|
| Status |
Public on Oct 18, 2022 |
| Title |
Exp2, st25-foxa1MO |
| Sample type |
SRA |
| |
|
| Source name |
epidermis, animal cap explant, st25
|
| Organism |
Xenopus laevis |
| Characteristics |
exp: 2
tissue: epidermis, animal cap explant
developmental stage: st25
genotype: wt
treatment: foxa1 MO injected
|
| Treatment protocol |
Control embryos remained untreated, while suh-dbm (100ng/ul), suh-dbm+dnmcidas (100ng/ul each), nicd (120ng/ul), and foxa1MO (3pmol) samples were injected 4 times into the animal hemisphere at four-cell stage with indicated mRNA/MO concentrations.
|
| 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 HiSeq4000 was conducted at the Vincent J. Coates Genomics Sequencing Lab, University of California at Berkeley.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
DESeq2_result_st25_FoxA1MOvsCTRL
|
| 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
Assembly: X. laevis v9.2 genome assembly
Supplementary files format and content: tabular results files derived from DESeq2 (column names: GeneID, Base mean, log2(FC), StdErr, Wald-Stats, P-value, P-adj)
Supplementary files format and content: GEO-XenIDSymbol_Walentek_2022 contains GeneIDs and Gene Names
|
| |
|
| Submission date |
Oct 13, 2022 |
| Last update date |
Nov 02, 2022 |
| 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 |
GPL22393 |
| Series (1) |
| GSE215373 |
Mucociliary epidermis RNA-seq data from controls and after manipulation of cell fates by Notch (suh-dbm, nicd) and cell type controlers (Foxa1MO, dnMCIDAS) |
|
| Relations |
| BioSample |
SAMN31266538 |
| SRA |
SRX18117919 |
