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Sample GSM5430136 Query DataSets for GSM5430136
Status Public on Aug 31, 2023
Title sd_zt16_6
Sample type SRA
 
Source name liquid culture
Organism Ostreococcus tauri
Characteristics strain: RCC4221
time point: ZT16
photoperiod: Continous darkness after short day
Treatment protocol Long day (16 hours light : 8 hours dark), short day (8 hours light : 16 hours dark), continous light, continous darkness.
Growth protocol Ostreococcus tauri was grown in column photochemostats under long day, short day, continous light and continous darkness conditions.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using E.Z.N.A.® Plant RNA Kit (Omega, R6827-01)
Libraries were prepared using 1 μg of total RNA with the VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina® (Vazyme, NR603) according to the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Quality control was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using HISAT2 (http://daehwankimlab.github.io/hisat2/)
Transcript assembly was performed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Subsequent data analysis and visualization was performed using the R bioconductor package ballgown (https://www.bioconductor.org/packages/release/bioc/html/ballgown.html)
Genome_build: ostta4221 v3 available from https://mycocosm.jgi.doe.gov/Ostta4221_3/Ostta4221_3.home.html
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
 
Submission date Jul 08, 2021
Last update date Aug 31, 2023
Contact name Francisco José Romero-Campero
E-mail(s) [email protected]
Organization name University of Sevilla
Department Institute for Plant Biochemistry and Photosynthesis
Street address Americo Vespucio 49
City Seville
ZIP/Postal code 41092
Country Spain
 
Platform ID GPL28953
Series (1)
GSE155535 Photoperiodic transcriptional responses in Ostreococcus tauri
Relations
BioSample SAMN20119688
SRA SRX11380012

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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