|
| Status |
Public on Jan 21, 2022 |
| Title |
vir_2_input [re-analysis] |
| Sample type |
SRA |
| |
|
| Source name |
virilizer input
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage/tissue: 2 weeks old, whole seedlings
ecotype: Columbia
genotype: vir
|
| Treatment protocol |
N/A
|
| Growth protocol |
Arabidopsis seeds were cultured in plates. Seeds planted in plates were sterilized by soaking in 5% NaClO for 4 min and then washed with sterile water for 5 times before being planted onto 0.5 × MS medium plus 1% sucrose. Plates were placed in the cold room (4°C, dark) for 2 days and then kept in the tissue culture room (16 h light: 8 h dark, 22°C) until used.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using hot phenol extration. Poly(A) RNA was prepared according to the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, NEB). m6A levels were measured by two-dimensional thin layer chromatography (TLC) analysis as described previously
The libraries from fragmented poly (A) RNA (100-150 nt) were prepared using ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina) followed by size selection using E-Gel SizeSelect II (Invitrogen), and quality checked on Agilent High Sensitivity DNA Chips (Agilent).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
B1-4-2_S3_ME
processed data file:
vir_diffE.csv
|
| Data processing |
reads trimmed with trimmomatic
alignment performed with Bowtie2 to TAIR10.48 genome
indexing with samtools
gene counting performed with htseq
differential expression analysis with DEseq2
Genome_build: TAIR10.48
Supplementary_files_format_and_content: .csv, differential expression analysis results
|
| |
|
| Submission date |
Nov 11, 2021 |
| Last update date |
Jan 21, 2022 |
| Contact name |
Nathan Archer |
| E-mail(s) |
nathan.archer1@nottingham.ac.uk
|
| Organization name |
University of Nottingham
|
| Department |
School of Veterinary Medicine and Sciences
|
| Lab |
ARCHER
|
| Street address |
Sutton Bonington
|
| City |
Loughborough |
| State/province |
East Midlands |
| ZIP/Postal code |
LE12 5RD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE188610 |
Two novel proteins with opposing m6A writing functions interact with HAKAI [RNA-seq] |
| GSE188611 |
Two zinc finger proteins with functions in m6A writing interact with HAKAI |
|
| Relations |
| Reanalysis of |
GSM5319979 |
| BioSample |
SAMN23068919 |
| SRA |
SRX13110160 |
