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: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:We aimed to study the impact of bacteria-derived metabolites in solid organ transplantation. The short-chain fatty acid butyrate was administered using a new drug-delivery method developed by Wang et al. (https://doi.org/10.1038/s41551-022-00972-5). This system is based on a micelle platform that carries and protects butyrate (ButM) from degradation in the upper gastrointestinal tract, to lower distal portions of the gut. Mice (adult B6 females) were treated for 21 days with ButM (100mg/mL) or 1x PBS. Splenic Ly6Chi CD11b+ monocytes were sorted for bulk RNAseq using the Takara SMART-Seq mRNA LP and Unique Dual Index kits. Libraries were sequenced using the Illumina NovaSeq 6000 platform.
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: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:Methods: Mouse bladder tumor organoids with Trp53, Pten, Rb1 mutation and Myc, KrasG12D amplification were treated with 10μM SRT1720 and Vehicle for 12 hours respectively. RNA libraries of SRT1720 and vehicle treated mouse bladder organoids were constructed according to standard Illumina protocols, and bulk RNA-seq were performed using Illumina NovaSeq 6000 sequencing platform.
Project description:The goal of the experiment was to identify which genes are differentially expressed between the unedited and SPI1-edited populations. The RS4:11 cell line was edited both mono and biallelicaly via electroporation with guides and Cas9. Following editing, RNA from unedited (SPI1 +/+), mono (SPI1 +/-) and biallellicaly edited (SPI1 -/-) cells were extracted through the Direct-zol RNA Microprep kit. cDNA libraries for sequencing were then prepared using the TruSeq Stranded mRNA Library Prep Kit and the IDT for Illumina-TruSeq RNA UD Indexes (Illumina). Samples were then sequenced on the Illumina NovaSeq platform.
Project description:Mice formed tumors either after an Hprt-Cre-initiated translocation between Ewsr1 and Atf1 genes on chromosomes 11 and 15. From tumor genomic DNA, libraries were generated and sequenced on an Ilumina NovaSeq instrument to measure copy number variation.
Project description:Purpose: 1. Compare transcriptomes of hESC-derived MSCs (EMSCs) and somatic MSCs (SMCS); 2. Reveal transriptomic profiles of EMSCs post injection into mouse blastocyst. Methods: For bulk seq on cultured human MSCs, mRNA was isolated using RNeasy Mini Kit (QIAGEN) and libraries was constructed using an Illumina kit, and then sequenced on NovaSeq platform. For single cell (sc) RNAseq on cultured human MSCs, cells were dissociated and lysed in the Oil-droplet Single Cell Capture System (Nadia Dolomite) and libraries were constructed using Nextera kits (Illumina), and then sequenced on Hiseq 150PE (Illumina). For EMSCs injected into mouse blastocyst, 30~70 embryos were pulled and lyzed in 10uL of Lysis Buffer for SmartSeq. Results: 1. Both in bulk and in single cell level, all types of MSCs share typical common markers; 2. Unignorable differences exhist among hES-derived and somatic MSCs; 3. Rapid mRNA profile shifts in metabolism, cellular skeleton, and immunoregulatory response happen in hES-derived MSCs post injection to mouse embryos. Conclusions: These experiments reveal transcriptomic alterations of EMSCs after injection into mouse blastocyst and transcriptomic profiles of human MSCs from different sources.
