|
| Status |
Public on Mar 25, 2022 |
| Title |
C.reinhardtii 6uM Mn rep3 |
| Sample type |
SRA |
| |
|
| Source name |
liquid cultures of microalgae
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
strain: CC-4532
growth conditions: mid-log photoheterotrophic growth
mn in media: 6 uM
|
| Treatment protocol |
TAP media with 1000 uM or 6 uM Mn.
|
| Growth protocol |
Flasks containing 1 L of Tris-Acetate-Phosphate (TAP) medium supplemented with either 6 uM Mn (control) or 1000 uM Mn (experimental) were innoculated with Chlamydomonas reinhardtii (strain CC-4532) at 1x10^4 cells/mL. These cultures were grown on shaking platforms (180 rpm) at 24°C under continuous light (~50 umol * m^-2 * s^-1) until they reached 3x10^6 cells/mL.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
SDS+proteinase K digestion and phenol/chloroform extraction.
Standard Illumina HiSeq poly-A selected libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA
Alignment of reads to reference genome with STAR --alignIntronMax 3000
FPKMs calculated with cuffdiff (v2.2.1) --multi-read-correct --max-bundle_frags 1000000000 --library-type fr-firststrand
FPKM table prepared with cummeRbund in R.
Genome_build: Chlamydomonas reinhardtii v5.6 (phytozome.net)
Supplementary_files_format_and_content: tab-delimited text file of FPKMs for each gene in each sample
|
| |
|
| Submission date |
Mar 26, 2021 |
| Last update date |
Mar 25, 2022 |
| Contact name |
Sean D. Gallaher |
| Organization name |
UC Berkeley
|
| Department |
California Institute for Quantitative Biosciences
|
| Lab |
Sabeeha Merchant
|
| Street address |
176 Stanley Hall, room 408
|
| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL15922 |
| Series (1) |
| GSE169756 |
Transcriptomics study of excess Mn (1000 uM) in Chlamydomonas reinhardtii |
|
| Relations |
| BioSample |
SAMN18511466 |
| SRA |
SRX10459646 |
