GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1701912 Query DataSets for GSM1701912
Status Public on Jun 03, 2015
Title Flag-Barx1_ChIP
Sample type SRA
Source name Immortalized E13.5 stomach mesenchymal cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Stomach
passage: 8-11
chip antibody: Flag M2 Antibody Sigma
Treatment protocol Infected with 3xFLAG-BARX1-P2A-EGFP lentivirus generated from 293FT cells, cultured for 7 days
Growth protocol Dulbecco's Modified Eagle Medium (DMEM) supplemented with 20% FBS and 1% Penicillin-Streptomycin
Extracted molecule genomic DNA
Extraction protocol Cells were fixed in 1.1% formaldehyde in phosphate-buffered saline for 10 min at room temperature. Nuclei were extracted in a hypotonic buffer and chromatin was sheared by sonication. Immunoprecipitation was done using 10 ug of Flag M2 antibody (Sigma) and Protein G dynabeads (Invitrogen).
DNA was amplified using ThruPLEX kit (Rubicon Genomics)
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing Basecalls performed using CASSAVA
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.2.1 with default settings. Only uniquely aligned tags were retained and PCR duplicates were removed
Peaks were called using MACS2 with the following settings: Q value <=0.01, bandwith = 220.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files and Peak Bed file generated with MACS2
Submission date Jun 02, 2015
Last update date May 15, 2019
Contact name Chenura Jayewickreme
Organization name Weill Cornell Medical College
Street address 1300 York Avenue
City New York
State/province NY
ZIP/Postal code 10021
Country USA
Platform ID GPL19057
Series (1)
GSE69483 Control of stomach smooth muscle development and intestinal rotation by transcription factor BARX1 (ChIP-seq)
BioSample SAMN03757641
SRA SRX1047225
Named Annotation

Supplementary file Size Download File type/resource 274.2 Mb (ftp)(http) BW
GSM1701912_ISMC_ChIP_peaks.bed.gz 3.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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