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| Status |
Public on May 11, 2024 |
| Title |
Tbx1-/- rep 2 |
| Sample type |
SRA |
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| Source name |
E14-Tg2a 4D
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| Organism |
Mus musculus |
| Characteristics |
cell line: E14-Tg2a 4D
genotype: Tbx1-/-
treatment: in vitro differentiation
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| Treatment protocol |
Cell Differentiation in precardiac mesoderm according to the paper by Andersen et al Nat Commun 9, 3140 (2018)
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| Growth protocol |
The culture medium consisted of GMEM (Sigma Cat# G5154) supplemented with 10^3 U/ml ESGRO LIF (Millipore, Cat# ESG1107), 15% fetal bovine serum (ES Screened Fetal Bovine Serum, US Euroclone Cat# CHA30070L), 0.1 mM non-essential amino acids (Gibco, Cat# 11140-035), 0.1 mM 2-mercaptoethanol (Gibco, Cat# 31350-010), 0.1 mM L-glutamine (Gibco, Cat# 25030081), 0.1 mM Penicillin/Streptomycin (Gibco, Cat# 10378016), and 0.1 mM sodium pyruvate (Gibco, Cat# 11360-070).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiagen RNeasy micro/mini plus Kit for RNA isolation and provide 10 μl of RNA at the exact concentration of 50 ng/μL
Quantseq 3′-biased protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequence reads were trimmed using bbduk softwareto remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6)
Alignment was performed with STAR on the reference genome mm10 provided by UCSC Genome Browser
The expression levels of genes were determined with featureCounts from Rsubread counting the reads that align to the forward strand
To account for biological variability, we used the noiseqbio function, setting the cutoff for the posterior probability to 0.95, to identify the differentially expressed genes. Gene ontology of the differentially expressed genes was performed with the gprofiler online tool (https://biit.cs.ut.ee/gprofiler/gost) using the entire set of expressed genes as the background.
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw count for each sample
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| Submission date |
Mar 08, 2024 |
| Last update date |
May 11, 2024 |
| Contact name |
Antonio Baldini |
| E-mail(s) |
antonio.baldini@unina.it
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| Organization name |
University of Naples Federico II
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| Department |
Department of Molecular Medicine and Medical Biotechnology
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| Street address |
Via Sergio Pansini 5
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| City |
Naples |
| State/province |
Naples |
| ZIP/Postal code |
80131 |
| Country |
Italy |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE261206 |
Cardiac Outflow tract septation defects in a DiGeorge syndrome model respond to Minoxidil treatment |
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| Relations |
| BioSample |
SAMN40339370 |
| SRA |
SRX23884927 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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