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| Status |
Public on Dec 20, 2013 |
| Title |
Small RNA_root-treat |
| Sample type |
SRA |
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| Source name |
drought-treated root_small RNA
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| Organism |
Nicotiana tabacum |
| Characteristics |
cultivar: Honghua Dajinyuan
tissue: mixed roots of six leaves plants under 6 and 48h drought treatment
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tag library preparation for three root samples (three tobacco roots tag-based DGE libraries treated at three time points (0, 6 and 48 h) with 20% PEG6000) was performed in parallel by using the Illumina gene expression sample preparation kit. Each sample was sequenced in a single lane of a flow cell. Each lane includes library preparations from both DpnII and NlaIII digests for that sample. Sequences from DpnII digests start with GATC and those from NlaIII digests start with ATG. The samples for four small RNA libraries was used based on the result of physiological index measurement as follows: equal quantities (10 ug) of total RNA isolated from tobacco roots treated with two time points (6 and 48 h) were mixed together to construct the drought -treated small RNA library (Root-treat), and total RNA prepared from the control roots sample was used to construct the control small RNA library (Root-ck). In addition, we also constructed another two libraries from leaves and stems of control plants, respectively. These libraries were constructed using the Small RNA Sample Prep Kit (Illumina, San Diego, CA) as described by Tang et al.[PMID 22353177].
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
DGE sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Nicotiana benthamiana whole genome using SOAPdenovo. For small RNA sequencing data, the 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags. Length distribution of clean tags are then summarized. Afterwards, the standard bioinformatics analysis will annotate the clean tags into different categories and take those which can not be annotated to any category to predict the novel miRNA and base edit of potential known miRNA.
To compare the DE of gene across samples (N6H/NCK, N48H/NCK and N48H/N6H), the number of raw clean tags in each library was normalized to TPM (number of transcripts per million clean tags) to obtain normalized gene expression level. DE detection of gene or tag across samples was performed according to Audic S (Genome Research, 1997, 7:986-995). In addition to the P value, False Discovery Rate (FDR) was manipulated to determine differentially expressed genes. Briefly, among R differentially expressed genes, S of those really indicates differential expression, and V actually indicates no difference, which are false positive. If the error ratio Q = V/R must remain below a cutoff (5%), FDR should not exceed 0.05. After multiple testing between pairwise comparisons, we use "FDR≤0.001 and the absolute value of log2Ratio≥1" as the threshold to judge the significance of gene expression difference. More stringent criteria with smaller FDR and bigger fold-change value can be used to identify DEGs.
The relative change of individual miRNA families of detected reads for root-ck and root-treat and P-values of the t-test were calculated; differentially detected miRNA families were those with P-values <0.01.
Genome_build: Nicotiana benthamiana genome database (v.0.4.4)
Supplementary_files_format_and_content: *GeneExpression.txt: all expression genes in three DGE libraries for each Sample
Supplementary_files_format_and_content: *result_advance.txt: tab-delimited text files include clean tags values for each Sample
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| Submission date |
Dec 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
hongjun liu |
| E-mail(s) |
lhj20305@163.com
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| Organization name |
Sichuan Agricultural University
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| Street address |
211 Huimin Road
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| City |
Wenjiang,Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
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| Platform ID |
GPL16416 |
| Series (1) |
| GSE43058 |
A genome-wide functional investigation into the roles of differentially expressed genes and microRNAs, including 24 transcription factor families, in tobacco roots during the drought stress response |
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| Relations |
| SRA |
SRX212161 |
| BioSample |
SAMN01832289 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1055738_root-treatA_result_advance.txt.gz |
54.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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