|
| Status |
Public on Feb 03, 2024 |
| Title |
RNA-Seq KWe284 |
| Sample type |
SRA |
| |
|
| Source name |
mouse forelimb
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mouse forelimb
genotype: Prx+/+;Smarcc1c/c
cell type: Right- and left forelimb pair (~700K cells)
Stage: E11.5 (39s)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole forelimb pairs/sample flash frozen, RNA-extracted in 500ul of Trizol and Dnase treated. RNA was run on a BioAnalyzer to assess quality (all samples had RIN numbers > 7.5) and 100-200ng of RNA was taken into cDNA prep.
Libraries were prepped by the BGI team as follows: libraries were 3'adenylated, adaptor-ligated, UDG digested and PCR amplified. Libraries were then circularized and amplified to make DNA nanoball to be sequenced on DNBseq platform.
Proprietary BGI DNB-seq platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
Forelimb pairs from individually genotyped embryos were were flash-frozen, prepped in 500ul Trizol for RNA and Dnase treated. 580ng total RNA; RIN number of 10
|
| Data processing |
Sequenced reads were aligned to the mm10 mouse genome using Salmon (version 1.9.0).
Transcripts per million (TPM) were obtained usinng R package tximeta (version 1.16.0).
|
| |
|
| Submission date |
Feb 03, 2023 |
| Last update date |
Feb 03, 2024 |
| Contact name |
Steven A. Vokes |
| E-mail(s) |
svokes@austin.utexas.edu
|
| Organization name |
University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Street address |
2500 Speedway, STOP A5000
|
| City |
Austin |
| State/province |
Texas |
| ZIP/Postal code |
78757 |
| Country |
USA |
| |
|
| Platform ID |
GPL28457 |
| Series (2) |
| GSE224505 |
The BAF complex does not mediate GLI repression (RNA-Seq) |
| GSE224510 |
The BAF complex does not mediate GLI repression |
|
| Relations |
| BioSample |
SAMN33059256 |
| SRA |
SRX19278550 |
