|
Status |
Public on Dec 31, 2017 |
Title |
P2_Non-Mes_Igf2-KO-rep2 |
Sample type |
SRA |
|
|
Source name |
pancreas
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 cell type: non-mesenchymal cells age: post natal day 2 genotype: Mutants 1 (Igf2+/fl; Nkx3.2Cre/+)
|
Extracted molecule |
total RNA |
Extraction protocol |
P2 pancreata were dissected and dissociated into single cells using trypsin-EDTA. Cells were then isolated by FACS into mesenchymal cells (YFP+) and non-mesenchymal cells (YFP-). Total RNA was extracted using RNEasy Micro kit (Qiagen-74004) 2ng total RNA was whole-transcriptome amplified using the Ovation RNA–seq System V2 (NuGEN). 2 ?g amplified cDNA was then used to prepare the RNA–seq libraries using the Ovation Rapid DR Library System (NuGEN). RNA-seq using Illumina HiSeq 2500 system for single-end 50-bp sequencing
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
Mus musculus post natal day 2 non-mesenchymal cells-Mutants 1 (Igf2+/fl; Nkx3.2Cre/+) data1.tsv SLX-8880.L2DRBC06
|
Data processing |
Reads were aligned to the GRCm38/Ensembl V54 transcriptome using Tophat v2.0.8 with default parameters FPKM values and differential gene expression were determined using CuffLinks v2.2.1 using default parameters Genome_build: GRCm38 Supplementary_files_format_and_content: Fastq files for raw data and raw count values in tab-delimted txt format
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|
|
Submission date |
Jul 09, 2017 |
Last update date |
Jun 28, 2019 |
Contact name |
Brian Yee Hong Lam |
E-mail(s) |
yhbl2@cam.ac.uk
|
Organization name |
University of Cambridge
|
Department |
Metabolic Research Laboratories
|
Street address |
Box 289 Addenbookes Hospital, Hills Road
|
City |
Cambridge |
ZIP/Postal code |
CB2 0QQ |
Country |
United Kingdom |
|
|
Platform ID |
GPL17021 |
Series (1) |
GSE100981 |
Mesenchymal Igf2 is a major regulator of pancreatic growth and function |
|
Relations |
BioSample |
SAMN07337614 |
SRA |
SRX2992302 |