 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 15, 2023 |
| Title |
spike for sgIkzf1_Tpex_5 |
| 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 50μl ATAC-seq lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10min. Resulting nuclei were pelleted at 500gfor 10min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50μl transposase reaction mix (25μl 2×TD buffer, 22.5μl nuclease-free water, 2.5μl transposase) and incubated for 30min 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 +4bp for the sense strand and −5bp 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 bedtoolsif within 100bp) for individual samples
Assembly: mm10
Supplementary files format and content: Consensus peaks and fragment counts for all samples
|
| |
|
| Submission date |
Aug 01, 2023 |
| 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) |
| GSE216800 |
Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer |
| GSE239802 |
Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [Ikzf1 ATAC-Seq] |
|
| Relations |
| BioSample |
SAMN36794179 |
| SRA |
SRX21218117 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
