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Status |
Public on May 13, 2024 |
Title |
leaf_h2az+HsH2A.Z.1_2 |
Sample type |
SRA |
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|
Source name |
third or fourth pair of rosette leaves
|
Organism |
Arabidopsis thaliana |
Characteristics |
tissue: third or fourth pair of rosette leaves genotype: h2az+HsH2A.Z.1
|
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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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
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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 |
SAMN40761415 |
SRA |
SRX24165944 |