NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3908314 Query DataSets for GSM3908314
Status Public on Dec 31, 2021
Title G1E-R307C_input
Sample type SRA
 
Source name cell line
Organism Mus musculus
Characteristics cell line: G1E
gata1 protein construct: R307C
chip antibody: none
Treatment protocol n/a
Growth protocol IMDM, 15% FBS, 1xPen/Strep, 4.5E-5M mono-thio-glycerate, 50ng/ml murine SCF and 2U/ml erythropoietin
Extracted molecule genomic DNA
Extraction protocol 1% formaldehyde fixation followed by sonication to shear chromatin
chromatin-immunoprecipitation-sequencing using ChIP-grade anti-HA antibody (ab9110)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Raw sequencing data was processed using bcl2fastq
Paired-end reads were aligned to the mm10 reference genome using bowtie2
Duplicate reads were removed using Picard and peaks were called with macs2. A consensus peak file was generated using a strategy discussed in the DiffBind workflow (input samples were used in the inference of peak summits).
Bigwig files were generated using macs2 on the merged treated and input bam files and normalized using the SPMR flag.
Genome_build: mm10
Supplementary_files_format_and_content: Per-sample raw peak / counts matrix; bigwig track views of merged replicates
 
Submission date Jun 27, 2019
Last update date Dec 31, 2021
Contact name Caleb Lareau
E-mail(s) lareauc@mskcc.org
Organization name Memorial Sloan Kettering
Street address 417 E 68th St, Zuckerman - ZRC 1132
City New York
State/province New York
ZIP/Postal code 10065
Country USA
 
Platform ID GPL19057
Series (2)
GSE133409 A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1 [G1E_ChIPseq]
GSE133417 A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1
Relations
BioSample SAMN12147619
SRA SRX6370148

Supplementary file Size Download File type/resource
GSM3908314_G1E-R307C_ChIP.bw 323.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap