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| Status |
Public on Apr 11, 2017 |
| Title |
K326_ShootApex_ZT12_R1 |
| Sample type |
SRA |
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| Source name |
K326_ShootApex_ZT12
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| Organism |
Nicotiana tabacum |
| Characteristics |
cultivar: K326
tissue: ShootApex
timepoint: ZT12
age (days): 56
photoperiod: 18l/6d
replicate: 1
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| Treatment protocol |
Tissue was harvested at ZT0, 6, 12 and 18
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| Growth protocol |
Plants were grown under long day conditions (18h light, 6h dark) at 23 degrees.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using QIAzol followed by clean up, including on-column DNase treatment, using Qiagen RNeasy spin columns. RNA was QC'd using Bioanalyzer RNAnano protocol. RNA with RIN>=8.0 was used in library preparation
Random primed cDNA-libraries were prepared at GATC Biotech (Konstanz, Germany) using propritary methods
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
A6212
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| Data processing |
Basecalls performed using HiSeq Control Software 2.2.38
Deconvolution of multiplexed reads was carried out using Casava 1.9.4
Data were filtered and multiplex adaptors trimmed from reads using fastq-mcf 1.04.803 with the following configurations: -q 30 -l 50 -P 30
Reads were aligned to Nitab4.5 gene models and quantified using rsem 1.2.7 and bowtie 1.1.0
Genome_build: nitab45_transcripts.fasta
Supplementary_files_format_and_content: tab-delimited text files including gene model, TPM and FPKM were produced for each sample
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| Submission date |
Mar 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kieron David Edwards |
| E-mail(s) |
kieron_edwards@bat.com
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| Phone |
01223429502
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| Organization name |
British American Tobacco
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| Department |
Plant Biotechnology
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| Street address |
GR&D Cambridge, 210 Cambridge Science Park
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| City |
Cambridge |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB4 0WA |
| Country |
United Kingdom |
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| Platform ID |
GPL13760 |
| Series (1) |
| GSE95717 |
Nicotinana tabacum cv. K326 long day diurnal timecourse: Root, Shoot, Shoot Apex |
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| Relations |
| BioSample |
SAMN06480933 |
| SRA |
SRX2613998 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2522547_A6212.genes.results.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
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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