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Sample GSM7207854 Query DataSets for GSM7207854
Status Public on Aug 07, 2023
Title Wild-type inflorescence RNA, CMC-treated, replicate 7
Sample type SRA
 
Source name inflorescence
Organism Arabidopsis thaliana
Characteristics tissue: inflorescence
genotype: Col-0
treatment: CMC
Treatment protocol N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide (CMC); pseudouridine antibody (D347-3, MBL)
Extracted molecule total RNA
Extraction protocol tissue ground in liquid nitrogen, Trizol total RNA extraction, 15% urea PAGE fractionation, 17-40nt cut and eluted ON
NEBNext small RNA sequencing kit (CMC samples); Perkin Elmer Nextflex v3 (IP samples)
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Data processing Adapter trimming (Fastx clipper, v0.0.14)
De-multiplexing (Fastx collapser v0.0.14)
Mapping (Bowtie2 v2.3.4.1)
feature counts (bedtools v2.29.0)
Assembly: TAIR10
Supplementary files format and content: Gene/TE name, sequence length, and RPM
Supplementary files format and content: Sequence, readcount (for pus7 and pus10 samples)
 
Submission date Apr 21, 2023
Last update date Aug 07, 2023
Contact name Rowan Paul Herridge
E-mail(s) rowan.herridge@otago.ac.nz
Organization name University of Otago
Department Biochemistry
Street address 710 Cumberland Street
City Dunedin
ZIP/Postal code 9016
Country New Zealand
 
Platform ID GPL19580
Series (1)
GSE230228 Pseudouridine in small RNAs
Relations
BioSample SAMN34276899
SRA SRX20032308

Supplementary file Size Download File type/resource
GSM7207854_WT_inf_CMC+_rep7_counts.txt.gz 1.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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