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Sample GSM5747759 Query DataSets for GSM5747759
Status Public on Dec 31, 2023
Title RNA-seq FL bud E10-E10.25 Hand2_WT replicate 3
Sample type SRA
 
Source name forelimb buds
Organism Mus musculus
Characteristics strain: Swiss albino
tissue: forelimb buds
developmental stage: E10-10.25 (31-33 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 (Prrx1-Cre;Hand2+/+) at E10-10.25 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 SAMN24300617
SRA SRX13488218

Supplementary file Size Download File type/resource
GSM5747759_H2_FL_WT_rep3.txt.gz 216.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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