 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 07, 2019 |
| Title |
uuo-day3-2 (RNA-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
uuo-day3, kidney
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
Sex: male
treatment: unilateral ureter obstruction
time: 3 days
tissue: kidney
|
| Treatment protocol |
Unilateral ureter obstruction (UUO) model: Before surgery, mice were anaesthetized with an intraperitoneal injection of sodium pentobarbital (50 mg/kg of body weight), the left kidney was exposed via a flank incision and 3.0 silk suture thread was used to tie off the ureter at the lower pole. Before the obstruction and 3, 7, and 14 days later, mice were sacrificed, kidneys were removed and immediately snap frozen in liquid nitrogen.
|
| Growth protocol |
Male BALC/c mice were obtained from Charles River Laboratories (USA). All experimental protocols concerning the use of laboratory animals were performed according to the NIH guidelines for the care and use of laboratory animals, and approved by the Institutional Animal Care and Use Committees (IACUC) of Harvard Medical School. Mice were housed in groups of three on a 12-h light/dark cycle with access to food and water ad libitum. At the age of 8-10 weeks they entered the experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Qiagen’s RNeasy Mini Kit. Quality and quantity of the RNA was assessed photometrically and with the Bioanalyzer (Agilent).
330 ng total RNA were transcribed utilizing Illumina‘s TruSeq Stranded mRNA Library Prep Kit. Libraries were pooled and sequenced on Illumina’s NextSeq500 as single end, 75 bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
for mRNA seq
|
| Data processing |
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org).
Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing were suitable for further analysis. Adapter sequences, other contaminant sequences (such as polyA tails and low quality sequences with PHRED quality scores less than five) were trimmed from reads using atropos15.
Trimmed reads were aligned to UCSC build mm10 of the Mus musculus genome, augmented with transcript information from Ensembl release GRCm38.84 using STAR 16. Alignments were checked for evenness of coverage, rRNA content, genomic context of alignments (for example, alignments in known transcripts and introns), complexity and other quality checks using a combination of FastQC, Qualimap17, MultiQC18 and custom code within the bcbio-nextgen pipeline. Counts of reads aligning to known genes were generated by featureCounts19.
In parallel, Transcripts Per Million (TPM) measurements per isoform were generated by quasialignment using Salmon 20. Differential expression at the gene level was called with DESeq219–21, preferring to use counts per gene estimated from the Salmon quasialignments by tximport 19–22
The DEGreport Bioconductor package was used for QC and clustering analysis (10.18129/B9.bioc.DEGreport).
Genome_build: mm10
Supplementary_files_format_and_content: TPMs
|
| |
|
| Submission date |
Aug 09, 2018 |
| Last update date |
May 08, 2019 |
| Contact name |
Lorena Pantano |
| E-mail(s) |
lpantano@iscb.org
|
| Organization name |
Harvard Chan School of Public Health
|
| Department |
Biostatistics
|
| Lab |
Bioinformatic Core
|
| Street address |
655 Huntington Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE118339 |
Multi Omics analysis of fibrotic kidneys in two mouse models [RNA-Seq] |
| GSE118341 |
Multi Omics analysis of fibrotic kidneys in two mouse models |
|
| Relations |
| BioSample |
SAMN09787180 |
| SRA |
SRX4524251 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3325578_day3_5.tpm.txt.gz |
262.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
