|
| 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 |
| E-mail(s) |
chj2018@med.cornell.edu
|
| 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) |
|
| Relations |
| BioSample |
SAMN03757641 |
| SRA |
SRX1047225 |
| Named Annotation |
GSM1701912_ISMC_ChIP.bw |
