|
| Status |
Public on May 07, 2015 |
| Title |
Healthy #2 (48h MSC treatment) |
| Sample type |
SRA |
| |
|
| Source name |
Male SCID mouse kidney
|
| Organism |
Mus musculus |
| Characteristics |
strain: SCID
tissue: Kidney
treatment: 48h MSC treatment
|
| Growth protocol |
Studies were approved by the Ethic Committee of Turin University and conducted in accordance with the National Institute of Health Guide for the Care and Use of Laboratory Animals. A model of rhabdomyolisis-induced acute kidney injury (AKI) was performed in male SCID mice as previous described. On day 3 after glycerol administration, mice received an intravenous injection into the tail vein of 75.000 MSC-CTRL or MSC-Dsh cells; and EV-CTRL or EV-Dsh in 150 μl saline, or saline alone. The number of particles injected (2.2x108 particles/mice) corresponds to an average of the amount of EVs released overnight by 75.000 MSCs (average of 2.900 EVs/cell), which showed a therapeutic effect on this AKI model. Mice were killed at day 5 (n =8 per group) after glycerol administration and blood samples for BUN determination and kidney specimens were collected. For gene expression, RNA was extracted using TRIzol from small pieces of the kidney cortical regions.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from kidney was extracted using TRIzol (Invitrogen). RNA extraction was performed following manufacturer protocol.
For RNA-Seq library preparation, approximately 2 μg of TRIzol (Invitrogen) isolated total RNA from whole kidney was subjected to polyA+ selection and library preparation using the TruSeq RNA Sample Prep Kit (Illumina), following manufacturer instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Reads quality was estimated using FastQC v0.10.1. Positions with a quality score behind 20 (Phred33 scale) were trimmed using the fastx_trimmer tool from the FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads mapping was performed using TopHat v2.0.10 (http://tophat.cbcb.umd.edu/, parameters: -a 5 --bowtie1). Wiggle file were generated from BAM alignment using the Wiggles v1.2.0 tool.
Genome_build: mm9
|
| |
|
| Submission date |
Jul 31, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Francesco Neri |
| E-mail(s) |
francesco.neri@unito.it
|
| Organization name |
University of Torino
|
| Street address |
Via Nizza 52
|
| City |
Torino |
| State/province |
Italy |
| ZIP/Postal code |
10126 |
| Country |
Italy |
| |
|
| Platform ID |
GPL16173 |
| Series (1) |
| GSE59958 |
Role of miRNAs in acute kidney injury recovery induced by mesenchymal stromal cells and derived extracellular vesicles. |
|
| Relations |
| BioSample |
SAMN02948378 |
| SRA |
SRX667366 |
