|
| Status |
Public on Dec 18, 2020 |
| Title |
IRX3_OTX2_Rep1_RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Tissue
|
| Organism |
Xenopus tropicalis |
| Characteristics |
cell line: none
Stage: stage10 .5 (Gastrula)
antibody: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from animal caps using our in-house adapted Trizol-Zymo Hybrid protocol.
The concentrations of all the RNA samples were measured using the DeNovix dsDNA High Sensitivity Assay (Catalog number: KIT-DSDNA-HIGH-1). The cDNA was constructed using KAPA RNA HyperPrep with RiboErase (Catalogue Number: 08278555702, Kapa Biosystems). We checked the quality of the samples by RT-qPCR using primers spanning coding regions of candidate and housekeeping genes. The prepared libraries were quantified with the KAPA Library Quantification Kit (Kapa Biosystems #KK4844), and then sequenced in a paired-ended manner using the NextSeq 500 (Illumina) according to standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
samplename_reads.tab file is generated with STAR 2.5.0 with the option of --quantMode GeneCounts
Genome_build: xt9
|
| |
|
| Submission date |
Feb 20, 2020 |
| Last update date |
Dec 18, 2020 |
| Contact name |
Ann Rose Bright |
| Organization name |
RIMLS
|
| Department |
Department of Molecular Biology
|
| Street address |
Geert Grooteplein Zuid 30
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24884 |
| Series (1) |
| GSE145619 |
Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates |
|
| Relations |
| BioSample |
SAMN14145527 |
| SRA |
SRX7759416 |
