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| Status |
Public on Jun 22, 2015 |
| Title |
X24_45_1 |
| Sample type |
SRA |
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| Source name |
BP-1_cold stress 45°C_24hr
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| Organism |
Thermosynechococcus vestitus BP-1 |
| Characteristics |
strain: BP-1
temperature ©: cold stress 45°C
time (hr): 24
replicate: 1
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| Treatment protocol |
Samples were collected over time (starting at time zero). For RNA analysis, 50-100 ml was poured into a manifold and fast-filtered through MF Membrane Filters (0.45 um HAWP, Millipore). The cells were washed off the filter with 1 ml of 1:1 TE buffer-Bacteria Protect, spun, and then stored at -80 ° C until RNA Extraction.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen cell pellets were mixed in Trizol preheated to 65 °C then incubated 15 minutes for RNA extraction. The sample was solvent separated with chloroform, purified on an miRNEasy kit, processed with TurboDNAse, and cleaned up with an miRNEasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq, analyzed as single-end 100 bp, ≥ 12 million reads on an Illumina HiSeq 2500.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence using cutadapt
Trimmed reads were mapped and annotated to the BP-1 reference genome on Rockhopper, version 2.0.3, http://cs.wellesley.edu/~btjaden/Rockhopper/index.html
Non-protein coding RNA was computationally removed and sample count data for each gene probe was exported to individual .txt files
Genome_build: GCF_000011345.1
Supplementary_files_format_and_content: File contains probe list in first column and count data for each sample, saved in .txt format
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| Submission date |
Jun 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Rebecca Knight |
| E-mail(s) |
[email protected]
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| Organization name |
University of Texas
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| Department |
Plant Biology
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| Lab |
UTEX
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| Street address |
1 University St. A6700
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| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78705 |
| Country |
USA |
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| Platform ID |
GPL20600 |
| Series (1) |
| GSE70086 |
RNA-seq analysis of gene expression after exposure to hot and cold stress in WT cells of Thermosynechococcus elongatus, BP-1 |
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| Relations |
| SRA |
SRX1067277 |
| BioSample |
SAMN03784653 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1716924_X24_45_1.txt.gz |
12.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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