|
| Status |
Public on Jul 08, 2009 |
| Title |
H3K4me2_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human breast adenocarcinoma cell line
|
| Growth protocol |
MDA-MB-231 cells were grown in DMEM containing 15% FBS, L-glutamine, non-essential amino acids, and penicillin/streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation was performed with rabbit anti-trimethyl histone H3K36 (Abcam, ab32356) and rabbit anti-dimethyl histone H3K4 (Abcam, ab9050) according to previously described methods (Steger et al. 2008). Following elution, IP samples were treated with RNaseA at 65ºC overnight followed by proteinase K at 42ºC for 2 hours. DNA was isolated by phenol:chloroform extraction and ethanol precipitation. ChIP DNA was prepared for Illumina sequencing according to the protocol described by Robertson et al (Robertson et al. 2007) and the manufacturer's recommendations.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin IP against H3K4me2
|
| Data processing |
Alignment: Sequence reads from ChIP-seq experiments were mapped to the human genome (March 2006) with the RMAP program, allowing at most 2 mismatches in 36 bases. Reads mapped ambiguously to multiple locations in the genome were ignored in subsequent analysis.
|
| |
|
| Submission date |
Jul 08, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Emily Hodges |
| E-mail(s) |
hodges@cshl.edu
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Street address |
1 Bungtown Road
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE17001 |
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing |
|
| Relations |
| SRA |
SRX007141 |
| BioSample |
SAMN02198685 |
| Named Annotation |
GSM425484_MB231_H3K4_aligned.bed.gz |
