|
| Status |
Public on Mar 08, 2017 |
| Title |
F6B2_1NP |
| Sample type |
SRA |
| |
|
| Source name |
Mouse ES Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: 46C-ES
strain: 129/Ola
|
| Growth protocol |
Cells were grown at 37°C in a 5% CO2 incubator in Glasgow Modified Eagles Medium, supplemented with 10% fetal bovine serum, 2 ng/ml LIF and 1 mM 2-mercaptoethanol, on 0.1% gelatin-coated dishes. Cells were passaged every other day. After the last passage 24h before harvesting, ES cells were re-plated in serum-free ESGRO Complete Clonal Grade medium (Millipore Inc.)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTCAGAA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 3
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
library strategy: DNA-seq
|
| Data processing |
Basecalls were made using RTA version 1.17.21.3, with default filter and quality settings. The reads were demultiplexed (allowing 0 or 1 mismatches in the index sequence) with CASAVA 1.8.2
Reads were mapped to the mm9 genome assembly using bowtie v2.0.5 with all default settings. Non-unique reads or reads with low mapping quality were filtered using the command “sed '/XS:/d' | samtools view -q 20 -F 4 -bS -”. PCR duplicates were removed with the “samtools rmdup” command.
Samples were checked for contamination using fastq_screen v0.4.2. Samples with <15% of reads mapped or with more than 20% of reads mapped to the Human hg19 reference were excluded from further processing (but are included in this submission).
Coverage depth of each sample in 30kb windows was calculated using bedtools v2.17 and the command “multiBamCov -bed <(bedtools makewindows -w 30000 -g mm9.chrom.sizes)”. Each 30kb window was then called as positive or negative using a custom python script.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix files (ending .txt.gz) are tab-delimited tables containing one row/column per genomic locus, where the score in each cell of the matrix indicates the strength of the interaction between the corresponding two genomic loci. Segmentation files contain one row for every genomic locus, and one column for every raw data file which passed QC parameters, with the values representing the segmentation score for each sample at that genomic location.
|
| |
|
| Submission date |
Jan 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert A Beagrie |
| E-mail(s) |
robert.beagrie@ndcls.ox.ac.uk
|
| Organization name |
MRC Weatherall Institute of Molecular Medicine
|
| Department |
Molecular Haematology Unit
|
| Street address |
Headley Way
|
| City |
Oxford |
| ZIP/Postal code |
OX39DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE64881 |
Genome Wide Characterization of Genome Organization in Mouse ES cells |
|
| Relations |
| BioSample |
SAMN03283018 |
| SRA |
SRX839631 |
