|
| Status |
Public on Nov 26, 2024 |
| Title |
P06KOM_13_540 |
| Sample type |
SRA |
| |
|
| Source name |
whole kidney
|
| Organism |
Mus musculus |
| Characteristics |
tissue: whole kidney
postnatal age: Day 6
genotype: Pkd2 KO
Sex: M
|
| Treatment protocol |
All animals underwent intraperitoneal injection of tamoxifen in canola oil on postndatal day 2.
Mice were sacrificed and bilateral kidneys collected for RNA extraction at the designated time points.
|
| Growth protocol |
C5/BL6 background. Experimental "KO" were CAGG-CreER; Pkd2null/flox. Control "WT" were CAGG-CreER; Pkd2+/flox and Cre-negative; Pkd2null/flox.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using the Qiagen RNeasy minikits, with on-column DNA digestion. Samples were submitted to BGI for library preparation.
RNA sequencing libraries were prepared by BGI according to manufacturer's protocols.
Eukaryotic small RNA RNA sequencing
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
p06_omiras.xlsx
|
| Data processing |
The sequences were demultiplexed and underwent bar code and adapter sequence removal using the SOAPnuke software (Chen et al 2018). The steps for demultiplexing, bar code removal and adapter removal were carried out by BGI.
Omiras (Müller et al 2013) pipeline:
Mirdeep2 package (Friedländer MR et al 2012) for mapping processed reads, quanitfying reads, and predicting secondary structure
Deseq for differential miRNA expression
Assembly: mm10
Supplementary files format and content: "p06_omiras.xlsx" and "p10_omiras.xlsx" contain normalized and raw read counts for all samples for all identified small RNAs and differential expression analysis. Normalization by DESeq median of ratios.
Supplementary files format and content: Individual sample files "Title.xlsx" contain raw counts, normalized by # of mapping loci, molecule type, most prominent tag sequence, raw count and number of loci.
|
| |
|
| Submission date |
Jan 11, 2023 |
| Last update date |
Nov 26, 2024 |
| Contact name |
Gregory Pazour |
| Organization name |
UMass Chan School of Medicine
|
| Department |
Program in Molecular Medicine
|
| Lab |
Pazour Lab
|
| Street address |
373 Plantation St.
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE222610 |
Small noncoding RNA expression in pre-cystic mouse kidneys after Pkd2 deletion. |
|
| Relations |
| BioSample |
SAMN32675349 |
| SRA |
SRX19001663 |
