|
| Status |
Public on Aug 01, 2013 |
| Title |
RNA-Seq_Prox |
| Sample type |
SRA |
| |
|
| Source name |
proximal colon crypts
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain/background: Sprague Dawley
age: 14 weeks
tissue: proximal colon crypts
|
| Growth protocol |
Samples from 7 rats, 14 weeks old, were pooled together for each sequencing run.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Colonic crypts were isolated from distal and proximal regions of the colon. RNA was extracted from colonic crypt cells.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Processed data file: RNAseq_gene_exp.txt (sample_1)
|
| Data processing |
Illumina Casava software used for basecalling.
RNA-Seq reads were filtered for adapter sequences and trimmed based on sequence quality (threshold of Q20) using ea-utils toolkit. Spliced alignment was performed against the rat genome (Baylor 3.4/rn4) using tophat2 without allowing any mismatches to reduce the number of false positives and the resultant alignments were further processed using cufflinks2 to perform reference annotation based transcript assembly with bias and multi-read correction. Differential expression analyses were performed using cuffdiff2 and cummeRbund.
Genome_build: RGSC_v3.4
Supplementary_files_format_and_content: RNAseq_gene_exp.txt is a tab-delimited text file that includes FPKM values for each Sample.
|
| |
|
| Submission date |
Jul 31, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Karen Triff |
| E-mail(s) |
ktriff@tamu.edu
|
| Phone |
979 845 0448
|
| Organization name |
Texas A&M University
|
| Street address |
321 Kleberg Center, 5523 TAMU
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77840 |
| Country |
USA |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE49389 |
Genome-wide analysis of the rat colon reveals site-specific differences in histone modifications and proto-oncogene expression |
|
| Relations |
| BioSample |
SAMN02298419 |
| SRA |
SRX330079 |
