|
| Status |
Public on Jun 17, 2024 |
| Title |
at-endosperm-RNAseq_replicate1_col_Cm_x_ler |
| Sample type |
SRA |
| |
|
| Source name |
endosperm
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: endosperm
cell line: AT F1-Endosperm Columbia TEmob x Landsberg
genotype: TEmob Col (maternal) x Ler (paternal)
|
| Treatment protocol |
Material was generated by manually crossing of pistillata (Ler) mutants with pollen of INT TEmob line (Col) and the INT TEmob line pollinated with Ler. TEmob (Cm) line was generated as follows: Seeds were germinated in 1⁄2MS agar plates supplemented with 5,44μM α-amanitin (Sigma Cat. No. A2263) and 40μM zebularine (Sigma Cat. No.Z4775) and incubated at 4°C degrees for 24h and subsequently at 37°C in the dark. Line was cross to cenh3 CENH3-TAILSWAPplants (Ravi & Chan, 2010) and offspring haploids were grown and treated with colchicine; a diploid line was identified (TEmob).
|
| Growth protocol |
Seeds were surface sterilized with 70% ethanol and washed three times with sterile water. Sterilized seeds were sown on 1⁄2MS plates containing 0.5% sucrose and 0.8% agar, stratified for 2 days at 4°C and germinated under long-day conditions (16h light/8h darkness) at 21°C. Seedlings were transferred to soil after 10–12 days and grown in phytotrons under long day conditions (day 21°C, night 20°C 70% humidity, 150μE light intensity).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from INTACT isolated endosperm nuclei using the mirVana kit.
NEBNext Poly(A) mRNA Magnetic Isolation kit, NEBNext® Ultra II RNA Library Prep Kit for Illumina® ,NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1)
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| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Arabidopsis thaliana F1-endosperm of TEmob Columbia-0 INT (female) crossed with Landsberg-erecta (male)
|
| Data processing |
The 150 bp reads were trimmed and mapped in single-end mode to the Arabidopsis (TAIR10) genome masked for rRNA genes using TopHat v2.1.0 (Trapnell et al., 2009) (parameters adjusted as -g 1 -a 10 -i 40 -I 5000 F 0 r 130). Transcript counts and RPKM values were calculated using GFOLD.
Assembly: The 150 bp reads were trimmed and mapped in single-end mode to the Arabidopsis (TAIR10) genome masked for rRNA genes using TopHat v2.1.0 (Trapnell et al., 2009) (parameters adjusted as -g 1 -a 10 -i 40 -I 5000 F 0 r 130). Transcript counts and RPKM values were calculated using GFOLD.
Supplementary files format and content: Expression levels (RPKM) are shown for genes in the genome annotation for Arabidopis thaliana TAIR10 at each condition and replicate.
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| |
|
| Submission date |
Mar 04, 2024 |
| Last update date |
Jun 17, 2024 |
| Contact name |
Juan C Santos-González |
| E-mail(s) |
juan.santos@slu.se
|
| Organization name |
SLU
|
| Department |
Department of Plant Biology and Forest Genetics
|
| Lab |
Köhler's lab
|
| Street address |
Almas Allé 5
|
| City |
Uppsala |
| State/province |
Uppsala |
| ZIP/Postal code |
75007 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE260821 |
Epigenetic and transcriptional consequences of chemically induced transposon mobilization in the endosperm (RNA-Seq) |
| GSE260822 |
Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis |
|
| Relations |
| BioSample |
SAMN40254850 |
| SRA |
SRX23831143 |
