|
| Status |
Public on Jun 02, 2020 |
| Title |
Neurog3:Cre_3 |
| Sample type |
SRA |
| |
|
| Source name |
Neurog3:Cre_e16.5 whole pancreas
|
| Organism |
Mus musculus |
| Characteristics |
strain background: mixed, C57Bl6/129SV
genotype/variation: Neurog3:cre
Stage: e16.5
tissue: pancreas
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole pancreas was dissected from e16.5 mouse embryos, pulverized in buffer RLT +beta mercaptoethanol (RNAeasy Mini Kit Qiagen, Cat# 74134), frozen on dry ice. RNA was extracted using Qiagen RNAeasy Mini kit, eluted in 30ul RNAse free H20.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT_7_S8_L001
|
| Data processing |
FastQC for quality check
Cutadapt to trim adapters
HiSAT2 to align to Mm10 ( using Ensembl Mus_musculus.GRCm38.95.gtf)
HT-Seq to generate counts (.txt files)
Bedtools to Align and Sort to create .sam and .bam files
DESeq2 for differential expression analysis
Genome_build: Mm10 (Mus_musculus.GRCm38.95.gtf)
Supplementary_files_format_and_content: .txt file with column 1 (gene) and column 2 (read counts)
|
| |
|
| Submission date |
Feb 07, 2020 |
| Last update date |
Jun 06, 2020 |
| Contact name |
David Lorberbaum |
| E-mail(s) |
[email protected]
|
| Phone |
303-724-6894
|
| Organization name |
University of Colorado Denver
|
| Department |
Barbara Davis Center for Diabetes
|
| Lab |
Lori Sussel
|
| Street address |
1775 Aurora Court
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE144953 |
Retinoic acid signaling within pancreatic endocrine progenitors regulates mouse and human pancreatic islet cell specification |
|
| Relations |
| BioSample |
SAMN14060206 |
| SRA |
SRX7692800 |
