|
| Status |
Public on Aug 01, 2014 |
| Title |
Anther_MACE |
| Sample type |
SRA |
| |
|
| Source name |
Anther
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: Anther
cultivar: Moneymaker
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Tomato plants (cv Moneymaker) were grown in a glasshouse under a 16/8h day/night cycle (24-20°C). Young leaves and anther from different developmental stages were collected from 8-week old plants for transcriptome analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the NucleoSpin® RNA isolation kit (Macherey and Nagel) following the manufacturer’s instructions.
The mRNA was enriched by binding the poly-A-tail at the 3'-end and the last 500 bp were sequenced so that each transcript is represented by one read in the library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Massive Analysis of cDNA ends (MACE)
|
| Data processing |
FastQC preprocessing
Filtering for sequences shorter than 14bp
MACE reads were aligned using SSAHA2 via the pipeline CRACPipe; kmer 14, skip 1
Data were weighted concerning equal hits and filtered for mapping with a max. of 1 insertion, deletion or mismatches
Genome_build: http://plants.ensembl.org ; ITAG2.3
Supplementary_files_format_and_content: comma separated files (csv) representing the Transcript per million (TPM) for the mRNAs.
|
| |
|
| Submission date |
Apr 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefan Simm |
| Organization name |
University Medicine Greifswald
|
| Department |
Bioinformatics
|
| Lab |
Applied Bioinformatics
|
| Street address |
Walter-Rathenau-Straße 48
|
| City |
Greifswald |
| ZIP/Postal code |
17489 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE56610 |
Expression of orthologs of ribosome biogenesis factors in vegetative and reproductive tissues in Solanum lycopersicum |
|
| Relations |
| BioSample |
SAMN02721476 |
| SRA |
SRX513216 |
