Project description: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:Single cell RNA sequencing (scRNA-seq) was performed with peripheral blood cells before (Day 0, T0), during nivolumab treatment (Day 7, T1; Day 21, T2), and when plasma EBV turned negative (Day 76, T3) in 1 patient (patient 7). scRNA-seq libraries were generated following the recommended protocol of the 3’ scRNA-seq 10X genomics platform and using v2 chemistry, and sequenced data was collected by illumina NovaSeq 6000 sequencing.
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:Bulk RNA sequencing was performed on neural stem/progenitor cell (NSPC) cultures derived from six adult human spinal cord donors (thoracic, lumbar, and conus regions). Samples were sequenced using the Illumina NovaSeq 6000 platform with paired-end 150 bp reads. Transcript abundances were quantified with Salmon (GENCODE v35 reference). This dataset supports the study “Aging and Clinical Exposures Shape Proliferation Dynamics of Adult Human Spinal Cord Neural Stem/Progenitor Cells,” providing a resource for examining donor- and region-specific transcriptional programs influencing NSPC proliferation.
Project description:We performed RNA-seq experiments on a total of 12 mouse immune organs, including spleen (SP), bone marrow (BM), lymph node (LN) and Peripheral blood mononuclear cell (PBMC). Briefly, RNA-Seq libraries were constructed after rRNA depletion using a NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB). The E6310L NEBNext Ultra RNA Library Prep Kit for Illumina（NEB, E7530S）(NEB) was used according to the manufacturer’s instructions and the cDNAs were sequenced with the Hiseq X10 platform(Illumina)
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: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.
Project description:This study evaluates the effects of 96h stimulus with Interleukin 4 (100 ng/mL) on the transcriptome of human umbilical cord blood derived mast cells. Through this approach, we identify upregulation of key intraepithelial mast cell-associated transcripts and downregulation of subepithelial mast cell-associated transcripts. Replicates are technical duplicates. Samples were sequenced on an Illumina NextSeq 500.
Project description:RNA-seq analysis of human endothelial cells overexpressing PTP4A1 and treated with Angiotensin II revealed transcriptional programs involved in angiogenesis and vascular stabilization. Libraries were prepared using QuantSeq 3′ mRNA-Seq and sequenced on Illumina NovaSeq.
