Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB10679 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR253532_1.fastq.gz | Fastqsanger.gz | |||
| DRR253532_2.fastq.gz | Fastqsanger.gz | |||
| DRR253533_1.fastq.gz | Fastqsanger.gz | |||
| DRR253533_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 709 |
Similar Datasets
Project description:Investigation of mRNA expression level changes in RWPE1 cells with AR,HOXC6 and NKX2-2 overexpression. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
2017-06-13 | GSE81232 | GEO
Project description:Our goal was to create a DNA chip that is as easy, convenient and inexpensive as an agarose gel. For a first generation solution, we describe a low cost, easy to use de novo synthesis oligonucleotide microarray technology that draws on the inherent flexibility of the maskless array synthesizer for in situ synthesis of thousands of photolithographically produced oligonucleotides covalently attached to a microscope slide. The method involves physically subdividing the slide into 1 x 1 mm 'millichips' that are hybridized to fluorescent RNA or DNA of biological origin, in a microfuge tube at an ordinary laboratory benchtop, rather than in dedicated hybridization chambers. Fluorescence intensity is then measured with a standard microxcope rather than sophisticated DNA chip scanners. For proof of principle, we measured changes in the transcriptome of Arabidopsis plants induced by growth in the presence of three major environmental abiotic stresses (temperature, light and water status), in all possible combinations. Validation by comparison with qRT-PCR showed a high correlation coefficient and analysis of variance indicated a high technical reproducibility. These experiments demonstrate that low cost DNA 'millichips' can be made and reliably used at the benchtop in a normal laboratory setting, without assistance of core facilities containing costly specialized instrumentation.
2012-04-12 | GSE37118 | GEO
Project description:Two fiber tissues harvested 10 days post anthesis from upland cotton trees grown under the same green house conditions except for different seasons of the year were used for RNA extraction. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer according to the manufacturer's instructions. The 35nt sequence tags from sequencing went through data cleaning first, which included getting rid of the low-quality tags and several kinds of contaminants from the 35nt tags. All clean tag sequences with copy numbers were then summarized into a fasta format file.
2011-07-01 | GSE27697 | GEO
Project description:Sequencing based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale mapping of DNA methylation have been employed, throughput has been a key limitation for most. To further facilitate the mapping of DNA methylation, we describe a protocol for gel-free multiplexed reduced representation bisulfite sequencing (mRRBS) that reduces the workload dramatically and enables processing of 96 or more samples per week. mRRBS achieves similar CpG coverage as the original RRBS protocol, while the higher throughput and lower cost make it better suited for large-scale DNA methylation mapping studies including cohorts of cancer samples. Libraries of 96 human samples
2012-08-29 | E-GEOD-40429 | biostudies-arrayexpress
Project description:Sequencing based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale mapping of DNA methylation have been employed, throughput has been a key limitation for most. To further facilitate the mapping of DNA methylation, we describe a protocol for gel-free multiplexed reduced representation bisulfite sequencing (mRRBS) that reduces the workload dramatically and enables processing of 96 or more samples per week. mRRBS achieves similar CpG coverage as the original RRBS protocol, while the higher throughput and lower cost make it better suited for large-scale DNA methylation mapping studies including cohorts of cancer samples.
2012-08-29 | GSE40429 | GEO
Project description:The genomic DNA of rearranged chromosome VIII (~900kb) of EC9 diploid strain was extracted from the gel of pulsed field gel electrophoresis (PFGE), and analyzed by array-CGH to identify it's amplified regions After PFGE, The ChrVIII DNA was purified from agarose gel and purified by column. Then the DNA was amplified by GenomePlex Whole Genome Amplification Kit for Array-comparative genomic hybridization.
2012-05-17 | E-GEOD-38034 | biostudies-arrayexpress
Project description:With the near eradication of poliovirus due to global vaccination campaigns, attention has shifted to other enteroviruses that can cause polio-like paralysis syndrome (now termed acute flaccid myelitis (AFM)). In particular, enterovirus D68 (EV-D68) is believed to be the main driver of epidemic outbreaks of AFM in recent years, yet not much is known about EV-D68 host interactions. EV-D68 is a respiratory virus but, in rare cases, can spread to the central nervous system to cause severe neuropathogenesis. We use genome-scale CRISPR screens to identify genes important for EV-D68 infection. A549 and U87-MG cells were stably transduced with lentiCas9-Blast (Addgene, #52962) and subsequently selected using Blasticidin. Then, 300 million cells that constitutively express Cas9 were transduced with lentiGuide-Puro from the Brunello library (MOI 0.3). Cells were then selected with puromycin, expanded to 3 billion cells, and then pooled together and cryofrozen in aliquots. One hundred million cells were thawed constituting over 1000× genome coverage worth of mutagenized library,expanded, and seeded for the screens. Each screen had over 500x genome coverage. The cells were infected with EV-D68 IL (BEI USA/2014/18952) (MOI 0.1). Virus-resistant colonies were harvested. The uninfected reference used was the unselected starting population. The unselected and selected cells were both processed with QIAamp DNA columns to purify the gDNA. A first round of PCR was used to amplify the guide RNA sequences encoded in the gDNA, followed by a second round of PCR to add the barcodes/adapters for amplicon sequencing. 2% agarose gels and a QIAquick gel extraction kit were used to purify the amplicons. The amplicons were then subjected to next-generation sequencing on a HiSeq instrument lane (Illumina) via Novogene.
2025-02-25 | E-MTAB-14765 | biostudies-arrayexpress
Project description:This dataset contains mass spectrometry data from 'Gel-assisted mass spectrometry imaging enables sub-micrometer spatial lipidomics'.
2024-05-16 | MSV000094777 | GNPS
Project description:Our goal was to create a DNA chip that is as easy, convenient and inexpensive as an agarose gel. For a first generation solution, we describe a low cost, easy to use de novo synthesis oligonucleotide microarray technology that draws on the inherent flexibility of the maskless array synthesizer for in situ synthesis of thousands of photolithographically produced oligonucleotides covalently attached to a microscope slide. The method involves physically subdividing the slide into 1 x 1 mm 'millichips' that are hybridized to fluorescent RNA or DNA of biological origin, in a microfuge tube at an ordinary laboratory benchtop, rather than in dedicated hybridization chambers. Fluorescence intensity is then measured with a standard microxcope rather than sophisticated DNA chip scanners. For proof of principle, we measured changes in the transcriptome of Arabidopsis plants induced by growth in the presence of three major environmental abiotic stresses (temperature, light and water status), in all possible combinations. Validation by comparison with qRT-PCR showed a high correlation coefficient and analysis of variance indicated a high technical reproducibility. These experiments demonstrate that low cost DNA 'millichips' can be made and reliably used at the benchtop in a normal laboratory setting, without assistance of core facilities containing costly specialized instrumentation. An average of three to four technical replicates and six biological replicates for each treatment and control group were performed resulting in a total of 457 individual millichip experiments for this study.
2012-04-11 | E-GEOD-37118 | biostudies-arrayexpress