|
| Status |
Public on Jul 29, 2022 |
| Title |
ID:K3987 Tis:Colon Group:RD |
| Sample type |
SRA |
| |
|
| Source name |
Proximal Colon Tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
rat: K3987
litterdateofbirth: 2019-01-31
age: 168
Sex: Male
diabetic: Y
diabetesonsetage: 146
diabetesdays: 22
bodyweight: 597
group: RD
colonlength: 25.1
fastingglucose: 102.5
flowcell: 2
flowcell_id: 4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ileum and colon tissues were removed, flash frozen in liquid nitrogen. Total RNA was isolated using TRI reagent and Rneasy mini columns. Illumina TruSeq mRNA 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
Directional mRNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
F2-4
|
| Data processing |
Sequencing was performed using Nextseq 500 (1 X 75 bp). Reads were demultiplexed using Illumina Basespace. Reads were trimmed for adapters and filtered for quality using FASTX toolkit. Filtered reads were aligned to the rat genome (rn6) using STAR with default settings. Bam files were imported into SeqMonk and gene level read count quantitation was performed.
Supplementary_files_format_and_content: comma delimited matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: comma delimited matrix table with counts per million values for every gene and every sample
|
| |
|
| Submission date |
Aug 01, 2021 |
| Last update date |
Jul 29, 2022 |
| Contact name |
Brian Piccolo |
| E-mail(s) |
[email protected]
|
| Organization name |
Arkanssa Children's Nutrition Center
|
| Street address |
15 Children's Way
|
| City |
Little Rock |
| State/province |
AR |
| ZIP/Postal code |
72202 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE181275 |
RNA-seq profiling of colon and ileum tissues from the UC Davis Type 2 Diabetes Mellitus Rat Model |
|
| Relations |
| BioSample |
SAMN20515354 |
| SRA |
SRX11623791 |
