|
| Status |
Public on Jun 01, 2015 |
| Title |
LN-REP1_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP_GATA2_ChIP-seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
cell type: prostate cancer cells
passages: 32-34
chip antibody: GATA2
chip antibody vendor: Santa cruz
chip antibody cat. #: sc-9008
chip antibody lot #: J1607
|
| Treatment protocol |
3 days before ChIP assay, the full medium was changed to RPMI medium supplied with 5% charcal treated FBS.
|
| Growth protocol |
LNCaP cells were routinely cutured in RPMI medium supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and GATA2-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 11257074). 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 (3' to 5' 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 16 cycles and library fragments of ~225 bp (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 Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Sample 1
|
| Data processing |
ChIP-seq reads were aligned to the hg19 genome assembly using the Bowtie aligner with default parameters.
Peaks were called using MACS with a threshold p-value < 1E-8 on the combined alignment of the two replicate samples.
Genome_build: hg19
Supplementary_files_format_and_content: bed file of peak calling by MACS
|
| |
|
| Submission date |
Jun 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhenqing Ye |
| E-mail(s) |
yez@uthscsa.edu
|
| Organization name |
The University of Texas Health Science Center at San Antonio
|
| Department |
Department of Molecular Medicine
|
| Street address |
7703 Floyd Curl Drive
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE38391 |
Next generation sequencing facilitates quantitative analysis of GATA2 binding profile in LNCaP cells. |
| GSE38452 |
A Class of H3K4me1/H3K9me2 marked active GATA2 enhancers directs a GATA2-dependent transcription program underlying prostate cancer progression. |
|
| Relations |
| SRA |
SRX150911 |
| BioSample |
SAMN01001646 |
