|
| Status |
Public on Apr 28, 2020 |
| Title |
H3K27ac_ChIPSeq_shPbrm1_2 |
| Sample type |
SRA |
| |
|
| Source name |
shPbrm1
|
| Organism |
Mus musculus |
| Characteristics |
cell line: OP9
cell type: Stromal Cell line
chip antibody: H3K27ac (Abcam, Cat. ab4729, Lot GR254707-1)
knockdown: shPbrm1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were precipitated with specific antibody.
ChIP-seq library preparation was performed using TruSeqChIP Sample Prep Kit (Illumina) according to the manufacturer’s instructions.10ng of input ChIP-enriched DNA was used for ChIP-seq library preparation. Final libraries were checked using High Sensitivity chips in 2100 Bioanalyzer (Agilent). Average fragment size of final libraries was found to be 277 ± 13bp. Paired-end sequencing (2 x 100 bp) of these libraries were performed in HiSeq-2500 (Illumina) according to the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 18
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using deeptools
|
| |
|
| Submission date |
Oct 21, 2019 |
| Last update date |
Apr 29, 2020 |
| Contact name |
Amitava Sengupta |
| E-mail(s) |
sayantani0904@gmail.com
|
| Phone |
+91 9681155400
|
| Organization name |
CSIR - Indian Institute of Chemical Biology (Translational Research Unit of Excellence)
|
| Department |
Cancer Biology & Inflammatory Disorder Division
|
| Lab |
Stem Cell & Leukemia Lab
|
| Street address |
CN 6, Sector V, Salt Lake
|
| City |
Kolkata |
| State/province |
West Bengal |
| ZIP/Postal code |
700091 |
| Country |
India |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE139216 |
Genome-wide maps of histone modification and chromatin remodeler binding in mouse calvaria derived stromal cell line (OP9) |
|
| Relations |
| BioSample |
SAMN13071604 |
| SRA |
SRX7031681 |
