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Sample GSM665908 Query DataSets for GSM665908
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
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
SRA SRX040561
BioSample SAMN00205406

Supplementary file Size Download File type/resource
GSM665908_Lin9_2.bam 669.6 Mb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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