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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 01, 2024 |
| Title |
KOOTI-WT2 |
| Sample type |
SRA |
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| Source name |
tumor
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| Organism |
Mus musculus |
| Characteristics |
tissue: tumor
cell line: primary cells
cell type: Tumor-infiltrating CD8 T cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
To analyze the function of CD8+ T cells in the TME, we sorted tumor-infiltrating CD8+ T cells from tumor-bearing mice.
Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay. The cells were then thawed in a 37oC water bath, pelleted, washed with cold PBS, and tagmented , with some = modifications based on (Corces et al. 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Analysis of ATAC-seq data was very similar to the analysis of ChIP Seq data. Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Assembly: mm10
Supplementary files format and content: bw
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| Submission date |
Apr 18, 2023 |
| Last update date |
Apr 01, 2024 |
| Contact name |
YUNA JO |
| E-mail(s) |
yoona8987@gmail.com
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| Phone |
+821080048987
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| Organization name |
Pusan National University
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| Street address |
49, Busandaehak-ro
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| City |
Yangsan |
| ZIP/Postal code |
50612 |
| Country |
South Korea |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE229990 |
Chromatin accessibility analysis of tumor-infiltrating CD8+ T cells from tumor-bearing mice transferred Nrf2-deficient CD8+ T cells. [ATACseq] |
| GSE229994 |
tumor-infiltrating CD8+ T cells from tumor-bearing mice transferred Nrf2-deficient CD8+ T cells. |
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| Relations |
| BioSample |
SAMN34237638 |
| SRA |
SRX20002662 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7182526_4_099F_01AUPNU_KOOTITg-WT2_ATAC_mm10_i227_uniqnorm_signal.bw |
97.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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