title: SS2_15_0063_J23


title: SS2_15_0063_J22

status: Public on Apr 02 2019

type: SRA

city: New York

first: Ruslan

last: Soldatov

state: New York

address: 323 E 61st Street

department: Computational Oncology

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
cells collected at E8.5
E8.5_whole_embryo_Wnt1_counts.txt

library_source: transcriptomic

data_processing:
ScRNA-seq reads were aligned to the UCSC mm10 genome assembly using STAR aligner
Per-gene read counts in each cell were determined using feature Counts software
Individual single-cell datasets were pre-processed using PAGODA1/PAGODA2 packages, which includes normalization, clustering of cells, and t-SNE embedding for visualization
Joint analysis of multiple datasets was performed using CONOS package
Genome_build: mm10
Supplementary_files_format_and_content: text files include gene counts matrices for each spatio-temporal condition

molecule: polyA RNA

organism: Mus musculus

source_name: neural crest and neural tube

extract_protocol:
Wnt1-tomato+ or Sox10-tomato+ embryos were selected following macroscopical observation using a stereoscope equiped with a UV-lamp. TOMATO+ embryo  tissue was dissociated using trypsin digestion as previously described (Furlan A et al Science 2017)
TOMATO+ single cells were sorted using a BD FACSAria III Cell Sorter B5/R3/V3 system  in 384-well plates. Library construction was performed as described in Picelli S et al, Nat Protoc. 2014.
Library pooling and sequencing was performed as described in Picelli S et al, Nat Protoc. 2014.

tag: age

tag: genotype

tag: segment

tag: plate


title: SS2_15_0063_J11


title: SS2_15_0063_J21


title: SS2_15_0063_J20


title: SS2_15_0063_J10


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title: SS2_15_0063_I7


title: SS2_15_0063_J19


title: SS2_15_0063_J18


title: SS2_15_0063_J13


title: SS2_15_0063_I2


title: SS2_15_0063_I4


title: SS2_15_0063_J5


title: SS2_15_0063_I9


title: SS2_15_0063_J12


title: SS2_15_0063_I8


title: SS2_15_0063_I5


title: SS2_15_0063_I24


title: SS2_15_0063_I6


title: SS2_15_0063_I21


title: SS2_15_0063_I3


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title: SS2_15_0063_I22


title: SS2_15_0063_I14


title: SS2_15_0063_I1


title: SS2_15_0063_I16


title: SS2_15_0063_I20


title: SS2_15_0063_I10


title: SS2_15_0063_I17


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title: SS2_15_0063_H6


title: SS2_15_0063_H5


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title: SS2_15_0063_H22


title: SS2_15_0063_H24


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title: SS2_15_0063_C15


title: SS2_15_0063_D11


title: SS2_15_0063_C13


title: SS2_15_0063_C12


title: SS2_15_0063_C20


title: SS2_15_0063_B7


title: SS2_15_0063_B4


title: SS2_15_0063_C10


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title: SS2_15_0063_B23


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title: SS2_15_0063_B21


title: SS2_15_0063_B2


title: SS2_15_0063_C11


title: SS2_15_0063_B19


title: SS2_15_0063_B1


title: SS2_15_0063_B20


title: SS2_15_0063_B9


title: SS2_15_0063_B15


title: SS2_15_0063_B14


title: SS2_15_0063_B8


title: SS2_15_0063_B18


title: SS2_15_0063_C14


title: SS2_15_0063_B17


title: SS2_15_0063_B6


title: SS2_15_0063_B16


title: SS2_15_0063_B12


title: SS2_15_0063_B11


title: SS2_15_0063_B10


title: SS2_15_0063_A8


title: SS2_15_0063_A9


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title: SS2_15_0063_F9


title: SS2_15_0063_A6


title: SS2_15_0063_A3


title: SS2_15_0063_A4


title: SS2_15_0063_A5


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title: SS2_15_0063_A22


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title: SS2_15_0063_A11


title: SS2_15_0063_A10


title: SS2_15_0063_A12


title: SS2_15_0087_P8

description:
cells collected at E9.5
E9.5_trunk_Wnt1_counts.txt

value: trunk


title: SS2_15_0087_P9


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title: SS2_15_0087_O12


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title: SS2_15_0087_O10


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title: SS2_15_0087_M7


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title: SS2_15_0087_M20


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title: SS2_15_0087_M15


title: SS2_15_0087_M14


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title: SS2_15_0087_M6


title: SS2_15_0087_M11


title: SS2_15_0087_M10


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title: SS2_15_0087_O2


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title: SS2_15_0087_L2


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title: SS2_15_0087_L22


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title: SS2_15_0087_L10


title: SS2_15_0087_K8


title: SS2_15_0087_K4


title: SS2_15_0087_K5


title: SS2_15_0087_K24


title: SS2_15_0087_K22


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title: SS2_15_0087_E5


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title: SS2_15_0087_E17


title: SS2_15_0087_E18


title: SS2_15_0087_E13


title: SS2_15_0087_E15


title: SS2_15_0087_E14


title: SS2_15_0087_E6


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title: SS2_15_0087_D8


title: SS2_15_0087_E10


title: SS2_15_0087_E11


title: SS2_15_0087_D6


title: SS2_15_0087_D4


title: SS2_15_0087_D7


title: SS2_15_0087_D5


title: SS2_15_0087_D2


title: SS2_15_0087_D3


title: SS2_15_0087_D24


title: SS2_15_0087_D23


title: SS2_15_0087_D21


title: SS2_15_0087_D22


title: SS2_15_0087_D20


title: SS2_15_0087_D1


title: SS2_15_0087_E16


title: SS2_15_0087_D18


title: SS2_15_0087_D19


title: SS2_15_0087_D17


title: SS2_15_0087_D16


title: SS2_15_0087_D13


title: SS2_15_0087_E23


title: SS2_15_0087_D15


title: SS2_15_0087_D14


title: SS2_15_0087_D12


title: SS2_15_0087_D11


title: SS2_15_0087_D10


title: SS2_15_0087_D9


title: SS2_15_0087_C9


title: SS2_15_0087_C8


title: SS2_15_0087_C2


title: SS2_15_0087_C24


title: SS2_15_0087_C4


title: SS2_15_0087_C3


title: SS2_15_0087_C23


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title: SS2_15_0085_K13


title: SS2_15_0085_K12


title: SS2_15_0085_K14


title: SS2_15_0085_J8


title: SS2_15_0085_K11


title: SS2_15_0085_K10


title: SS2_15_0085_J9


title: SS2_15_0085_J6


title: SS2_15_0085_L19


title: SS2_15_0085_J4


title: SS2_15_0085_J3


title: SS2_15_0085_J2


title: SS2_15_0085_J5


title: SS2_15_0085_J23


title: SS2_15_0085_J19


title: SS2_15_0085_J1


title: SS2_15_0085_J22


title: SS2_15_0085_J17


title: SS2_15_0085_J15


title: SS2_15_0085_J12


title: SS2_15_0085_J18


title: SS2_15_0085_J14


title: SS2_15_0086_A10


title: SS2_15_0085_J13


title: SS2_15_0085_J7


title: SS2_15_0085_J10


title: SS2_15_0085_I9


title: SS2_15_0085_J11


title: SS2_15_0085_I8


title: SS2_15_0085_I6


title: SS2_15_0085_I4


title: SS2_15_0085_I5


title: SS2_15_0085_I3


title: SS2_15_0085_J24


title: SS2_15_0085_I24


title: SS2_15_0085_I23


title: SS2_15_0085_J21


title: SS2_15_0085_J20


title: SS2_15_0085_I22


title: SS2_15_0085_J16


title: SS2_15_0085_I2


title: SS2_15_0085_I20


title: SS2_15_0085_I18


title: SS2_15_0085_K2


title: SS2_15_0085_I1


title: SS2_15_0085_I19


title: SS2_15_0085_I21


title: SS2_15_0085_I14


title: SS2_15_0085_I16


title: SS2_15_0085_I15


title: SS2_15_0085_I13


title: SS2_15_0085_I12


title: SS2_15_0085_I7


title: SS2_15_0085_I10


title: SS2_15_0085_H8


title: SS2_15_0085_H7


title: SS2_15_0085_H6


title: SS2_15_0085_H5


title: SS2_15_0085_I17


title: SS2_15_0085_H3


title: SS2_15_0085_H2


title: SS2_15_0085_H4


title: SS2_15_0085_H24


title: SS2_15_0085_H22


title: SS2_15_0085_H21


title: SS2_15_0085_H23


title: SS2_15_0085_H20


title: SS2_15_0085_H1


title: SS2_15_0085_H17


title: SS2_15_0085_H16


title: SS2_15_0085_H15


title: SS2_15_0085_H18


title: SS2_15_0085_H19


title: SS2_15_0085_I11


title: SS2_15_0085_H14


title: SS2_15_0085_H12


title: SS2_15_0085_H13


title: SS2_15_0085_G9


title: SS2_15_0085_G8


title: SS2_15_0085_H10


title: SS2_15_0085_G7


title: SS2_15_0085_G6


title: SS2_15_0085_G5


title: SS2_15_0085_G2


title: SS2_15_0085_G4


title: SS2_15_0085_G23


title: SS2_15_0085_G24


title: SS2_15_0085_G3


title: SS2_15_0085_G21


title: SS2_15_0085_G20


title: SS2_15_0085_G22


title: SS2_15_0085_G18


title: SS2_15_0085_G17


title: SS2_15_0085_H9


title: SS2_15_0085_G1


title: SS2_15_0085_G16


title: SS2_15_0085_G19


title: SS2_15_0085_G15


title: SS2_15_0085_G12


title: SS2_15_0085_F9


title: SS2_15_0085_G10


title: SS2_15_0085_G14


title: SS2_15_0085_F8


title: SS2_15_0085_G13


title: SS2_15_0085_F7


title: SS2_15_0085_F6


title: SS2_15_0085_F5


title: SS2_15_0085_F24


title: SS2_15_0085_F2


title: SS2_15_0085_F22


title: SS2_15_0085_F4


title: SS2_15_0085_G11


title: SS2_15_0085_F19


title: SS2_15_0085_F21


title: SS2_15_0085_F23


title: SS2_15_0085_F18


title: SS2_15_0085_F16


title: SS2_15_0085_F13


title: SS2_15_0085_F17


title: SS2_15_0085_F20


title: SS2_15_0085_F14


title: SS2_15_0085_F15


title: SS2_15_0085_F11


title: SS2_15_0085_F12


title: SS2_15_0085_E9


title: SS2_15_0085_E6


title: SS2_15_0085_E7


title: SS2_15_0085_E5


title: SS2_15_0085_E24


title: SS2_15_0085_E22


title: SS2_15_0085_E23


title: SS2_15_0085_E21


title: SS2_15_0085_E2


title: SS2_15_0085_F1


title: SS2_15_0085_E20


title: SS2_15_0085_H11


title: SS2_15_0085_E3


title: SS2_15_0085_E1


title: SS2_15_0085_E16


title: SS2_15_0085_E19


title: SS2_15_0085_E18


title: SS2_15_0085_E15


title: SS2_15_0085_E10


title: SS2_15_0085_E14


title: SS2_15_0085_F10


title: SS2_15_0085_D8


title: SS2_15_0085_E13


title: SS2_15_0085_D9


title: SS2_15_0085_E8


title: SS2_15_0085_E11


title: SS2_15_0085_E4


title: SS2_15_0085_D7


title: SS2_15_0085_D5


title: SS2_15_0085_D6


title: SS2_15_0085_D3


title: SS2_15_0085_D4


title: SS2_15_0085_D2


title: SS2_15_0085_D24


title: SS2_15_0085_D20


title: SS2_15_0085_E17


title: SS2_15_0085_D22


title: SS2_15_0085_D21


title: SS2_15_0085_D19


title: SS2_15_0085_D1


title: SS2_15_0085_E12


title: SS2_15_0085_D16


title: SS2_15_0085_D17


title: SS2_15_0085_D12


title: SS2_15_0085_D18


title: SS2_15_0085_D14


title: SS2_15_0085_D15


title: SS2_15_0085_D13


title: SS2_15_0085_D11


title: SS2_15_0085_D10


title: SS2_15_0085_C9


title: SS2_15_0085_C7


title: SS2_15_0085_C8


title: SS2_15_0085_C5


title: SS2_15_0085_C3


title: SS2_15_0085_C6


title: SS2_15_0085_C4


title: SS2_15_0085_D23


title: SS2_15_0085_C23


title: SS2_15_0085_C22


title: SS2_15_0085_C21


title: SS2_15_0085_C18


title: SS2_15_0085_C19


title: SS2_15_0085_C16


title: SS2_15_0085_C1


title: SS2_15_0085_C17


title: SS2_15_0085_C11


title: SS2_15_0085_C15


title: SS2_15_0085_C12


title: SS2_15_0085_C13


title: SS2_15_0085_C14


title: SS2_15_0085_C10


title: SS2_15_0085_B9


title: SS2_15_0085_B8


title: SS2_15_0085_B7


title: SS2_15_0085_C2


title: SS2_15_0085_B5


title: SS2_15_0085_B4


title: SS2_15_0085_B3


title: SS2_15_0085_B23


title: SS2_15_0085_B24


title: SS2_15_0085_B22


title: SS2_15_0085_C24


title: SS2_15_0085_B6


title: SS2_15_0085_B2


title: SS2_15_0085_C20


title: SS2_15_0085_B21


title: SS2_15_0085_B20


title: SS2_15_0085_B1


title: SS2_15_0085_B17


title: SS2_15_0085_B18


title: SS2_15_0085_B15


title: SS2_15_0085_B11


title: SS2_15_0085_B12


title: SS2_15_0085_B10


title: SS2_15_0085_A9


title: SS2_15_0085_A5


title: SS2_15_0085_A4


title: SS2_15_0085_A2


title: SS2_15_0085_A24


title: SS2_15_0085_A3


title: SS2_15_0085_A23


title: SS2_15_0085_A22


title: SS2_15_0085_A21


title: SS2_15_0085_A19


title: SS2_15_0085_A1


title: SS2_15_0085_A20


title: SS2_15_0085_A18


title: SS2_15_0085_B19


title: SS2_15_0085_A17


title: SS2_15_0085_A15


title: SS2_15_0085_B13


title: SS2_15_0085_B14


title: SS2_15_0085_A13


title: SS2_15_0085_A8


title: SS2_15_0085_A11


title: SS2_15_0085_A6


title: SS2_15_0085_B16


title: SS2_15_0085_A7


title: SS2_15_0085_A12


title: SS2_15_0085_A10


title: SS2_15_0085_A16


title: SS2_18_108_C16

description:
cells collected at E10.5
E10.5_tail_Wnt1_counts.txt

source_name: neural crest-derived cells

value: tail


title: SS2_18_108_C22


title: SS2_18_108_C24


title: SS2_18_108_C17


title: SS2_18_108_D9


title: SS2_18_108_D8


title: SS2_18_108_D6


title: SS2_18_108_D4


title: SS2_18_108_C15


title: SS2_18_108_C20


title: SS2_18_108_C23


title: SS2_18_108_C21


title: SS2_18_108_C18


title: SS2_18_108_C19


title: SS2_15_0085_A14


title: SS2_18_108_C13


title: SS2_18_108_D12


title: SS2_18_108_C9


title: SS2_18_108_D7


title: SS2_18_108_C7


title: SS2_18_108_C11


title: SS2_18_108_C4


title: SS2_18_108_C6


title: SS2_18_108_B19


title: SS2_18_108_B20


title: SS2_18_108_C10


title: SS2_18_108_B16


title: SS2_18_108_C8


title: SS2_18_108_C12


title: SS2_18_108_C3


title: SS2_18_108_B18


title: SS2_18_108_C2


title: SS2_18_108_B24


title: SS2_18_108_B17


title: SS2_18_108_B22


title: SS2_18_108_C14


title: SS2_18_108_C1


title: SS2_18_108_B21


title: SS2_18_108_B14


title: SS2_18_108_B23


title: SS2_18_108_B9


title: SS2_18_108_C5


title: SS2_18_108_B10


title: SS2_18_108_B8


title: SS2_18_108_B13


title: SS2_18_108_B11


title: SS2_18_108_A4


title: SS2_18_108_A16


title: SS2_18_108_A8


title: SS2_18_108_A18


title: SS2_18_108_B7


title: SS2_18_108_A3


title: SS2_18_108_B15


title: SS2_18_108_B6


title: SS2_18_108_A9


title: SS2_18_108_B12


title: SS2_18_108_A10


title: SS2_18_108_A6


title: SS2_18_108_A2


title: SS2_18_108_A15


title: SS2_18_108_A20


title: SS2_18_108_A22


title: SS2_18_108_A17


title: SS2_18_108_A13


title: SS2_18_108_A19


title: SS2_18_108_B3


title: SS2_18_108_A14


title: SS2_18_108_A21


title: SS2_18_108_A11


title: SS2_18_108_B4


title: SS2_18_108_B2


title: SS2_18_108_A1


title: SS2_18_108_B1


title: SS2_18_108_A5


title: SS2_18_108_A7


title: SS2_18_108_B5


title: SS2_18_108_A12


title: SS2_18_108_A23


title: SS2_18_107_P20


title: SS2_18_107_P21


title: SS2_18_107_P22


title: SS2_18_108_A24


title: SS2_18_107_P18


title: SS2_18_107_P7


title: SS2_18_107_P17


title: SS2_18_107_P16


title: SS2_18_107_P10


title: SS2_18_107_P3


title: SS2_18_107_P23


title: SS2_18_107_P9


title: SS2_18_107_P14


title: SS2_18_107_P5


title: SS2_18_107_P12


title: SS2_18_107_P8


title: SS2_18_107_O24


title: SS2_18_107_O22


title: SS2_18_107_P6


title: SS2_18_107_O23


title: SS2_18_107_P13


title: SS2_18_107_O14


title: SS2_18_107_P19


title: SS2_18_107_O13


title: SS2_18_107_P24


title: SS2_18_107_O15


title: SS2_18_107_P15


title: SS2_18_107_O21


title: SS2_18_107_O12


title: SS2_18_107_O20


title: SS2_18_107_P2


title: SS2_18_107_O6


title: SS2_18_107_P11


title: SS2_18_107_N23


title: SS2_18_107_N22


title: SS2_18_107_O18


title: SS2_18_107_O19


title: SS2_18_107_O5


title: SS2_18_107_O17


title: SS2_18_107_N21


title: SS2_18_107_O16


title: SS2_18_107_O9


title: SS2_18_107_O1


title: SS2_18_107_O10


title: SS2_18_107_O2


title: SS2_18_107_O11


title: SS2_18_107_O7


title: SS2_18_107_N24


title: SS2_18_107_P1


title: SS2_18_107_N11


title: SS2_18_107_N4


title: SS2_18_107_N1


title: SS2_18_107_N17


title: SS2_18_107_N20


title: SS2_18_107_N18


title: SS2_18_107_N19


title: SS2_18_107_N8


title: SS2_18_107_M17


title: SS2_18_107_N2


title: SS2_18_107_N10


title: SS2_18_107_M16


title: SS2_18_107_N3


title: SS2_18_107_M11


title: SS2_18_107_N15


title: SS2_15_0085_F3


title: SS2_18_107_M12


title: SS2_18_107_N6


title: SS2_18_107_N12


title: SS2_18_107_M21


title: SS2_18_107_M9


title: SS2_18_107_N7


title: SS2_18_107_M23


title: SS2_18_107_M19


title: SS2_18_107_N5


title: SS2_18_107_L23


title: SS2_18_107_M10


title: SS2_18_107_M22


title: SS2_18_107_L18


title: SS2_18_107_M18


title: SS2_18_107_M7


title: SS2_18_107_M8


title: SS2_18_107_M13


title: SS2_18_107_M24


title: SS2_18_107_O4


title: SS2_18_107_O3


title: SS2_18_107_M14


title: SS2_18_107_M5


title: SS2_18_107_M20


title: SS2_18_107_M4


title: SS2_18_107_L11


title: SS2_18_107_M2


title: SS2_18_107_M6


title: SS2_18_107_L17


title: SS2_18_107_M15


title: SS2_18_107_L16


title: SS2_18_107_L14


title: SS2_18_107_L24


title: SS2_18_107_L19


title: SS2_18_107_L22


title: SS2_18_107_N16


title: SS2_18_107_L21


title: SS2_18_107_L10


title: SS2_18_107_M3


title: SS2_18_107_N13


title: SS2_18_107_L7


title: SS2_18_107_L20


title: SS2_18_107_L5


title: SS2_18_107_M1


title: SS2_18_107_P4


title: SS2_18_107_L13


title: SS2_18_107_K24


title: SS2_18_107_K22


title: SS2_18_107_L15


title: SS2_18_107_L8


title: SS2_18_107_K19


title: SS2_18_107_K17


title: SS2_18_107_L4


title: SS2_18_107_L9


title: SS2_18_107_L3


title: SS2_18_107_L12


title: SS2_18_107_L1


title: SS2_18_107_K20


title: SS2_18_107_O8


title: SS2_18_107_L2


title: SS2_18_107_K13


title: SS2_18_107_K11


title: SS2_18_107_K18


title: SS2_18_107_K21


title: SS2_18_107_K15


title: SS2_18_107_L6


title: SS2_18_107_K9


title: SS2_18_107_K14


title: SS2_18_107_K10


title: SS2_18_107_K12


title: SS2_18_107_K8


title: SS2_18_107_K5


title: SS2_18_107_K3


title: SS2_18_107_J23


title: SS2_18_107_K6


title: SS2_18_107_K7


title: SS2_18_107_J14


title: SS2_18_107_N14


title: SS2_18_107_J20


title: SS2_18_107_J24


title: SS2_18_107_K4


title: SS2_18_107_J19


title: SS2_18_107_J12


title: SS2_18_107_K2


title: SS2_18_107_J10


title: SS2_18_107_J21


title: SS2_18_107_J22


title: SS2_18_107_J11


title: SS2_18_107_K16


title: SS2_18_107_J15


title: SS2_18_107_K1


title: SS2_18_107_J18


title: SS2_18_107_N9


title: SS2_18_107_J17


title: SS2_18_107_J4


title: SS2_18_107_J13


title: SS2_18_107_J7


title: SS2_18_107_J5


title: SS2_18_107_J9


title: SS2_18_107_J16


title: SS2_18_107_J8


title: SS2_18_107_J1


title: SS2_18_107_I22


title: SS2_18_107_K23


title: SS2_18_107_I23


title: SS2_18_107_I12


title: SS2_18_107_J6


title: SS2_18_107_I24


title: SS2_18_107_J2


title: SS2_18_107_I18


title: SS2_18_107_I19


title: SS2_18_107_J3


title: SS2_18_107_I10


title: SS2_18_107_I13


title: SS2_18_107_I8


title: SS2_18_107_I17


title: SS2_18_107_I3


title: SS2_18_107_I16


title: SS2_18_107_I6


title: SS2_18_107_I2


title: SS2_18_107_I11


title: SS2_18_107_I9


title: SS2_18_107_I15


title: SS2_18_107_H24


title: SS2_18_107_I5


title: SS2_18_107_I7


title: SS2_18_107_I14


title: SS2_18_107_I4


title: SS2_18_107_I20


title: SS2_18_107_H12


title: SS2_18_107_H19


title: SS2_18_107_H21


title: SS2_18_107_H6


title: SS2_18_107_H14


title: SS2_18_107_H16


title: SS2_18_107_H22


title: SS2_18_107_G21


title: SS2_18_107_H17


title: SS2_18_107_H18


title: SS2_18_107_H20


title: SS2_18_107_H9


title: SS2_18_107_I1


title: SS2_18_107_H5


title: SS2_18_107_H15


title: SS2_18_107_H2


title: SS2_18_107_H3


title: SS2_18_107_H10


title: SS2_18_107_G22


title: SS2_18_107_H7


title: SS2_18_107_G20


title: SS2_18_107_G19


title: SS2_18_107_G10


title: SS2_18_107_H1


title: SS2_18_107_G11


title: SS2_18_107_G15


title: SS2_18_107_H8


title: SS2_18_107_G17


title: SS2_18_107_H13


title: SS2_18_107_G24


title: SS2_18_107_H23


title: SS2_18_107_G8


title: SS2_18_107_H4


title: SS2_18_107_I21


title: SS2_18_107_G16


title: SS2_18_107_G12


title: SS2_18_107_G2


title: SS2_18_107_G6


title: SS2_18_107_G23


title: SS2_18_107_G9


title: SS2_18_107_G13


title: SS2_18_107_F21


title: SS2_18_107_F24


title: SS2_18_107_G5


title: SS2_18_107_F16


title: SS2_18_107_F20


title: SS2_18_107_G7


title: SS2_18_107_F15


title: SS2_18_107_F11


title: SS2_18_107_G1


title: SS2_18_107_F13


title: SS2_18_107_H11


title: SS2_18_107_F22


title: SS2_18_107_F5


title: SS2_18_107_F14


title: SS2_18_107_F10


title: SS2_18_107_G14


title: SS2_18_107_F9


title: SS2_18_107_F6


title: SS2_18_107_F19


title: SS2_18_107_E24


title: SS2_18_107_F7


title: SS2_18_107_F17


title: SS2_18_107_F4


title: SS2_18_107_E23


title: SS2_18_107_F18


title: SS2_18_107_E15


title: SS2_18_107_E12


title: SS2_18_107_E16


title: SS2_18_107_E17


title: SS2_18_107_E10


title: SS2_18_107_F3


title: SS2_18_107_F8


title: SS2_18_107_F2


title: SS2_18_107_E22


title: SS2_18_107_E20


title: SS2_18_107_E19


title: SS2_18_107_E8


title: SS2_18_107_E6


title: SS2_18_107_F1


title: SS2_18_107_E5


title: SS2_18_107_E14


title: SS2_18_107_E11


title: SS2_18_107_E7


title: SS2_18_107_E3


title: SS2_18_107_E2


title: SS2_18_107_E9


title: SS2_18_107_D23


title: SS2_18_107_D24


title: SS2_18_107_D22


title: SS2_18_107_E18


title: SS2_18_107_E1


title: SS2_18_107_E4


title: SS2_18_107_D19


title: SS2_18_107_D20


title: SS2_18_107_D16


title: SS2_18_107_D17


title: SS2_18_107_D15


title: SS2_18_107_D18


title: SS2_18_107_F23


title: SS2_18_107_E13


title: SS2_18_107_D10


title: SS2_18_107_E21


title: SS2_18_107_D7


title: SS2_18_107_G4


title: SS2_18_107_D4


title: SS2_18_107_D8


title: SS2_18_107_D6


title: SS2_18_107_G3


title: SS2_18_107_D21


title: SS2_18_107_D13


title: SS2_18_107_D5


title: SS2_18_107_D1


title: SS2_18_107_D3


title: SS2_18_107_D2


title: SS2_18_107_C16


title: SS2_18_107_D9


title: SS2_18_107_C21


title: SS2_18_107_D14


title: SS2_18_107_C19


title: SS2_18_107_C23


title: SS2_18_107_C22


title: SS2_18_107_C20


title: SS2_18_107_C18


title: SS2_18_107_D11


title: SS2_18_107_C12


title: SS2_18_107_F12


title: SS2_18_107_C10


title: SS2_18_107_C11


title: SS2_18_107_C9


title: SS2_18_107_C14


title: SS2_18_107_D12


title: SS2_18_107_C5


title: SS2_18_107_C7


title: SS2_18_107_B21


title: SS2_18_107_C8


title: SS2_18_107_B18


title: SS2_18_107_C2


title: SS2_18_107_G18


title: SS2_18_107_B20


title: SS2_18_107_B19


title: SS2_18_107_B16


title: SS2_18_107_C13


title: SS2_18_107_B17


title: SS2_18_107_C6


title: SS2_18_107_B15


title: SS2_18_107_C15


title: SS2_18_107_C1


title: SS2_18_107_C4


title: SS2_18_107_B14


title: SS2_18_107_B23


title: SS2_18_107_B13


title: SS2_18_107_B10


title: SS2_18_107_B24


title: SS2_18_107_B11


title: SS2_18_107_B22


title: SS2_18_107_B9


title: SS2_18_107_B7


title: SS2_18_107_A24


title: SS2_18_107_B8


title: SS2_18_107_A23


title: SS2_18_107_A20


title: SS2_18_107_A13


title: SS2_18_107_A19


title: SS2_18_107_C24


title: SS2_18_107_A14


title: SS2_18_107_A11


title: SS2_18_107_B4


title: SS2_18_107_A21


title: SS2_18_107_A12


title: SS2_18_107_A18


title: SS2_18_107_A9


title: SS2_18_107_A8


title: SS2_18_107_B1


title: SS2_18_107_A17


title: SS2_18_107_B12


title: SS2_18_107_A2


title: SS2_18_107_C17


title: SS2_18_107_B5


title: SS2_18_107_A1


title: SS2_18_107_A15


title: SS2_18_107_B3


title: SS2_18_107_A22


title: SS2_18_107_A4


title: SS2_18_107_B2


title: SS2_18_107_A3


title: SS2_18_107_A5


title: SS2_18_102_P4

description:
tracing induced at E8.5 and cells collected at E9.5
E9.5_anterior_Sox10_counts.txt

value: anterior


title: SS2_18_107_A7


title: SS2_18_102_P6


title: SS2_18_102_P1


title: SS2_18_102_P9


title: SS2_18_107_A16


title: SS2_18_102_P3


title: SS2_18_102_P10


title: SS2_18_102_P5


title: SS2_18_102_P2


title: SS2_18_102_P7


title: SS2_18_102_O8


title: SS2_18_102_O7


title: SS2_18_102_O4


title: SS2_18_107_A10


title: SS2_18_102_O3


title: SS2_18_102_O10


title: SS2_18_102_O5


title: SS2_18_102_O6


title: SS2_18_102_O1


title: SS2_18_102_O9


title: SS2_18_102_N10


title: SS2_18_102_P8


title: SS2_18_102_N4


title: SS2_18_102_N6


title: SS2_18_102_N7


title: SS2_18_102_N5


title: SS2_18_102_N9


title: SS2_18_102_N8


title: SS2_18_102_M9


title: SS2_18_102_M7


title: SS2_18_102_N2


title: SS2_18_102_M6


title: SS2_18_102_M10


title: SS2_18_102_M8


title: SS2_18_102_M5


title: SS2_18_102_M1


title: SS2_18_102_L10


title: SS2_18_102_M3


title: SS2_18_102_M4


title: SS2_18_102_L9


title: SS2_18_107_A6


title: SS2_18_107_B6


title: SS2_18_102_L8


title: SS2_18_102_N1


title: SS2_18_102_L6


title: SS2_18_102_L3


title: SS2_18_102_N3


title: SS2_18_102_L2


title: SS2_18_102_L5


title: SS2_18_102_L4


title: SS2_18_102_K7


title: SS2_18_102_K9


title: SS2_18_102_K6


title: SS2_18_102_K5


title: SS2_18_102_K1


title: SS2_18_102_L7


title: SS2_18_102_K4


title: SS2_18_102_K3


title: SS2_18_102_K8


title: SS2_18_102_J10


title: SS2_18_102_K2


title: SS2_18_102_M2


title: SS2_18_102_J9


title: SS2_18_102_J7


title: SS2_18_102_J8


title: SS2_18_102_J4


title: SS2_18_102_J1


title: SS2_18_102_J2


title: SS2_18_102_K10


title: SS2_18_102_I10


title: SS2_18_102_J5


title: SS2_18_102_I8


title: SS2_18_102_I7


title: SS2_18_102_I6


title: SS2_18_102_I4


title: SS2_18_102_I5


title: SS2_18_102_I9


title: SS2_18_102_I2


title: SS2_18_102_I3


title: SS2_18_102_H9


title: SS2_18_102_I1


title: SS2_18_102_H8


title: SS2_18_102_J6


title: SS2_18_102_H10


title: SS2_18_102_J3


title: SS2_18_102_H4


title: SS2_18_102_H5


title: SS2_18_102_H2


title: SS2_18_102_H1


title: SS2_18_102_G9


title: SS2_18_102_H3


title: SS2_18_102_H6


title: SS2_18_102_G10


title: SS2_18_102_G6


title: SS2_18_102_G7


title: SS2_18_102_G8


title: SS2_18_102_G4


title: SS2_18_102_G2


title: SS2_18_102_G3


title: SS2_18_102_H7


title: SS2_18_102_F8


title: SS2_18_102_G1


title: SS2_18_102_F7


title: SS2_18_102_G5


title: SS2_18_102_F6


title: SS2_18_102_E8


title: SS2_18_102_E10


title: SS2_18_102_F5


title: SS2_18_102_E7


title: SS2_18_102_F2


title: SS2_18_102_F1


title: SS2_18_102_F3


title: SS2_18_102_F4


title: SS2_18_102_E6


title: SS2_18_102_E3


title: SS2_18_102_E2


title: SS2_18_102_E5


title: SS2_18_102_E1


title: SS2_18_102_F10


title: SS2_18_102_F9


title: SS2_18_102_D7


title: SS2_18_102_D4


title: SS2_18_102_D6


title: SS2_18_102_D3


title: SS2_18_102_D1


title: SS2_18_102_D5


title: SS2_18_102_D8


title: SS2_18_102_D9


title: SS2_18_102_D2


title: SS2_18_102_C9


title: SS2_18_102_C7


title: SS2_18_102_E9


title: SS2_18_102_C10


title: SS2_18_102_C4


title: SS2_18_102_E4


title: SS2_18_102_C5


title: SS2_18_102_D10


title: SS2_18_102_C1


title: SS2_18_102_C2


title: SS2_18_102_C6


title: SS2_18_102_B4


title: SS2_18_102_B9


title: SS2_18_102_B8


title: SS2_18_102_A10


title: SS2_18_102_C3


title: SS2_18_102_A7


title: SS2_18_102_A6


title: SS2_18_102_B10


title: SS2_18_102_A2


title: SS2_18_102_B1


title: SS2_18_102_B7


title: SS2_18_102_C8


title: SS2_18_102_B6


title: SS2_18_102_A4


title: SS2_18_102_A9


title: SS2_18_102_A3


title: SS2_18_102_A8


title: SS2_17_554_P20


title: SS2_17_554_P22


title: SS2_17_554_P19


title: SS2_18_102_B3


title: SS2_17_554_P24


title: SS2_18_102_L1


title: SS2_17_554_P21


title: SS2_18_102_B5


title: SS2_17_554_P17


title: SS2_18_102_A1


title: SS2_17_554_P23


title: SS2_17_554_P12


title: SS2_17_554_P15


title: SS2_17_554_P18


title: SS2_17_554_P13


title: SS2_17_554_P9


title: SS2_17_554_P7

description:
tracing induced at E8.5 and cells collected at E9.5
E9.5_posterior_Sox10_counts.txt

value: posterior


title: SS2_17_554_P14


title: SS2_17_554_P11


title: SS2_18_102_O2


title: SS2_18_102_A5


title: SS2_17_554_P5


title: SS2_17_554_P10


title: SS2_18_102_B2


title: SS2_17_554_P6


title: SS2_17_554_P4


title: SS2_17_554_P8


title: SS2_17_554_P3


title: SS2_17_554_P2


title: SS2_17_554_P1


title: SS2_17_554_O24


title: SS2_17_554_O22


title: SS2_17_554_O20


title: SS2_17_554_O21


title: SS2_17_554_O23


title: SS2_17_554_O19


title: SS2_17_554_O16


title: SS2_17_554_P16


title: SS2_17_554_O18


title: SS2_17_554_O17


title: SS2_17_554_O15


title: SS2_17_554_O14


title: SS2_17_554_O12


title: SS2_17_554_O9


title: SS2_17_554_O13


title: SS2_17_554_O7


title: SS2_17_554_O11


title: SS2_17_554_O10


title: SS2_17_554_O8


title: SS2_17_554_O5


title: SS2_17_554_O6


title: SS2_17_554_O3


title: SS2_17_554_N23


title: SS2_17_554_O4


title: SS2_17_554_N22


title: SS2_17_554_N24


title: SS2_17_554_N20


title: SS2_17_554_O1


title: SS2_17_554_N21


title: SS2_17_554_N13


title: SS2_17_554_N18


title: SS2_17_554_N15


title: SS2_17_554_O2


title: SS2_17_554_N10


title: SS2_17_554_N19


title: SS2_18_109_P13


title: SS2_18_109_P18


title: SS2_18_109_P14


title: SS2_18_109_P11


title: SS2_18_109_P10


title: SS2_18_109_P15


title: SS2_18_109_P9


title: SS2_18_109_P3


title: SS2_18_109_P5


title: SS2_18_109_P6


title: SS2_18_109_P2


title: SS2_18_109_P4


title: SS2_18_109_P7


title: SS2_18_109_O22


title: SS2_18_109_P1


title: SS2_18_109_O20


title: SS2_17_554_N14


title: SS2_18_109_O18


title: SS2_18_109_O19


title: SS2_18_109_O14


title: SS2_17_554_N17


title: SS2_18_109_P12


title: SS2_18_109_O16


title: SS2_18_109_O17


title: SS2_18_109_O12


title: SS2_18_109_O13


title: SS2_18_109_P8


title: SS2_18_109_O15


title: SS2_18_109_O11


title: SS2_18_109_O8


title: SS2_18_109_O9


title: SS2_18_109_O23


title: SS2_18_109_O7


title: SS2_18_109_O4


title: SS2_18_109_O3


title: SS2_18_109_O1


title: SS2_18_109_O5


title: SS2_18_109_N19


title: SS2_18_109_O2


title: SS2_18_109_N23


title: SS2_18_109_O24


title: SS2_18_109_N21


title: SS2_18_109_N20


title: SS2_18_109_O21


title: SS2_18_109_N24


title: SS2_18_109_N22


title: SS2_18_109_N17


title: SS2_18_109_N14


title: SS2_18_109_N16


title: SS2_18_109_N15


title: SS2_18_109_N10


title: SS2_18_109_O10


title: SS2_18_109_N18


title: SS2_18_109_N11


title: SS2_18_109_O6


title: SS2_18_109_N7


title: SS2_18_109_N13


title: SS2_18_109_N5


title: SS2_18_109_N9


title: SS2_18_109_N3


title: SS2_18_109_N6


title: SS2_18_109_N1


title: SS2_18_109_M23


title: SS2_18_109_M19


title: SS2_18_109_M18


title: SS2_18_109_M21


title: SS2_18_109_M17


title: SS2_18_109_M22


title: SS2_18_109_N2


title: SS2_18_109_N4


title: SS2_18_109_M20


title: SS2_18_109_M24


title: SS2_18_109_M10


title: SS2_18_109_N12


title: SS2_18_109_M12


title: SS2_18_109_M11


title: SS2_18_109_M16


title: SS2_18_109_M3


title: SS2_18_109_M7


title: SS2_18_109_M13


title: SS2_18_109_M14


title: SS2_18_109_M9


title: SS2_18_109_M15


title: SS2_18_109_M5


title: SS2_18_109_N8


title: SS2_18_109_M4


title: SS2_18_109_L21


title: SS2_18_109_L19


title: SS2_18_109_M8


title: SS2_18_109_M1


title: SS2_18_109_M6


title: SS2_18_109_L18


title: SS2_18_109_L20


title: SS2_18_109_L24


title: SS2_18_109_M2


title: SS2_18_109_L17


title: SS2_18_109_L14


title: SS2_18_109_L16


title: SS2_18_109_L10


title: SS2_18_109_L23


title: SS2_18_109_L13


title: SS2_18_109_L22


title: SS2_18_109_L15


title: SS2_18_109_L8


title: SS2_18_109_L7


title: SS2_18_109_L11


title: SS2_18_109_L12


title: SS2_18_109_L5


title: SS2_18_109_L6


title: SS2_18_109_L4


title: SS2_18_109_L1


title: SS2_18_109_L9


title: SS2_18_109_K17


title: SS2_18_109_K23


title: SS2_18_109_K22


title: SS2_18_109_K13


title: SS2_18_109_K15


title: SS2_18_109_L3


title: SS2_18_109_K20


title: SS2_18_109_K16


title: SS2_18_109_K21


title: SS2_18_109_K24


title: SS2_18_109_K10


title: SS2_18_109_K11


title: SS2_18_109_K18


title: SS2_18_109_K9


title: SS2_18_109_K7


title: SS2_18_109_K12


title: SS2_18_109_K8


title: SS2_18_109_K5


title: SS2_18_109_K4


title: SS2_18_109_K1


title: SS2_18_109_K14


title: SS2_18_109_K3


title: SS2_18_109_J23


title: SS2_18_109_J19


title: SS2_18_109_J24


title: SS2_18_109_K19


title: SS2_18_109_K2


title: SS2_18_109_J21


title: SS2_18_109_J17


title: SS2_18_109_L2


title: SS2_18_109_J22


title: SS2_18_109_J16


title: SS2_18_109_J15


title: SS2_18_109_J13


title: SS2_18_109_J11


title: SS2_18_109_J20


title: SS2_18_109_J9


title: SS2_18_109_J10


title: SS2_18_109_J5


title: SS2_18_109_J4


title: SS2_18_109_K6


title: SS2_18_109_I22


title: SS2_18_109_J2


title: SS2_18_109_I23


title: SS2_18_109_I20


title: SS2_18_109_J6


title: SS2_18_109_J14


title: SS2_18_109_I21


title: SS2_18_109_I18


title: SS2_18_109_J3


title: SS2_18_109_I24


title: SS2_18_109_J1


title: SS2_18_109_J7


title: SS2_18_109_I17


title: SS2_18_109_J8


title: SS2_18_109_I16


title: SS2_18_109_I13


title: SS2_18_109_J12


title: SS2_18_109_I10


title: SS2_18_109_J18


title: SS2_18_109_I14


title: SS2_18_109_I4


title: SS2_18_109_I7


title: SS2_18_109_I15


title: SS2_18_109_I19


title: SS2_18_109_I12


title: SS2_18_109_I9


title: SS2_18_109_I11


title: SS2_18_109_I8


title: SS2_18_109_I3


title: SS2_18_109_I6


title: SS2_18_109_I5


title: SS2_18_109_I2


title: SS2_18_109_H22


title: SS2_18_109_H24


title: SS2_18_109_H17


title: SS2_18_109_H21


title: SS2_18_109_H18


title: SS2_18_109_H15


title: SS2_18_109_H20


title: SS2_18_109_H19


title: SS2_18_109_H11


title: SS2_18_109_H14


title: SS2_18_109_I1


title: SS2_18_109_H16


title: SS2_18_109_H10


title: SS2_18_109_H13


title: SS2_18_109_H6


title: SS2_18_109_H3


title: SS2_18_109_H1


title: SS2_18_109_H9


title: SS2_18_109_H2


title: SS2_18_109_G24


title: SS2_18_109_H12


title: SS2_18_109_G19


title: SS2_18_109_H8


title: SS2_18_109_G20


title: SS2_18_109_H23


title: SS2_18_109_G17


title: SS2_18_109_G22


title: SS2_18_109_G18


title: SS2_18_109_G21


title: SS2_18_109_G13


title: SS2_18_109_G14


title: SS2_18_109_G12


title: SS2_18_109_G15


title: SS2_18_109_G16


title: SS2_18_109_G11


title: SS2_18_109_H7


title: SS2_18_109_H5


title: SS2_18_109_H4


title: SS2_18_109_G10


title: SS2_18_109_G1


title: SS2_18_109_G4


title: SS2_18_109_G8


title: SS2_18_109_F21


title: SS2_18_109_G23


title: SS2_18_109_G2


title: SS2_18_109_G3


title: SS2_18_109_F23


title: SS2_18_109_F12


title: SS2_18_109_F16


title: SS2_18_109_G7


title: SS2_18_107_C3


title: SS2_18_109_G6


title: SS2_18_109_F20


title: SS2_18_109_F19


title: SS2_18_109_G9


title: SS2_18_109_F24


title: SS2_18_109_F17


title: SS2_18_109_F15


title: SS2_18_109_G5


title: SS2_18_109_F14


title: SS2_18_109_F7


title: SS2_18_109_F8


title: SS2_18_109_F5


title: SS2_18_109_F9


title: SS2_18_109_F11


title: SS2_18_109_F13


title: SS2_18_109_F4


title: SS2_18_109_E24


title: SS2_18_109_F2


title: SS2_18_109_E22


title: SS2_18_109_F1


title: SS2_18_109_E19


title: SS2_18_109_E18


title: SS2_18_109_E20


title: SS2_18_109_E16


title: SS2_18_109_F18


title: SS2_18_109_E14


title: SS2_18_109_E7


title: SS2_18_109_F10


title: SS2_18_109_E23


title: SS2_18_109_E21


title: SS2_18_109_F22


title: SS2_18_109_E15


title: SS2_18_109_E11


title: SS2_18_109_F6


title: SS2_18_109_F3


title: SS2_18_109_E8


title: SS2_18_109_E9


title: SS2_18_109_E10


title: SS2_18_109_E17


title: SS2_18_109_E3


title: SS2_18_109_D21


title: SS2_18_109_E4


title: SS2_18_109_E6


title: SS2_18_109_E12


title: SS2_18_109_E5


title: SS2_18_109_D24


title: SS2_18_109_E2


title: SS2_18_109_D22


title: SS2_18_109_D20


title: SS2_18_109_E1


title: SS2_18_109_D23


title: SS2_18_109_D19


title: SS2_18_109_D17


title: SS2_18_109_D13


title: SS2_18_109_D12


title: SS2_18_109_D18


title: SS2_18_109_D10


title: SS2_18_109_D15


title: SS2_18_109_D16


title: SS2_18_109_E13


title: SS2_18_109_D9


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title: SS2_18_110_H2


title: SS2_18_110_E17


title: SS2_18_110_E24


title: SS2_18_110_E13


title: SS2_18_110_E20


title: SS2_18_110_E22


title: SS2_18_110_E16


title: SS2_18_110_E18


title: SS2_18_110_D24


title: SS2_18_110_E14


title: SS2_18_110_D21


title: SS2_18_110_D19


title: SS2_18_110_D23


title: SS2_18_110_D18


title: SS2_18_110_D22


title: SS2_18_110_F20


title: SS2_18_110_D17


title: SS2_18_110_D20


title: SS2_18_110_D16


title: SS2_18_110_C19


title: SS2_18_110_C21


title: SS2_18_110_C18


title: SS2_18_110_C14


title: SS2_18_110_E15


title: SS2_18_110_C24


title: SS2_18_110_C23


title: SS2_18_110_D14


title: SS2_18_110_F18


title: SS2_18_110_C20


title: SS2_18_110_D15


title: SS2_18_110_D13


title: SS2_18_110_C16


title: SS2_18_110_C17


title: SS2_18_110_B24


title: SS2_18_110_C15


title: SS2_18_110_B19


title: SS2_18_110_B16


title: SS2_18_110_B15


title: SS2_18_110_B18


title: SS2_18_110_B20


title: SS2_18_110_B22


title: SS2_18_110_B13


title: SS2_18_110_B17


title: SS2_18_110_A15


title: SS2_18_110_B21


title: SS2_18_110_A20


title: SS2_18_110_A23


title: SS2_18_110_A16


title: SS2_18_110_A18


title: SS2_18_110_A17


title: SS2_18_110_A21


title: SS2_18_110_A14


title: SS2_18_110_A22


title: SS2_18_110_C22


title: SS2_18_110_A19


title: SS2_18_110_A24


title: SS2_18_110_B23


title: SS2_18_109_P21


title: SS2_18_110_B14


title: SS2_18_109_P24


title: SS2_18_110_C13


title: SS2_18_109_P20


title: SS2_18_109_P22


title: SS2_18_109_P17


title: SS2_18_109_P23


title: SS2_18_109_P16


title: SS2_18_109_P19


title: P3 Input Serum

status: Public on Mar 06 2019

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: processed data file not provided, bam file was used to determine barcode representation

library_source: genomic

data_processing:
Demultiplexing and deduplication: Sequencing was performed using 50:8:34 cycles (Read1:Index1:Read2) Illumina bcl2fastq was used to demultiplex paired-end sequencing reads by 8nt index1 read (PCR barcode). NextSeq lanes were merged into single fastq files, creating the primary fastq files. Read1 starts with 6nt UMI and 8nt barcode in the format NNNNNNABCDEFGH. A sample sheet was used with four columns corresponding to sample name, replicate name, barcode sequence, primary fastq name. For each line in the sample sheet, reads matching the barcode sequence were extracted from the primary fastq file, allowing up to two mismatches. Duplicate reads identified by identical first 24nt of read1 were discarded. Read pairs matching parts of the adaptor sequence (SBS3 or T7 promoter) in either read1 or read2 were removed. Demultiplexed and deduplicated reads were written into sample-specific fastq file used for subsequent mapping.
Mapping: Sample-specific paired fastq files were mapped using botwie2 (v2.3.4.3) using --fast parameter to the mouse genome (mm9). Alignments were processed into sorted BAM files with samtools (v1.9). Blacklisted regions were removed from BAM file using BEDTools (v2.27.1). Reads were also mapped to a metagenome of RepBase murine repetitive sequences using botwie2.
Scaling: Input coverage tracks with 1bp resolution in BigWig format were generated from BAM files using deepTools (v3.1.0) bamCoverage and scaled to a reads-per-genome-coverage of one (1xRPGC, also referred to as ‘1x normalization’) using mm9 genome size 2654895218. ChIP coverage tracks were generated from BAM files using deepTools (v3.1.0) bamCoverage. Quantitative scaling amongst samples within each pool was based on their total mapped read counts, as well as the total mapped read counts of the respective input data. One condition in the pool served as a reference (Serum condition, no treatment), which was scaled to 1xRPGC. All other samples were scaled relative to the reference using an explicit scaling factor. The RPGC was calculate by the following formula: ( #mapped[ChIP] / #mapped[Input] ) / ( #mapped[ChIP_Reference] / #mapped[Input_Reference] ).
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files are scaled according to MINUTE quantification with respect to the reference of each pool (Serum condition, 1xRPGC)

molecule: genomic DNA

source_name: Embryonic Stem Cell

growth_protocol: Murine embryonic stem cells (mESCs) were cultured feeder-free in 0.1% gelatin-coated dishes.  "Serum" condition: Knockout DMEM (Life Technologies), 2 mM Glutamax (Gibco), 0.1 mM non-essential amino acids (Gibco), 15% ESC-grade fetal bovine serum (FBS) (Gibco), 0.1 mM β-mercaptoethanol, and leukemia inhibitory factor (LIF) (Millipore), "Serum2i" condition: above medium supplemented with 2i; 1 μM MEK inhibitor PD0325901 (Sigma) and 3 μM GSK3 inhibitor CHIR99021 (Sigma). "2i" condition: serum free ESGRO Complete Basal medium (Millipore) with 0.1mM LIF and 2i as described above. For all conditions cells were passaged in 48 h intervals, using accutase (Sigma) for detachment. Cell line was tested for mycoplasma contamination.

extract_protocol:
Cell lysis immediately followed by MNase digestion of native chromatin, T7-adapter ligation, pool-and-split multiplexing, immunoprecipitation and magnetic bead isolation of immunoprecipitated DNA.
Illumnina library preparation by in vitro transcription, reverse transcription and library PCR (see manuscript).

treatment_protocol: Medium was supplemented with 10 μM GSK-J4 (Sigma) for 96 h, 50 μM Zebularin for 96 h or 10 μM EPZ-6438 (BioVision) for 7 days.

tag: background

tag: condition

value: Serum

tag: antibody

value: Input

tag: minute-pool

tag: supplementary file scaling

value: 1x genome coverage


title: SS2_18_110_A13


title: P3 Input 2i EPZ-6438


title: P3 H3K27me3-ChIP (07-449) Serum EPZ-6438

description: contains data from three replicates with different barcodes provided as raw files

value: Millipore 07-449

value: relative to P3 H3K27me3-ChIP Serum


title: P3 Input 2i GSK-J4


title: P3 H3K27me3-ChIP (CS9733) Serum

value: Cell signaling 9733


title: P3 Input 2i


title: P3 H3K27me3-ChIP (07-449) Serum GSK-J4


title: P3 H3K27me3-ChIP (07-449) Serum


title: Sample_61506_LLF23

status: Public on Feb 18 2019

city: Ann Arbor

first: Natalie

middle: Celia

last: Tronson

state: MI

address: 530 Church st

department: Psychology

institute: University of Michigan

description: Sample 61506

data_processing:
RNA-Seq was performed using Illumina 4000 High-seq platform
Base-calling software: Illumina Casava 1.8 software
Alignment was conducted using TopHat (version 2.0.13) and Bowtie (version 2.2.1), with default parameter settings, with exception of: "---b2-very-sensitive" for additional search of valid alignments
Cufflinks/Cuffdiff (version 2.2.1) was used for expression quantification, normalization, and differential expression analysis, with UCSC mm10.fa as the reference genome
Normalization of expression values included "--compatible-hits-norm" and "--upper-quartile-norm", adjustments of expression calculations for reads that map unto more than one locus with the "--multi-read-correct" parameter
Genome_build: mm10.fa
Supplementary_files_format_and_content: Raw counts from Tophat

growth_protocol: Single housed

extract_protocol:
Whole hippocampus was harvested, flash frozen in liquid nitrogen, and RNA was extracted using Life Technologies PureLink RNA Mini kit (cat. no. 12183018A) with 20 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols, single end, poly-A selection

treatment_protocol: Subchronic immune challenge = 5 intraperitoneal injections of LPS (250 µg/kg), each spaced 3 days apart, acute immune challenge = 1 intraperitoneal injection LPS (250 µg/kg)

tag: strain

value: 8-9 weeks old

tag: Sex

value: Female

tag: tissue

value: Whole hippocampus

tag: treatment


title: P3 H3K27me1-ChIP Serum GSK-J4

value: Cell signaling 5326S

value: relative to P3 H3K27me1-ChIP Serum


title: P3 H3K27me1-ChIP Serum EPZ-6438


title: Sample_61504_LLF19

description: Sample 61504


title: Sample_61500_VLF22

description: Sample 61500


title: Sample_61503_LVF31

description: Sample 61503


title: Sample_61505_LLF21

description: Sample 61505


title: Sample_61502_LVF29

description: Sample 61502


title: Sample_61498_VLF22

description: Sample 61498


title: Sample_61501_LVF27

description: Sample 61501


title: Sample_61499_VLF20

description: Sample 61499


title: Sample_61497_VVF30

description: Sample 61497


title: Sample_61495_VVF26

description: Sample 61495


title: Sample_61494_LLM13

description: Sample 61494

value: Male


title: Sample_61496_VVF28

description: Sample 61496


title: Sample_61490_LVM11

description: Sample 61490


title: Sample_61489_LVM1

description: Sample 61489


title: P3 H3K27me3-ChIP (CS9733) Serum GSK-J4


title: Sample_61491_LVM15

description: Sample 61491


title: Sample_61493_LLM9

description: Sample 61493


title: P3 H3K27me3-ChIP (CS9733) Serum EPZ-6438


title: Sample_61486_VLM4

description: Sample 61486


title: Sample_61484_VVM12

description: Sample 61484


title: Sample_61485_VVM16

description: Sample 61485


title: P3 H3K27me1-ChIP Serum


title: Sample_61487_VLM6

description: Sample 61487


title: Sample_61488_VLM14

description: Sample 61488


title: Sample_61483_VVM2

description: Sample 61483


title: WT rep2

status: Public on Feb 12 2019

city: Shanghai

first: Yunli

last: Xie

state: Shanghai

address: 131 Dong'an Road, Shanghai

department: Institutes of Brain Science

country: China

institute: Fudan University

data_processing:
Base calling was performed using bcl2fastq v1.8.4
Adapter trimming and quality filtering were performed using trim_gaplore v0.4.4
Alignment to the reference genome was performed using STAR v2.5.4b
Read counting was performed using featureCounts v1.6.1
Differential expression analysis was performed using R v3.4.1 and the R package DESeq2 v1.22.1
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited spreadsheet, FPKM values

molecule: total RNA

source_name: cortex

extract_protocol:
Cortex were removed on ice, and RNA was harvested using Trizol reagent.
TruSeq RNA Library Prep Kit

value: cortex

value: embryonic day 12.5


title: Hdac1&2 cKO rep1


title: WT rep1


title: Hdac1&2 cKO rep2


title: WT rep3


title: Sample_61492_LLM5

description: Sample 61492


title: CDK11-1 KD 1

status: Public on Dec 07 2018

city: Bethesda

first: Jianyi

last: Ding

state: MD

address: 9000 Rockville Pike

department: CMTB

institute: NHLBI, NIH

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequences are aligned to transcriptome with BWA
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using RSEM
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Homo sapiens

source_name: human embryonic stem cells

growth_protocol: SHhES8 cells were cultured in mTESR1

extract_protocol:
Total RNA were extracted using Trizol reagent (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocol

treatment_protocol: NC and CDK11 siRNA transfected SHhES8 cells were cultured in conditioned medium for 4 days

tag: cell line

tag: transfection

value: CDK11 siRNA


title: NC KD 1

value: NC siRNA


title: Hdac1&2 cKO rep3


title: CDK11-2 KD 2


title: CDK11-1 KD 2


title: NC KD 2


title: CDK11-2 KD 1


title: 5158476

status: Public on Nov 07 2018

type: RNA

city: Little Rock

first: Brian

last: Walker

state: AR

address: 4301 W Markham St.

institute: University of Arkansas for Medical Sciences

description:
CD138+
Gene expresion data from newly diagnosed Smouldering patient

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on human GeneChip. U133 plus 2.0 chips are washed and stained further in affymetrix fluidics station

scan_protocol: Chips were scanned using the HG-U133 Plus 2.0 v2.2 on a Affymetrix Genechip scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: CD138+ selected bone marrow plasma cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from200ng  total RNA

extract_protocol: RNA extraction and isolation was performed with the AllPrep kit by Qiagen

tag: patient id

tag: swog id

tag: patient group

value: AMM

tag: patient disease timepoint

value: Baseline

tag: sample type

value: RNAS-Random Aspirate

tag: molecular subgroup

value: LB

tag: gep70 score


title: 5158411


title: 5155671

description:
CD138+
Gene expresion data 12 Mo Follow-Up from Smouldering patient

value: 12 Mo Follow-Up

value: MF


title: 5159747


title: 5158494


title: 5161613


title: 5418300


title: 5152665


title: 5152670

value: HY


title: 4989909

value: MS


title: 4963603

description:
CD138+
Gene expresion data 12 Mo Follow-Up from MGUS patient

value: MGUS


title: 4839736


title: 4945131


title: 4928348


title: 4982710


title: 5336713

description:
CD138+
Gene expresion data from newly diagnosed MGUS patient

value: PR


title: 4805124


title: 5150040


title: 4956204


title: 4828627


title: 4815861


title: 4810881


title: 4791464


title: 4764931


title: 5020505


title: 4913028


title: 4784464


title: 4798763


title: 4750869


title: 4733648


title: 4710710


title: 4707271


title: 4693023


title: 4694043


title: 4720468


title: 4781710


title: 4726513


title: 4744430


title: 4714695


title: 4751203


title: 4707368


title: 4703661


title: 4657604


title: 4656694


title: 4714213


title: 4710775


title: 4676864


title: 4657570


title: 4666417


title: 4605973


title: 4674241


title: 4639241


title: 4639243


title: 4611361


title: 4729874


title: 4661717


title: 4706768


title: 4624305


title: 4597931


title: 4580715


title: 4557460

description:
CD138+
Gene expresion data from newly diagnosed Waldenstrom's patient

value: WM


title: 4567958


title: 4402274


title: 4580719


title: 4451788


title: 4554658


title: 4593874


title: 4551004


title: 4534784


title: 4582247


title: 4562173


title: 4386019


title: 4535364


title: 4540916


title: 4395418


title: 4557458


title: 4394131


title: 4574332


title: 4451765


title: 4383430


title: 4377370


title: 4540979


title: 4368371


title: 4402838


title: 4554627


title: 4577454


title: 4375958


title: 4373687


title: 4367187


title: 4364165


title: 4316975


title: 4350120


title: 4313114


title: 4363237


title: 4303608


title: 4340242


title: 4276521


title: 4313076

description:
CD138+
Gene expresion data from newly diagnosed Multiple Myeloma patient

value: MM


title: 4340252


title: 4269238


title: 4291001


title: 4309320


title: 4340243


title: 4362000


title: 4309350


title: 4342850


title: 4280194


title: 4272425


title: 4280150


title: 4239466


title: 4305572


title: 4250845


title: 4269229


title: 4254256


title: 4346776


title: 4254249


title: 4293926


title: 4313087


title: 4236057


title: 4262270


title: 4232137


title: 4229244


title: 4212139


title: 4196853


title: 4185254


title: 4230554


title: 4221163


title: 4212148


title: 4199595


title: 4217032


title: 4181111


title: 4194709


title: 4212115


title: 4162651


title: 4162648


title: 4162647


title: 4226079


title: 4199590


title: 4162661


title: 4162621


title: 4088855


title: 4078140


title: 4156687


title: 4151567


title: 4151564


title: 4088852


title: 4066703


title: 4088890


title: 4207874


title: 4156681


title: 4015527


title: 3985845


title: 3985842


title: 4036831


title: 4066708


title: 3985080


title: 3985081


title: 4015513


title: 3985086


title: 4006014


title: 3984800


title: 3957834


title: 3926208


title: 3925953


title: 3925659


title: 3886336


title: 3922866


title: 3814203


title: 3848441


title: 3925995


title: 3466162


title: 3509938


title: 3886362


title: 3418695


title: 3767288


title: 3517054


title: 3369119


title: 3714567


title: 4141035


title: 3451884


title: 3224473


title: 3391861


title: 3223720


title: 3012740


title: 2770226


title: 3056193


title: 3313812


title: 3942943


title: 3062984


title: 2579564


title: 2799526


title: 2728326


title: 2092143


title: 2753612


title: 2009062


title: 1842336


title: 2489343


title: 2651928


title: 2063364


title: 1842700


title: 2651965


title: 1842301


title: homeostatic Hydra, neuron enriched -rep 2 (D12-N2)

status: Public on Nov 02 2018

city: Davis

first: Celina

middle: E

last: Juliano

state: California

address: 149 Briggs Hall

department: MCB

institute: University of California Davis

description:
D12-N2_S2
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt

data_processing:
library strategy: Drop-seq
Data was processed using Drop-seq tools v1.01, according to Drop-seq protocol v3.1 (http://www.dropseq.org/). Read 2 was aligned with Bowtie2 v 2.2.6 to 1) the Hydra vulgaris 105 2.0 genome using 2.0 genome gene models and 2) a Hydra vulgaris AEP transcriptome reference (aepLRv2)(references available at https://research.nhgri.nih.gov/hydra/). Each aligned read was tagged with its mate-pair UMI and cell barcode (which comprise Read 1). Each aligned exonic read was tagged with a gene name. Cell barcodes were corrected for synthesis errors. A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes. The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample. Genome UMI counts are provided in supplementary file Hydra_DS_genome_UMICounts.txt. Transcriptome UMI counts are provided in supplementary file Hydra_DS_transcriptome_UMICounts.txt.
genome build: Hydra vulgaris 2.0 genome, Hydra vulgaris AEP transcriptome (aepLRv2)(https://research.nhgri.nih.gov/hydra/)
Supplementary_files_format_and_content: tab-delimited text files of UMI counts for genome mapping (Hydra_DS_genome_UMICounts.txt) and transcriptome mapping (Hydra_DS_transcriptome_UMICounts.txt)
Supplementary_files_format_and_content: tab-delimited text file of isoform level expression estimates

organism: Hydra vulgaris

source_name: cell suspension from homeostatic Hydra vulgaris AEP, enriched for neuronal cells FACS

growth_protocol: Hydra vulgaris AEP were cultured according to standard protocol (Lenhoff, 1983)  at 18˚C.

extract_protocol:
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org).
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 15 cycles of PCR amplification and 200 STAMPs per PCR reaction.

treatment_protocol: Prior to Drop-seq cells were dissociated for 90min using Pronase E (VWR, E629-1G) as described previously (Greber et al.,1992) at a concentration of ~75u/mL. 40-50 Hydra were washed twice in sterile filtered Hydra medium and transferred into a 1.5mL eppendorf tube. The medium was removed and 1mL Pronase solution was added. Cells were dissociated for 90min at room temperature (22-24C) with agitation on a nutator. Cells were washed twice and resuspended in resuspended in Hydra dissociation medium. Neuronal cells were enriched using FACS.

value: Hydra vulgaris AEP (transgenic line nGreen, Robert E. Steele)

value: whole animal


title: homeostatic Hydra, neuron enriched -rep 1 (D12-N1)

description:
D12-N1_S1
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt

source_name: cell suspension from homeostatic Hydra vulgaris AEP, enriched for neuronal cells using FACS

extract_protocol:
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org).
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 16 cycles of PCR amplification and 200 STAMPs per PCR reaction.


title: 1869228


title: 2822679


title: 1783332


title: homeostatic Hydra -rep 9 (D11-PO)

description:
D11-PO_S1
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt

source_name: cell suspension from homeostatic Hydra vulgaris AEP

extract_protocol:
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org).
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 16 cycles of PCR amplification and 130 STAMPs per PCR reaction.

treatment_protocol: Prior to Drop-seq cells were dissociated for 90min using Pronase E (VWR, E629-1G) as described previously (Greber et al.,1992) at a concentration of ~75u/mL. 40-50 Hydra were washed twice in sterile filtered Hydra medium and transferred into a 1.5mL eppendorf tube. The medium was removed and 1mL Pronase solution was added. Cells were dissociated for 90min at room temperature (22-24C) with agitation on a nutator. Cells were washed twice and resuspended in resuspended in Hydra dissociation medium {Greber:1992iw} containing 0.01% BSA.

value: Hydra vulgaris AEP


title: homeostatic Hydra -rep 7 (D06-KI)

description:
D06-KI_S4
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt

extract_protocol:
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org).
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 12 cycles of PCR amplification and 133 STAMPs per PCR reaction.


title: 1737305


title: 1840815


title: homeostatic Hydra, male (D06-MA)

description:
D06-MA_S3
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt

extract_protocol:
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org).
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 12 cycles of PCR amplification and 145 STAMPs per PCR reaction.


title: 1704901


title: homeostatic Hydra, budding -rep 8 (D11-BU)

description:
D11-BU_S2
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt

extract_protocol:
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org).
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 14 cycles of PCR amplification and 130 STAMPs per PCR reaction.


title: 1837730


title: 1842276


title: homeostatic Hydra, female (D06-FM)

description:
D06-FM_S1
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt

treatment_protocol: Prior to Drop-seq cells were dissociated for 90min using Pronase E (VWR, E629-1G) as described previously (Greber et al.,1992) at a concentration of ~75u/mL. 40-50 Hydra were washed twice in sterile filtered Hydra medium and transferred into a 1.5mL eppendorf tube. The medium was removed and 1mL Pronase solution was added. Cells were dissociated for 90min at room temperature (22-24C) with agitation on a nutator. Cells were washed twice and resuspended in resuspended in Hydra-PBS(iso) (10 mM PO43−, 2mM NaCL, 2.7mM KCl, 0.05% BSA, pH7.6, iso-osmolar to Hydra dissociation medium).


title: 1719941


title: homeostatic Hydra, male spike-in (D03-MA)

description:
D03-MA_S2
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt

extract_protocol:
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org).
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 14 cycles of PCR amplification and 148 STAMPs per PCR reaction.

treatment_protocol: Prior to Drop-seq cells were dissociated for 90min using Pronase E (VWR, E629-1G) as described previously (Greber et al.,1992) at a concentration of ~75u/mL. 40-50 Hydra were washed twice in sterile filtered Hydra medium and transferred into a 1.5mL eppendorf tube. The medium was removed and 1mL Pronase solution was added. Cells were dissociated for 90min at room temperature (22-24C) with agitation on a nutator. Cells were washed twice and resuspended in resuspended in a salt-adjusted Hydra-PBS (10 mM PO43−, 2mM NaCL, 0.1mM KCl, 0.05% BSA, pH7.6).


title: 3985096


title: 1735475