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| Status |
Public on Nov 07, 2022 |
| Title |
Cc Hydrogren peroxide N3 |
| Sample type |
SRA |
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| Source name |
algal cell
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| Organism |
Cylindrotheca closterium |
| Characteristics |
cell type: algal cell
strain: CCMP340
treatment: Hydrogen peroxide treated
growth conditions: 24C, Aquil, Aquil, 5days
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| Growth protocol |
16:8 hours light:dark cycles and a light intensity of about 100 μmol photons·m-2·sec-1. Specific growth conditions for each species marked under 'growth conditions' as: temprature (C), salts, nutrients, and day of harvest after initiating the experiment, in replete or no iron media. Hydrogen peroxide was added to replete cultures about 2 hours before harvest for RNA-Seq.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 0.2 µm membrane filters with the Zymo Direct-zol RNA MiniPrep Plus kit.
Poly-A-selection, library preparation and sequencing were performed at the Northwest Genomics Center (University of Washington) with standard Illumina NextSeq protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
c_closterium_TPM.csv
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| Data processing |
Sequence reads were trimmed using Trimmomatic 0.39,25 run in paired-end mode with cut adaptor and other Illumina-specific sequences (ILLUMINACLIP) set to TruSeq3-PE.fa:2:30:10:1:true, Leading and Trailing thresholds of 25, a sliding window trimming approach (SLIDINGWINDOW) of 4:15, an average quality level (AVGQUAL) of 20, and a minimum length (MINLEN) of 60.
Reads were mapped to the genome of T. pseudonana or T. oceanica using Hisat2-2.1.0. De-novo transcriptome assemblies were generated from RNA sequences extracted from isolate cultures of Amphora, Chaetoceros, and Cylindrotheca. Each species' quality-controlled RNA sequencing data was assembled using Trinity v2.12.0 using default settings and with sequences provided as un-merged paired end reads. The pre-assembly RNA sequencing reads were then mapped back to their respective assemblies as a quality control step, and at least 85% of the reads from all cultures successfully mapped onto the resulting assemblies. The assembly resulted in 53,401 contigs for Amphora, 37,507 contigs for Chaetoceros, and 73,553 contigs for Cylindrotheca
We calculated the number of T. pseudonana or T. oceanica reads that aligned to the gene models from resulting SAM alignment files with aligned sequences used in subsequent analyses.
Assembly: Thaps3 FilteredModels2 or ThaOc_1.0
Supplementary files format and content: csv files include TPM values for each sample,
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| Submission date |
Nov 07, 2022 |
| Last update date |
Nov 09, 2022 |
| Contact name |
Shiri Graff van Creveld |
| E-mail(s) |
shirig@uw.edu
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| Organization name |
University of Washingtom
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| Department |
Oceanography
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| Lab |
Armbrust
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| Street address |
616 NE Northlake Place
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98105 |
| Country |
USA |
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| Platform ID |
GPL32841 |
| Series (1) |
| GSE217467 |
Five diatoms transcriptomes under iron limitation and oxidative stress |
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| Relations |
| BioSample |
SAMN31645497 |
| SRA |
SRX18196701 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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