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| Status |
Public on May 09, 2020 |
| Title |
Hacha root control [13_S14] |
| Sample type |
SRA |
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| Source name |
Roots of 11-day old Hacha rice plants that were previously grown under control conditions for 2 days
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| Organism |
Oryza sativa |
| Characteristics |
line: Hacha (derived from a cross of CRM 53 X IR 64)
age: 11 days
tissue: whole root
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| Treatment protocol |
9-days old plants were treated for two days with Fe stress with full-strength Hoagland medium plus 15 mM Fe sulfate at pH 5.2 was applied or plants were exposed to control conditions (50 µM Fe).
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| Growth protocol |
Plant growth was conducted in a controlled growth chamber, with a 16-hour light/ 8-hour dark cycle, 70 % humidity, a light intensity of 220 µmol*m-2*s-1, a day/night temperature of 26 °C. Rice seeds were disinfected using 1 % sodium hypochlorite for 15 min. Subsequently, seeds were soaked in water for one day at 4 °C and transferred for three days in the dark to 30 °C for germination. Homogenously grown seedlings were transplanted into 1 l pots filled with half-strength modified Hoagland solution for two days. Then, half-strength nutrient solution was replaced with a full-strength solution containing 1 mM calcium nitrate, 2.5 mM potassium nitrate, 2.86 mM ammonium nitrate, 1 mM potassium dihydrogen phosphate, 1 mM magnesium sulfate, 0.045 μM boric acid, 0.009 µM manganese chloride, 0.666 μM zinc sulfate, 0.4 μM copper sulfate, and 0.0176 μM sodium molybdate and 50 µM Fe sodium EDTA, pH 6.2, which also represented the control treatment condition. The nutrient solutions were renewed every second day.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from 100 mg plant material using the RNeasy plant mini kit (Qiagen) according to the manufacturer‘s instructions.
Libraries were constructed with the TruSeq RNA Sample Prep Kit v2 (Illumina Technologies). Double-stranded cDNA was purified for end repair, adaptor ligation, and DNA fragment enrichment.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls were performed and demultiplexed using bcl2fastq2.
Sequenced reads were trimmed for adapter sequence and masked for low-complexity or low-quality sequence, then mapped to the IRGSP 1.0 reference transcriptome using kallisto.
TSV files with TPM (transcripts per million) values were generated using kallisto.
Average insert length information was extracted from the command line output of kallisto.
Genome_build: IRGSP 1.0
Supplementary_files_format_and_content: TSV files were generated using kallisto. Besides normalized TPM values they contain counts and length information.
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| Submission date |
May 08, 2020 |
| Last update date |
May 09, 2020 |
| Contact name |
Hans-Joerg Mai |
| E-mail(s) |
[email protected]
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| Organization name |
Heinrich Heine University
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| Department |
Institute of Botany
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| Lab |
Prof. Dr. Petra Bauer
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| Street address |
Universitaetsstrasse 1
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| City |
Dusseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
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| Platform ID |
GPL13160 |
| Series (1) |
| GSE150103 |
Transcriptomic expression patterns of two contrasting lowland rice varieties reveal high iron stress tolerance |
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| Relations |
| BioSample |
SAMN14854222 |
| SRA |
SRX8293167 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4523694_S14.tsv.gz |
609.7 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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