|
| Status |
Public on Jan 25, 2012 |
| Title |
LIN9_ChIPSeq_HeLa_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa cell line
chip antibody: LIN9
|
| Growth protocol |
Asynchronously growing HeLa cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP protocol is modified from Rayman et al, 2002. The purification and extraction of ChIP DNA from the IPs is described in the protocol (pdf file) attached to the Series record. Briefly, it involves purification using the Qiagen QiaQuick PCR purification columns (Cat. No. 28104). The LIN9 antibody used in ChIP was manufactured in-house in collaboration with Bethyl labs. The B-Myb antibody used in ChIP was from Bethyl labs, Cat. No. A301-656A. The average insert size of the ChIP-Seq libraries was 150-300 bp including adapters, 50-150 without adapters, as determined by running 1 ul of the library on the Agilent BioAnalyzer.
Chromatin from HeLa cells was used to immunoprecipitate B-Myb or LIN9 using specific antibodies. From ~30 ng of chromatin IPed DNA or input DNA, libraries were prepared using Illumina's ChIP-Seq sample prep kit. ChIP-Seq DNA libraries were quantified using Nanodrop (Thermo-Scientific) and a sharp peak at 200-400 nt was confirmed on the BioAnalyzer (Agilent) before sequencing. Diluted libraries were used for cluster generation and single-end sequencing using the Genome Analyzer II (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin IP DNA
|
| Data processing |
Base calling and mapping of the 36-bp reads to the human genome (Build 37, hg19) was done using Bowtie using very strict alignment criteria: only perfect matches (-n 0) and only unique alignments (-m 1). Enriched genomic regions from ChIP-Seq experiments were determined using CisGenome version 1.2 by two-sample analysis using the Input signal as negative control.
The ChIP-Seq libraries were used for cluster generation and single-end sequencing (36-bp reads) using the Genome Analyzer II (Illumina) following the manufacturer's protocol.
|
| |
|
| Submission date |
Feb 02, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Subhashini Sadasivam |
| E-mail(s) |
subhashini.sadasivam@gmail.com
|
| Organization name |
Dana Farber Cancer Insitute
|
| Department |
Medical Oncology
|
| Lab |
Laboratory of James DeCaprio, Mayer 444
|
| Street address |
450 Brookline Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE27030 |
Genome-wide binding profiles of the B-Myb-MuvB complex in HeLa cells |
| GSE27031 |
The MuvB complex sequentially recruits B-Myb and FoxM1 to promote mitotic gene expression |
|
| Relations |
| SRA |
SRX040561 |
| BioSample |
SAMN00205406 |
