|
| Status |
Public on Feb 04, 2020 |
| Title |
uninjected_st41_repl1 |
| Sample type |
SRA |
| |
|
| Source name |
uninjected_st41
|
| Organism |
Xenopus laevis |
| Characteristics |
developmental stage: stage 41
tissue: whole embryo
|
| Growth protocol |
Injected and uninjected Xenopus laevis embryos were cultivated in 0.1x MBS culture buffer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (peqGOLD TriFast reagent, peQlab) according to instructions.
TruSeq RNA Library Preparation Kit v2, Set A (48 samples, 12 indexes)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
JM11-control-st41_S11_L002
|
| Data processing |
Fluorescence images were transformed to BCL files with the Illumina BaseCaller software and samples were demultiplexed to FASTQ files using bcl2fastq 2.17.1.14
Assessment of quality control of sequences using FastQC 0.11.5
Alignment of sequences to Xenopus Laevis reference genome using STAR 2.5.2a
Counting unique reads within genes using featureCounts 1.5.0-p1
Data normalization and testing for differentially expressed genes using DESeq2 1.8.2
Genome_build: Xenla9.1 (http://www.xenbase.org)
Supplementary_files_format_and_content: gene counts
|
| |
|
| Submission date |
Feb 04, 2019 |
| Last update date |
Feb 05, 2020 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
Gabriela.Salinas-Riester@medizin.uni-goettingen.de
|
| Organization name |
Universitaetsmedizin Goettingen
|
| Department |
Department of Pathology
|
| Lab |
NGS Integrative Genomics
|
| Street address |
Kreuzbergring 57
|
| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22393 |
| Series (1) |
| GSE126058 |
Identification of genes regulated by Erythroferrone (ERFE) in Xenopus embryos at tadpole stages. |
|
| Relations |
| BioSample |
SAMN10869408 |
| SRA |
SRX5330029 |
