|
| Status |
Public on Oct 18, 2011 |
| Title |
MCF7_cMYC_REP1 |
| Sample type |
SRA |
| |
|
| Source name |
breast adenocarcinoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: breast adenocarcinoma cells
cell line: MCF7
antibody: cMYC
antibody (vender, cat#, lot#): Santa Cruz, sc-764X, C1309
|
| Growth protocol |
Cells were grown according to the approved ENCODE cell culture protocols.Specific protocol descriptions can be found at http://genome.ucsc.edu/ENCODE/cellTypes.html.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
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, library fragments of ~230 bp (insert plus adaptor and PCR primer sequences) were selected from an agarose gel. The final size-selected lib. was amplified by 15 cycle of PCR followed by column purification of amplified DNA. 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.
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution (Bhinge et al. 2007; Birney et al. 2007). Immunoprecipitated DNA were sequenced using Illumina sequencers, (ChIP-seq). Input sequencing data were generated for GM12878, K562, HeLa-S3, HepG2, and HUVEC by cross-linking chromatin, shearing and reversing cross-links without immunoprecipitating.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against c-Myc
|
| Data processing |
peaks were identified using a Parzen window based algorithm as described previously with minor modifications (Shivaswamy et al. 2008. PLoS Biol 6: e65. )
|
| |
|
| Submission date |
Oct 05, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Vishy Iyer |
| E-mail(s) |
iyerlab@gmail.com
|
| Phone |
5122327833
|
| Organization name |
University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Street address |
2500 Speedway Dr. MBB 3.212
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE32692 |
Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells [new ChIP-Seq samples] |
| GSE32883 |
Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells |
|
| Relations |
| SRA |
SRX099865 |
| BioSample |
SAMN00737704 |
