 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 26, 2015 |
| Title |
HiC_rabbit_liver, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
cell type: primary liver cells
developmental stage: Young adult
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After liver homogenisation, cells were immediately fixed with 1% formaldehyde before proceeding with Hi-C protocol.
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 HiSeq 2000 |
| |
|
| Data processing |
Read alignment was done by using Bowtie v0.12.8 with the parameters "-v 3 -a -m 1 --best --strata".
HiC data analysis was done using hicpipe v1.01 (Yaffe and Tanay, 2011)
genome_build: mm10,oryCun2,rheMac2,canFam3
Supplementary_files_format_and_content: HiCseq_summary' is a tab-delimited text file summarizing alignment results for all samples. All other processed data files are cis-interaction maps reporting observed and expected values for contacts between 50 Kb bins separated by up to 2 Mb. One processed data file is supplied for each replicate plus a merge of the two replicates for each species. The files are in a modified bed format (with header) in which the first three columns are the coordinate of the first bin (chrom1, start1, end1), the second three columns are the coordinates of the second bin (chrom2, start2, end2) and the last two columns are the expected and observed interaction counts.
|
| |
|
| Submission date |
Jan 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Suzana Hadjur |
| E-mail(s) |
s.hadjur@ucl.ac.uk
|
| 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 |
GPL18453 |
| Series (1) |
| GSE65126 |
Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. |
|
| Relations |
| BioSample |
SAMN03292455 |
| SRA |
SRX851864 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1587704_HiC_rabbit_liver_rep2_50000.txt.gz |
24.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
|
|
|
|
 |
