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| Status |
Public on Jun 18, 2022 |
| Title |
Seedlings, bbx4-1 rep1 |
| Sample type |
SRA |
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| Source name |
seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col
tissue: seedlings
genotype: BBX4-1
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| Growth protocol |
Arabidopsis Col and bbx4-1 mutant seeling were grown in constant red light in a growth chamber at 22ºC for 4 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from approximately 80~100 mg powder of each sample using the RNeasy plant mini kit (Qiagen, www.qiagen.com) according to the manufacturer’s protocol.
The complementary DNA (cDNA) libraries were prepared according to Zhang et al. (2016) by performing a series of procedures, including poly(A) enrichment, RNA fragmentation, cDNA synthesis, linker ligation, size selection and PCR amplification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
BBX4-FPKM.txt
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| Data processing |
After trimming adapter sequences and filtering low-quality reads with Q < 20 from the 5' and 3' ends of the remaining reads, the clean reads were mapped onto the TAIR10 reference genome using hisat2 (version 2.1.0). Differential expression between accessions was assessed statistically using the R/Bioconductor package edgeR (v.3.0.8). Genes with P value < 0.05 and foldchange >1.5, as determined using edgeR, were identified as differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values
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| Submission date |
Jun 19, 2019 |
| Last update date |
Jun 18, 2022 |
| Contact name |
Xuncheng Wang |
| E-mail(s) |
1706380435@pku.edu.cn
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| Organization name |
Peiking University
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| Street address |
5 Yiheyuan Road
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL13222 |
| Series (1) |
| GSE132980 |
Transcriptomic analysis of B-box containing protein (BBX4)-regulated genes in response to light |
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| Relations |
| BioSample |
SAMN12094967 |
| SRA |
SRX6093635 |
| 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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