|
| Status |
Public on Aug 13, 2013 |
| Title |
Input DP (for Input DP for Nipbl and Med1 ChIP) |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ CD8+ Double Positive Thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD4+ CD8+ Double Positive Thymocytes
chip antibody: input DNA
genotype: wild type
genetic background: C57BL\6 and 129 mixed
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sorted CD4+ CD8+ DP thymocytes were fixed in 10% FCS DMEM media containing 1% formaldehyde. The cells were lysed and sonicated in [20 mM Tris-HCl, pH8, 150 mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X, protease inhibitors]. Lysates were cleared by centrifugation and incubated with a mixture of RNaseA and proteinaseK for 2 hours at 37° and then 16 hours at 65° to reverse the cross-links. DNA was purified by phenol-chloroform extraction and 10ng was used with a Illumina ChIP-seq sample preparation according to the manufacturer instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
DEKKER ICE METHOD - all relevant HiC data (binned at 4 resolutions) raw + iced data
UCSC GENOME BROWSER BED FILE - coordinates of all chip-seq peaks
Tab delmited file of all gene expression values (count equivalents) across all 4 samples.
Genome_build: mm9
Supplementary_files_format_and_content: peak bed (ChIP-seq), counts (RNA-Seq), and HiC data
|
| |
|
| Submission date |
Jul 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Andre J Faure |
| E-mail(s) |
andre.faure@crg.eu
|
| Organization name |
Centre for Genomic Regulation (CRG)
|
| Department |
EMBL-CRG Systems Biology Unit
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE48763 |
Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments. |
|
| Relations |
| SRA |
SRX320064 |
| BioSample |
SAMN02230610 |
