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| Status |
Public on Mar 21, 2018 |
| Title |
EW14_CACCTC_L007_R1_001 |
| Sample type |
SRA |
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| Source name |
root
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| Organism |
Boechera depauperata |
| Characteristics |
treatment: 43°C
tissue: root
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| Treatment protocol |
Plants were grown at 22°C[normal], 38°C [Basal] and 43°C [Acquired]
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA 88 was isolated using AMBION RNAeasy isolation kits.The quality of RNA was examined using a BioAnalyzer.
A 1:1 ratio of Agencourt AMPure XP beads (Beckman Coulter Inc., Brea, CA) were used to purify resulting cDNA, and 1 ng cDNA was subsequently used to prepare a sequencing library with the Nextera XT DNA Library Prep Kit (Illumina, San Diego, CA). Both whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR pre-amplification cycles, and fragment size selection.
RNAseq libraries were sequenced using Illumina HiSeq 2500 according to the standard protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Bd_counts_file.txt
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| Data processing |
Filtered reads were mapped against the human TAIR10 and Boechera Stricta reference using Tophat v1.4.1 (--library-type fr-firststrand)
Alternative splicing events were identified used rMATS.3.0.9
Differentially expressed genes were identified using DeSeq2
Genome_build: TAIR10, Bstricta.v1.2 (https://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Bstricta)
Supplementary_files_format_and_content: count matrix
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| Submission date |
Dec 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
sumetha kannan |
| E-mail(s) |
sumetha.kannan@gmail.com
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| Organization name |
San DIego State University
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| Department |
Biology
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| Lab |
Waters lab
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| Street address |
5500 Campanile Dr
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| City |
Sn diego |
| State/province |
California |
| ZIP/Postal code |
92182 |
| Country |
USA |
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| Platform ID |
GPL24352 |
| Series (1) |
| GSE107820 |
Heat stress induced alternative splicing in a species-dependent manner |
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| Relations |
| BioSample |
SAMN08145778 |
| SRA |
SRX3455467 |
| 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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