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| Status |
Public on May 24, 2014 |
| Title |
Soybean Early Maturation Axis Epidermis- biological replicate 2 |
| Sample type |
SRA |
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| Source name |
Soybean Early Maturation Stage-Axis Epidermis
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| Organism |
Glycine max |
| Characteristics |
cultivar: Williams 82
seed compartments/tissue: Soybean Early Maturation Stage-Axis Epidermis
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| Growth protocol |
Soybean plants were grown at the UC Davis Greenhouses with a 16:8 day:night cycle at 22°C-30°C. Seeds were germinated in Modified UC Mix (equal parts of ground canadian sphagnum, horticultural grade sand, white pumice, redwood compost) for 10 days. Individual seedlings were transfered to 1 gallon pots where they were grown for an additional 3 weeks before being transplanted to 3 gallon pots. Plants were watered as needed with water containing 190 ppm Nitrogen, 40 ppm Phosphorus and 140 ppm Potassium and micronutrients.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Soybean seeds (Williams 82) were fixed in 3:1 ethanol:acetic acid for 16-20 hours at 4°C, then dehydrated with 75% ethanol, 85% ethanol, 95% ethanol, and three times with 100% ethanol, each wash in one hour intervals. Then they were infiltrated with 3:1 ethanol-xylenes, 1:1 ethanol-xylenes, 1:3 ethanol-xylenes, and three times with 100% xylenes, dilution in two hour intervals. They were then infiltrated with molten paraffin at 60 deg C for 1-4 days, depending on the size of the tissue. Laser capture microdissection was used to isolate specific compartments of the seed after tissues were sectioned in 5-10um sections. Total RNA was isolated with Ambion RNaqueous-Micro kit (Grand Island, NY) and quantified with Quant-iT™ RiboGreen® RNA reagent (Grand Island, NY) on a Nanodrop ND-3300.
Amplification was performed using NuGen Ovation Pico WTA V1 (San Carlos, CA), starting with 15ng total RNA. Double-stranded cDNA was generated using the NuGen WT-Ovation Exon-Module (San Carlos, CA). Illumina-complatible libraries were made starting with one microgram of double-stranded cDNA using Illumina TruSeq DNA Sample prep kit (Hayward, CA), according to manufacturer's instructions except for the PCR enrichment step where Agilent Pfu Turbo Cx hotstart DNA polymerase was used for 15 cycles of amplification. Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument. Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Compartments collected from seeds ranging 6.0-7.0mm in length
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| Data processing |
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file. The sequence data are in the fastq format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to Glycine max gene models (v1.1) using bowtie v0.12.7 with parameters -v 2 -5 10 -3 4 -m 1 --best --strata
Read counts for each gene models were computed using a custom script. Normalized counts are obtained using the EdgeR package v3.0.8 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140).
Genome_build: Glycine max V1.1
Supplementary_files_format_and_content: tab-delimited text file including the normalized counts for each sample.
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| Submission date |
May 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
John Harada |
| E-mail(s) |
jjharada@ucdavis.edu
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| Organization name |
University of California
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| Department |
Plant Biology
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| Lab |
Harada lab
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| Street address |
One Shields Avenue
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL15008 |
| Series (2) |
| GSE46096 |
Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage |
| GSE116036 |
mRNA profiling of soybean seed regions and tissues at five developmental stages |
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| Relations |
| BioSample |
SAMN02799123 |
| SRA |
SRX552860 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1398252_em.AX.EPD.2.norm.counts.txt.gz |
254.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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