|
| Status |
Public on Sep 23, 2016 |
| Title |
CF-1 |
| Sample type |
SRA |
| |
|
| Source name |
small intestine
|
| Organism |
Rattus norvegicus |
| Characteristics |
disease state: cystic fibrosis
strain: Sprague Dawley
tissue: small intestine
age: post natal day 21
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The entire length of the small intestine was removed to ice cold PBS and trimmed free of fat and mesentery. The tissue was then flushed with PBS containing 10 mM dithiothreitol to remove the majority of digesta and mucus from the lumen. The tissue was then opened along the mesenteric border and cut lengthwise. Total RNA was isolated from the entire length of the small intestine by homogenization in Trizol followed by processing with a Phase Lock Gel Heavy according to the manufacturer's instructions. Stranded mRNA-Seq was performed using the Illumina HiSeq2500 Sequencing System. Total RNA (0.5 g) was used to initiate the Stranded mRNA-Seq library preparation protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
stranded mRNA
|
| Data processing |
bcl2fastq Conversion Software v1.8.4 from illumina was used to generate fastq files
reads were trimmed with cutadapt and mapped to the Rat Rnor_6.0 genome with STAR_2.3.1z --genomeDir Rnor_6.0 --readFilesIn R1.fastq R2.fastq --runThreadN 24 --outSAMstrandField intronMotif
differential gene expression was deterimined using stringtie -p 24 -G cuffmerge -g -p 24 and cuffdiff -p 24 -u -v --emit-count-tables --max-bundle-frags 100000000 --max-mle-iterations 500000
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab delimited files containing fpkm counts by group or sample, differential gene expression by gene.
|
| |
|
| Submission date |
May 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert C De Lisle |
| E-mail(s) |
[email protected]
|
| Phone |
913-588-2742
|
| Organization name |
Univ Kansas Med Ctr
|
| Department |
Anatomy & Cell Biology
|
| Street address |
3901 Rainbow Blvd
|
| City |
Kansas City |
| State/province |
KS |
| ZIP/Postal code |
66160 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE81114 |
RNA-Seq analysis of the cystic fibrosis rat small intestine |
|
| Relations |
| BioSample |
SAMN04942900 |
| SRA |
SRX1743009 |
