NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1693803 Query DataSets for GSM1693803
Status Public on Feb 01, 2016
Title 7SK ChIRP-seq - HeLa - Input
Sample type SRA
 
Source name HeLa cells
Organism Homo sapiens
Characteristics cell type: Cervical cancer cells
cell line: HeLa
gender: female
Treatment protocol All cells were fixed with 1% gluteraldehyde for 10 minutes at room temperature.
Growth protocol mES cells were grown on gelatin plates with serum and LIF. Human ES cells were grown on matrigel plates. HeLa cells were grown on untreated plates
Extracted molecule genomic DNA
Extraction protocol Lysates were produced from soncated cell material and 7SK snRNA enriched with antisense oligonucleotide enrichment.
Libraries were prepared according to the standard ChIRP-seq protocol (PMID: 21963238)
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description Affinity purified genomic DNA
processed data file: hg19_7SK_ChIRP-seq_HeLa_Input.bw
Data processing Library strategy: ChIRP-seq
After demultiplexing, reads were stripped adaptors and mapped to the mouse (mm9) or human (hg19) genome using Bowtie2. Even and Odd datasets were merged as described previously (PMID:21963238) and visualized as bigWig files. Peaks from the merged datasets were called using MACS2.
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: bigWig files of merged (even and odd probe sets) 7SK ChIRP-seq read density
 
Submission date May 21, 2015
Last update date May 15, 2019
Contact name Ryan Alexander Flynn
E-mail(s) raflynn@stanford.edu
Organization name Stanford University
Street address 380 Roth Way, Room 265
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL11154
Series (2)
GSE69141 7SK-BAF axis controls pervasive transcription at enhancers [ChIRP-Seq]
GSE69143 7SK-BAF axis controls pervasive transcription at enhancers
Relations
BioSample SAMN03704208
SRA SRX1036405

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.