|
| Status |
Public on Nov 09, 2023 |
| Title |
WT_0h_1 |
| Sample type |
SRA |
| |
|
| Source name |
maize seed
|
| Organism |
Zea mays |
| Characteristics |
tissue: maize seed
cell type: maize seed cells
genotype: WT
treatment: 0h after imbibition
|
| Treatment protocol |
28°C with dark condition,Samples were taken after 0 h and 6 h of imbibition.
|
| Growth protocol |
Seeds of KN5585 and ereb92 mutants were sterilized with 10% NaClO solution for 20 min and washed 5 times with sterile water. After that, 30 seeds were evenly placed on the filter paper infiltrated with sterile water in the germination box.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the seeds of ereb92 knockout mutant lines and KN5585 using standard extraction methods
The starting RNA for library construction is total RNA, which is enriched with polyA tailed mRNA using Oligo (dT) magnetic beads. Subsequently, the resulting mRNA is randomly interrupted with divalent cations in the Fragmentation Buffer. Using fragmented mRNA as a template and random oligonucleotides as primers, the first strand of cDNA was synthesized in the M-MuLV reverse transcriptase system. Subsequently, the RNA strand was degraded using RNaseH, and the second strand of cDNA was synthesized using dNTPs as raw material in the DNA polymerase I system. The purified double stranded cDNA undergoes end repair, A-tailed addition, and sequencing connections. cDNA of approximately 370-420 bp was screened using AMPure XP beans, amplified by PCR, and the PCR product was purified again using AMPure XP beans, ultimately obtaining a library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
WT_0h_1_fpkm
|
| Data processing |
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit. 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost 2 insertion cost 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using Cl _C genomic benchwork
Assembly: B73V4_ctg23
Supplementary files format and content: tab-delimited text file includes fpkm for each Sample
Supplementary files format and content: tab-delimited text file includes raw counts each Sample
|
| |
|
| Submission date |
Jun 13, 2023 |
| Last update date |
Nov 09, 2023 |
| Contact name |
wenzheng Pei |
| E-mail(s) |
peij10j20@sina.com
|
| Phone |
13966885074
|
| Organization name |
Sichuan Agricultural University
|
| Department |
State Key Laboratory of Crop Gene Exploraion and Utilization in Southwest China
|
| Lab |
State Key Laboratory of Crop Gene Exploraion and Utilization in Southwest China
|
| Street address |
No. 211, Huimin Road, Fair Street, Wenjiang District, Chengdu, Sichuan Province
|
| City |
Chengdu |
| State/province |
Sichuan Province |
| ZIP/Postal code |
611134 |
| Country |
China |
| |
|
| Platform ID |
GPL9141 |
| Series (1) |
| GSE234833 |
ZmEREB92 plays a negative role in seed germination by regulating ethylene signaling and starch mobilization in maize |
|
| Relations |
| BioSample |
SAMN35726100 |
| SRA |
SRX20672589 |
