NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2734730 Query DataSets for GSM2734730
Status Public on Aug 07, 2017
Title Late-maturation stage whole seed
Sample type SRA
 
Source name Soybean seeds containing late-maturation-stage embryos
Organism Glycine max
Characteristics cultivar: Williams 82
tissue: whole seeds
developmental stage: late-maturation-stage embryos
Growth protocol Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., 2010). Whole seeds containing globular stage, heart stage, cotyledon stage, early-, mid-, and late-maturation stage embryos were collected. Dry seeds weighed approximately 200 mg. Seedlings were isolated from seeds imbibed for six days. Vegetative tissues (trifoliate leaves, roots, stems) were isolated from a mature plant 3-4 months old. Floral buds consists of unopened buds with no signs of dehisced anthers.
Extracted molecule total RNA
Extraction protocol Collected tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Total RNA was isolated from the powder using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer√Ęs instructions. Isolated total RNA was treated with RNase-free DNase I (Ambion, Austin, TX) and was subjected to two rounds of poly-A+ RNA selection using oligo-d(T)25 magnetic beads (Dynabeads, Invitrogen, Carlsbad, CA).
Sequencing libraries were prepared using 100 nanograms of twice-selected polyA+ RNA following the Illumina mRNA-Seq Protocol (Part #1004898 Rev. D). Briefly, polyA+ RNA was fragmented and used as template for random-primed cDNA synthesis. Double-stranded cDNAs were treated with T4 and Klenow DNA Polymerases and T4 PNK to generate blunt-end cDNAs. An 'A' base was added to the 3√Ę ends of the phosphorylated blunt-end cDNAs, followed by the ligation of Illumina adapters. Adapter-ligated cDNAs were size selected on an agarose gel for the desired size of ~ 200 bp. Purified cDNAs were amplified by PCR for 15 cycles. Quantification of cDNA libraries was carried out using a Nanodrop ND-3300 Fluoro-spectrophotometer (Thermo Scientific, Waltham, MA). Amplified cDNA size was determined by agarose gel electrophoresis. Single-end 76-bp reads were generated for each library by the UCLA Genome Sequencing Center (http://gsc.ucla.edu/) using an Illumina Genome Analyzer IIx and HiSeq 2000.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Whole seeds 1.2 - 1.5 cm in length and have a fresh weight between 230 - 350 mg were collected. The entire embryo is yellow including the axis and cotyledons.
Data processing Original unprocessed and unfiltered data file from the Illumina sequencing pipeline. Each lane of sequencing is attached as an individual compressed file. The sequence data are in the QSEQ format
Raw sequence reads were initially filtered using the Illumina purity filter parameter. Then, the remaining reads were mapped to a reference containing soybean ribosomal RNA (rRNA) sequences using Bowtie [Langmead et al., Genome Research, (2009)]. The final filtered reads have passed the Illumina purity filter and are devoid of rRNA sequences. These sequences were used to map against the soybean reference genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net). Only uniquely mapped reads (i.e. reads that map to one position within the genome) were used for subsequent analysis.
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 1.01
Supplementary_files_format_and_content: tab-delimited text file including normalized RPKM count of each sampled gene
 
Submission date Aug 07, 2017
Last update date May 15, 2019
Contact name Bob Goldberg
E-mail(s) bobglab@mcdb.ucla.edu
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)
GSE29163 Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle
Relations
BioSample SAMN07457101
SRA SRX3067926

Supplementary file Size Download File type/resource
GSM2734730_wm.lm.seed.rnaseq.rpkm.txt.gz 349.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap