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Sample GSM3273122

Query DataSets for GSM3273122

Status

Public on Jul 27, 2018

Title

MS3

Sample type

SRA

Source name

Microspore

Organism

Solanum lycopersicum

Characteristics

tissue: Microspore

Growth protocol

The tomato cultivar Heinz 1706 (Solanum lycopersicum) was planted in a climate-controlled chamber under 14-h light/10-h dark at 28°C for 2 weeks, then fully expanded leaves were collected. One-month-old friable callus was generated from tomato hypocotyls on solid Murashige and Skoog medium containing 1 mg/L 2,4-dichlorophenoxyacetic acid and 0.5 mg/L kinetin in a 12-h light/12-h dark cycle at 25°C.

Extracted molecule

total RNA

Extraction protocol

Generative cells and sperm cells were isolated from just-germinated pollen cultured in vitro for 20 min and 10-h-cultured pollen tubes(Lu et al., 2015), respectively. For microspore isolation, flowers 7 mm long were excised and anthers 5 mm long were squashed in ice-cold 0.6 M mannitol solution. The released microspore was filtered through a 75-μm nylon mesh and collected by centrifugation at 200 g for 2 min.
Strand-specific sequencing libraries were generated by using the rRNA-depleted RNA and NEBNext Ultra directional RNA library prep kit for Illumina (NEB) following the manufacturer’s recommendations. The libraries were qualified on the Agilent Bioanalyzer 2100 system, sequenced on an Illumina Hiseq 2000 platform, and 100-bp paired-end reads were generated.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Redundant reads and low-quality reads were removed by Trinity kmer filteri.
The filtered dataset was assembled by using SOAPDenovo-Trans and treated as EST evidence. Protein-encoding and non-coding RNA genes were predicted by an evidence-based approach (Liang et al., 2009)
Cuffdiff (v2.1.1) was used to calculate fragments per kilobase of exon per million reads (FPKM) for both lncRNA and protein-coding genes in each sample (Trapnell et al., 2010).
Genome_build: SL2.5
Supplementary_files_format_and_content: xlsx file includes FPKM values for each sample

Submission date

Jul 16, 2018

Last update date

Jul 27, 2018

Contact name

Tai Wang

E-mail(s)

twang@ibcas.ac.cn

Organization name

Institute of Botany, CAS

Street address

Nanxincun 20, Xiangshan