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| Status |
Public on Oct 15, 2019 |
| Title |
PG-lAna-1: Late_Anagen Sample 1 |
| Sample type |
SRA |
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| Source name |
SKIN
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| Organism |
Capra hircus |
| Characteristics |
breed: Chanthangi Pashmina Goat
tissue: skin
age: 26 months
pashmina fiber cycling: Late Anagen
Sex: Male
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| Extracted molecule |
total RNA |
| Extraction protocol |
The skin sample was collected from the flanking region of each goat at same time point. Prior to sampling, the site was sheared, shaved and locally anesthetized with 2% lignocaine. Approximately 7mm diameter skin samples were harvested aseptically with a single-use biopsy punch.
The quality of purified total RNA provided will be checked on the Agilent Tapestation using the RNA cartridge. Total RNA with RNA Integrity Number (RIN) value greater than or equal to 8 is considered good quality. ~4ug of total RNA will be used to prepare the RNA seq library using the TruSeq RNA Sample Prep Kits (Illumina). The libraries will be prepared as per the kit protocol. In short, poly-A containing mRNA molecules will be purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA will be fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments will be used to synthesize first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments will then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products will be purified and enriched with PCR to create the final cDNA library. Bioanalyzer plots will be used at every step to assess mRNA quality, enrichment success, fragmentation sizes, and final library sizes. Both Qubit and qPCRwill be used for measuring the quantity of the library before sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
2x100 paired-end sequence reads
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Capra hircus whole genome using bowtie v2 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
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| Submission date |
Jul 13, 2018 |
| Last update date |
Oct 15, 2019 |
| Contact name |
Basharat Ahmad Bhat |
| E-mail(s) |
bb284@snu.edu.in
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| Phone |
9469662374
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| Organization name |
Sher-e-Kashmir University of Agricultural Sciences and Technology
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| Department |
Animal Biotechnology
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| Street address |
Shuhama
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| City |
Gandarbal |
| State/province |
Kashmir |
| ZIP/Postal code |
190006 |
| Country |
India |
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| Platform ID |
GPL19149 |
| Series (1) |
| GSE117065 |
Comparative transcriptome analysis reveals genetic basis of the annual Pashmina fiber cycle in Changthangi Pashmina goats |
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| Relations |
| BioSample |
SAMN09654147 |
| SRA |
SRX4388411 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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