|
| Status |
Public on Nov 21, 2016 |
| Title |
ChIP-seq_BT16_NoDox_SMARCC1 |
| Sample type |
SRA |
| |
|
| Source name |
ChIP-seq_BT16_NoDox
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT16
cell type: brain rhabdoid tumor derived cell line
treatment/condition: untreated
chip antibody: SMARCC1/BAF155 (Santa Cruz, R-8, sc-9746)
|
| Treatment protocol |
Cells were treated with doxycycline to induce SNF5 re-expression for 48 hours.
|
| Growth protocol |
G401, BT16 cells were cultured in DMEM with 10% FBS; TTC549 cells were cultured in RPMI with 10% FBS. All cell lines are maintained with Tet-System Approved FBS (Clonetech, cat.# 631106)
|
| 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 hg19 genome assembly using Bowtie 0.12.6, allowing up to 10 matches (‘-m 10 --best’ options).
Reads on the 24 assembled chromosomes excluding the encode blacklisted regions were kept for downstream analysis.
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: hg19
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) |
[email protected]
|
| 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 |
GPL11154 |
| Series (2) |
| GSE71504 |
SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation [cell line_ChIP-seq] |
| GSE71506 |
SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation |
|
| Relations |
| BioSample |
SAMN03943812 |
| SRA |
SRX1123853 |
