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| Status |
Public on Aug 11, 2015 |
| Title |
408_rep1 |
| Sample type |
SRA |
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| Source name |
fruit
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| Organism |
Cucumis sativus |
| Characteristics |
cucumber line: 408
tissue: fruits
age: early fruits about 2-4cm
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| Treatment protocol |
Early fruits about 2-4 cm were collected from 408 or 409 lines at the same time on the same day. Three-to-five fruits from different plants were pooled together as one biological sample for each cucumber line.
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| Growth protocol |
The cucumber line 408 and its near-isogenic line 409 were grown in the Jinliuhuan experimental station of Beijing under standard greenhouse condition. Pest control and water management were performed according to standard practices.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen fruit samples were grinded in a mortar with liquid nitrogen, and total RNA was isolated using RNA extraction kit (Huayueyang, China). RNA degradation and contamination was checked on 1% agarose gels, followed by Nano Photometer spectrophotometer (IMPLEN, CA, USA) to examine RNA purity. Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA) was used to measure RNA concentration, and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) was used to evaluate RNA integrity. Only RNA samples that passed the quality test were chosen for RNA-SEQ analyses.
RNA-seq library construction was performed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) following manufacturer’s instruction and four index codes were added to attribute sequences to each sample45. Briefly, mRNA was enriched from 3ug total RNA using magnetic beads with Oligo (dT) (Life technologies, CA, USA), and then fragmented using divalent cations under elevated temperature in NEB proprietary fragmentation buffer. Double-stranded cDNAs were synthesized using random hexamers and M-MuLV Reverse Transcriptase (RNase H-), followed by DNA Polymerase I and RNase H. After adenylation of 3’ ends of DNA fragments, NEBNext adaptor oligonucleotides were ligated to cDNA fragments, and AMPure XP beads system (Beckman Coulter, Beverly, USA) were used to select cDNA fragments of approximately 200 bp in length. DNA fragments with ligated adaptor molecules on both ends were selectively enriched using NEB Universal PCR Primer and Index primer in a 10 cycles PCR reaction. Products were purified (AMPure XP beads system) and quantified using the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. RNA-seq library were sequenced on an Illumina Hiseq 2000 platform and 100 bp single-end reads were generated.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Raw reads were pre-processed to remove low quality regions and adapter sequences. Reads passed quality filtering and minimum length (Q > 17 and length >= 25 bp) were clean reads and used to map to the cucumber genome using TopHat. The genome data that we used were downloaded from the cucumber genome database (http://cucumber.genomics.org.cn/page/cucumber/index.jsp).
Genome_build: v2i
Supplementary_files_format_and_content: Fasta file with id and clean sequence; the normalized data (reads per million per gene), Cucumber_fruits_RPM.txt
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| Submission date |
Aug 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Renyi Liu |
| E-mail(s) |
[email protected]
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| Phone |
02157078228
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| Organization name |
Shanghai Center for Plant Stress Biology
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| Department |
Bioinformatics
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| Street address |
3888 Chenhua Road
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
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| Platform ID |
GPL16310 |
| Series (1) |
| GSE60346 |
Comparative transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus) |
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| Relations |
| BioSample |
SAMN02988317 |
| SRA |
SRX679272 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1474130_408_rep1.clean.fa.gz |
470.5 Mb |
(ftp)(http) |
FA |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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