Colon tissue lysates from DSS-induced acute colitis in Twist2Cre;Lkb1fl/+ or Lkb1fl/+ mice
Ontology highlight
ABSTRACT: Mice were exposed to 3% DSS in the drinking water for 7 days followed by 3 days of recovery. Colon tissues were collected at 3 day after recovery in RNA later and RNA was extracted using DNA, RNA, protein purification kit from Macherey-Nagel.
Project description:RNA from primary intestinal fibroblasts derived from Lkb1fl/fl mice (biological replicate n=4). Cells were adenotransducted with either AdCre or AdGFP to deplete Lkb1 and at day 4 after adenotransduction treated 24h with or without LPS. RNA sequencing method used was 3′UTR RNA sequencing.
Project description:To characterize murine ASPCs we performed bulk RNA-seq (BRB-seq, Alpern et al., 2019) of total, CD142− and CD142+ (Aregs) mouse adipose stem and progenitor cells (ASPCs). ASPCs were collected as Lin− (CD31− CD45− TER119−) CD29+ CD34+ SCA1+ cells of the mouse subcutaneous stromal vascular fraction using FACS. The cells were sequenced directly after sort or after expansion.
Project description:To validate that the robustness of Aregs' (CD142+ ASPCs') molecular identity regardless of the antibody used, we performed transcriptomic profiling of freshly isolated CD142− and CD142+ mouse adipose stem and progenitor cells (ASPCs) sorted using four different anti-CD142 antibodies. ASPCs were collected as Lin− (CD31− CD45− TER119−) CD29+ CD34+ SCA1+ CD142+/− cells of the mouse subcutaneous stromal vascular fraction using FACS.
Project description:To explore the molecular identity of mouse adipose stem and progenitor cells (ASPCs) and more specifically of CD142+ ASPCs (Aregs), we performed bulk RNA-seq on freshly isolated total, CD142− and CD142+ ASPCs of new-born pups (P0), post-natal day 16 mice (P16), 4 week-old (4wo), 7wo and 11wo mice. ASPCs were collected as Lin− (CD31− CD45− TER119−) CD29+CD34+ SCA1+ cells of the mouse subcutaneous stromal vascular fraction using FACS.
Project description:To characterize CD142+ ASPCs (Aregs) after exposure to an adipogenic cocktail we performed bulk RNA-seq (using BRB-seq) of total, CD142− and CD142+ mouse adipose stem and progenitor cells (ASPCs), sorted using four different anti-CD142 antibodies. ASPCs were collected as Lin− (CD31− CD45− TER119−) CD29+ CD34+ SCA1+ cells of the mouse subcutaneous stromal vascular fraction using FACS.
Project description:To study the involvement of key Areg (CD142+ ASPC)-specifics factors in the inhibitory capacity of CD142+ ASPCs on adipogenesis, we performed transcriptomic profiling of CD142− ASPCs exposed to the secretome of CD142+ ASPCs carrying knockdowns of the indicated genes. CD142− ASPCs were co-cultured and co-differentiated (within the transwell set-up) with CD142+ ASPCs in which siRNA-based knockdowns of specific genes were performed. ASPCs were collected as Lin− (CD31− CD45− TER119−) CD29+ CD34+ SCA1+ cells of the mouse subcutaneous stromal vascular fraction using FACS.
Project description:To study the impact of retinoic acid treatment on the transcriptome of CD142− ASPCs, we performed bulk RNA-seq on CD142− ASPCs treated with different RA concentrations ranging between 0.01 to 100 μM, with 100 ng/ml of BSA (negative control), DMSO (negative control) or 100 ng/ml of EGF (positive control).
Project description:Here, we validate a novel protocol, Bulk RNA Barcoding and sequencing (BRB-seq), that combines the multiplexing-driven cost-effectiveness of a single-cell RNA-seq protocol with the efficiency of a bulk RNA-seq procedure. For this we use BRB-seq protocol on human pre-adipocytes and differentiated adipocytes, and compare its effectiveness as compared to TruSeq. Indeed, one of the principal limitations of bulk RNA-seq is the time and costs of library preparation, which makes it difficult to profile many samples simultaneously. Here, BRB-seq produces 3’ libraries that exhibit similar gene expression quantification to TruSeq and maintain this quality even with low quality RNA samples.
Project description:We performed RNA sequencing of wing discs at the wandering L3 larval stage from 32 inbred lines of Drosophila genetic reference panel (DGRP) that consists of 16 big and 16 small wing lines. We aimed to understand system-wide gene regulatory mechanisms that attain the observed natural variation in wing size including the sexual size dimorphism.
Project description:The development of therapeutic anticancer vaccines calls for the identification of tumor-specific antigens (TSAs). Though a combination of four cutting-edge proteogenomic approaches, we performed a deep exploration of the MHC-I presented peptides (MAPs) of 19 acute myeloid leukemia (AML) patients and identified various TSAs that could serve for the design of an anti-AML vaccine.