|
| Status |
Public on Nov 01, 2022 |
| Title |
db/m4 |
| Sample type |
SRA |
| |
|
| Source name |
islet cells
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Wild type
tissue: Pancreas
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Islets were isolated by collagenase digestion followed by purification on Histopaque (Sigma Aldrich, Germany) density gradient and used directly for RNA extraction.
The library for sequencing was constructed by removing ribosomal RNA from the total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
processed data file: all.counts.exp.txt
|
| Data processing |
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15, b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome.
Count counting.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: all.counts.exp.txt: Tab-delimited text file contains counts for each sample.
|
| |
|
| Submission date |
Nov 01, 2019 |
| Last update date |
Nov 01, 2022 |
| Contact name |
Li Xiong |
| E-mail(s) |
xiongl8@mail2.sysu.edu.cn
|
| Phone |
86-020-87755766-8450
|
| Organization name |
The First Affiliated Hospital of Sun Yat-sen University
|
| Department |
Department of Endocrinology
|
| Street address |
58 Zhongshan Road 2
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE139823 |
Next-generation sequencing facilitates quantitative analysis of wild type and diabetic db/db mice islets transcriptomes |
|
| Relations |
| BioSample |
SAMN13178332 |
| SRA |
SRX7085332 |
