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Sample GSM2026766 Query DataSets for GSM2026766
Status Public on Oct 25, 2016
Title ChIP-seq of GFP-tagged ZNF22 in HEK293 cells [ZNF22_rep2]
Sample type SRA
 
Source name HEK293 cells expressing GFP-tagged protein
Organism Homo sapiens
Characteristics uniprotkb id: P17026
cell line: HEK293
Treatment protocol Expression of the gene of interest was induced by addition of doxycycline to the culture medium 24 hours prior to harvesting. HEK293 cells were cross-linked for 10 min in 1% formaldehyde.
Growth protocol HEK293 cells were cultured in Dulbecco's modified Eagle's medium with 10% fetal bovine serum and antibiotics. Gateway-compatible entry clones were cloned into the pDEST pcDNA5/FRT/TO-eGFP vector according to the manufacturer's instructions and co-transfected into Flp-In T-REx 293 cells together with the pOG44 Flp recombinase expression plasmid. Cells were selected for FRT site-specific recombination into the genome, following instructions by the manufacturer.
Extracted molecule genomic DNA
Extraction protocol Lysates were sonicated to a DNA fragment length range of 200-300 bp using a Bioruptor (Diagenode). GFP-tagged transcription factors were immunoprecipitated with a polyclonal anti-GFP antibody (ab290, Abcam) and Dynabeads Protein G (Invitrogen). Subsequently, crosslinks were reversed at 65°C over night and bound DNA fragments were purified (EZ-10 Spin Column PCR Product Purification kit, Bio Basic).
Sequencing libraries were constructed using the TruSeq ChIP-seq library kits (Illumina) according the manufacturer's instructions followed by PCR amplification and agarose gel size selection.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing ChIP-seq reads were mapped to the human genome build hg19 using Bowtie 2. The 3’ end of reads were trimmed to a final length of 50 nucleotides, mapped with the Bowtie “--very-sensitive” preset of parameters, and duplicate reads were removed using SAMtools.
MACS v1.4 was used for peak calling, using experiment-specific background models constructed by pooling multiple control datasets.
Genome_build: hg19
Supplementary_files_format_and_content: MACS v1.4 output, containing the coordinates of peaks and summits based on hg19 genome assembly, as well as associated scores.
Supplementary_files_format_and_content: combined_summits.per_protein.hg19.tar: Tar of peak summits per protein.
Supplementary_files_format_and_content: combined_summits.motif_hits.per_protein.hg19.tar: Tar of motif hit locations within peaks per protein.
Supplementary_files_format_and_content: motifs.pfm.txt: Tab-delimited text file includes motifs identified for each protein.
 
Submission date Jan 04, 2016
Last update date May 15, 2019
Contact name Hamed S Najafabadi
Organization name McGill University
Department Human Genetics
Lab Computational and Statistical Genomics Lab
Street address 740 Dr. Penfield Avenue, Room 7202
City Montreal
State/province QC
ZIP/Postal code H3A 0G1
Country Canada
 
Platform ID GPL11154
Series (2)
GSE76494 Identification of in vivo binding sites of human GFP-tagged C2H2-ZF proteins
GSE76496 Multiparameter functional diversity of human C2H2 zinc finger proteins
Relations
BioSample SAMN04383220
SRA SRX1514943

Supplementary file Size Download File type/resource
GSM2026766_ZNF22_rep2.macs.out.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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