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| Status |
Public on May 19, 2023 |
| Title |
mRNA, ndx1-4, rep1 |
| Sample type |
SRA |
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| Source name |
flower
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: flower
developmental stage: 5-week-old
ecotype: Col-0
genotype: ndx1-4 mutant
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| Growth protocol |
Inflorescence tissues of 5-week-old Col-0 and ndx1-4 flowering plants were collected.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from Col-0 and ndx1-4 flowers using the phenol-chloroform extraction method. The quality of total RNA samples was checked by an Agilent bioanalyzer (RIN > 9).
cDNA libraries were prepared according to Illumina's TruSeq RNA Library Preparation Kit v2 protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ndx1.4_rep1_count, ndx1.4_rep1_fpkm
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| Data processing |
NGS libraries were sequenced (1x75 bp reads) using an Illumina NextSeq 500 instrument.
Reads were mapped to the A. thaliana reference transcriptome (Araport11, coding and noncoding genes) to quantify gene expression and reads were mapped to transposable elements (Araport11) themselves to quantify their expression using Salmon. Transcript quantities were corrected for GC bias to reduce isoform quantification errors.
Differentially expressed genes and differentially expressed transposable elements between Col-0 and ndx1-4 samples were identified by DESeq2 (FDR < 0.01 and FDR < 0.05 respectively).
For data visualisation, reads were aligned to the A. thaliana reference sequence (TAIR10) using HISAT2 allowing for reporting spliced alignments. We used deepTools bamCoverage to create RPKM (Reads per Kilobase per Million) normalized coverage files.
Assembly: A. thaliana (Araport11)
Supplementary files format and content: Coverage data (bigWig) files are RPKM normalized read coverage data of mapped reads.
Supplementary files format and content: Differentially expressed genes data (tab-delimited text) files are the results of DESeq2 analyses. Comparisons are: ndx1-4 vs Col-0 flower samples, Col-0 flower vs seedling (GSE207842) samples, ndx1-4 flower vs seedling (GSE207842) samples. Data table includes count, FPKM, log2(Fold Change), adjusted p-value of differentially expressed coding and noncoding genes.
Supplementary files format and content: Differentially expressed transposon data (tab-delimited text file) is a result of DESeq2 analysis between Col-0 and ndx1-4 samples. Data table includes count, FPKM, log2(Fold Change), adjusted p-value of differentially expressed transposable elements.
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| Submission date |
Jan 24, 2023 |
| Last update date |
May 19, 2023 |
| Contact name |
Lorant Szekvolgyi |
| Organization name |
University of Debrecen
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| Department |
Department of Pharmacy
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| Lab |
Genome Architecture and Recombination Research Group
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| Street address |
Egyetem ter 1.
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| City |
Debrecen |
| ZIP/Postal code |
4032 |
| Country |
Hungary |
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| Platform ID |
GPL19580 |
| Series (2) |
| GSE223589 |
Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX) deficient Arabidopsis inflorescence [RNA-Seq] |
| GSE223591 |
Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX) deficient Arabidopsis inflorescence |
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| Relations |
| BioSample |
SAMN32886718 |
| SRA |
SRX19147912 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6965100_at_rnaseq_ndx1-4_flower_r1.bw |
55.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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