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Sample GSM5529937 Query DataSets for GSM5529937
Status Public on Mar 23, 2022
Title TAP_2_0mm, replicate 1
Sample type SRA
 
Source name LCM isolated tapetal cells
Organism Zea mays
Characteristics tissue: Isolated tapetal cells from fixed 2.0 mm maize anthers
genotype: W23 inbred
Stage: 2.0 mm
Treatment protocol Anthers were dissected from tassels and then measured using a micrometer (Fisher Scientific).
Growth protocol Maize (Zea mays) W23 bz2 inbred line plants were grown in Stanford, CA, USA under greenhouse conditions (31℃/21℃, 14 h day/10 h night light cycle with supplemental LED and UV-A lamps providing ~50% of summer sun conditions).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from three different LCM cell samples and FA samples at 1.5 mm and 2.0 mm using the RNAqueous™-Micro Kit (Invitrogen).
RealSeq®-AC kits (SomaGenics) were used for ultra-low amounts of total RNA starting with 100 ng from whole anthers or 1 to 10 ng from LCM cell samples.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model NextSeq 550
 
Description LCM isolated tapetal cells from fixed 2.0 mm anthers of W23 inbred maize, provided by Walbot lab at Stanford
For small RNA library preparation, RealSeq®-AC kits (SomaGenics) were used for ultra-low amounts of total RNA starting with 100 ng from whole anthers or 1 to 10 ng from LCM cell samples. Sequencing in a single-end mode on an Illumina NextSeq (University of Delaware) yielded 75 bp reads for sRNA-seq.
Data processing Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the maize genome (Maize Genome Database).
Genome_build: version 4 of the B73 maize genome
 
Submission date Aug 19, 2021
Last update date Mar 23, 2022
Contact name Blake C. Meyers
E-mail(s) bmeyers@danforthcenter.org
Phone 314-587-1422
Organization name Donald Danforth Plant Science Center
Lab Meyers lab
Street address 975 N Warson Road
City St. Louis
State/province MO
ZIP/Postal code 63132
Country USA
 
Platform ID GPL27775
Series (1)
GSE182476 24-nt phasiRNAs move from tapetal to meiotic cells in maize anthers
Relations
BioSample SAMN20863910
SRA SRX11828791

Supplementary file Size Download File type/resource
GSM5529937_8941_chopped.txt.gz 6.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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