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| Status |
Public on Feb 08, 2018 |
| Title |
TXNS278-Root-T1 |
| Sample type |
SRA |
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| Source name |
TXNS278
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| Organism |
Solanum tuberosum |
| Characteristics |
tissue: Root
age: 66 day old
selection: TXNS278
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| Growth protocol |
Tubers were planted in Springlake, TX and plant were grown on commercial field
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| Extracted molecule |
total RNA |
| Extraction protocol |
Plant Sample were collected in the field place in RNA-later, kept on ice till brought back in the lab and Frozen. and removed, flash frozen on dry ice, and RNA was harvested using Qiagen Plant RNeasy. TruSeq RNA Library Preparation Kit v2 was used on poly(A) RNA enriched.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
analyses was performed on CyVerse.org
The pre-filtered reads were quality-filtered using FASTQC tools.
The RNA-seq reads that passed the quality filters were mapped to the potato reference genome (PGSC_DM_v3.4 gene models ensemblv19-preinstalled in iplantcollaborative.org) using the Tuxedo RNA-seq pipeline (Trapnell et al., 2013, Trapnell et al., 2009, Trapnell et al., 2010).
The Tuxedo pipeline comprised TopHat2 (mapping), Cufflinks2 (transcript assembly), and Cuffmerge2 (transcript merging).
Identification of differential gene expression was conducted using Cuffdiff2, following the defaults parameters in CyVerse.
Genome_build: PGSC_DM_v3.4
Supplementary_files_format_and_content: .gtf file
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| Submission date |
Oct 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Cecilia Tamborindeguy |
| E-mail(s) |
ctamborindeguy@tamu.edu
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| Phone |
979 845 2619
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| Organization name |
Texas A&M University
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| Street address |
Heep Center
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| City |
College Station |
| ZIP/Postal code |
77843 |
| Country |
USA |
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| Platform ID |
GPL16436 |
| Series (1) |
| GSE87857 |
Global transcriptome comparison reveals stress adaptation between Russet Norkotah and its Clonal Selection, TXNS278 |
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| Relations |
| BioSample |
SAMN05897968 |
| SRA |
SRX2239238 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2341977_278RootT1Transcripts.gtf.gz |
5.9 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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