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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 30, 2024 |
| Title |
KO_Sti, rep 3, ATACseq |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
cell type: NK cells
genotype: KO
treatment: stimulated with IL12/18
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
NK cells were subjected to ATAC-seq analysis using ATAC-Seq Kit (Active Motif) following the manufacturer’s instructions (Active Motif). 100,000 cells were washed with PBS and resuspended in ATAC lysis buffer followed by Tagmentation reaction and purification.
Purified Tagmented DNA was amplified using a combination of indexed primers and resulting libraries were purified again.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Quality control of sequenced reads was assessed by FastQC (version 0.11.9). Cutadapt (version 4.1) was used to remove adapters sequences.
Trimmed sequenced reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.3.4.1) and filtered with samtools (version 1.15.1).
Normalized coverage tracks (CPM normalization in bigWig format) were generated with bamCoverage from deepTools (version 3.4.2).
Peaks were called with MACS (version 2.1.1.20160309) and loaded into R with rtracklayer package.Consensus peaks were calculated with reduce function in GenomicsRanges and reads mapping to the consensus peaks were computed with summarizeOverlaps function in GenomicAlignments.
Assembly: mm10
Supplementary files format and content: count.rds
Supplementary files format and content: bigwig and narrowPeak
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| Submission date |
Jul 18, 2023 |
| Last update date |
May 30, 2024 |
| Contact name |
Xin Sun |
| E-mail(s) |
sunxin@ifrec.osaka-u.ac.jp
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| Organization name |
IFReC, Osaka University
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| Street address |
3-1 Yamadaoka, Suita
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| City |
Osaka |
| ZIP/Postal code |
5650871 |
| Country |
Japan |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE237637 |
The transcriptional landscape associated with the deletion of Regnase-1 [ATAC-Seq] |
| GSE237643 |
Deletion of the mRNA endonuclease Regnase-1 promotes NK cell anti-tumor activity via OCT2- dependent transcription of Ifng |
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| Relations |
| BioSample |
SAMN36518387 |
| SRA |
SRX21062782 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7635044_KO-3_Sti.bw |
154.8 Mb |
(ftp)(http) |
BW |
| GSM7635044_KO-3_Sti_peaks.narrowPeak.gz |
1.2 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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