|
Status |
Public on Dec 31, 2023 |
Title |
RNA-seq FL bud E9.75-E10 Tbx3_WT replicate 3 |
Sample type |
SRA |
|
|
Source name |
forelimb buds
|
Organism |
Mus musculus |
Characteristics |
strain: Swiss albino tissue: forelimb buds developmental stage: E9.75-10.0 (28-31 somites) genotype: WT
|
Treatment protocol |
For both Hand2 and Tbx3 samples, three replicates were analyzed per genotype. One replicate consists of one pair of forelimb buds, which were flash frozen in liquid nitrogen and stored at -80°C until RNA extraction.
|
Extracted molecule |
total RNA |
Extraction protocol |
Samples were defrosted and total RNA extracted using QIAGEN RNeasy kit according to manufactures instructions. The RNA quality was evaluated using the Fragment Analyzer in combination with the High Sensitivity RNA Analysis kit (Advanced Analytical). Only samples with a RIN ≥8.0 were used for library construction. RNA-seq libraries were constructed using the using the Clontech SMARTer kit and 85bp single end reads were sequenced on the Illumina NextSeq 500.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Total RNA extracted from forelimb buds of wild-type mouse at E9.75-10.0 stage
|
Data processing |
Raw single-end sequencing reads of 85bp read length from Tbx3 and Hand2 samples of mouse forelimb buds were subjected to quality check using FastQC v0.11.4 (FastQC: a quality control tool for high throughput sequence data) High-quality sequencing reads were aligned on reference genome and transcriptome (ensembl release-91) of mouse (mm10) using a fast accurate aligner STAR v2.5.2 (Dobin A et al., 2012). Subsequently, rsem-calculate-expression utility of RSEM v1.3.0 (Li, Bo, and Colin N. Dewey, 2011) was used to quantify expression levels of genes and transcripts across all the samples. Genome_build: mm10 Supplementary_files_format_and_content: .txt, rsem quantifications
|
|
|
Submission date |
Dec 22, 2021 |
Last update date |
Dec 31, 2023 |
Contact name |
Aimee Zuniga |
E-mail(s) |
devgenlab-dbm@unibas.ch
|
Organization name |
University of Basel
|
Department |
Department of Biomedicine
|
Lab |
Developmental Genetics
|
Street address |
Mattenstrasse, 28 4058
|
City |
Basel |
ZIP/Postal code |
4058 |
Country |
Switzerland |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE192485 |
Identification of TBX3 and shared HAND2-TBX3 target gene in early mouse limb buds [RNA-seq] |
GSE192486 |
Identification of TBX3 and shared HAND2-TBX3 target genes in early mouse limb buds |
|
Relations |
BioSample |
SAMN24300623 |
SRA |
SRX13488212 |