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| Status |
Public on Dec 31, 2018 |
| Title |
W14_root |
| Sample type |
SRA |
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| Source name |
root
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| Organism |
Manihot esculenta |
| Characteristics |
cultivar: W14
age: 90 days
treated with: normal condition
tissue: root
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh samples were frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
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 |
Sequence quality was examined using FastQC
low quality reads were filtered also using FASTX-toolkit
Clean reads weremapped to cassava genome (version 4.1) using Tophat v2.0.13
Raw count data were obtained and normalized by Cufflinks pipeline v2.1.1
Genome_build: cassava genome version 4.1 The genome assembly file (‘Mesculenta_147.fa.gz’) and GFF annotation file (‘Mesculenta_147_gene.gff3.gz’) were downloaded from phytozome website (Version 9) at http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Jan 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Zehong Ding |
| E-mail(s) |
dingzehong@itbb.org.cn
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| Organization name |
ITBB
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| Street address |
No.4 XueYuan Rd
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| City |
HaiKou |
| State/province |
HaiNan |
| ZIP/Postal code |
571101 |
| Country |
China |
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| Platform ID |
GPL17194 |
| Series (1) |
| GSE93098 |
Genome-wide expression of HD-Zip genes in cassava |
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| Relations |
| BioSample |
SAMN06198842 |
| SRA |
SRX2458897 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2443752_W14_root.txt.gz |
167.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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