 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 31, 2019 |
| Title |
Callus II rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Callus
|
| Organism |
Sorghum bicolor |
| Characteristics |
strain: Hiro-1
tissue: Callus
age: 3 weeks callus induced from young embryo,and additional 20 days subculture
genotype: wild type
phenotype: Callus II
|
| Growth protocol |
Sorghum bicolor (L.) Hiro-1 were used in this study. Young embryos (about 1-2 mm) were collected from 13-15 day-old plants after flowering, and subsequently inoculated on callus induction medium (CIM) and cultured under sterile and non-light conditions at 25 °C. After 3 weeks, after removing the buds and outer membranes of the immature embryos, three types of callus was excised from the explants, and separately transferred to the new CIM for additional 20 days subculture before being moved into differentiation medium and cultured under condition of 16/8 h of light/dark at 25 °C and 2000 lx of light intensity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from Callus I, Callus II, Callus III and leaves generated from Callus II by using Trizol reagent (Invitrogen). Four RNA samples were then separately subjected to transcriptome analysis using Illumina sequencing with two biological replicates.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA-seq data were first cleaned by removing contaminations and low quality reads by Trimmomatic. The clean data were aligned with Tophat 2.0 (Kim et al., 2013) using the Phytozome Sorghum bicolor (BTx623) genome as the reference under default parameters (Paterson et al., 2009). Then, the gene counts were calculated with Cufflink, and the differentially expressed genes (greater than 2, P value < 0.05) were calculated by Cuffdiff. The up- or down-regulated genes were subjected to GO analysis and KEGG analysis to see which pathways the differential gene function was concentrated on.
Genome_build: sorghum BTx623
Supplementary_files_format_and_content: tab-delimited text files include gene ID, gene locus and FPKM values for each sample.
|
| |
|
| Submission date |
Nov 25, 2019 |
| Last update date |
Jan 01, 2020 |
| Contact name |
chao zhou |
| E-mail(s) |
zhouchao@ctgu.edu.cn
|
| Organization name |
CTGU
|
| Street address |
No.8,daxuelu Street
|
| City |
yichang |
| ZIP/Postal code |
443002 |
| Country |
China |
| |
|
| Platform ID |
GPL21615 |
| Series (1) |
| GSE140958 |
Transcriptome sequencing analysis of sorghum callus with various regeneration capacities |
|
| Relations |
| BioSample |
SAMN13383589 |
| SRA |
SRX7213629 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4191356_Callus_II_rep2_FPKM.txt.gz |
511.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
