|
| Status |
Public on Dec 15, 2022 |
| Title |
Assemblage of eggs, 3 Hours, Subitaneous, Replicate A |
| Sample type |
SRA |
| |
|
| Source name |
Assemblage of eggs
|
| Organism |
Acartia tonsa |
| Characteristics |
tissue: Assemblage of eggs
time: 3 Hours
developmental stage: 4-16 cell stage
type of_development: Subitaneous
|
| Treatment protocol |
Subitaneous samples were kept under the same environmentl conditions as growth protocol while quiescent samples were put at 4ºC and anoxic conditions
|
| Growth protocol |
An Acartia tonsa population was kept in 60L tanks under a dark environment with salt water (32), and a temperature of 16.9ºC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Rneasy mini kit (Qiagen)
0,3 ug RNA was used for the construction of sequencing libraries
RNA libraries were constructed using the TruSeq kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
The supplementary file contains the differentially expressed transcripts for all the subitaneous samples with an alpha value of 0.001 and fold change of 2.
see supplementary file
Transcriptome.annotated.fasta
3A_S5
|
| Data processing |
Bcl2fastq was used for both basecalling and demultiplexing
Trinity v2.13.2
The reads were assembled into a transcriptome using Trinity (settings: Forward stranded library, minimun contig length: 200, minimun k-mers to be assembled: 1)
Reads werealigned from the transcriptome and abundance estimated with Trinity
Both raw and normalized expression matrixes were built with Trinity and edgeR included with Trinity was used for differential expression analysis
Supplementary files format and content: tab-delimited text files include TMM values for each sample
|
| |
|
| Submission date |
Aug 04, 2022 |
| Last update date |
Dec 15, 2022 |
| Contact name |
Miguel Cifuentes Acebal |
| Organization name |
Roskilde university
|
| Department |
Department of Science and Environment
|
| Street address |
Universitetsvej 1
|
| City |
Roskilde |
| State/province |
Sjaelland |
| ZIP/Postal code |
4000 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL32548 |
| Series (1) |
| GSE210554 |
Transcriptome analysis of Acartia tonsa embryogenesis and its quiescent stage |
|
| Relations |
| BioSample |
SAMN30154107 |
| SRA |
SRX16848973 |
