|
| Status |
Public on Jul 31, 2015 |
| Title |
ICC Colon |
| Sample type |
SRA |
| |
|
| Source name |
ICC in colon
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
strain: KitcopGFP/+
strain name (jackson lab): B6.129S7-Kittm1Rosay/J
age: 4 weeks
tissue: Colon
cell type: ICC
cell population: Sorted primary cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mirVana miRNA Isolation Kit
TruSeq RNA Sample Preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 4
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Reads were aligned against mouse genome (mm9) for junction identification using Tophat v1.4.1.
Abundance estimation and differential expression analysis are done using Cufflinks v2.0.2.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: isoforms_fpkm_tracking_04172013.xlsx: differential expression analysis using Cuffdiff
|
| |
|
| Submission date |
May 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Seungil Ro |
| E-mail(s) |
sro@medicine.nevada.edu
|
| Phone |
775-784-1462
|
| Organization name |
University of Nevada School of Medicine
|
| Department |
Physiology and Cell Biology
|
| Street address |
1664 North Virginia St
|
| City |
Reno |
| State/province |
NV |
| ZIP/Postal code |
89557 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE57776 |
Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFRα+ Cells |
|
| Relations |
| BioSample |
SAMN02786507 |
| SRA |
SRX546216 |
