ABSTRACT: SmMIP libraries using DNA from patients diagnosed with myeloid malignancies were generated in replicates and were sequenced on the NovaSeq SP platform (Illumina)
Project description:SmMIP libraries using bulk cell line DNA and DNA mixes were generated in replicates and were sequenced on the NovaSeq SP platform (Illumina)
Project description:Purpose: The goal of this study was compare the transcriptional profile of CD34+ AML stem/progenitors derived from newly diagnosed AML patients at diagnosis and after treatment with the anti-CD70 antibody cusatuzumab as a monotherapy on a single cell level. Methods: Barcoded cDNA from at least 977 CD34+ cells from patients C8 and C10 was prepared using the Chromium Single Cell 3′ Library (v2 Chemistry) & Gel Bead Kit on a Chromium Controller according to the manufacturer’s recommendations (10XGenomics). The barcoded cDNA was further processed into scRNA-seq libraries and sequenced on a NovaSeq 6000 instrument using NovaSeq Control Software v1.6 (Illumina). Libraries were sequenced with 100 cycle S1 flow cell kits using the following paired-end configuration: 26 bp Read 1, 91 bp Read 2. Results/Conclusion: Cusatuzumab monotherapy triggers gene signatures related to myeloid differentiation and apoptosis in CD34+ AML stem/progenitor cells
Project description:Over 16,000 nuclei were isolated from human postmartum brain frozen prefrontal cortex samples of alcoholic and control individuals. Libraries were prepared with 10X Genomics platform and sequenced using NovaSeq 6000.
Project description:Nuclei were isolated from human postmartum brain frozen dorsolateral prefrontal cortex samples of AUD and control individuals. Libraries were prepared with 10X Genomics platform and sequenced using NovaSeq 6000. Post-filtering and site integration resulted in 464, 716 nuclei for downstream analysis.
Project description:H1299 human lung adenocarcinoma cells were transfected with tRF3019a antisense inhibitor (tRF3019asi) or a negative control. Total RNA was extracted and polyA-enriched mRNA libraries were prepared and sequenced on the Illumina NovaSeq 6000 platform (paired-end, 150 bp). The goal was to identify genes and pathways regulated by tRF3019a.
Project description:CT26 cells with or without PHF8 knockout were processed using the High-Sensitivity Open Chromatin Profile Kit according to the manufacturer’s instructions.DNA was extracted using Tagment DNA Extract Beads, purified with NovoNGS DNA Clean Beads, and amplified by PCR. Libraries that passed quality control were sequenced on an Illumina NovaSeq X Plus platform.
Project description:CT26 cells with or without PHF8 knockout were processed using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit according to the manufacturer’s instructions.DNA was extracted using Tagment DNA Extract Beads, purified with NovoNGS DNA Clean Beads, and amplified by PCR. Libraries that passed quality control were sequenced on an Illumina NovaSeq X Plus platform.
Project description:Controlled human infection experiments enable longitudinal profiling of immune responses to a pathogen. 36 healthy volunteers aged 18-29 years, with no evidence of previous infection or vaccination, were inoculated with SARS-CoV-2 virus and quarantined for 14 days. Blood samples for RNA sequencing were collected into PAXgene tubes before virus challenge, 6 hours after challenge, daily thereafter for 14 days and on day 28. Mid-turbinate nose swabs for RNA sequencing were collected before virus challenge, and on days 1, 3, 5, 7, 10 and 14 after challenge, preserved in RNAprotect. 18 of 36 participants developed a replicative SARS-CoV-2 infection as evidenced by consecutive PCR-positive swabs for the virus. For every participant, blood RNA from selected days were extracted and depleted for genomic DNA and globin mRNA, before cDNA libraries were constructed using KAPA RNA HyperPrep with RiboErase kits. Libraries were sequenced on the Illumina NovaSeq 6000 platform using NovaSeq 6000 S4 Reagent Kits (200 cycles). Nose swab RNA samples were extracted and depleted for genomic DNA before cDNA libraries were constructed using KAPA mRNA HyperPrep Kits. Libraries were sequenced on the Illumina NextSeq platform the using the NextSeq 500/550 High Output Kit (75 cycles).
Project description:The goal of the experiment was to understand the epigenetic effects of PU.1 haploinsufficiency on pro-B cells. The RS4:11 cell line was edited both mono and biallelicaly via electroporation of Cas9 and guides. Following editing, aliquots of unedited (SPI1 +/+), mono (SPI1 +/-) and biallellicaly edited (SPI1 -/-) cells were lysed before undergoing the transposition reaction. After transposition, the ATAC-seq libraries were purified and then amplified via PCR. Libraries were sequenced using the Illumina Novaseq platform.
