|
| Status |
Public on Jun 19, 2017 |
| Title |
tfcp2l1 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Metanephric Mesenchyme
|
| Organism |
Rattus norvegicus |
| Characteristics |
transduction: Tfcp2l1 adenoviruses
developmental stage: Embryonic Day 13.5 (E13.5)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10 mesenchymes were pulled to produce one replicate, total RNA was extracted using Qiagen RNAeasy Mini Kit according to manufacturer's instructions, quality and amount was analyzed on Bioanalyzer
Illumina TruSeq RNA prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base calling using RTA( (Illumina)
Read mapping using Tophat version 2.0.4 with 4 mismatches and 10 maximum multiple hits
Estimation of relative abundance of genes using cufflinks version 2.0.2
identification of differentially expressed genes using R limma
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimeted text files include FPKM values for each gene
|
| |
|
| Submission date |
Oct 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Max Werth |
| Organization name |
Columbia University
|
| Department |
Medicine
|
| Street address |
1150 St. Nicholas Ave.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL14844 |
| Series (2) |
| GSE87744 |
RNA-Seq Gene Expression Analysis in Rat Metanephric Mesenchyme overexpressing Transcription Factor Tfcp2l1 |
| GSE87769 |
Identification of Tfcp2l1 target genes in the mouse kidney |
|
| Relations |
| BioSample |
SAMN05879389 |
| SRA |
SRX2229383 |
