|
| Status |
Public on Jan 24, 2019 |
| Title |
JLDD4ABV4 Biological Replicate #2 |
| Sample type |
SRA |
| |
|
| Source name |
Chlamydomonas reinhardtii 4A+ wild-type
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
strain: 4A+
treatment: 0.1 mM
light: 4h white light
|
| Treatment protocol |
Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit.
|
| Growth protocol |
All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Illumina's RNA-Seq whole transcriptome analysis
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%.
Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2).
Genome_build: version 5.5 assembly of the Chlamydomonas genome
Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs.
|
| |
|
| Submission date |
Jan 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sabeeha Merchant |
| E-mail(s) |
merchant@chem.ucla.edu
|
| Phone |
310-825-8300
|
| Organization name |
University of California Los Angeles
|
| Department |
Department of Chemistry and Biochemistry
|
| Street address |
607 Charles E. Young Drive East
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095-1569 |
| Country |
USA |
| |
|
| Platform ID |
GPL15922 |
| Series (1) |
| GSE77388 |
Bilin-dependent photoacclimation in Chlamydomonas reinhardtii |
|
| Relations |
| BioSample |
SAMN04448189 |
| SRA |
SRX1553142 |
