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Sample GSM7207869 Query DataSets for GSM7207869
Status Public on Aug 07, 2023
Title Wild-type pollen RNA, CMC-treated, replicate 2
Sample type SRA
Source name pollen
Organism Arabidopsis thaliana
Characteristics tissue: pollen
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 MiSeq
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
Organization name University of Otago
Department Biochemistry
Street address 710 Cumberland Street
City Dunedin
ZIP/Postal code 9016
Country New Zealand
Platform ID GPL17970
Series (1)
GSE230228 Pseudouridine in small RNAs
BioSample SAMN34276884
SRA SRX20032323

Supplementary file Size Download File type/resource
GSM7207869_WT_pollen_CMC+_rep2_counts.txt.gz 1.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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