|
| Status |
Public on Feb 22, 2014 |
| Title |
4C_Ibtk_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Trophoblast Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: F1 hybrid trophoblast stem cells derived from blastocyst
passage: 17
strain: Cast/EiJ x C57BL/6
|
| Treatment protocol |
TS cells were removed from feeder cells and grown feeder-free for 2 passages prior to fixation.
|
| Growth protocol |
TS cells were cultured as previously described (Calabrese et al., 2012, Quinn et al., 2006)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted as fixed chromatin from nuclear lysates and fragmented by restriction digest. See methods in Williams et al., 2013
4C libraries were constructed using a modified, locus-specific protocol for 4C-Seq. See methods in Williams et al., 2013
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Sequences processed by CASAVA v1.8
Raw sequences were filtered for 4C-primers to identify anchor and allele of origin
Raw sequences were mapped using Bowtie v0.12.7 (-n 2 -l 100 -m 1 --best --strata)
Mapped sequences were processed using custom Perl scripts and the fourSig analysis package to identify significant interacting regions of the genome
Interacting regions were analyzed using custom R scripts to identify interacting fragments between replicate libraries and alleles
Genome_build: mm9
Supplementary_files_format_and_content: All text files are tab delimited and contain genomic coordinates for interactions and read counts.
|
| |
|
| Submission date |
Sep 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Rex Lee Williams |
| Organization name |
University of North Carolina
|
| Department |
Genetics
|
| Lab |
Magnuson Lab
|
| Street address |
120 Mason Farm Road
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE50907 |
fourSig: A Method for Determining Chromosomal Interactions in 4C-Seq Data |
|
| Relations |
| BioSample |
SAMN02356748 |
| SRA |
SRX351937 |
