|
| Status |
Public on Feb 09, 2017 |
| Title |
WT - rep1 |
| Sample type |
SRA |
| |
|
| Source name |
anther, wild type
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Rutgers
genotype/variation: wild type
tissue: anther
|
| Growth protocol |
The 7B-1 mutant and wild type (cv. Rutgers) tomatoes were grown in a growth chamber set for long day condition (16/8 h light/dark). Flower buds of different sizes, smaller, equal and larger than 4-5 mm were collected from WT and 7B-1 flowers and the stamens were dissected under a microscope.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy plant miniRNA extraction kit (Qiagen) from 7B-1 and WT anthers of different sizes and pooled separately in equimolar ratio.
Two mRNA libraries were constructed using the TruSeq mRNA Sample Preparation Kit from Illumina (Illumina, San Diego, CA, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
S. Lycopersicum cv. Rutgers
Processed data file: SLycopersicum_GeneExpressionLevels_allGenes.xlsx
Processed data file: SLycopersicum_GeneExpressionLevels_DEG.xlsx
|
| Data processing |
All reads containing unassigned nucleotides were discarded.
The matching to the genome (v2.5, Sly) was done full length, with 2 mismatches allowed.
The gene expression was calculated as indicated in Mortazavi et al. 2008.
The differential expression analysis was conducted using NoiSeq.
Genome_build: SL2.50
Supplementary_files_format_and_content: SLycopersicum_GeneExpressionLevels_allGenes.xlsx: Excel file includes raw counts and normalized expression values (RPKMs) of all genes.
Supplementary_files_format_and_content: SLycopersicum_GeneExpressionLevels_DEG.xls: Excel file includes normalized expression values (FPKMs) of the differentially expressed genes. The "log2" column indicates the log2 of the ratio between the normalized expression levels for wild type and mutant; the "Pr" is the corrected p-value under the NoiSeq model.
|
| |
|
| Submission date |
Aug 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Irina Mohorianu |
| E-mail(s) |
irina.mohorianu@paediatrics.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
Medical Sciences Division
|
| Lab |
Oxford Vaccine Group
|
| Street address |
Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7LE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE85859 |
Transcriptional regulation of male-sterility in 7B-1 male-sterile tomato mutant |
|
| Relations |
| BioSample |
SAMN05597304 |
| SRA |
SRX2035825 |
