|
| Status |
Public on Nov 30, 2012 |
| Title |
H3K4me2_ChIPSeq_abl |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP-abl (abl) prostate cancer cells
genotype/variation: androgen-independent prostate cancer cells
passages: 61-64
chip antibody: anti-H3K4me2 (Millipore (07-030))
|
| Treatment protocol |
For the purpose of ChIP experiments, the cells were kept in androgen-depleted medium for 3 days and then treated with either 10 nM 5α-dihydrotestosterone (DHT, for LNCaP cells) or with ethanol only (for abl cells) for 24 hours before the cells were collected.
|
| Growth protocol |
LNCaP cells were routinely maintained in RPMI-1640 with 10% fetal bovine serum (FBS) plus 1% antibiotics (penicillin and streptomycin). LNCaP-abl (abl) cells were routinely maintained in phenol-red-free RPMI with 10% charcoal-stripped FBS plus 1% antibiotics.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for up to 18 cycles and library fragments of 250-400 bp range (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina GAII system following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
anti-H3K4me2
|
| Data processing |
Basecalls performed using CASAVA 1.6.0
ChIP-Seq reads are aligned to hg18 using Eland with default configurations, only uniqly mapped reads are kept
Redundant reads (reads mapped to exactly the same location) are removed
All libraries are sampled down to 10 million reads
Peaks are called using MACS2 2.0.9
Genome_build: hg18
bigwig files are generated using MACS2+bedGraphToBigWig
Supplementary_files_format_and_content: peaks.bed files: These bed files are the ChiP enriched regions generated by MACS
Supplementary_files_format_and_content: .bw files: The bigwig files are generated from the pile up track of MACS. Files treat_pileup.bw, normalized_sorted-norm-10M.bw, treat_pileup-norm-10000000.bw are all generated in the same way (but the naming is not consistent).
|
| |
|
| Submission date |
Jul 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kexin Xu |
| E-mail(s) |
kxuthscsa@gmail.com
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Molecular Medicine
|
| Street address |
7703 Floyd Curl, MC 8257
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE39459 |
Genome-wide maps of PRC2 complex components and chromatin states in prostate cancer cell lines |
| GSE39461 |
Role of PRC2 complex components in prostate cancer cell lines |
|
| Relations |
| SRA |
SRX160737 |
| BioSample |
SAMN01091306 |
