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Sample GSM1259355 Query DataSets for GSM1259355
Status Public on Nov 06, 2013
Title s_8
Sample type SRA
 
Source name HeLa S3_FOXM1 ChIP
Organism Homo sapiens
Characteristics cell line: HeLa S3
cell type: epithelial
chip antibody: FOXM1 Antibody (C-20)
chip antibody vendor: Santa Cruz
chip antibody cat. #: SC-502
chip antibody lot #: H0408
Growth protocol HeLa cells were passaged in a 37C, humidity controlled, CO2 equilibrated incubator in DMEM (Life Technologies) media containing 10% FBS (Life Technologies), and 1% Penn-Strep (Life Technologies)
Extracted molecule genomic DNA
Extraction protocol HeLa cells were fixed with 1% formaldehyde before the DNA was sonicated to a fragment length of 200-600bp with a Bioruptor® (Diagenode, Sparta, NJ). Antibodies were bound to a mix of Protein A and Protein G Dynabeads® (Life Technologies, Grand Island, NY) before an 18 hour incubation at 4°C with the fragmented DNA. DNA was washed and crosslinks reversed before purification with a QIAquick™ PCR purification kit (QIAGEN, Valencia, CA). DNA concentrations were measured using Quant-iT™ PicoGreen® (Life Technologies, Grand Island, NY).
A library was constructed from the bound fragments per manufacturer’s protocols and the DNA fragments from each independent ChIP were sequenced independently at the UNC High Throughput Sequencing Facility using an Illumina Genome Analyzer II.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description Sample 2
Data processing Reads were aligned to hg19 using Bowtie software (v 0.12.7)
Enriched peaks were identified independently in each dataset using MACS (v. 1.4.1)
Genome_build: HG19
Supplementary_files_format_and_content: s_7_peaks.bed.gz contains the peaks called by MACS for sample s_7
Supplementary_files_format_and_content: s_8_peaks.bed.gz contains the peaks called by MACS for sample s_8
 
Submission date Nov 05, 2013
Last update date May 15, 2019
Contact name Gavin D Grant
Organization name Geisel School of Medicine
Department Genetics
Lab Whitfield
Street address 7400 Remsen
City Hanover
State/province NH
ZIP/Postal code 05001
Country USA
 
Platform ID GPL9115
Series (2)
GSE52098 Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors [ChIP-seq]
GSE52100 Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors
Relations
BioSample SAMN02393621
SRA SRX373257

Supplementary file Size Download File type/resource
GSM1259355_s_8_peaks.bed.gz 42.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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