|
| Status |
Public on Nov 21, 2016 |
| Title |
ChIP-seq_WT_SMARCC1 |
| Sample type |
SRA |
| |
|
| Source name |
MEF_WT
|
| Organism |
Mus musculus |
| Characteristics |
strain background: B6/129
genotype/variation: WT
cell type: mouse embryonic fibroblast
chip antibody: SMARCC1/BAF155 (Santa Cruz, R-8, sc-9746)
|
| Treatment protocol |
Cells were infected with retrovisur expressing Cre, and selected with puromycine. 72 hours post selection, cells were harvested and used to extract chromatin.
|
| Growth protocol |
MEFs were cultured in DMEM with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Cat.# IP-202-1012)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The sequenced reads were aligned to the mm9 genome assembly using Bowtie 0.12.6, allowing up to 10 matches (‘-m 10 --best’ options).
1kb sized bins with more than mean+3standard deviation signal in any of the input samples were marked as noisy blacklist regions (total 287kb).
Reads on the 19 autosomal chromosomes excluding blacklisted regions were kept for downstream analysis.
For batches with low library complexity (<70% in any sample), only one read was preserved mapping to each position (denoted "PCRclean" or "clean1" in file names)
Peaks of cross-correlation profiles were identified to estimate the typical fragment size for each sample. Each read was considered to represent a signal at half typical fragment size from the 5' end.
Genomic profiles for visualization were generated using a sigma=100bp Gaussian smoothing after library size normalization
Genome_build: mm9
Supplementary_files_format_and_content: wig files depict genomic profiles after a sigma=100bp Gaussian smoothing.
|
| |
|
| Submission date |
Jul 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter J Park |
| E-mail(s) |
peter_park@harvard.edu
|
| Phone |
617-432-7373
|
| Organization name |
Harvard Medical School
|
| Department |
Center for Biomedical Informatics
|
| Street address |
10 Shattuck St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE71507 |
The SWI/SNF chromatin remodeling complex is required for lineage specific enhancer activity [MEF_ChIP] |
| GSE71509 |
The SWI/SNF chromatin remodeling complex is required for lineage specific enhancer activity |
|
| Relations |
| BioSample |
SAMN03943898 |
| SRA |
SRX1123929 |
