Project description:Akap1 KO and Wt mice were exposed to normoxia or hyperoxia for 48h. Total RNA was extracted from lungs of Wt Normoxia (n=3), Wt hyperoxia (n=3), Akap1 KO (n=3) and Akap1 hyperoxia (n=3) mice. RNA-sequencing was carried out followed by differential expression of genes in the following groups. Wt Normoxia vs Wt Hyperoxia, Akap1 KO Normoxia versus Akap1 KO Hyperoxia, Wt Normoxia versus Akap1 KO Normoxia and Wt Hperoxia versus Akap1 Hyperoxia.
Project description:To compare the inflammatory responses of WT and SIRPα KO macrophage, we performed a complete transcript profiling of WT and SIRPα-KO M1 macrophage using transcriptome sequencing as a discovery platform. SIRPα-KO mice and WT mice were kept under the same condition. BMDMs were produced from WT and SIRPα-KO mice followed by M1 polarization. RNA was then isolated from the same number of BMDMs.
2021-03-19 | GSE169177 | GEO
Project description:RNA sequencing from LOX KO and WT mice
Project description:To study the transcriptome differences of tumor transplanted into WT and KO host, E0771 tumors harvested from WT and KO host were extracted for total RNA and mRNA sequencing was performed. To study the transcriptome differences of WT and KO fat tissue, visceral fat tissue were harvested from obese WT and KO mice and total RNA was extracted and sequenced.
Project description:To identify soluble factors released from Dnmt3a KO macrophages that might drive differences in osteoclast differentiation, we performed RNA sequencing on unstimulated BMDMs from WT and Dnmt3a KO mice. To investigate the mechanistic basis for the inflammatory phenotype. of myeloid cells with loss of Dnmt3a,we performed reduced representation bisulfite sequencing (RRBS) on Dnmt3a KO and WT BMDMs to assess methylation changes. Concurrently, we performed ATAC-sequencing (ATAC-seq) to assess differences in chromatin accessibility between WT and Dnmt3a KO BMDMs in the context of changes in methylation. We performed chromatin immunoprecipitation sequencing (CHIP-seq) for Irf3 and Rela based on ATAC-seq analysis.
Project description:To identify the direct m6A demethylation targets of ALKBH5 at the onset of renal IRI, we performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) using RNA isolated from IRI mouse kidney of WT and KO mice 24h after I/R (WT n=3 vs. KO n=3)
Project description:WT mice and claudin 4 KO mice were exposed to ventilator-induced lung injury (VILI) for 2 hours. We found that in some Cldn4 KO mice, injury was similar to WT, while in others, injury was higher, as assessed by amount of protein leak into broncho-alveolar lavage fluid. We performed RNAseq to find which genes were responsible for higher injury in Cldn4 KO mice. WT mice and claudin 4 KO mice were exposed to ventilator-induced lung injury (VILI) for 2 hours. RNA were extracted from whole lungs and RNA sequencing was performed. The samples are (all in duplicates): WT no VILI, Cldn4 KO no VILI, WT VILI, Cldn4 KO VILI with similar injury to WT (Cldn4 KOlow), and Cldn4 KO VILI with higher injury than WT (Cldn4 KOhigh)
Project description:WT and H2BE-KO primary cortical neurons were isolated from E16.5 mice and culture for 12 days for ATAC-sequencing (n=3 WT biological replicates, 4 KO biological replicates).
Project description:Global RNA sequencing analysis of the hypothalamus, BAT, inguinal WAT and muscle of long-term cold exposed WT, FGF21 KO, UCP1 KO and UCP1/FGF21 double KO mice
Project description:Loss of Tet1 expression causes global 5mC and 5hmC changes in stem and progenitor cells in mice and causes enhanced Pro-B cell self-renewal, increased DNA damage and B-lymphomageneis. In this study we performed reduced representative bisulfite sequencing (RRBS) of DNA from WT and Tet1 KO LSK cells. DNA methylation sequencing was performed and analyzed using an enhanced reduced representation (ERRBS) methodology as previously described. DNA was extracted from purified LSK cells of 6-month old WT and Tet1 KO mice, Bisulphite treatment was performed using the EZ DNA Methylation Kit (Zymo Research). Libraries were amplified according to illumina protocols and sequenced on an Illumina HiSeq2500 machine DNA methylation profiling of LSK cells in WT and Tet1 KO mice.
