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Sample GSM1639669 Query DataSets for GSM1639669
Status Public on Mar 24, 2015
Title Albion Rep 3
Sample type SRA
 
Source name Developing pods
Organism Phaseolus vulgaris
Characteristics genotype: Albion
zn condition: Low zinc concentration
age: 20 days after anthesis
Extracted molecule total RNA
Extraction protocol Two pods per replication were ground to a fine powder with a mortar and pestle while completely frozen. Liquid nitrogen was continuously added to ensure tissue remained frozen throughout the grinding process. Total RNA was extracted from the samples using an RNA easy Plant kit (Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description Genotype grown at sufficient Zn supply
Data processing The RNA sequence was received in FASTQ formatted files containing 75-bp paired-end reads. The file contained sequences and quality information about each sequence. The data were filtered using scripts from FASTX-Toolkit (FASTQ Quality Trimmer and FASTQ Quality Filter http://hannonlab.cshl.edu/fastx_toolkit/ ). FASTQ Quality Trimmer clipped the low quality ends with a quality threshold of 20 and removed the reads shorter than 64 bp. Subsequently, FASTQ Quality Filter script was used to remove low quality sequences with quality scores of 20 or less.
The P. vulgaris reference genome sequence v. 1.0 (DOE-JGI and USDA-NIFA and corresponding gene model annotation files were obtained directly from http://www.phytozome.net). A P. vulgaris genome index was built using Bowtie v. 0.12.7 [22]. Paired-end clean reads for each individual were aligned to the reference genome by TopHat v 1.4.1 [23] with the provided guidance of annotated gene models (GTF file)
The transcript profile and abundance estimation was carried out using Cufflinks v1.3.0 with default parameters [26]. The resulting alignment of RNA-seq reads to the common bean reference genome from TopHat was used into Cufflinks to assemble into transcripts [27]. Normalization, estimated abundance, and tests for differential expression between tissue samples were performed using the program Cuffdiff with default parameters. The value of the test statistic used to compute significance of the observed change of the transcript abundance was measured in fragments per kilobase of transcript per million mapped reads (FPKM)
Genome_build: common bean reference genome
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample.
 
Submission date Mar 20, 2015
Last update date May 15, 2019
Contact name Carolina Astudillo
E-mail(s) carolinastudillor@gmail.com
Organization name Michigan State University
Street address A494 PSSB 1066 Bogue St.
City East Lansing,
State/province MI
ZIP/Postal code 48824
Country USA
 
Platform ID GPL14000
Series (1)
GSE67121 Transcriptome Characterization of developing bean (Phaseolus vulgaris L.) pods from two genotypes with contrasting seed zinc concentrations.
Relations
BioSample SAMN03436096
SRA SRX963058

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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