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:We comprehensively investigated the neural-splicing using P19 cells, set up nine filtering conditions, and obtained 262 candidate exons (236 genes). Results of semi-quantitative RT-PCR in randomly selected 30 candidates suggested that 87% of the candidates were actually changed more than double compared with the undifferentiated and differentiated cells. GO analysis and pathway analysis also showed that these 236 candidate genes were highly involved in the neural events. These results suggested that our extraction of alternative exons was quite reasonable and successful. We have biological duplicates in this project. We essentially compared Day 7 (neural-differentiated) against Day0 (Undifferentiated)
2011-03-10 | E-GEOD-23710 | biostudies-arrayexpress
Project description:This dataset consists of 60 mRNA sequencing runs from full blood of 31 myotonic dystrophy type 1 patients, of which for 27 patients reliable data is available before and after 10 months of cognitive behavioural therapy.
>30 million 150 bp paired end reads were obtained with UMI-labeled adapters to facilitate filtering of PCR duplicates.
Via UMI-analysis we found samples with the aliases sample_01 and sample_02 to contain a very high number of PCR duplicates and recommend the use of these samples only with highest caution or not at all.
| EGAD00001008383 | EGA
Project description:ATAC sequencing of Tspan8posMHCIIlo, Tspan8posMHCIIhi, Tspan8negMHCIIlo and Tspan8negMHCIIhi mTECs was performed in biological duplicates.
2024-02-14 | GSE234363 | GEO
Project description:Human nontransformed retinal pigment epithelia RPE-PPM1D-T2 cells carrying a truncating mutation in exon 6 of the PPM1D were exposed to ionising radiation (3 Gy) and subsequently were grown in semisolid media for 8 weeks. Six spheroid clones (RPE-PPM1D-T2-SA clones 1-6) were recovered and then were cultivated in adherent conditions. DNA was isolated from asynchronically growing parental RPE-PPM1D-T2 and transformed RPE-PPM1D-T2-SA-1 to 6 cells and was subjected to whole exome sequencing. DNA sequencing libraries were prepared using KAPA EvoPlus Kit (Roche) and were sequenced on the NovaSeq 6000 system using NovaSeq S1 Reagent Kit v1.5, 200 cycles (Illumina) with mean coverage >35 DNA samples, respectively. DNA fastq files were mapped to the hg19 reference using Novoalign (novoalign_2.08.03). PCR duplicates were removed from the BAM files using Picard Tools (picard-tools 1.129), and variant calling was performed using GATK HaplotypeCaller (3.8). Copy number variations (CNV) were analyzed using CNVkit version 0.7.4. Areas with median coverage >20 were included in the analysis. RNA fastq files were mapped to the hg19 reference using STAR (STAR-2.5.2b). The PCR duplicates were removed using Picard Tools (picard-tools 1.129).
2024-04-05 | E-MTAB-13923 | biostudies-arrayexpress
Project description:Simulated oral microbiome with artificial duplicates
| PRJEB26333 | ENA
Project description:The project aimed to characterize the protein composition from 3 Pleistocene bone specimens (AR-7, AR-16, AR-30). Analysed extracts concern standard ZooMS tryptic digests (AR-7, AR-16, AR-30) and additional palaeoproteomic extracts (AR-30A and AR-30B). The latter concern two biological duplicates. All extractions were performed at the Department of Human Evolution, MPI-EVA (Germany) under sterile conditions. Analyses took place on a Q-Exactive Hybrid Quadrupole-Orbitrap MS.
2016-09-27 | PXD003208 | Pride
Project description:This dataset includes the whole-genome sequencing data from a study entitled "Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma". Whole-genome sequencing libraries were generated by PCR-free methods, and sequencing run was made in HiSeq X Ten machines. PCR duplicates-marked, indel-realigned, and base-recalibrarted BAM files are provided in our dataset.
| EGAD00001004793 | EGA
Project description:Gene duplication and deletion are pivotal processes shaping the structural and functional repertoire of genomes, with implications for disease, adaptation and evolution. We employed an experimental evolution framework partnered with high-throughput genomics to assess the molecular and transcriptional characteristics of novel gene copy-number variants (CNVs) in Caenorhabditis elegans populations subjected to varying intensity of selection. Here, we report a direct spontaneous genome-wide rate of gene duplication of 2.9 × 10-5 /gene/generation in C. elegans, the highest for any species to date. The increase in average transcript abundance of new duplicates arising under minimal selection is significantly greater than two-fold compared to single-copies of the same gene, suggesting that genes in segmental duplications are frequently overactive at inception. The average increase in transcriptional activity of gene duplicates is greater in MA lines that passed through single individual bottlenecks than in MA lines with larger population bottlenecks. Furthermore, there is an inverse relationship between the ancestral transcription levels of newly originating gene duplicates and population size, with duplicate copies of highly expressed genes less likely to accumulate in larger populations. The results demonstrate that there is a fitness cost of superfluous gene expression and purifying selection against new gene duplicates. However, on average, duplications also provide a significant increase in gene expression that can facilitate adaptation to novel environmental challenges.
2018-04-07 | GSE112821 | GEO
Project description:This dataset includes the high-throughput sequencing data from a study entitled "Clonal History and Genetic Predictors of Transformation into Small Cell Carcinomas from Lung Adenocarcinomas". Whole-genome sequencing libraries were generated by PCR-free methods, and sequencing run was made in HiSeq X or HiSeq 2500 machines. PCR duplicates-marked, indel-realigned, and base-recalibrarted BAM files are provided in our dataset.
| EGAD00001003315 | EGA