|
| Status |
Public on May 31, 2023 |
| Title |
osg1l2 R3 |
| Sample type |
SRA |
| |
|
| Source name |
meristems at early developmental stages enriched in PBMs and ePBM/Ams
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Nipponbare
tissue: meristems at early developmental stages enriched in PBMs and ePBM/Ams
cell type: meristematic cells
genotype: osg1l2 single mutant
treatment: pants sown in growth chamber under LD conditions, sampled after 12 days in SD conditions
|
| Treatment protocol |
12 day of induction in SD conditions (70% humidity, 12h light at 28°C/12h dark at 26°C)
|
| Growth protocol |
pants sown in growth chamber under LD condition (70% humidity, 16h light at 28°C/8h dark at 26°C) sampled after 12 day of induction in SD conditions (70% humidity, 12h light at 28°C/12h dark at 26°C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the samples using RNeasy Plant Mini Kit from Qiagene.
cDNA libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7370) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw RNA-seq files were processed using the TuxNet interface (Spurney et al., 2019).
Reads were cleaned, mapped on the O. sativa reference genome (IRGSP-1.0), normalised, and FPKMs (Fragment per kilobase of transcript per million mapped reads) were calculated
performing a pairwise differential expression analysis between the wild type and mutant, the TuxNet interface generated Differentially Expressed Gene (DEG) datasets
Assembly: reference genome IRGSP-1.0
Supplementary files format and content: FPKM_Replicates.xlsx excel file that contains the FPKM values of each of the replicates
Supplementary files format and content: complete_table.xlsx excel file that contains the expression values, log2 fold changes, and q-values
|
| |
|
| Submission date |
Mar 20, 2023 |
| Last update date |
May 31, 2023 |
| Contact name |
Veronica Maria Beretta |
| E-mail(s) |
[email protected]
|
| Phone |
3349337306
|
| Organization name |
Università degli Studi di Milano
|
| Street address |
Via A. Vivaldi 36
|
| City |
Cassina Rizzardi |
| State/province |
Co |
| ZIP/Postal code |
22070 |
| Country |
Italy |
| |
|
| Platform ID |
GPL27860 |
| Series (1) |
| GSE227706 |
The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice |
|
| Relations |
| BioSample |
SAMN33831457 |
| SRA |
SRX19732262 |
