|
| Status |
Public on Sep 26, 2015 |
| Title |
Smad3_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cell
strain: J1 ES cells containing BirA
chip antibody: Smad3 (Abcam, ab28379)
|
| Growth protocol |
Mouse J1 ES cells were cultivated in 0.1% gelatin coated dishes using DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 15% fetal bovine serum (FBS), 2 mM of L-glutamine, 0.1 mM of non-essential amino acid, 1% of nucleoside mix, 0.1 mM of ß-mercaptoethanol, 1000U/ml of recombinant leukemia inhibitory factor and 50 U/ml of Penicillin/Streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution in J1 mouse ES cells. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNA was applied for the generation of sequencing libraries using the NEB ChIP-seq library prep. kit (E6200L ) following by manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Chromatin IP against Smad3
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse mm9 genome using BWA version 0.5.9-r16.
Peaks were called using MACS peak caller with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak
|
| |
|
| Submission date |
Feb 26, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bum-Kyu Lee |
| E-mail(s) |
bklee92@gmail.com
|
| Phone |
512-232-8046
|
| Organization name |
University of Texas at Austin
|
| Street address |
2506 Speedway Stop A5000
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE55404 |
TG-interacting factor1 (Tgif1) maintains the identity of mouse ES cells by counterbalancing the expression of ES cell core factors |
| GSE55437 |
TG-interacting factor1 (Tgif1) maintains the identity of mouse ES cells by counterbalancing the expression of core pluripotency factors and ES cell core factors |
|
| Relations |
| BioSample |
SAMN02666514 |
| SRA |
SRX477547 |
