|
| Status |
Public on Feb 11, 2020 |
| Title |
ATAC-seq_DP_F1_34_Rep1B_Rep2T |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ CD8+ thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Thymus
strain: (NOD/ShiLtJ X C57BL/6) F1 mice
|
| Treatment protocol |
Thymi of mice were dissociated through a 70µM mesh filter (Falcon) in RPMI 1640 (Corning) with 1% FBS (Sigma-Aldrich), and single cell suspensions were stained with 7AAD (Biolegend) for live cell distinction, as well as PE CD4 (RM404) and APC CD8a (53-6.7) for double-positive CD4+ CD8+ T cell isolation. Sorting was performed on FACS Aria II (BD Biosciences), with forward scatter–height by forward scatter–width and side scatter–height by side scatter–width parameters being used to exclude doublets. Purity was verified after sorting.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed as previously described with minor modifications (Buenrostro et al., 2013). Fifty thousand cells were pelleted at 550 x g and washed with 1 mL 1x PBS, followed by treatment with 50 μL lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After pelleting nuclei, the pellets were resuspended in 50 μL transposition reaction with 2.5 μL Tn5 transposase (FC-121-1030; Illumina). The reaction was incubated in a 37°C water bath for 45 minutes. Tagmented DNA was purified using a MinElute Reaction Cleanup Kit (Qiagen) and amplified with varying cycles, depending on the side reaction results. Libraries were purified using a QIAQuick PCR Purification Kit (Qiagen).
Libraries were paired-end sequenced (38bp+38bp) on a NextSeq 550 (Illumina). Libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ATAC-seq libraries were pair-end sequenced by Illumina NextSeq 500. Bowtie2 was used for alignment. In NOD mice, aligned reads were shifted to BL6 coordinates with MMARGE (PMID: 29893919) utilizing the NOD VCF files (version 5) from the Mouse Genomes Project (PMID: 21921910). Reads aligned to the mitochondrial genome or chrY as well as reads mapping to multiple genomic loci were discarded from downstream analyses. Additionally, Picard was used to mark and remove duplicates. Furthermore, for each ATAC-seq library the insert size was calculated by Picard.
Genome_build: GRCm38
Supplementary_files_format_and_content: Bigwig files were generated by bedtools genomecov and wigToBigWig normalizing tracks to tags-per-million
|
| |
|
| Submission date |
Dec 11, 2019 |
| Last update date |
Feb 12, 2020 |
| Contact name |
Naomi Goldman |
| Organization name |
University of Pennsylvania
|
| Lab |
Golnaz Vahedi
|
| Street address |
324 BRB II/III, 421 Curie Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE141845 |
Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [ATAC-seq] |
| GSE141853 |
Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells |
|
| Relations |
| BioSample |
SAMN13541870 |
| SRA |
SRX7348106 |
