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| Status |
Public on Jun 24, 2024 |
| Title |
Untreated, old processing, rep 4 |
| Sample type |
SRA |
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| Source name |
Leaf 6 of rosette
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Leaf 6 of rosette
genotype: Col-0
treatment: Untreated
timepoint: Untreated
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| Extracted molecule |
total RNA |
| Extraction protocol |
Rneasy plant mini kit (Qiagen) according to the manufacturer's instructions. Included on-column DNAse step.
TruSeq mRNA Sample Prep Kit (Illumina), according to the manufacturer's instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Reads were aligned to the Arabidopsis genome (TAIR v10) using TOPHAT v2.0.4 with the settings ‘transcriptome-mismatches 3’, ‘N 3’, ‘bowtie1’, ‘no-novel-juncs’, ‘genome-read-mismatches 3’, ‘p 6’, ‘read-mismatches 3’, ‘G’, ‘min-intron-length 40’, ‘max-intron-length 2000’. Reads were assigned to annotated gene models of TAIR v10 using HTSeq-count v0.6.1 with default settings except ‘-s no’. Normalization was done using the medium count ratio, following the principle applied in the DESeq2 R package.
Assembly: TAIR v10
Supplementary files format and content: Rows: genes, columns: samples
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| Submission date |
May 16, 2024 |
| Last update date |
Jun 24, 2024 |
| Contact name |
Niels Aerts |
| E-mail(s) |
n.aerts@uu.nl
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| Organization name |
Utrecht University
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| Department |
Biology
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| Lab |
Plant-Microbe Interactions
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| Street address |
Padualaan 8
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| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CH |
| Country |
Netherlands |
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| Platform ID |
GPL13222 |
| Series (2) |
| GSE267647 |
Time series study of ABA-treated Arabidopsis thaliana rosettes [Illumina TruSeq mRNA Sample Prep Kit] |
| GSE267649 |
Time series study of ABA-treated Arabidopsis thaliana rosettes |
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| Relations |
| BioSample |
SAMN02380810 |
| SRA |
SRX384011 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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