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:Bulk RNA sequencing was performed on central canal–associated spinal cord cells isolated from adult pig (Sus scrofa) and rat (Rattus norvegicus) spinal cords and expanded under ex vivo culture conditions. Libraries were sequenced on the Illumina NovaSeq 6000 platform using 150 bp single-end reads. Transcript abundances were quantified using Salmon (v1.x) against species-specific reference transcriptomes (pig: ss11; rat: rn6). This dataset enables cross-species analysis of transcriptional programs associated with proliferative activation and progenitor-associated states in the mammalian spinal cord.
Project description:MKN-45 gastric cancer cells were subjected to NNMT knockdown or negative control treatment and cultured in three independent biological replicates per group. Total RNA was extracted using TRIzol reagent, and RNA integrity was confirmed with RIN > 8.0. RNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads. Differential gene expression analysis was performed to identify transcriptomic changes induced by NNMT knockdown.
Project description:ATAC-seq was conducted to map open chromatin regions in five individual primary human melanocyte cultures. The ATAC libraries were sequenced using paired-end sequencing on an Illumina NovaSeq platform. In total, we sequenced 15 ATAC libraries from these five independent primary melanocyte cultures (C24, C27, C56, C140, C205), with three technical replicates for each culture.
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: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.
