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| Status |
Public on Mar 09, 2019 |
| Title |
H: 0240_REP3 |
| Sample type |
SRA |
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| Source name |
pool of two youngest leaves from each of three replica plants
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| Organism |
Nicotiana tabacum |
| Characteristics |
tissue: de-etiolating tobacco leaves
treatment: Extended dark
harvest time after treatment: 0240 minutes
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| Treatment protocol |
Whole plants were submitted to extended dark treatment. Young growing leaves were pale (etiolated). Leaf tissue was taken following return to the light (t=0) to observe de-etiolation. Samples were taken the middle section (excluding leaf-tip and basal region) of two leaves of each of three replica plants. These samples were pooled to make one biological repeat.
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| Growth protocol |
Nicotiana tabacum plants were grown on soil until near maturity under long day (16 hours light, 350 uE/m2/s), and subjected to extended dark treatment.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Leaf harvests at day 3 were done at 10 h and 15 h after dawn and at day 4 at 9 h after dawn. Frozen leaf tissue (40 - 100 mg) from three independent replicates each of bacteria-primed and mock treated plants was ground (2 x 45 s, maximum frequency) by a Retsch mill (MM 400, Retsch, Haan, Germany). Each harvest was a single young systemic leaf from a single rosette. The harvested systemic leaves were all developmentally younger than the previously locally infected leaves. RNA was extracted with the RNeasy Plant Mini Kit according to the manual (QIAGEN GmbH, Hilden, Germany). RNA was quantified with a Qubit® RNA HS Assay Kit (ThermoFisher Scientific Life Technologies GmbH, Darmstadt, Germany) and RNA quality was further assessed by agarose gel electrophoresis.
RNA samples were sequenced at the Max Planck Genome Centre (MP-GC, Cologne, Germany), with an Illumina HiSeq2500 (Illumina, San Diego, CA). Single end, 100 bp reads to a minimum of 30 million (± 10%) reads per sample were undertaken using a TruSeq RNA library prepared by the MP-GC.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Quality control: Quality of obtained Illumina single-end sequences was tested with FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). As no overrepresented sequences were detected, an additional 3'-trimming step was skipped.
Mapping: To reduce complexity, and because the project aimed to defined and identify evolutionarily conserved features, we mapped to the tobacco maternal (Renny-Byfield et al., 2011) progenitor N. sylvestris, as opposed to N. tabacum (Sierro et al., 2014). Mapping was undertaken using BWA v0.70 in aln mode with default parameters (Li and Durbin, 2009). Samtools v1.0 was used to create, sort and index the alignment data in BAM format and calculate transcript counts (Li et al., 2009).
Read counting: Samtools v1.0 was used to create, sort and index the alignment data in BAM format and calculate transcript counts (Li et al., 2009).
Genome_build: N. sylvestris (ftp://ftp.ncbi.nlm.nih.gov/genomes/Nicotiana_sylvestris/RNA/rna.fa.gz; file date 10/24/14
Supplementary_files_format_and_content: Read count output files (ASCII format): NCBI GI identifier, Read count
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| Submission date |
Mar 08, 2019 |
| Last update date |
Mar 09, 2019 |
| Contact name |
Tegan Armarego-Marriott |
| E-mail(s) |
armarego@mpimp-golm.mpg.de
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| Phone |
17695492258
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| Organization name |
Max Planck Institute of Molecular Plant Physiology
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| Street address |
Am Muehlenberg, 1
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| City |
Potsdam-Golm |
| ZIP/Postal code |
14476 |
| Country |
Germany |
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| Platform ID |
GPL22345 |
| Series (1) |
| GSE128049 |
Highly resolved systems biology to dissect the etioplast-to-chloroplast transition in tobacco leaves |
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| Relations |
| BioSample |
SAMN11089761 |
| SRA |
SRX5495069 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3660854_1252_H_transcriptCounts.txt.gz |
209.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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