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Sample GSM1341816 Query DataSets for GSM1341816
Status Public on Dec 02, 2014
Title TBP ChIP-seq (Human K562 cells) Rep 1
Sample type SRA
 
Source name TBP ChIP-seq (Human K562 cells) Rep 1
Organism Homo sapiens
Characteristics cell line: K562 cells
chip antibody: anti-TBP rabbit polyclonal, Santa Cruz Technology, catalog # sc-204X (ChIP-grade), lot # C-0513
multiplex barcode: GTGGCC
Treatment protocol no treatment, only fixation by formaldehyde
Growth protocol grown at 37C, 5% CO2 w/ humidity in Iscove's DMEM media with 10% fetal bovine serum
Extracted molecule genomic DNA
Extraction protocol cells were cross-linked in 1.0% formaldehyde. Cells were then dounced to bread down cells and extract nuclei. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. 300 ul soluble chromatin from ~ 10 million cells was used
DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step using AmPure beads (200-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description UCSC hg19
Data processing Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were trimmed to 50 bp and aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were extended to each library's estimated insert size
Genome-wide coverage counts were calculated and saved in BigWig format
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base
 
Submission date Mar 07, 2014
Last update date May 15, 2019
Contact name Julia Zeitlinger
E-mail(s) jbz@stowers.org
Organization name Stowers Institute for Medical Research
Lab Zeitlinger Lab
Street address 1000 E 50th St
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
 
Platform ID GPL11154
Series (1)
GSE55306 ChIP-nexus: a novel ChIP-exo protocol for improved detection of in vivo transcription factor binding footprints
Relations
BioSample SAMN02677504
SRA SRX482859

Supplementary file Size Download File type/resource
GSM1341816_hsap_k562_tbp_chipseq_01.bw 71.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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