|
| Status |
Public on Nov 26, 2021 |
| Title |
RNA extracted from batch 1 of embryos transfected with epiB::ciHMX and epiB:YFP |
| Sample type |
SRA |
| |
|
| Source name |
Transfected late tailbud embryos
|
| Organism |
Ciona intestinalis |
| Characteristics |
developmental stage: Late tailbud
tissue: Whole embryos
genotype: ciHMX overexpression
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Fluorescent transfected embryos were collected in 1.5ml tubes. Embryos were dissociated in TRIZOL, dissociating via gentling passing through a needle. RNA was subsequently extracted using phase separation with chlorofom, pricipitated with isopropanol, followed by ethanol washes and re-suspension in nuclease free water.
The mRNA fraction was selected from the total RNA provided before conversion to cDNA. Second strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated. Prior to amplification, samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and QC’ed before paired end sequencing was carried out over four lanes.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
HMX1
|
| Data processing |
fastQC was used to assess sequencing quality
Trimmomatic was used to trim off adapters and Sickle to trim low quality reads
Remaining reads were then mapped to the Ciona robusta genome (KH2012) using STAR
Genome_build: Ciona robusta genome (KH2012)
Supplementary_files_format_and_content: ciHMXsequencing_countTable.csv (the gene IDs correspond to gene models of the KH2012 Ciona robusta genome. The models and genome can all be found in https://www.aniseed.cnrs.fr/aniseed/ and https://www.aniseed.cnrs.fr/aniseed/download/download_data)
|
| |
|
| Submission date |
Nov 26, 2019 |
| Last update date |
Nov 26, 2021 |
| Contact name |
Vasileios Papadogiannis |
| Organization name |
University of Oxford
|
| Department |
Zoology
|
| Street address |
Solonos 2
|
| City |
Aigaleo Athens |
| ZIP/Postal code |
12244 |
| Country |
Greece |
| |
|
| Platform ID |
GPL27816 |
| Series (1) |
| GSE141046 |
ciHMX overexpression in Ciona intestinalis embryos |
|
| Relations |
| BioSample |
SAMN13390080 |
| SRA |
SRX7217844 |
