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Sample GSM7996478 Query DataSets for GSM7996478
Status Public on Mar 31, 2024
Title 4Y-1
Sample type SRA
 
Source name testis
Organism Bos grunniens
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model PromethION
 
Description 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
 
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 GPL34047
Series (1)
GSE252198 Nanopore-based full-length transcriptome sequencing of yak (Bos grunniens) testis
Relations
BioSample SAMN39182385
SRA SRX23052705

Supplementary file Size Download File type/resource
GSM7996478_4Y-1.full_length_filtered.fa.gz 2.3 Gb (ftp)(http) FA
SRA Run SelectorHelp
Raw data are available in SRA

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