|
| Status |
Public on Nov 30, 2022 |
| Title |
WT4 |
| Sample type |
SRA |
| |
|
| Source name |
mouse larynx
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Swiss Webster WT
tissue: 3-pooled larynx tissues (~60K cells)
developmental stage: E10.5 (32-35S)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
3 larynxes/sample were collected in 150ul of Trizol and prepped for RNA and Dnase treated. RNA was run on a BioAnalyzer to assess quality (all samples had RIN numbers > 7.5) and 100-150ng of RNA was taken into cDNA prep.
Libraries were enriched for PolyA by magnetic isolation and libraries were amplified for 10 cycles. Excess primers were removed from PCR reactions using AmpureXP beads (A63880) at a ratio of 0.8x beads. NEBNext Ultra II Directional RNA Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
3 larynxes were collected in 150ul of Trizol and prepped for RNA and Dnase treated. 210ng total RNA; 110ng RNA taken in cDNA prep; RIN number of 7.7
|
| Data processing |
Base calling was done using Illumina bcl2fasq version 1.37.0
Sequenced reads were mapped to mouse reference genome mm10 usinng HISAT2 v2.1.0.
Transcripts per million (TPM) were obtained usinng StringTie v1.3.6.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.
|
| |
|
| Submission date |
Dec 06, 2021 |
| Last update date |
Nov 30, 2022 |
| 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 |
GPL19057 |
| Series (1) |
| GSE190281 |
Hedgehog signaling is essential to maintain epithelial identity during larynx and foregut morphogenesis. |
|
| Relations |
| BioSample |
SAMN23704722 |
| SRA |
SRX13327401 |
