title: Motoneuron_P8E10


title: MCRL_wk0_ATD_p1_B08_AE

status: Public on Feb 11 2022

type: SRA

city: Kensington

first: Jerome

last: Samir

state: NSW

address: Level 5, Wallace Wurth Building, High Street

department: IVPP

country: Australia

institute: Kirby Institute

library_source: transcriptomic

data_processing:
Illumina NextSeq was used
Sequenced paired-end reads were trimmed using Trimmomatic (v0.39) (using parameters:  LEADING = 3, TRAILING = 3, SLIDINGWINDOW = 4:10, MINLEN = 50), then aligned to the human reference genome (GRCh38) using STAR (v2.7.3a). Gene expression was then quantified at the counts and TPM level with RSEM (v1.3.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: .mtx.gz files contain matrices including raw counts, TPM and scaled TPM values for each sample and each gene.
Supplementary_files_format_and_content: .txt and and .tsv files contain tab delimited information on sample names and gene names (as per ordering in matrices), and gene annotation information.

molecule: total RNA

organism: Homo sapiens

source_name: CD8+ T cell

extract_protocol:
Single HCV-specific CD8+ T cells were sorted using flow cytometry, with RNA isolation and sequencing library construction performed according to the Smart-seq2 protocol.
Single cell RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject

value: CL-MCRL

tag: epitope

value: ATD

tag: dpi

tag: cell type

value: CD8+ T cell


title: Motoneuron_P8E11

city: Heidelberg

first: Jessica

last: Velten

address: Im Neuenheimer Feld 230

department: Centre for Organismal Studies

country: Germany

institute: University of Heidelberg

data_processing:
Adapter trimming, perl
Pseudoalignment, kallisto 0.43.0
Count tables, R 3.5.1/scater 1.10.1
Genome_build: Drosophila melanogaster, BDGP6 ensemble
Supplementary_files_format_and_content: Kallisto output (tsv)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Motoneuron

extract_protocol:
Collections of 19-20h old Drosophila embryos were collected and dissociated. Cells were stained with Dapi and DRAQ5 to exclude debris. Single cells were sorted into 96-well-plates in Smart-seq2 lysis buffer. Full-length cDNA from individual cells were produced following the SmartSeq2 protocol.
Smart-Seq2 (modified from Picelli et al., Nature Protocols 2014) Tagmentation using Homemade Tn5 (Hennig et al., G3 2018)

tag: population

value: Ok371>RFP+ DAPI- DRAQ5+


title: Motoneuron_P8E8


title: MCRL_wk0_ATD_p1_B04_AE


title: Motoneuron_P8F12


title: Motoneuron_P8E6


title: MCRL_wk0_ATD_p1_A04_AE


title: MCRL_wk0_ATD_p1_B07_AE


title: Motoneuron_P8E12


title: Motoneuron_P8F3


title: MCRL_wk0_ATD_p1_B05_AE


title: MCRL_scrn_ATD_p1_H07_AE


title: Motoneuron_P8E7


title: MCRL_wk0_ATD_p1_A10_AE


title: MCRL_wk0_ATD_p1_A01_AE


title: MCRL_scrn_ATD_p1_H05_AE


title: Motoneuron_P8E2


title: Motoneuron_P8E5


title: Motoneuron_P8D9


title: MCRL_scrn_ATD_p1_H02_AE


title: MCRL_scrn_ATD_p1_H04_AE


title: Motoneuron_P8D8


title: Motoneuron_P8D10


title: Motoneuron_P8D11


title: Motoneuron_P8E3


title: MCRL_scrn_ATD_p1_H03_AE


title: MCRL_scrn_ATD_p1_G08_AE


title: MCRL_scrn_ATD_p1_G07_AE


title: MCRL_scrn_ATD_p1_G05_AE


title: Motoneuron_P8D5


title: Motoneuron_P8C12


title: Motoneuron_P8C10


title: MCRL_scrn_ATD_p1_G04_AE


title: Motoneuron_P8C9


title: MCRL_scrn_ATD_p1_G03_AE


title: MCRL_scrn_ATD_p1_G02_AE


title: Motoneuron_P8C7


title: Motoneuron_P8C6


title: MCRL_scrn_ATD_p1_G01_AE


title: Motoneuron_P8C5


title: MCRL_scrn_ATD_p1_F08_AE


title: MCRL_scrn_ATD_p1_F07_AE


title: Motoneuron_P8C2


title: MCRL_wk0_ATD_p1_C09_AE


title: Motoneuron_P8D2


title: MCRL_scrn_ATD_p1_F06_AE


title: MCRL_scrn_ATD_p1_F05_AE


title: MCRL_scrn_ATD_p1_H01_AE


title: Motoneuron_P8B7


title: MCRL_scrn_ATD_p1_F04_AE


title: Motoneuron_P8B6


title: Motoneuron_P8B9


title: MCRL_scrn_ATD_p1_F01_AE


title: Motoneuron_P8B3


title: MCRL_scrn_ATD_p1_F02_AE


title: MCRL_scrn_ATD_p1_E05_AE


title: MCRL_scrn_ATD_p1_E08_AE


title: Motoneuron_P8B4


title: Motoneuron_P8B5


title: MCRL_scrn_ATD_p1_E07_AE


title: Motoneuron_P8B8


title: Motoneuron_P8B12


title: MCRL_scrn_ATD_p1_E06_AE


title: MCRL_scrn_ATD_p1_E04_AE


title: Motoneuron_P8A9


title: Motoneuron_P8B2


title: Motoneuron_P8A5


title: MCRL_scrn_ATD_p1_E03_AE


title: MCRL_scrn_ATD_p1_E01_AE


title: Motoneuron_P8A6


title: MCRL_scrn_ATD_p1_F03_AE


title: Motoneuron_P8A8


title: MCRL_scrn_ATD_p1_E02_AE


title: Motoneuron_P8A3


title: MCRL_scrn_ATD_p1_D08_AE


title: Motoneuron_P8A4


title: MCRL_scrn_ATD_p1_D06_AE


title: Motoneuron_P8A2


title: MCRL_scrn_ATD_p1_D07_AE


title: MCRL_scrn_ATD_p1_D04_AE


title: MCRL_scrn_ATD_p1_D05_AE


title: Motoneuron_P7G9


title: MCRL_scrn_ATD_p1_D03_AE


title: Motoneuron_P7G8


title: Motoneuron_P7F9


title: Motoneuron_P8A10


title: MCRL_scrn_ATD_p1_D02_AE


title: MCRL_scrn_ATD_p1_D01_AE


title: MCRL_scrn_ATD_p1_C08_AE


title: MCRL_scrn_ATD_p1_C05_AE


title: Motoneuron_P7E10


title: MCRL_scrn_ATD_p1_C07_AE


title: Motoneuron_P7E9


title: MCRL_scrn_ATD_p1_C02_AE


title: Motoneuron_P7E8


title: Motoneuron_P7G10


title: MCRL_scrn_ATD_p1_BULK_G06_AE


title: Motoneuron_P7D4


title: Motoneuron_P7E6


title: MCRL_scrn_ATD_p1_B07_AE


title: Motoneuron_P7D9


title: MCRL_scrn_ATD_p1_C01_AE


title: Motoneuron_P7D7


title: Motoneuron_P7D6


title: Motoneuron_P7B10


title: Motoneuron_P7E11


title: Motoneuron_P7B9


title: MCRL_scrn_ATD_p1_B06_AE


title: MCRL_scrn_ATD_p1_B05_AE


title: MCRL_scrn_ATD_p1_B04_AE


title: Motoneuron_P7A8


title: MCRL_scrn_ATD_p1_C06_AE


title: MCRL_scrn_ATD_p1_C03_AE


title: Motoneuron_P12H7


title: Motoneuron_P12H6


title: MCRL_wk0_ATD_p1_F10_AE


title: Motoneuron_P7C3


title: MCRL_scrn_ATD_p1_B02_AE


title: MCRL_scrn_ATD_p1_B01_AE


title: Motoneuron_P12H3


title: MCRL_scrn_ATD_p1_A08_AE


title: Motoneuron_P12H4


title: Motoneuron_P12H2


title: MCRL_scrn_ATD_p1_A04_AE


title: Motoneuron_P12H5


title: Motoneuron_P12H1


title: Motoneuron_P12G12


title: MCRL_scrn_ATD_p1_A03_AE


title: MCRL_scrn_ATD_p1_A05_AE


title: MCRL_scrn_ATD_p1_A06_AE


title: Motoneuron_P12G8


title: Motoneuron_P12G9


title: MCRL_scrn_ATD_p1_A01_AE


title: Motoneuron_P12G7


title: MCRL_scrn_ATD_p1_B03_AE


title: Motoneuron_P12G6


title: Motoneuron_P12G3


title: Motoneuron_P12G5


title: Motoneuron_P12G2


title: Motoneuron_P12G4


title: Motoneuron_P12F12


title: MCRL_scrn_ATD_p1_A02_AE


title: Motoneuron_P12G1


title: Motoneuron_P12F11


title: Motoneuron_P12F8


title: 3023_wk24_CIN_p1_F07_CC

value: CIN


title: 3023_wk24_CIN_p1_G07_CC


title: Motoneuron_P12F10


title: Motoneuron_P12F7


title: Motoneuron_P12F9


title: 3023_wk24_CIN_p1_A08_CC


title: Motoneuron_P12F5


title: 3023_wk24_CIN_p1_G06_CC


title: 3023_wk24_CIN_p1_D07_CC


title: 3023_wk24_CIN_p1_A05_CC


title: 3023_wk24_CIN_p1_F06_CC


title: 3023_wk24_CIN_p1_B05_CC


title: 3023_wk24_CIN_p1_G04_CC


title: 3023_wk24_CIN_p1_F04_CC


title: 3023_wk24_CIN_p1_B07_CC


title: Motoneuron_P12F4


title: 3023_wk24_CIN_p1_F05_CC


title: 3023_wk24_CIN_p1_H06_CC


title: 3023_wk24_CIN_p1_A06_CC


title: 3023_wk24_CIN_p1_H04_CC


title: 3023_wk24_CIN_p1_D04_CC


title: 3023_wk24_CIN_p1_H03_CC


title: Motoneuron_P12E12


title: Motoneuron_P12E11


title: Motoneuron_P12E10


title: 3023_wk24_CIN_p1_B03_CC


title: Motoneuron_P12E9


title: Motoneuron_P12F6


title: Motoneuron_P12E8


title: 3023_wk24_CIN_p1_H02_CC


title: 3023_wk24_CIN_p1_G02_CC


title: Motoneuron_P12E6


title: 3023_wk24_CIN_p1_G01_CC


title: Motoneuron_P12E5


title: 3023_wk24_CIN_p1_F02_CC


title: Motoneuron_P12E1


title: Motoneuron_P12E3


title: Motoneuron_P12D11


title: 3023_wk24_CIN_p1_B02_CC


title: Motoneuron_P12F3


title: 3023_wk24_CIN_p1_A02_CC


title: 3023_wk24_CIN_p1_F01_CC


title: 3023_wk24_CIN_p1_H01_CC


title: 3023_wk24_CIN_p1_E02_CC


title: 3023_wk24_CIN_p1_C03_CC


title: 3023_wk24_CIN_p1_F03_CC


title: Motoneuron_P12E2


title: 3023_wk24_CIN_p1_D01_CC


title: 3023_wk24_CIN_p1_C01_CC


title: Motoneuron_P12E7


title: Motoneuron_P12D8


title: Motoneuron_P12D9


title: 3023_wk24_CIN_p1_A03_CC


title: 3023_wk24_CIN_p1_E01_CC


title: 3023_wk24_CIN_p1_A01_CC


title: Motoneuron_P12D3


title: Motoneuron_P12E4


title: 3023_wk12_CIN_p1_H11_CC


title: Motoneuron_P12D6


title: Motoneuron_P12D2


title: Motoneuron_P12D10


title: 3023_wk12_CIN_p1_G11_CC


title: 3023_wk12_CIN_p1_E11_CC


title: Motoneuron_P12C11


title: 3023_wk12_CIN_p1_D11_CC


title: Motoneuron_P12C9


title: 3023_wk12_CIN_p1_F11_CC


title: Motoneuron_P12C8


title: 3023_wk12_CIN_p1_B11_CC


title: 3023_wk12_CIN_p1_C11_CC


title: 3023_wk12_CIN_p1_A11_CC


title: 3023_wk24_CIN_p1_B01_CC


title: Motoneuron_P12C6


title: Motoneuron_P12D7


title: Motoneuron_P12C7


title: 3023_wk24_CIN_p1_H05_CC


title: Motoneuron_P12C4


title: Motoneuron_P12C5


title: 3023_wk12_CIN_p1_F08_CC


title: Motoneuron_P12C3


title: 3023_wk12_CIN_p1_E08_CC


title: Motoneuron_P12D1


title: 3023_wk24_CIN_p1_G05_CC


title: 3023_wk12_CIN_p1_F10_CC


title: Motoneuron_P12C2


title: Motoneuron_P12C1


title: 3023_wk12_CIN_p1_D08_CC


title: Motoneuron_P12B6


title: 3023_wk12_CIN_p1_D07_CC


title: 3023_wk12_CIN_p1_F07_CC


title: 3023_wk12_CIN_p1_E10_CC


title: 3023_wk12_CIN_p1_C07_CC


title: Motoneuron_P12B5


title: 3023_wk12_CIN_p1_D10_CC


title: Motoneuron_P12A10


title: Motoneuron_P12A11


title: Motoneuron_P12B4


title: Motoneuron_P12B8


title: 3023_wk12_CIN_p1_C10_CC


title: 3023_wk12_CIN_p1_F06_CC


title: Motoneuron_P12A9


title: 3023_wk12_CIN_p1_D06_CC


title: 3023_wk12_CIN_p1_C06_CC


title: 3023_wk12_CIN_p1_E06_CC


title: Motoneuron_P12C10


title: 3023_wk12_CIN_p1_B10_CC


title: Motoneuron_P12A7


title: Motoneuron_P12A5


title: Motoneuron_P12A6


title: 3023_wk12_CIN_p1_E07_CC


title: Motoneuron_P12B11


title: 3023_wk12_CIN_p1_A10_CC


title: 3221_12m1_GPR_p1_H05_CC

value: GPR


title: Motoneuron_P12A3


title: Motoneuron_P11H9


title: 3221_12m1_GPR_p1_G05_CC


title: 3023_wk12_CIN_p1_F05_CC


title: Motoneuron_P12A2


title: Motoneuron_P11H4


title: 3221_12m1_GPR_p1_C05_CC


title: 3221_12m1_GPR_p1_F05_CC


title: Motoneuron_P12B2


title: Motoneuron_P11H3


title: 3221_12m1_GPR_p1_A05_CC


title: Motoneuron_P11G12


title: 3221_12m1_GPR_p1_B05_CC


title: Motoneuron_P12A8


title: Motoneuron_P11G11


title: Motoneuron_P11H2


title: 3023_wk12_CIN_p1_E05_CC


title: Motoneuron_P11G6


title: Motoneuron_P11G7


title: 3221_12m1_GPR_p1_G04_CC


title: Motoneuron_P11G5


title: 3221_12m1_GPR_p1_F04_CC


title: Motoneuron_P11G4


title: Motoneuron_P12A4


title: 3221_12m1_GPR_p1_C04_CC


title: Motoneuron_P11G3


title: Motoneuron_P11G2


title: 3221_12m1_GPR_p1_H03_CC


title: 3221_12m1_GPR_p1_B04_CC


title: 3221_12m1_GPR_p1_G03_CC


title: Motoneuron_P11G1


title: 3221_12m1_GPR_p1_F03_CC


title: 3221_12m1_GPR_p1_A04_CC


title: 3221_12m1_GPR_p1_E03_CC


title: Motoneuron_P11F8


title: Motoneuron_P11F10


title: 3221_12m1_GPR_p1_H04_CC


title: Motoneuron_P11F12


title: 3221_12m1_GPR_p1_C03_CC


title: Motoneuron_P11F9


title: Motoneuron_P11F3


title: 3023_wk12_CIN_p1_D05_CC


title: 3221_12m1_GPR_p1_E04_CC


title: Motoneuron_P11F7


title: 3221_12m1_GPR_p1_E05_CC


title: 3221_12m1_GPR_p1_A03_CC


title: Motoneuron_P11F2


title: 3221_12m1_GPR_p1_B03_CC


title: Motoneuron_P11E12


title: 3221_12m1_GPR_p1_G02_CC


title: Motoneuron_P11E10


title: 3221_12m1_GPR_p1_E02_CC


title: Motoneuron_P11F11


title: Motoneuron_P11E6


title: Motoneuron_P11G10


title: 3221_12m1_GPR_p1_B02_CC


title: 3221_12m1_GPR_p1_C02_CC


title: 3221_12m1_GPR_p1_H01_CC


title: 3023_wk12_CIN_p1_C05_CC


title: Motoneuron_P11E2


title: Motoneuron_P11E3


title: 3221_12m1_GPR_p1_G01_CC


title: Motoneuron_P11E5


title: Motoneuron_P11E1


title: 3221_12m1_GPR_p1_F01_CC


title: 3221_12m1_GPR_p1_C01_CC


title: 3221_12m1_GPR_p1_H02_CC


title: 3221_12m1_GPR_p1_E01_CC


title: Motoneuron_P11D11


title: Motoneuron_P11D10


title: Motoneuron_P11D12


title: 3221_12m1_GPR_p1_F02_CC


title: 3221_scrn_GPR_p1_H05_CC


title: Motoneuron_P11D6


title: 3221_12m1_GPR_p1_B01_CC


title: Motoneuron_P11E11


title: Motoneuron_P11D8


title: 3221_12m1_GPR_p1_A01_CC


title: Motoneuron_P11D9


title: Motoneuron_P11D5


title: Motoneuron_P11E4


title: 3221_scrn_GPR_p1_E05_CC


title: 3221_scrn_GPR_p1_G05_CC


title: Motoneuron_P11D4


title: 3023_wk12_CIN_p1_B05_CC


title: Motoneuron_P11D3


title: 3221_scrn_GPR_p1_B05_CC


title: 3221_scrn_GPR_p1_C05_CC


title: Motoneuron_P11D2


title: Motoneuron_P11D1


title: Motoneuron_P11C10


title: 3221_scrn_GPR_p1_E04_CC


title: Motoneuron_P11C7


title: Motoneuron_P11C8


title: Motoneuron_P11C12


title: 3221_scrn_GPR_p1_G04_CC


title: 3221_scrn_GPR_p1_F04_CC


title: 3221_scrn_GPR_p1_H03_CC


title: Motoneuron_P11C3


title: 3221_scrn_GPR_p1_G03_CC


title: 3221_scrn_GPR_p1_A04_CC


title: 3221_scrn_GPR_p1_F03_CC


title: 3221_scrn_GPR_p1_B04_CC


title: Motoneuron_P11C2


title: Motoneuron_P11C5


title: 3023_wk12_CIN_p1_A05_CC


title: 3221_scrn_GPR_p1_C03_CC


title: Motoneuron_P11B12


title: Motoneuron_P11B6


title: Motoneuron_P11B11


title: 3221_scrn_GPR_p1_B03_CC


title: Motoneuron_P11B10


title: 3221_scrn_GPR_p1_E03_CC


title: 3221_scrn_GPR_p1_F05_CC


title: Motoneuron_P11B3


title: Motoneuron_P11C6


title: Motoneuron_P11B4


title: Motoneuron_P11A9


title: 3221_scrn_GPR_p1_H02_CC


title: 3221_scrn_GPR_p1_G02_CC


title: 3221_scrn_GPR_p1_A03_CC


title: 3221_scrn_GPR_p1_E02_CC


title: Motoneuron_P11A7


title: 3221_scrn_GPR_p1_C02_CC


title: Motoneuron_P11A6


title: 3221_scrn_GPR_p1_B02_CC


title: 3221_scrn_GPR_p1_F02_CC


title: Motoneuron_P11A5


title: 3221_scrn_GPR_p1_A02_CC


title: Motoneuron_P11A3


title: Motoneuron_P11A2


title: 3221_scrn_GPR_p1_H01_CC


title: Motoneuron_P10H12


title: 3023_wk12_CIN_p1_F09_CC


title: 3221_scrn_GPR_p1_F01_CC


title: 3221_scrn_GPR_p1_E01_CC


title: Motoneuron_P10H9


title: Motoneuron_P10H4


title: 3221_scrn_GPR_p1_C01_CC


title: Motoneuron_P11B2


title: Motoneuron_P10G12


title: 3221_scrn_GPR_p1_A01_CC


title: Motoneuron_P10G11


title: Motoneuron_P10H8


title: MCRL_wk0_GPR_p3_F10_CC


title: Motoneuron_P11A4


title: 3023_wk12_CIN_p1_E09_CC


title: MCRL_wk0_GPR_p3_F09_CC


title: Motoneuron_P10G10


title: Motoneuron_P10G7


title: Motoneuron_P10G9


title: 3221_scrn_GPR_p1_G01_CC


title: MCRL_wk0_GPR_p3_D07_CC


title: Motoneuron_P10G4


title: Motoneuron_P10G8


title: MCRL_wk0_GPR_p3_D08_CC


title: Motoneuron_P10H11


title: Motoneuron_P10G6


title: MCRL_wk0_GPR_p3_B03_CC


title: Motoneuron_P10F12


title: Motoneuron_P10F11


title: Motoneuron_P10F10


title: MCRL_wk0_GPR_p2_A10_CC


title: MCRL_wk0_GPR_p2_E07_CC


title: MCRL_wk0_GPR_p3_B04_CC


title: Motoneuron_P10F7


title: MCRL_wk0_GPR_p2_A08_CC


title: Motoneuron_P10F9


title: Motoneuron_P10F6


title: Motoneuron_P10F8


title: 3023_wk12_CIN_p1_F04_CC


title: MCRL_wk0_GPR_p2_B07_CC


title: Motoneuron_P10F4


title: MCRL_wk0_GPR_p3_C06_CC


title: MCRL_wk0_GPR_p3_C05_CC


title: MCRL_wk0_GPR_p2_D05_CC


title: MCRL_wk0_GPR_p2_D04_CC


title: MCRL_wk0_GPR_p2_F04_CC


title: Motoneuron_P10E11


title: Motoneuron_P10F3


title: Motoneuron_P10E12


title: Motoneuron_P10G2


title: MCRL_wk0_GPR_p3_A02_CC


title: MCRL_wk0_GPR_p2_F03_CC


title: Motoneuron_P10E10


title: MCRL_wk0_GPR_p2_E03_CC


title: MCRL_wk0_GPR_p2_C04_CC


title: Motoneuron_P10E9


title: Motoneuron_P10E8


title: Motoneuron_P10E7


title: MCRL_wk0_GPR_p2_A03_CC


title: MCRL_wk0_GPR_p2_B03_CC


title: Motoneuron_P10F5


title: MCRL_wk0_GPR_p2_G02_CC


title: Motoneuron_P10E6


title: Motoneuron_P10F2


title: 3023_wk12_CIN_p1_E04_CC


title: MCRL_wk0_GPR_p2_G01_CC


title: MCRL_wk0_GPR_p2_F01_CC


title: Motoneuron_P10E5


title: MCRL_wk0_GPR_p2_C01_CC


title: MCRL_wk0_GPR_p2_D01_CC


title: Motoneuron_P10E4


title: MCRL_wk0_ATD_p1_B11_CC


title: Motoneuron_P10E2


title: MCRL_wk0_GPR_p2_D03_CC


title: MCRL_wk0_ATD_p1_C11_CC


title: exo10cKO_1_4_p20_RM

city: Ashburn

first: Di

last: Wu

state: Virginia

address: 19700 Helix Drive

country: USA

institute: HHMI Janelia

description: plus ERCC spike-in mix #4456740

data_processing:
For RNA-seq: Raw sequence reads were trimmed with Cutadapt 2.5 to remove adapters while performing light quality trimming with parameters "-m 10 -q 20, 20". For CUT&Tag seq: data analysis were performed according to CUT&Tag Data Processing and Analysis Tutorial
For RNA-seq, the sequencing library quality was assessed with FastQC v0.11.8 with default parameters. Trimmed reads were mapped to the Mus musculus mm10 reference genome plus ERCC.fasta using STAR v2.7.2a.
Multi-mapping reads were filtered using samtools 1.9. Uniquely aligned reads were then mapped to gene features using HTseq v0.9.1 as an unstranded library with default parameters (for polyA RNA-seq) and using stranded=yes for ribominus analysis.
A gene/ERCC count was considered valid when present in at least 5 reads in at least 2 libraries. Differential expression between groups of samples was tested using R version 3.5.1 (2018-07-02) with DESeq2 v1.24.0. The oocyte libraries were normalized by ERCC counts by defining the ERCC genes as the controlGenes when estimating the sizeFactors in DESeq2.
Genome_build: mm10, ERCC
Supplementary_files_format_and_content: RNA-seq: provide tab deliminated original counts of each gene obtained form Htseq-count. For CUT&Tag: provide tab diliminated bed files of all peaks from each library obtained by SEACR using igg as negative control. The protocol follows CUT&Tag Data Processing and Analysis Tutorial.

organism: Mus musculus

source_name: single mouse oocyte

growth_protocol: All GV oocytes and 3 hr oocytes were dissected from ovaries and cultured ex vivo in M2 medium. MII eggs are dissected from oviducts from superovulated mice.

extract_protocol:
polyA RNAs: Each oocyte was lysed in RLT-plus buffer. The oligo-dT beads were used to isolate the polyA RNA. RiboMinus RNAs and ribosomal RNA: with Ovation Solo kit. CUT&Tag: oocytes were collected according to Bench top CUT&Tag V.3 protocol
For polyA RNA seq: Single oocyte RNA-seq libraries were prepared according to a published single-cell RNA seq pipeline with subtle modifications (Macaulay et al., 2016). Briefly, the oocytes at desired stages were collected individually into 2.5 ml RLT plus and stocked at -80 °C until all samples were collected. In the beginning of RNA purification, ERCC RNA spike-in mix (ThermoFisher 4456740) was diluted 10^5 fold, and 1 ml of the diluted ERCC mix was added to each lysis. Poly(A) RNA were isolated by oligo (dT) beads, reverse transcribed, amplified and purified. The purified cDNAs were analyzed by Bioanalyzer 2100 to confirm successful amplification range and quality. cDNAs passing a quality test were further constructed into sequencing libraries by Nextera DNA Sample Preparation Kit. For RiboMinus Total RNA-seq: single oocyte libraries were prepared according to the Ovation Solo system, but random hexamer primer is used for reverse transcription. For CUT&Tag sequencing: libraries were constructed according to the protocol Bench top CUT&Tag V.3, with fresh GV oocytes without light fixation.

treatment_protocol: Mutant oocytes were dissected from the mutant mice (constructed by CRISPR/Cas9)

value: single mouse oocyte

tag: Stage

tag: genotype


title: MCRL_wk0_GPR_p2_A01_CC


title: MCRL_wk0_GPR_p2_E01_CC


title: exo10cKO_2_2_p20_RM

description: plus ERCC spike-in mix #4456740


title: exo10cKO_2_3_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk0_GPR_p2_B01_CC


title: exo10cKO_2_1_p20_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P10E3


title: exo10cKO_2_4_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk0_ATD_p1_A11_CC


title: Motoneuron_P10D12


title: exo10cKO_1_2_p20_RM

description: plus ERCC spike-in mix #4456740


title: exo10cKO_1_3_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk0_ATD_p1_F10_CC


title: MCRL_wk0_ATD_p1_E10_CC


title: 3023_wk12_CIN_p1_D04_CC


title: Motoneuron_P10D9


title: Motoneuron_P10D11


title: MCRL_wk0_ATD_p1_D10_CC


title: exo10cKO_1_1_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk0_GPR_p3_A01_CC


title: dis3cKO_2_4_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk0_ATD_p1_F09_CC


title: MCRL_wk0_ATD_p1_A10_CC


title: Motoneuron_P10D7


title: MCRL_wk0_ATD_p1_C09_CC


title: MCRL_wk0_ATD_p1_B09_CC


title: Motoneuron_P10D6


title: Motoneuron_P10D5


title: MCRL_wk0_ATD_p1_A09_CC


title: dis3cKO_2_1_p20_RM

description: plus ERCC spike-in mix #4456740


title: dis3cKO_2_2_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk0_ATD_p1_A08_CC


title: Motoneuron_P10D8


title: MCRL_wk0_ATD_p1_B07_CC


title: MCRL_wk0_ATD_p1_B10_CC


title: MCRL_wk0_ATD_p1_F05_CC


title: dis3cKO_1_1_p20_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P10D2


title: Motoneuron_P10D3


title: dis3cKO_2_3_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk0_ATD_p1_D05_CC


title: 3023_wk12_CIN_p1_C04_CC


title: MCRL_wk0_ATD_p1_C05_CC


title: dis3cKO_1_3_p20_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P10C12


title: dcKO_2_4_p20_RM

description: plus ERCC spike-in mix #4456740

value: dcKO


title: 3023_wk12_CIN_p1_A04_CC


title: MCRL_wk0_ATD_p1_B05_CC


title: MCRL_wk0_ATD_p1_E09_CC


title: MCRL_wk0_ATD_p1_A04_CC


title: dcKO_2_3_p20_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P10C10


title: MCRL_wk0_ATD_p1_G02_CC


title: dis3cKO_1_2_p20_RM

description: plus ERCC spike-in mix #4456740


title: dcKO_2_2_p20_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P10C9


title: MCRL_wk0_ATD_p1_E02_CC


title: dcKO_2_1_p20_RM

description: plus ERCC spike-in mix #4456740


title: dcKO_1_4_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk0_ATD_p1_C02_CC


title: Motoneuron_P10C11


title: MCRL_wk0_ATD_p1_D02_CC


title: MCRL_wk0_ATD_p1_G01_CC


title: MCRL_wk0_ATD_p1_F01_CC


title: Motoneuron_P10C8


title: 3023_wk12_CIN_p1_D09_CC


title: dcKO_1_3_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk0_ATD_p1_C01_CC


title: MCRL_wk0_ATD_p1_B01_CC


title: Motoneuron_P10C7


title: Motoneuron_P10C3


title: dcKO_1_2_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk0_ATD_p1_A01_CC


title: Motoneuron_P10C4


title: dcKO_1_1_p20_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P10C2


title: ctr_2_4_p20_RM

description: plus ERCC spike-in mix #4456740

value: control


title: MCRL_wk24_GPR_p1_F11_CC


title: MCRL_wk24_GPR_p1_G11_CC


title: MCRL_wk0_ATD_p1_D01_CC


title: MCRL_wk24_GPR_p1_H10_CC


title: MCRL_wk24_GPR_p1_G10_CC


title: Motoneuron_P10B6


title: MCRL_wk24_GPR_p1_F10_CC


title: ctr_2_2_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_GPR_p1_D10_CC


title: Motoneuron_P10B4


title: ctr_2_1_p20_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P10B3


title: MCRL_wk24_GPR_p1_H09_CC


title: 3023_wk12_CIN_p1_C09_CC


title: MCRL_wk24_GPR_p1_B10_CC


title: ctr_1_4_p20_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P10B2


title: MCRL_wk24_GPR_p1_C10_CC


title: MCRL_wk24_GPR_p1_B09_CC


title: MCRL_wk24_GPR_p1_D09_CC


title: Motoneuron_P10A11


title: ctr_1_3_p20_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P10B11


title: ctr_1_2_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_GPR_p1_A09_CC


title: Motoneuron_P10A10


title: ctr_1_1_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_GPR_p1_H08_CC


title: Motoneuron_P10A9


title: MCRL_wk24_GPR_p1_B08_CC


title: ctr_2_3_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_GPR_p1_H07_CC


title: Motoneuron_P10A8


title: GV_cKO_AM1757_4_RM

description: plus ERCC spike-in mix #4456740

value: GV


title: 3023_wk12_CIN_p1_F03_CC


title: MCRL_wk24_GPR_p1_G07_CC


title: GV_cKO_AM1757_3_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_GPR_p1_F09_CC


title: MCRL_wk24_GPR_p1_C07_CC


title: Motoneuron_P10A7


title: Motoneuron_P10A6


title: MCRL_wk24_GPR_p1_B07_CC


title: MCRL_wk24_GPR_p1_A07_CC


title: GV_cKO_AM1757_1_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_GPR_p1_B06_CC


title: MCRL_wk24_GPR_p1_H06_CC


title: Motoneuron_P10A5


title: MCRL_wk24_GPR_p1_A06_CC


title: GV_cKO_AM1713_4_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P10A4


title: MCRL_wk24_GPR_p1_F05_CC


title: MCRL_wk24_GPR_p1_G08_CC


title: GV_cKO_AM1713_3_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_GPR_p1_E05_CC


title: Motoneuron_P10A3


title: MCRL_wk24_GPR_p1_D05_CC


title: GV_cKO_AM1713_2_RM

description: plus ERCC spike-in mix #4456740


title: 3023_wk12_CIN_p1_E03_CC


title: GV_cKO_AM1713_1_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P10A2


title: GV_cKO_AM1757_2_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_GPR_p1_A05_CC


title: MCRL_wk24_GPR_p1_B05_CC


title: MCRL_wk24_GPR_p1_H04_CC


title: Motoneuron_P6H12


title: GV_ctr_AM1759_4_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_GPR_p1_F04_CC


title: MCRL_wk24_GPR_p1_G04_CC


title: GV_ctr_AM1759_3_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6H11


title: MCRL_wk24_GPR_p1_B04_CC


title: GV_ctr_AM1759_2_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6H10


title: MCRL_wk24_GPR_p1_A04_CC


title: MCRL_wk24_GPR_p1_C04_CC


title: MCRL_wk24_GPR_p1_H03_CC


title: MCRL_wk24_GPR_p1_G03_CC


title: Motoneuron_P6H8


title: 3023_wk12_CIN_p1_D03_CC


title: GV_ctr_AM1759_1_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_GPR_p1_F03_CC


title: Motoneuron_P6H9


title: MCRL_wk24_GPR_p1_C03_CC


title: Motoneuron_P6H7


title: GV_ctr_AM1758_3_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6H6


title: MCRL_wk24_GPR_p1_H02_CC


title: MCRL_wk24_GPR_p1_D02_CC


title: MCRL_wk24_GPR_p1_C02_CC


title: MCRL_wk24_GPR_p1_B02_CC


title: GV_ctr_AM1758_2_RM

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6H5


title: MCRL_wk24_GPR_p1_A02_CC


title: Motoneuron_P6H4


title: Motoneuron_P10D4


title: MCRL_wk0_ATD_p1_D08_CC


title: MCRL_wk0_ATD_p1_B08_CC


title: MCRL_wk0_ATD_p1_F02_CC


title: MCRL_wk0_ATD_p1_C10_CC


title: MCRL_wk0_ATD_p1_C08_CC


title: Motoneuron_P6H3


title: dis3cKO_1_4_p20_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_GPR_p1_H01_CC


title: Dis3_MII_cKO_16

description: plus ERCC spike-in mix #4456740

value: MII


title: Motoneuron_P6H2


title: MCRL_wk24_GPR_p1_E01_CC


title: GV_ctr_AM1758_4_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_GPR_p1_G01_CC


title: Dis3_MII_cKO_14

description: plus ERCC spike-in mix #4456740


title: 3023_wk12_CIN_p1_C03_CC


title: MCRL_wk24_GPR_p1_F01_CC


title: MCRL_wk24_GPR_p1_D01_CC


title: MCRL_wk24_GPR_p1_C01_CC


title: Motoneuron_P6H1


title: MCRL_wk24_GPR_p1_A01_CC


title: Dis3_MII_cKO_15

description: plus ERCC spike-in mix #4456740


title: GV_ctr_AM1758_1_RM

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_B11_CC


title: Dis3_MII_cKO_12

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_B09_CC


title: MCRL_wk24_GPR_p1_B01_CC


title: Motoneuron_P6G11


title: Motoneuron_P6G10


title: MCRL_wk24_ATD_p1_C11_CC


title: Motoneuron_P6G12


title: MCRL_wk24_ATD_p1_A09_CC


title: Dis3_MII_cKO_10

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6G8


title: Motoneuron_P6G7


title: MCRL_wk24_ATD_p1_H08_CC


title: Dis3_MII_cKO_8

description: plus ERCC spike-in mix #4456740


title: 3023_wk12_CIN_p1_B03_CC


title: MCRL_wk24_ATD_p1_E08_CC


title: MCRL_wk24_ATD_p1_C08_CC


title: Dis3_MII_cKO_9

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_A08_CC


title: MCRL_wk24_ATD_p1_F08_CC


title: Motoneuron_P6G6


title: MCRL_wk24_ATD_p1_G08_CC


title: Dis3_MII_cKO_13

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_F07_CC


title: Motoneuron_P6G5


title: Motoneuron_P6G3


title: MCRL_wk24_ATD_p1_B08_CC


title: 3023_wk12_CIN_p1_A03_CC


title: Dis3_MII_cKO_6

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6G4


title: Dis3_MII_cKO_4

description: plus ERCC spike-in mix #4456740


title: Dis3_MII_cKO_5

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6G2


title: MCRL_wk24_ATD_p1_B07_CC


title: Dis3_MII_cKO_11

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6F12


title: MCRL_wk24_ATD_p1_D07_CC


title: MCRL_wk24_ATD_p1_G06_CC


title: MCRL_wk24_ATD_p1_H06_CC


title: MCRL_wk24_ATD_p1_D08_CC


title: MCRL_wk24_ATD_p1_A07_CC


title: Dis3_MII_cKO_1

description: plus ERCC spike-in mix #4456740


title: Dis3_MII_cKO_2

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_D06_CC


title: MCRL_wk24_ATD_p1_E06_CC


title: MCRL_wk24_ATD_p1_E07_CC


title: Motoneuron_P6F10


title: Dis3_MII_cKO_7

description: plus ERCC spike-in mix #4456740


title: Dis3_MII_ctr_7

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_H07_CC


title: Motoneuron_P6G1


title: Motoneuron_P6F11


title: Motoneuron_P6F9


title: Dis3_MII_ctr_8

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_H05_CC


title: Motoneuron_P6F7


title: MCRL_wk24_ATD_p1_G05_CC


title: Dis3_MII_ctr_5

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_C06_CC


title: MCRL_wk24_ATD_p1_C05_CC


title: Dis3_MII_ctr_3

description: plus ERCC spike-in mix #4456740


title: Dis3_MII_cKO_3

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_A06_CC


title: 3023_wk12_CIN_p1_B09_CC


title: MCRL_wk24_ATD_p1_G04_CC


title: Dis3_MII_ctr_6

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6F3


title: MCRL_wk24_ATD_p1_F05_CC


title: Motoneuron_P6F6


title: Dis3_MII_ctr_1

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_F06_CC


title: Motoneuron_P6F1


title: MCRL_wk24_ATD_p1_E04_CC


title: Dis3_MII_ctr_4

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6F5


title: Dis3_GV3h_cKO_15

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_D05_CC


title: MCRL_wk24_ATD_p1_C04_CC


title: MCRL_wk24_ATD_p1_B05_CC


title: Motoneuron_P6E11


title: MCRL_wk24_ATD_p1_B04_CC


title: MCRL_wk24_ATD_p1_G03_CC


title: MCRL_wk24_ATD_p1_F03_CC


title: Dis3_GV3h_cKO_13

description: plus ERCC spike-in mix #4456740


title: Dis3_MII_ctr_2

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6F4


title: Dis3_GV3h_cKO_14

description: plus ERCC spike-in mix #4456740


title: Dis3_GV3h_cKO_16

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6E8


title: Dis3_GV3h_cKO_12

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_F04_CC


title: 3023_wk12_CIN_p1_A09_CC


title: Motoneuron_P6E12


title: Motoneuron_P6E5


title: MCRL_wk24_ATD_p1_C03_CC


title: MCRL_wk24_ATD_p1_A03_CC


title: MCRL_wk24_ATD_p1_H04_CC


title: MCRL_wk24_ATD_p1_E03_CC


title: MCRL_wk24_ATD_p1_A05_CC


title: Motoneuron_P6E10


title: MCRL_wk24_ATD_p1_D04_CC


title: MCRL_wk24_ATD_p1_D03_CC


title: MCRL_wk24_ATD_p1_F02_CC


title: MCRL_wk24_ATD_p1_D02_CC


title: 3023_wk12_CIN_p1_F02_CC


title: MCRL_wk24_ATD_p1_C02_CC


title: MCRL_wk24_ATD_p1_B03_CC


title: MCRL_wk24_ATD_p1_E05_CC


title: MCRL_wk24_ATD_p1_B02_CC


title: MCRL_wk24_ATD_p1_H01_CC


title: Motoneuron_P6D10


title: MCRL_wk24_ATD_p1_G02_CC


title: Motoneuron_P6D12


title: Dis3_GV3h_cKO_8

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6E3


title: Dis3_GV3h_cKO_7

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6D9


title: Dis3_GV3h_cKO_5

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6D7


title: Motoneuron_P6E2


title: 3023_wk12_CIN_p1_E02_CC


title: Dis3_GV3h_cKO_10

description: plus ERCC spike-in mix #4456740


title: Dis3_GV3h_cKO_6

description: plus ERCC spike-in mix #4456740


title: Dis3_GV3h_cKO_9

description: plus ERCC spike-in mix #4456740


title: 3023_wk24_CIN_p1_C11_CC


title: MCRL_wk24_ATD_p1_G01_CC


title: Dis3_GV3h_cKO_3

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_E02_CC


title: 3023_wk24_CIN_p1_D11_CC


title: MCRL_wk24_ATD_p1_A02_CC


title: 3023_wk24_CIN_p1_E11_CC


title: Motoneuron_P6D6


title: 3023_wk24_CIN_p1_B11_CC


title: Dis3_GV3h_cKO_2

description: plus ERCC spike-in mix #4456740


title: 3023_wk24_CIN_p1_A11_CC


title: Motoneuron_P6D5


title: 3023_wk24_CIN_p1_G10_CC


title: Motoneuron_P6D11


title: 3023_wk24_CIN_p1_H10_CC


title: Motoneuron_P6D4


title: 3023_wk12_CIN_p1_D02_CC


title: 3023_wk24_CIN_p1_F10_CC


title: Dis3_GV3h_ctr_8

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_F01_CC


title: Dis3_GV3h_cKO_1

description: plus ERCC spike-in mix #4456740


title: Dis3_GV3h_cKO_4

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6D3


title: Dis3_GV3h_ctr_6

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_D01_CC


title: Motoneuron_P6D2


title: Motoneuron_P6C12


title: MCRL_wk24_ATD_p1_A01_CC


title: Dis3_GV3h_ctr_7

description: plus ERCC spike-in mix #4456740


title: MCRL_wk24_ATD_p1_C01_CC


title: MCRL_wk24_ATD_p1_B01_CC


title: Motoneuron_P6C11


title: Dis3_GV3h_ctr_5

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6D1


title: 3023_wk24_CIN_p1_G11_CC


title: 3023_wk24_CIN_p1_F11_CC


title: Motoneuron_P6C9


title: 3023_wk12_CIN_p1_C02_CC


title: MCRL_wk24_ATD_p1_E01_CC


title: 3023_wk24_CIN_p1_E10_CC


title: 3023_wk24_CIN_p1_A10_CC


title: 3023_wk24_CIN_p1_C10_CC


title: 3023_wk24_CIN_p1_B10_CC


title: Motoneuron_P6C10


title: Dis3_GV3h_ctr_2

description: plus ERCC spike-in mix #4456740


title: 3023_wk24_CIN_p1_H09_CC


title: Dis3_GV3h_ctr_3

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6C8


title: 3023_wk24_CIN_p1_G09_CC


title: Dis3_GV3h_ctr_1

description: plus ERCC spike-in mix #4456740


title: 3023_wk24_CIN_p1_F09_CC


title: Motoneuron_P6C7


title: 3023_wk24_CIN_p1_B09_CC


title: 3023_wk24_CIN_p1_D09_CC


title: Dis3_GV_cKO_16

description: plus ERCC spike-in mix #4456740


title: Dis3_GV3h_ctr_4

description: plus ERCC spike-in mix #4456740


title: 3023_wk24_CIN_p1_F08_CC


title: Motoneuron_P6C6


title: Dis3_GV_cKO_15

description: plus ERCC spike-in mix #4456740


title: Dis3_GV_cKO_14

description: plus ERCC spike-in mix #4456740


title: 3023_wk24_CIN_p1_G08_CC


title: 3023_wk24_CIN_p1_C08_CC


title: Motoneuron_P6C5


title: 3023_wk24_CIN_p1_B08_CC


title: Dis3_GV_cKO_13

description: plus ERCC spike-in mix #4456740


title: 3023_wk12_CIN_p1_B02_CC


title: 3023_wk12_CIN_p1_A02_CC


title: Dis3_GV_cKO_12

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6C3


title: 3023_wk12_CIN_p1_F01_CC


title: Motoneuron_P6C4


title: Motoneuron_P6B11


title: Motoneuron_P6B12


title: 3023_wk12_CIN_p1_E01_CC


title: Dis3_GV_cKO_10

description: plus ERCC spike-in mix #4456740


title: 3023_wk12_CIN_p1_C01_CC


title: 3023_wk12_CIN_p1_D01_CC


title: 3023_wk12_CIN_p1_G01_CC


title: Motoneuron_P6B10


title: Dis3_GV_cKO_8

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6B9


title: Dis3_GV_cKO_7

description: plus ERCC spike-in mix #4456740


title: 3023_wk12_CIN_p1_A01_CC


title: Dis3_GV_cKO_6

description: plus ERCC spike-in mix #4456740


title: 3023_wk12_CIN_p1_B01_CC


title: Motoneuron_P6B7


title: 3023_wk6_KSK_p3_D07_CC

value: KSK


title: 3023_wk12_CIN_p1_H01_CC


title: Motoneuron_P6B6


title: 3023_wk6_KSK_p3_C07_CC


title: 3023_wk6_KSK_p3_B07_CC


title: Dis3_GV_cKO_5

description: plus ERCC spike-in mix #4456740


title: Dis3_GV3h_cKO_11

description: plus ERCC spike-in mix #4456740


title: 3023_wk6_KSK_p3_H06_CC


title: Motoneuron_P6B5


title: Dis3_GV_cKO_4

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6B4


title: 3023_wk6_KSK_p3_D06_CC


title: 3023_wk6_KSK_p3_H05_CC


title: 3023_wk6_KSK_p3_B06_CC


title: 3023_wk6_KSK_p3_E05_CC


title: 3023_wk6_KSK_p3_F07_CC


title: 3023_wk6_KSK_p3_E07_CC


title: Motoneuron_P6B3


title: 3023_wk6_KSK_p3_D05_CC


title: Dis3_GV_cKO_3

description: plus ERCC spike-in mix #4456740


title: 3023_wk6_KSK_p3_C05_CC


title: Dis3_GV_cKO_2

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6B2


title: 3023_wk6_KSK_p3_B05_CC


title: 3023_wk6_KSK_p3_A05_CC


title: Motoneuron_P6A11


title: 3023_wk6_KSK_p3_G04_CC


title: Dis3_GV_cKO_11

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6A10


title: Dis3_GV_cKO_1

description: plus ERCC spike-in mix #4456740


title: 3023_wk6_KSK_p3_F04_CC


title: 3023_wk6_KSK_p3_E06_CC


title: 3023_wk6_KSK_p3_D04_CC


title: Motoneuron_P6A9


title: Motoneuron_P6A8


title: Dis3_GV_ctr_7

description: plus ERCC spike-in mix #4456740


title: Dis3_GV_ctr_6

description: plus ERCC spike-in mix #4456740


title: 3023_wk6_KSK_p3_E04_CC


title: Dis3_GV_ctr_5

description: plus ERCC spike-in mix #4456740


title: 3023_wk6_KSK_p3_G03_CC


title: 3023_wk6_KSK_p3_F03_CC


title: 3023_wk6_KSK_p3_D03_CC


title: 3023_wk6_KSK_p3_E03_CC


title: Dis3_GV_ctr_4

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6A6


title: 3023_wk6_KSK_p3_C03_CC


title: 3023_wk6_KSK_p3_B03_CC


title: Dis3_GV_ctr_8

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6A7


title: Dis3_GV_ctr_3

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P6A2


title: 3023_wk6_KSK_p3_A03_CC


title: 3023_wk6_KSK_p3_G02_CC


title: Motoneuron_P5H10


title: 3023_wk6_KSK_p3_B04_CC


title: Dis3_GV_ctr_2

description: plus ERCC spike-in mix #4456740


title: Motoneuron_P5H9


title: 3023_wk6_KSK_p3_E02_CC


title: 3023_wk6_KSK_p3_F02_CC


title: 3023_wk6_KSK_p3_D02_CC


title: Dis3_GV_ctr_1

description: plus ERCC spike-in mix #4456740


title: 3023_wk6_KSK_p3_C02_CC


title: Motoneuron_P5H4


title: 3023_wk6_KSK_p3_B02_CC


title: Motoneuron_P5H8


title: 3023_wk6_KSK_p3_A02_CC


title: 3023_wk6_KSK_p3_E01_CC


title: Motoneuron_P5G9


title: 3023_wk6_KSK_p3_D01_CC


title: 3023_wk6_KSK_p3_F01_CC


title: Motoneuron_P5G8


title: Motoneuron_P5G11


title: 3023_wk6_KSK_p3_A01_CC


title: MCRL_wk104_ATD_p2_F12_CC


title: MCRL_wk104_ATD_p2_C12_CC


title: ESCC tissue_11_rep4

type: RNA

city: Beijing

first: Fen

last: Liu

address: Youanmenwai Street

department: Department of Epidemiology and Health Statistics

country: China

institute: Capital Medical University

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: ESCC tissue from patient 11

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US).

tag: tissue

value: esophageal squamous cell carcinoma


title: 3023_wk6_KSK_p3_B01_CC


title: adjacent normal tissue_11_rep4

source_name: adjacent normal tissue from patient 11

value: normal adjacent esophageal tissue


title: MCRL_wk104_ATD_p2_E12_CC


title: MCRL_wk104_ATD_p2_A12_CC


title: Motoneuron_P5G7


title: MCRL_wk104_ATD_p2_F11_CC


title: MCRL_wk104_ATD_p2_C11_CC


title: Motoneuron_P5G6


title: Motoneuron_P5G4


title: MCRL_wk104_ATD_p2_E11_CC


title: 3023_wk6_KSK_p3_G01_CC


title: MCRL_wk104_ATD_p2_A11_CC


title: ESCC tissue_01_rep1

source_name: ESCC tissue from patient 01


title: MCRL_wk104_ATD_p2_E10_CC


title: adjacent normal tissue_05_rep2

source_name: adjacent normal tissue from patient 05


title: Motoneuron_P5F12


title: ESCC tissue_08_rep3

source_name: ESCC tissue from patient 08


title: adjacent normal tissue_08_rep3

source_name: adjacent normal tissue from patient 08


title: ESCC tissue_05_rep2

source_name: ESCC tissue from patient 05


title: MCRL_wk104_ATD_p2_C10_CC


title: MCRL_wk104_ATD_p2_D10_CC


title: Motoneuron_P5F10


title: Motoneuron_P5F11


title: adjacent normal tissue_01_rep1

source_name: adjacent normal tissue from patient 01


title: MCRL_wk104_ATD_p2_F10_CC


title: MCRL_wk104_ATD_p2_F09_CC


title: Motoneuron_P5F9


title: MCRL_wk104_ATD_p2_E09_CC


title: MCRL_wk104_ATD_p2_A09_CC


title: MCRL_wk104_ATD_p2_B11_CC


title: MCRL_wk104_ATD_p2_A10_CC


title: MCRL_wk104_ATD_p2_D09_CC


title: MCRL_wk104_ATD_p2_E08_CC


title: MCRL_wk104_ATD_p2_B09_CC


title: MCRL_wk104_ATD_p2_D08_CC


title: MCRL_wk104_ATD_p2_C08_CC


title: MCRL_wk104_ATD_p2_F08_CC


title: Motoneuron_P5F8


title: Motoneuron_P5G3


title: Motoneuron_P5F5


title: Motoneuron_P5F6


title: MCRL_wk104_ATD_p2_F07_CC


title: MCRL_wk104_ATD_p2_E07_CC


title: MCRL_wk104_ATD_p2_B07_CC


title: MCRL_wk104_ATD_p2_B10_CC


title: Motoneuron_P5F4


title: MCRL_wk104_ATD_p2_C06_CC


title: Motoneuron_P5F1


title: MCRL_wk104_ATD_p2_E06_CC


title: MCRL_wk104_ATD_p2_A07_CC


title: Motoneuron_P5F7


title: Motoneuron_P5E12


title: Motoneuron_P5E9


title: 3256_wk4_GPR_p1_C3_CC


title: MCRL_wk104_ATD_p2_F05_CC


title: 3256_wk4_GPR_p1_C4_CC


title: MCRL_wk104_ATD_p2_G05_CC


title: Motoneuron_P5E8


title: MCRL_wk104_ATD_p2_E05_CC


title: 3256_wk4_GPR_p1_C2_CC


title: MCRL_wk104_ATD_p2_B05_CC


title: 3256_wk4_GPR_p1_C1_CC


title: MCRL_wk104_ATD_p2_B08_CC


title: MCRL_wk104_ATD_p2_E04_CC


title: Motoneuron_P5E7


title: 3023_wk6_CIN_p2_H12_CC


title: 3256_wk4_GPR_p1_B7_CC


title: 3023_wk6_CIN_p2_F12_CC


title: 3256_wk4_GPR_p1_B8_CC


title: 3023_wk6_CIN_p2_D12_CC


title: Motoneuron_P5E5


title: 3023_wk6_CIN_p2_G12_CC


title: 3256_wk4_GPR_p1_B6_CC


title: Motoneuron_P5E4


title: 3023_wk6_CIN_p2_B12_CC


title: MCRL_wk104_ATD_p2_D04_CC


title: Motoneuron_P5E2


title: 3023_wk6_CIN_p2_C12_CC


title: 3023_wk6_CIN_p2_G11_CC


title: 3023_wk6_CIN_p2_A12_CC


title: MCRL_wk104_ATD_p2_B06_CC


title: 3256_wk4_GPR_p1_B3_CC


title: MCRL_wk104_ATD_p2_C05_CC


title: 3256_wk4_GPR_p1_B4_CC


title: 3023_wk6_CIN_p2_F11_CC


title: 3023_wk6_CIN_p2_D11_CC


title: Motoneuron_P5E6


title: Motoneuron_P5D11


title: 3023_wk6_CIN_p2_B11_CC


title: Motoneuron_P5D12


title: 3023_wk6_CIN_p2_C11_CC


title: 3256_wk4_GPR_p1_B2_CC


title: Motoneuron_P5D10


title: 3023_wk6_CIN_p2_G10_CC


title: 3256_wk4_GPR_p1_B12_CC


title: 3023_wk6_CIN_p2_F10_CC


title: 3023_wk6_CIN_p2_A11_CC


title: Motoneuron_P5E1


title: Motoneuron_P5D9


title: 3023_wk6_CIN_p2_D10_CC


title: 3256_wk4_GPR_p1_B5_CC


title: 3023_wk6_CIN_p2_E10_CC


title: 3256_wk4_GPR_p1_A7_CC


title: Motoneuron_P5D7


title: 3023_wk6_CIN_p2_C10_CC


title: 3023_wk6_CIN_p2_E11_CC


title: 3023_wk6_CIN_p2_B10_CC


title: 3023_wk6_CIN_p2_G09_CC


title: 3023_wk6_CIN_p2_A10_CC


title: 3256_wk4_GPR_p1_A3_CC


title: Motoneuron_P5D6


title: Motoneuron_P5D3


title: 3023_wk6_CIN_p2_E09_CC


title: 3023_wk6_CIN_p2_D09_CC


title: 3256_wk4_GPR_p1_A2_CC


title: Motoneuron_P5D5


title: 3256_wk4_GPR_p1_A12_CC


title: MCRL_wk104_ATD_p2_A04_CC


title: MCRL_wk104_ATD_p2_G03_CC


title: Motoneuron_P5D8


title: 3023_wk6_CIN_p2_F09_CC


title: 3023_wk6_CIN_p2_C09_CC


title: 3256_wk4_GPR_p1_B1_CC


title: Motoneuron_P5C12


title: 3256_wk24_HYP_p2_G4_CC

value: HYP


title: 3023_wk6_CIN_p2_B09_CC


title: Motoneuron_P5C9


title: 3023_wk6_CIN_p2_H08_CC


title: 3256_wk24_HYP_p2_F9_CC


title: Motoneuron_P5C7


title: 3256_wk24_HYP_p2_F2_CC


title: 3023_wk6_CIN_p2_G08_CC


title: 3023_wk6_CIN_p2_A09_CC


title: 3023_wk6_CIN_p2_E08_CC


title: 3023_wk6_CIN_p2_D08_CC


title: 3256_wk24_HYP_p2_E8_CC


title: Motoneuron_P5C6


title: Motoneuron_P5B12


title: 3256_wk24_HYP_p2_E5_CC


title: MCRL_wk104_ATD_p2_E03_CC


title: Motoneuron_P5B11


title: 3023_wk6_CIN_p2_H07_CC


title: 3023_wk6_CIN_p2_G07_CC


title: 3023_wk6_CIN_p2_F07_CC


title: 3023_wk6_CIN_p2_E07_CC


title: 3023_wk6_CIN_p2_D07_CC


title: 3256_wk4_GPR_p1_A8_CC


title: 3256_wk24_HYP_p2_E10_CC


title: 3023_wk6_CIN_p2_C07_CC


title: 3023_wk6_CIN_p2_F08_CC


title: 3256_wk24_HYP_p2_D4_CC


title: 3023_wk6_CIN_p2_B07_CC


title: 3023_wk6_CIN_p2_G06_CC


title: 3256_wk24_HYP_p2_D1_CC


title: Motoneuron_P5A6


title: Motoneuron_P3H12


title: Motoneuron_P5C4


title: 3256_wk24_HYP_p2_C8_CC


title: 3023_wk6_CIN_p2_F06_CC


title: 3023_wk6_CIN_p2_C08_CC


title: 3256_wk24_HYP_p2_E3_CC


title: 3023_wk6_CIN_p2_B08_CC


title: MCRL_wk104_ATD_p2_D03_CC


title: Motoneuron_P3H10


title: 3023_wk6_CIN_p2_E06_CC


title: Motoneuron_P5B8


title: 3023_wk6_CIN_p2_C06_CC


title: Motoneuron_P5B7


title: 3023_wk6_CIN_p2_B06_CC


title: Motoneuron_P3H9


title: 3256_wk24_HYP_p2_C3_CC


title: 3256_wk24_HYP_p2_D8_CC


title: Motoneuron_P3H8


title: 3023_wk6_CIN_p2_F05_CC


title: Motoneuron_P3H7


title: 3023_wk6_CIN_p2_D05_CC


title: 3023_wk6_CIN_p2_A07_CC


title: 3023_wk6_CIN_p2_A05_CC


title: 3256_wk24_HYP_p2_B6_CC


title: 3023_wk6_CIN_p2_H04_CC


title: Motoneuron_P3H6


title: 3023_wk6_CIN_p2_H05_CC


title: 3256_wk24_HYP_p2_C1_CC


title: 3023_wk6_CIN_p2_G05_CC


title: 3023_wk6_CIN_p2_G04_CC


title: 3256_wk24_HYP_p2_B3_CC


title: MCRL_wk104_ATD_p2_C03_CC


title: 3256_wk24_HYP_p2_C5_CC


title: 3256_wk24_HYP_p2_B5_CC


title: 3023_wk6_CIN_p2_F04_CC


title: 3023_wk6_CIN_p2_E04_CC


title: Motoneuron_P3H4


title: Motoneuron_P3H3


title: 3023_wk6_CIN_p2_D04_CC


title: 3023_wk6_CIN_p2_C04_CC


title: 3256_wk24_HYP_p2_A9_CC


title: 3256_wk24_HYP_p2_B1_CC


title: 3023_wk6_CIN_p2_H03_CC


title: 3023_wk6_CIN_p2_A04_CC


title: Motoneuron_P3H2


title: 3256_wk24_HYP_p2_A8_CC


title: 3023_wk6_CIN_p2_G03_CC


title: 3023_wk6_CIN_p2_F03_CC


title: Motoneuron_P3H1


title: 3023_wk6_CIN_p2_B04_CC


title: 3023_wk6_CIN_p2_D03_CC


title: Motoneuron_P3G12


title: 3256_wk24_HYP_p2_A4_CC


title: MCRL_wk104_ATD_p2_A03_CC


title: Motoneuron_P3G11


title: 3256_wk24_HYP_p2_A6_CC


title: Motoneuron_P3H5


title: 3023_wk6_CIN_p2_B03_CC


title: 3023_wk6_CIN_p2_H02_CC


title: 3256_wk24_HYP_p2_A1_CC


title: 3023_wk6_CIN_p2_C03_CC


title: Motoneuron_P3G10


title: 3023_wk6_CIN_p2_G02_CC


title: 3256_wk0_HYP_p2_H9_CC


title: Motoneuron_P3G9


title: 3023_wk6_CIN_p2_F02_CC


title: 3023_wk6_CIN_p2_E02_CC


title: Motoneuron_P3G8


title: 3023_wk6_CIN_p2_D02_CC


title: 3023_wk6_CIN_p2_C02_CC


title: 3256_wk0_HYP_p2_G9_CC


title: Motoneuron_P3G7


title: 3023_wk6_CIN_p2_E01_CC


title: 3023_wk6_CIN_p2_D01_CC


title: Motoneuron_P3G6


title: MCRL_wk104_ATD_p2_G02_CC


title: 3256_wk24_HYP_p2_A3_CC


title: 3256_wk0_HYP_p2_G2_CC


title: Motoneuron_P3G4


title: 3023_wk6_KSK_p3_H12_CC


title: 3023_wk6_CIN_p2_C01_CC


title: 3023_wk6_CIN_p2_B01_CC


title: 3023_wk6_KSK_p3_G12_CC


title: 3256_wk0_HYP_p2_G1_CC


title: 3256_wk0_HYP_p2_F9_CC


title: 3023_wk6_KSK_p3_C12_CC


title: 3256_wk0_HYP_p2_F4_CC


title: 3023_wk6_KSK_p3_B12_CC


title: 3023_wk6_KSK_p3_A12_CC


title: 3023_wk6_KSK_p3_D12_CC


title: 3256_wk0_HYP_p2_F2_CC


title: 3023_wk6_KSK_p3_H11_CC


title: Motoneuron_P3F12


title: Motoneuron_P3G1


title: Motoneuron_P3G3


title: 3256_wk0_HYP_p2_G4_CC


title: 3256_wk0_HYP_p2_F1_CC


title: 3023_wk6_KSK_p3_G11_CC


title: Motoneuron_P3F11


title: 3023_wk6_KSK_p3_F11_CC


title: 3256_wk0_HYP_p2_E9_CC


title: 3023_wk6_KSK_p3_E11_CC


title: Motoneuron_P3G5


title: Motoneuron_P3F10


title: MCRL_wk104_ATD_p2_F02_CC


title: 3023_wk6_KSK_p3_C11_CC


title: 3256_wk0_HYP_p2_E4_CC


title: Motoneuron_P3F7


title: 3256_wk0_HYP_p2_E2_CC


title: 3023_wk6_KSK_p3_H10_CC


title: Motoneuron_P3F6


title: 3023_wk6_KSK_p3_A11_CC


title: 3023_wk6_KSK_p3_G10_CC


title: Motoneuron_P3F5


title: 3023_wk6_KSK_p3_D10_CC


title: 3023_wk6_KSK_p3_F10_CC


title: MCRL_wk104_ATD_p2_E02_CC


title: 3256_wk0_HYP_p2_D9_CC


title: 3256_wk0_HYP_p2_D4_CC


title: 3023_wk6_KSK_p3_D11_CC


title: Motoneuron_P3F4


title: Motoneuron_P3F1


title: 3023_wk6_KSK_p3_B10_CC


title: 3256_wk0_HYP_p2_D3_CC


title: 3023_wk6_KSK_p3_A10_CC


title: 3256_wk0_HYP_p2_E1_CC


title: 3023_wk6_KSK_p3_C10_CC


title: Motoneuron_P3E11


title: 3023_wk6_KSK_p3_G09_CC


title: 3256_wk0_HYP_p2_D1_CC


title: 3023_wk6_KSK_p3_F09_CC


title: 3023_wk6_KSK_p3_E09_CC


title: 3023_wk6_KSK_p3_B11_CC


title: Motoneuron_P3E10


title: 3023_wk6_KSK_p3_D09_CC


title: 3023_wk6_KSK_p3_C09_CC


title: 3256_wk0_HYP_p2_C9_CC


title: 3256_wk0_HYP_p2_C4_CC


title: Motoneuron_P3E9


title: 3023_wk6_KSK_p3_B09_CC


title: 3256_wk0_HYP_p2_D2_CC


title: MCRL_wk104_ATD_p2_D02_CC


title: 3023_wk6_KSK_p3_H08_CC


title: 3023_wk6_KSK_p3_H09_CC


title: 3256_wk0_HYP_p2_C2_CC


title: Motoneuron_P3E12


title: 3023_wk6_KSK_p3_F08_CC


title: 3256_wk0_HYP_p2_C1_CC


title: 3023_wk6_KSK_p3_G08_CC


title: Motoneuron_P3E8


title: Motoneuron_P3E6


title: 3023_wk6_KSK_p3_D08_CC


title: 3256_wk0_HYP_p2_B9_CC


title: 3023_wk6_KSK_p3_E08_CC


title: 3023_wk6_KSK_p3_A08_CC


title: Motoneuron_P3E5


title: Motoneuron_P3E4


title: 3023_wk6_KSK_p3_C08_CC


title: 3256_wk0_HYP_p2_B4_CC


title: 3256_wk0_HYP_p2_B3_CC


title: 3023_wk6_KSK_p3_H07_CC


title: Motoneuron_P3E3


title: MCRL_wk104_ATD_p2_C02_CC


title: 3023_wk6_KSK_p3_G07_CC


title: 3023_wk6_KSK_p3_B08_CC


title: Motoneuron_P3E7


title: MCRL_wk104_ATD_p2_B02_CC


title: Motoneuron_P3E2


title: 3256_wk0_HYP_p2_B1_CC


title: MCRL_wk104_ATD_p2_A02_CC


title: MCRL_wk104_ATD_p2_F01_CC


title: MCRL_wk104_ATD_p2_G01_CC


title: Motoneuron_P3E1


title: MCRL_wk104_ATD_p2_E01_CC


title: 3256_wk0_HYP_p2_B2_CC


title: 3256_wk0_HYP_p2_A4_CC


title: MCRL_wk104_ATD_p2_D01_CC


title: Motoneuron_P3D12


title: 3256_wk0_HYP_p2_A9_CC


title: MCRL_wk104_ATD_p2_B01_CC


title: Motoneuron_P3D11


title: ELT2219A1_9-37683615


title: Motoneuron_P3D9


title: 3256_wk0_HYP_p2_A2_CC


title: ELT2219A1_8-37683614


title: MCRL_wk104_ATD_p2_C01_CC


title: ELT2219A1_7-37683613


title: Motoneuron_P3D8


title: MCRL_wk104_ATD_p2_A01_CC


title: 3256_wk0_HYP_p2_A1_CC


title: HOKD_wk24_HPV_p1_H9_CC

value: CH-HOKD

value: HPV


title: ELT2219A1_5-37683611

value: CL-MCRL


title: ELT2219A1_4-37683610


title: Motoneuron_P3D6


title: ELT2219A1_6-37683612

value: ATD


title: HOKD_wk24_HPV_p1_H8_CC

value: CD8+ T cell


title: ELT2219A1_3-37683609


title: Motoneuron_P3D5

value: Ok371>RFP+ DAPI- DRAQ5+


title: ELT2219A1_12-37683618


title: ELT2219A1_11-37683617


title: HOKD_wk24_HPV_p1_H6_CC


title: ELT2219A1_10-37683616


title: HOKD_wk24_HPV_p1_H2_CC


title: ELT2219A1_1-37683607


title: Motoneuron_P3D3


title: 3256_wk0_HYP_p2_A3_CC


title: HOKD_wk24_HPV_p1_H11_CC


title: 3023_wk12_KSK_p2_G11_CC


title: 3023_wk12_KSK_p2_F11_CC


title: 3023_wk12_KSK_p2_A11_CC


title: HOKD_wk24_HPV_p1_H1_CC


title: Motoneuron_P3D7


title: 3023_wk12_KSK_p2_C11_CC


title: 3023_wk12_KSK_p2_E10_CC


title: HOKD_wk24_HPV_p1_H10_CC


title: 3023_wk12_KSK_p2_F10_CC


title: Motoneuron_P3C11


title: 3023_wk12_KSK_p2_D10_CC


title: Motoneuron_P3C10


title: HOKD_wk24_HPV_p1_G9_CC


title: 3023_wk12_KSK_p2_C10_CC


title: Motoneuron_P3C9


title: 3023_wk12_KSK_p2_B10_CC


title: ELT2219A1_2-37683608


title: Motoneuron_P3D4


title: HOKD_wk24_HPV_p1_G8_CC


title: 3023_wk12_KSK_p2_A10_CC


title: 3023_wk12_KSK_p2_G07_CC


title: Motoneuron_P3C8


title: HOKD_wk24_HPV_p1_G6_CC


title: 3023_wk12_KSK_p2_F07_CC


title: Motoneuron_P3C12


title: 3023_wk12_KSK_p2_E07_CC


title: HOKD_wk24_HPV_p1_G2_CC


title: Motoneuron_P3C7


title: 3023_wk12_KSK_p2_D07_CC


title: 3023_wk12_KSK_p2_C07_CC


title: Motoneuron_P3C5


title: 3023_wk12_KSK_p2_B07_CC


title: HOKD_wk24_HPV_p1_G10_CC


title: Motoneuron_P3C3


title: 3023_wk12_KSK_p2_A07_CC


title: HOKD_wk24_HPV_p1_G1_CC


title: 3023_wk12_KSK_p2_F06_CC


title: 3023_wk12_KSK_p2_D06_CC


title: Motoneuron_P3C2


title: 3023_wk12_KSK_p2_E06_CC


title: 3023_wk12_KSK_p2_C06_CC


title: 3023_wk12_KSK_p2_B06_CC


title: HOKD_wk24_HPV_p1_F9_CC


title: HOKD_wk24_HPV_p1_F8_CC


title: 3023_wk12_KSK_p2_G05_CC


title: 3023_wk12_KSK_p2_F05_CC


title: Motoneuron_P3B11


title: Motoneuron_P3B10


title: 3023_wk12_KSK_p2_E05_CC


title: Motoneuron_P3B9


title: 3023_wk12_KSK_p2_C05_CC


title: HOKD_wk24_HPV_p1_F6_CC


title: HOKD_wk24_HPV_p1_G11_CC


title: Motoneuron_P3C4


title: 3023_wk12_KSK_p2_B05_CC


title: HOKD_wk24_HPV_p1_F3_CC


title: Motoneuron_P3B8


title: 3023_wk12_KSK_p2_G06_CC


title: Motoneuron_P3B6


title: 3023_wk12_KSK_p2_A05_CC


title: 3023_wk12_KSK_p2_E04_CC


title: Motoneuron_P3C1


title: HOKD_wk24_HPV_p1_F11_CC


title: Motoneuron_P3B7


title: 3023_wk12_KSK_p2_F04_CC


title: HOKD_wk24_HPV_p1_F10_CC


title: 3023_wk12_KSK_p2_C04_CC


title: 3023_wk12_KSK_p2_A06_CC


title: Motoneuron_P3B5


title: 3023_wk12_KSK_p2_D05_CC


title: HOKD_wk24_HPV_p1_F1_CC


title: 3023_wk12_KSK_p2_B04_CC


title: 3023_wk12_KSK_p2_G03_CC


title: Motoneuron_P3B4


title: HOKD_wk24_HPV_p1_E8_CC


title: 3023_wk12_KSK_p2_A04_CC


title: HOKD_wk24_HPV_p1_E9_CC


title: 3023_wk12_KSK_p2_F03_CC


title: 3023_wk12_KSK_p2_D03_CC


title: 3023_wk12_KSK_p2_E03_CC


title: HOKD_wk24_HPV_p1_E6_CC


title: Motoneuron_P3A12


title: HOKD_wk24_HPV_p1_E3_CC


title: 3023_wk12_KSK_p2_C03_CC


title: 3023_wk12_KSK_p2_B03_CC


title: 3023_wk12_KSK_p2_A03_CC


title: HOKD_wk24_HPV_p1_E2_CC


title: 3023_wk12_KSK_p2_D04_CC


title: 3023_wk12_KSK_p2_G02_CC


title: Motoneuron_P3A10


title: 3023_wk12_KSK_p2_E02_CC


title: 3023_wk12_KSK_p2_F02_CC


title: HOKD_wk24_HPV_p1_E11_CC


title: 3023_wk12_KSK_p2_D02_CC


title: Motoneuron_P3B2


title: HOKD_wk24_HPV_p1_E10_CC


title: HOKD_wk24_HPV_p1_F2_CC


title: Motoneuron_P3A9


title: 3023_wk12_KSK_p2_C02_CC


title: HOKD_wk24_HPV_p1_D9_CC


title: Motoneuron_P3A7


title: 3023_wk12_KSK_p2_B02_CC


title: 3023_wk12_KSK_p2_C01_CC


title: 3023_wk12_KSK_p2_B01_CC


title: Motoneuron_P3A8


title: HOKD_wk24_HPV_p1_D8_CC


title: Motoneuron_P3A11


title: Motoneuron_P3A6


title: 3023_wk12_KSK_p2_A01_CC


title: HOKD_wk24_HPV_p1_D6_CC


title: 3023_wk24_KSK_p2_B11_CC


title: 3023_wk24_KSK_p2_G11_CC


title: 3023_wk24_KSK_p2_D10_CC


title: HOKD_wk24_HPV_p1_D3_CC


title: Motoneuron_P3A3


title: 3023_wk12_KSK_p2_E01_CC


title: HOKD_wk24_HPV_p1_E1_CC


title: 3023_wk24_KSK_p2_G09_CC


title: 3023_wk24_KSK_p2_B09_CC


title: Motoneuron_P3A1


title: 3023_wk12_KSK_p2_D01_CC


title: HOKD_wk24_HPV_p1_D11_CC


title: 3023_wk24_KSK_p2_H08_CC


title: HOKD_wk24_HPV_p1_D10_CC


title: HOKD_wk24_HPV_p1_D2_CC


title: Motoneuron_P2H12


title: 3023_wk24_KSK_p2_B08_CC


title: Motoneuron_P2H10


title: Motoneuron_P3A4


title: 3023_wk24_KSK_p2_H07_CC


title: 3023_wk24_KSK_p2_G08_CC


title: Motoneuron_P2H9


title: 3023_wk24_KSK_p2_E07_CC


title: 3023_wk12_KSK_p2_G04_CC


title: 3023_wk24_KSK_p2_H06_CC


title: 3023_wk24_KSK_p2_C10_CC


title: Motoneuron_P2H8


title: 3023_wk24_KSK_p2_G06_CC


title: Motoneuron_P3A2


title: 3023_wk24_KSK_p2_H09_CC


title: 3023_wk24_KSK_p2_G07_CC


title: HOKD_wk24_HPV_p1_C9_CC


title: HOKD_wk24_HPV_p1_C8_CC


title: 3023_wk24_KSK_p2_E06_CC


title: Motoneuron_P2H7


title: 3023_wk24_KSK_p2_G05_CC


title: 3023_wk24_KSK_p2_B05_CC


title: HOKD_wk24_HPV_p1_C6_CC


title: 3023_wk24_KSK_p2_H05_CC


title: 3023_wk24_KSK_p2_A05_CC


title: HOKD_wk24_HPV_p1_C3_CC


title: Motoneuron_P2H5


title: Motoneuron_P2H4


title: HOKD_wk24_HPV_p1_C2_CC


title: HOKD_wk24_HPV_p1_D1_CC


title: 3023_wk24_KSK_p2_H04_CC


title: 3023_wk24_KSK_p2_F04_CC


title: Motoneuron_P2H3


title: 3023_wk24_KSK_p2_E04_CC


title: HOKD_wk24_HPV_p1_C11_CC


title: 3023_wk24_KSK_p2_D04_CC


title: Motoneuron_P2H2


title: 3023_wk24_KSK_p2_C04_CC


title: HOKD_wk24_HPV_p1_C10_CC


title: 3023_wk24_KSK_p2_B04_CC


title: 3023_wk24_KSK_p2_G03_CC


title: Motoneuron_P2G12


title: 3023_wk24_KSK_p2_H03_CC


title: HOKD_wk24_HPV_p1_B9_CC


title: Motoneuron_P2H1


title: 3023_wk24_KSK_p2_B03_CC


title: Motoneuron_P2G11


title: Motoneuron_P2G10


title: 3023_wk24_KSK_p2_H02_CC


title: HOKD_wk24_HPV_p1_B8_CC


title: 3023_wk24_KSK_p2_G02_CC


title: HOKD_wk24_HPV_p1_B6_CC


title: 3023_wk24_KSK_p2_E02_CC


title: 3023_wk24_KSK_p2_D02_CC


title: 3023_wk24_KSK_p2_A03_CC


title: Motoneuron_P2G9


title: HOKD_wk24_HPV_p1_B2_CC


title: 3023_wk24_KSK_p2_C02_CC


title: 3023_wk24_KSK_p2_A02_CC


title: HOKD_wk24_HPV_p1_B10_CC


title: 3023_wk24_KSK_p2_A04_CC


title: Motoneuron_P2G7


title: Motoneuron_P2G3


title: 3023_wk24_KSK_p2_F01_CC


title: HOKD_wk24_HPV_p1_B11_CC


title: HOKD_wk24_HPV_p1_B1_CC


title: 3023_wk24_KSK_p2_C01_CC


title: HOKD_wk24_HPV_p1_C1_CC


title: HOKD_wk24_HPV_p1_A9_CC


title: Motoneuron_P2G5


title: 3023_wk24_KSK_p2_E01_CC


title: Motoneuron_P2F12


title: 3023_wk24_KSK_p2_H01_CC


title: 3221_12m1_GPR_p3_C06_CC


title: 3023_wk24_KSK_p2_A01_CC


title: Motoneuron_P2F11


title: 3221_12m1_GPR_p3_F05_CC


title: 3221_12m1_GPR_p3_D06_CC


title: 3023_wk24_KSK_p2_B02_CC


title: Motoneuron_P2F9


title: HOKD_wk24_HPV_p1_A2_CC


title: HOKD_wk24_HPV_p1_A8_CC


title: HOKD_wk24_HPV_p1_A6_CC


title: 3221_12m1_GPR_p3_B06_CC


title: Motoneuron_P2F7


title: Motoneuron_P2F10


title: 3221_12m1_GPR_p3_D04_CC


title: 3221_12m1_GPR_p3_A06_CC


title: 3221_12m1_GPR_p3_E05_CC


title: Motoneuron_P2F8


title: 3221_12m1_GPR_p3_D03_CC


title: 3221_12m1_GPR_p3_D05_CC


title: 3023_wk24_KSK_p2_B01_CC


title: HOKD_wk24_HPV_p1_A11_CC


title: 3221_12m1_GPR_p3_A05_CC


title: HOKD_wk24_HPV_p1_A1_CC


title: Motoneuron_P2F5


title: 3221_12m1_GPR_p3_C01_CC


title: HOKD_wk24_HPV_p1_A10_CC


title: 3221_12m1_GPR_p3_C03_CC


title: Motoneuron_P2F6


title: 3221_12m1_GPR_p3_B03_CC


title: HOKD_wk2_HPV_p3_H8_CC


title: HOKD_wk2_HPV_p3_H9_CC


title: 3221_12m1_GPR_p2_D06_CC


title: 3221_12m1_GPR_p2_B07_CC


title: HOKD_wk2_HPV_p3_H6_CC


title: 3221_12m1_GPR_p3_A01_CC


title: 3221_12m1_GPR_p2_A06_CC


title: Motoneuron_P2F1


title: 3221_12m1_GPR_p2_A07_CC


title: Motoneuron_P2F3


title: Motoneuron_P2E12


title: 3221_12m1_GPR_p2_D04_CC


title: HOKD_wk2_HPV_p3_H5_CC


title: 3221_12m1_GPR_p2_C01_CC


title: 3221_scrn_GPR_p2_H06_CC


title: HOKD_wk2_HPV_p3_H2_CC


title: 3221_12m1_GPR_p2_A01_CC


title: 3221_scrn_GPR_p2_F06_CC


title: 3221_scrn_GPR_p2_E06_CC


title: Motoneuron_P2E11


title: HOKD_wk2_HPV_p3_H10_CC


title: 3221_scrn_GPR_p2_C06_CC


title: Motoneuron_P2E10


title: HOKD_wk2_HPV_p3_H1_CC


title: Motoneuron_P2E9


title: Motoneuron_P2F4


title: 3221_scrn_GPR_p2_H04_CC


title: HOKD_wk2_HPV_p3_G9_CC


title: 3221_scrn_GPR_p2_G04_CC


title: Motoneuron_P2E8


title: HOKD_wk2_HPV_p3_G8_CC


title: Motoneuron_P2E7


title: 3221_scrn_GPR_p2_D04_CC


title: 3221_scrn_GPR_p2_C04_CC


title: HOKD_wk2_HPV_p3_G6_CC


title: 3221_scrn_GPR_p2_B04_CC


title: Motoneuron_P2E6


title: 3221_scrn_GPR_p2_H03_CC


title: HOKD_wk2_HPV_p3_G5_CC


title: 3221_scrn_GPR_p2_G03_CC


title: Motoneuron_P2E5


title: HOKD_wk2_HPV_p3_G3_CC


title: 3221_scrn_GPR_p2_C03_CC


title: Motoneuron_P2E4


title: 3221_scrn_GPR_p2_A02_CC


title: 3221_scrn_GPR_p2_C02_CC


title: 3221_scrn_GPR_p2_D03_CC


title: Motoneuron_P2E2


title: 3221_scrn_GPR_p2_A01_CC


title: 3221_scrn_GPR_p2_C01_CC


title: HOKD_wk2_HPV_p3_G1_CC


title: HOKD_wk2_HPV_p3_G10_CC


title: Motoneuron_P2D12


title: 3221_scrn_GPR_p2_E04_CC


title: HOKD_wk2_HPV_p3_G2_CC


title: 3221_scrn_GPR_p2_F04_CC


title: Motoneuron_P2D11


title: 4059_wk12_CIN_p2_H06_CC

value: CIN


title: 4059_wk12_CIN_p2_C07_CC


title: 4059_wk12_CIN_p2_B07_CC


title: HOKD_wk2_HPV_p3_F9_CC


title: Motoneuron_P2D10


title: 4059_wk12_CIN_p2_E06_CC


title: 4059_wk12_CIN_p2_G05_CC


title: Motoneuron_P2D8


title: HOKD_wk2_HPV_p3_F8_CC


title: 4059_wk12_CIN_p2_F05_CC


title: HOKD_wk2_HPV_p3_F6_CC


title: 4059_wk12_CIN_p2_D05_CC


title: 4059_wk12_CIN_p2_C05_CC


title: Motoneuron_P2D7


title: 4059_wk12_CIN_p2_A05_CC


title: HOKD_wk2_HPV_p3_F3_CC


title: HOKD_wk2_HPV_p3_F5_CC


title: Motoneuron_P2D5


title: Motoneuron_P2D6


title: HOKD_wk2_HPV_p3_F2_CC


title: Motoneuron_P2D4


title: 4059_wk12_CIN_p2_B04_CC


title: 4059_wk12_CIN_p2_F04_CC


title: 4059_wk12_CIN_p2_C04_CC


title: 4059_wk12_CIN_p2_G06_CC


title: HOKD_wk2_HPV_p3_F1_CC


title: HOKD_wk2_HPV_p3_F10_CC


title: 4059_wk12_CIN_p2_D03_CC


title: 4059_wk12_CIN_p2_A04_CC


title: Motoneuron_P2D3


title: 4059_wk12_CIN_p2_E04_CC


title: 4059_wk12_CIN_p2_H03_CC


title: Motoneuron_P2D2


title: 4059_wk12_CIN_p2_C03_CC


title: 4059_wk12_CIN_p2_H02_CC


title: HOKD_wk2_HPV_p3_E8_CC


title: 4059_wk12_CIN_p2_B03_CC


title: Motoneuron_P2D1


title: HOKD_wk2_HPV_p3_E9_CC


title: 4059_wk12_CIN_p2_E02_CC


title: 4059_wk12_CIN_p2_C02_CC


title: HOKD_wk2_HPV_p3_E6_CC


title: Motoneuron_P2C11


title: 4059_wk12_CIN_p1_G01_CC


title: 4059_wk12_CIN_p1_E03_CC


title: HOKD_wk2_HPV_p3_E5_CC


title: Motoneuron_P2C10


title: 4059_wk12_CIN_p1_D01_CC


title: HOKD_wk2_HPV_p3_E3_CC


title: 4059_wk4_CIN_p2_C04_CC


title: HOKD_wk2_HPV_p3_E2_CC


title: 4059_wk12_CIN_p2_H04_CC


title: 4059_wk4_CIN_p2_H02_CC


title: 4059_wk4_CIN_p2_E02_CC


title: Motoneuron_P2C7


title: Motoneuron_P2C6


title: Motoneuron_P2C5


title: 4059_wk4_CIN_p2_C03_CC


title: 4059_wk4_CIN_p2_D03_CC


title: HOKD_wk2_HPV_p3_E1_CC


title: 4059_wk4_CIN_p1_E05_CC


title: HOKD_wk2_HPV_p3_E10_CC


title: 4059_wk4_CIN_p2_A01_CC


title: 4059_wk12_CIN_p1_B04_CC


title: 4059_wk4_CIN_p2_G01_CC


title: Motoneuron_P2C12


title: 4059_wk4_CIN_p1_D04_CC


title: HOKD_wk2_HPV_p3_D9_CC


title: 4059_wk4_CIN_p1_G05_CC


title: 4059_wk4_CIN_p1_B01_CC


title: Motoneuron_P2C9


title: 4059_wk4_CIN_p1_H01_CC


title: HOKD_wk2_HPV_p3_D8_CC


title: Motoneuron_P2C3


title: 4059_wk6_CIN_p3_C06_CC


title: 4059_wk6_CIN_p3_B06_CC


title: 4059_wk6_CIN_p3_A06_CC


title: HOKD_wk2_HPV_p3_D5_CC


title: Motoneuron_P2C1


title: HOKD_wk2_HPV_p3_D3_CC


title: 4059_wk6_CIN_p3_H05_CC


title: 4059_wk6_CIN_p3_G05_CC


title: 4059_wk6_CIN_p3_F05_CC


title: HOKD_wk2_HPV_p3_D2_CC


title: 4059_wk6_CIN_p3_E05_CC


title: 4059_wk6_CIN_p3_D05_CC


title: Motoneuron_P2B11


title: Motoneuron_P2B10


title: HOKD_wk2_HPV_p3_D10_CC


title: 4059_wk6_CIN_p3_A05_CC


title: Motoneuron_P2B8


title: 4059_wk6_CIN_p3_B05_CC


title: HOKD_wk2_HPV_p3_D6_CC


title: Motoneuron_P2C4


title: Motoneuron_P2B7


title: Motoneuron_P2C2


title: HOKD_wk2_HPV_p3_C8_CC


title: 4059_wk6_CIN_p3_H02_CC


title: HOKD_wk2_HPV_p3_D1_CC


title: 4059_wk6_CIN_p3_C02_CC


title: Motoneuron_P2B12


title: 4059_wk6_CIN_p3_E02_CC


title: Motoneuron_P2B6


title: HOKD_wk2_HPV_p3_C6_CC


title: 4059_wk6_CIN_p3_B02_CC


title: HOKD_wk2_HPV_p3_C9_CC


title: Motoneuron_P2B4


title: HOKD_wk2_HPV_p3_C5_CC


title: 4059_wk6_CIN_p3_F01_CC


title: 4059_wk6_CIN_p3_D01_CC


title: 4059_wk6_CIN_p3_B01_CC


title: 4059_wk6_CIN_p3_G02_CC


title: Motoneuron_P2B3


title: Motoneuron_P2B2


title: 4059_wk6_CIN_p1_F08_CC


title: Motoneuron_P2A11


title: HOKD_wk2_HPV_p3_C2_CC


title: 4059_wk6_CIN_p3_D02_CC


title: HOKD_wk2_HPV_p3_C10_CC


title: 4059_wk6_CIN_p1_B08_CC


title: Motoneuron_P2A10


title: 4059_wk6_CIN_p1_H07_CC


title: HOKD_wk2_HPV_p3_C1_CC


title: 4059_wk6_CIN_p1_F07_CC


title: Motoneuron_P2A8


title: 4059_wk6_CIN_p3_H01_CC


title: HOKD_wk2_HPV_p3_B9_CC


title: Motoneuron_P2A6


title: 4059_wk6_CIN_p1_A07_CC


title: 4059_wk6_CIN_p1_B07_CC


title: 4059_wk6_CIN_p1_D07_CC


title: HOKD_wk2_HPV_p3_B8_CC


title: 4059_wk6_CIN_p1_H08_CC


title: HOKD_wk2_HPV_p3_C3_CC


title: 4059_wk6_CIN_p1_F06_CC


title: HOKD_wk2_HPV_p3_B6_CC


title: 4059_wk6_CIN_p1_D06_CC


title: 4059_wk6_CIN_p1_H06_CC


title: 4059_wk6_CIN_p1_B06_CC


title: HOKD_wk2_HPV_p3_B5_CC


title: 4059_wk6_CIN_p1_A06_CC


title: HOKD_wk2_HPV_p3_B3_CC


title: 4059_wk6_CIN_p1_D08_CC


title: Motoneuron_P2A5


title: 4059_wk6_CIN_p1_G07_CC


title: 4059_wk6_CIN_p1_E05_CC


title: Motoneuron_P2A4


title: Motoneuron_P2A2


title: 4059_wk6_CIN_p1_D05_CC


title: Motoneuron_P2A1


title: 4059_wk6_CIN_p1_F04_CC


title: Motoneuron_P1H11


title: HOKD_wk2_HPV_p3_B10_CC


title: 4059_wk6_CIN_p1_E04_CC


title: 4059_wk6_CIN_p1_C04_CC


title: HOKD_wk2_HPV_p3_B1_CC


title: 4059_wk6_CIN_p1_G03_CC


title: HOKD_wk2_HPV_p3_A9_CC


title: Motoneuron_P1H9


title: Motoneuron_P1H8


title: 4059_wk6_CIN_p1_F03_CC


title: Motoneuron_P2A3


title: 4059_wk6_CIN_p1_B04_CC


title: 4059_wk6_CIN_p1_F05_CC


title: HOKD_wk2_HPV_p3_A6_CC


title: 4059_wk6_CIN_p1_E03_CC


title: 4059_wk6_CIN_p1_C03_CC


title: 4059_wk6_CIN_p1_H04_CC


title: 4059_wk6_CIN_p1_A03_CC


title: 4059_wk6_CIN_p1_D02_CC


title: Motoneuron_P1H5


title: 4059_wk6_CIN_p1_D03_CC


title: 4059_wk6_CIN_p1_A02_CC


title: HOKD_wk2_HPV_p3_A4_CC


title: HOKD_wk2_HPV_p3_B2_CC


title: Motoneuron_P1H7


title: HOKD_wk2_HPV_p3_A5_CC


title: 4059_wk8_CIN_p2_G10_CC


title: Motoneuron_P1H2


title: HOKD_wk2_HPV_p3_A3_CC


title: 4059_wk6_CIN_p1_G04_CC


title: 4059_wk8_CIN_p2_B10_CC


title: 4059_wk8_CIN_p2_F10_CC


title: 4059_wk8_CIN_p2_H09_CC


title: HOKD_wk2_HPV_p3_A2_CC


title: 4059_wk8_CIN_p2_H08_CC


title: Motoneuron_P1G10


title: Motoneuron_P1G12


title: Motoneuron_P1H6


title: 4059_wk8_CIN_p2_G08_CC


title: Motoneuron_P1G9


title: HOKD_wk2_HPV_p3_A1_CC


title: 4059_wk8_CIN_p2_F08_CC


title: 4059_wk8_CIN_p2_E08_CC


title: THDS_wk8_KLV_p1_H9_CC

value: CH-THDS

value: KLV


title: 4059_wk8_CIN_p2_C08_CC


title: 4059_wk8_CIN_p2_H07_CC


title: Motoneuron_P1G7


title: Motoneuron_P1G8


title: 4059_wk8_CIN_p2_G07_CC


title: 4059_wk8_CIN_p2_A07_CC


title: Motoneuron_P1G6


title: 4059_wk8_CIN_p2_H06_CC


title: 4059_wk8_CIN_p2_C07_CC


title: THDS_wk8_KLV_p1_H5_CC


title: Motoneuron_P1G5


title: THDS_wk8_KLV_p1_H6_CC


title: 4059_wk8_CIN_p2_E09_CC


title: 4059_wk8_CIN_p2_C06_CC


title: Motoneuron_P1G4


title: 4059_wk8_CIN_p2_H05_CC


title: THDS_wk8_KLV_p1_H2_CC


title: THDS_wk8_KLV_p1_H11_CC


title: Motoneuron_P1G3


title: 4059_wk8_CIN_p2_F06_CC


title: 4059_wk8_CIN_p2_H03_CC


title: HOKD_wk2_HPV_p3_A8_CC


title: 4059_wk8_CIN_p2_A03_CC


title: 4059_wk8_CIN_p2_H02_CC


title: THDS_wk8_KLV_p1_G9_CC


title: THDS_wk8_KLV_p1_H10_CC


title: 4059_wk8_CIN_p2_G02_CC


title: Motoneuron_P1F11


title: 4059_wk8_CIN_p2_F02_CC


title: 4059_wk8_CIN_p2_E02_CC


title: 4059_wk8_CIN_p2_C02_CC


title: THDS_wk8_KLV_p1_G5_CC


title: Motoneuron_P1F10


title: Motoneuron_P1F9


title: THDS_wk8_KLV_p1_G2_CC


title: Motoneuron_P1F5


title: HOKD_wk2_HPV_p3_A10_CC


title: 4059_wk8_CIN_p2_H04_CC


title: 4059_wk8_CIN_p2_H01_CC


title: 4059_wk8_CIN_p2_A02_CC


title: THDS_wk8_KLV_p1_G11_CC


title: 4059_wk8_CIN_p2_G01_CC


title: 4059_wk8_CIN_p2_F01_CC


title: 4059_wk8_CIN_p2_E01_CC


title: Motoneuron_P1F12


title: Motoneuron_P1F4


title: THDS_wk8_KLV_p1_F9_CC


title: 4059_wk8_CIN_p2_B01_CC


title: THDS_wk8_KLV_p1_G10_CC


title: THDS_wk8_KLV_p1_G6_CC


title: 4059_wk8_CIN_p2_C01_CC


title: Motoneuron_P1F3


title: Motoneuron_P1E12


title: 4059_wk8_CIN_p1_C09_CC


title: 4059_wk8_CIN_p2_D01_CC


title: 4059_wk8_CIN_p1_C10_CC


title: Motoneuron_P1E11


title: 4059_wk8_CIN_p1_B08_CC


title: 4059_wk8_CIN_p2_B02_CC


title: 4059_wk8_CIN_p1_A08_CC


title: 4059_wk8_CIN_p1_C07_CC


title: THDS_wk8_KLV_p1_F5_CC


title: Motoneuron_P1E10


title: 4059_wk8_CIN_p1_B07_CC


title: Motoneuron_P1E9


title: 4059_wk8_CIN_p1_C06_CC


title: 4059_wk8_CIN_p1_B06_CC


title: THDS_wk8_KLV_p1_F11_CC


title: THDS_wk8_KLV_p1_F10_CC


title: 4059_wk8_CIN_p1_C05_CC


title: 4059_wk8_CIN_p1_B05_CC


title: 4059_wk8_CIN_p1_A06_CC


title: Motoneuron_P1E8


title: THDS_wk8_KLV_p1_F1_CC


title: Motoneuron_P1E7


title: 4059_wk8_CIN_p1_A10_CC


title: Motoneuron_P1E6


title: THDS_wk8_KLV_p1_E9_CC


title: Motoneuron_P1E5


title: 4059_wk8_CIN_p1_A05_CC


title: THDS_wk8_KLV_p1_E6_CC


title: 4059_wk8_CIN_p1_B04_CC


title: THDS_wk8_KLV_p1_E5_CC


title: 4059_wk8_CIN_p1_C03_CC


title: Motoneuron_P1E1


title: THDS_wk8_KLV_p1_E3_CC


title: THDS_wk8_KLV_p1_F6_CC


title: THDS_wk8_KLV_p1_F3_CC


title: Motoneuron_P1D12


title: 4059_wk8_CIN_p1_C02_CC


title: Motoneuron_P1D11


title: Motoneuron_P1D10


title: 4059_wk8_CIN_p1_A02_CC


title: 4059_wk8_CIN_p1_B02_CC


title: Motoneuron_P1D9


title: THDS_wk8_KLV_p1_E2_CC


title: THDS_wk8_KLV_p1_E11_CC


title: THDS_wk8_KLV_p1_E10_CC


title: 4059_wk8_CIN_p1_C01_CC


title: Motoneuron_P1D7


title: 3132_24m1_ATD_p2_H04_CC


title: 4059_wk8_CIN_p1_B01_CC


title: Motoneuron_P1D5


title: THDS_wk8_KLV_p1_E1_CC


title: Motoneuron_P1D4


title: Motoneuron_P1D3


title: THDS_wk8_KLV_p1_D3_CC


title: THDS_wk8_KLV_p1_D9_CC


title: 3132_24m1_ATD_p2_H03_CC


title: 3132_24m1_ATD_p2_A04_CC


title: Motoneuron_P1D2


title: THDS_wk8_KLV_p1_D2_CC


title: 3132_24m1_ATD_p2_G03_CC


title: 4059_wk8_CIN_p1_A01_CC


title: 3132_24m1_ATD_p2_D03_CC


title: THDS_wk8_KLV_p1_D11_CC


title: Motoneuron_P1D1


title: Motoneuron_P1C12


title: THDS_wk8_KLV_p1_D5_CC


title: THDS_wk8_KLV_p1_D10_CC


title: 3132_24m1_ATD_p2_H02_CC


title: Motoneuron_P1C11


title: 3132_24m1_ATD_p2_E02_CC


title: 3132_24m1_ATD_p2_D02_CC


title: THDS_wk8_KLV_p1_C9_CC


title: THDS_wk8_KLV_p1_D1_CC


title: Motoneuron_P1D6


title: Motoneuron_P1C10


title: THDS_wk8_KLV_p1_D6_CC


title: 3132_24m1_ATD_p2_A02_CC


title: THDS_wk8_KLV_p1_C6_CC


title: Motoneuron_P1C8


title: THDS_wk8_KLV_p1_C3_CC


title: THDS_wk8_KLV_p1_C4_CC


title: Motoneuron_P1C4


title: THDS_wk8_KLV_p1_C2_CC


title: Motoneuron_P1C5


title: 3132_24m1_ATD_p1_D05_CC


title: 3132_24m1_ATD_p1_B05_CC


title: 3132_24m1_ATD_p1_F05_CC


title: THDS_wk8_KLV_p1_C5_CC


title: 3132_24m1_ATD_p1_A05_CC


title: THDS_wk8_KLV_p1_C11_CC


title: 3132_24m1_ATD_p2_B05_CC


title: Motoneuron_P1C6


title: Motoneuron_P1C9


title: THDS_wk8_KLV_p1_C10_CC


title: THDS_wk8_KLV_p1_C1_CC


title: Motoneuron_P1C3


title: THDS_wk8_KLV_p1_B9_CC


title: Motoneuron_P1C2


title: 3132_24m1_ATD_p1_C03_CC


title: 3132_24m1_ATD_p1_B03_CC


title: Motoneuron_P1B11


title: Motoneuron_P1B12


title: Motoneuron_P1B8


title: THDS_wk8_KLV_p1_B6_CC


title: 3132_24m1_ATD_p1_G02_CC


title: Motoneuron_P1B7


title: 3132_24m1_ATD_p2_C06_CC


title: 3132_24m1_ATD_p1_E02_CC


title: THDS_wk8_KLV_p1_B5_CC


title: Motoneuron_P1B4


title: THDS_wk8_KLV_p1_B11_CC


title: Motoneuron_P1B2


title: Motoneuron_P1A10


title: Motoneuron_P1A11


title: 3132_24m1_ATD_p1_F01_CC


title: THDS_wk8_KLV_p1_B10_CC


title: 3132_30m_ATD_p1_E5_CC


title: THDS_wk8_KLV_p1_B4_CC


title: THDS_wk8_KLV_p1_B2_CC


title: 3132_24m1_ATD_p1_C01_CC


title: THDS_wk8_KLV_p1_B1_CC


title: 3132_30m_ATD_p1_E1_CC


title: Motoneuron_P1A5


title: Motoneuron_P1A4


title: 3132_24m1_ATD_p1_G01_CC


title: Motoneuron_P1A3


title: THDS_wk8_KLV_p1_A5_CC


title: Motoneuron_P1A8


title: 3132_12m1_ATD_p9_F01_CC


title: THDS_wk8_KLV_p1_A4_CC


title: Motoneuron_P1A2


title: 3132_12m1_ATD_p9_D01_CC


title: THDS_wk8_KLV_p1_A3_CC


title: 3132_12m1_ATD_p9_C01_CC


title: 3132_30m_ATD_p1_C1_CC


title: THDS_wk8_KLV_p1_A9_CC


title: TLSCC57/SPR ATAC

city: GuangZhou

first: Hanwen

last: Yu

state: GuangDong

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-*Sen Road, Yuexiu District, Guangzhou City, Guangdong Province, 510080, PRC

institute: SUN YAT-SEN UNIVERSITY

description: TLSCC57/SPR ATAC

library_source: genomic

data_processing:
The bioinformatics analysis of ATAC-seq datasets generated in this study or downloaded from publicly available repositories and data portals were performed by custom shell scripts in which raw data were first trimmed and filtered by TrimGalore with default parameter. Qualified read pairs were then aligned to mouse genome (mm10) by Bowtie2 (release 2.4.1). Biological and optical duplicates were removed with Sambamba (release 0.7.1). Last we used MACS2 (release 2.2.7.1; parameters for narrow peaks such as H3K27ac and H3K4me3: -p 0.05 -g mm -f BAMPE; broad peaks such as H3K27me3, H3K4me1, H3K79me2, H3K79me3 and H3K4me3: --broad --broad-cutoff 0.05 -g mm -f BAMPE; ATAC-seq: --broad --broad-cutoff 0.05 -g mm -f BAMPE) to call peaks. The highly reproducible peaks were identified by package IDR, which is a uni?ed approach to measure the reproducibility of ?ndings identi?ed from replicate experiments and provide highly stable thresholds based on reproducibility.!Sample_data_processing = Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content:
Peak bed files.
wig files were generated using deeptools; Scores represent RPKM values.

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol: Mouse ESCs were cultured in N2B27 medium comprising 10ng/ml of LIF, 1 μM PD03, 3 μM CHIR9901 (Nichols and Ying, 2006) or in KnockOut medium comprising 20% KnockOut serum replacement, 1X non-essential amino acids solution, 2 mM L-glutamine, 55 µM 2-mercaptoethanol and 10 ng/ml LIF. The medium was changed every another day. When passaging, cells were dissociated by 0.05% Trypsin-EDTA into single cells and re-plated every 3 days at a ratio of 1:8-1:10.

extract_protocol:
A total of 50,000 cells were washed once with 50 µl of cold PBS and resuspended in 50 µl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) NP-40). To perform transposition reaction, the collected nuclei by centrifuged for 10 minutes at 500g at 4°C was mixed with the transposition reaction mix (10 µl TTBL, 5 µl TTE Mix V50 and nuclease-free H2O up to 50 µl in total) of TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, catalog. no. TD501-01) for 10 minutes at 55 °C.
Samples were then PCR amplified. Post-PCR clean-up was performed by adding 1.2 volume of DNA clean beads (Vazyme, catalog. no. N411-02). Library concentration was measured with Qubit. Library integrity was checked by the Agilent bioanalyzer. Finally, the ATAC library was sequenced on an Illumina Hiseq X10 platform and 150 bp paired-end reads were generated.

treatment_protocol: 2C::GFP+/SGC cells were cultured in in KnockOut medium comprising 20% KnockOut serum replacement, 1X non-essential amino acids solution, 2 mM L-glutamine, 55 µM 2-mercaptoethanol and 10 ng/ml LIF, under treatment with SGC0946 (2 µM). 2C::GFP+/SA cells were cultured in in KnockOut medium comprising 20% KnockOut serum replacement, 1X non-essential amino acids solution, 2 mM L-glutamine, 55 µM 2-mercaptoethanol and 10 ng/ml IL6/sIL-6R, under treatment with SGC0946 (2 µM) and AS8351 (2 μM).

value: mouse embryonic stem cells

tag: treatment

value: TPSC medium


title: TLSC2C ATAC

description: TLSC2C ATAC


title: THDS_wk8_KLV_p1_A10_CC


title: 3132_12m1_ATD_p2_G04_CC


title: 3132_12m1_ATD_p9_B01_CC


title: 3132_12m1_ATD_p9_A01_CC


title: 3132_12m1_ATD_p2_H04_CC


title: THDS_wk2_KLV_p1_H9_CC


title: THDS_wk2_KLV_p1_H7_CC


title: THDS_wk8_KLV_p1_A11_CC


title: mESC IgG

description: mESC IgG

data_processing:
Library strategy: CUT&Tag-sequencing
The bioinformatics analysis of CUT&Tag datasets generated in this study or downloaded from publicly available repositories and data portals were performed by custom shell scripts in which raw data were first trimmed and filtered by TrimGalore with default parameter. Qualified read pairs were then aligned to mouse genome (mm10) by Bowtie2 (release 2.4.1). Biological and optical duplicates were removed with Sambamba (release 0.7.1). Last we used MACS2 (release 2.2.7.1; parameters for narrow peaks such as H3K27ac and H3K4me3: -p 0.05 -g mm -f BAMPE; broad peaks such as H3K27me3, H3K4me1, H3K79me2, H3K79me3 and H3K4me3: --broad --broad-cutoff 0.05 -g mm -f BAMPE; ATAC-seq: --broad --broad-cutoff 0.05 -g mm -f BAMPE) to call peaks. The highly reproducible peaks were identified by package IDR, which is a uni?ed approach to measure the reproducibility of findings identied from replicate experiments and provide highly stable thresholds based on reproducibility.genome build mm10
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content:
peak bed files.
wig files were generated using deeptools; Scores represent RPKM values.

extract_protocol:
A hyperactive pA-Tn5 transposon for the illumina platform was first generated. Cells were harvested and washed twice. Then the nuclei were isolated by ice-cold NE1 buffer and re-suspended in wash buffer. 10 μl of activated concanavalin A beads were added per sample and incubated at room temperature for 10 minutes. Primary antibody (1:50 dilution of anti-IgG, anti-H3K4me1,H34me3,H3K27me3 and H3K27ac) incubation was performed on a rotator at 4°C overnight. To increase the number of protein A binding sites, a secondary antibody (such as guinea pig anti-Rabbit IgG antibody for a rabbit primary antibody, and rabbit anti-mouse IgG for a mouse primary antibody) was diluted 1:100 in wash buffer and incubated at RT for 1h. After removing unbound antibodies, cells were mixed with 1:100 dilution of pA-Tn5 (0.04 µM) and incubated at room temperature for 1 hour on rotator. Next, cells were re-suspended in 300 µl tagmentation buffer and incubated at 37 °C for 1 h. To stop tagmentation, 10 µl 0.5 M EDTA, 3µl 10% SDS and 2.5 µl of 20 mg/mL Proteinase K was added to sample, which was incubated overnight at 37 °C. DNA was extracted by PCI and dissolved in 30 μl TE buffer.
To amplify libraries, we added P5 primer, P7 primer (Vazyme, catalog. no. TD202), TruePrep Amplify Enzyme (Vazyme catalog. no. TD601) and performed PCR with the conditions below: 72°C for 3 minutes; 98°C for 30 seconds; 18 cycles of 98°C for 15 seconds, 63°C for 15 seconds; 72°C for 5 minutes. Post-PCR clean-up was performed by adding 1.2 volume of DNA clean beads (Vazyme, catalog. no. N411) and libraries were eluted in 20 μl nuclease-free water.

tag: celltype

tag: chip antibody

value: IgG(Abcam, ab171870)

value: untreated


title: 3132_12m1_ATD_p9_G01_CC


title: TLSC IgG

description: TLSC IgG


title: mESC H3K9me2

description: mESC H3K9me2

value: H3K9me2(Abcam, ab1220)


title: TLSC H3K9me2

description: TLSC H3K9me2


title: 3132_12m1_ATD_p2_F04_CC


title: THDS_wk8_KLV_p1_A2_CC


title: 3132_12m1_ATD_p2_D04_CC


title: TLSC H3K4me3

description: TLSC H3K4me3

value: H3K4me3(Millipore, 07-473)


title: THDS_wk2_KLV_p1_H6_CC


title: 3132_12m1_ATD_p2_E04_CC


title: sc.E15.5.placenta

description: E15.5 placenta scRNAseq

data_processing:
The scRNA-seq data generated by SMART-seq2 and bulk RNA-seq data were pre-processed according to the following pipeline. Sequencing quality of all high-throughput sequencing data were first comprehensively examined by FastQC (release 0.11.9). Next, adapter sequences and bases with sequencing quality < 20 were trimmed from raw data by TrimGalore (release 0.6.5; default parameter). Trimmed read pairs were aligned to mouse genome (mm10) with STAR (release 2.7.4a). For quantification of gene and repeat locus expression, the following command-line arguments were used: --outSAMmapqUnique 255 ?outFilterMultimapNmax 10. We computed the number of uniquely mapped reads of each gene and repeat element using the featureCounts package (release 2.0.0; default parameter). The 10X Genomics scRNA-seq reads were demultiplexed, aligned to the mm10 reference genome and quantified using the toolkit Cell Ranger (release v6.0.2).!Sample_data_processing = Genome_build: mm10 (GRCm38)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content:
TPM values for each sample.
Matrix table with raw gene counts for every gene and every sample.

source_name: E15.5 placenta

extract_protocol:
Total RNA was extracted from  mESC, 2C::GFP+, 2C::GFP+/SGC and 2C::GFP+/SA cells using the Trizol kit (Thermo Fisher Scientific, catalog. no. 15596018) following the manufacturer’s instructions. PolyA(+) RNA was isolated for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: E15.5 placenta


title: THDS_wk2_KLV_p1_H5_CC


title: 3132_12m1_ATD_p2_B04_CC


title: THDS_wk2_KLV_p1_H4_CC


title: 3132_12m1_ATD_p2_A04_CC


title: sc.E15.5.embryo

description: E15.5 embryo scRNAseq

source_name: E15.5 embryo

value: E15.5 embryo


title: mESC H3K4me3

description: mESC H3K4me3


title: sc.E13.5.ep

description: E13.5 embryo + placenta scRNAseq

source_name: E13.5 embryo + placenta

value: E13.5 embryo + placenta


title: THDS_wk2_KLV_p1_H8_CC


title: THDS_wk2_KLV_p1_H3_CC


title: mESCC57/SPR

description: mESCC57/SPR RNA-seq

value: 2i medium


title: 3132_12m1_ATD_p2_G03_CC


title: rESCTLSC

description: rESCTLSC RNA-seq


title: 2CLCC57/SPR

description: 2CLCC57/SPR RNA-seq

value: KOSR medium


title: THDS_wk2_KLV_p1_H2_CC


title: THDS_wk2_KLV_p1_G7_CC


title: TLSCC57/SPR(P4)

description: TLSCC57/SPR(P4) RNA-seq


title: 3132_12m1_ATD_p2_E03_CC

value: ATD


title: 3132_12m1_ATD_p2_D03_CC

value: CD8+ T cell


title: THDS_wk2_KLV_p1_G6_CC


title: THDS_wk2_KLV_p1_G5_CC


title: 3132_12m1_ATD_p2_C03_CC


title: TLSC2C(P14)

description: TLSC2C(P14) RNA-seq


title: THDS_wk2_KLV_p1_G4_CC


title: 3132_12m1_ATD_p2_H03_CC


title: TLSC2C(P8)

description: TLSC2C(P8) RNA-seq


title: 3132_12m1_ATD_p2_B03_CC


title: 3132_12m1_ATD_p2_H02_CC


title: 2C::GFP+/SA ATAC rep2

description: 2C::GFP+/SA ATAC rep2

treatment_protocol: 2C::GFP+/SGC cells were cultured in KnockOut medium comprising 20% KnockOut serum replacement, 1X non-essential amino acids solution, 2 mM L-glutamine, 55 µM 2-mercaptoethanol and 10 ng/ml LIF, under treatment with SGC0946 (2 µM). 2C::GFP+/SA cells were cultured in KnockOut medium comprising 20% KnockOut serum replacement, 1X non-essential amino acids solution, 2 mM L-glutamine, 55 µM 2-mercaptoethanol and 10 ng/ml IL6/sIL-6R, under treatment with SGC0946 (2 µM) and AS8351 (2 μM).

tag: genotype/variation

value: SGCAS treated


title: THDS_wk2_KLV_p1_G2_CC


title: 2C::GFP+/SA ATAC rep1

description: 2C::GFP+/SA ATAC rep1


title: 3132_12m1_ATD_p2_G02_CC


title: 3132_12m1_ATD_p2_F02_CC


title: THDS_wk2_KLV_p1_G1_CC


title: THDS_wk2_KLV_p1_H1_CC


title: 3132_12m1_ATD_p2_F03_CC


title: TLSCC57/SPR(P12)

description: TLSCC57/SPR(P12) RNA-seq


title: THDS_wk2_KLV_p1_F6_CC


title: 2C::GFP+/SGC ATAC rep1

description: 2C::GFP+/SGC ATAC rep1

value: SGC treated


title: 3132_12m1_ATD_p2_D02_CC


title: THDS_wk2_KLV_p1_F5_CC

value: CH-THDS


title: 3132_12m1_ATD_p2_F01_CC


title: 2C::GFP+ ATAC rep2

description: 2C::GFP+ ATAC rep2


title: THDS_wk2_KLV_p1_F4_CC

value: KLV


title: 2C::GFP+ ATAC rep1

description: 2C::GFP+ ATAC rep1

value: mouse embryonic stem cells


title: THDS_wk2_KLV_p1_G3_CC


title: 3132_12m1_ATD_p2_D01_CC


title: mESC ATAC rep2

description: mESC ATAC rep2

value: WT


title: 3132_12m1_ATD_p2_B01_CC


title: 3132_12m1_ATD_p2_C01_CC


title: 2C::GFP+/SA IgG rep2

description: 2C::GFP+/SA IgG rep2

extract_protocol:
A hyperactive pA-Tn5 transposon for the Illumina platform was first generated. Cells were harvested and washed twice. Then the nuclei were isolated by ice-cold NE1 buffer and re-suspended in wash buffer. 10 μl of activated concanavalin A beads were added per sample and incubated at room temperature for 10 minutes. Primary antibody (1:50 dilution of anti-IgG, anti-H3K4me1, H34me3, H3K27me3 and H3K27ac) incubation was performed on a rotator at 4°C overnight. To increase the number of protein A binding sites, a secondary antibody (such as guinea pig anti-Rabbit IgG antibody for a rabbit primary antibody, and rabbit anti-mouse IgG for a mouse primary antibody) was diluted 1:100 in wash buffer and incubated at RT for 1h. After removing unbound antibodies, cells were mixed with 1:100 dilution of pA-Tn5 (0.04 µM) and incubated at room temperature for 1 hour on rotator. Next, cells were re-suspended in 300 µl tagmentation buffer and incubated at 37 °C for 1 h. To stop tagmentation, 10 µl 0.5 M EDTA, 3µl 10% SDS and 2.5 µl of 20 mg/mL Proteinase K was added to sample, which was incubated overnight at 37 °C. DNA was extracted by PCI and dissolved in 30 μl TE buffer.
To amplify libraries, we added P5 primer, P7 primer (Vazyme, catalog. no. TD202), TruePrep Amplify Enzyme (Vazyme catalog. no. TD601) and performed PCR with the conditions below: 72°C for 3 minutes; 98°C for 30 seconds; 18 cycles of 98°C for 15 seconds, 63°C for 15 seconds; 72°C for 5 minutes. Post-PCR clean-up was performed by adding 1.2 volume of DNA clean beads (Vazyme, catalog. no. N411) and libraries were eluted in 20 μl nuclease-free water.

value: IgG (Abcam, ab171870)


title: 3132_12m1_ATD_p2_A01_CC


title: mESC ATAC rep1

description: mESC ATAC rep1

value: untreated


title: THDS_wk2_KLV_p1_F1_CC


title: 2C::GFP+/SA IgG rep1

description: 2C::GFP+/SA IgG rep1


title: THDS_wk2_KLV_p1_E7_CC


title: THDS_wk2_KLV_p1_F2_CC


title: 3132_12m1_ATD_p9_F02_CC


title: 2C::GFP+/SA H3K4me3 rep2

description: 2C::GFP+/SA H3K4me3 rep2

value: H3K4me3 (Millipore, 07-473)


title: THDS_wk2_KLV_p1_E6_CC


title: THDS_wk2_KLV_p1_F7_CC


title: 3132_12m1_ATD_p9_E02_CC


title: 3132_12m1_ATD_p2_G01_CC


title: 2C::GFP+/SA H3K4me3 rep1

description: 2C::GFP+/SA H3K4me3 rep1


title: 2C::GFP+/SGC ATAC rep2

description: 2C::GFP+/SGC ATAC rep2


title: 3132_12m1_ATD_p9_D02_CC


title: 3132_12m1_ATD_p9_B02_CC


title: THDS_wk2_KLV_p1_E5_CC


title: 3132_12m1_ATD_p1_G02_CC


title: 2C::GFP+/SA H3K4me1 rep1

description: 2C::GFP+/SA H3K4me1 rep1

value: H3K4me1 (Abcam, ab8895)


title: THDS_wk2_KLV_p1_F3_CC


title: 2C::GFP+/SA H3K27ac rep2

description: 2C::GFP+/SA H3K27ac rep2

value: H3K27ac (Abcam, ab4729)


title: THDS_wk2_KLV_p1_E2_CC


title: 2C::GFP+/SA H3K27ac rep1

description: 2C::GFP+/SA H3K27ac rep1


title: 3132_12m1_ATD_p1_F02_CC


title: 3132_12m1_ATD_p1_D02_CC


title: THDS_wk2_KLV_p1_E1_CC


title: THDS_wk2_KLV_p1_D8_CC


title: 2C::GFP+/SA H3K27me3 rep2

description: 2C::GFP+/SA H3K27me3 rep2

value: H3K27me3 (Millipore, 07-449)


title: THDS_wk2_KLV_p1_D7_CC


title: 3132_12m1_ATD_p1_C02_CC


title: 2C::GFP+/SA H3K27me3 rep1

description: 2C::GFP+/SA H3K27me3 rep1


title: 2C::GFP+/SGC IgG rep2

description: 2C::GFP+/SGC IgG rep2


title: 3132_12m1_ATD_p1_B02_CC


title: THDS_wk2_KLV_p1_D6_CC


title: THDS_wk2_KLV_p1_E4_CC


title: THDS_wk2_KLV_p1_D5_CC


title: 3132_12m1_ATD_p1_G01_CC


title: THDS_wk2_KLV_p1_D4_CC


title: 2C::GFP+/SGC IgG rep1

description: 2C::GFP+/SGC IgG rep1


title: 2C::GFP+/SA H3K4me1 rep2

description: 2C::GFP+/SA H3K4me1 rep2


title: 3132_12m1_ATD_p1_A02_CC


title: 2C::GFP+/SGC H3K4me3 rep2

description: 2C::GFP+/SGC H3K4me3 rep2


title: THDS_wk2_KLV_p1_E3_CC


title: 2C::GFP+/SGC H3K4me3 rep1

description: 2C::GFP+/SGC H3K4me3 rep1


title: 3132_12m1_ATD_p1_F01_CC


title: 3132_12m1_ATD_p1_D01_CC


title: 2C::GFP+/SGC H3K4me1 rep2

description: 2C::GFP+/SGC H3K4me1 rep2


title: 3132_12m1_ATD_p1_C01_CC


title: THDS_wk2_KLV_p1_D2_CC


title: 3132_12m1_ATD_p1_B01_CC


title: THDS_wk2_KLV_p1_D1_CC


title: THDS_wk2_KLV_p1_C8_CC


title: 2C::GFP+/SGC H3K27ac rep1

description: 2C::GFP+/SGC H3K27ac rep1


title: THDS_wk2_KLV_p1_C7_CC


title: r-SLAMF7 4

city: Boston

first: Daimon

last: Simmons

state: MA

address: 75 Francis Street

institute: Brigham and Women's Hospital

description: Sample 11

data_processing:
Reads were pseudoaligned and quantified using kallisto version 0.46.0
Genome_build: GRCh38.97
Supplementary_files_format_and_content: tab-delimited text files include transcript counts and TPM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Monocyte derived macrophages

growth_protocol: Monocytes were cultured in M-CSF (20 ng/ml)

extract_protocol:
Cells were lysed in TCL buffer and stored at -80C.
Libraries were processed at the Broad Institute using the Smart-seq2 protocol.

treatment_protocol: Cells were incubated for 24 hours with IFN-g. Then, they were either left unstimulated for 4 hours, or treated with 10 ug/ml anti-SLAMF7 or 1 ug/ml recombinant SLAMF7.

value: Peripheral blood

value: Monocyte-derived macrophage

tag: disease state

value: healthy

tag: donor

value: Donor D


title: THDS_wk8_KLV_p1_A6_CC

value: CD8+ T cell


title: 2C::GFP+/SGC H3K27me3 rep2

description: 2C::GFP+/SGC H3K27me3 rep2


title: THDS_wk2_KLV_p1_C6_CC


title: 2C::GFP+/SGC H3K27me3 rep1

description: 2C::GFP+/SGC H3K27me3 rep1


title: THDS_wk2_KLV_p1_C5_CC


title: 2C::GFP+ IgG rep2

description: 2C::GFP+ IgG rep2


title: r-SLAMF7 2

description: Sample 9

value: Donor B


title: THDS_wk2_KLV_p1_C4_CC


title: r-SLAMF7 1

description: Sample 8

value: Donor A


title: 2C::GFP+ IgG rep1

description: 2C::GFP+ IgG rep1


title: anti-SLAMF7 4

description: Sample 7


title: THDS_wk2_KLV_p1_C3_CC

value: CH-THDS


title: THDS_wk2_KLV_p1_D3_CC

value: KLV


title: 2C::GFP+ H3K4me3 rep2

description: 2C::GFP+ H3K4me3 rep2

value: mouse embryonic stem cells


title: 2C::GFP+/SGC H3K4me1 rep1

description: 2C::GFP+/SGC H3K4me1 rep1

value: SGC treated


title: THDS_wk2_KLV_p1_C2_CC


title: anti-SLAMF7 1

description: Sample 5


title: THDS_wk2_KLV_p1_C1_CC


title: 2C::GFP+/SGC H3K27ac rep2

description: 2C::GFP+/SGC H3K27ac rep2


title: anti-SLAMf7 3

description: Sample 6

value: Donor C


title: 2C::GFP+ H3K4me1 rep2

description: 2C::GFP+ H3K4me1 rep2

value: untreated


title: 2C::GFP+ H3K4me3 rep1

description: 2C::GFP+ H3K4me3 rep1

value: H3K4me3 (Millipore, 07-473)


title: 3132_12m1_ATD_p1_A01_CC

value: ATD


title: THDS_wk2_KLV_p1_B8_CC


title: r-SLAMF7 3

description: Sample 10


title: 2C::GFP+ H3K27ac rep2

description: 2C::GFP+ H3K27ac rep2

value: H3K27ac (Abcam, ab4729)


title: THDS_wk2_KLV_p1_B7_CC


title: 2C::GFP+ H3K4me1 rep1

description: 2C::GFP+ H3K4me1 rep1

value: H3K4me1 (Abcam, ab8895)


title: Unstimulated 2

description: Sample 2

value: Peripheral blood

value: Unstimulated


title: Unstimulated 1

description: Sample 1

value: Monocyte-derived macrophage

value: healthy


title: 2C::GFP+ H3K27me3 rep2

description: 2C::GFP+ H3K27me3 rep2

value: H3K27me3 (Millipore, 07-449)


title: THDS_wk2_KLV_p1_B4_CC

value: CD8+ T cell


title: Donor 14 Peripheral blood CD14+CD16+ SLAMF7 High

description: Sample 88

data_processing:
Reads were aligned using STAR version 2.4.2a
Transcripts were quantified using RSEM version 1.2.2.1
Genome_build: GRCh38.83
Supplementary_files_format_and_content: tab delimited text files with gene level TPM, FPKM, counts

source_name: Peripheral blood

value: Monocyte

value: Control

value: Donor 14

tag: monocyte population

tag: slamf7  expression

value: High


title: 2C::GFP+ H3K27ac rep1

description: 2C::GFP+ H3K27ac rep1

value: mouse embryonic stem cells


title: mESC IgG rep2

description: mESC IgG rep2

value: WT

value: IgG (Abcam, ab171870)


title: THDS_wk2_KLV_p1_B3_CC

source_name: CD8+ T cell

value: CH-THDS

value: KLV


title: Donor 14 Peripheral blood CD14+CD16+ SLAMF7 Low

description: Sample 87

value: Low


title: Donor 14 Peripheral blood CD14++CD16- SLAMF7 High

description: Sample 84


title: mESC IgG rep1

description: mESC IgG rep1

value: untreated


title: THDS_wk2_KLV_p1_B5_CC


title: THDS_wk2_KLV_p1_A8_CC


title: Donor 14 Peripheral blood CD14++CD16+ SLAMF7 High

description: Sample 86

value: Peripheral blood


title: Unstimulated 4

description: Sample 4

value: Unstimulated

value: Donor D


title: THDS_wk2_KLV_p1_B2_CC


title: 2C::GFP+ H3K27me3 rep1

description: 2C::GFP+ H3K27me3 rep1


title: THDS_wk2_KLV_p1_B1_CC


title: mESC H3K4me3 rep1

description: mESC H3K4me3 rep1

value: H3K4me3 (Millipore, 07-473)


title: Unstimulated 3

description: Sample 3

value: Monocyte-derived macrophage

value: healthy

value: Donor C


title: Donor 14 Peripheral blood CD14++CD16- SLAMF7 Low

description: Sample 83

value: Monocyte

value: Control


title: Donor 14 Peripheral blood CD14++CD16+ SLAMF7 Low

description: Sample 85

value: Donor 14


title: THDS_wk2_KLV_p1_A6_CC

value: CD8+ T cell


title: Donor 13 Peripheral blood CD14+CD16+ SLAMF7 High

description: Sample 82

value: Donor 13

value: High


title: mESC H3K4me1 rep2

description: mESC H3K4me1 rep2

value: mouse embryonic stem cells

value: WT

value: H3K4me1 (Abcam, ab8895)


title: THDS_wk2_KLV_p1_B6_CC

value: CH-THDS

value: KLV


title: THDS_wk2_KLV_p1_A5_CC


title: Donor 13 Peripheral blood CD14+CD16+ SLAMF7 Low

description: Sample 81

value: Peripheral blood

value: Low


title: mESC H3K4me1 rep1

description: mESC H3K4me1 rep1

value: untreated


title: mESC H3K4me3 rep2

description: mESC H3K4me3 rep2

value: H3K4me3 (Millipore, 07-473)


title: THDS_wk2_KLV_p1_A3_CC


title: mESC H3K27ac rep2

description: mESC H3K27ac rep2

value: H3K27ac (Abcam, ab4729)


title: THDS_wk2_KLV_p1_A4_CC


title: Donor 13 Peripheral blood CD14++CD16+ SLAMF7 High

description: Sample 80


title: Donor 13 Peripheral blood CD14++CD16+ SLAMF7 Low

description: Sample 79


title: mESC H3K27me3 rep2

description: mESC H3K27me3 rep2

value: H3K27me3 (Millipore, 07-449)


title: THDS_wk2_KLV_p1_A2_CC


title: mESC H3K27ac rep1

description: mESC H3K27ac rep1


title: Donor 13 Peripheral blood CD14++CD16- SLAMF7 High

description: Sample 78

value: Monocyte


title: mESC H3K27me3 rep1

description: mESC H3K27me3 rep1


title: THDS_wk2_KLV_p1_A7_CC


title: WTC NCdCas9 TBX18/g6

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

data_processing:
ChIP-seq reads were trimmed and aligned to hg19 using bowtie2, and bigWig coverage files were generated using UCSC tools.
Genome_build: hg19

source_name: hiPSC WTC #11

extract_protocol:
Protocol used for ATAC-seq is described in  Corces et al., 2017. Briefly frozen cell pellets were thawed and permeabilized on ice. Tagmentation occurred in the same tube followed by quenching and phenol:chloroform:isoamyl alcohol DNA purification and PCR. Exact temperatures, times, buffer composition were identical to Corces et al., 2017.
PMID: 28846090

value: WTC NCdCas9

tag: transfection

value: TBX18 g6 RNA


title: Donor 13 Peripheral blood CD14++CD16- SLAMF7 Low

description: Sample 77

value: Control


title: THDS_91m_KLV_p1_H1_CC

tag: subject

value: CD8+ T cell


title: mESC Input rep2

description: mESC Input rep2

data_processing:
The bioinformatics analysis of ChIP-seq datasets generated in this study or downloaded from publicly available repositories and data portals were performed by custom shell scripts in which raw data were first trimmed and filtered by TrimGalore with default parameter. Qualified read pairs were then aligned to mouse genome (mm10) by Bowtie2 (release 2.4.1). Biological and optical duplicates were removed with Sambamba (release 0.7.1). Last we used MACS2 (release 2.2.7.1; parameters for narrow peaks such as H3K27ac and H3K4me3: -p 0.05 -g mm -f BAMPE; broad peaks such as H3K27me3, H3K4me1, H3K79me2, H3K79me3 and H3K4me3: --broad --broad-cutoff 0.05 -g mm -f BAMPE; ATAC-seq: --broad --broad-cutoff 0.05 -g mm -f BAMPE) to call peaks. The highly reproducible peaks were identified by package IDR, which is a uni?ed approach to measure the reproducibility of ?ndings identi?ed from replicate experiments and provide highly stable thresholds based on reproducibility.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content:
Peak bed files.
wig files were generated using deeptools; Scores represent RPKM values.

growth_protocol: Mouse ESCs were cultured in N2B27 medium comprising 10ng/ml of LIF, 1 μM PD03, 3 μM CHIR9901 (Nichols and Ying, 2006) or in KnockOut medium comprising 20% KnockOut serum replacement, 1X non-essential amino acids solution, 2 mM L-glutamine, 55 µM 2-mercaptoethanol and 10 ng/ml LIF. The medium was changed every other day. When passaging, cells were dissociated by 0.05% Trypsin-EDTA into single cells and re-plated every 3 days at a ratio of 1:8-1:10.

extract_protocol:
For each ChIP, 5×10^6 cells were used. Cells were fixed in 1% formalin/mESC medium (v/v) for 10 min with gentle agitation on a rotator at room temperature. Fixation was stopped by the addition of glycine (125 mM) and agitation for 5 minutes at room temperature. Fixed cells were washed twice in ice-cold PBS, re-suspended in LB1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5%NP-40, 0.25% Triton X-100 and protease inhibitors). After 10 min of incubation, cells were pelleted by centrifugation and resuspended in LB2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitors). After 10 min of incubation, cells were pelleted and resuspended in 0.25ml of freshly prepared LB3 (10 mM Tris-HCl, pH 8.0,100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5%N-lauroylsarcosine and protease inhibitors) and sonicated to about 100 - 500 bp fragments using a Bioruptor (Diagenode). Anti-H3K79me2 and anti-H3K79me3 antibodies were diluted into 5 mg/ml BSA (PBS/BSA) and incubated with preblocked protein G magnetic beads (Invitrogen) at 4°C with gentle agitation on a rotator for 4 hours. Antibody-bead complexes were rotated overnight with sonicated chromatin solution at 4°C. Immune chromatin-bead precipitates were collected by the magnetic device (Invitrogen). Precipitates were washed sequentially with high-salt wash buffer (20 mMTris·HCl, pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, and 1% Triton X-100), then with LiCl wash buffer (10 mM Tris·HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, and 1% Nonidet P-40), and then with Tris-EDTA (TE)-NaCl buffer (1 mM EDTA, 10 mM Tris·HCl, pH 8.0, and 50 mM NaCl). Immunoprecipitated DNA was eluted by incubating the beads with 100 µl elution buffer (50 mM Tris·HCl, pH 8.0, 10 mM EDTA, and 1% SDS), shaking at room temperature at a setting of 1300 rpm for one hour. To reverse crosslinking, sample was treated with proteinase K and incubated at 65°C for 4 hours. Add 100 µl TE buffer to each sample. The DNA was purified using phenol-chloroform extraction, and suspended in 40 µl TE buffer.
ChIP-seq library was constructed with the Accel-NGS 2S Plus DNA Library kit (Swift Biosciences, catalog. no. 21096) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.


title: WTC EBdCas9 TBX18/g6

value: WTC EBdCas9


title: THDS_wk2_KLV_p1_A1_CC

tag: epitope


title: Donor 12 Peripheral blood CD14+CD16+ SLAMF7 High

description: Sample 76

value: Donor 12

value: High