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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 25, 2022 |
| Title |
WT naive CD8, IgG Cut&Run |
| Sample type |
SRA |
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| Source name |
CD8 T cells
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| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
time point: 0h
tissue: splenocytes
cell phenotype: GFP+ TCRbeta+ CD62Lhi CD44lo-med CD8+
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Naïve CD8+ T cells were sort-purified from the spleen, and stimulated with IL-7 and IL-15 in vitro for 0 or 72 hrs. The live cells were permeabilized, and then incubated with CTCF antibody overnight, followed by incubation with Protein A/G-MNase, calcium-mediated MNase activation. The reaction was stopped and then genomic DNA fragments were extracted.
The DNA segments from CTCF Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-X platform.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
CTCF_WT_na_IgG
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| Data processing |
Library strategy: Cut&Run
The sequencing quality of Cut&Run libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For Cut&Run libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a q value of < 0.05, 4 fold change at peak summit as identified binding sites.
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak
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| Submission date |
Jul 08, 2021 |
| Last update date |
Apr 26, 2022 |
| Contact name |
Shaoqi Zhu |
| E-mail(s) |
zsq@email.gwu.edu
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| Phone |
5714572498
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| Organization name |
The George Washington University
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| Street address |
725 21st st nw
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| City |
washington dc |
| State/province |
District of Columbia |
| ZIP/Postal code |
20052-0051 |
| Country |
USA |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE179723 |
Tcf1-CTCF cooperativity shapes genomic architecture to promote CD8+ T cell homeostasis [CTCF Cut&Run] |
| GSE179775 |
Tcf1-CTCF cooperativity shapes genomic architecture to promote CD8+ T cell homeostasis |
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| Relations |
| BioSample |
SAMN20119390 |
| SRA |
SRX11379634 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5429997_WT_na_IgG_peaks.narrowPeak.gz |
250 b |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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