NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM942077 Query DataSets for GSM942077
Status Public on Jul 09, 2012
Title Chip Seq H3K9me3 in ER:Ras expressing IMR90 with no 4OHT with sh-HMGA1/SIN SLX3591
Sample type SRA
 
Source name IMR90 Human Diploid Fibroblasts
Organism Homo sapiens
Characteristics treatment: no 4OHT with sh-HMGA1/SIN
transgene: ER:Ras
gender: female
cell line: IMR90
chip antibody: H3K4me3 CMA318
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) rafik.salama@ndm.ox.ac.uk
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 SRX151354
BioSample SAMN01036617

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap