Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12183032.fastq.gz | Fastqsanger.gz | |||
| SRR12183033.fastq.gz | Fastqsanger.gz | |||
| SRR12183034.fastq.gz | Fastqsanger.gz | |||
| SRR12183035.fastq.gz | Fastqsanger.gz | |||
| SRR12183036.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:We investigated the toxicity of soil samples derived from a former municipal landfill site in the South of the Netherlands, where a bioremediation project is running aiming at reusing the site for recreation. Both an organic soil extract and the original soil sample was investigated using the ISO standardised Folsomia soil ecotoxicological testing and gene expression analysis. The 28 day survival/reproduction test revealed that the ecologically more relevant original soil sample was more toxic than the organic soil extract. Microarray analysis showed that the more toxic soil samples induced gene regulatory changes in twice as less genes compared to the soil extract. Consequently gene regulatory changes were highly dependent on sample type, and were to a lesser extent caused by exposure level. An important biological process shared among the two sample types was the detoxification pathway for xenobiotics (biotransformation I, II and III) suggesting a link between compound type and observed adverse effects. Finally, we were able to retrieve a selected group of genes that show highly significant dose-dependent gene expression and thus were tightly linked with adverse effects on reproduction. Expression of four cytochrome P450 genes showed highest correlation values with reproduction, and maybe promising genetic markers for soil quality. However, a more elaborate set of environmental soil samples is needed to validate the correlation between gene expression induction and adverse phenotypic effects.
2012-04-16 | GSE37154 | GEO
Project description:Root transcriptomes of acidic soil adapted rice genotypes viz. Sahbhagi Dhan (SD) and Chakhao Poreiton (CP) was done in response to low phosphorus (P) levels. RNAseq approach after 15 days of low P treatment was employed to understand long term molecular processes involved in low P tolerance. Note: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
2015-06-08 | E-MTAB-4431 | biostudies-arrayexpress
Project description:Purpose: The goals of this study is to determine the best method of gene expression quantification (RNA-seq, Microarray, NanoString) and amplification kits adapted to low-input and/or low-quality RNA samples (FFPE samples) Methods: Mouse bladder cancer cell line (mouse bladder cancer cell line, BC57) and mouse normal mouse normal urothelium were fixed in formalin and embedded in paraffin (FFPE), andfesh frozen (FF) in liquid nitrogen. The total RNA of these 4 samples were tested by 3 technologies (NanoString, RNA-seq and Microarray) and the results were compared to its reference (high-quality and high-input RNA of mouse bladder cancer cell line and mouse normal mouse normal urothelium). For NanoString with low-input RNA samples, each sample was tested by NanoString quantification after amplification by SMARTer Stranded Total RNA-Seq Kit - Pico Input mammelian and Ovation SoLo NuGEN RNA-seq System, and NanoString based on PCR approach with three input quantities: 50pg, 250pg and 2ng of total RNA, except for NanoString quantification after amplification by SMARTer Stranded Total RNA-Seq Kit - Pico Input mammelian kit for which the minimum recommended quantity was 250pg of total RNA. NanoString direct quantification was also done for FF and FFPE samples at high amount (50ng of total RNA) and results obtained from FF samples were considered as the reference. To determine which is the method for NanoString technology, low-input and low-quality RNA samples, we performed NanoString control quality metrics, principal component analysis, and a differential analysis between the mouse bladder cancer cell lines and the mouse normal mouse normal urothelium for each input quantity, amplification method and method of sample preservation (FF or FFPE). Results: The NanoString based PCR based approach is recommended for quantification of gene expression of FFPE and FF samples from 250pg of total RNA. However, NanoString quantification after amplification by SMARTer Stranded Total RNA-Seq Kit - Pico Input mammelian and Ovation SoLo NuGEN RNA-seq System is not recommended for FF and FFPE from low-input samples.
2024-07-19 | GSE117670 | GEO
Project description:Intense selective breeding of broiler breeds of chickens has resulted in suboptimal egg production in broiler breeder hens. Ad libitum feeding which leads to excessive and disorganized follicular growth exacerbates this reproductive phenotype. One strategy used to improve broiler breeder hen reproductive efficiency is restricted feeding. In this study, we sought to identify transcriptional changes which translate level of dietary intake to increased follicle selection. Broiler breeder hens were raised according to commercial guidelines until 28 weeks of age and then randomly assigned to an ad libitum diet (FF) or continued on a restricted diet (RF) for 6 weeks. Following dietary treatment, granulosa cells from growing 6-8 mm follicles from FF hens (n=3) and RF hens (n=3) were collected, RNA was extracted, and samples were processed for RNA-sequencing on Illumina NextSeq 500. Transcriptomes of granulosa cells from 6-8 mm follicles were sequenced to identify transcriptional differences in the population from which follicles are selected into the preovulatory stage. FastQ files were first processed through trim-galore and reads were aligned to the Galgal6 genome using the RNA-seq aligner, STAR. A cluster analysis using hclust in R identified a FF sample as an outlier and this sample was removed from the analysis. Differential expression analysis was conducted using DeSEQ2 and resulted in 350 differentially expressed genes. Several genes involved in follicle selection were upregulated in prehierarchal follicles of FF hens, suggesting an effect of dietary treatment at early stages in follicle development.
2021-09-23 | GSE175887 | GEO
Project description:The present invention relates to methods for determining soil quality, and especially soil pollution, using the invertebrate soil organism Folsomia candida also designated as springtail. Specifically, the present invention relates to a method for determining soil quality comprising: contacting Folsomia Candida with a soil sample to be analysed during a time period of 1 to 5 days; isolating said soil contacted Folsomia Candida; extracting RNA from said isolated soil contacted Folsomia Candida; determing a gene expression profile based on said extracted RNA using microarray technology; comparing said gene expression profile with a reference gene expression profile; and determing soil quality based expression level differences between said gene expression profile and said control expression profile.
2014-07-19 | GSE59588 | GEO
Project description:In this study we have performed expression analysis using paired FF-FFPE glioma samples. We show that expression data from FFPE glioma material is concordant with expression data from matched FF tissue, and can be used for molecular profiling in gliomas. In this study we have performed expression analysis using 55 paired FF-FFPE glioma samples (HU133 plus 2.0 arrays (FF) and Human Exon 1.0 ST arrays (FFPE)). The most informative probe sets were selected based on variance This Series contains the FFPE data only. FF data set was previously submitted (GSE16011).
2012-06-30 | E-GEOD-30472 | biostudies-arrayexpress
Project description:This study was performed to evaluated RNA extraction and gene expression analysis of FFPE specimen stored for more than 20 years. Using long time stored FFPE material; large retrospective studies correlating molecular features with therapeutic response and clinical outcome, can be performed. Quantitative PCR (qPCR) was used to evaluate RNA extraction methods and to compare gene expression profiles of FFPE and fresh frozen (FF) tissue. Extracted RNA was subsequently subjected to microarray analysis and compared to qPCR data. The Ambion RecoverAll kit appears to be particularly suited for RNA extraction of long time stored FFPE tissues. Gene expression analysis using Affymetrix platform displayed a high degree of correlation for endogenous control genes comparing FF and FFPE tissues. We conclude that high quality gene expression signatures can be recognized using Affymetrix gene expression platform on FFPE tissue stored for more than 20 years. However, a general interpretation must be done with caution as different FFPE procedures have varying effects on RNA quality. Three RNA extraction methods from Roche (Basel, Switzerland), Ambion (Austin, TX, USA) and Qiagen (Hilden, Germany), designed for FFPE material was used. The methods were compared using qPCR. For the qPCR analysis, two different concentrations of input cDNA were used (20ng and 100ng) and 32 human endogenous control genes were examined. RNA from the Ambion FFPE kit was further analyzed by using microarray. Amplification of RNA prior to microarray analysis was performed using Nugen technologies (San Carlos, CA, USA). Nugen has developed amplification kits both for FFPE and FF materials: WT- ovation FFPE RNA amplification System V2 (Nugen FFPE), Ovation FF RNA Amplification System V2 (Nugen V2 FF) and Ovation FF Pico RNA Amplification System (Nugen PICO FF). The Nugen FFPE kit, designed for FFPE material was only used for FFPE tissue. The Nugen Pico FF kit, designed to target small amounts of FF RNA (>500 pg) and the Nugen V2 FF kit designed to target total FF RNA, were only used for FF tissue. Affymetrix standard amplification protocol (Affy FF) designed for FF RNA was also included as the standard method for amplification.
2011-09-14 | E-GEOD-31735 | biostudies-arrayexpress
Project description:We profiled human DLBCL tumor samples (FF and FFPE matched pairs) to identify the transcripts which are less prone to degradation in FFPE Keywords: DLBCL FF FFPE RNA profiles of human FF and FFPE samples (DLBCL)
2011-03-16 | E-GEOD-18377 | biostudies-arrayexpress
Project description:Broiler breeder hens given ad libitum access to feed have excessive ovarian follicle development with poor reproductive outcome. One strategy to improve their reproductive capacity is by restricting their feed intake. In this study, we sequenced the liver transcriptomes of hens fed ad libitum (FF, n=3) and hens given a restricted fed diet (RF, n=3) to get insight into possible signaling pathways affected by dietary treatment. Hens were reared according to commercial guidelines until 38 weeks of age, when they were assigned to either FF or continued on RF for 6 weeks. Liver mRNA samples from three hens in each group were sequenced using the Illumina HiSeq 2000/2500 technology at a depth of 100 bp. The sequencing quality of the data was determined using FastQC. Reads were aligned to UCSC Galgal4 using Tophat (v2.0.13) and transcripts were counted using cuffdiff (v.2.2.1). A multidimensional scaling plot (MDS plot) was generated to evaluate the variance among biological replicates and identified one FF hen as a sample outlier and this animal was removed from the analysis. Differential gene expression analysis was conducted using edgeR and yielded 120 differentially expressed genes. This study identified transcriptional differences in the livers of FF and RF hens which may signal metabolic status to the ovary.
2022-02-03 | GSE175780 | GEO