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| Status |
Public on Mar 01, 2024 |
| Title |
12-day-old SPCHΔ49 seedlings [C2] |
| Sample type |
SRA |
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| Source name |
whole seedling
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole seedling
genotype: 35S:SPCH{delta}49
treatment: none
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| Growth protocol |
After 3-day imbibition at 4 °C, seeds were sown on ½ MS medium, grown under 16 h light/8 h dark cycle with 100µmol m-2 s-1 light density at 22 °C
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 12-day-old Arabidopsis seedlings by the Plant RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample Prep Kit v2 LS protocol (Illumina, San Diego, CA, USA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
C2
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| Data processing |
Raw reads were trimmed and filtered by removing adapters sequence and bases with low quality score (Q30 score < 15) using Trimmomatic v0.38
Clean reads were mapped to Arabidopsis thaliana (version 11) primary transcript sequences (https://phytozome.jgi.doe.gov) to calculate the gene expression in transcript per million (TPM) using Kallisto v 0.44.0 (Bray, et.al., Nat Biotechnol, 2016).
Candidates with TPM ≥10 in all biological replicates of any group, and with parameters |b| ≥ 0.692 and q-value < 0.05 were identified differentially expressed genes (DEGs) using Sleuth program (Pimentel, et.al., Nat Methods, 2017).
Assembly: Arabidopsis thaliana (version 11) primary transcript sequences
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Mar 02, 2023 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Wang Ming Lin |
| E-mail(s) |
[email protected]
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| Organization name |
shenyang agricultural university
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| Street address |
120 Dongling Road
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| City |
Shenyang |
| ZIP/Postal code |
110866 |
| Country |
China |
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| Platform ID |
GPL13222 |
| Series (1) |
| GSE226455 |
Transcriptome analysis of wild type and transgenic plants with excessive stomatal lineage cells |
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| Relations |
| BioSample |
SAMN33574823 |
| SRA |
SRX19554663 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7075862_C2.txt.gz |
218.6 Kb |
(ftp)(http) |
TXT |
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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