|
| Status |
Public on Jan 30, 2024 |
| Title |
empty vector, Rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Sorghum bicolor |
| Characteristics |
tissue: leaf
genotype: empty vector
|
| Growth protocol |
4-week-old sorghum plants
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated using the TRIzol Reagent (Invitrogen) and treated with DNase I (Invitrogen) to remove genomic DNA contamination
Libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw data with adapter sequences or low-quality sequences was filtered using SOAPnuke (v 2.1.7) with parameters: "-n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim --minReadLen 150"
clean reads were aligned to the Sorghum bicolor genome v3.1.1 (Phytozome) using HISAT2 (v2.2.1)
Transcripts were then assembled using StringTie (v2.2.1).
DEGs were identified using DESeq2 (v2.11.40.7)
Assembly: Sorghum bicolor genome v3.1.1
Supplementary files format and content: tab-delimited tabular files include raw counts for each sample
|
| |
|
| Submission date |
Jul 21, 2023 |
| Last update date |
Jan 30, 2024 |
| Contact name |
Meng Xie |
| E-mail(s) |
mxie@bnl.gov
|
| Organization name |
Brookhaven National Laboratory
|
| Street address |
50 Bell Ave
|
| City |
Upton |
| State/province |
NY |
| ZIP/Postal code |
11973 |
| Country |
USA |
| |
|
| Platform ID |
GPL21615 |
| Series (2) |
| GSE237989 |
Sorghum SbGhd7 is a major regulator of floral transition and directly represses genes crucial for flowering activation |
| GSE238095 |
Sorghum SbGhd7 is a major regulator of floral transition and directly represses genes crucial for flowering activation |
|
| Relations |
| BioSample |
SAMN36678933 |
| SRA |
SRX21126189 |
