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Sample GSM1213858 Query DataSets for GSM1213858
Status Public on Aug 22, 2013
Title Early maturation-stage seed coat [small-RNA]
Sample type SRA
Source name Soybean early maturation-stage seed coat
Organism Glycine max
Characteristics cultivar: Williams 82
developmental stage: Early maturation-stage
tissue: seed coat
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. The TruSeq Small RNA Sample Preparation kit was used to generate libraries with modifications (Illumina, San Diego, CA).  Specifically, 250 ng total RNA was used as input and 15 PCR cycles was used for the final PCR enrichment step. 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 size fractionation
Instrument model Illumina HiSeq 2000
Description Seed coats from seeds 6.0 - 7.0 mm in length were 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.
Small RNA sequences were first selected for reads containing adapters. Reads were trimmed at the adapter site and reads between 18 – 24 nucleotides were kept for further analysis.
Trimmed reads were first filtered by removing reads that mapped to rRNA and tRNA sequences.  The remaining trimmed reads were aligned to the genome using Bowtie (version 0.12.7) with no mismatch allowed.
Genome_build: Glyma version 1.0
Supplementary_files_format_and_content: tab-delimited text files containing read counts for each trimmed unique sequence
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 SAMN02324427
SRA SRX337856

Supplementary file Size Download File type/resource 9.0 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data provided as supplementary file

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