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| Status |
Public on Jul 01, 2023 |
| Title |
FS40-c |
| Sample type |
SRA |
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| Source name |
fruit
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| Organism |
Vitis vinifera |
| Characteristics |
tissue: fruit
cultivar: Flame Seedless
age: 40 days after full blooming
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a Plant RNA EASYspin Plus Kit (aidlab, Peking, China) according to the instructions of the manufacturer, and treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm and 280 nm (A260 and A280) using SmartSpec Plus (BioRad, USA). RNA integrity was further verified by electrophoresis using a 1.5% agrose gel. To avoid individual variation, we selected three biological replicates for each sample, and extracted total RNA separately, and then we pooled the replicates together for the following experiments.
Construction of cDNA library was independently prepared using 10 ug of total RNA. Polyadenylated RNAs were purified and concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen) before being used for the directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95oC followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 oC until used for sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
T09
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic-0.36 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
To evaluate the quality of clean reads , fastqc was used with default parameters
clean reads were mapped to vitis vinifera genome(ftp://ftp.ensemblgenomes.org/pub/plants/release-25/fasta/vitis_vinifera/) by tophat2 using default paremeters and fpkm values were calculated by cufflinks
DEGs were identified by R package EdgeR
Genome_build: vitis vinifera
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Jul 06, 2020 |
| Last update date |
Jul 01, 2023 |
| Contact name |
Guosong Jiang |
| E-mail(s) |
jiangguosongdoc@hotmail.com
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| Organization name |
Union Hospital, Tongji Medical College, Huazhong University of Science and Technology
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| Department |
Department of Urology
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| Street address |
Jiefang Road, No. 1277
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| City |
WuHan |
| State/province |
Hubei Province |
| ZIP/Postal code |
430022 |
| Country |
China |
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| Platform ID |
GPL25271 |
| Series (2) |
| GSE153870 |
Comparative study on berry development of two grape cultivars by transcriptomic analyses [Flame Seedless] |
| GSE153999 |
Comparative study on berry development of two grape cultivars by transcriptomic analyses |
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| Relations |
| BioSample |
SAMN15458228 |
| SRA |
SRX8673517 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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