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Sample GSM6578832 Query DataSets for GSM6578832
Status Public on Feb 07, 2024
Title BrainC_Cattle
Sample type SRA
 
Source name Brain
Organism Bos taurus
Characteristics tissue: Brain
development stage: adult
Extracted molecule total RNA
Extraction protocol Total RNA were extracted using TRIzol method from frozen Brain samples
mRNA were enriched using magnetic beads with Oligo(dT) and sheared. The cDNA was synthesized using random hexamers, end-repaired, and ligated to A base and sequencing adapters.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing The adapter sequences and low-quality bases were filtered using Trimmomatic v0.39
The trimmed reads were mapped to the Ensembl 103 version of reference genomes with annotated genes using STAR aligner v 2.7.6 with the following options: “--outFilterMismatchNmax 3 –outFilterType BySJout –quantMode GeneCounts –outFilterMismatchNoverLmax 0.04 –outSAMtype SAM SortedByCoordinate”.
Gene expression levels were quantified as counts using featureCounts
Assembly: ARS-UCD1.2, Oar_rambouillet_v1.0, ARS1
Supplementary files format and content: tab-delimited text files include gene counts for each Sample
 
Submission date Sep 14, 2022
Last update date Feb 07, 2024
Contact name Siqian Chen
E-mail(s) siqianchen1994@gmail.com
Phone 15652765993
Organization name China Agricultural University
Department College of Animal Science and Technology
Lab National Engineering Laboratory for Animal Breeding
Street address 2rd, Yuanmingyuan West Road
City Beijing
ZIP/Postal code 100193
Country China
 
Platform ID GPL24230
Series (1)
GSE213317 Comparative gene expressions profiling of brain and muscle across ruminants
Relations
BioSample SAMN30846018
SRA SRX17564658

Supplementary file Size Download File type/resource
GSM6578832_BrainC_Cattle.featureCounts.txt.gz 2.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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