|
| Status |
Public on Dec 28, 2022 |
| Title |
GoatSkin6 |
| Sample type |
SRA |
| |
|
| Source name |
Goat Skin
|
| Organism |
Capra hircus |
| Characteristics |
tissue: Skin
treatment: Control
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Skin tissue was chopped into fine pieces and lysed by adding Buffer ATL, ProteinaseK and Buffer AL. The lysate was bound to Dneasy Mini Spin Column and the DNA was eluted in Buffer AE after subsequent washes. (Dneasy® Blood& Tissue Kit Cat.No.69506)
The purified gDNAwas bisulfite converted using Lightning Conversion Reagent and amplified with specific PreAmp primeres followed by Amplification with Library Amp Primers and Index primers. (Pico Methyl-Seq Library Prep Kit for Illumina-based sequencing; Cat.No. D5456-A)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Quality trimming using fastp
Alignment against Goat reference genome using Bismark
PCA using R
differential gene expression analysis using methyl kit
Annotation using Homer
Genome_build: goat genome GCF_001704415.1_ARS1
Supplementary_files_format_and_content: tab delimited format of methylation estimated
|
| |
|
| Submission date |
Jan 10, 2022 |
| Last update date |
Dec 28, 2022 |
| Contact name |
Veerasamy Sejian |
| E-mail(s) |
Sejian.V@icar.gov.in
|
| Organization name |
National Institute of Animal Nutrition and Physiology
|
| Street address |
National Institute of Animal Nutrition and Physiology
|
| City |
BENGALURU |
| ZIP/Postal code |
560030 |
| Country |
India |
| |
|
| Platform ID |
GPL25639 |
| Series (1) |
| GSE193343 |
Assessing the productive and adaptive capability of two different goat breeds to heat stress based on differences in the phenotypic and genotypic traits |
|
| Relations |
| BioSample |
SAMN24794092 |
| SRA |
SRX13691808 |
