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| Status |
Public on Feb 04, 2019 |
| Title |
L4440_rep2 |
| Sample type |
SRA |
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| Source name |
whole organism
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| Organism |
Caenorhabditis elegans |
| Characteristics |
growth: grown at 15 C during six days
diet: E.coli feeding
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| Treatment protocol |
Synchronization worms at the first larval stage were silenced by feeding for genes of the different components of integrator complex
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| Growth protocol |
Wild-type nematodes were obtained from the Caenorhabditis Genetic Center (CGC, University of Minesota). Worm populations were synchronized by “bleaching” with hypochlorite solution, maintained in M9 medium during 20 hours to allow hatching eggs and synchronization at the first larval stage (L1). Then, worms were grown in plates seeded with the corresponding RNAi clones and they were kept at 15ºC during six days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
mirVana (miRNA Isolation Kit, Ambion), and treated with DNase I (Qiagen) following manufacturer’s instructions.
Sequencing libraries were prepared by following the TruSeq RNA Library (LS) Preparation Kit v2 (Illumina Inc., San Diego, CA) from 1 ug of totalRNA (after rRNA depletion with RiboZero H/M/R protocol).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence and low-quality sequence with TrimGalore default parameters
Clean reads were mapped to c.elegans whole genome (WBcel235.85) with Tophat2 (v2.1.1 & default parameters). Then, resulting .bam file was sorted by position and indexed with Samtools.
Bam files were processed with FeatureCounts tool (Liao et al., 2014) in order to obtain raw counts on exonic features, provided by the GTF file.
Quantitative differential expression analysis between conditions was performed both by DESeq2 (Love et al., 2014) and edgeR (Robinson et al., 2010) implementations, to compare all groups in pairs to analyze the effect of the two variables of this study: food sources (E. coli diet vs B. subtilis diet) and growth temperatures (15ºC vs 20ºC vs 25ºC). Both of them, implemented as R Bioconductor packages, perform read-count normalization by following a negative binomial distribution model. In order to automate this process and facilitate all group combination analysis, the SARTools pipeline (Varet et al., 2016) was used.
Resulting charts, containing raw and normalized data were annotated with additional data from Biomart, WormBase and the org.Ce.eg.db databases.
Gene Ontology enrichment analysis was performed for common up/down regulated genes by using clusterProfiler package (Yu et al., 2012) through its enrichGO tool.
The regularized log2 transformation (rlog) data was represented into a 2-dimension Principal Component Analysis (PCA) plot, by tacking DESeq2 expression values
Sample-to-sample Euclidean distances were calculated from the rld data and represented in a heatmap, showing the adjacent clustering information
Genome_build: WBcel235.85
Supplementary_files_format_and_content: The tab delimited files with extension .counts contain raw counts data, generated with FeatureCounts software
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| Submission date |
Feb 25, 2018 |
| Last update date |
Feb 04, 2019 |
| Contact name |
María de Toro |
| E-mail(s) |
mthernando@riojasalud.es
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| Organization name |
Centro de Investigación Biomédica de La Rioja
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| Department |
Genomics & Bioinformatics Core Facility
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| Street address |
C/Piqueras 98
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| City |
Logrono |
| State/province |
La Rioja |
| ZIP/Postal code |
26006 |
| Country |
Spain |
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| Platform ID |
GPL18730 |
| Series (1) |
| GSE111083 |
C. elegans total RNA profiles of worms treated with RNAi for different Integrator complex |
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| Relations |
| BioSample |
SAMN08605713 |
| SRA |
SRX3741120 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3021852_L4440_rep2.counts.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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