|
| Status |
Public on Jul 09, 2012 |
| Title |
Chip Seq H3K4me3 in ER:Ras-induced senescent IMR90 with Lenti-sh-Rb SLX3617 |
| Sample type |
SRA |
| |
|
| Source name |
IMR90 Human Diploid Fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody catalog #: 307-34813
chip antibody manufacturer: Wako
treatment: Lenti-sh-Rb
transgene: ER:Ras
gender: female
cell line: IMR90
chip antibody: H3K4me3 CMA304
|
| Treatment protocol |
100 nM 4OHT for 6 days in ER:Ras-expressing IMR90 cells to induced ER:Ras
|
| Growth protocol |
DMEM supplemented with 10% FBS and antibiotics in 5% oxygen for IMR90 cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. After end-repair and addition of an ‘A’ base to the 3’ ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of fourtyfold diluted ‘Adapter oligo mix’ in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with MinElute PCR Purification Kit, and eluted with 32 µl of 10 mM tris buffer at pH8.5. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg18 genome assembly using bwa 0.6.1 with the default parameters
BAM files were filtered and all reads with quality score below 15 are skipped, then the resulting BAM is filtered using the UCSC Duke excluded regions for hg18
Rseg differential was used to identify significant domains in the data using mode 2 versus input
Genome_build: NCBI Build 36.1 (HG18)
Supplementary_files_format_and_content: UCSC bed format of significant regions identified by Rseg
|
| |
|
| Submission date |
Jun 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Rafik Salama |
| E-mail(s) |
[email protected]
|
| Organization name |
Cancer Research UK
|
| Street address |
Li Ka Shing Centre, Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE38442 |
Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation (ChIP-Seq) |
| GSE38448 |
Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation |
|
| Relations |
| SRA |
SRX151392 |
| BioSample |
SAMN01036655 |
