s_G24


title: aorta_912s_H05


title: aorta_912s_G20


title: aorta_912s_G22


title: aorta_912s_G23


title: HC32 memory B


title: HC12 memory B


title: HC27 memory B


title: HC33 naive B

description: This sample failed quality control. Processed data are not provided this sample.

value: naive B


title: HC34 naive B


title: HC36 naive B


title: aorta_912s_G18


title: SLE18 naive B


title: aorta_912s_G17


title: SLE16 naive B


title: SLE71-pre naive B


title: SLE25 naive B


title: SLE71-pre memory B


title: HC35 naive B


title: aorta_912s_G16


title: SLE71-post naive B


title: aorta_912s_G19


title: aorta_912s_G13


title: aorta_912s_G12


title: aorta_912s_G11


title: aorta_912s_G10


title: aorta_912s_G14


title: HC30 naive B


title: aorta_912s_F23


title: aorta_912s_G06


title: aorta_912s_G03


title: aorta_912s_G01


title: aorta_912s_F22


title: aorta_912s_G09


title: aorta_912s_G02


title: aorta_912s_G04


title: aorta_912s_G07


title: aorta_912s_F21


title: aorta_912s_F20


title: aorta_912s_F19


title: aorta_912s_F17


title: aorta_912s_F18


title: aorta_912s_F16


title: SLE71-post memory B


title: aorta_912s_F15


title: aorta_912s_F11


title: aorta_912s_F14


title: HC29 memory B


title: aorta_912s_F10


title: aorta_912s_F09


title: aorta_912s_F07


title: SLE39 naive B


title: SLE64-pre memory B


title: SLE47-post naive B


title: HC31 naive B


title: HC29 naive B


title: aorta_912s_F06


title: SLE23 naive B


title: SLE16 mDC

value: mDC


title: SLE71-post mDC


title: aorta_912s_F05

value: aorta


title: SLE51-pre mDC


title: HC35 mDC


title: SLE31 naive B


title: HC30 mDC


title: SLE18 mDC


title: SLE38 naive B


title: HC32 mDC


title: HC32 naive B


title: aorta_912s_F04

value: 10 weeks


title: SLE39 mDC

value: SLE


title: SLE47-post mDC


title: SLE36 naive B


title: HC28 naive B


title: SLE25 mDC


title: SLE38 mDC


title: HC36 mDC


title: HC12 naive B


title: SLE71-pre mDC


title: aorta_912s_F03


title: HC33 mDC


title: SLE64-pre mDC


title: HC34 mDC


title: aorta_912s_F02


title: SLE29 mDC


title: HC31 mDC


title: aorta_912s_E24


title: aorta_912s_E23


title: SLE37 mDC


title: HC29 mDC


title: HC28 mDC


title: aorta_912s_E20


title: aorta_912s_E19


title: aorta_912s_E17


title: HC27 mDC


title: HC12 mDC


title: SLE71-pre PBMC


title: SLE71-post PBMC


title: HC36 PBMC


title: SLE45 Tcell

value: Tcell


title: aorta_912s_E16


title: SLE71-pre Tcell

value: F


title: HC34 PBMC


title: aorta_912s_E15


title: aorta_912s_E14


title: aorta_912s_E21


title: aorta_912s_E18


title: aorta_912s_E13


title: aorta_912s_E12


title: aorta_912s_E11


title: aorta_912s_E10


title: aorta_912s_E09


title: HC36 Tcell


title: aorta_912s_E07


title: aorta_912s_E06


title: aorta_912s_E05


title: aorta_912s_E04


title: aorta_912s_E02


title: aorta_912s_E03


title: aorta_912s_E01


title: aorta_912s_D24


title: aorta_912s_D23


title: aorta_912s_D22


title: aorta_912s_D19


title: aorta_912s_D20


title: aorta_912s_D18


title: SLE38 Tcell

value: Negative, 1:Positive):0


title: aorta_912s_D17


title: HC30 Tcell


title: aorta_912s_D16


title: HC31 Tcell


title: HC33 Tcell


title: SLE16 Tcell


title: SLE47-pre Tcell


title: SLE24 Tcell


title: SLE43-post Tcell

value: post


title: HC34 Tcell


title: SLE47-post Tcell

value: treat


title: HC29 Tcell

value: Healthy control


title: SLE37 Tcell


title: SLE51-post Tcell


title: aorta_912s_D15


title: SLE64-pre Tcell

value: pre


title: SLE23 Tcell


title: SLE29 Tcell


title: HC35 Tcell


title: SLE36 Tcell


title: SLE28 Tcell


title: HC12 Tcell


title: SLE39 Tcell


title: SLE51-pre Tcell

value: untreat


title: HC32 Tcell


title: HC27 Tcell


title: aorta_912s_D10


title: aorta_912s_D11


title: aorta_912s_D13


title: aorta_912s_D05


title: aorta_912s_D04


title: aorta_912s_F01


title: aorta_912s_C24


title: aorta_912s_D02


title: SLE47-post Bcell

value: Bcell


title: aorta_912s_C23


title: aorta_912s_E22


title: aorta_912s_C22


title: HC36 Bcell


title: SLE71-post monocyte

value: monocyte


title: SLE71-pre monocyte


title: aorta_912s_D06


title: HC36 monocyte


title: aorta_912s_C19


title: HC34 monocyte


title: HC35 monocyte


title: aorta_912s_D03


title: HC35 Bcell


title: aorta_912s_C18


title: aorta_912s_C21


title: aorta_912s_C20


title: aorta_912s_C17


title: aorta_912s_C16


title: aorta_912s_C15


title: aorta_912s_C14


title: aorta_912s_C13


title: aorta_912s_C12


title: aorta_912s_C10


title: aorta_912s_C11


title: SLE16 pDC

value: pDC

value: Negative, 1:Positive):1


title: aorta_912s_C07


title: HC36 pDC


title: SLE71-post pDC


title: aorta_912s_C06


title: HC35 pDC


title: SLE36 monocyte


title: aorta_912s_C09


title: aorta_912s_C04


title: SLE71-pre pDC


title: HC33 monocyte


title: SLE16 monocyte


title: aorta_912s_C03


title: HC34 pDC


title: SLE47-post monocyte


title: SLE39 monocyte


title: HC12 monocyte

value: M


title: HC27 monocyte


title: HC28 monocyte


title: aorta_912s_C05


title: HC32 monocyte


title: SLE51-pre monocyte


title: HC29 monocyte


title: aorta_912s_C02


title: SLE23 monocyte


title: SLE51-post monocyte


title: aorta_912s_B24


title: HC31 monocyte


title: SLE45 monocyte


title: HC30 monocyte


title: SLE29 pDC


title: aorta_912s_B23


title: aorta_912s_B22


title: aorta_912s_B21


title: aorta_912s_B20


title: aorta_912s_B18


title: aorta_912s_B19


title: aorta_912s_B17


title: aorta_912s_B16


title: SLE51-pre pDC


title: SLE37 pDC


title: aorta_912s_B15


title: SLE1 pDC


title: aorta_912s_B14


title: aorta_912s_B11


title: aorta_912s_B13


title: aorta_912s_B12


title: HC32 pDC


title: HC16 pDC


title: aorta_912s_B10


title: SLE29 PBMC

value: PBMC


title: SLE47 PBMC


title: SLE37 PBMC


title: HC15 pDC


title: HC12 pDC


title: SLE51 PBMC


title: aorta_912s_B07

value: aorta


title: aorta_912s_D07

value: 10 weeks


title: aorta_912s_B06


title: aorta_912s_B05


title: SLE24 PBMC

value: SLE


title: aorta_912s_B03


title: HC16 PBMC


title: aorta_912s_B02


title: SLE45 mDC

value: mDC


title: HC15 PBMC

value: F


title: aorta_912s_B01


title: SLE31 mDC

value: Negative, 1:Positive):0


title: SLE24 mDC


title: SLE36 mDC


title: aorta_912s_A23


title: SLE1 mDC


title: SLE45 PBMC


title: aorta_912s_A22


title: aorta_912s_B04


title: aorta_912s_A20


title: aorta_912s_A21


title: HC14 mDC


title: HC16 mDC


title: aorta_912s_A19


title: aorta_912s_A18


title: HC15 mDC


title: aorta_912s_A17


title: aorta_912s_A15


title: aorta_912s_A16


title: SLE43 PBMC


title: aorta_912s_A12


title: SLE36 PBMC


title: SLE27 PBMC


title: aorta_912s_A10


title: aorta_912s_A11


title: SLE1 PBMC


title: aorta_912s_A09


title: HC-03 PBMC


title: SLE31 Tcell

value: Tcell


title: HC14 PBMC


title: SLE28 PBMC

value: treat


title: aorta_912s_A07


title: SLE23 PBMC


title: aorta_912s_A06


title: SLE27 Tcell


title: aorta_912s_A05


title: aorta_912s_A03


title: aorta_912s_A04


title: SLE43 Tcell


title: aorta_912s_A01


title: SLE1 Tcell


title: HC16 Tcell

value: Healthy control


title: aorta_594s_P22


title: aorta_594s_P21


title: aorta_594s_P20


title: HC15 Tcell


title: aorta_594s_P19


title: HC-03 Tcell


title: HC14 Tcell


title: aorta_594s_P18


title: aorta_594s_P17


title: SLE24 memory-B

value: memory-B


title: aorta_594s_P14


title: aorta_594s_P15


title: aorta_594s_P13


title: SLE51 memory-B

value: pre

value: untreat


title: SLE45 memory-B


title: aorta_594s_P12


title: aorta_594s_P11


title: HC16 memory-B


title: SLE31 memory-B


title: aorta_594s_P10


title: SLE64 naiveB

value: naiveB


title: aorta_594s_P16


title: aorta_594s_P09


title: HC14 memory-B


title: SLE47 naiveB


title: SLE24 naiveB


title: SLE1 memory-B


title: SLE51 naiveB


title: aorta_594s_P08


title: SLE28 naiveB


title: aorta_594s_P07


title: HC-03 memory-B


title: SLE64 monocyte

value: monocyte


title: aorta_594s_P06


title: aorta_594s_P05


title: HC16 naiveB


title: aorta_594s_P04


title: SLE1 naiveB


title: aorta_594s_P03


title: aorta_594s_P02


title: aorta_594s_P01


title: aorta_594s_O22


title: aorta_594s_O19


title: aorta_594s_O20


title: SLE1 monocyte


title: SLE24 monocyte


title: H9c2, DOX + DXZ, rep3

city: Shanghai

first: Minfeng

last: Huo

state: Shanghai

address: 500 Zhennan Road

institute: School of Medicine, Tongji University

description:
DOX + DXZ
D_DXZ3

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38/mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values for all Samples

growth_protocol: H9c2 cells were cultured using DMEM medium containing 4 mM L-Glutamine, 4,500 mg l-1 glucose, 10 % fatal bovine serum (FBS), 100 units ml-1 streptomycin and 100 units ml-1 penicillin. H9c2 cells were inoculated into the 96-well plate with a cell density of 8000 cells per well and incubated for 12 h for cell attachment.

extract_protocol:
The total RNA from the H9c2 cells were harvested using TRIzol (Invitrogen).
A total amount of 1 µg RNA per sample was used as input material for the RNAsample preparations. Sequencing libraries were generated using NEBNext®UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’srecommendations and index codes were added to attribute sequences to each sample

treatment_protocol: After cell attachment, the medium was then discarded and rinsed with cold PBS three times. Cells were subjected to different treatments including untreated (Unt), DOX treatment (DOX), combinational DOX + MgHCF treatment (D_MgHCF) and combinational DOX + DXZ treatment (D_DXZ) for 6 h.

tag: cell line

value: myoblast

tag: genotype

value: WT

value: DOX and DXZ treatment, 6h


title: H9c2, DOX + MgHCF, rep2

description:
DOX + MgHCF
D_MgPB2

tag: treatment

value: DOX and MgHCF NCs treatment, 6h


title: H9c2, DOX + MgHCF, rep3

description:
DOX + MgHCF
D_MgPB3


title: SLE43 monocyte

tag: diagnosis

value: Negative, 1:Positive):1


title: H9c2, DOX + DXZ, rep2

description:
DOX + DXZ
D_DXZ2

tag: cell type


title: H9c2, DOX + DXZ, rep1

description:
DOX + DXZ
D_DXZ1


title: HC15 monocyte

tag: date measured


title: H9c2, DOX + MgHCF, rep1

description:
DOX + MgHCF
D_MgPB1


title: SLE47 monocyte

value: SLE

tag: Sex


title: aorta_594s_O18

value: aorta

value: 10 weeks


title: HC14 monocyte

value: F

tag: sex (1 vs 2)


title: aorta_594s_O17


title: HC16 monocyte


title: H9c2, DOX, rep2

description:
DOX
DOX2

value: DOX treatment, 6h


title: aorta_594s_O15


title: aorta_594s_O21


title: H9c2, Untreated, rep2

description:
Untreated
Unt2

value: Untreated, 6h


title: aorta_594s_O12


title: aorta_594s_O14


title: aorta_594s_O13


title: H9c2, Untreated, rep3

description:
Untreated
Unt3


title: H9c2, DOX, rep1

description:
DOX
DOX1


title: H9c2, Untreated, rep1

description:
Untreated
Unt1


title: aorta_594s_O11


title: aorta_594s_O10


title: aorta_594s_O09


title: H9c2, DOX, rep3

description:
DOX
DOX3


title: aorta_594s_O04


title: Exercise_AdipoR1_m_rep3

city: kunming

first: Yi-Cheng

last: Ma

email: 290361200@qq.com, mayc@ynu.edu.cn

state: yunnan

address: NO.2 North Cuihu Road

institute: Yunnan University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 2*150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads.
Differential expression analysis of two conditions/groups (four biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value.The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and log2(Fold change) of 1 were set as the threshold for significantly differential expression.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: xlsx files include RPKM values for each Sample

source_name: gastrocnemius muscle

growth_protocol: C57BL/6J mice (male, 16 months old) were housed in standard cages with unrestricted access to food and water. The temperature and humidity in the room were maintained at 20 ± 2°C and 50 ± 5%, respectively.

extract_protocol:
The gastrocnemius muscle of exercised mice flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At the age of 16 months, all mice were acclimated to a motorized running wheel apparatus (#YLS-10B, Yiyan, Jinan, China) (0.6 m/revolution, 15 rpm for 30 minutes every other day) for 3 days prior to beginning the training protocol. After a total of 16 weeks of restricted wheel running exercise regimen, gastrocnemius muscle of mice were collected.

value: gastrocnemius muscle

value: male

value: exercise

value: AdipoR1 knockdown

tag: developmental stage

value: 16 months


title: aorta_594s_O03


title: aorta_594s_O07


title: aorta_594s_O05


title: Pooled high-affinity IBC samples hashtag library

city: Aurora

first: John

last: Cambier

state: CO

department: Immunology & Microbiology

country: USA

institute: University of Colorado

description:
10x Genomics
C0301 = VH125.NOD mouse #1
C0302 = VH125.NOD mouse #2
C0303 = VH125.NOD mouse #3

library_source: other

data_processing:
Raw base call files were processed with the 10x Genomics Cell Ranger pipeline package (version 3.1.0) using a standard protocol and with mouse reference genomes: mm10 (GENCOD vM23/Ensemble 98) and vdj-GRCm38-alts-ensembl-3.1.0 available on the 10xGenomics website. The Cell Ranger package demultiplexed raw base call files into FASTQ 372 files, aligned, filtered cells using quality metrics, counted 373 nucleotide barcodes, performed gene expression analysis in 374 reference to VDJ sequences and hashtag data. The total number of reads assigned to the gene expression library was 288,478,010 and VDJ – 200,957,192. Fraction of reads with valid barcodes and unique molecular identifiers was 91.5% for gene expression and 96.7% for VDJ library. Sequencing saturation reflecting library complexity as well as sequencing depth reached 88.8%. Mean read pairs per cell were 45,287 for gene expression and hashtag library and 36,873 for antibody VDJ library. Further analysis was performed with 10x Genomics software: Loupe Cell and Loupe VDJ Browsers.
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files and feature files

molecule: other

source_name: spleen

extract_protocol:
Splenocytes were treated with 2.4G2 anti-Fc gRIIB antibody to block FcR binding. In primary staining, cells were incubated with anti-B220 (clone: RA3-6B2) and anti-IgM antibodies (clone: B-7-6), and 0.1 mg biotinylated human recombinant insulin (Sigma) for 30 min on ice. In secondary staining, cells were stained with 2 μg Alexa FluorTM 647 conjugated streptavidin (Invitrogen) for 20 min on ice. Cells were washed and resuspended in MACS buffer (1X PBS;0.5% BSA;2 mmol/L EDTA), and incubated with anti-Cy5/anti-Alexa 647 microbeads (Miltenyi Biotec) for 15 min at 4°C. To enrich IBCs, cells were passed through LS column mounted on a magnet (Miltenyi Biotec).  FACS sorting was then done on MoFlo Astrios EQ (Beckman Coulter), isolating B220+ cells with high signal for both mIgM and biotinylated insulin. To distinguish individual mice, splenocytes were additionally labeled during primary staining  with TotalSeq-C antibodies (BioLegend) with anti-MHC antibody conjugated to unique oligonucleotide tags, termed hashtags. prediabetic VH125.NOD mouse 1 – TotalSeq-CO301 hashtag 1 with 5′–ACCCACCAGTAAGAC–3′ barcode, mouse 2 – TotalSeq-CO302 hashtag 2 with 5′– GGTCGAGAGCATTCA–3′barcode, and mouse 3 – TotalSeq-CO303 hashtag 3 with 5′–CTTGCCGCATGTCAT–3′ barcode. Labelling with hashtag antibodies was performed on ice for 30 min. After sorting,  high-affinity IBCs from three VH125.NOD mice were pooled for library construction using 10X Genomics protocols and submitted for Illumina sequencing. High-affinity IBCs were sorted into PBS supplemented with 10% FBS, counted, and assessed for cell viability. Cells were diluted into a final concentration of 400 cells/μl in 50ml volume.
Single-cell RNA-sequencing (scRNA-seq) was performed with 10X Genomics technology and protocols. Briefly, about 7,000 cells were loaded onto the Chromium Controller microfluidics device and cells were encapsulated in oil-droplets containing beads and cDNA synthesis reagents (10X Genomics). Three sequencing libraries were prepared: 5′ total gene expression, hashtag, and VDJ antibody, according to the manufacturer’s instructions. Reverse transcription (RT) of total mRNA occurred in each individual droplet to generate cDNA. Simultaneously, hashtag barcodes were captured and overlap-extended with mRNA transcripts within the same droplet to generate DNA. After RT, droplets were broken, and the cDNA and DNA were amplified by PCR, purified, and separated with size selection beads. VDJ was amplified with additional PCR with mouse B cell Chromium Single-Cell V(D)J Enrichment Kit (10x Genomics). Sequencing was performed on a NovaSEQ 6000 system (Illumina).

value: spleen

value: insulin-reactive B cells

value: Cg-Tg (Igh-6/Igh-V125)2Jwt/JwtJ] on NOD/ShiLtJ


title: Pooled high-affinity IBC samples VDJ library

description: 10x Genomics


title: Exercise_EV_m_rep4

value: wild type


title: Exercise_AdipoR1_m_rep1


title: Exercise_AdipoR1_m_rep4


title: aorta_594s_O01


title: Exercise_EV_m_rep3


title: Exercise_EV_m_rep2


title: aorta_594s_N22


title: aorta_594s_O02


title: Pooled high-affinity IBC samples GEX  library

description: 10x Genomics


title: Control_EV_m_rep4

value: control


title: aorta_594s_N18


title: Control_EV_m_rep3


title: Control_EV_m_rep2


title: Exercise_EV_m_rep1


title: aorta_594s_O06


title: aorta_594s_N20


title: Exercise_AdipoR1_m_rep2


title: Control_EV_m_rep1


title: aorta_594s_N17


title: PSAPP_TAM3

city: New York

first: Philip

last: Hasel

address: 435 E 30th St

institute: NYU Langone Medical Centre

data_processing:
10xGenomics Visium libraries were processed using SpaceRanger (1.3.1)
Assembly: mm10
Supplementary files format and content: processed files include aligned fiducials, hi and low res tissue images, detected tissue image, tissue positon list, scalefactor, matrix, filtered feature bc matrix, features and barcodes

source_name: Inpp5dfl/fl/Cx3cr1CreER/+ crossed to APPKM670/671NL/PSEN1Δexon9 (PSAPP) treated with tamoxifen

extract_protocol:
Brain sections were cryosectioned to 10 um
Dual Index Illumina libraries were prepared following 10xGenomics Visium instructions

treatment_protocol: mice were treated with either cornoil or tamoxifen (75 mg/kg) at 3 months of age for 5 consecutive days

value: coronal brain section

value: tamoxifen

value: Inpp5dfl/fl/Cx3cr1CreER/+ crossed to APPKM670/671NL/PSEN1{delta}exon9 (PSAPP)


title: aorta_594s_N16

value: aorta

value: 10 weeks


title: aorta_594s_N21


title: aorta_594s_N15


title: aorta_594s_N19


title: aorta_594s_N13


title: WT_TAM3

source_name: Inpp5dfl/fl/Cx3cr1CreER/+ treated with tamoxifen


title: aorta_594s_N11


title: aorta_594s_N12


title: aorta_594s_N14


title: PSAPP_TAM2


title: WT_TAM2


title: aorta_594s_N09


title: PSAPP_CO2

source_name: Inpp5dfl/fl/Cx3cr1CreER/+ crossed to APPKM670/671NL/PSEN1Δexon9 (PSAPP) treated with cornoil

value: cornoil


title: aorta_594s_N07


title: aorta_594s_N08


title: WT_CO2

source_name: Inpp5dfl/fl/Cx3cr1CreER/+ treated with cornoil


title: PSAPP_TAM1


title: PSAPP_CO1


title: aorta_594s_N05


title: WT_TAM1


title: WT_CO1


title: PSAPP_CO3


title: WT_CO3


title: aorta_594s_N04


title: Swap2-iRFPGFP-Low

first: Hani

last: Shayya

state: New York

address: 3227 Broadway

department: Biochemistry and Mol Biophysics

institute: Columbia University

data_processing:
Transcript annotations were downloaded from Ensembl (GRCm38, Ensembl version 92). Extended OR gene models were included from Ibarra-Soria et al., PLOS Genetics, 2014. The coding sequence for each extended OR gene model was annotated based on the Ensembl annotations for that OR. Only transcripts from a localized contig and containing an annotated coding sequence were retained in the final transcript set.
A fasta file of transcript sequences was generated using the GRCm38 (mm10) sequence, the above annotation set and custom python scripts. Sequences were indexed using salmon (verson 0.13.1, -k 31).
Demultiplexed fastq files were quantified against the reference transcriptome using Salmon (version 0.13.1, --libType A, --seqBias, --gcBias, --validateMappings).
Assembly: mm10
Supplementary files format and content: Tab-delimited quant.sf files generated by Salmon. Each row is a transcript (ENSMUST = Ensembl transcripts, CUFFORT = extended OR gene models, egfp/tdtomato/lacZ as above). Columns indicate Length (nt), EffectiveLength (as modeled by Salmon), TPM (abundance in transcripts per million) and NumReads (expected number of reads originating from each transcript).

source_name: Olfactory epithelium

extract_protocol:
For experiments on OSN developmental populations (INPs, iOSNs, mOSNs), cells were sorted across multiple days, pelleted (10 minutes at 800g) and frozen at -80 until the day of extraction. Lysates were prepared from roughly 1e6 cells per condition using a lysis buffer (20mM Tris pH=7.5, 150mM NaCl, 5mM MgCl2, 1mM DTT, 100ug/mL cycloheximide, 1%(v/v) Triton X-100 and 25U/mL TURBO DNAse), RNA was quantified by Quant-iT RiboGreen assay (Thermo Fisher) and lysate containing 100ng of RNA was mixed with 300uL of Trizol (Invitrogen). In all other experiments, 10-20k cells were sorted directly into 500uL of Trizol LS (Sigma). RNA was recovered from Trizol using the Direct-Zol RNA Miniprep kit (Zymo), precipitated overnight with 300mM sodium acetate and 1.5 volumes of isopropanol, digested for 30min at 37°C with TURBO DNAse (Invitrogen) and cleaned up on 1.8x Ampure Beads (Beckman Coulter). <10ng RNA was used for library prep, as measured by Quant-iT RiboGreen assay.
Libraries were prepared using the SMARTER Stranded Total RNA-seq Kit v2 - Pico Input Mammalian (Takara Bio) and the manufacturer’s instructions.

treatment_protocol: Mice were sacrificed by decapitation (if younger than postnatal day 14) or CO2 followed by cervical dislocation, and the main olfactory epithelium (MOE) was isolated by dissection into ice-cold 1xPBS without calcium or magnesium. Single-cell suspensions were prepared using a papain dissociation system (Worthington) following a modified version of the manufacturer’s protocol. Dissociations were for 30-45 minutes at 37°C, centrifugation steps for 5min at 400g and the discontinuous density gradient was not performed. Cells were re-suspended for FACS in a buffer containing 2%FBS (Gibco), 5mM MgCl2, DAPI (1:10k, Invitrogen) and the remaining DNAase I from the dissociation kit. For experiments where iRFP intensity was measured to determine stress levels in mice containing the Atf5-reporter allele, cycloheximide (Sigma, 100µg/mL) was added to all solutions during dissociation and cytometry to block new protein synthesis and minimize the effects of dissociation or sorting-related stress on these measurements. Dissociated cells were filtered through a 40µm cell strainer and analyzed on a Beckman Coulter MoFlo Astrios EQ sorter.

value: Olfactory epithelium

value: mOSN


title: Swap2-iRFPGFP-High


title: aorta_594s_N10


title: Swap2-iRFP-High

value: iOSN


title: aorta_594s_N06


title: Swap2-iRFP-Low


title: aorta_594s_N01


title: aorta_594s_N02


title: aorta_594s_M22


title: aorta_594s_M20


title: Swap1-iRFPGFP-High


title: Swap1-iRFP-Low


title: aorta_594s_M21


title: Swap1-iRFP-High


title: OmpCreDdit3-Het2


title: aorta_594s_N03


title: aorta_594s_M18


title: aorta_594s_M16


title: OmpCreDdit3-cKO1


title: aorta_594s_M19


title: aorta_594s_M17


title: OmpCreDdit3-Het1


title: aorta_594s_M14


title: Ctrl4-iRFPGFP-Low

value: Atf5(rep/+); Omp(iresGFP/+)


title: Ctrl4-iRFPGFP-High


title: Ctrl3-iRFPGFP-Low


title: aorta_594s_M13


title: Ctrl4-iRFP-High


title: Swap1-iRFPGFP-Low


title: aorta_594s_M12


title: Ctrl3-iRFPGFP-High


title: Ctrl4-iRFP-Low


title: aorta_594s_M09


title: Ctrl3-iRFP-Low


title: aorta_594s_M07


title: aorta_594s_M08


title: aorta_594s_M05


title: aorta_594s_M04


title: aorta_594s_M03


title: aorta_594s_M10


title: aorta_594s_M06


title: aorta_594s_M01


title: aorta_594s_M11


title: aorta_594s_L24


title: aorta_594s_L23


title: aorta_594s_L22


title: aorta_594s_M02


title: patent ductus arteriosus postnatal 5 day

city: Los Angeles

first: Feiyang

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Sequencing was performed on NovaSeq 6000 (Pair-end, 100 base pairs per read).
The digital expression matrix was generated by demultiplexing, barcode processing, and gene unique molecular index counting using the Cellranger count pipeline (version 4.0.0, 10X Genomics).
Multiple samples were merged using the Cellranger aggr pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: Raw expression values in sparse matrix format

source_name: patent ductus arteriosus

growth_protocol: For scRNA-seq experiments, C57BL/6 mice at the following stages were used: E18.5, P0.5 and P5. Libraries were generated from ducti of pooled littermates (8-9 mice per library, both sexes).

extract_protocol:
For cell isolation, aorta and ducti were dissected in versene, vessels were minced into small pieces and placed in 1mL of digestion buffer containing DNase1, 1M HEPES, Libase, and HBSS at 37C for 20mins. Once tissue was digested into a single cell suspension, cells were washed, pelleted, and passed through a 40m filter. The final cell suspension was in 0.04% BSA.
scRNA-seq libraries were generated using 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cells were loaded accordingly following the 10X Genomics protocol with an estimated targeted cell recovery of 6000 cells.

value: patent ductus arteriosus

value: postnatal 5 day


title: 4wkM28Ddit3-cKO1-tdtomato


title: 4wkM28Ddit3-Het2-tdtomato


title: Ctrl3-iRFP-High


title: 4wkM28Ddit3-Het3-tdtomato


title: 4wkM28Ddit3-cKO1-GFP


title: 4wkM28Ddit3-cKO2-GFP


title: 4wkM28Ddit3-Het3-GFP


title: patent ductus arteriosus postnatal 0.5 day

value: postnatal 0.5 day


title: patent ductus arteriosus embryo 18.5 day

value: embryo 18.5 day


title: aorta postnatal 5 day

source_name: aorta


title: aorta postnatal 0.5 day


title: 4wkM28Ddit3-WT1-GFP


title: 4wkM28Ddit3-WT1-tdtom


title: aorta_594s_L14


title: aorta_594s_L19


title: aorta_594s_L16


title: aorta_594s_L20


title: aorta_594s_L18


title: aorta_594s_L15


title: aorta_594s_L21


title: aorta_594s_L17


title: aorta_594s_L10


title: aorta_594s_L12


title: βRicKO+Ad-GFP-1(KO1)

first: canqi

last: cui

address: 197 Ruijin 2nd Road

institute: shanghai national reaearch center for endocrine and metabolic diseases

library_source: genomic

data_processing:
Raw sequence reads were initially processed by FastQC for quality control, and then adapter sequences and poor quality reads were removed by using Trimmomatic.
Quality filtered reads were then mapped to hg38/GRCh38 reference genome using BWA(0.7.10), and only uniquely mapped reads were kept.
Sam files were converted to Bam format using Samtools and used for peak calling. MACS2(2.1.1)was used to call peaks and an initial threshold q-value of 0.05 as cutoff.
Visualization of read count data was performed by converting raw bam files to bigwig files using IGV tools.
Genome_build: hg38

molecule: genomic DNA

source_name: islet

growth_protocol: Individual islets were hand-picked and cultured in RPMI 1640, isolated islets were digested by 0.25% trypsin with EDTA .

extract_protocol:
Selected 50 average size islets were lysed in lysis buffer.Nuclei were then incubated with the Tn5 transposome and tagmentation.
Libaray was prepared according to protocols of TruePrep DNA Library Prep Kit V2 for illumina(Vazyme Biotech, Nanjing, China) .PCR was performed to amplify the library for 12 cycles.The libraries were sequenced on HiSeq (X Ten) platform and using PE50 sequencing strategy

treatment_protocol: Adenovirus packaged with Acsl4 or control was transfected with 48h ex vivo

value: islet

value: BetaRicKO


title: aorta_594s_L08

source_name: male mouse


title: aorta embryo 18.5 day


title: aorta_594s_L09


title: Con+Ad-GFP-2(WT2)

value: wildtype


title: 4wkM28Ddit3-Het2-GFP


title: aorta_594s_L13


title: aorta_594s_L07


title: aorta_594s_L06


title: aorta_594s_L04


title: aorta_594s_L05


title: aorta_594s_L03


title: 4wkM28Ddit3-cKO3-GFP


title: aorta_594s_L02


title: 4wkM28Ddit3-cKO2-tdtomato


title: 4wkM28Ddit3-Het1-GFP


title: 4wkM28Ddit3-cKO3-tdtom


title: aorta_594s_L01


title: 4wkM28Ddit3-Het1-tdtomato


title: aorta_594s_K24


title: Con+Ad-GFP-1(WT)


title: βRicKO+Ad-Acsl4-1(KA1)

value: BetaRicKO with Acsl4 overexpression


title: βRicKO+Ad-GFP-2(KO2)


title: βRicKO+Ad-Acsl4-2(KA3)


title: aorta_594s_L11


title: aorta_594s_K21


title: aorta_594s_K23


title: aorta_594s_K20


title: aorta_594s_K22


title: aorta_594s_M15


title: aorta_594s_K19


title: aorta_594s_K18


title: aorta_594s_K17


title: aorta_594s_K16


title: aorta_594s_K15


title: aorta_594s_K14


title: aorta_594s_K13


title: aorta_594s_K12


title: aorta_594s_K11


title: aorta_594s_K10


title: aorta_594s_K09