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Sample GSM5686771 Query DataSets for GSM5686771
Status Public on Jan 21, 2022
Title hakai_2_input [re-analysis]
Sample type SRA
 
Source name hakai input
Organism Arabidopsis thaliana
Characteristics developmental stage/tissue: 2 weeks old, whole seedlings
ecotype: Columbia
genotype: hakai
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 B2-2-4_S2_ME
processed data file:
hakai_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 GSM5319983
BioSample SAMN23068923
SRA SRX13110164

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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