|
| Status |
Public on May 04, 2018 |
| Title |
UV2 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Xenopus tropicalis |
| Characteristics |
strain: wild-type (out-bred Nigerian)
tissue: embryo
developmental stage: gastrula (stage NF11-11.5)
treatment: UV
|
| Treatment protocol |
Embryos were exposed to 0.3M LiCl at 32-cell stage or irradiated with UV for 2 minutes within the first 30 minutes after fertilisation.
|
| Growth protocol |
Embryos were grown to the indicated developmental stage in 5% MMR at 25ºC.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
10 embryos were homogenised in 400 µl TRIzol (Thermo Fisher Scientific) by vortexing. For phase separation, 80 µl of chloroform was added to the homogenate, shaken vigorously for 15 secs before spinning for 5 mins at 16,000 g at 4ºC. The aqueous phase containing total RNA which was precipitated with one volume of 100% ethanol and cleaned using the RNA Clean and Concentrator 5 or 25 (Zymo Research) with in-column 3 U Turbo DNase (Thermo Fisher Scientific) treatment according to the manufacturer’s instructions.
Libraries were made from ~2 µg total RNA by following version 2 of the TruSeq RNA low sample protocol (Illumina) following the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Embryos treated with UV, replicate 2
|
| Data processing |
Bases were called using Casava version 1.8.2
Paired-end reads were aligned to a revised version of X. tropicalis gene models 7.2 using Tophat2 (version 2.1.1) with the following parameters: -p 12 --transcriptome-index= xenTro7 --no-novel-juncs --no-coverage-search.
Only read pairs that uniquely align to one gene were counted using HTSeq-count (Anders, Pyl, and Huber, 2015). Differential expression analysis was performed with raw fragment counts using DESeq2 (Love et al., 2014)
For genome browser visualisation, paired-end reads were mapped to the X. tropicalis genome assembly 7.1 and known off-genome EST assemblies using Tophat (version 2.0.10) with the following parameters: -r 77 --mate-std-dev 110 -G v7.2 (gene models of version 7.2 as used above) -g 200 --report-secondary-alignments.
Genome_build: X. tropicalis v7.1 available at ftp://ftp.xenbase.org/pub/Genomics/JGI/Xentr7.1/xenopus_tropicalis_v7.1.tar.gz
Supplementary_files_format_and_content: text file with raw counts. The GTF with gene IDs and chromosomal locations is available on the series record.
|
| |
|
| Submission date |
Nov 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Rita Monteiro |
| E-mail(s) |
rita.monteiro@crick.ac.uk
|
| Organization name |
The Francis Crick Institute
|
| Department |
Developmental Biology Laboratory
|
| Lab |
Jim Smith
|
| Street address |
1 Midland Road
|
| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21875 |
| Series (1) |
| GSE107424 |
Transcriptomics of Dorso-Ventral axis determination in Xenopus tropicalis |
|
| Relations |
| BioSample |
SAMN08104858 |
| SRA |
SRX3426357 |
