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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 09, 2023 |
| Title |
Mouse # 66624 CAF ATAC-seq |
| Sample type |
SRA |
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| Source name |
Sorted CAF
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| Organism |
Mus musculus |
| Characteristics |
genotype: dKO
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
5 × 10^4 sorted CAFs were processed for ATAC-seq as described in PMID: 26083756: Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015 Jul 23;523(7561):486-90. doi:10.1038/nature14590. Epub 2015 Jun 17.
Libraries were constructed as described in PMID: 26083756: Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015 Jul 23;523(7561):486-90. doi:10.1038/nature14590. Epub 2015 Jun 17. Libraries were subjected to double-sided size selection using SPRIselect beads (Beckman Coulter) at ratios of 0.55 and 1.2X prior to sequencing.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ATAC-seq of cancer-associated fibroblasts sorted from melanoma tissue at 50 days post induction
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| Data processing |
ATAC-seq: Read pairs were merged and adapters removed using NGmerge v.0.3, followed by alignment to the mm10 assembly with bowtie2 v.2.4.1. Low-quality (MAPQ < 30), mitochondrial genome and duplicated reads were removed using samtools v.1.9 and genome coverage calculation for visualization purposes on the UCSC genome browser was performed using deepTools v.3.5.1 excluding blacklisted regions.
ChIP-seq: Adapters were trimmed with Trimmomatic v.0.36. Alignment, read filtering and genome coverage calculation were performed as for ATAC-seq.
CUT&RUN: Reads were processed as for ATAC-seq.
Assembly: Gencode M25 (GRCm38.p6)
Supplementary files format and content: fastq - raw Illumina reads. BigWig - aligned reads pileup produced with deeptools
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| Submission date |
Apr 13, 2022 |
| Last update date |
Jun 11, 2023 |
| Contact name |
Dan Filipescu |
| Organization name |
Icahn School of Medicine at Mount Sinai
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| Department |
Oncological Sciences
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| Lab |
Emily Bernstein
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| Street address |
1470 Madison Ave
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE200734 |
MacroH2A restricts melanoma progression via inhibition of chemokine expression in cancer-associated fibroblasts [epigenomics] |
| GSE200751 |
MacroH2A restricts melanoma progression via inhibition of chemokine expression in cancer-associated fibroblasts. |
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| Relations |
| BioSample |
SAMN27566522 |
| SRA |
SRX14843287 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6042893_66624-CAF-ATAC.bw |
171.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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