|
| Status |
Public on Nov 10, 2021 |
| Title |
follicular granulosa cell layers-F1 Hi-C replicate_1 |
| Sample type |
SRA |
| |
|
| Source name |
follicular granulosa cell layers
|
| Organism |
Gallus gallus |
| Characteristics |
breed: Luhua hens
developmental stage: preovulatory follicles
age: 31 weeks
tissue: follicular granulosa cell layers
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C experiment were conducted using DpnII, according to the protocol published by Suhas S P Rao. et al. Cell 2014 (PMID: 25497547) .
DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S P Rao. et al. Cell 2014 (PMID: 25497547).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Reads were mapped to the chicken reference genome (GRCg6a) by BWA (v 0.7.15).
Juicer were used HiC data processing to filter duplication, low-quality alignment read pairs (MAPQ < 30) as well as intra-fragment read pairs.
High-quality reads normalized with Knight-Ruiz [KR] algorithm and quantile algorithm to structure contact matrixes at 20 or 100 kb resolution.
Compartments A/B were identified with principal component analysis (PCA) as described by Lieberman-Aiden E, et al. science 2009 (PMID: 19815776).
Locations of topologically associated domains (TADs) were computed by combining directionality index (Dixon et al. Nature. 2012 [PMID: 22495300]) and insulation index (Emily Crane et al. Nature. 2017)
Genome_build: GRCg6a
Supplementary_files_format_and_content: 20 and 100 kb matrixes, hic file
location of paired reads, gz file
A-B index, xls file
locations of TAD for each sample, bed file
|
| |
|
| Submission date |
Feb 18, 2021 |
| Last update date |
Nov 10, 2021 |
| Contact name |
hua kui |
| E-mail(s) |
2020102003@stu.sicau.edu.cn
|
| Organization name |
Sichuan Agricultural University
|
| Street address |
No 211 Huimin Road
|
| City |
chengdu |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL24517 |
| Series (1) |
| GSE167064 |
Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis |
|
| Relations |
| BioSample |
SAMN17980520 |
| SRA |
SRX10128372 |
