title: M120_HetCtrl_P1_H2_S306_quant


title: M120_HetCtrl_P1_G5_S28_quant

status: Public on Nov 12 2020

type: SRA

city: New York City

first: Katherine

last: Stewart

state: NY

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

country: USA

institute: The Rockefeller University

description:
stage-matched control mouse replicate #2
Infarinato_etal_2020_ALL_DATA_counts.csv
Infarinato_etal_2020_ALL_DATA_TPM.csv

library_source: transcriptomic

data_processing:
Sequence reads were obtained. Adaptors were trimmed from reads using Skewer (version 0.2.2), and the resulting reads were mapped to the mouse genome (GENCODE release M23 (GRCm38.p6)) using STAR (version 2.5.2a). ERCC spike-ins were added to the mouse genome as artificial chromosomes.
Expression values of each gene were quantified as transcript per million (TPM), as well as by raw counts, using Salmon (version 0.14.1) and Tximport (version 1.12.3).
Genome_build: GENCODE release M23 (GRCm38.p6)
Supplementary_files_format_and_content: comma separated value text files contain either TPMs or raw counts for all samples

molecule: total RNA

organism: Mus musculus

source_name: Mouse back skin

extract_protocol:
Single melanocyte lineage cells were FACS purified, and collected into 96-well plates containing lysis buffer and snap frozen in liquid nitrogen. Plates were stored at -80oC
Single cells were lyzed by incubating at 72oC for 3 min. Reverse transcription reaction and whole transcriptome amplification were performed according to Smart-seq2 protocol. The amplified cDNA libraries were purified by Ampure XP beads (Beckman Coulter), and the tagmentation reaction was performed by Illumina Nextera XT DNA Library Prep Kit. The libraries were pooled and sequenced on an Illumina NextSeq 500 with mid-output 38/37 cycles paired-end mode.

tag: cell stage

value: commited melanocyte progenitor

tag: Sex

value: male

tag: age

tag: hair cycle stage

value: wax-induced anagen (1 week post wax)

tag: strain

value: Bmpr1a fl/+, TyrCreER+, R26YFP fl/+ (C57Bl6 mix)

tag: sorting strategy

value: YFP+ dump (CD31, CD45, CD140a)-, Sca-1- and CD34-


title: M120_HetCtrl_P1_G7_S299_quant


title: M120_HetCtrl_P1_G9_S301_quant


title: M120_HetCtrl_P1_G2_S294_quant


title: M120_HetCtrl_P1_G10_S302_quant


title: M120_HetCtrl_P1_G12_S304_quant


title: M120_HetCtrl_P1_G11_S303_quant


title: M120_HetCtrl_P1_F9_S289_quant


title: M120_HetCtrl_P1_F8_S288_quant


title: M120_HetCtrl_P2_A4_S68_quant


title: M120_HetCtrl_P1_G3_S295_quant


title: M120_HetCtrl_P1_F7_S287_quant


title: M120_HetCtrl_P1_F3_S284_quant


title: M120_HetCtrl_P1_F2_S283_quant


title: M120_HetCtrl_P1_H11_S313_quant


title: M120_HetCtrl_P1_H5_S309_quant


title: M120_HetCtrl_P1_F12_S292_quant


title: M120_HetCtrl_P1_G4_S26_quant


title: M120_HetCtrl_P1_F5_S286_quant


title: M120_HetCtrl_P1_F10_S290_quant


title: M120_HetCtrl_P1_E9_S278_quant


title: M120_HetCtrl_P1_F11_S291_quant


title: M120_HetCtrl_P1_E7_S276_quant


title: M120_HetCtrl_P1_G1_S293_quant


title: M120_HetCtrl_P1_F1_S282_quant


title: M120_HetCtrl_P1_E6_S275_quant


title: M120_HetCtrl_P1_E4_S273_quant


title: M120_HetCtrl_P1_G8_S300_quant


title: M120_HetCtrl_P1_E12_S281_quant


title: M120_HetCtrl_P1_E11_S280_quant


title: M120_HetCtrl_P1_D8_S269_quant


title: M120_HetCtrl_P1_E2_S272_quant


title: M120_HetCtrl_P1_D7_S268_quant


title: M120_HetCtrl_P1_D6_S267_quant


title: M120_HetCtrl_P1_F4_S285_quant


title: M120_HetCtrl_P1_D5_S266_quant


title: M120_HetCtrl_P1_E10_S279_quant


title: M120_HetCtrl_P1_D12_S271_quant


title: M120_HetCtrl_P1_D4_S265_quant


title: M120_HetCtrl_P1_D3_S264_quant


title: M120_HetCtrl_P1_C7_S258_quant


title: M120_HetCtrl_P1_D10_S270_quant


title: M120_HetCtrl_P1_C5_S257_quant


title: M120_HetCtrl_P1_D1_S263_quant


title: M120_HetCtrl_P1_C9_S14_quant


title: M120_HetCtrl_P1_E8_S277_quant


title: M120_HetCtrl_P1_C10_S18_quant


title: M120_HetCtrl_P1_C1_S253_quant


title: M120_HetCtrl_P1_C2_S254_quant


title: M120_HetCtrl_P1_E5_S274_quant


title: M120_HetCtrl_P1_C12_S262_quant


title: M120_HetCtrl_P1_C11_S24_quant


title: M120_HetCtrl_P1_B7_S247_quant


title: M120_HetCtrl_P1_B5_S10_quant


title: M120_HetCtrl_P1_B4_S4_quant


title: M120_HetCtrl_P1_B12_S252_quant


title: M120_HetCtrl_P1_B11_S251_quant


title: M120_HetCtrl_P1_B3_S243_quant


title: M120_HetCtrl_P1_B9_S249_quant


title: M120_HetCtrl_P1_B8_S248_quant


title: M120_HetCtrl_P1_B10_S250_quant


title: M120_HetCtrl_P1_B6_S12_quant


title: M120_HetCtrl_P1_A8_S236_quant


title: M120_HetCtrl_P1_B2_S242_quant


title: M120_HetCtrl_P1_B1_S241_quant


title: M4_Bmpr1a_Het_Plate1_C11_S199_quant

description:
stage-matched control mouse replicate #3
Infarinato_etal_2020_ALL_DATA_counts.csv
Infarinato_etal_2020_ALL_DATA_TPM.csv


title: M120_HetCtrl_P1_A7_S235_quant


title: M120_HetCtrl_P1_C4_S256_quant


title: M120_HetCtrl_P1_A5_S233_quant


title: M120_HetCtrl_P1_A6_S234_quant


title: M120_HetCtrl_P1_C3_S255_quant


title: M120_HetCtrl_P1_A4_S232_quant


title: M120_HetCtrl_P1_A3_S231_quant


title: M120_HetCtrl_P1_A2_S230_quant


title: M120_HetCtrl_P1_A11_S239_quant


title: M120_HetCtrl_P1_A12_S240_quant


title: M51_BMP_WT_P4_H12_S318_quant

description:
stage-matched control mouse replicate #1
Infarinato_etal_2020_ALL_DATA_counts.csv
Infarinato_etal_2020_ALL_DATA_TPM.csv

value: Bmpr1a+/+, TyrCreER+, R26YFP fl/+ (C57Bl6 mix)


title: M51_BMP_WT_P4_H3_S314_quant


title: M51_BMP_WT_P4_H1_S312_quant


title: M51_BMP_WT_P4_H11_S317_quant


title: M120_HetCtrl_P1_A9_S237_quant


title: M51_BMP_WT_P4_H10_S316_quant


title: M51_BMP_WT_P4_G8_S309_quant


title: M51_BMP_WT_P4_H9_S315_quant


title: M51_BMP_WT_P4_G6_S307_quant


title: M51_BMP_WT_P4_G5_S306_quant


title: M51_BMP_WT_P4_G4_S305_quant


title: M51_BMP_WT_P4_G7_S308_quant


title: M51_BMP_WT_P4_G2_S303_quant


title: M51_BMP_WT_P4_G3_S304_quant


title: M51_BMP_WT_P4_G1_S302_quant


title: M51_BMP_WT_P4_F9_S298_quant


title: M51_BMP_WT_P4_G9_S310_quant


title: M51_BMP_WT_P4_F7_S296_quant


title: M51_BMP_WT_P4_F4_S293_quant


title: M51_BMP_WT_P4_F6_S295_quant


title: M51_BMP_WT_P4_F5_S294_quant


title: M51_BMP_WT_P4_F3_S292_quant


title: M51_BMP_WT_P4_G11_S311_quant


title: M51_BMP_WT_P4_F11_S300_quant


title: M120_HetCtrl_P1_A10_S238_quant


title: M51_BMP_WT_P4_H2_S313_quant


title: M51_BMP_WT_P4_F12_S301_quant


title: M51_BMP_WT_P4_F10_S299_quant


title: M51_BMP_WT_P4_F1_S291_quant


title: M51_BMP_WT_P4_E8_S286_quant


title: M51_BMP_WT_P4_E9_S287_quant


title: M51_BMP_WT_P4_E4_S283_quant


title: M51_BMP_WT_P4_E3_S282_quant


title: M51_BMP_WT_P4_E7_S285_quant


title: M51_BMP_WT_P4_E12_S290_quant


title: M51_BMP_WT_P4_E10_S288_quant


title: M51_BMP_WT_P4_F8_S297_quant


title: M51_BMP_WT_P4_D9_S277_quant


title: M51_BMP_WT_P4_D5_S275_quant


title: M51_BMP_WT_P4_D2_S272_quant


title: M51_BMP_WT_P4_D6_S276_quant


title: M51_BMP_WT_P4_D3_S273_quant


title: M51_BMP_WT_P4_E1_S281_quant


title: M51_BMP_WT_P4_D12_S280_quant


title: M51_BMP_WT_P4_D11_S279_quant


title: M51_BMP_WT_P4_D10_S278_quant


title: M51_BMP_WT_P4_C7_S266_quant


title: M51_BMP_WT_P4_C6_S265_quant


title: M51_BMP_WT_P4_C8_S267_quant


title: M51_BMP_WT_P4_C9_S268_quant


title: M51_BMP_WT_P4_C2_S261_quant


title: M51_BMP_WT_P4_C5_S264_quant


title: M51_BMP_WT_P4_C11_S270_quant


title: M51_BMP_WT_P4_E5_S284_quant


title: M51_BMP_WT_P4_C12_S271_quant


title: M51_BMP_WT_P4_C4_S263_quant


title: M51_BMP_WT_P4_B9_S257_quant


title: M51_BMP_WT_P4_C3_S262_quant


title: M51_BMP_WT_P4_D4_S274_quant


title: M51_BMP_WT_P4_B7_S255_quant


title: M51_BMP_WT_P4_B8_S256_quant


title: M51_BMP_WT_P4_B6_S254_quant


title: M51_BMP_WT_P4_B5_S253_quant


title: M51_BMP_WT_P4_E11_S289_quant


title: M51_BMP_WT_P4_C10_S269_quant


title: M51_BMP_WT_P4_B4_S252_quant


title: M51_BMP_WT_P4_B3_S251_quant


title: M51_BMP_WT_P4_B12_S260_quant


title: M51_BMP_WT_P4_B11_S259_quant


title: M51_BMP_WT_P4_A8_S246_quant


title: M51_BMP_WT_P4_B10_S258_quant


title: M51_BMP_WT_P4_A7_S245_quant


title: M51_BMP_WT_P4_A2_S240_quant


title: M51_BMP_WT_P4_A5_S243_quant


title: M51_BMP_WT_P4_A11_S248_quant


title: M51_BMP_WT_P4_A4_S242_quant


title: M51_BMP_WT_P4_A3_S241_quant


title: M51_BMP_WT_P4_A10_S247_quant


title: M51_BMP_WT_P3_H3_S238_quant


title: M51_BMP_WT_P3_H11_S239_quant


title: M51_BMP_WT_P3_H1_S236_quant


title: M51_BMP_WT_P3_H2_S237_quant


title: M51_BMP_WT_P3_G8_S232_quant


title: M51_BMP_WT_P3_G7_S231_quant


title: M51_BMP_WT_P3_G5_S230_quant


title: M51_BMP_WT_P3_G4_S229_quant


title: M51_BMP_WT_P3_G3_S228_quant


title: M51_BMP_WT_P3_G2_S227_quant


title: M51_BMP_WT_P3_G12_S235_quant


title: M51_BMP_WT_P3_G11_S234_quant


title: M51_BMP_WT_P3_F9_S222_quant


title: M51_BMP_WT_P4_B1_S250_quant


title: M51_BMP_WT_P3_G10_S233_quant


title: M51_BMP_WT_P3_G1_S226_quant


title: M51_BMP_WT_P3_F6_S220_quant


title: M51_BMP_WT_P3_F8_S221_quant


title: M51_BMP_WT_P4_A6_S244_quant


title: M51_BMP_WT_P3_F5_S219_quant


title: M51_BMP_WT_P4_A12_S249_quant


title: M51_BMP_WT_P3_F4_S218_quant


title: M51_BMP_WT_P3_F2_S216_quant


title: M51_BMP_WT_P3_F3_S217_quant


title: M51_BMP_WT_P3_F1_S215_quant


title: M51_BMP_WT_P3_F11_S224_quant


title: M51_BMP_WT_P3_E9_S211_quant


title: M51_BMP_WT_P3_E8_S210_quant


title: M51_BMP_WT_P3_E7_S209_quant


title: M51_BMP_WT_P3_E6_S208_quant


title: M51_BMP_WT_P3_E4_S206_quant


title: M51_BMP_WT_P3_E5_S207_quant


title: M51_BMP_WT_P3_E2_S204_quant


title: M51_BMP_WT_P3_E3_S205_quant


title: M51_BMP_WT_P3_E12_S214_quant


title: M51_BMP_WT_P3_E11_S213_quant


title: M51_BMP_WT_P3_E1_S203_quant


title: M51_BMP_WT_P3_E10_S212_quant


title: M51_BMP_WT_P3_D9_S199_quant


title: M51_BMP_WT_P3_D3_S193_quant


title: M51_BMP_WT_P3_D6_S196_quant


title: M51_BMP_WT_P3_D4_S194_quant


title: M51_BMP_WT_P3_D2_S192_quant


title: M51_BMP_WT_P3_D12_S202_quant


title: M51_BMP_WT_P3_D8_S198_quant


title: M51_BMP_WT_P3_D7_S197_quant


title: M51_BMP_WT_P3_F10_S223_quant


title: M51_BMP_WT_P3_D5_S195_quant


title: M51_BMP_WT_P3_F12_S225_quant


title: M51_BMP_WT_P3_D10_S200_quant


title: M51_BMP_WT_P3_D1_S191_quant


title: M51_BMP_WT_P3_D11_S201_quant


title: M51_BMP_WT_P3_C7_S185_quant


title: M51_BMP_WT_P3_C9_S187_quant


title: M51_BMP_WT_P3_C8_S186_quant


title: M51_BMP_WT_P3_C6_S184_quant


title: M51_BMP_WT_P3_C5_S183_quant


title: M51_BMP_WT_P3_C2_S180_quant


title: M51_BMP_WT_P3_C3_S181_quant


title: M51_BMP_WT_P3_C11_S189_quant


title: M51_BMP_WT_P3_C12_S190_quant


title: M51_BMP_WT_P3_C4_S182_quant


title: M51_BMP_WT_P3_C10_S188_quant


title: M51_BMP_WT_P3_C1_S179_quant


title: M51_BMP_WT_P3_B9_S176_quant


title: M51_BMP_WT_P3_B6_S173_quant


title: M51_BMP_WT_P3_B8_S175_quant


title: M51_BMP_WT_P3_B7_S174_quant


title: M51_BMP_WT_P3_B5_S172_quant


title: M51_BMP_WT_P3_B12_S178_quant


title: M51_BMP_WT_P3_B2_S169_quant


title: M51_BMP_WT_P3_B4_S171_quant


title: M51_BMP_WT_P3_B11_S177_quant


title: M51_BMP_WT_P3_A6_S163_quant


title: M51_BMP_WT_P3_B1_S168_quant


title: M51_BMP_WT_P3_B3_S170_quant


title: M51_BMP_WT_P3_A8_S164_quant


title: M51_BMP_WT_P3_A12_S167_quant


title: M51_BMP_WT_P1_H3_S77_quant


title: M51_BMP_WT_P3_A10_S166_quant


title: M51_BMP_WT_P1_H2_S76_quant


title: M51_BMP_WT_P3_A3_S161_quant


title: M51_BMP_WT_P3_A5_S162_quant


title: M51_BMP_WT_P1_H12_S80_quant


title: M51_BMP_WT_P3_A2_S160_quant


title: M51_BMP_WT_P1_H10_S78_quant


title: M51_BMP_WT_P1_G9_S71_quant


title: M51_BMP_WT_P1_H11_S79_quant


title: M51_BMP_WT_P1_H1_S75_quant


title: M51_BMP_WT_P1_G5_S67_quant


title: M51_BMP_WT_P1_G8_S70_quant


title: M51_BMP_WT_P1_G6_S68_quant


title: M51_BMP_WT_P1_G7_S69_quant


title: M51_BMP_WT_P1_G2_S65_quant


title: M51_BMP_WT_P3_A9_S165_quant


title: M51_BMP_WT_P1_G3_S66_quant


title: M51_BMP_WT_P1_G12_S74_quant


title: M51_BMP_WT_P1_F7_S60_quant


title: M51_BMP_WT_P1_F9_S61_quant


title: M51_BMP_WT_P1_F4_S58_quant


title: M51_BMP_WT_P1_F6_S59_quant


title: M51_BMP_WT_P1_F2_S56_quant


title: M51_BMP_WT_P1_G1_S64_quant


title: M51_BMP_WT_P1_G10_S72_quant


title: M51_BMP_WT_P3_A1_S159_quant


title: M51_BMP_WT_P1_F1_S55_quant


title: M51_BMP_WT_P1_E7_S50_quant


title: M51_BMP_WT_P1_E8_S51_quant


title: M51_BMP_WT_P1_F3_S57_quant


title: M51_BMP_WT_P1_E6_S49_quant


title: M51_BMP_WT_P1_F10_S62_quant


title: M51_BMP_WT_P1_E9_S52_quant


title: M51_BMP_WT_P1_E2_S45_quant


title: M51_BMP_WT_P1_E3_S46_quant


title: M51_BMP_WT_P1_E10_S53_quant


title: M51_BMP_WT_P1_E12_S54_quant


title: M51_BMP_WT_P1_E1_S44_quant


title: M51_BMP_WT_P1_G11_S73_quant


title: M51_BMP_WT_P1_D7_S38_quant


title: M51_BMP_WT_P1_D6_S37_quant


title: M51_BMP_WT_P1_D4_S35_quant


title: M51_BMP_WT_P1_F12_S63_quant


title: M51_BMP_WT_P1_D3_S34_quant


title: M51_BMP_WT_P1_D2_S33_quant


title: M51_BMP_WT_P1_D1_S32_quant


title: M51_BMP_WT_P1_D11_S42_quant


title: M51_BMP_WT_P1_E5_S48_quant


title: M51_BMP_WT_P1_D12_S43_quant


title: M51_BMP_WT_P1_C9_S28_quant


title: M51_BMP_WT_P1_C8_S27_quant


title: M51_BMP_WT_P1_E4_S47_quant


title: M51_BMP_WT_P1_C7_S26_quant


title: M51_BMP_WT_P1_C11_S30_quant


title: M51_BMP_WT_P1_C5_S24_quant


title: M51_BMP_WT_P1_C2_S22_quant


title: M51_BMP_WT_P1_D8_S39_quant


title: M51_BMP_WT_P1_C12_S31_quant


title: M51_BMP_WT_P1_C1_S21_quant


title: M51_BMP_WT_P1_C10_S29_quant


title: M51_BMP_WT_P1_D5_S36_quant


title: M51_BMP_WT_P1_B9_S19_quant


title: M51_BMP_WT_P1_B6_S16_quant


title: M51_BMP_WT_P1_B7_S17_quant


title: M51_BMP_WT_P1_B4_S14_quant


title: M51_BMP_WT_P1_B5_S15_quant


title: M51_BMP_WT_P1_B3_S13_quant


title: M51_BMP_WT_P1_C6_S25_quant


title: M51_BMP_WT_P1_B10_S20_quant


title: M51_BMP_WT_P1_B2_S12_quant


title: M51_BMP_WT_P1_A9_S7_quant


title: M51_BMP_WT_P1_C4_S23_quant


title: M51_BMP_WT_P1_A8_S6_quant


title: M51_BMP_WT_P1_A5_S4_quant


title: M51_BMP_WT_P1_A4_S3_quant


title: M51_BMP_WT_P1_A7_S5_quant


title: M51_BMP_WT_P1_A2_S2_quant


title: M51_BMP_WT_P1_A12_S10_quant


title: M51_BMP_WT_P1_B8_S18_quant


title: M51_BMP_WT_P1_A1_S1_quant


title: M51_BMP_WT_P1_A11_S9_quant


title: MP10_Mc_P2_H3_S149_quant

description:
mouse replicate #2
Infarinato_etal_2020_ALL_DATA_counts.csv
Infarinato_etal_2020_ALL_DATA_TPM.csv

value: differentiated melanocyte

value: morphogenesis

value: Dct-eGFP+, Lef1-RFP+ (CD1/C57Bl6J mix)

value: Dct-eGFP+, Lef1-RFP+, c-Kit+, integrin α6medium-low, dump (CD31, CD45, CD140a)-, Sca-1-, and CD34-


title: M51_BMP_WT_P1_A10_S8_quant


title: MP10_Mc_P2_H12_S153_quant


title: MP10_Mc_P2_H4_S150_quant


title: MP10_Mc_P2_H1_S147_quant


title: MP10_Mc_P2_H2_S148_quant


title: MP10_Mc_P2_G9_S143_quant


title: MP10_Mc_P2_H11_S152_quant


title: MP10_Mc_P2_G6_S140_quant


title: M51_BMP_WT_P1_B1_S11_quant


title: MP10_Mc_P2_G4_S138_quant


title: MP10_Mc_P2_G5_S139_quant


title: MP10_Mc_P2_G3_S137_quant


title: MP10_Mc_P2_G2_S136_quant


title: MP10_Mc_P2_G12_S146_quant


title: MP10_Mc_P2_H5_S151_quant


title: MP10_Mc_P2_G10_S144_quant


title: MP10_Mc_P2_G11_S145_quant


title: MP10_Mc_P2_F7_S131_quant


title: MP10_Mc_P2_F3_S128_quant


title: MP10_Mc_P2_F5_S129_quant


title: MP10_Mc_P2_F11_S134_quant


title: MP10_Mc_P2_F10_S133_quant


title: MP10_Mc_P2_F6_S130_quant


title: MP10_Mc_P2_G8_S142_quant


title: MP10_Mc_P2_F1_S126_quant


title: MP10_Mc_P2_F12_S135_quant


title: MP10_Mc_P2_E6_S120_quant


title: MP10_Mc_P2_E9_S122_quant


title: MP10_Mc_P2_E7_S121_quant


title: MP10_Mc_P2_E3_S117_quant


title: MP10_Mc_P2_F9_S132_quant


title: MP10_Mc_P2_E2_S116_quant


title: MP10_Mc_P2_F2_S127_quant


title: MP10_Mc_P2_E12_S125_quant


title: MP10_Mc_P2_E10_S123_quant


title: MP10_Mc_P2_E1_S115_quant


title: MP10_Mc_P2_D9_S111_quant


title: MP10_Mc_P2_D5_S108_quant


title: MP10_Mc_P2_D6_S109_quant


title: MP10_Mc_P2_D4_S107_quant


title: MP10_Mc_P2_D3_S106_quant


title: MP10_Mc_P2_E5_S119_quant


title: MP10_Mc_P2_D12_S114_quant


title: MP10_Mc_P2_D2_S105_quant


title: MP10_Mc_P2_C9_S100_quant


title: MP10_Mc_P2_D1_S104_quant


title: MP10_Mc_P2_C7_S98_quant


title: MP10_Mc_P2_C3_S94_quant


title: MP10_Mc_P2_C12_S103_quant


title: MP10_Mc_P2_C6_S97_quant


title: MP10_Mc_P2_C2_S93_quant


title: MP10_Mc_P2_E11_S124_quant


title: MP10_Mc_P2_C11_S102_quant


title: MP10_Mc_P2_C10_S101_quant


title: MP10_Mc_P2_E4_S118_quant


title: MP10_Mc_P2_D7_S110_quant


title: MP10_Mc_P2_B9_S88_quant


title: MP10_Mc_P2_B8_S87_quant


title: MP10_Mc_P2_B7_S86_quant


title: MP10_Mc_P2_C5_S96_quant


title: MP10_Mc_P2_G7_S141_quant


title: MP10_Mc_P2_D11_S113_quant


title: MP10_Mc_P2_C8_S99_quant


title: MP10_Mc_P2_B6_S85_quant


title: MP10_Mc_P2_D10_S112_quant


title: M51_BMP_WT_P1_D10_S41_quant


title: MP10_Mc_P2_B4_S84_quant


title: MP10_Mc_P2_B10_S89_quant


title: MP10_Mc_P2_A3_S78_quant


title: MP10_Mc_P2_B12_S91_quant


title: MP10_Mc_P2_B11_S90_quant


title: MP10_Mc_P2_A2_S77_quant


title: MP10_Mc_P2_B3_S83_quant


title: MP10_Mc_P2_B2_S82_quant


title: MP10_Mc_P2_C1_S92_quant


title: MP10_Mc_P2_A11_S80_quant


title: MP10_Mc_P2_C4_S95_quant


title: MP10_Mc_P2_A12_S81_quant


title: MP10_Mc_P1_H3_S155_quant


title: MP10_Mc_P1_H5_S157_quant


title: MP10_Mc_P1_H9_S158_quant


title: MP10_Mc_P1_H4_S156_quant


title: MP10_Mc_P2_A1_S76_quant


title: MP10_Mc_P1_H2_S154_quant


title: MP10_Mc_P1_H12_S160_quant


title: MP10_Mc_P1_H1_S153_quant


title: MP10_Mc_P1_G9_S149_quant


title: MP10_Mc_P1_G6_S146_quant


title: MP10_Mc_P1_H11_S159_quant


title: MP10_Mc_P1_G8_S148_quant


title: MP10_Mc_P1_G7_S147_quant


title: MP10_Mc_P1_G3_S143_quant


title: MP10_Mc_P1_G5_S145_quant


title: MP10_Mc_P1_G12_S152_quant


title: MP10_Mc_P1_G4_S144_quant


title: MP10_Mc_P1_G2_S142_quant


title: MP10_Mc_P1_G11_S151_quant


title: MP10_Mc_P1_G10_S150_quant


title: MP10_Mc_P1_F9_S138_quant


title: MP10_Mc_P2_A10_S79_quant


title: MP10_Mc_P1_F8_S137_quant


title: MP10_Mc_P1_F6_S135_quant


title: MP10_Mc_P1_F5_S134_quant


title: MP10_Mc_P1_F3_S132_quant


title: MP10_Mc_P1_F2_S131_quant


title: MP10_Mc_P1_F1_S130_quant


title: MP10_Mc_P1_E9_S126_quant


title: MP10_Mc_P1_F12_S141_quant


title: MP10_Mc_P1_F10_S139_quant


title: MP10_Mc_P1_F11_S140_quant


title: MP10_Mc_P1_E8_S125_quant


title: MP10_Mc_P1_E7_S124_quant


title: MP10_Mc_P1_E2_S119_quant


title: MP10_Mc_P1_E12_S129_quant


title: MP10_Mc_P1_E3_S120_quant


title: MP10_Mc_P1_E4_S121_quant


title: MP10_Mc_P1_E11_S128_quant


title: MP10_Mc_P1_D9_S114_quant


title: MP10_Mc_P1_E1_S118_quant


title: MP10_Mc_P1_E10_S127_quant


title: MP10_Mc_P1_D7_S112_quant


title: MP10_Mc_P1_F7_S136_quant


title: MP10_Mc_P1_D8_S113_quant


title: MP10_Mc_P1_D4_S109_quant


title: MP10_Mc_P1_D5_S110_quant


title: MP10_Mc_P1_F4_S133_quant


title: MP10_Mc_P1_D2_S107_quant


title: MP10_Mc_P1_D3_S108_quant


title: MP10_Mc_P1_D6_S111_quant


title: MP10_Mc_P1_D12_S117_quant


title: MP10_Mc_P1_D11_S116_quant


title: MP10_Mc_P1_D10_S115_quant


title: MP10_Mc_P1_E6_S123_quant


title: MP10_Mc_P1_E5_S122_quant


title: MP10_Mc_P1_C9_S102_quant


title: MP10_Mc_P1_C6_S99_quant


title: MP10_Mc_P1_C8_S101_quant


title: MP10_Mc_P1_C7_S100_quant


title: MP10_Mc_P1_C5_S98_quant


title: MP10_Mc_P1_C3_S96_quant


title: MP10_Mc_P1_C11_S104_quant


title: MP10_Mc_P1_C2_S95_quant


title: MP10_Mc_P1_C12_S105_quant


title: MP10_Mc_P1_B9_S90_quant


title: MP10_Mc_P1_B8_S89_quant


title: MP10_Mc_P1_C10_S103_quant


title: MP10_Mc_P1_B7_S88_quant


title: MP10_Mc_P1_B3_S84_quant


title: MP10_Mc_P1_B2_S83_quant


title: MP10_Mc_P1_B12_S93_quant


title: MP10_Mc_P1_C1_S94_quant


title: MP10_Mc_P1_B6_S87_quant


title: MP10_Mc_P1_B4_S85_quant


title: MP10_Mc_P1_B10_S91_quant


title: MP10_Mc_P1_B5_S86_quant


title: MP10_Mc_P1_A3_S79_quant


title: MP10_Mc_P1_A2_S78_quant


title: MP10_Mc_P1_A12_S82_quant


title: MP10_Mc_P1_A11_S81_quant


title: MP10_Mc_P1_A10_S80_quant


title: MP10_Mc_P1_C4_S97_quant


title: MP10_Mc_P1_A1_S77_quant


title: M37_P10_Mc_Plate4_H8_S336_quant

description:
mouse replicate #1
Infarinato_etal_2020_ALL_DATA_counts.csv
Infarinato_etal_2020_ALL_DATA_TPM.csv


title: M37_P10_Mc_Plate4_H7_S335_quant


title: M37_P10_Mc_Plate4_H9_S337_quant


title: M37_P10_Mc_Plate4_H5_S334_quant


title: M37_P10_Mc_Plate4_H3_S333_quant


title: M37_P10_Mc_Plate4_H2_S332_quant


title: M37_P10_Mc_Plate4_H10_S338_quant


title: M37_P10_Mc_Plate4_H11_S339_quant


title: M37_P10_Mc_Plate4_G9_S327_quant


title: M37_P10_Mc_Plate4_H1_S331_quant


title: M37_P10_Mc_Plate4_H12_S340_quant


title: M37_P10_Mc_Plate4_G7_S325_quant


title: M37_P10_Mc_Plate4_G8_S326_quant


title: M37_P10_Mc_Plate4_G6_S324_quant


title: M37_P10_Mc_Plate4_G5_S323_quant


title: MP10_Mc_P1_B11_S92_quant


title: M37_P10_Mc_Plate4_G2_S320_quant


title: M37_P10_Mc_Plate4_G3_S321_quant


title: M37_P10_Mc_Plate4_G4_S322_quant


title: M37_P10_Mc_Plate4_G12_S330_quant


title: M37_P10_Mc_Plate4_F9_S315_quant


title: M37_P10_Mc_Plate4_G1_S319_quant


title: M37_P10_Mc_Plate4_F3_S309_quant


title: M37_P10_Mc_Plate4_F8_S314_quant


title: M37_P10_Mc_Plate4_G10_S328_quant


title: M37_P10_Mc_Plate4_F5_S311_quant


title: M37_P10_Mc_Plate4_F2_S308_quant


title: M37_P10_Mc_Plate4_F7_S313_quant


title: M37_P10_Mc_Plate4_F4_S310_quant


title: M51_BMP_WT_P1_D9_S40_quant


title: M37_P10_Mc_Plate4_F6_S312_quant


title: M37_P10_Mc_Plate4_F11_S317_quant


title: M37_P10_Mc_Plate4_F12_S318_quant


title: M37_P10_Mc_Plate4_F10_S316_quant


title: M37_P10_Mc_Plate4_F1_S307_quant


title: M37_P10_Mc_Plate4_E5_S300_quant


title: M37_P10_Mc_Plate4_E9_S303_quant


title: M37_P10_Mc_Plate4_E7_S302_quant


title: M37_P10_Mc_Plate4_G11_S329_quant


title: M37_P10_Mc_Plate4_E6_S301_quant


title: M37_P10_Mc_Plate4_E12_S306_quant


title: M37_P10_Mc_Plate4_E2_S297_quant


title: M37_P10_Mc_Plate4_E4_S299_quant


title: M37_P10_Mc_Plate4_E3_S298_quant


title: M37_P10_Mc_Plate4_E1_S296_quant


title: M37_P10_Mc_Plate4_E11_S305_quant


title: M37_P10_Mc_Plate4_D9_S292_quant


title: M37_P10_Mc_Plate4_E10_S304_quant


title: M37_P10_Mc_Plate4_D8_S291_quant


title: M37_P10_Mc_Plate4_D7_S290_quant


title: M37_P10_Mc_Plate4_D2_S285_quant


title: M37_P10_Mc_Plate4_D12_S295_quant


title: M37_P10_Mc_Plate4_D4_S287_quant


title: M37_P10_Mc_Plate4_D6_S289_quant


title: M37_P10_Mc_Plate4_D3_S286_quant


title: M37_P10_Mc_Plate4_D10_S293_quant


title: M37_P10_Mc_Plate4_D1_S284_quant


title: M37_P10_Mc_Plate4_D11_S294_quant


title: M37_P10_Mc_Plate4_C6_S277_quant


title: M37_P10_Mc_Plate4_C12_S283_quant


title: M37_P10_Mc_Plate4_C9_S280_quant


title: M37_P10_Mc_Plate4_C8_S279_quant


title: M37_P10_Mc_Plate4_C5_S276_quant


title: M37_P10_Mc_Plate4_C10_S281_quant


title: M37_P10_Mc_Plate4_C4_S275_quant


title: M37_P10_Mc_Plate4_B7_S266_quant


title: M37_P10_Mc_Plate4_C7_S278_quant


title: M37_P10_Mc_Plate4_C3_S274_quant


title: M37_P10_Mc_Plate4_B5_S264_quant


title: M37_P10_Mc_Plate4_C11_S282_quant


title: M37_P10_Mc_Plate4_B6_S265_quant


title: M37_P10_Mc_Plate4_B9_S268_quant


title: M37_P10_Mc_Plate4_C1_S272_quant


title: M37_P10_Mc_Plate4_B10_S269_quant


title: M37_P10_Mc_Plate4_D5_S288_quant


title: M37_P10_Mc_Plate4_C2_S273_quant


title: M37_P10_Mc_Plate4_B11_S270_quant


title: M37_P10_Mc_Plate4_B1_S260_quant


title: M37_P10_Mc_Plate4_B12_S271_quant


title: M37_P10_Mc_Plate4_B2_S261_quant


title: M37_P10_Mc_Plate4_B8_S267_quant


title: M37_P10_Mc_Plate4_B4_S263_quant


title: M37_P10_Mc_Plate4_A8_S257_quant


title: M37_P10_Mc_Plate4_A7_S256_quant


title: MP10_Mc_P1_D1_S106_quant


title: M37_P10_Mc_Plate4_A5_S255_quant


title: M37_P10_Mc_Plate4_A3_S254_quant


title: M37_P10_Mc_Plate4_A2_S253_quant


title: M37_P10_Mc_Plate4_B3_S262_quant


title: M37_P10_Mc_Plate4_A10_S258_quant


title: M37_P10_Mc_Plate4_A1_S252_quant


title: M37_P10_Mc_Plate3_H9_S168_quant


title: M37_P10_Mc_Plate3_H7_S166_quant


title: M37_P10_Mc_Plate3_H5_S164_quant


title: M37_P10_Mc_Plate3_H1_S160_quant


title: M37_P10_Mc_Plate3_H8_S167_quant


title: M37_P10_Mc_Plate3_H6_S165_quant


title: M37_P10_Mc_Plate3_G7_S154_quant


title: M37_P10_Mc_Plate3_G8_S155_quant


title: M37_P10_Mc_Plate3_G6_S153_quant


title: M37_P10_Mc_Plate3_H10_S169_quant


title: M37_P10_Mc_Plate3_G12_S159_quant


title: M37_P10_Mc_Plate3_G5_S152_quant


title: M37_P10_Mc_Plate3_H3_S162_quant


title: M37_P10_Mc_Plate3_H2_S161_quant


title: M37_P10_Mc_Plate3_G9_S156_quant


title: M37_P10_Mc_Plate4_A11_S259_quant


title: M37_P10_Mc_Plate3_H12_S171_quant


title: M37_P10_Mc_Plate3_G11_S158_quant


title: M37_P10_Mc_Plate3_H11_S170_quant


title: M37_P10_Mc_Plate3_H4_S163_quant


title: M37_P10_Mc_Plate3_F9_S145_quant


title: M37_P10_Mc_Plate3_G1_S149_quant


title: M37_P10_Mc_Plate3_F7_S143_quant


title: M37_P10_Mc_Plate3_G2_S150_quant


title: M37_P10_Mc_Plate3_G3_S151_quant


title: M37_P10_Mc_Plate3_F6_S142_quant


title: M37_P10_Mc_Plate3_F8_S144_quant


title: M37_P10_Mc_Plate3_F5_S141_quant


title: M37_P10_Mc_Plate3_F3_S139_quant


title: M37_P10_Mc_Plate3_G10_S157_quant


title: M37_P10_Mc_Plate3_F12_S148_quant


title: M37_P10_Mc_Plate3_F11_S147_quant


title: M37_P10_Mc_Plate3_E9_S134_quant


title: M37_P10_Mc_Plate3_E5_S130_quant


title: M37_P10_Mc_Plate3_E8_S133_quant


title: M37_P10_Mc_Plate3_F1_S138_quant


title: M37_P10_Mc_Plate3_F10_S146_quant


title: M37_P10_Mc_Plate3_E3_S129_quant


title: M37_P10_Mc_Plate3_D8_S122_quant


title: M37_P10_Mc_Plate3_E1_S127_quant


title: M37_P10_Mc_Plate3_E12_S137_quant


title: M37_P10_Mc_Plate3_D9_S123_quant


title: M37_P10_Mc_Plate3_E2_S128_quant


title: M37_P10_Mc_Plate3_E11_S136_quant


title: M37_P10_Mc_Plate3_E10_S135_quant


title: M37_P10_Mc_Plate3_D7_S121_quant


title: M37_P10_Mc_Plate3_D6_S120_quant


title: M37_P10_Mc_Plate3_D4_S119_quant


title: M37_P10_Mc_Plate3_D11_S125_quant


title: M37_P10_Mc_Plate3_D3_S118_quant


title: M37_P10_Mc_Plate3_D2_S117_quant


title: M37_P10_Mc_Plate3_D10_S124_quant


title: M37_P10_Mc_Plate3_F4_S140_quant


title: M37_P10_Mc_Plate3_D1_S116_quant


title: M37_P10_Mc_Plate3_E7_S132_quant


title: M37_P10_Mc_Plate3_D12_S126_quant


title: M37_P10_Mc_Plate3_E6_S131_quant


title: M37_P10_Mc_Plate3_C9_S112_quant


title: M37_P10_Mc_Plate3_C6_S109_quant


title: M37_P10_Mc_Plate3_C7_S110_quant


title: M37_P10_Mc_Plate3_C5_S108_quant


title: M37_P10_Mc_Plate3_C4_S107_quant


title: M37_P10_Mc_Plate3_C3_S106_quant


title: M37_P10_Mc_Plate3_C11_S114_quant


title: M37_P10_Mc_Plate3_C12_S115_quant


title: M37_P10_Mc_Plate3_B7_S98_quant


title: M37_P10_Mc_Plate3_C1_S104_quant


title: M37_P10_Mc_Plate3_C10_S113_quant


title: M37_P10_Mc_Plate3_B8_S99_quant


title: M37_P10_Mc_Plate3_B9_S100_quant


title: M37_P10_Mc_Plate3_B4_S95_quant


title: M37_P10_Mc_Plate3_B3_S94_quant


title: M37_P10_Mc_Plate3_B2_S93_quant


title: M37_P10_Mc_Plate3_C8_S111_quant


title: M37_P10_Mc_Plate3_B11_S102_quant


title: M37_P10_Mc_Plate3_B1_S92_quant


title: M37_P10_Mc_Plate3_A7_S88_quant


title: M37_P10_Mc_Plate3_A8_S89_quant


title: M37_P10_Mc_Plate3_A4_S87_quant


title: M37_P10_Mc_Plate3_B10_S101_quant


title: M37_P10_Mc_Plate3_A2_S85_quant


title: M37_P10_Mc_Plate3_A3_S86_quant


title: M37_P10_Mc_Plate3_C2_S105_quant


title: M37_P10_Mc_Plate3_A10_S90_quant


title: M37_P10_Mc_Plate3_A1_S84_quant


title: M37_P10_Mc_Plate3_A11_S91_quant


title: M9_P21_P1_H8_S198_quant

description:
mouse replicate #3
Infarinato_etal_2020_ALL_DATA_counts.csv
Infarinato_etal_2020_ALL_DATA_TPM.csv

value: active melanocyte stem cell

value: 1st anagen

value: Dct-eGFP+ (CD1/C57Bl6 mix)

value: Dct-eGFP+, dump (CD31, CD45, CD140a)-, Sca1-, and CD34-


title: M9_P21_P1_H5_S196_quant


title: M37_P10_Mc_Plate3_B6_S97_quant


title: M9_P21_P1_H4_S195_quant


title: M9_P21_P1_H7_S197_quant


title: M37_P10_Mc_Plate3_B5_S96_quant


title: M37_P10_Mc_Plate3_B12_S103_quant


title: M9_P21_P1_H10_S200_quant


title: M9_P21_P1_H9_S199_quant


title: M9_P21_P1_H11_S201_quant


title: M9_P21_P1_G7_S188_quant


title: M9_P21_P1_G3_S186_quant


title: M9_P21_P1_G8_S189_quant


title: M9_P21_P1_G5_S187_quant


title: M9_P21_P1_G1_S185_quant


title: M9_P21_P1_G12_S193_quant


title: M9_P21_P1_F8_S180_quant


title: M9_P21_P1_F9_S181_quant


title: M9_P21_P1_F7_S179_quant


title: M9_P21_P1_G11_S192_quant


title: M9_P21_P1_G9_S190_quant


title: M9_P21_P1_F5_S178_quant


title: M9_P21_P1_E9_S170_quant


title: M9_P21_P1_E8_S169_quant


title: M9_P21_P1_E4_S166_quant


title: M9_P21_P1_F4_S177_quant


title: M9_P21_P1_F3_S176_quant


title: M9_P21_P1_E12_S173_quant


title: M9_P21_P1_F2_S175_quant


title: M9_P21_P1_F11_S183_quant


title: M9_P21_P1_H12_S202_quant


title: M9_P21_P1_E11_S172_quant


title: M9_P21_P1_E10_S171_quant


title: M9_P21_P1_D8_S160_quant


title: M9_P21_P1_D9_S161_quant


title: M9_P21_P1_D7_S159_quant


title: M9_P21_P1_D4_S157_quant


title: M9_P21_P1_D12_S163_quant


title: M9_P21_P1_E7_S168_quant


title: M9_P21_P1_D6_S158_quant


title: M9_P21_P1_F10_S182_quant


title: M9_P21_P1_E5_S167_quant


title: M9_P21_P1_F1_S174_quant


title: M9_P21_P1_C8_S149_quant


title: M9_P21_P1_E3_S165_quant


title: M9_P21_P1_G10_S191_quant


title: M9_P21_P1_F12_S184_quant


title: M9_P21_P1_C3_S146_quant


title: M9_P21_P1_C7_S148_quant


title: M9_P21_P1_H1_S194_quant


title: M9_P21_P1_E1_S164_quant


title: M9_P21_P1_B5_S141_quant


title: M9_P21_P1_B9_S142_quant


title: M9_P21_P1_D11_S162_quant


title: M9_P21_P1_B11_S144_quant


title: M9_P21_P1_B2_S139_quant


title: M9_P21_P1_D2_S155_quant


title: M9_P21_P1_D3_S156_quant


title: M9_P21_P1_B10_S143_quant


title: M8_P21_P1_H9_S133_quant


title: M9_P21_P1_A12_S137_quant


title: M8_P21_P1_H7_S132_quant


title: M8_P21_P1_H2_S129_quant


title: M9_P21_P1_D1_S154_quant


title: M9_P21_P1_C9_S150_quant


title: M8_P21_P1_H11_S134_quant


title: M8_P21_P1_G9_S125_quant


title: M9_P21_P1_C4_S147_quant


title: M9_P21_P1_C12_S153_quant


title: M9_P21_P1_C11_S152_quant


title: M9_P21_P1_C10_S151_quant


title: M8_P21_P1_G11_S127_quant


title: M8_P21_P1_G3_S121_quant


title: M8_P21_P1_G7_S123_quant


title: M8_P21_P1_F7_S115_quant


title: M8_P21_P1_G1_S120_quant


title: M9_P21_P1_B12_S145_quant


title: M9_P21_P1_B3_S140_quant


title: M9_P21_P1_B1_S138_quant


title: M9_P21_P1_A11_S136_quant


title: M8_P21_P1_H6_S131_quant


title: M8_P21_P1_F10_S117_quant


title: M8_P21_P1_F1_S113_quant


title: M8_P21_P1_H12_S135_quant


title: M8_P21_P1_H1_S128_quant


title: M8_P21_P1_E9_S109_quant


title: M8_P21_P1_E5_S106_quant


title: M8_P21_P1_E7_S107_quant


title: M8_P21_P1_E8_S108_quant


title: M8_P21_P1_G8_S124_quant


title: M8_P21_P1_G4_S122_quant


title: M8_P21_P1_F2_S114_quant


title: M8_P21_P1_G10_S126_quant


title: M8_P21_P1_D9_S100_quant


title: M8_P21_P1_E10_S110_quant


title: M8_P21_P1_F11_S118_quant


title: M8_P21_P1_D3_S98_quant


title: M8_P21_P1_H4_S130_quant


title: M8_P21_P1_F12_S119_quant


title: M8_P21_P1_D10_S101_quant


title: M8_P21_P1_D12_S103_quant


title: M8_P21_P1_C9_S93_quant


title: M8_P21_P1_C1_S91_quant


title: M8_P21_P1_B12_S90_quant


title: M8_P21_P1_E3_S105_quant


title: M8_P21_P1_E12_S112_quant


title: M8_P21_P1_E11_S111_quant


title: M8_P21_P1_F9_S116_quant


title: M8_P21_P1_E1_S104_quant


title: M8_P21_P1_B10_S88_quant


title: M8_P21_P1_A12_S84_quant


title: M7_P21_P2_H8_S265_quant


title: M8_P21_P1_C3_S92_quant


title: M8_P21_P1_A10_S82_quant


title: M7_P21_P2_H5_S263_quant


title: M8_P21_P1_D5_S99_quant


title: M8_P21_P1_D11_S102_quant


title: M7_P21_P2_H2_S261_quant


title: M8_P21_P1_D1_S97_quant


title: M8_P21_P1_B11_S89_quant


title: M7_P21_P2_H11_S268_quant


title: M8_P21_P1_C12_S96_quant


title: M7_P21_P2_H10_S267_quant


title: M7_P21_P2_G8_S255_quant


title: M7_P21_P2_H1_S260_quant


title: M8_P21_P1_C10_S94_quant


title: M8_P21_P1_C11_S95_quant


title: M8_P21_P1_B9_S87_quant


title: M8_P21_P1_B5_S86_quant


title: M7_P21_P2_G12_S259_quant


title: M8_P21_P1_B3_S85_quant


title: M7_P21_P2_G10_S257_quant


title: M7_P21_P2_G1_S249_quant


title: M8_P21_P1_A3_S81_quant


title: M7_P21_P2_F8_S245_quant


title: M8_P21_P1_A11_S83_quant


title: M7_P21_P2_F6_S243_quant


title: M8_P21_P1_A1_S80_quant


title: M7_P21_P2_F12_S248_quant


title: M7_P21_P2_F2_S241_quant


title: M7_P21_P2_F10_S247_quant


title: M7_P21_P2_H9_S266_quant


title: M7_P21_P2_E9_S236_quant


title: M7_P21_P2_F1_S240_quant


title: M7_P21_P2_H7_S264_quant


title: M7_P21_P2_E8_S235_quant


title: M7_P21_P2_H4_S262_quant


title: M7_P21_P2_E6_S233_quant


title: M7_P21_P2_E2_S232_quant


title: M7_P21_P2_E12_S239_quant


title: M7_P21_P2_E11_S238_quant


title: M7_P21_P2_H12_S269_quant


title: M7_P21_P2_G9_S256_quant


title: M7_P21_P2_E10_S237_quant


title: M7_P21_P2_G7_S254_quant


title: M7_P21_P2_D9_S227_quant


title: M7_P21_P2_D8_S226_quant


title: M7_P21_P2_D7_S225_quant


title: M7_P21_P2_D5_S224_quant


title: M7_P21_P2_D12_S230_quant


title: M7_P21_P2_G5_S252_quant


title: M7_P21_P2_D10_S228_quant


title: M7_P21_P2_G4_S251_quant


title: M7_P21_P2_D1_S222_quant


title: M7_P21_P2_G2_S250_quant


title: M7_P21_P2_C9_S218_quant


title: M7_P21_P2_G11_S258_quant


title: M7_P21_P2_C5_S216_quant


title: M7_P21_P2_F9_S246_quant


title: M7_P21_P2_B12_S213_quant


title: M7_P21_P2_F7_S244_quant


title: M7_P21_P2_G6_S253_quant


title: M7_P21_P2_B11_S212_quant


title: M7_P21_P2_F5_S242_quant


title: M7_P21_P2_A12_S208_quant


title: M7_P21_P2_A2_S204_quant


title: M7_P21_P2_A11_S207_quant


title: M7_P21_P2_B1_S209_quant


title: M7_P21_P1_H9_S76_quant


title: M7_P21_P2_E7_S234_quant


title: M7_P21_P1_H5_S75_quant


title: M7_P21_P1_H4_S74_quant


title: M7_P21_P2_A10_S206_quant


title: M7_P21_P2_A1_S203_quant


title: M7_P21_P1_H3_S73_quant


title: M7_P21_P1_H2_S72_quant


title: M7_P21_P2_E1_S231_quant


title: M7_P21_P2_C10_S219_quant


title: M7_P21_P2_D2_S223_quant


title: M7_P21_P2_D11_S229_quant


title: M7_P21_P1_H12_S79_quant


title: M7_P21_P2_C6_S217_quant


title: M7_P21_P2_C2_S215_quant


title: M7_P21_P1_H10_S77_quant


title: M7_P21_P1_G9_S67_quant


title: M7_P21_P2_C12_S221_quant


title: M7_P21_P2_C11_S220_quant


title: M7_P21_P2_C1_S214_quant


title: M7_P21_P2_B10_S211_quant


title: M7_P21_P1_G4_S63_quant


title: M7_P21_P1_G2_S62_quant


title: M7_P21_P1_G12_S70_quant


title: M7_P21_P1_G6_S64_quant


title: M7_P21_P2_A5_S205_quant


title: M7_P21_P2_B9_S210_quant


title: M7_P21_P1_G1_S61_quant


title: M7_P21_P1_F8_S57_quant


title: M7_P21_P1_H11_S78_quant


title: M7_P21_P1_H1_S71_quant


title: M7_P21_P1_F12_S60_quant


title: M7_P21_P1_F2_S51_quant


title: M7_P21_P1_G7_S65_quant


title: M7_P21_P1_F9_S58_quant


title: M7_P21_P1_G11_S69_quant


title: M7_P21_P1_G8_S66_quant


title: M7_P21_P1_F4_S53_quant


title: M7_P21_P1_F5_S54_quant


title: M7_P21_P1_F3_S52_quant


title: M7_P21_P1_E8_S45_quant


title: M7_P21_P1_F10_S59_quant


title: M7_P21_P1_F1_S50_quant


title: M7_P21_P1_E9_S46_quant


title: M7_P21_P1_E5_S42_quant


title: M7_P21_P1_E3_S40_quant


title: M7_P21_P1_F6_S55_quant


title: M7_P21_P1_E10_S47_quant


title: M7_P21_P1_E4_S41_quant


title: M7_P21_P1_E6_S43_quant


title: M7_P21_P1_G10_S68_quant


title: M7_P21_P1_F7_S56_quant


title: M7_P21_P1_E12_S49_quant


title: M7_P21_P1_E7_S44_quant


title: M7_P21_P1_E11_S48_quant


title: M7_P21_P1_E1_S38_quant


title: M7_P21_P1_E2_S39_quant


title: M7_P21_P1_D7_S32_quant


title: M7_P21_P1_D6_S31_quant


title: M7_P21_P1_D9_S34_quant


title: M7_P21_P1_D8_S33_quant


title: M7_P21_P1_D11_S36_quant


title: M7_P21_P1_D2_S27_quant


title: M7_P21_P1_D12_S37_quant


title: M7_P21_P1_C8_S23_quant


title: M7_P21_P1_D10_S35_quant


title: M7_P21_P1_C6_S21_quant


title: M7_P21_P1_C9_S24_quant


title: M7_P21_P1_C2_S19_quant


title: M7_P21_P1_C11_S26_quant


title: M7_P21_P1_C4_S20_quant


title: M7_P21_P1_C1_S18_quant


title: M7_P21_P1_B9_S14_quant


title: M7_P21_P1_B8_S13_quant


title: M7_P21_P1_C7_S22_quant


title: M7_P21_P1_B5_S10_quant


title: M7_P21_P1_D3_S28_quant


title: M7_P21_P1_B3_S8_quant


title: M7_P21_P1_B4_S9_quant


title: M7_P21_P1_B12_S17_quant


title: M7_P21_P1_D4_S29_quant


title: M7_P21_P1_B2_S7_quant


title: M7_P21_P1_B10_S15_quant


title: M7_P21_P1_A5_S3_quant


title: M7_P21_P1_B1_S6_quant


title: M7_P21_P1_A8_S4_quant


title: M7_P21_P1_A3_S2_quant


title: M7_P21_P1_A10_S5_quant


title: M7_P21_P1_A2_S1_quant


title: M7_P21_P1_C10_S25_quant


title: MP62_M2_McSC_H7_S226_quant

value: quiescent melanocyte stem cell

value: 2nd telogen

value: Dct-eGFP+ (CD1/C57Bl6J mix)

value: Dct-eGFP+, integrin α6medium-low, dump (CD31, CD45, CD140a)-, Sca1-, and CD34-


title: M7_P21_P1_D5_S30_quant

value: male


title: MP62_M2_McSC_H6_S225_quant


title: MP62_M2_McSC_H3_S222_quant


title: MP62_M2_McSC_H2_S221_quant


title: M7_P21_P1_B7_S12_quant


title: MP62_M2_McSC_G9_S216_quant


title: MP62_M2_McSC_G5_S212_quant


title: MP62_M2_McSC_G8_S215_quant


title: M7_P21_P1_B11_S16_quant


title: MP62_M2_McSC_G7_S214_quant


title: MP62_M2_McSC_G6_S213_quant


title: MP62_M2_McSC_G3_S210_quant


title: MP62_M2_McSC_G4_S211_quant


title: MP62_M2_McSC_G2_S209_quant


title: MP62_M2_McSC_G1_S208_quant


title: MP62_M2_McSC_G10_S217_quant


title: MP62_M2_McSC_F8_S203_quant


title: MP62_M2_McSC_G12_S219_quant


title: MP62_M2_McSC_G11_S218_quant


title: MP62_M2_McSC_F9_S204_quant


title: MP62_M2_McSC_H5_S224_quant


title: MP62_M2_McSC_H4_S223_quant


title: MP62_M2_McSC_F6_S201_quant


title: MP62_M2_McSC_F5_S200_quant


title: MP62_M2_McSC_F4_S199_quant


title: MP62_M2_McSC_F3_S198_quant


title: MP62_M2_McSC_H1_S220_quant


title: MP62_M2_McSC_F11_S206_quant


title: MP62_M2_McSC_F10_S205_quant


title: MP62_M1_McSC_D2_S195_quant


title: MP62_M2_McSC_F1_S196_quant


title: MP62_M2_McSC_F12_S207_quant


title: MP62_M1_McSC_C9_S190_quant


title: MP62_M1_McSC_C5_S186_quant


title: MP62_M1_McSC_C6_S187_quant


title: MP62_M1_McSC_C7_S188_quant


title: MP62_M1_McSC_C8_S189_quant


title: MP62_M1_McSC_D1_S194_quant


title: MP62_M1_McSC_C11_S192_quant


title: MP62_M2_McSC_F7_S202_quant


title: MP62_M1_McSC_B8_S180_quant


title: MP62_M1_McSC_C12_S193_quant


title: MP62_M1_McSC_B9_S181_quant


title: MP62_M1_McSC_B4_S176_quant


title: MP62_M1_McSC_C10_S191_quant


title: MP62_M1_McSC_C4_S185_quant


title: MP62_M1_McSC_B6_S178_quant


title: MP62_M1_McSC_B3_S175_quant


title: MP62_M2_McSC_F2_S197_quant


title: MP62_M1_McSC_B5_S177_quant


title: MP62_M1_McSC_B2_S174_quant


title: MP62_M1_McSC_B7_S179_quant


title: MP62_M1_McSC_B1_S173_quant


title: M7_P21_P1_B6_S11_quant


title: MP62_M1_McSC_B10_S182_quant


title: MP62_M1_McSC_A8_S168_quant


title: MP62_M1_McSC_A9_S169_quant


title: MP62_M1_McSC_A7_S167_quant


title: MP62_M1_McSC_A5_S165_quant


title: MP62_M1_McSC_A3_S163_quant


title: 0326-S5X_07

type: RNA

city: Taipei

first: Yung-Chi

last: Chang

address: Rm 736, No. 1, Sec. 1, Jei-Ai Rd

department: Microbiology

country: Taiwan

institute: National Taiwan University, College of Medicine

description: nCounter® Human Immunology v2 Panel (CodeSet Only)

data_processing: Gene expression data was analyzed by nSolverTM analysis software (NanoString Technologies). Background values were corrected from raw data and normalized using 15 housekeeping genes (ABCF1, ALAS1, EEF1G, G6PD, GAPDH, GUSB, HPRT1, OAZ1, POLR1B, POLR2A, PPIA, RPL19, SHDA, TBP, TUBB).

label: Nanostring bar coding

organism: Homo sapiens

source_name: THP-1 monocytic cell line

growth_protocol: THP-1 cells were maintained in RPMI 1640 supplemented with 10% FBS, 10 mM HEPES, 1 mM sodium pyruvate, 2.5 g/L glucose and 0.05 mM 2-mercaptoethanol. Pneumococcus were cultured in static liquid Todd-Hewitt broth containing 2% yeast extract at 37°C with 5% CO2 to mid-log phase for experiments

extract_protocol: Total RNA was manually extracted from THP-1 cells by Qiagen Rneasy Mini kit according to the manufacturer's protocol

treatment_protocol: THP-1 cells were uninfected or infected with pneumococcus for 6 hours

tag: cell line

value: THP-1 monocytic cell line

tag: infection

value: uninfected


title: MP62_M1_McSC_B11_S183_quant


title: 0326-S5WT_08

value: WT pneumococcus


title: MP62_M1_McSC_A11_S171_quant


title: 0321-S5d_03

value: DnanA


title: MP62_M1_McSC_A12_S172_quant


title: MP62_M1_McSC_A10_S170_quant


title: MP62_M1_McSC_A1_S161_quant


title: MP62_M1_McSC_B12_S184_quant


title: PAW3 [128-16-PAW_S16]

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

data_processing:
CLC genomic workbench
trimming and quality control
non-redundant list
small RNA analysis extract and count
Supplementary_files_format_and_content: trimmed small RNA sample files contains small RNA reads together with their lenghts and counts

organism: Catharanthus roseus

source_name: PAW_leaf and stem RNA

extract_protocol:
phenol-chlorophorm extraction (Szittya et al, 2002 doi:10.1105/tpc.010366)
modified Illumina Truesec small RNA library preparation (Czotter et al, 2018 doi:10.1007/978-1-4939-7683-6_9)

tag: treatment

value: plasma activated water (PAW)

tag: tissue

value: leaf and stem


title: NO1 [129-10-NO_S6]

source_name: control_leaf and stem RNA

value: control water


title: NO2 [130-11-NO_S2]


title: MP60_P2_McSC_G9_S73_quant


title: PAW2 [127-15-PAW_S3]


title: 0321-S5WT_02


title: MP60_P2_McSC_G7_S71_quant


title: 0321-S5X_01


title: PAW1 [126-14-PAW_S13]


title: MP60_P2_McSC_G6_S70_quant


title: MP60_P2_McSC_G4_S68_quant


title: MP60_P2_McSC_G3_S67_quant


title: MP62_M1_McSC_A6_S166_quant


title: MP60_P2_McSC_G2_S66_quant


title: MP62_M1_McSC_A2_S162_quant


title: MP60_P2_McSC_G10_S74_quant


title: MP62_M1_McSC_A4_S164_quant


title: MP60_P2_McSC_G5_S69_quant


title: MP60_P2_McSC_G8_S72_quant


title: MP60_P2_McSC_F9_S61_quant


title: 0326-S5d_09


title: MP60_P2_McSC_F4_S56_quant


title: MP60_P2_McSC_F12_S64_quant


title: MP60_P2_McSC_F6_S58_quant


title: MP60_P2_McSC_F2_S54_quant


title: MP60_P2_McSC_F5_S57_quant


title: S20

city: New York

first: Ana

last: Pavel

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
RNA-seq sample quality was assessed using FastQC and MultiQC.
Samples were aligned to human reference genome based on STAR RNA-sequencing aligner and sequencing reads were assigned to genomic features by featureCounts.
Genomic features with 0 counts in more than 20% of the samples were filtered out.
Data was then transfromed to log2-counts per million by voom-transform.
Fold changes (FCHs) vs. baseline were estimated and hypothesis testing was conducted with contrasts under the general framework for linear models in limma package. P-values were adjusted using the Benjamini-Hochberg procedure, which controls False Discovery Rate (FDR).
Genome_build: GRCh38
Supplementary_files_format_and_content: log2-counts per million

source_name: Skin biopsy

extract_protocol:
Total RNA was extracted from skin biopsy samples using Qiagen miRNeasy Mini kit.
The libraries were generated using TruSeq Stranded mRNA Library Prep kit following manufactory protocol. Briefly, mRNA was first extracted from 240ng of total RNA using oligo-dT magnetic beads and fragmented at high temperature. A cDNA library was then prepared from the fragemented mRNA by revervse transcription, second strand synthesis and ligation of specific adapters.
Next generation sequencing was performed on Illumina Hiseq 4000 with single-ended 100 red cycles. Image analysis and bases calling was conducted in real-time by the Illumina analysis pipeline.

tag: ptid

tag: timepoint

value: Cerdulatinib

value: skin

tag: disease state

value: Lesional

tag: patient diagnosis

value: Mild-to-Moderate Atopic Dermatitis


title: NO3 [131-12-NO_S1]


title: MP60_P2_McSC_F3_S55_quant


title: MP60_P2_McSC_G1_S65_quant


title: MP60_P1_McSC_E8_S48_quant


title: S17

value: BL


title: MP60_P2_McSC_F11_S63_quant

value: quiescent melanocyte stem cell


title: MP60_P1_McSC_E6_S46_quant

value: 2nd telogen


title: MP60_P1_McSC_E5_S45_quant

value: Dct-eGFP+ (CD1/C57Bl6J mix)


title: MP60_P1_McSC_E4_S44_quant

value: Dct-eGFP+, integrin α6medium-low, dump (CD31, CD45, CD140a)-, Sca1-, and CD34-


title: MP60_P2_McSC_F1_S53_quant

value: male


title: MP60_P2_McSC_F7_S59_quant


title: S4_S4


title: S14_S6


title: S11_S3


title: S15_S7


title: S18


title: S9_S1


title: MP60_P1_McSC_E2_S42_quant


title: S19_S11


title: S16_S8


title: MP60_P1_McSC_E1_S41_quant


title: MP60_P1_McSC_D4_S40_quant


title: MP60_P2_McSC_F10_S62_quant


title: MP60_P1_McSC_E9_S49_quant


title: S8_S8


title: MP60_P1_McSC_E11_S51_quant


title: S7_S7


title: MP60_P1_McSC_D2_S38_quant


title: MP60_P1_McSC_E10_S50_quant


title: S3_S3


title: S13_S5


title: MP60_P1_McSC_E7_S47_quant


title: MP60_P1_McSC_E3_S43_quant


title: MP60_P1_McSC_C9_S33_quant


title: MP60_P1_McSC_C6_S30_quant


title: WT_ChIPseq_hH3-3xFLAG-Input

city: Athens

first: Zachary

middle: A

last: Lewis

state: GA

address: 1000 Cedar St. Biosciences Bldg

institute: University of Georgia

library_source: genomic

data_processing:
Trimmed with TrimGalore! Version version 4.0 parameters --length 20 --fastqc
alignment with bwa mem version 0.7.15/ parameters -M or bowtie2 version 2.4.1/parameters --verysensitive
conversion to bam and sorted and indexed with samtools version 1.3.1/
bigwigs made with DeepTools 3.3.1/ parameters --normalizeUsing CPM
Deeptools for creation of heatmaps and metaplots
Genome_build: GCA_000182925.2 (NC12)
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Neurospora crassa

source_name: Mycelium

growth_protocol: vogel's 1.5% sucrose

extract_protocol: Illumina TruSeq

treatment_protocol: ATAC-seq, ChIP-seq

tag: genotype

value: Mycelial cultures

tag: chip antibody

value: none (input)


title: WT_ChIPseq_H3K27me2me3

value: WT

value: H3K27me2/3 (ActivMotif Cat# 39535)


title: MP60_P1_McSC_C7_S31_quant


title: WT_ChIPseq_hH3-3xFLAG-8h

value: FLAG (Sigma Cat# F1804)


title: MP60_P1_McSC_C8_S32_quant


title: WT_ChIPseq_H3K36me3

value: H3K36me3 (Abcam Cat# ab9050)


title: WT_ChIPseq_hH3-3xFLAG-0h


title: WT_ChIPseq_H3K4me3

value: H3K4me3 (Abcam Cat# ab1012)


title: WT_ChIPseq_H3K4me1

value: H3K4me1 (Abcam Cat# ab9885)


title: MP60_P1_McSC_E12_S52_quant


title: S12_S4

value: Cerdulatinib

value: skin


title: MP60_P1_McSC_C11_S35_quant


title: WT_ChIPseq_H3K9me3

value: H3K9me3 (ActivMotif Cat# 39161)


title: MP60_P1_McSC_C5_S29_quant


title: MP60_P1_McSC_C4_S28_quant


title: WT_ChIPseq_H3K4me2

value: H3K4me2 (ActivMotif Cat# 29679)


title: MP60_P1_McSC_C3_S27_quant

value: quiescent melanocyte stem cell


title: MP60_P1_McSC_B9_S21_quant

value: 2nd telogen


title: MP60_P1_McSC_C2_S26_quant

value: Dct-eGFP+ (CD1/C57Bl6J mix)


title: MP60_P1_McSC_B8_S20_quant

value: Dct-eGFP+, integrin α6medium-low, dump (CD31, CD45, CD140a)-, Sca1-, and CD34-


title: MP60_P1_McSC_C12_S36_quant

value: male


title: MP60_P1_McSC_D1_S37_quant


title: MP60_P1_McSC_B5_S17_quant


title: WT_ChIPseq_H3K27ac

value: Mycelial cultures


title: WT_ATACseq_Rep2


title: dHTZ_ATACseq_Rep1


title: dWC2_ATACseq_Rep1


title: MP60_P1_McSC_C10_S34_quant


title: dHTZ_ATACseq_Rep2


title: MP60_P1_McSC_C1_S25_quant


title: dWC2_ATACseq_Rep2


title: WT_ATACseq_unsortedNuclei


title: MP60_P1_McSC_B7_S19_quant


title: MP60_P1_McSC_B2_S14_quant


title: MP60_P1_McSC_B6_S18_quant


title: WT_ATACseq_sortedNuclei


title: MP60_P1_McSC_B4_S16_quant


title: Control-2-Sequences

city: Irvine

first: QIN

last: YANG

address: 825 Health Science Rd.

department: Physiology and Biophysics

institute: University of California, Irvine

description: LSD1-LKO RNA-seq processed data

data_processing:
RNA-STAR for mapping
StringTie for transcript assembly
DESeq2 for differential expression
Genome_build: mm10
Supplementary_files_format_and_content: Excel file

source_name: Liver

extract_protocol:
Total RNA was extracted from liver of LSD1-Lko and control mice using the RNeasy kit (QIAGEN).
poly-A enrichment

treatment_protocol: Liver specific LSD1 knockout in adult mice.

value: Liver

tag: genotype/variation

value: control


title: Control-3-Sequences

description: LSD1-LKO RNA-seq processed data


title: MP60_P1_McSC_B12_S24_quant

tag: cell stage


title: MP60_P1_McSC_B3_S15_quant

tag: Sex


title: MP60_P1_McSC_B1_S13_quant

tag: age


title: WT_ ATACseq_Rep1

value: WT


title: LSD1-LKO-1-Sequences

description: LSD1-LKO RNA-seq processed data


title: LSD1-LKO-2-Sequences

description: LSD1-LKO RNA-seq processed data


title: MP60_P1_McSC_B11_S23_quant

tag: hair cycle stage


title: LSD1-LKO-3-Sequences

description: LSD1-LKO RNA-seq processed data

tag: strain


title: MP60_P1_McSC_B10_S22_quant

tag: sorting strategy


title: MP60_P1_McSC_A7_S7_quant


title: Time course 3, time point 60

city: Troy

first: Jennifer

middle: Marie

last: Hurley

institute: Rensselaer Polytechnic Institute

data_processing:
sequenced on Illumina HiSeq in a 2x150 bp configuration in High Output mode
aligned to the Mus musculus GRCm38.87 reference genome using the DRAGEN RNA-seq aligner
hit counts were calculated using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Hit counts for every gene and every sample

source_name: Bone Marrow Derived Macrophages

growth_protocol: Bone marrow progenitor cells were harvested from femurs/tibias of 3-6 month old male mice and differentiated in DMEM based media with M-CSF for 6 days until fully confluent

extract_protocol:
At specified time point, RNA collected with Qiagen RNeasy kit's Buffer RLT, homogenized via QIAshredder and then flash frozen. After all samples collected, RNeasy column extraction protocol continued according to Qiagen's instructions for animal tissue.
RNA libraries created by Genewiz using rRNA depletion step and standard Illumina protocols for Paired End sequencing with Illumina HiSeq

treatment_protocol: Prior to time course, Per2 rhythms were synchronized in differentiated macrophages by

tag: cell type

value: M-CSF Differentiated Bone Marrow Derived Macrophages


title: MP60_P1_McSC_A9_S9_quant


title: Control-1-Sequences

description: LSD1-LKO RNA-seq processed data


title: Time course 3, time point 62


title: Time course 3, time point 58


title: Time course 3, time point 50


title: MP60_P1_McSC_A8_S8_quant


title: Time course 3, time point 48


title: MP60_P1_McSC_A5_S5_quant


title: Time course 3, time point 52


title: MP60_P1_McSC_A4_S4_quant


title: Time course 3, time point 56


title: MP60_P1_McSC_A12_S12_quant


title: MP60_P1_McSC_A2_S2_quant


title: Time course 3, time point 46


title: MP60_P1_McSC_A3_S3_quant


title: MP60_P1_McSC_A10_S10_quant


title: Time course 3, time point 42


title: MP60_P1_McSC_A6_S6_quant


title: Time course 3, time point 36


title: Time course 3, time point 38


title: MP60_P1_McSC_A1_S1_quant


title: MP60_P1_McSC_A11_S11_quant


title: Cre control NK 2

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Reads were aligned to mm10 using STAR
Gene-wise counts were obtained using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: txt file of gene-wise counts

source_name: Sorted splenic NK cells

extract_protocol:
RNA isolation from sorted NK cells were extracted using a RNeasy Plus Mini Kit (QIAGEN), according to the manufacturer’s protocol.
Next-generation sequencing libraries were prepared with quality-controlled RNA samples (RIN > 7.0) from at least three biological replicates per genotype using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). cDNA libraries were pooled and subjected to 75 bp single end sequencing.

value: Spleen

value: NK

tag: cell markers

value: Cre control


title: Cre control NK 3


title: Cre control NK 1


title: Time course 3, time point 34


title: Hhex KO NK 4

value: Hhex KO


title: Time course 3, time point 40


title: Time course 3, time point 32


title: Time course 3, time point 28


title: Hhex KO NK 2


title: Hhex KO NK 3


title: Time course 3, time point 54


title: Time course 3, time point 44


title: Hhex KO NK 1


title: Time course 3, time point 26


title: MP60_P2_McSC_F8_S60_quant


title: Time course 3, time point 24


title: Sham2

city: Edison

first: Ashutosh

last: Dharap

state: NJ

address: 65 James st

department: Neuroscience

institute: HackensackMeridian Health JFK Medical Center

data_processing:
The sequencing reads were aligned to the mouse reference genome GRCm38 using HISAT2 (v2.0). StringTie (v1.3) was then used to assemble the transcripts of each sample independently using mouse transcript annotations from Ensembl 81 as a guide.StringTie and gffcompare was then used to merge all the assemblies to create a StringTie merged gtf. Finally, the mRNA profiling was done using StringTie and Differentially expressed mRNAs were identified using Rpackage Ballgown.
Genome_build: mm10
Supplementary_files_format_and_content: gtf files

source_name: Cerebral cortex

extract_protocol:
Animals were euthanized and the infarcted ipsilateral cortical tissues were immediately harvested and snap-frozen in liquid nitrogen before storing in -80°C. Total RNA was then isolated from the tissues using the mirVana total RNA isolation kit, followed by Dnase I tratment. The RNA integrity was evaluated using Bioanalyzer.
For  Negative control and Knockdown samples Poly(A) RNA sequencing, the library was prepared following Illumina’s truseq-stranded-mRNA sample preparation protocols. RNA integrity of total RNA sample received was checked using an Agilent Technologies 2100 Bioanalyzer.  The polyA containing mRNA molecules were purified using poly-T oligo attached magnetic beads and using two rounds of purification.  After purification the polyA RNA was fragmented using divalent cation containing buffer and elevated temperature. Quality control analysis and quantification of the DNA library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip.  Paired-end sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.For the Sham samples,previously generated data from our lab was used. Please refer to  GEO accession number GSE112348 for the relevant details regarding sham samples.

treatment_protocol: In order to understand the role of eRNAs in mediating the post-stroke pathophysiology in vivo, we knocked-down the expression of eRNA_06347 in the mouse brain using sequence-specific locked nucleic acid (LNA) antisense oligos delivered via the lateral ventricles. Cohorts of mice underwent either eRNA_06347 knockdown or  Negative control oligo treatment, followed by a 1 h  Middle cerebral arterey occlusion(MCAO) and 6 h of reperfusion (n=3/group). A sham cohort (n=3/group) receiving  undergoing sham surgery served as healthy controls.Transient focal ischemia was induced using the MCAO method. Mice were anesthetized with 5% isoflurane and a midline neck incision was made to expose the common  carotid artery (CCA). A nick was made in CCA and a 6-0 silicon-coated filament was inserted and advanced through the internal carotid artery up to the middle cerebral artery (MCA) and left in place for 1 h to occlude blood flow into the MCA. Cerebral blood flow and body tem- perature were continuously monitored. The incision was sutured and the animals were returned to warm cages for recovery. After 1 h of occlusion, the filament was removed, the incision was sutured, and the mice were returned to their cages. Reperfusion was allowed for 6 h. For the sham cohort, midline neck incision was similarly done to expose the ECA; however, no filament was inserted to occlude the MCA.

tag: gender

value: Male

value: 9-12 weeks

tag: treatment

value: sham surgery


title: Sham3


title: Sham1


title: Time course 3, time point 20


title: Cerebral cortex, Sham_H3K27Ac_ChIPSeq

data_processing:
processing of llumina base-call data and demultiplexing using bcl2fastq2(v2.20)
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Animals were euthanized and the infarcted ipsilateral cortical tissues were immediately harvested and snap-frozen in liquid nitrogen before storing in -80°C. Cortices from three separate animals were pooled for both the sham and the stroke groups and processed as follows:Brain tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield.An aliquot of chromatin (25 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against H3K27Ac (Active Motif, Cat. 39133, Lot 8). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.Quantitative PCR (QPCR) reactions were carried out in triplicate on specific genomic regions using SYBR Green Supermix (Bio-Rad).  The resulting signals were normalized for primer efficiency by carrying out QPCR for each primer pair using Input DNA.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: Transient focal ischemia was induced using the MCAO method. Mice were anesthetized with 5% isoflurane and a midline neck incision was made to expose the external carotid artery (ECA). A nick was made and a 6-0 silicon-coated filament was inserted and advanced through the internal carotid artery up to the middle cerebral artery (MCA) and left in place for 1 h to occlude blood flow into the MCA. Cerebral blood flow and body tem- perature were continuously monitored. The incision was sutured and the animals were returned to warm cages for recovery. After 1 h of occlusion, the filament was removed, the incision was sutured, and the mice were returned to their cages. Reperfusion was allowed for 6 h. For the sham cohort, midline neck incision was similarly done to expose the ECA; however, no filament was inserted to occlude the MCA.

tag: stress

value: sham

value: H3K27Ac (Active Motif, 39133, lot 8)

tag: tissue

value: Cerebral cortex


title: Time course 2, time point 62


title: Cerebral cortex, Stroke_H3K27Ac_ChIPSeq

value: stroke


title: Time course 2, time point 60


title: Time course 3, time point 22


title: Time course 2, time point 58


title: Cerebral cortex, Pooled_Input


title: Time course 2, time point 56


title: Rh36 cell xenograft_GR14_S16_GANT61+RITA treated

city: Huddinge

first: Ani

last: Azatyan

state: Stockholm

address: Hälsovägen 7C

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

data_processing:
Illumina bcl2fastq (v2.20.0) was used for basecalling and demultiplexing.
Read quality was checked for each sample using FastQC (v0.11.8).
Reads were aligned to Ensemble GRCh38 reference genome using STAR (v2.6.1d).
Read summarization to gene counts was performed using featureCounts (v1.5.1).
Normalized counts were generated using DESeq2 (v1.22.2).
Genome_build: GRCm38/mm10.
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts for each sample.

source_name: Human Embryonal Rhabdomyosarcoma cell line Rh36

growth_protocol: Human Embryonal Rhabdomyosarcoma Rh36 cells were cultured in RPMI-1640 medium with L-glutamine (Gibco, USA) and 10% FBS and MCF7 cells in DMEM (Sigma-Aldrich, USA) with 10% FBS, supplemented with 100 IU/ml penicillin/Streptomycin (Sigma-Aldrich, USA) and maintained in a 5% CO2 humidified incubator at 37 °C. 3 × 10^6 Rh36 cells in suspension were mixed with equal volume (1/1 ratio) of Matrigel (#356234, Corning, USA) and were injected subcutaneously into the right flank of immunodeficient nude mice (female 5–6 week old, NMRI-nu/nu, Scanbur, Denmark), n=44.

extract_protocol:
4 tumor samples were selected from each treatment group (16 samples in total), and total RNA extracted from each sample was isolated with E.Z.N.A. total RNA kit I (#R6834-02, Omega Bio-tek, USA) according to the manufacturer's instructions. For RNA isolation from tumor samples, small pieces of tumors (20–40 mg) were homogenized by Qiagen TissueRuptor (Germany) and proceeded further according to the manufacturer's instructions.
≈100 ng of total RNA was used to generate stranded mRNA libraries with the TruSeq®Stranded mRNA Low Throughput Sample Preparation kit according to manufacturer's instructions (#15031047, Illumina, USA). The concentration and quality of the cDNA libraries were assessed by Qubit (Life Technologies, USA) and TapeStation, respectively.

treatment_protocol: RITA was purchased from Santa Cruz Biotechnology (#sc-202753, USA) or obtained from NCI (USA), GANT61 was a kind gift of Rune Toftgård (Karolinska Institutet, Stockholm, Sweden). At palpable xenograft tumor size, volume ≥0.150 mL, animals were randomized to receive RITA (dissolved in 100% DMSO and administered by intraperitoneal injection at a dose of 10 mg/kg in 100–140 μL PBS solution), GANT61 (dissolved in 70% ethanol and administered by oral gavage feeding at a dose of 75 mg/kg in 200–300 μL glucose solution), combination treatment of 10 mg/kg RITA (intraperitoneal injection) and 75 mg/kg GANT61 (oral gavage feeding) or no treatment (control). Tumors were measured daily and tumor volume was calculated as V = (tumor width)2 x (tumor length) x 0.44. In this study, mice received daily treatments of RITA or/and GANT61 for 20 consecutive days and then sacrificed.

tag: sample type

value: Rhabdomyosarcoma cell line Rh36 mouse xenograft tumor

tag: mouse strain

value: NMRI-nu/nu mouse strain

value: GANT61+RITA treated


title: Time course 3, time point 30

tag: genotype


title: Rh36 cell xenograft_GR30_S15_GANT61+RITA treated


title: Time course 2, time point 54


title: Rh36 cell xenograft_GR26_S14_GANT61+RITA treated


title: Rh36 cell xenograft_GR22_S13_GANT61+RITA treated


title: Rh36 cell xenograft_R31_S12_RITA treated

value: RITA treated


title: Rh36 cell xenograft_R17_S11_RITA treated


title: Rh36 cell xenograft_R25_S10_RITA treated


title: Time course 2, time point 50


title: Time course 2, time point 48


title: Time course 3, time point 16


title: Time course 3, time point 18


title: Time course 2, time point 46


title: Time course 2, time point 44


title: Rh36 cell xenograft_R42_S9_RITA treated


title: Rh36 cell xenograft_G16_S8_GANT61 treated

value: GANT61 treated


title: Time course 2, time point 42

value: M-CSF Differentiated Bone Marrow Derived Macrophages


title: Time course 2, time point 40


title: Rh36 cell xenograft_G44_S6_GANT61 treated


title: Rh36 cell xenograft_C1_S2_control

value: control


title: Time course 2, time point 52


title: Time course 2, time point 38


title: Time course 2, time point 32


title: Time course 2, time point 30


title: Time course 2, time point 36


title: Rh36 cell xenograft_G21_S5_GANT61 treated


title: Rh36 cell xenograft_C32_S3_control


title: Rh36 cell xenograft_C40_S4_control


title: Time course 2, time point 34


title: Time course 2, time point 22


title: Rh36 cell xenograft_C38_S1_control


title: Time course 2, time point 20


title: Time course 2, time point 28


title: Time course 2, time point 26


title: Time course 2, time point 24


title: Target rep3

city: Hatay

first: Ceyhun

last: Bereketoglu

address: Iskenderun Technical University Main Campus, Iskenderun

department: Biomedical Engineering

country: Turkey

institute: Iskenderun Technical University

description: Gene expression data from yeast RNA

data_processing:
RNA-Seq data was analyzed using Partek Genomic Flow software (Partek).
The raw data files were first analyzed for sequence quality using pre-alignment QA/QC.
The reads were then aligned to the S. cerevisiae genome (R64-1-1) using STAR 2.5.3a aligner index.
Genome assembly and annotation files were obtained from Ensembl genome browser.
The generated counts were normalized using counts per million (CPM) method and the differentially regulated genes were identified using differential gene expression (GSA) algorithm.
Gene ontology (GO) enrichment anaylsis was performed to determine GO terms. For pathway analysis KEGG pathway database was used. False discovery rate (FDR) was set to 0.05, p value to 0.05 and fold change +/- 1.5 fold.
Genome_build: R64-1-1
Supplementary_files_format_and_content: xlsx file includes differentially expressed genes, GO terms and pathways

organism: Saccharomyces cerevisiae

source_name: Target, yeast cells

growth_protocol: YPD broth was inoculated with 1% of yeast pre-culture and incubated at 30⁰C, 180 RPM in incubator shaker

extract_protocol:
Extraction of total RNA was performed with RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. 1μg of total RNA was used for RNA-seq analysis.Libraries for RNA-Seq were prepared using the following procedure. At first, poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. After purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR amplification. Then the PCR yield was quantified by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for further data analysis. For this step, the BGISEQ-500 platform was combined the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Cultures at the beginning of incubation were treated with 2 mg/L NP prepared in ethanol while controls were treated with the same volume of ethanol for 22 h.  At the end of 22 hour of exposure, 1 mL sample was taken from each of the cultures, centrifuged, and supernatants were discarded. The precipitated cells were suspended in 1 mL of liquid YPD medium. This process was repeated three times to remove possible NP residuals. After the washing procedure, suspended cells were transferred to the new 100 mL YPD in 500 mL flasks and NP was added to the cultures to reach the above mentioned final concentrations of NP,  and the second round of the exposure was initiated. The long-term exposure was performed for 40 rounds by repeating the above steps.

value: 2 mg/L NP


title: Time course 2, time point 18


title: MEP1+Metformin

city: Birmingham

first: Charles

middle: O

last: Elson

state: Alabama

address: 1825 University Blvd

department: Gastroenterology - Medicine

institute: University of Alabama at Birmingham

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample; Unique gene hit counts

source_name: CBir1 TCR Tg CD4+ T cells

extract_protocol:
Remaining donor-derived CBir1 TCR Tg CD4+ cells in the spleen were sorted with BD FACSAria and stored in Trizol at -80C until RNA was extracted. RNA extraction, purification, library preparation were performed by Genewiz.
RNA libraries were prepared for sequencing using Ultra-low library preparation protocols at Genewiz.

treatment_protocol: C57BL/6.CD45.2 mice were transferred with 2x10^6 CBir1 TCR Tg.CD45.1.CD4+CD44- cells on Day0, followed with 50ug CBir1 flagellin plus 1ug CT i.p. immunization on Days1 and 7. On Days28 and 35, mice in treatment groups received 3ug MEP1 i.v., followed with i.p. injection of vehicle CMC, metformin+CMC, rapamycin+CMC, or the combination of both plus CMC for 5 consecutive days. Recipient mice in No treatment group received neither MEP1 or metabolic inhibitors at this period. On Day56, all recipient mice were chanllenged with 3ug MEP1 i.v.. Mice were sacrificed on Day63 for analyses.

value: spleen

value: CBir1 TCR Tg CD4+ T cells


title: Rh36 cell xenograft_G13_S7_GANT61 treated


title: MEP1+Metformin+Rapamycin


title: MEP1+CMC


title: No treatment

description: A-No-treatment

value: No treatment


title: 161088C_D-4

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

description: RNA from single cells

data_processing:
Transcripts from human donors were mapped to the reference genome (GRCh38) using Cell Ranger Version 3.0.2
Transcripts from mice were mapped to the reference genome (GRCm38/mm10) using Cell Ranger Version 2.0.1
Quality control of all data sets was performed using Seurat (Version 3.0.0)
Processed files were analyzed with Seurat V3.1.0, Monocle V2.10.1, scEpath V1 and Velocyto.R V0.6.
Genome_build: mm10
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output

source_name: Dorsal skin epidermis

growth_protocol: N/A. Primary cells were used in this study.

extract_protocol:
Human: Human EMPD (Patient ID; n=1) and normal skin (Patient ID; n=1; normal skin constitutes site adjacent to EMPD lesion). Samples were surgically excised and placed in tissue storage solution (MACS). Samples were processed for single cell isolation within 10 hours post-surgery. Excess subcutaneous adipose and dermal tissues were excised. Samples were cut into pieces with a maximum diameter of 4 mm. Skin specimens were then washed twice with cold 1X PBS. Single cells were isolated using the human epidermis isolation kit (MACS) as per manufacturer’s instructions with minor modifications. Mouse: Skin epidermal cells were collected from DTG (n=1) and control (n=1) newborn mice (post-natal day 0.5) 5 days after Doxycycline treatment. Mice were euthanized, and consecutively immersed in 70% ethanol and cold 1X PBS twice for 3 minutes. Fore and hind limbs and tail were cut off and skin was peeled along the ventral midline axis with blunt tweezers. Subcutaneous adipose tissue was micro-dissected. 12 mm skin biopsies were laid on EpiLife CF basal media (STEM CELL) droplets (300 μL) on a 12-well plate with skin dermis side down. 2 ml (2.5 U/mL) Dispase solution (STEM CELL)  was added to skin and incubated at 4℃ for 12 hrs. Epidermis was separated from dermis with two sharp tweezers and placed on Accutase (ThermoFisher) droplets (500 μL) for 30 min (dermis side down) at RT to create single cell suspensions.
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v2 chemistry (mouse samples) and Single Cell 3' v3 chemistry (human samples). Cell capture, library preparation, quality control, and sequencing was performed at Beijing CapitalBio Technology (Beijing, China).
Single Cell 3’ v2 chemistry (mouse samples) - 10X Genomics

value: Msi1-overexpressing dorsal skin

value: Newborn mouse


title: MEP1+Rapamycin


title: 161088C_D-1

description: RNA from single cells

treatment_protocol: N/A. Primary cells were used in this study.


title: CBir1 TCR Tg naïve CD4 control

value: naïve CD4 control


title: Time course 2, time point 16


title: Time course 1, time point 62


title: 161088C_D-3

description: RNA from single cells


title: Target rep2

description: Gene expression data from yeast RNA


title: MP60_P1_McSC_D3_S39_quant

value: quiescent melanocyte stem cell

value: male

value: 2nd telogen

value: Dct-eGFP+ (CD1/C57Bl6J mix)

value: Dct-eGFP+, integrin α6medium-low, dump (CD31, CD45, CD140a)-, Sca1-, and CD34-


title: Time course 1, time point 60


title: S10_S2

tag: ptid

tag: timepoint

value: Cerdulatinib

value: skin

tag: disease state

value: Lesional

tag: patient diagnosis

value: Mild-to-Moderate Atopic Dermatitis


title: 161088C_D-2

description: RNA from single cells

tag: age


title: Time course 1, time point 58

value: M-CSF Differentiated Bone Marrow Derived Macrophages


title: Control rep2

description: Gene expression data from yeast RNA

source_name: Control, yeast cells

value: control


title: 161088C_C-2

description: mRNA from single cells

value: Control dorsal skin


title: 161088C_C-3

description: mRNA from single cells


title: Control rep1

description: Gene expression data from yeast RNA


title: 161088C_C-1

description: mRNA from single cells


title: Time course 1, time point 56


title: Control rep3

description: Gene expression data from yeast RNA


title: Sample T7 technical replicate c

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: Tolerant rat, sample T7 technical replicate c

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.0-beta5. Before mapping, reads ≤40 bases were removed, and reads with  quality mean ≤30 were discarded. Reads were then aligned against the Rattus norvegicus genome (rnor6 genome assembly from Ensembl version 84) using the STAR mapper (version 2.4.0k, with --outSAMunmapped Within parameter). Alignments from reads matching more than once on the genome were removed. Rattus norvegicus GFF3 genome annotation from from Ensembl version 84 was used to compute gene expression. All overlapping regions between alignments and referenced exons were counted with HTSeq-count 0.5.3.
Genome_build: rnor6 version Ensembl 84
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

organism: Rattus norvegicus

source_name: Dorsal striatum

extract_protocol:
Total RNA was extracted from bilateral nucleus accumbens and caudate putamen with RNeasy Qiagen mini kit according to the lipid tissue protocol of the manufacturer (Qiagen, Courtaboeuf, France)
Messenger (polyA+) RNAs were purified from 500 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina)

tag: genetic background

value: Sprague-Dawley

value: 15 cocaine injections


title: Target rep1

description: Gene expression data from yeast RNA

tag: strain

value: 2 mg/L NP


title: Sample T7 technical replicate d

description: Tolerant rat, sample T7 technical replicate d


title: Time course 1, time point 54


title: Time course 1, time point 52


title: Sample T7 technical replicate a

description: Tolerant rat, sample T7 technical replicate a


title: Sample T6 technical replicate d

description: Tolerant rat, sample T6 technical replicate d


title: Sample T7 technical replicate b

description: Tolerant rat, sample T7 technical replicate b


title: 161088C_C-4

description: mRNA from single cells

value: Newborn mouse


title: TM22A-CC-A647Pos

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415 Curie Boulevard

institute: University of Pennsylvania

description:
processed data file:
WM989_timeMachineSort_TPMdata.csv
meltedData_TM22A.tsv

data_processing:
bcl2fastq conversion performed on BaseSpace using Illumina's default generate fastq workflow
Aligned to hg19 using STAR version 2.5.2a with default parameters
Filtered uniquely mapped reads using ngsutils/bamutils
Sorted using samtools-0.1.19
enumerated read counts per gene using HTseq-0.6.1 in union mode
normalized by sequencing depth and gene length using custom R script
Genome_build: aligned to hg19, ensembl GRCh37.75 gtf used for gene annotations
Supplementary_files_format_and_content:
tsv files contain gene level RNA-seq counts generated using HTSeq with GRCh37.75 gene annotations. csv files contain RPM, RPKM, and TPM normalized counts as well as basic gene annotations (e.g. protein-coding, etc, lincRNA, rRNA etc.).
meltedData_TM13_TM16.tsv: HTSeq counts. For WM989 and WM983b samples (1 biological replicate each)
meltedData_TM21B.tsv: HTSeq counts. For WM983b samples (2nd biological replicate)
meltedData_TM22A.tsv: HTSeq counts. For WM989 samples (2nd biological replicate)
WM989_timeMachineSort_TPMdata.csv: Normalized counts for WM989 samples
WM983b_timeMachineSort_TPMdata.csv: Normalized counts for WM983b samples

molecule: polyA RNA

source_name: WM989 A6-G3 melanoma

growth_protocol: Grown in TU2% media

extract_protocol:
RNA extracted using Macharey-Nagel Nucleospin total RNA FFPE XS kit
NEBNext single cell/low input RNA library prep kit for illumina
mRNA-seq, poly-dT primed RT, unstranded.

treatment_protocol: When indicated, treated with 1 micromolar PLX4032 for 3-4 weeks

tag: cell line

value: clonal melanoma cell line

tag: clone

tag: experiment name (replicate)

tag: technical replicate


title: TM22A-PLX-GFPPos

tag: cell type

tag: treatment

value: 1 micromolar PLX4032 for 3 weeks


title: Sample T6 technical replicate c

description: Tolerant rat, sample T6 technical replicate c


title: TM22A-PLX-A647Pos


title: TM22A-CC-A647Neg3


title: Time course 1, time point 50


title: Sample T6 technical replicate b

description: Tolerant rat, sample T6 technical replicate b


title: Sample T6 technical replicate a

description: Tolerant rat, sample T6 technical replicate a


title: Sample T5 technical replicate d

description: Tolerant rat, sample T5 technical replicate d


title: Sample T5 technical replicate c

description: Tolerant rat, sample T5 technical replicate c


title: Time course 1, time point 46


title: TM22A-CC-A647Neg2


title: Sample T5 technical replicate b

description: Tolerant rat, sample T5 technical replicate b


title: Time course 1, time point 42


title: TM22A-CC-A647Neg1


title: Control AtHMGB15_2

type: genomic

city: Kolkata

first: Shubho

last: Chaudhuri

state: West Bengal

address: P1/12 C.I.T Scheme VII M

country: India

institute: Bose Institute

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The value is log e R normalized using blank substraction and Lowess

organism: Arabidopsis thaliana

source_name: AtHMGB15 ChIP DNA from 22 days old control seedlings

label_protocol: not provided

growth_protocol: Arabidopsis col 0 lines were grown on MS medium for 22 days at 22C under long day conditions.

extract_protocol: 2gms tissue was fixed with 1% formaldehyde for 15 min at room temperature followed by quenching with 150mM glycine for 10 min. The tissue was washed twice with water and frozen in liquid nitrogen. The tissue was crushed, and nuclei was isolated from control and 2hrs cold stress treated seedlings using Plant Nuclei Isolation/Extraction kit (Cell Lytic TM PN) (Sigma-Aldrich) as per manufacturer’s protocol. The crosslinked chromatin was sheared to an average size of 500 bp by fifteen 30-second pulses using a Biorupter sonicator (Diagenode). The lysate was then centrifuged to remove cell debris and the chromatin was diluted in dilution buffer (1.1% Triton X-100, 1.2 mM EDTA ,16.7 mM Tris pH8.10, 167 mM NaCl). The chromatin supernatant was then incubated overnight with purified antibody at 4C. After incubation with Magna chip beads (30 µl) for 2h at 4C, the immune complexes were collected using a magnetic rack and washed with the following buffers each for 10 min at 4C; Low  salt buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 500 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C. The chromatin was then de-crosslinked with NaCl at 65°C overnight. Phenol-chloroform extraction was used to purify the chromatin following a proteinase K treatment.

tag: tissue

value: 22 days old seedlings

tag: chip antibody

source_name: Arabidopsis Input DNA from 22 days old cold seedlings

value: None, input DNA_2


title: Time course 1, time point 44


title: Sample A7 technical replicate d

description: Acute response rat, sample A7 technical replicate d

value: 13 physiological serum injections + 3 cocaine injections


title: TM21B-PLX-GFPPos

description:
processed data file:
WM983b_timeMachineSort_TPMdata.csv
meltedData_TM21B.tsv

source_name: WM983b E9-C6 melanoma


title: Sample A5 technical replicate d

description: Acute response rat, sample A5 technical replicate d


title: TM21B-CC-A647Neg2


title: Time course 1, time point 48


title: Time course 1, time point 40


title: Sample A6 technical replicate d

description: Acute response rat, sample A6 technical replicate d


title: Sample A6 technical replicate b

description: Acute response rat, sample A6 technical replicate b


title: Sample A7 technical replicate a

description: Acute response rat, sample A7 technical replicate a


title: Sample A5 technical replicate c

description: Acute response rat, sample A5 technical replicate c


title: Time course 1, time point 34


title: Sample A7 technical replicate c

description: Acute response rat, sample A7 technical replicate c


title: Sample A6 technical replicate c

description: Acute response rat, sample A6 technical replicate c


title: TM21B-CC-A647Pos


title: Time course 1, time point 38


title: Cold 2hrs AtHMGB15_2

source_name: AtHMGB15 ChIP DNA from 22 days old cold stressed seedlings

treatment_protocol: 22 days old plants were incubated at 4C for 2 hrs prior to harvesting in liquid nitrogen

source_name: Arabidopsis Input DNA from 22 days old control stressed seedlings


title: TM21B-CC-A647Neg3


title: Sample T5 technical replicate a

description: Tolerant rat, sample T5 technical replicate a


title: Time course 1, time point 36


title: Sample A6 technical replicate a

description: Acute response rat, sample A6 technical replicate a


title: Sample A5 technical replicate b

description: Acute response rat, sample A5 technical replicate b


title: Sample S7 technical replicate d

description: Saline rat, sample S7 technical replicate d

value: 15 physiological serum injections


title: TM21B-CC-A647Neg1


title: Time course 1, time point 32


title: Sample S7 technical replicate a

description: Saline rat, sample S7 technical replicate a


title: Sample S7 technical replicate b

description: Saline rat, sample S7 technical replicate b


title: TM16-1uMA-PLX-barcodePos

description:
processed data file:
WM989_timeMachineSort_TPMdata.csv
meltedData_TM13_TM16.tsv


title: Sample S6 technical replicate c

description: Saline rat, sample S6 technical replicate c


title: Time course 1, time point 30


title: Sample A7 technical replicate b

description: Acute response rat, sample A7 technical replicate b


title: Time course 1, time point 28


title: Sample S6 technical replicate d

description: Saline rat, sample S6 technical replicate d


title: TM16-1uMA-CarbonCopy-barcodeNeg2


title: Sample A5 technical replicate a

description: Acute response rat, sample A5 technical replicate a


title: Sample S5 technical replicate b

description: Saline rat, sample S5 technical replicate b


title: Sample S5 technical replicate a

description: Saline rat, sample S5 technical replicate a


title: TM16-1uMA-CarbonCopy-barcodePos


title: Sample S6 technical replicate a

description: Saline rat, sample S6 technical replicate a


title: TM16-1uMA-CarbonCopy-barcodeNeg1


title: TM16-1uMA-PLX-barcodeNeg


title: Control AtHMGB15_1

value: None, input DNA_1


title: TM13-PLX-barcodePos

description:
processed data file:
WM983b_timeMachineSort_TPMdata.csv
meltedData_TM13_TM16.tsv


title: Cold 2hrs AtHMGB15_1


title: Time course 1, time point 22


title: Sample S7 technical replicate c

description: Saline rat, sample S7 technical replicate c


title: TM13-PLX-barcodeNeg2


title: Sample A3 technical replicate b

description: Acute response rat 3 technical replicate b

data_processing:
Illumina bcl2fastq 2.17.1.14 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.0-beta4. Before mapping, reads ≤40 bases were removed, and reads with  quality mean ≤30 were discarded. Reads were then aligned against the Rattus norvegicus genome (rnor6 genome assembly from Ensembl version 84) using the STAR mapper (version 2.4.0k, with --outSAMunmapped Within parameter). Alignments from reads matching more than once on the genome were removed. Rattus norvegicus GFF3 genome annotation from from Ensembl version 84 was used to compute gene expression. All overlapping regions between alignments and referenced exons were counted with HTSeq-count 0.5.3.
Genome_build: rnor6 version Ensembl 84
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

source_name: Nucleus accumbens

tag: phenotype

value: Saline Rat


title: Sample A3 technical replicate c

description: Acute response rat 3 technical replicate c


title: Sample S6 technical replicate b

description: Saline rat, sample S6 technical replicate b


title: Time course 1, time point 18

tag: genotype


title: TM13-CarbonCopy-barcodePos


title: Sample A3 technical replicate d

description: Acute response rat 3 technical replicate d


title: Time course 1, time point 26


title: Time course 1, time point 24


title: TM13-PLX-barcodeNeg1


title: Time course 1, time point 16


title: Time course 1, time point 20


title: Sample S5 technical replicate c

description: Saline rat, sample S5 technical replicate c


title: Sample S5 technical replicate d

description: Saline rat, sample S5 technical replicate d


title: TM13-CarbonCopy-barcodeNeg1


title: TM27-Dot1Li-PLX-Independent

description:
processed data file:
WM989_timeMachineSort_Dot1Li_TPMdata.csv
meltedData_TM27.tsv

data_processing:
bcl2fastq conversion performed on BaseSpace using Illumina's default generate fastq workflow
Aligned to hg19 using STAR version 2.5.2a with default parameters
Filtered uniquely mapped reads using ngsutils/bamutils
Sorted using samtools-0.1.19
enumerated read counts per gene using HTseq-0.6.1 in union mode
normalized by sequencing depth and gene length using custom R script
Genome_build: aligned to hg19, ensembl GRCh37.75 gtf used for gene annotations
Supplementary_files_format_and_content: tsv files contain gene level RNA-seq counts generated using HTSeq with GRCh37.75 gene annotations. csv files contain RPM, RPKM, and TPM normalized counts as well as basic gene annotations (e.g. protein-coding, etc, lincRNA, rRNA etc.).

treatment_protocol: When indicated, treated with 4 micromolar pinometostat or equal concentration DMSO for 5 days (replacing media with drug on day 3). When indicated, treated with 1 micromolar PLX4032 for 3 weeks (replacing media with drug every ~ 3 days).

tag: clone id

value: 4 micromolar pinometostat for 5 days then 1 micromolar PLX4032 for 3 weeks


title: TM13-CarbonCopy-barcodeNeg3


title: Sample A1 technical replicate c

description: Acute response rat 1 technical replicate c


title: Sample A1 technical replicate b

description: Acute response rat 1 technical replicate b


title: Sample A2 technical replicate a

description: Acute response rat 2 technical replicate a


title: Sample A1 technical replicate d

description: Acute response rat 1 technical replicate d


title: Sample T3 technical replicate c

description: Tolerant rat 3 technical replicate c

value: Vulnerable Rat


title: Sample A2 technical replicate b

description: Acute response rat 2 technical replicate b


title: Sample T3 technical replicate b

description: Tolerant rat 3 technical replicate b


title: Sample A1 technical replicate a

description: Acute response rat 1 technical replicate a


title: Sample A3 technical replicate a

description: Acute response rat 3 technical replicate a


title: Sample A2 technical replicate d

description: Acute response rat 2 technical replicate d


title: Sample T2 technical replicate c

description: Tolerant rat 2 technical replicate c


title: TM13-CarbonCopy-barcodeNeg2

description:
processed data file:
WM983b_timeMachineSort_TPMdata.csv
meltedData_TM13_TM16.tsv


title: Sample T2 technical replicate d

description: Tolerant rat 2 technical replicate d


title: Sample T2 technical replicate b

description: Tolerant rat 2 technical replicate b


title: Sample A2 technical replicate c

description: Acute response rat 2 technical replicate c


title: IRF4-CUT&RUN resting Tcon rep2

city: Shanghai

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

country: China

institute: SJTU

data_processing:
Library strategy: CUT&RUN
Align ATAC-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ATAC-seq duplicates: Picard v1.141
Call ATAC-seq peaks: MACS2 v2.1.1
Align RNA-seq reads: STAR v2.5.0c
Remove RNA-seq duplicates: Picard v1.141
Count RNA-seq reads: GenomicAlignments v1.2.2
Align ChIP-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ChIP-seq duplicates: Picard v1.141
Call ChIP-seq peaks: MACS2 v2.1.1
Align CUT&RUN reads: STAR v2.5.0c [disable splicing alignment]
Remove CUT&RUN duplicates: Picard v1.141
Call CUT&RUN peaks: MACS2 v2.1.1
Genome_build: GRCm38 and CAST/EiJ
Supplementary_files_format_and_content: raw read count

extract_protocol:
Antibody targeted pA/G-MNase cleavage followed by Qiagen MinElute reaction cleanup
Kapa hyper prep kit

value: B6/Cast F1

value: CD44-CD62L+ Foxp3- CD4 T cells


title: cJun-CUT&RUN resting Tcon rep2


title: IRF4-CUT&RUN resting Treg rep2

value: CD44-CD62L+ Foxp3+ CD4 T cells


title: IRF4-CUT&RUN activated Treg rep1

value: CD44+CD62L- Foxp3+ CD4 T cells


title: IRF4-CUT&RUN resting Treg rep1


title: IRF4-CUT&RUN resting Tcon rep1


title: TM27-Dot1Li-PLX-Dependent


title: TM27-Dot1Li-CC-Neg-2

value: 4 micromolar pinometostat for 5 days


title: TM27-Dot1Li-PLX-GFP


title: Sample T2 technical replicate a

description: Tolerant rat 2 technical replicate a

value: Sprague-Dawley

value: 15 cocaine injections


title: Sample T3 technical replicate a

description: Tolerant rat 3 technical replicate a


title: cJun-CUT&RUN resting Tcon rep1


title: TM27-Dot1Li-CC-Neg-1

value: clonal melanoma cell line


title: TM27-Dot1Li-CC-Independent


title: cJun-CUT&RUN activated Treg rep2


title: Sample T1 technical replicate d

description: Tolerant rat 1 technical replicate d


title: cJun-CUT&RUN activated Treg rep1


title: Sample T1 technical replicate a

description: Tolerant rat 1 technical replicate a


title: TM27-Dot1Li-CC-Dependent


title: TM21B-PLX-A647Pos

description:
processed data file:
WM983b_timeMachineSort_TPMdata.csv
meltedData_TM21B.tsv

value: 1 micromolar PLX4032 for 3 weeks


title: Sample T1 technical replicate b

description: Tolerant rat 1 technical replicate b


title: Sample S3 technical replicate d

description: Saline rat 3 technical replicate d


title: Sample S3 technical replicate c

description: Saline rat 3 technical replicate c


title: cJun-CUT&RUN resting Treg rep2


title: IRF4-CUT&RUN activated Treg rep2


title: TM27-DMSO-PLX-GFP

value: DMSO 5 days then 1 micromolar PLX4032 for 3 weeks


title: Sample S3 technical replicate a

description: Saline rat 3 technical replicate a


title: Sample S2 technical replicate d

description: Saline rat 2 technical replicate d


title: TM27-DMSO-PLX-Dependent


title: cJun-CUT&RUN resting Treg rep1


title: Sample S2 technical replicate b

description: Saline rat 2 technical replicate b


title: Lef1-CUT&RUN activated Tcon rep2

value: CD44+CD62L- Foxp3- CD4 T cells


title: Lef1-CUT&RUN activated Tcon rep1


title: Sample T3 technical replicate d

description: Tolerant rat 3 technical replicate d


title: Sample S1 technical replicate d

description: Saline rat 1 technical replicate d


title: Sample S2 technical replicate a

description: Saline rat 2 technical replicate a


title: TM27-DMSO-CC-Neg-2

value: DMSO 5 days


title: TM27-DMSO-CC-Neg-1


title: TM27-DMSO-CC-Independent


title: Sample S1 technical replicate b

description: Saline rat 1 technical replicate b

value: 15 physiological serum injections


title: Sample T1 technical replicate c

description: Tolerant rat 1 technical replicate c


title: Sample S1 technical replicate a

description: Saline rat 1 technical replicate a


title: Lef1-CUT&RUN resting Tcon rep1


title: Lef1-CUT&RUN resting Tcon rep2


title: Lef1-CUT&RUN activated Treg rep2


title: Sample S3 technical replicate b

description: Saline rat 3 technical replicate b