|
| Status |
Public on Nov 21, 2022 |
| Title |
single protoplasts transfected with a pool of bHLHs; protoplast #86 |
| Sample type |
SRA |
| |
|
| Source name |
leaf protoplasts
|
| Organism |
Zea mays |
| Characteristics |
cell type: leaf protoplasts
genotype: B73
|
| 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 |
CEL-seq2
CEL-seq2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
24merTFs_cell_86
|
| Data processing |
The raw CEL-seq2 reads were demultiplexed based on cell-specific barcodes using Fastq-Multx. The UMI sequences from read 1 were added to the read 2 sequence names and then filtered and trimmed with Fastp (parameters: -y -x -3 -f 6). The clean reads were mapped to B73 RefGen_v3 with Hisat2, and the UMIs quantified with SAMtools and UMI-tools. The counts of UMIs mapped to each gene/locus/construct were normalized to transcripts per million.
Assembly: B73 RefGen_v3
Supplementary files format and content: tab-delimited text file including TPM values for each gene
|
| |
|
| 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) |
| GSE210327 |
Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci [scRNA-seq] |
| GSE210330 |
Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci |
|
| Relations |
| BioSample |
SAMN30103145 |
| SRA |
SRX16771241 |
