|
Status |
Public on Apr 30, 2019 |
Title |
Exp2-st24-TP63MO |
Sample type |
SRA |
|
|
Source name |
animal cap explant
|
Organism |
Xenopus laevis |
Characteristics |
tissue: Xenopus animal cap explant Stage: 24 treatment: deltaN-TP63 MO injected
|
Treatment protocol |
Control embryos remained untreated, while DN-TP63 MO samples were injected 4 times into the animal hemisphere at four-cell stage with 4-6 pmol morpholino oligonucleotide targeting the ATG of DN-tp63 (sequence: 5’-GATACAACATCTTTGCAGTGAGGTT-3’).
|
Growth protocol |
Explants were cut from the animal portion of stage 8 Xenopus laevis embryos in 1x Modified Barth's Saline (MBS), then they were maintained in the medium for at least 1 hour to heal. After healing of explants, they were transferred to 0.5x MBS containing 0.1% of Gentamycin and cultured in that medium until they reached the indicated stage.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using the standard Trizol protocol. 500 ng total RNA per sample was used, poly-A selection and RNA-sequencing library preparation was done using non strand massively-parallel cDNA sequencing (mRNA-Seq) protocol from Illumina, the TruSeq RNA Library Preparation Kit v2, Set A (Illumina #RS-122-2301) according to manufacturer’s recommendation. Quality and integrity of RNA was assessed with the Fragment Analyzer from Advanced Analytical by using the standard sensitivity RNA Analysis Kit (Advanced Analytical #DNF-471). All samples selected for sequencing exhibited an RNA integrity number over 8. For accurate quantitation of cDNA libraries, the QuantiFluor™dsDNA System from Promega was used. The size of final cDNA libraries was determined using the dsDNA 905 Reagent Kit (Advanced Bioanalytical #DNF-905) exhibiting a sizing of 300 bp on average. Libraries were pooled and paired-end 100bp sequencing on a HiSeq2500 was conducted at the Transcriptome and Genome Analysis Laboratory, University of Göttingen.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Quality control was done using FastQC v0.11.5 paired-end reads were mapped to Xenopus laevis genome assembly v9.2 using RNA STAR v2.6.0b-1 featureCounts v1.6.3 was used to count uniquely mapped reads per gene statistical analysis of differential gene expression was conducted in DEseq2 v1.22.1 Genome_build: X. laevis v9.2 genome assembly Supplementary_files_format_and_content: tabular results files dervied from DESeq2; raw gene count tables from featurecounts
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|
|
Submission date |
Apr 29, 2019 |
Last update date |
Apr 30, 2019 |
Contact name |
Peter Walentek |
E-mail(s) |
peter.walentek@medizin.uni-freiburg.de
|
Organization name |
University Freiburg Medical Center
|
Department |
Internal Medicine IV & IMITATE
|
Lab |
Walentek
|
Street address |
Breisacherstr. 113
|
City |
Freiburg |
State/province |
BW |
ZIP/Postal code |
79106 |
Country |
Germany |
|
|
Platform ID |
GPL18936 |
Series (1) |
GSE130448 |
Mucociliary epidermis RNA-seq data from comparison of controls and DN-tp63 morpholino knockdown in Xenopus animal cap explants. |
|
Relations |
BioSample |
SAMN11527038 |
SRA |
SRX5765504 |