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Sample GSM2671003 Query DataSets for GSM2671003
Status Public on Aug 01, 2017
Title RNAseq HCT116 Rep3
Sample type SRA
Source name HCT116
Organism Homo sapiens
Characteristics cell line: HCT116
genotype: wildtype
Treatment protocol WT HCT116 and Cdk7as cells were treated with 10mM NM-PP1 for 24 hr before cross-linking and harvesting for ChIP-seq or RNA-seq
Growth protocol McCoy's 10% FCS, 10mM NM-PP1, 24hr
Extracted molecule total RNA
Extraction protocol Ribosomal RNA was removed using the NEB ribosome removal kit and libraries were prepared using the NEB ultra directional kit, with RNA fragmentation for 8 min and 15 PCR cycles.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description rRNA depleted total RNA
Data processing Single-end 50 base reads (after removing barcodes) or 151 base reads (after removing barcodes and trimming adaptor sequences) were mapped to the hg19 UCSC human genome with Bowtie version 0.12.5 for ChIP-seq and with Hisat2 version 2.0.4 for RNA-seq
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: bigwig files for ChIP-seq, TDF files for RNA-seq
Submission date Jun 15, 2017
Last update date May 15, 2019
Contact name David L. Bentley
Organization name U. Colorado School of Medicine
Department Biochemistry and Mol. Genetics
Street address 12801 E. 17th Ave
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
Platform ID GPL20301
Series (1)
GSE100040 Human TFIIH kinase CDK7 regulates transcription-associated epigenetic modification
BioSample SAMN07247114
SRA SRX2922522

Supplementary file Size Download File type/resource
GSM2671003_hct116_wt_3.tdf 106.7 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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