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Sample GSM5643204 Query DataSets for GSM5643204
Status Public on Mar 30, 2022
Title IELp Ctrl_rep_1 [ATAC-seq]
Sample type SRA
Source name Thymus
Organism Mus musculus
Characteristics strain: C57BL/6
population: TCRb+CD4–CD8a–CD5hi CD122+H-2Kb+ CD44–PD-1hi
genotype: Cd4 Cre- lrffl/fl
Extracted molecule genomic DNA
Extraction protocol Chrominum Single Cell ATAC reagent Kits v1.1 per the manufacturer instructions (10X genomics)
IELp Ctrl/KO_rep_1: 2 10x Genomics Single Cell Chromium ATAC libraries were sequenced on one NextSeq 2000 P3 run and combined with a previous NextSeq 2000 P2 run. The sequencing run was setup as a 2x51 cycles symmetric run. R1: 51bp, Index1: 8bp, Index2: 16bp, R2: 51bp. IELp Ctrl/KO_rep_2: 2 10x Genomics Single Cell Chromium ATAC libraries were sequenced on one NextSeq 2000 run. The sequencing run was setup as a 50 cycles + 50 cycles symmetric run. R1: 50bp, Index1: 8bp, Index2: 16bp, R2: 50bp.
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model NextSeq 2000
Data processing Basecalling was performed using RTA 2.4.11 for IELp Ctrl/KO_rep_1, using RTA 3.9.2 for IELp Ctrl/KO_rep_2
Barcode was demultiplexed with mkfastq in Cellranger 1.2.0
Alignment, tagging and gene counting were done with Cellranger 1.2.0
Genome_build: mm10
Supplementary_files_format_and_content: h5, tsv.gz,
Submission date Oct 20, 2021
Last update date Mar 30, 2022
Contact name Jia Nie
Organization name National Cancer Institute
Department Center for Cancer Research
Lab Laboratory of Immune cell Biology
Street address Building 37, Room 3016
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
Platform ID GPL30172
Series (1)
GSE186291 Single-cell ATAC of WT thymic IEL precursors (IELp)
BioSample SAMN22444678
SRA SRX12710507

Supplementary file Size Download File type/resource
GSM5643204_filtered_peak_bc_matrix_Ctrl_1.h5 109.0 Mb (ftp)(http) H5
GSM5643204_fragments_Ctrl_1.tsv.gz 1.4 Gb (ftp)(http) TSV
GSM5643204_fragments_Ctrl_1.tsv.gz.tbi.gz 819.4 Kb (ftp)(http) TBI
GSM5643204_raw_peak_bc_matrix_Ctrl_1.h5 119.0 Mb (ftp)(http) H5
GSM5643204_singlecell_Ctrl_1.csv.gz 4.8 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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