|
| Status |
Public on Nov 16, 2022 |
| Title |
Wildtype LEC zero hour sample 1 |
| Sample type |
SRA |
| |
|
| Source name |
lens capsule
|
| Organism |
Mus |
| Characteristics |
tissue: lens capsule
strain: C57BL/6
cell type: lens epithelial cells (LEC)
age: 2 months
genotype: wildtype
time point: 0 hr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (50) from Qiagen (Cat No./ID: 74104).
Takara SMARTer Stranded Pico v2
Paired end, ribodepletion
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT_0H_1
|
| Data processing |
Aligned reads using HISAT2 ( -fr --rna-strandedness RF, default otherwise)
Quantified genes using htseq-count -m union
Normalized counts using TMM (in edgeR)
Tested for differential expression using edgeR's Quasi-Likelihood F-Test
Assembly: GRCm38.p6 / Ensembl v100
Supplementary files format and content: Differential Expression analysis results in an excel spreadsheet
Supplementary files format and content: AVG RPKM
|
| |
|
| Submission date |
Jun 21, 2022 |
| Last update date |
Apr 26, 2024 |
| Contact name |
Melinda K. Duncan |
| E-mail(s) |
duncanm@udel.edu
|
| Phone |
3028310533
|
| Organization name |
University of Delaware
|
| Department |
Biological Sciences
|
| Lab |
Vertebrate Development
|
| Street address |
327 Wolf Hall
|
| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19716 |
| Country |
USA |
| |
|
| Platform ID |
GPL31136 |
| Series (1) |
| GSE206563 |
The six-hour injury response in lens epithelial cells |
|
| Relations |
| BioSample |
SAMN29222194 |
| SRA |
SRX15808451 |
