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.
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)
Project description:ATAC sequencing of Tspan8posMHCIIlo, Tspan8posMHCIIhi, Tspan8negMHCIIlo and Tspan8negMHCIIhi mTECs was performed in biological duplicates.
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.
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.