|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Dec 31, 2018 |
Title |
KU50_ESR |
Sample type |
SRA |
|
|
Source name |
early storage root
|
Organism |
Manihot esculenta |
Characteristics |
cultivar: KU50 age: 90 days treated with: normal condition tissue: early storage root
|
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
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
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
|
|
|
Submission date |
Jan 03, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Zehong Ding |
E-mail(s) |
dingzehong@itbb.org.cn
|
Organization name |
ITBB
|
Street address |
No.4 XueYuan Rd
|
City |
HaiKou |
State/province |
HaiNan |
ZIP/Postal code |
571101 |
Country |
China |
|
|
Platform ID |
GPL17194 |
Series (1) |
GSE93098 |
Genome-wide expression of HD-Zip genes in cassava |
|
Relations |
BioSample |
SAMN06198840 |
SRA |
SRX2458899 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2443754_KU50_ESR.txt.gz |
168.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|