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| Status |
Public on May 14, 2024 |
| Title |
WT_45FR_rep1 |
| Sample type |
SRA |
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| Source name |
Whole 12 days old seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Whole 12 days old seedlings
cell line: Col-0
cell type: Wild-type seedlings
genotype: WT
treatment: 45 minutes FR-enriched light
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using either the Spectrum Plant Total RNA Kit (Sigma)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
WT_45_1Aligned.out.sam
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| Data processing |
BASH command line, FastQC and R
Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic (Leading = 25, Trailing = 25, MINLEN = 35, Sliding Window = 5:35). Reads quality was checked using FastQC.
Mapping was done using STAR in R
Read counts extraction and normalization were performed in R
The counts from each sample were merged together in a merged count file of that biological replicate, after checking the replicates by PCA
Assembly: TAIR10
Supplementary files format and content: Tab delimited text files combining raw counts of each replicate in one text file per biological sample
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| Submission date |
Aug 30, 2023 |
| Last update date |
May 14, 2024 |
| Contact name |
Stephan Wenkel |
| E-mail(s) |
stephan.wenkel@umu.se
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| Organization name |
Umeå Plant Science Center
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| Street address |
Parallellvägen 21
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| City |
Umeå |
| ZIP/Postal code |
907 36 |
| Country |
Sweden |
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| Platform ID |
GPL21785 |
| Series (2) |
| GSE241974 |
The ATHB2 microProtein affects plant development and the shade avoidance response (RNA-Seq) |
| GSE241976 |
The ATHB2 microProtein affects plant development and the shade avoidance response |
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| Relations |
| BioSample |
SAMN37207072 |
| SRA |
SRX21543790 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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