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| Status |
Public on Nov 24, 2024 |
| Title |
miRNA Caenorhabditis elegans-control-rep2 |
| Sample type |
SRA |
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| Source name |
whole individual
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: wild type
treatment: untreated
treatment: control
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| Treatment protocol |
CdCl2 was dissolved to 1000 μM as the standard solution and gradiently diluted to 60 μmol/L; and the L4-larvae of C. elegans was exposed to CdCl2 at this concentration mixed with NGM and then added with OP50 with the colony forming units (CFUs) of 4 × 106 at 20 °C.
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| Growth protocol |
Wild type N2 nematodes grew in standard NGM medium.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For per 50-100mg tissue sample, 1ml TRI REAGENT was added and an electric homogenizer used to mix it. After that, the sample was incubated for 5 minutes at 15 to 30℃ to completely dissociate the nucleic acid protein complex. Add 0.2ml chloroform to 0.2ml chloroform was added in per 1ml mixture, and close the tube cap tightly. After shaking the tube vigorously by hand for 15 seconds, it was incubated at 15 to 30℃ for 2 to 3 minutes. Centrifuge at 12000xg for 15 minutes at 4℃. After that, the mixture will be divided into the lower red phenol-chloroform phase, the middle layer and the upper colorless water phase. The RNA is all distributed in the water phase. The volume of the water phase is approximately 60% of the TRI REAGENT reagent added during the homogenization. Transfer the aqueous phase to a new centrifuge tube. The aqueous phase is mixed with 0.5ml isopropanol to precipitate the RNA. After mixing, it was incubated at 15 to 30°C for 10 minutes, and centrifuged at 12000xg at 4℃ for 10 minutes. Remove the supernatant, and add at least 1ml 75% ethanol to every 1ml mixture to wash the RNA precipitate. After shaking, centrifuge at 7500xg at 4℃ for 5 minutes. Remove the ethanol solution and dry the RNA pellet in the air for 5-10 minutes. When dissolving RNA, add RNase-free water and pipe repeatedly with a gun several times, and then incubate at 55 to 60°C for 10 minutes. The obtained RNA solution was stored at -70℃.
The library of miRNA of C. elegans was constructed using Multiplex Small RNA Library Prep Set for Illumina (E7508L, New England Biolabs, Netherlands). After degrading to ssDNA, it was captured in Illumina flow cell and conducted in situ amplification. According to the manufacturer’s operating manual, it was sequenced on the platform of Illumina NextSeq 500 (50 cycles). Other steps were similar to the mRNA sequencing.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
After quality control by FastQC (0.11.9) and discarding 3’ and 5’ adapter by Cutadapt (3.4) and as well as short fragments (≤20bp) in reads, the trimmed data was aligned to reference genome (WBcel235) by Hisat2 (2.2.1) and then determined whether to use its results for further analysis according to the quality. The StringTie (2.1.5) software was applied to estimate transcription abundance and get the count data of genes and transcripts. The Fragments per kilobase of transcript per million mapped reads (FPKM) in gene and transcript level was calculated by “Ballgown” of the R package; while the average FPKM of gene and transcript in treat or control group less than 0.1 was excluded. After exclusion, the FPKM value in gene level was used to conduct the spearman correlation analysis for validation of the samplesconcordance, which the spearman correlation should greater than 0.9, according to the standard of ENCODE (https://www.encodeproject.org). Then, the count data of genes and transcripts were employed to explore the differentially expressed genes (DEGs) and differentially expressed transcripts using R package “DESeq2”, with the standards of P < 0.05 and |log2FC| > 0.585. According to the file of gene transfer format (Caenorhabditis_elegans.WBcel235.103.gtf, GTF file, http://www.ensembl.org/), the protein-coding RNA (mRNA) and lncRNA were identified. CircRNAs were identified and quantitated by the software of bowtie2 (2.4.2) and find_circ (1.2). Count data of circRNA were used to perform differentially expressed analysis for circRNA using “edgeR”of R package with the standards of P < 0.05 and |log2FC| > 0.585. The differentially expressed mRNAs (DEmRNAs), lncRNA (DElncRNAs) and circRNAs (DEcircRNAs) were prepared for further analysis.
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include count, CPM values for each Sample.
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| Submission date |
Nov 27, 2021 |
| Last update date |
Nov 24, 2024 |
| Contact name |
Panpan Wang |
| E-mail(s) |
[email protected]
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| Organization name |
郑州大学
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| Department |
College of Public Health
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| Street address |
郑州市高新区科学大道100号郑州大学
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| City |
Zhengzhou |
| State/province |
1995-07-13 |
| ZIP/Postal code |
450001 |
| Country |
China |
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| Platform ID |
GPL19757 |
| Series (2) |
| GSE189664 |
Whole transcriptome sequencing explored the toxic effect of cadmiun on Caenorhabditis elegans [miRNA-seq] |
| GSE189666 |
Whole transcriptome sequencing explored the toxic effect of cadmiun on Caenorhabditis elegans |
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| Relations |
| BioSample |
SAMN23470158 |
| SRA |
SRX13242131 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5705705_2-2-microRNA_CPM.txt.gz |
3.1 Kb |
(ftp)(http) |
TXT |
| GSM5705705_2-2-microRNA_countsdata.txt.gz |
1.8 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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