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| Status |
Public on Apr 19, 2019 |
| Title |
CK2 |
| Sample type |
SRA |
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| Source name |
control_root cells
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype/variation: wild type
age: 5-day-old
treated with: none (control)
tissue: root
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| Treatment protocol |
Narciclasine was purchased from Sigma-Aldrich (http://www.sigmaaldrich.com/catalog/product/ sigma/n9789?lang=zh®ion=CN) with the CAS number 29477-83-6. For narciclasine treatment, 5 day-old seedlings were transferred to the plates containing 1/2 MS medium with or without 0.5 µM narciclasine and incubated for 2 or 12 hr.
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| Growth protocol |
Seeds were surface sterilized with 70% ethanol containing 0.05% Tween 20 for 30 seconds and then 15% sodium hypochlorite for 15 min, and rinsed at least three times with sterilized water before sowing on agar plates of 1/2 × MS medium (pH5.7) containing 1% (W/V) sucrose, 0.8% (W/V) agar. After stratification for 4 days at 4 ℃, the plates were placed vertically in a climate chamber at 21～22 ℃ under 200 µM m-2s-1 light conditions (16/8 h light cycle) for 5 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
At each time point, total RNA was extracted with Trizol (Invitrogen) from 3 mm samples of excised root tips (100 mg), and RNA quality was monitored on 1% agarose gels. RNA purity was analyzed with a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Prior to differential gene expression analysis for each sequenced library, the read counts were adjusted by edger program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.12.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2 (Fold change) of 1 were set as the threshold for significantly differential expression.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Apr 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Na Xiaofan |
| E-mail(s) |
nxf-0324@163.com
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| Organization name |
Ningxia univertisty
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| Department |
school of life science
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| Street address |
Helanshan west road
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| City |
yinchuan |
| State/province |
Ningxia |
| ZIP/Postal code |
750021 |
| Country |
China |
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| Platform ID |
GPL17639 |
| Series (1) |
| GSE80815 |
Transcriptomic analysis reveals the early signaling events of narciclasine in Arabidopsis root apex |
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| Relations |
| BioSample |
SAMN04880535 |
| SRA |
SRX1716761 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2138303_CK2.txt.gz |
254.7 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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