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| Status |
Public on Aug 01, 2019 |
| Title |
Leaf_P5_Aux_2 |
| Sample type |
SRA |
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| Source name |
Leaf #5, P5 stage
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| Organism |
Solanum lycopersicum |
| Characteristics |
line: M82
tissue: Leaf #5, P5 stage
treatment: Picloram 1 µM
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| Treatment protocol |
For root response assay, 4 days after germination, seedlings were transferred to plates containing 1µM of the auxin analog 2,4-D (Sigma D7299) for 3h. For shoot samples, plants were sprayed with either mock or 1 µM of the auxin analog Picloram (Sigma P5575) for 3 hours
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| Growth protocol |
For the root response, tomato seedlings were germinated on ½ Murashige and Skoog plates in a growth chamber at 22C of continuous light. For the shoot response, tomato plants were grown in a greenhouse for three weeks
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| Extracted molecule |
total RNA |
| Extraction protocol |
For root tissues, 1cm root tips were cut and flash frozen in liquid nitrogen. For shoot, 15 young leaf primordia (Leaf number 5 at the P5 stage) were collected and flash frozen. RNA-extraction was performed using Qiagen RNAEasy Microkit
sequencing libraries prepared using Lexigen 3’ Quant-Seq kit, according to the manufacturer instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Expression calling was performed using Salmon 0.8.2, by aligning to the tomato genome ITAG3.2. As the library is 3’ biased, we extended all genes to cover 500 additional base pairs downstream.
Expression data were normalized using Deseq2 and genes induced at False Discovery Rate (FDR )<0.01 were selected
Genome_build: Solanum lycopersicum ITAG3.2
Supplementary_files_format_and_content: Normalized expression reads for all samples
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| Submission date |
Feb 11, 2019 |
| Last update date |
Aug 01, 2019 |
| Contact name |
Idan Efroni |
| E-mail(s) |
[email protected]
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| Organization name |
Hebrew University
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| Department |
Plant Sciences
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| Street address |
POB 12
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| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
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| Platform ID |
GPL21762 |
| Series (1) |
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| Relations |
| BioSample |
SAMN10909746 |
| SRA |
SRX5358393 |
| 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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