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Sample GSM7567338 Query DataSets for GSM7567338
Status Public on Aug 27, 2023
Title AireWT_ATAC
Sample type SRA
Source name Thymic epithelial cells
Organism Mus musculus
Characteristics cell line: Thymic epithelial cells
cell type: WT
Extracted molecule genomic DNA
Extraction protocol Thymi from 4 pooled 5 week old B6.Adig mice were dissociated by enzymatic digestion using Liberase TH and DNase in RPMI at 37°C until complete digestion. The single cell suspension was then filtered through a 52 µm mesh filter and resolved on a Percoll gradient. The Percoll gradient was centrifuged at 2700rpm at 4°C with no break, for 30 minutes. Stromal cells where collected and washed followed by centrifugation. Single cell suspensions were further enriched for thymic epithelial cells by staining for EpCAM-APC Cy7 followed by positive selection using anti-APC microbeads and the enriched fraction was stained for cell sorting. 60,000 viable (DAPI negative) CD45-EpCAM+ TECs were sorted into 500 ul PBS supplemented with 0.04% bovine serum albumin and then supplemented with 6,800 CD45-EpCAM+IA-IEloItgb4lo/neg cells. Cells were processed as per manufacturer’s instructions for low cell input nuclei isolation. Briefly, cells were resuspended in 100 μl cold lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40 substitute, 0.01% digitonin, 1% BSA, 1 mM DTT, RNase inhibitor 1 U/µl) and divided into 2 tubes for 3 min lysis. Nuclei were then washed and resuspended in nuclei buffer to target 7,000 recovered nuclei.
Nuclei transposition and mRNA barcoding were followed by library preparation per the manufacturer’s (10x genomics) instructions which were sequenced with paired-end 100-bp reads on an Illumina NovaSeq6000.
single cell 3' RNA-seq and single cell ATAC-seq
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
Description 10x Genomics
Data processing Single cell multiome ATAC + Gene Expression data was processed using the Cell Ranger ARC analysis pipeline (10x Genomics version 2.0.0), with reference data file refdata-cellranger-arc-mm10-2020-A.
Assembly: mm10
Supplementary files format and content: Filtered feature-barcode matrix and fragment files from cellranger
Submission date Jul 06, 2023
Last update date Aug 27, 2023
Contact name Jakub Abramson
Organization name Weizmann Institute of Science
Department Department of Immunology
Street address 234 Herzl st.
City Rehovot
ZIP/Postal code 7610001
Country Israel
Platform ID GPL24247
Series (2)
GSE236075 Thymic mimetic cells function beyond self-tolerance
GSE236667 Thymic mimetic cells function beyond self-tolerance [scATAC-Seq Multiome]
BioSample SAMN36345320
SRA SRX20928454

Supplementary file Size Download File type/resource
GSM7567338_atac_fragments.tsv.gz 2.6 Gb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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