|
| Status |
Public on Dec 31, 2017 |
| Title |
P2_Mes_H19-C-rep4 |
| Sample type |
SRA |
| |
|
| Source name |
pancreas
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: mesenchymal cells
age: post natal day 2
genotype: Controls 2 (H19DMD+/+; Nkx3.2+/Cre)
|
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Mus musculus post natal day 2 mesenchymal cells-Controls 2 (H19DMD+/+; Nkx3.2+/Cre)
data2.tsv
SLX-9736.L2DRBC15
|
| 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
|
| |
|
| Submission date |
Jul 09, 2017 |
| Last update date |
May 15, 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 |
SAMN07337609 |
| SRA |
SRX2992307 |
