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| Status |
Public on May 22, 2018 |
| Title |
CYP_2h-B |
| Sample type |
SRA |
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| Source name |
animal cap explants
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| Organism |
Xenopus laevis |
| Characteristics |
injected rna: VegT/Noggin/Cyp16a1
treatment: untreated
time: 2h
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| Treatment protocol |
Treatments with 5 µM RA (all-trans RA, SIGMA) were done in the corresponding buffer at stage 11 for one hour at 12 °C under light protection. Treatments with 10 µg/ml Cyclohexamide (SIGMA) started 30 min prior to additional treatments.
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| Growth protocol |
Ectodermal explants were dissected from the blastocoel roof of stage 8/9 embryos and cultured in salt solution (88 mM NaCl, 1 mM KCl, 0.82 mM MgSO4, 2.4 mM NaHCO3, 0.41 mM CaCl2, 0.33 mM Ca(NO3)2, 10 mM HEPES, pH 7.8 ) with antibiotics (Ampicillin (100 µg/ml), Kanamycin (10µg/ml) and Gentamycin (10 µg/ml)) on 0.7% agarose at 14°C until control embryos had reached the desired stage.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using peqGOLD Trifast reagent (peQlab)
Library preparation for RNA-Seq was performed using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit removing both cytoplasmic and mitochondrial rRNA (Illumina, Cat. No. RS-122-2201, San Diego, CA, USA). About 200 ng of total RNA was used as start material. Accurate quantitation of cDNA libraries was performed by using the QuantiFluorTM dsDNA System (Promega,Madison, WI, USA). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina with 50bp Single-end chemistry.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
CASAVA 1.8.2 software was used for demultiplexing
Quality check was performed using Babraham Bioinformatics FastQC v.0.10.1
Sequenced reads were mapped to Xenopus laevis 9.1 whole genome using bowtie v 2.1.0
Read Counting and detection of differentially regulated genes was performed using edgeR
Candidate genes with log2Foldchange of 2 and p-value 0.05 were filtered
Genome_build: Xenopus laevis 9.1
Supplementary_files_format_and_content: Tab-delimited text file containing normalized values, candidate genes
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| Submission date |
Apr 04, 2018 |
| Last update date |
May 22, 2018 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
Gabriela.Salinas-Riester@medizin.uni-goettingen.de
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| Organization name |
Universitaetsmedizin Goettingen
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| Department |
Department of Pathology
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| Lab |
NGS Integrative Genomics
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| Street address |
Kreuzbergring 57
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| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
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| Platform ID |
GPL17682 |
| Series (1) |
| GSE112718 |
Retinoic acid induced expression of Hnf1β and Fzd4 is required for pancreas development in Xenopus laevis |
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| Relations |
| BioSample |
SAMN08865896 |
| SRA |
SRX3885767 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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