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Sample GSM8189456 Query DataSets for GSM8189456
Status Public on May 13, 2024
Title leaf_WT_2 (h2a.z + HsH2A.Z control)
Sample type SRA
 
Source name third or fourth pair of rosette leaves
Organism Arabidopsis thaliana
Characteristics tissue: third or fourth pair of rosette leaves
genotype: WT
Treatment protocol NA
Growth protocol Plants were grown in soil in growth chambers at +20°C under a 16 hour-light/8-hour dark cycle.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted per the RNeasy Plant Mini kit (Qiagen). An RLT suspension of frozen leaf powder was split into three equal aliquots of 400 μl for 3 replicates. Total RNA was DNase-treated (Ambion) and quantified using Nanodrop One (Thermo Scientific). 100 nanograms for each of the three replicates from every sample were then used as input to generate RNA-seq libraries following the Universal RNA-seq with NuQuant protocol (Tecan).
RNA-seq libraries were constructed following the Universal RNA-seq with NuQuant protocol (Tecan).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Reads were trimmed of adapter content using Trimgalore. Trimmed reads were mapped to the Arabidopsis thaliana TAIR10 genome assembly, converted to the BAM file format, and sorted by coordinate using STAR. Aligned reads were indexed and quality filtered using Samtools. Mapped fragments overlapping with exons were counted using featureCounts. Gene counts were then analyzed for differential enrichment using DESeq.
Reads were trimmed of adapter content using Trimgalore. Trimmed reads were mapped to the Arabidopsis thaliana TAIR10 genome assembly, converted to the BAM file format, and sorted by coordinate using STAR. Aligned reads were indexed and quality filtered using Samtools. Mapped fragments overlapping with exons were counted using featureCounts. Gene counts were then analyzed for differential enrichment using DESeq.
Assembly: TAIR10
Supplementary files format and content: tab delimited text file including raw read counts at each TAIR10 gene via featureCounts
 
Submission date Apr 05, 2024
Last update date May 13, 2024
Contact name Roger B Deal
E-mail(s) roger.deal@emory.edu
Phone 404-727-8087
Organization name Emory University
Department Biology
Street address 1510 Clifton Rd NE
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
 
Platform ID GPL26208
Series (2)
GSE263311 Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development (WT, h2a.z + HsH2A.Z. RNA-Seq)
GSE263313 Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development
Relations
BioSample SAMN40761412
SRA SRX24165947

Supplementary file Size Download File type/resource
GSM8189456_WT2_unique.count.txt.gz 133.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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