|
| Status |
Public on Aug 24, 2011 |
| Title |
Smad3 - ESC |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: V6.5 embryonic stem cells
chip antibody: Smad3
antibody vendor: Abcam
antibody catalog number: AB28379
|
| Treatment protocol |
Normal culture conditions
|
| Growth protocol |
V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
08082008_309DNAAXX_B2
Chromatin IP against Smad3
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
Reads aligned to mouse NCBI build 36 (mm8 for mouse samples and hg18 for human) using BOWTIE.
For ChIP-Seq, sequences from all lanes were extended 200bp downstream (with respect to strand), and allocated into 25 bp bins. Reads from replicates were merged and genomic bins containing statistically significant ChIP-seq enrichment were identified by comparison to a Poissonian background model, using a p-value threshold of 10-9. Additionally, we used an empirical background model obtained from identical Solexa sequencing of DNA from whole cell extract (WCE) or IgG IP's from matched cell samples (>5X normalized enrichment across the entire region). WIG tracks show bins with at least 2 counts in the respective dataset (after replicate merging, where appropriate).
|
| |
|
| Submission date |
Apr 30, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE21614 |
Cell-Type-Specific TGF-beta Signaling is Targeted to Genes that Control Cell Identity: ChIP-Seq |
| GSE21621 |
Cell-Type-Specific TGF-beta Signaling is Targeted to Genes that Control Cell Identity |
|
| Relations |
| SRA |
SRX026242 |
| BioSample |
SAMN00014814 |
