|
| Status |
Public on Nov 26, 2024 |
| Title |
P06KOM_11_568 |
| Sample type |
SRA |
| |
|
| Source name |
KO
|
| Organism |
Mus musculus |
| Characteristics |
tissue: whole kidney
postnatal age: Day 6
genotype: CAGG-CreER; Pkd2null/flox
strain: C5/BL6
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 |
RNA was harvested using Rneasy mini kit with on-column DNA digestion (Qiagen). RNA samples were submitted to BGI for library preparation.
RNA sequencing libraries were prepared by BGI according to manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
p06_kallisto_count_data_genes_expression_expected_count.csv
deseq2_p06WTKO_alldetected.csv
|
| Data processing |
DolphinNext RNA-seq Pipeline
Read quality was assessed using FastQC (v0.11.8)
Transcript abundance was estimated based on pseudoalignments using Kallisto (v0.46.0)
Differential gene expression analysis was performed in DEBrowser (v1.19.0) using DESeq2. Low count filtering by counts per million (cpm) >2 in 19/20 samples (Day 10) or >2 in 27/28 samples (Day 6)
Assembly: mm10
Supplementary files format and content: comma-separated text files include raw transcript abundances from kallisto pseudoalignment for each sample
Supplementary files format and content: comma-separated text files include gene expression normalized counts using median of ratios and differential expression analysis performed using DESeq2
|
| |
|
| Submission date |
Dec 07, 2022 |
| 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) |
| GSE220322 |
Gene expression in pre-cystic mouse kidneys after Pkd2 deletion. |
|
| Relations |
| BioSample |
SAMN32092902 |
| SRA |
SRX18524972 |
