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| Status |
Public on Dec 11, 2020 |
| Title |
42_Seedcoat_rep3 |
| Sample type |
SRA |
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| Source name |
42 DAF seedcoat
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| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Moneymaker
tissue: Seed coat
age (daf): 42
developmental stage: 42 DAF
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| Treatment protocol |
Seeds were manually extracted from the equatorial section of the fruit. The embryo, endosperm and seed coat were hand-dissected, immediately frozen in liquid nitrogen and stored at -80°C prior to RNA isolation.
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| Growth protocol |
Plants were grown under controlled greenhouse conditions in 10 L pots containing substrate (Irish peat, perlite, coconut fiber; 50/40/10; v/v/v), watered with a nutrient solution and supplemented with 16 h of 250 µmol m2 s-1 light. The day and night temperatures were maintained at > 23°C/20°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from the frozen grinded seed tissues using the NucleoSpin® RNA Plant and Fungi kit (Macherey-Nagel, Düren, Germany), according to the manufacturer instructions (protocol 5.1) without the incubation step at 56°C using the following recommended sample type: alfalfa for embryo, potato tuber for the endosperm and grape vine leaf for seed coat.
Samples were sent to BGI, Hong Kong, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth). After mRNA enrichment, RNA was fragmented and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on BGISEQ-500 platform, generating an average 20M reads of 50bp per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
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| Description |
42_SC_3
AllSamples_GeneExpression_Count.txt
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| Data processing |
Clean reads were mapped to the reference genome tomato SL4.0 using SALMON to calculate gene expression level.
Genome_build: SL4.0
Supplementary_files_format_and_content: AllSamples_GeneExpression_Count.txt: Tab-delimited text file with count values for every gene and every sample.
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| Submission date |
Aug 06, 2020 |
| Last update date |
Dec 11, 2020 |
| Contact name |
Julia Buitink |
| E-mail(s) |
julia.buitink@inrae.fr
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| Phone |
+33241225544
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| Organization name |
INRAE
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| Department |
BAP
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| Lab |
SEED
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| Street address |
42 rue Georges Morel
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| City |
Beaucouze |
| ZIP/Postal code |
49070 |
| Country |
France |
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| Platform ID |
GPL28981 |
| Series (1) |
| GSE155838 |
RNA sequencing of tomato seed tissues during seed development |
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| Relations |
| BioSample |
SAMN15751173 |
| SRA |
SRX8902078 |
| 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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