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| Status |
Public on Jun 26, 2021 |
| Title |
3h 2 |
| Sample type |
SRA |
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| Source name |
pollen tubes
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| Organism |
Nicotiana tabacum |
| Characteristics |
tissue: pollen tubes
condition: 3 h RT
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| Growth protocol |
200 mg Nicotiana tabacum pollen were resuspended in 2 ml pollen tube medium (2.5 % w/v PEG 4000, 5 % w/v sucrose, 15 mM MES-KOH pH 5.9, 1 mM CaCl2,1 mM KCl, 0.8 mM MgSO4, 0.01 % v/v H3BO3, 30 µM CuSO4) and spread onto cellophane foil that was placed in a square petri dish on 50 ml of solid pollen tube medium (2 % Agarose w/v, 5 % sucrose w/v, 6 % PEG-4000 w/v, 15 mM MES-KOH pH 5.9, 1 mM CaCl2,1 mM KCl, 0.8 mM MgSO4, 0.01 % H3BO3 v/v, 30 µM CuSO4)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction kit (SpectrumTM Plant Total RNA Kit, Sigma-Aldrich)
RNA-seq libraries were performed using the non stranded mRNA Kit from Illumina (Cat. N°RS-122-2001)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
s3h5
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| Data processing |
Illumina software BaseCaller was used to generate BCL files, which were demultiplexed using bcl2fastq v2.17.1.14
STAR version 2.5.2a was used to align the reads to the Nitab-v4.5 using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in Nitab-v4.5
Genome_build: Nicotiana tabacum version 4.5 (Nitab-v4.5) from Sol Genomic Network
Supplementary_files_format_and_content: Tab-delimited gene counts
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| Submission date |
Jun 29, 2020 |
| Last update date |
Jun 27, 2021 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
[email protected]
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| Organization name |
Universitaetsmedizin Goettingen
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| Department |
Department of Pathology
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| Lab |
NGS Integrative Genomics
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| Street address |
Kreuzbergring 57
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| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
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| Platform ID |
GPL25653 |
| Series (1) |
| GSE153474 |
Transcriptome analysis of heat stressed Nicotiana tabacum pollen tubes |
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| Relations |
| BioSample |
SAMN15398428 |
| SRA |
SRX8632183 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4644883_s3h5_geneCounts.txt.gz |
229.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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