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Sample GSM3738805 Query DataSets for GSM3738805
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.
 
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
 
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

Supplementary file Size Download File type/resource
GSM3738805_featureCounts_Exp2DNtp63MOSt24_Counts.tab.gz 222.2 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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