|
| Status |
Public on Feb 19, 2022 |
| Title |
Control 109 |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Mus musculus |
| Characteristics |
brg1 allele: Brg1 flx/flx
developmental stage: E17.5
tissue: kidney
|
| Treatment protocol |
Fresh kidney tissue harvested.
|
| Growth protocol |
In utero mouse kidney growth to E17.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from three E17.5 kidneys for each genotype using an RNeasy Mini Kit (Qiagen 74104) with on the column DNAse I treatment. Ribosomal RNA was depleted from 1 μg of total RNA using Ribominus Eukaryote System v2 (Life Technologies).
Construction of barcoded sequencing libraries was performed using the Ion Total RNA-seq v2 kits (Life Technologies) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
ribosomal RNA-depleted RNA
|
| Data processing |
Basecalling was performed by Torrent Suite version 4 and 5 software using the default settings
Alignment to mus musculus genome mm10 sequence was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
The total sequencing base pair coverage in all exons was summed for all annotated genes in each sample and normalized to total coverage using BEDtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics 11:e1005655.
Normalization factors were calculated by averaging the total exon coverage for all replicates and dividing this average by the total exon coverage for each individual sample. The total coverage for each gene in each replicate was then multiplied by these factors after adding an offset of 1 to each gene to preclude division by 0 in subsequent calculations.
The averages and p values of the coverage values for all genes in the individual groups were calculated using Microsoft Office Excel. The expression values for each gene are the normalized strand-specific total nucleotide coverage for each gene.
Genome_build: mus musculus mm10
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated expressed genes and statistical comparison of expression in wild type kidney to mutant kidney.
|
| |
|
| Submission date |
Feb 18, 2022 |
| Last update date |
Feb 23, 2022 |
| Contact name |
Jeannine M Basta |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University in St. Louis
|
| Department |
Internal Medicine/Nephrology
|
| Lab |
Rauchman
|
| Street address |
660 S Euclid Ave, MSC 8126-0012-08
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (2) |
| GSE196996 |
The core SWI/SNF catalytic subunit Brg1 regulates nephron progenitor cell proliferation and differentiation [RNA-seq] |
| GSE196997 |
The core SWI/SNF catalytic subunit Brg1 regulates nephron progenitor cell proliferation and differentiation |
|
| Relations |
| BioSample |
SAMN26082977 |
| SRA |
SRX14222441 |
