|
| Status |
Public on Apr 26, 2017 |
| Title |
RNAseq_kidney_KS_tamoxifen_2 |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Mus musculus |
| Characteristics |
tissue: kidney
kidney region: cortex
genotype: Sav1-/-
treatment: tamoxifen
genotype abbreviations: KS
background strain: mixed
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Qiagen Rneasy Kit
Libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
KS-tamox-2168_S10
|
| Data processing |
75b paired-end reads were sequenced on a NextSeq 500 Desktop Sequencer using a high output flow cell kit (Illumina), yielding an average of over 28M reads per sample.
QC-passed reads were aligned to the mouse reference genome (mm9) using MapSplice
The alignment profile was determined by Picard Tools v1.64 (http://broadinstitute.github.io/picard/).
Aligned reads were sorted and indexed using SAMtools and translated to transcriptome coordinates then filtered for indels, large inserts, and zero mapping quality using UBU v1.0 (https://github.com/mozack/ubu).
Transcript abundance estimates for each sample were performed using RSEM, an expectation-maximization algorithm using the UCSC knownGene transcript and gene definitions.
Raw RSEM read counts for all RNAseq samples were normalized to the overall upper quartile
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RSEM values for each sample
|
| |
|
| Submission date |
Apr 25, 2017 |
| Last update date |
Jun 30, 2020 |
| Contact name |
William Y. Kim |
| E-mail(s) |
william_kim@med.unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Medicine and Genetics
|
| Lab |
William Kim Lab
|
| Street address |
450 West Dr.
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE98197 |
Sav1 Loss Induces Senescence and Stat3 Activation Coinciding with Tubulointerstitial Fibrosis |
|
| Relations |
| BioSample |
SAMN06830636 |
| SRA |
SRX2764628 |
