|
| Status |
Public on Oct 15, 2016 |
| Title |
mutant rep1 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic islets
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Pancreatic islets
age: 5-6 weeks
genotype: mutGCK(Y214C)
|
| Treatment protocol |
no treatment prior to RNA extraction
|
| Growth protocol |
mice were kept in SPF facility
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pancreatic islets were isolated from transgenic GCK mutant (GCK Y214C) and control littermates. RNA was extracted using Qiagen RNA extraction Mini Kit
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 column: F0_ZM
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse mm9 genome and Refseq transcriptome, as well as for transcript quantitation .
Differential expression analysis was carried out using a custom script implementing EdgeR software
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited file of raw read counts
|
| |
|
| Submission date |
Sep 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sharona Tornovsky Babaey |
| E-mail(s) |
btsharona@gmail.com
|
| Organization name |
Hebrew University-Hadassah Medical Center
|
| Department |
Endocrinology and Metabolism
|
| Street address |
Jerusalem 91120, Israel
|
| City |
Jerusalem |
| ZIP/Postal code |
12000 |
| Country |
Israel |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE86949 |
RNAseq data from mouse beta-cells expressing mutant (GCK Y214C) versus wild-type Glucokinase |
|
| Relations |
| BioSample |
SAMN05773533 |
| SRA |
SRX2165332 |
