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: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: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: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:Mitochondrial DNA mutations in components of the electron transport chain disrupt mitochondrial activity and can alter how cells take up and utilize nutrients. To investigate how mtND6 (Complex I) mutations reshape the transcriptional profile of human pluripotent stem cells, we performed bulk RNA sequencing on hESCs carrying levels of mtND6 mutations: wild-type, 5%, 56%, and 77% heteroplasmy. All four lines were profiled in mTeSR+, and wild-type and 77% mutant hESCs were additionally profiled in Essential 8 (E8) medium to identify transcriptional changes robust to differences in culture nutrient composition. Each sample was sequenced in biological triplicate (n = 18). Total RNA was poly(A)-selected, and libraries were sequenced on an Illumina NovaSeq platform, paired-end read, 20 million reads per sample.
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:Primary human dermal fibroblasts were obtained from four young donors (ages 23–33) and five aged donors (ages 64–72) through the San Diego Nathan Shock Center (SD-NSC) Human Cell Models of Aging Core. Cells were cultured under standard conditions and subjected to bulk RNA sequencing to investigate age-associated transcriptional changes. Libraries were prepared using polyA selection and sequenced on the Illumina NovaSeq 6000 platform. Differential gene expression analysis was performed using the HOMER pipeline.
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.
