|
Status |
Public on Mar 31, 2024 |
Title |
TES-3 |
Sample type |
SRA |
|
|
Source name |
testis
|
Organism |
Bos grunniens x Bos taurus |
Characteristics |
tissue: testis Sex: male age: four years
|
Treatment protocol |
The testicular tissue was washed with PBS and quickly placed in a freezer tube, immediately stored in liquid nitrogen.
|
Growth protocol |
Five groups of 6-month-old (6M), 18-month-old (18M), 30-month-old (30M), 4-year-old (4Y) male yaks and 4-year-old adult male cattle-yak (TES) were selected from the same cooperative in Xiahe County (N34°51'50', E102°26'9') in Gannan Tibetan Autonomous Prefecture for castration.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from each testicular sample using TRIzol reagent. RNA quality was assessed using Nanodrop-2000 and 1% agarose gel electrophoresis. Qualified RNA was used to prepare 1μg total RNA for cDNA library construction by cDNA-PCR sequencing kit. The cDNA library was sequenced on PromethION sequencer (Oxford Nanopore Technologies, Oxford, UK). These testing processes were conducted according to the protocol of the manufacturer.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
PromethION |
|
|
Description |
cattle-yak
|
Data processing |
Pychopper was used to identify full-length sequences in valid sequencing data and NanoFilt was used to filter the full-length sequence. Minimap2 was used to align the filtered full-length sequence with the reference gene and quickly construct a non-redundant transcript set. The gffcompare was used to compare transcripts with known transcripts in the genome. The alternative splicing types of each sample were obtained by suppa2. Use Tofu (version: 13.0.0; parameter: default) alignment and search for fusion transcripts. Using MISA software for SSR prediction. The transcription factors were identified using the animal transcription factor database animalTFDB. TAPAS combined with the reference sequence of RefSeq database to identify APA. Assembly: LU_Bosgru_v3.0 Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample. Supplementary files format and content: Tab-delimited text files include DESeq2 results. Supplementary files format and content: FASTA files
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|
|
Submission date |
Dec 28, 2023 |
Last update date |
Mar 31, 2024 |
Contact name |
shaoke guo |
E-mail(s) |
YDKang0901@outlook.com
|
Phone |
15036009308
|
Organization name |
Chinese Academy of Agricultural Sciences
|
Department |
Lanzhou institute of husbandry and pharmaceutical sciences
|
Street address |
West Lake Street
|
City |
Lanzhou |
State/province |
Gansu |
ZIP/Postal code |
730050 |
Country |
China |
|
|
Platform ID |
GPL34048 |
Series (1) |
GSE252198 |
Nanopore-based full-length transcriptome sequencing of yak (Bos grunniens) testis |
|
Relations |
BioSample |
SAMN39182380 |
SRA |
SRX23052710 |