|
| Status |
Public on Nov 21, 2022 |
| Title |
p35S-GFP-ZHD5; protoplast prep #3 |
| Sample type |
SRA |
| |
|
| Source name |
leaf protoplasts
|
| Organism |
Zea mays |
| Characteristics |
cell type: leaf protoplasts
genotype: B73
tf: ZHD5
|
| Growth protocol |
Seeds of the B73 maize were germinated and grown in constant darkness at 25oC and 50–70% humidity. Leaves were collected from more than 10 etiolated seedlings 10 to 12 days after germination for each protoplast isolation.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the TRI reagent (Sigma-Aldrich).
RNA-seq libraries were made using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) following the manufacturer’s protocol for use with the NEBNext Poly(A) mRNA magnetic isolation module.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Prep3_ZHD5
|
| Data processing |
RNA-seq reads were mapped to the maize reference genomeusing Hisat v2.1.0. Reads mapped to each gene/locus were counted using the featureCounts program of the Subread package (v1.6.3). Read counts were normalized using edgeR v3.20.9.
Assembly: B73 RefGen_v3
Supplementary files format and content: tab-delimited text file including RPKM values
|
| |
|
| Submission date |
Aug 02, 2022 |
| Last update date |
Nov 21, 2022 |
| Contact name |
Junpeng Zhan |
| E-mail(s) |
[email protected]
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
1 Shizishan Street, Hongshan District
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL27775 |
| Series (2) |
| GSE210322 |
Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci [bulk RNA-seq] |
| GSE210330 |
Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci |
|
| Relations |
| BioSample |
SAMN30102818 |
| SRA |
SRX16770838 |
