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Sample GSM6432378 Query DataSets for GSM6432378
Status Public on Dec 15, 2022
Title Assemblage of eggs, 7 hours, Subitaneous, Replicate A
Sample type SRA
 
Source name Assemblage of eggs
Organism Acartia tonsa
Characteristics tissue: Assemblage of eggs
time: 7 Hours
developmental stage: Gastrulation
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 see supplementary file
Transcriptome.annotated.fasta
7A_S7
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 SAMN30154102
SRA SRX16848978

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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