|
| Status |
Public on Nov 21, 2022 |
| Title |
D-06-f-Mesa-1 |
| Sample type |
SRA |
| |
|
| Source name |
Mesangail cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mesangail cells
genotype: BTBR ob/ob
treatment: BTBR ob/ob (DN)
time: 6 weeks
Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy Micro Kit(Qiagen). 12ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The quality of the bulk RNA-seq reads was assessed using FastQC (v0.11.5).
The reads were aligned to the mouse reference genome (mm10) with Bowtie2 (v2.3.3.1) using RSEM (v1.3.0) with the default parameters. The function rsem-calculate-expression was used to align the reads and quantify the gene and isoform abundance.
Assembly: mm10
Supplementary files format and content: plain file including read count and transcripts per million (TPM) value
|
| |
|
| Submission date |
Nov 16, 2022 |
| Last update date |
Nov 22, 2022 |
| Contact name |
Tianran Zhang |
| E-mail(s) |
tianran.zhang@zmnh.uni-hamburg.de
|
| Organization name |
University Medical Center Hamburg-Eppendorf
|
| Street address |
Falkenried 94
|
| City |
Hamburg |
| ZIP/Postal code |
20251 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE218086 |
Bulk RNA-sequencing of FACS-sorted kidney glomerular cell types from BTBR ob/ob mice and glomeruli isolated from ex vivo perfused kidneys |
|
| Relations |
| BioSample |
SAMN31752211 |
| SRA |
SRX18285097 |
