|
| Status |
Public on Mar 15, 2012 |
| Title |
WT_SA1 |
| Sample type |
SRA |
| |
|
| Source name |
Chromatin IP against SA1
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: wild type
developmental stage: E12.5
cell type: Mouse Embryonic Fibroblasts (MEF)
strain: C57BL/6 x 129 Sv
chip antibody: SA1
|
| Treatment protocol |
Untreated
|
| Growth protocol |
MEFs were grown in DMEM supplemented with 20% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Input and chromatin immunoprecipitated DNA samples were provided by the user. Available sample amounts from 4 to 15ng of DNA (as quantitated by fluorometry) were electrophoresed on agarose gel and independent sample-specific fractions of 100-200 bp were taken. Extracted DNA was processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "ChIP Sequencing Sample Prep Guide" (part # 11257047 Rev. A), with the exception that gel extraction was replaced with Agencourt AMPure XP (BeckmanCoulter) bead purification. Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (14 cycles). The resulting purified DNA libraries were applied to an Illumina flow cell for cluster generation and sequenced on the Genome Analyzer IIx by following manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
WT Mouse Embryonic Fibroblasts
|
| Data processing |
Image analysis was performed with Illumina Real Time Analysis software (RTA1.8). Sequence alignment to the reference genome (mm9) was made with Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. ELANDv2 performs multiseed alignment with consecutive read substrings of 16 to 32 bases separately. The seeds are aligned to multiple candidate positions in the reference genome, with a maximum of two mismatches allowed per 32 bases seed; then they are extended to the full read using gapped alignment, allowing for any number of mismatches and potential gaps (indels) of up to 20 bases. The best alignment among the multiple candidate positions is chosen based on quality scores.
Genome Build:
WT_SA1vsInput.FDR10.AllFC.bed: mm9
|
| |
|
| Submission date |
Sep 22, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Silvia Remeseiro |
| E-mail(s) |
sremeseiro@cnio.es
|
| Organization name |
Spanish National Cancer Research Centre (CNIO)
|
| Lab |
Ana Losada's lab
|
| Street address |
Calle Melchor Fernandez Almagro 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE32319 |
A unique role of Cohesin-SA1 in gene regulation and development [ChIP-Seq] |
| GSE32320 |
A unique role of Cohesin-SA1 in gene regulation and development |
|
| Relations |
| SRA |
SRX099211 |
| BioSample |
SAMN00727944 |
