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Status |
Public on Jul 04, 2019 |
Title |
Heat Shock noFT_Hsrep-2 |
Sample type |
SRA |
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Source name |
stem
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Organism |
Solanum lycopersicum |
Characteristics |
experiment: Heat Shock genotype/variation: Treated sft
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Extracted molecule |
total RNA |
Extraction protocol |
Five, seemingly homogeneous plants were selected from a larger population to represent the natural variation among greenhouse tomato plants. Independent stem samples consisted of 5 mid-segments of internodes harvested in duplicates 2 h after dawn. Total RNA was extracted using the RNeasy Mini Kit (Qiagen), and treated with DNase I using the RNase-Free DNase set (Qiagen) RNA samples were processed for sequencing, quality control, and differential expression analysis at the Technion Genome Center. Libraries of single 50 bp reads were prepared using the Ilumina TruSeq RNA library preparation kit v2. The barcoded libraries were sequenced on Ilumina Hiseq 2500, six samples per lane (~30,000,000 reads). If an experiment included more than 6 samples, each sample was divided equally, in all the lanes.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Description |
Sample_477B
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Data processing |
Library quality control was conducted using FASTQC, version 0.11.5 Sequences were trimmed by quality using trim galore Sequences were aligned using Tophat2, version 2.1.0 (uses Bowtie2 version 2.2.6). Raw gene expression levels were counted by HTseq-count, version 0.6.1 Genome_build: ITAG version 2.5 genome (ftp://ftp.sgn.cornell.edu/genomes/Solanum_lycopersicum/annotation/ITAG2.5_release), Supplementary_files_format_and_content: counts
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Submission date |
Jun 06, 2019 |
Last update date |
Jul 04, 2019 |
Contact name |
Eliezer Lifschitz |
Organization name |
Technion
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Department |
Faculty of Biology
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Street address |
Technion City
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City |
Haifa |
ZIP/Postal code |
3200003 |
Country |
Israel |
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Platform ID |
GPL19694 |
Series (1) |
GSE132280 |
Florigen Accelerates Secondary Cell Wall Biogenesis to Harmonize Vascular Maturation with flowering and reproductive phase Development |
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Relations |
BioSample |
SAMN11967526 |
SRA |
SRX5980224 |
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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