|
| Status |
Public on Dec 11, 2013 |
| Title |
HadjurLab-HiC-mNSC-Rad21-floxed, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
neural stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: neural stem cells
genotype/variation: floxed--conditional mutants
|
| Treatment protocol |
To delete Rad21, cells were grown in OHT for 48hr (for NSCs) or AdCre for 96hr (for ASTs)
|
| Growth protocol |
Cells were grown in serum-free media containing EGF+FGF (for NSCs) or BMP+FGF (for ASTs) and Laminin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were treated with accutase and immediately fixed with 1% formaldehyde before proceeding with Hi-C protocol.The PE library preparations for the HiC were also done according to illuminas PE kit procedure.
Ligated material was sonicated, enriched for biotinylated ligation junctions and PE sequencing adapters were added according to Illumina standard protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Read alignment was done by using Bowtie v1.0.0 with the parameters as "-n 3 -a -m 1 --best --strata".
Genome_build: mm9
Supplementary_files_format_and_content: The tab-delimited text file summaries alignment results for all samples.
|
| |
|
| Submission date |
Jul 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Suzana Hadjur |
| E-mail(s) |
[email protected]
|
| Phone |
+44 7798957199
|
| Organization name |
Ucl
|
| Department |
Cancer biology
|
| Lab |
Genome organization
|
| Street address |
72 Huntley street
|
| City |
London |
| ZIP/Postal code |
Wc1e6bt |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE49017 |
Cohesin is a key determinant of interphase chromosome domain architecture (HiC) |
| GSE49018 |
Cohesin is a key determinant of interphase chromosome domain architecture |
|
| Relations |
| Reanalyzed by |
GSE87112 |
| BioSample |
SAMN02260381 |
| SRA |
SRX326537 |
