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Sample GSM4712825 Query DataSets for GSM4712825
Status Public on Dec 11, 2020
Title 49_Embryo_rep3
Sample type SRA
 
Source name 49 DAF embryo
Organism Solanum lycopersicum
Characteristics cultivar: Moneymaker
tissue: Embryo
age (daf): 49
developmental stage: 49 DAF
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.
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Description 49_Em_3
AllSamples_GeneExpression_Count.txt
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.
 
Submission date Aug 06, 2020
Last update date Dec 11, 2020
Contact name Julia Buitink
E-mail(s) julia.buitink@inrae.fr
Phone +33241225544
Organization name INRAE
Department BAP
Lab SEED
Street address 42 rue Georges Morel
City Beaucouze
ZIP/Postal code 49070
Country France
 
Platform ID GPL28981
Series (1)
GSE155838 RNA sequencing of tomato seed tissues during seed development
Relations
BioSample SAMN15751161
SRA SRX8902090

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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