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Sample GSM1213857 Query DataSets for GSM1213857
Status Public on Aug 22, 2013
Title Early maturation-stage embryonic axis [RNA-seq]
Sample type SRA
Source name Soybean early maturation-stage embryonic axis part
Organism Glycine max
Characteristics cultivar: Williams 82
developmental stage: Early maturation-stage
tissue: embryonic axis part
Growth protocol Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010). Whole seeds containing early-maturation (EM) stage embryos were collected. The embryo was dissected out of the seed coat and the axis was manually separated from the cotyledons of the EM-stage embryo
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from three seed parts (axis, cotyledon, and seed coat) using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions.  Total RNA was treated with RNase-free DNaseI (Ambion, Austin, TX) and quantified with Quant-iT™ RiboGreen® RNA reagent (Grand Island, NY) on a Nanodrop ND-3300. Approximately 20 nanogram of total RNA was amplified with Nugen Ovation Pico WTA system v.1 (Nugen, San Carlos, CA).  Double-stranded cDNA was generated using WT-Ovation Exon Module (Nugen, San Carlos, CA) and quantified with Picogreen on the Nanodrop ND-3300 (Nanodrop Technologies).  One microgram of double-stranded cDNA was fragmented using NEB Fragmentase for 15 minutes at 37oC for the standard protocol (NEB, Ipswich, MA).  The Illumina TruSeq DNA Sample prep kit was used to prepare the Illumina library with modifications (Illumina, San Diego, CA).  Specifically, the Covaris shearing step was omitted, the final PCR enrichment step was performed using Agilent Pfu Turbo Cx DNA polymerase (Agilent, Santa Clara, CA) instead of the TruSeq PCR mix, and 12 cycles of PCR were performed. 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
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Whole embryonic axis devoid of the plumule from seeds 6.0 - 7.0 mm in length was collected.
Data processing Basecalls performed using RTA version
Each lane of sequencing for each sample is attached as an individual compressed file. The sequence data are in the qseq format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to Glycine max genome (v1.0) using bowtie v0.12.7 with parameters -v 2 -5 6 -3 0 -m 3 --best --strata.
Read counts to Glycine max gene models (v1.1) models were computed using BedTools.
Reads per kilobase per million (RPKM) value was calculated according to Mortazavi et al. (Mortazavi et al., 2008).
Genome_build: Glyma version 1.0
Supplementary_files_format_and_content: tab-delimited text file including gene model and normalized RPKM value.
Submission date Aug 21, 2013
Last update date Aug 26, 2013
Contact name Bob Goldberg
Phone 310-825-3270
Organization name University of California, Los Angeles
Department Molecular, Cell and Developmental Biology
Street address 610 Charles E Young Drive East
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
Platform ID GPL15008
Series (1)
GSE37895 Methylation Changes in Soybean Early Maturation Seed Parts
BioSample SAMN02324424
SRA SRX337948

Supplementary file Size Download File type/resource
GSM1213857_wm.em.axis.rnaseq.rpkm.txt.gz 392.4 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data provided as supplementary file

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