|
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.
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|
|
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 |