|
| Status |
Public on Feb 07, 2013 |
| Title |
WT Hi-C |
| Sample type |
SRA |
| |
|
| Source name |
Floral tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
tissue: floral
genotype/variation: wild-type
|
| Treatment protocol |
Two grams of 3-week-old seedling leaves were crosslinked with formaldehyde as previously described (PMID: 17337630)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C was carried out essentially as described previously (Lieberman-Aiden et al., 2009), with the exception that plant nuclei were prepared following a previously published Arabidopsis ChIP protocol (PMID: 17337630)
The ligation products were fragmented by Covaris sonication to an average size of 200 bp and then the ideal size for Illumina sequencing (100-300 bp) was selected by Ampure fractionation. The DNA ends were prepared for Illumina sequencing adapter ligation by repairing the DNA ends and adding an ‘A’ to each end. The biotinylated junctions were then pulled down using MyOne streptavidin beads. Illumina paired end adapters were ligated onto the DNA ends and then the fragments were PCR amplified. Samples were sequenced on an Illumina HiSeq 2000 instrument using the Paired End 50 bp module.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing reads were mapped to the TAIR8 A. thaliana reference genome using Bowtie 1 to obtain all zero-mismatch hits of ends independently and keeping only unique paired end reads. Paired reads with ends aligning to the same HindIII fragment were discarded.
Reads were assigned to genomic bins of 50 kb or 200 kb, according to the center of their corresponding restriction fragment. HindIII fragments which overlapped regions of poor reference genome quality were excluded from the analysis. Genomic 1-D bins (rows and columns) in which > 50% of the sequence length was excluded by these filters were treated as missing data. The binned interaction maps were then corrected for systematic biases by equalizing the total coverage (1D sum across the matrix) of every bin in the genome using 50 iterations of a normalization procedure previously described (PMID: 22341456). Genomic bins with a total 1-D coverage more than 3 standard deviations greater or less than the mean were excluded.
Genome_build: tair8
Supplementary_files_format_and_content: IntMatrix files: Contains a matrix of normalized interaction frequencies for every pair of 50 kb or 200 kb bins in the genome. Bin names and genomic coordinates are listed in row and column headers and then iteratively corrected interaction frequencies are listed in each pair of row and column.
|
| |
|
| Submission date |
Feb 05, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Shawn J. Cokus |
| Organization name |
UCLA
|
| Street address |
UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE37644 |
MORC family ATPases required for heterochromatin condensation and gene silencing |
|
| Relations |
| SRA |
SRX227441 |
| BioSample |
SAMN01914969 |
