|
| Status |
Public on Jun 03, 2019 |
| Title |
Spermatogonia_HiC |
| Sample type |
SRA |
| |
|
| Source name |
Spermatogonia
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Spermatogonia
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Enriched cell populations were processed following the in situ Hi-C protocol described by Rao et. al 2014.
Hi-C libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Hi-C: Reads were quality-checked and filtered using BBDuk version10/2015 and then aligned using TADbit version 0.2.0.23. Data was binned and normalised using an in-house script taht read the map files generated after filtering, obtaining matrix that were stored into a file in NPZ format (raw).
ChIP-seq: Reads were quality-checked and mapped with BWA. Mapped reads were filtered with SAMtools. Coverage files were obtained from bam files using DeepTools:bamCoverage. All the mentioned tools were used through the Galaxy server (https://usegalaxy.org/).
RNA-seq: Reads were analysed using AIR (https://transcriptomics.cloud), were reads were filtered according to quality, mapped using STAR (Dobin et al 2013) and gene expression quantification was done using featureCounts (Liao et al 2014).
Genome_build: mm10
|
| |
|
| Submission date |
May 31, 2019 |
| Last update date |
Jun 05, 2019 |
| Contact name |
Covadonga Vara |
| E-mail(s) |
covavara92@gmail.com
|
| Organization name |
Universitat Autònoma de Barcelona
|
| Department |
Biologia cel·lular, Fisiologia i Immunologia
|
| Lab |
Citologia
|
| Street address |
Campus UAB
|
| City |
Cerdanyola del Vallès (Bellaterra) |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE132054 |
Three-dimensional genomic structure and cohesin occupancy correlates with transcriptional activity during spermatogenesis |
|
| Relations |
| BioSample |
SAMN11935450 |
| SRA |
SRX5951657 |
