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| Status |
Public on Jun 09, 2023 |
| Title |
iDF culture genomic DNA input for ChIP-seq |
| Sample type |
SRA |
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| Source name |
Serum-starved and stimulated cultured iDF
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| Organism |
Mus musculus |
| Characteristics |
genotype: WT and dKO combined
antibody: none
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
~ 8 × 10^6 cultured iDFs after 30min serum stimulation were single-cross-linked and processed for ChIP as described in Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R, Agrawal P, Chowdhury A, Gantz M, de Pablos-Aragoneses A, Morgenstern A, Wu P, Filipescu D, Valle-Garcia D, Darvishian F, Roe JS, Davies MA, Vakoc CR, Hernando E, Bernstein E. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Mol Cell. 2017 Nov 16;68(4):731-744.e9. doi: 10.1016/j.molcel.2017.11.004. PMID: 29149598; PMCID: PMC5993436.
Libraries were constructed as described in Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R, Agrawal P, Chowdhury A, Gantz M, de Pablos-Aragoneses A, Morgenstern A, Wu P, Filipescu D, Valle-Garcia D, Darvishian F, Roe JS, Davies MA, Vakoc CR, Hernando E, Bernstein E. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Mol Cell. 2017 Nov 16;68(4):731-744.e9. doi: 10.1016/j.molcel.2017.11.004. PMID: 29149598; PMCID: PMC5993436.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
H3K27ac ChIP in immortalized dermal fibroblasts fibroblasts 30 minutes after serum stimulation
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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 |
| E-mail(s) |
dan.filipescu@mssm.edu
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| Phone |
2128249265
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| 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 |
SAMN27566513 |
| SRA |
SRX14843296 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6042902_iDF-mixed-input.bw |
90.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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