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Sample GSM2340123 Query DataSets for GSM2340123
Status Public on Oct 09, 2019
Title VRTN_ChIPSeq
Sample type SRA
Source name HEK293T cells
Organism Homo sapiens
Characteristics cell line: HEK293T
cell type: Human Embryonic Kidney
passages: 15-18
chip antibody: Anti-FLAG M2 Affinity Gel (Sigma)
Treatment protocol The full-length coding sequence of pig VRTN was subcloned into pNTAP-2×flag expression vectors. HEK293T cells were transfected with pNTAP-2×flag-VRTN.
Growth protocol HEK293T cells were cultured in high-glucose DMEM (Gibco) supplemented with 10% fetal bovine serum (Hyclone) and an antibiotic solution
Extracted molecule genomic DNA
Extraction protocol ChIP samples were prepared from VRTN-overexpressing HEK293T cells using the SimpleChIP Enzymatic Chromatin IP kit (CST) according to the manufacturer’s instructions. The cells were harvested and chemically cross-linked with 1% formaldehyde for 10 minutes at 16-20°C. The cell nuclei were released via sonication using an Ultrasonic Processor (SONXI). The collected nuclei were digested with micrococcal nuclease (CST) for 20 minutes at 37 °C. Sheared chromatin was incubated with Anti-FLAG M2 Affinity Gel (Sigma) for 4 hours. Immunoprecipitated DNA was treated with RNase A (CST) and purified with the SimpleChIP kit (CST).
A sequencing library was constructed from enriched DNA fragments using the TruSeq ChIP Library Prep kit (Illumina). Final DNA libraries were validated and sequenced at 50 bp per sequence read using a HiSeq 2000 sequencer (Illumina) at a depth of approximately 20 million sequences.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Data processing ChIP-seq reads were mapped to the human genome (GRCh38.p5) using BEDtools.
Only the alignments with fewer than two mismatches were considered for enriched-region (peak) identification (peak calling) using the Model-based Analysis of ChIP-seq (MACS) algorithm.
MEME 4.6.1 software was used to identify the VRTN binding motif.
PeakAnalyzer software was used for peak annotation and the analysis of the nearest downstream gene.
Genome_build: the human genome (GRCh38.p5)
Supplementary_files_format_and_content: wig files were generated with MACS algorithm.
Submission date Oct 09, 2016
Last update date Oct 09, 2019
Contact name Yanyu Dean
Phone 86-791-83813080
Organization name Jiangxi Agricultural University
Lab State Key Laboratory of Pig Genetic Improvement and Production Technology
Street address Lushanzhong888, Changbei district
City Nanchang
ZIP/Postal code 330044
Country China
Platform ID GPL9052
Series (2)
GSE87774 VRTN Regulates the Number of Thoracic Vertebrae During Vertebrate Development [ChIP-seq]
GSE87776 VRTN Regulates the Number of Thoracic Vertebrae During Vertebrate Development
BioSample SAMN05891564
SRA SRX2234299

Supplementary file Size Download File type/resource
GSM2340123_1.wiggle.tar.gz 54.6 Mb (ftp)(http) TAR
GSM2340123_peaks.txt.gz 30.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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