|
| Status |
Public on Nov 15, 2023 |
| Title |
ATAC-seq_spike for sgRbpj_Tex_1_ day 7 |
| Sample type |
SRA |
| |
|
| Source name |
sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor
|
| Organism |
Mus musculus |
| Characteristics |
cell type: sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor
strain: C57BL/6
|
| Growth protocol |
OT-I cells transduced with indicatd sgRNAs were sorted from B16-OVA tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10 min. Resulting nuclei were pelleted at 500g for 10 min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 μl transposase reaction mix (25 μl 2 × TD buffer, 22.5 μl nuclease-free water, 2.5 μl transposase) and incubated for 30 min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Adapter sequences were removed using cutadapt v.1.9
and aligned them to the mouse genome mm10 (GRCm38_68 from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/GRCm38_68.fa) using the Burrows–Wheeler algorithm32 (version 0.5.9-r26-dev, default parameter)
duplicated reads were then marked with Picard (version 1.65 (1160)) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.0.20150603, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Assembly: mm10
Supplementary files format and content: Consensus peaks and fragment counts for all samples
|
| |
|
| Submission date |
Oct 28, 2022 |
| Last update date |
Nov 15, 2023 |
| Contact name |
Hongbo Chi |
| E-mail(s) |
hongbo.chi@stjude.org
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Immunology
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE216797 |
Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [Rbpj_ATAC-seq] |
| GSE216800 |
Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer |
|
| Relations |
| BioSample |
SAMN31509390 |
| SRA |
SRX18064719 |
