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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
E-mail(s) jia.nie@nih.gov
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)
Relations
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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