|
| Status |
Public on Aug 01, 2019 |
| Title |
R1 |
| Sample type |
SRA |
| |
|
| Source name |
Islets
|
| Organism |
Rattus norvegicus |
| Characteristics |
age: Fetal (GD22)
treatment: Control
strain: Sprague Dawley
|
| Treatment protocol |
Islets were extracted from 2 fetal pancreata after 48 hours of 4mg/min glucose infusion and recovered 24hrs in culture media
|
| Growth protocol |
RPMI with 5mM glucose
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Qiagen RNEasy Plus micro kit.
Illumina TruSeq Stranded mRNA Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NextSeq 500.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featurecounts.txt (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.12.1).
Genome_build: UCSC rn6
Supplementary_files_format_and_content: Raw counts.txt and normalized abundance measurement from edgeR
|
| |
|
| Submission date |
Aug 08, 2018 |
| Last update date |
Aug 01, 2019 |
| Contact name |
Kok Lim Kua |
| E-mail(s) |
kkua@iu.edu
|
| Organization name |
Indiana University
|
| Department |
PED-NEONATAL MEDICINE
|
| Street address |
RR208 PNEO IN
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE118323 |
Hyperglycemia Alters the Fetal Islet Transcriptome and Leads to Progeny Islet Dysfunction |
|
| Relations |
| BioSample |
SAMN09785762 |
| SRA |
SRX4522568 |
