Project description:We used Illumina Small RNA and RNA-Seq kits to prepare both small RNA and RNA-Seq libraries from total RNA isolated from either leptotenze/zygotene or pachytene spermatocytes purified from either Dgcr8 or Dicer germline conditional knockout mice. Conditional knockout mice were generated by using a Ddx4 promoter to drive cre excision of either Dgcr8 or Dicer at embryonic day 18. Mixed leptotene/zygotene or pachytene spermatocytes were then isolated from the testis of adult conditional knockout mice, along with paired WT littermates as a control. RNA was isolated from these spermatocytes using Trizol. Small RNA or RNA-Seq libraries were then prepped using Illumina's sequencing library preparation kits.
Project description:RNA-seq analysis documented mRNA changes in total pancreatic RNA preparations 14 days after Ptf1a inactivation. pancreas mRNA profiles of Tamoxifen treated adult control mice [Ptf1a(CreER/+)] and Ptf1a conditional knockout mice [Ptf1a(CreER/fl)] were generated by deep sequencing using an Illumina Hiseq 2500.
Project description:To investigate the function of Rcrin in liver, we established Rcrin flox mice and crossed with Alb-cre mice, then we generated Rcrin conditional knockout mice. Then we got liver tissues from Rcrin conditional knockout mice and Rcrin flox mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of Rcrin conditional knockout mice (Rcrin knockout) and Rcrin flox mice (WT) at age of 8 weeks old.
Project description:Spinal cord mRNA profiles of 14-day-old control (Brg1c/+;Olig1-Cre) and Smarca4/Brg1 conditional knockout (Brg1c/c;Olig1-Cre) mice were generated by RNA-seq. Differential expressed genes are identified using Cuffdiff and validated with qPCR. Spinal cord mRNA profiles of 14-day old control and Brg1c/c;Olig1-Cre mice were generated by RNA-sequencing.
Project description:RNA-Seq was performed on pancreatic islets from four transgenic mouse strains affecting LKB1 and AMPK. A conditional LKB1 knockout strain was generated. Double conditional knockouts for AMPK alpha1 and AMPK alpha2 were also generated. These conditional strains were crossed with RIP-Cre (driven by rat insulin promoter) or Ins1-Cre mice to generate LKB1 knockout and AMPK double knockout strains.
Project description:To elucidate the mechanisms underlying the role of Atf4 deficiency in erythropoiesis, we performed 10X Genomics single-cell RNA sequencing on Lin-cKit+ cells from Atf4 hematopoietic cell-specific conditional knockout mice (KO) and Atf4 floxed mice (WT) at steady state (referred to KO_BM and WT_BM) and after secondary transplantation (referred to cKO_t and WT_t). Furthermore, we also sorted CMP cells from Atf4 hematopoietic cell-specific conditional knockout mice (KO) and ATF4 floxed mice (WT) for 10X Genomics scRNA-seq.
Project description:Gains and losses in DNA methylation are prominent genomic features of all mammalian cell types. To gain insight into mechanisms that could promote shifts in DNA 5-hydroxymethylation (5hmc) patterns and thus contribute to cell fate, including malignant transformation, we performed genome-wide mapping of 5hmc in purified wild type and Dnmt3a conditional knockout hematopoietic stem cells (HSCs) using cytosine-5-methylenesulphonate sequencing (CMS-seq). Comparing anti-CMS pulldown to input control, we identified 107,549 and 175,682 peaks of 5hmc enrichment in control and Dnmt3a knockout HSCs, respectively. Whole genome CMS-enriched bisulfite sequencing of secondarily-transplanted wild-type and Dnmt3a conditional knockout hematopoietic stem cells using Illumina HiSeq 2000
Project description:Hopx conditional knockout mouse (Hopx-/-) was generated. We then studied the biological effects of Hopx knockout on the hematopoietic system of young mice, via whole-transcriptome RNA-seq.