|
| Status |
Public on Jul 01, 2013 |
| Title |
Chlamydomonas reinhardtii crr1:CRR1 - Dark anoxic 6 hours |
| Sample type |
SRA |
| |
|
| Source name |
Chlamydomonas cultured cells
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
strain: crr1:CRR1
treatment: dark-anoxic
|
| Treatment protocol |
Cells were grown to the early-logarithmic growth phase (ca. 3 ∙ 106 cells ∙ ml-1). 100 ml culture aliquots were then transferred to squared glass bottles sealed with Red Rubber Suba Seals 37 ), which had a total volume of 118 ml after insertion of the Suba Seals. The flasks were subsequently incubated in a dark-room on magnetic stirrers. Reference cultures were 100 ml culture aliquots removed from the main cultures, transferred to 500 ml Erlenmeyer flasks and placed back to growth conditions in order to prevent the establishment of microaerobic conditions. RNA of the reference cells was isolated when the other incubation flasks had been placed in the dark room, thus 10 min after their removal from the main culture.
|
| Growth protocol |
Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 700 ml TAP-medium in 2 l flasks in the light (100 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 2.2 to 2.7 cells ∙ ml-1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated at time-points indicated in the text according to a method described before (Hill et al., 1991, PMID: 1714451) with the following modifications: 100 ml of cell suspension was harvested by centrifugation (3,440 g) at 4°C and resuspended in 1.6 ml ice-cold lysis buffer (Schmidt et al., 1984; PMID: 6202701) without SDS. After addition of 0.4 ml 10 % (w/v) SDS, cells were vigorously vortexed and RNA was extracted and precipitated according to (Hill et al., 1991, PMID: 1714451). RNA integrity was checked by formaldehyde gel electrophoresis and ethidium bromide staining, by Agilent 2100 Bioanalyzer analysis. DNA was removed from total RNA using TURBO™ DNase from Ambion/Applied Biosystems (www.ambion.com) according to the manufacturer’s recommendations. For quantitative transcriptomes, RNAs were sequenced at JGI by Illumina's whole transcriptome analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Illumina's RNA-Seq whole transcriptome analysis
|
| Data processing |
Illumina's proprietary software was used for basecalling.
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome.
Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates.
Genome_build: version 4.0 assembly of the Chlamydomonas genome
Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs.
|
| |
|
| Submission date |
Nov 05, 2012 |
| 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 |
GPL9100 |
| Series (1) |
| GSE42035 |
The acclimation of Chlamydomonas reinhardtii to anaerobiosis involves plant and animal strategies |
|
| Relations |
| SRA |
SRX202849 |
| BioSample |
SAMN01801589 |
