|
Status |
Public on Feb 05, 2019 |
Title |
CSB+/- rep1 |
Sample type |
SRA |
|
|
Source name |
CSB+/-_cerebellum
|
Organism |
Rattus norvegicus |
Characteristics |
strain background: Sprague-Dawly (SD) age: 10-week old age genotype/variation: heterozygous mutant for CSB; CSBR571X/- tissue: Cerebellum cortex
|
Extracted molecule |
total RNA |
Extraction protocol |
Cerebellar cortex tissues were removed, flash frozen and homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
|
|
Description |
F1-1
|
Data processing |
FastQC was conducted for Quality control (QC) of RNA-seq reads Trimming was performed by seqtk for known Illumina TruSeq adapter sequences, poor reads, and ribosomal RNA reads Trimmed reads were mapped to the Rattus norvegicus reference genome by the Hisat 2(version:2.0.4) String Tie(version:1.3.0) was performed for each gene count from trimmed reads Gene counts were normalized by trimmed mean of M-values, and fragments per kilobase of transcript per million mapped reads (FPKM) in Perl script Genome_build: rn6 Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
|
|
Submission date |
Feb 04, 2019 |
Last update date |
Feb 12, 2019 |
Contact name |
Yuming Wang |
E-mail(s) |
wangyuming2006@hotmail.com
|
Phone |
008602037103555
|
Organization name |
Guangzhou medical university
|
Department |
School of Basic Medical Science
|
Street address |
Room 512, Anatomy Building
|
City |
Guangzhou |
State/province |
Guangdong |
ZIP/Postal code |
511436 |
Country |
China |
|
|
Platform ID |
GPL24688 |
Series (1) |
GSE126032 |
Gloable gene expression is affected by loss of CSB function in the rat model for Cockayne syndrome |
|
Relations |
BioSample |
SAMN10868556 |
SRA |
SRX5329405 |