SHAMAN MOCK
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB34705 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The goal of this study was to titrate the amount of adapters for picogram amounts of ChIP DNA to determine the optimal conditions for library generation. H3K4me3 ChIP DNA from human Raji cells was diluted to the indicated amount and sequencing libraries generated using a range of adapter concentrations. The optimal adapter:DNA ratios were sequenced in technical duplicate to determine the reproducibility at each starting ChIP DNA amount. Additionally, for two samples we altered the number of cycles during the PCR amplification to determine the effect of PCR on library complexity and read duplicates.
2020-08-20 | GSE71700 | GEO
Project description:Gene expression profiles generated with RNA sequencing can be biased by RNA amount and methods utilised for cDNA library generation. Polymerase chain reaction (PCR) amplification can generate high PCR duplicate proportions and introduce bias in transcript counts. In this study, we investigate the impact of input amount and PCR cycle number on the PCR duplication rate and on the RNA-seq data quality. We used a range of inputs (1 ng - 1,000 ng) and assessed the PCR duplication rate using unique molecular identifiers (UMIs). For broader applicability, we sequenced the data on four different short-read sequencing platforms: Illumina NovaSeq 6000, Illumina NovaSeq X, Element Biosciences AVITI, and Singular Genomics G4. We highlight the limitations of using input amounts below 125 ng and the advantages for using UMIs for deduplication. We contrast the data obtained from different sequencers and discuss the benefits and drawbacks of using Illumina library conversion kits.
2024-03-13 | GSE261432 | GEO
Project description:Bacterial mock community, species derived from eight different genera, including Alcaligenes sp. (Accession number JF698681), Arthrobacter sp. (Accession number FJ851358), Bacillus sp. (Accession number KU556329), Cupriavidus sp. (Accession number KU
| PRJNA623498 | ENA
Project description:We recently identified recurrent mutations of cohesin complex in myeloid neoplasms through whole-exome sequencing analysis. RAD21 is one of the main components of the cohesin complex. In this study, to investigate the biological impact of wild-type RAD21 on Kasumi1 cells harboring RAD21 mutation, Kasumi1 cells were retrovirally transduced with either mock or wild-type RAD21, and expression array was performed.
2013-07-16 | GSE47641 | GEO
Project description:We recently identified recurrent mutations of cohesin complex in myeloid neoplasms through whole-exome sequencing analysis. RAD21 is one of the main components of the cohesin complex. In this study, to investigate the biological impact of wild-type RAD21 on Kasumi1 cells harboring RAD21 mutation, Kasumi1 cells were retrovirally transduced with either mock or wild-type RAD21, and expression array was performed. Expression analysis was performed for mock- or wild-type RAD21-transduced Kasumi-1 cells in triplicate. The experiment was performed twice independently.
2013-07-16 | E-GEOD-47641 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived H2O2-treated HCC transcriptome profiling (RNA-seq) to NGS-derived mock-treated HCC transcriptome profiling. Methods: HCC mRNA profiles of mock-treated Huh7 cells and H2O2-treated Huh7 cells were generated by deep sequencing, in duplicate, using Illumina Pipeline (CASAVA) v1.8.2. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: RNA-seq data validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.90. Conclusions: We conclude that our study represents the first detailed analysis of H2O2-treated HCC cells transcriptomes compared to mocke-treated HCC cells, with biologic replicates, generated by RNA-seq technology.
2021-01-30 | GSE109915 | GEO
Project description:In this study, RNA-seq analysis was performed to generally understand the circRNA profiles of mock-infected and HCMV-infected HELF cells. Totally, 27,409 and 35,515 host circRNAs were identified in mock-infected and HCMV-infected HELF cells by RNA-seq respectively. Among them, 278 circRNAs were significantly modified filtrating by a threshold value of >2 (or <-2) fold-change and q-value <0.05. GO and KEGG pathway enrichment analysis suggested that the remarkably changed circRNAs might play important roles in viral entry, cell proliferation, and inhibition of apoptosis. Verification of four selected circRNAs ( circSP100, circMAP3K1, circTRIO, and circPLEKHM1) was performed using RT-PCR and Sanger sequencing. Moreover, further verification of circSP100 was performed using northern blotting and RT-qPCR and proteins binding directly to circSP100 were purified using RNA antisense purification (RAP).
2020-09-05 | GSE138836 | GEO
Project description:In this study we developed metaproteomics based methods for quantifying taxonomic composition of microbiomes (microbial communities). We also compared metaproteomics based quantification to other quantification methods, namely metagenomics and 16S rRNA gene amplicon sequencing. The metagenomic and 16S rRNA data can be found in the European Nucleotide Archive (Study number: PRJEB19901). For the method development and comparison of the methods we analyzed three types of mock communities with all three methods. The communities contain between 28 to 32 species and strains of bacteria, archaea, eukaryotes and bacteriophage. For each community type 4 biological replicate communities were generated. All four replicates were analyzed by 16S rRNA sequencing and metaproteomics. Three replicates of each community type were analyzed with metagenomics. The "C" type communities have same cell/phage particle number for all community members (C1 to C4). The "P" type communities have the same protein content for all community members (P1 to P4). The "U" (UNEVEN) type communities cover a large range of protein amounts and cell numbers (U1 to U4). We also generated proteomic data for four pure cultures to test the specificity of the protein inference method. This data is also included in this submission.
2017-05-12 | PXD006118 | Pride