Ontology highlight
ABSTRACT:
PROVIDER: PRJNA495928 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:FDA metagenomic data sets related to food safety
| PRJNA390622 | ENA
Project description:Cells were treated as described in the material and methods section of the manuscript. Briefly, RNA-seq experiments were performed with sorted populations with an size of about 10_E6 Corynebacterium glutamicum cells. As a reference data set RNA-Seq. analysis of unsorted cells were conducted (n=3, induced vs uninduced =2, 2 x 3 = 6 data sets). For the sorting and the counter-silencer based prophage induction, RNAprotect and RNAlater were used and for each agent data sets with two biological relicates were generated (n = 2, RNAprotect + RNAlater = 2, induced vs uninduced = 2, 2 x 2 x 2 = 8 data sets). One data set was generated using 10_E5 cells (n = 1, induced vs uninduced =2, 2 x 1 = 2 data sets) For the subpopulation caused by iron-shift experiments RNAprotect was used (n = 3, positive vs negative, 3 x 2 = 6 data sets). In sum 26 data sets are uploaded. Each consist of two fastq files (due to paired-end sequencing).
2018-09-15 | E-MTAB-6809 | biostudies-arrayexpress
Project description:Peripheral blood lymphocytes from a total of 15 healthy individuals without history of cancer (NoCa) were immortalized with Epstein-Barr virus. Cells were exposed to mock treatment (Mock), ultra-violet radiation (UV), or ionizing radiation (IR). For UV radiation treatment, cells were exposed to 10 J/m^2 and harvested for RNA 24 hours later. For IR treatment, cells were exposed to 5 Gy of IR and harvested for RNA 4 hours later. For example, NoCa1-Mock refers to cells from healthy patient 1 exposed to mock treatment. The published manuscript (NAR 32:4786, 2004) can be found at http://nar.oupjournals.org/cgi/content/abstract/32/16/4786 Data were analyzed with Affymetrix MAS version 4.0. Normalization – A reference data set was generated by averaging the expression of each gene over all data sets. The data for each hybridization were compared with the reference data set in a cube root scatter plot. A linear least-squares fit to the cube root scatter plot was then used to normalize each hybridization. Keywords: repeat sample
2004-11-16 | GSE1977 | GEO
Project description:This data set contains ChEC-seq binding profiles of various TF in yeast strains deleted of other TFs. Each sample has a pair-end sequencing file and a processed file (.out) is a genomic signal track after alignment to S.cerevisiae (R64) reference genome. Mapping was done using the read end. This dataset also contains raw and processed MNase-seq data files for nucleosome occupancy. Data related to manuscript: The architecture of binding cooperativity between densely bound transcription factors.
2023-08-01 | GSE222268 | GEO
Project description:Baltic Sea reference metagenome assembly and data sets; transect and redoxcline.
| PRJEB22997 | ENA
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized system-based cell pathway analysis. The purposes of this study were to compare and analyze the expression differences of skin squamous cell line A431 in stem cells after Mir-22 deletion. Methods: mRNA profiles of control and case cells were generated by deep sequencing, in duplicate, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods:Bowtie2 to map clean reads to reference gene and use HISAT to reference genome.Bowtie2 parameters forSE reads:-q--phred64--sensitive--dpad0--gbar and HISTAparameters forSE reads:-p8--phred64--sensitive-I1-X 1000. qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 24 million sequence reads per sample to the human genome (build hg19) and identified 17000 transcripts in control and case cells with RSEM workflow. Approximately 5% of the transcripts showed differential expression between control and case cells, with a fold change ≥1.5 and p value <0.01. Altered expression of 10 candidate genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.
2020-08-15 | GSE156255 | GEO
Project description:This experiment set contains the raw data for 8 arrays that were used in the genomic typing of the pre- and post-mouse H. pylori strains SS1 and SS2000. 10700 is the pre-mouse clinical isolate of SS1 and PMSS2000 is the pre-mouse clinical isolate of SS2000. gDNA from these strains were labeled and hybridized to H. pylori microarrays as described in Salama et al. {Salama et al. 2000 PNAS 97:14668-73}. In each case the test gDNA sample was labeled with Cy5 (red) and this was hybridized with Cy3 (green) labeled reference DNA of equal amount. The reference DNA consisted of equal amounts of gDNA from the two H. pylori strains used to make the H. pylori microarray, 26695 and J99. This data was used for the manuscript: L. J. Thompson, S. J. Danon, J.E. Wilson, J. L. O'Rourke, N. R. Salama, S. Falkow, H. Mitchell, and A. Lee. (2004) Chronic Helicobacter pylori infection in C57BL/6 and BALB/c mice using SS1 and a newly identified mouse-adapted strain (SS2000). Infect. Immun. (in press).
2005-11-03 | E-SMDB-1734 | biostudies-arrayexpress
Project description:Eosinophilia–myalgia syndrome (EMS) is characterized by subacute onset of myalgias and peripheral eosinophilia, followed by chronic neuropathy and skin induration. The EMS epidemic in 1989 was linked to L-tryptophan consumption originating from a single source. Following the Food and Drug Administration (FDA) ban on the sale of L-tryptophan, the incidence of EMS declined rapidly. Moreover, no new cases have been published since the FDA ban was lifted in 2005. We report the clinical, histopathological and immunogenetic features of a new case of L-tryptophan-associated EMS along with evidence of activated transforming growth factor-ß and interleukin-4 signaling in the lesional skin. 6 samples were analyzed to include EMS patient and two replicates along with three normal controls
2012-01-28 | E-GEOD-26934 | biostudies-arrayexpress