|
| Status |
Public on Aug 31, 2023 |
| Title |
ld_zt04_3 |
| Sample type |
SRA |
| |
|
| Source name |
liquid culture
|
| Organism |
Ostreococcus tauri |
| Characteristics |
strain: RCC4221
time point: ZT4
photoperiod: Long Day
|
| Treatment protocol |
Long day (16 hours light : 8 hours dark), short day (8 hours light : 16 hours dark) and continous light.
|
| Growth protocol |
Ostreococcus tauri was grown in column photochemostats under long day, short day and continous light 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 |
Aug 02, 2020 |
| 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 |
SAMN15698466 |
| SRA |
SRX8864836 |
