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Sample GSM1065007 Query DataSets for GSM1065007
Status Public on Mar 02, 2013
Title Input DNA
Sample type SRA
Source name HCT116 cells
Organism Homo sapiens
Characteristics cell type: colorectal carcinoma
passages: 15-18
cell line: HCT116 cells
chip antibody: None
Treatment protocol For TAF3, RNAPII, and H3K4me3 ChIP-seq, cells in monolayer were fixed with 1% Formaldehyde for 10 min at room temperature and quenched by adding glycine to a final concentration of 125 mM (Sigma). 10-50 million cells were used per IP.
Growth protocol HCT116 cells were cultured on uncoated tissue-culture plates in Dulbecco’s modified Eagle medium (DMEM, Gibco).
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated and precleared chromatin was immunoprecipitated with antibody.
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 was PCR amplified with Illumina primers for 15 cycles and library fragments of ~200 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 for 36 bp on the Genome Analyzer IIx following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing Basecalls performed using Illumina RTA
ChIP-seq reads were aligned to the hg19 genome assembly using Illumina Casava 1.8.2
Data were filtered using the following specifications: only unique alignments were used.
peaks were called using MACS version 1.4.2 with the default setting.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files were generated using MACS version 1.4.2 and then converted to bigWig format using the bedGraphToBigWig program. Peaks are filtered by fold_enrichment > 5 and FDR < 0.05.
Submission date Jan 16, 2013
Last update date May 15, 2019
Contact name Xiaolin Wu
Phone 301-846-7677
Organization name Frederick National Laboratory for Cancer Research/SAIC-Frederick Inc
Department Cancer Research Technology Program
Lab Genomics Laboratory
Street address 8560 Progress Drive, C3001
City Frederick
State/province MD
ZIP/Postal code 21701
Country USA
Platform ID GPL10999
Series (2)
GSE43539 H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation [ChIP-Seq]
GSE43542 H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation
SRA SRX217737
BioSample SAMN01888183

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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