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| Status |
Public on Sep 11, 2021 |
| Title |
Top Internode section of the maize stem, rep 2 |
| Sample type |
SRA |
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| Source name |
Puma hybrid maize
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| Organism |
Zea mays |
| Characteristics |
genotype: Puma hybrid
developmental stage: 60 DAS before pollination
tissue: Top internode section of the stem
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| Growth protocol |
Puma hybrid maize plants were grown in 10 L plastic pots containing 1/1 v/v peatmoss and vermiculite sterile soil mixture under greenhouse conditions. Plants were collected at early reproductive stage R1 (60 DAS). Tissues collected were the top internode section of the stem, TI. And the female inflorescences (FI) which were bagged prior to silk emergence. Samples were frozen, milled with Restch mill in liquid nitrogen and storage at -80°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from female inflorescences (FI) and top internodes of the stem (TI) at 60 DAS were extracted using the PureLink RNA-micro-to-midi Kit (Invitrogen Corp., Carlsbad, CA, USA) as described by the manufacturer. The purity and integrity of RNA samples were evaluated by electrophoresis on 2% RNase-free agarose gels, spectrophotometry (A260/A280 and A260/A230 ratios) using a NanoDrop 2000 (Thermo Scientific) and quality analysis using the Agilent 2100 Bioanalyzer system (Agilent technologies, Inc, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Data processing |
RNA-seq read quality was assessed with FastQC v0.11.2 and cleaned using the Trimmomatic software (Bolger, Lohse & Usadel, 2014).
Reads were aligned to the maize B73 reference genome (ZmB73_RefGen_v3.25, www.maizegdb.org) using the TopHat v2.0.13 software.
The expression level was calculated in fragments per kilobase of transcript per million fragments mapped (FPKM) as described previously (Trapnell, Pachter & Salzberg, 2009; Trapnell et al., 2012).
Data analysis were updated using CLC Genomics Workbench 20.0 (QIAGEN) software mapping to the B73 reference genome v4 .
Only the genes with FPKM results that met the criteria of FDR <0.05 and fold change > |2| between the two conditions were considered to be significantly differentially expressed
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for every gene and every sample including FPKM values
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Updated expression data with CLC Workbench software. Tab-delimited text file with expression values including FPKM
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| Submission date |
Aug 12, 2021 |
| Last update date |
Sep 11, 2021 |
| Contact name |
Stewart Gillmor |
| E-mail(s) |
[email protected]
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| Phone |
4621663013
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| Organization name |
CINVESTAV
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| Department |
UNIDAD DE GENOMICA AVANZADA
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| Street address |
CARR. LEON-IRAPUATO
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| City |
IRAPUATO |
| State/province |
GUANAJUATO |
| ZIP/Postal code |
36660 |
| Country |
Mexico |
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| Platform ID |
GPL19255 |
| Series (1) |
| GSE181998 |
Analysis of global gene expression in vegetative and reproductive tissues of maize (Zea mays) that differ in accumulation of starch and sucrose |
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| Relations |
| BioSample |
SAMN20748658 |
| SRA |
SRX11729140 |
| 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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