Project description:In this study: (1) we distinguished Tet3 target genes that are regulated by its catalytic vs. noncatalytic functions in neuroectoderm (NE) cells by transcriptomic profiling of Tet3 wildtype (WT), Tet3 catalytic mutant (Mut), and Tet3 knockout (KO) NE cells by RNA-seq. (2) We mapped genome-wide DNA methylation of Tet3-WT, Tet3-Mut, and Tet3-KO NE cells by WGBS. (3) We determined Tet3 genome-wide occupancy in Tet3-WT NE cells by CUT&Tag. (4) We mapped 5hmC rich regions in Tet3-WT, Tet3-Mut, and Tet3-KO NE cells by hmeDIP. (5) We overexpressed (OE) the Tet3 target gene Dnmt1 (D) or an empty vector (EV) in Tet3-WT, Tet3-Mut, and Tet3-KO NE cells and assessed gene expression by RNA-seq. (6) We overexpressed (OE) Tet3 (T) or an empty vector (EV) in Tet3-WT, Tet3-Mut, and Tet3-KO NE cells and examined gene expression changes in these cells by RNA-seq.
Project description:Purpose: To further identify the genes and pathways involved in the necrotic phenotype of NtCBL5A-OE lines, the leaf transcriptome profiling of WT and OE-2 lines grown under control conditions and salt stress (100 mM NaCl) at 4 DAT were sequenced and compared. Methods: Two datasets of differentially expressed genes (DEGs) were made in which we identified the genes that were differentially expressed as a result of the overexpression of NtCBL5A: Control-WT vs Control-OE2 (C-WT/C-OE2), Salt-WT vs Salt-OE2 (S-WT/S-OE2). Another two datasets were also used to identify the transcripts that were responsive to the salt treatments: Control-WT vs Salt-WT (C-WT/S-WT) and Control-OE2 vs Salt-OE2 (C-OE2/S-OE2). DEGs from C-WT/C-OE2 and S-WT/S-OE2 were compared to select the transcripts affected by NtCBL5A overexpression only under salt stress. We also compared DEGs from C-WT/S-WT and C-OE2/S-OE2 to identify the specific transcripts affected by salt stress and only in NtCBL5A-OE lines. This procedure was done for two independent experiments, and only DEGs that were identified in both experiments were considered. Results: The OE-affected DEGs and salt-affected DEGs together resulted in 2079 up-regulated DEGs and 1154 down-regulated DEGs, strongly affected by the combination of NtCBL5A overexpression and salt stress.
Project description:There are three projects including AE155LQ, RE161LQ, RE235LQ. AE155LQ is about the proteomes of wild type cells (WT) and E. coli RelA* OE strain during exponential growth in glucose cAA medium. E1 & E2 corresponds to the wild type cells (two biological replicate samples) and E3 & E4 corresponds to RelA* OE data (two biological replicate samples). RE161LQ is about the time-course proteome of wild type (four samples including WT_0, WT_20, WT_40 and WT_80) vs relA-deficient strain (relA_0, relA_1.5 h, relA_3 h and relA_4.5 h) during AA downshift. RE235Q is about the time-course proteome of wild type (three samples including WT_0, WT_60, WT_160) vs relA-deficient strain (three samples including relA_0, relA_60 and relA_160) during carbon downshift.
Project description:RNA-seq was used to characterize the LMP1 mediated regulation of host target gene regulation. Here, we stably expressed doxycycline-induced HA-tagged wildtype (WT) LMP1 or TES1 mutant (TES1m) oe TES2 mutant(TES2m) in GM12878 LCL. We then depleted LMP1 from these cells using CRISPR-Cas9 approach and treated the cells with 400ng/ml of doxycycline to induce expression of WT, TES1m or TES2m LMP1 to rescue from the LMP1 depletion mediated effects (including loss of cell viability) to understand and differenciate the role of LMP1 TES1 vs TES2 domains in LCL.
Project description:We carried out strand-specific RNA-seq libraries followed by deep sequencing (RNA-seq) to explore the transcriptional profile of the PfRrp6-DD-1C,PfRrp6-DD-1B,PfRrp6-DD-4C,WT 3D7-G7, WT NF54 and PfMaf1-OE lines.
2020-01-01 | GSE133236 | GEO
Project description:RNA-seq of SlPGR5-RNAi, SlPGR5-OE and WT
Project description:Transcriptional profiling of Arabidopsis rossette leaves comparing WT Col-0 with a transgenic line overexpressing AhERF or AhDOF genes from Amaranthus hypochondriacus under different conditions. Three-condition experiment of WT vs AhERF OE plant leaves. The analyzed conditions were: normal growth conditions, 5 days of water stress (no irrigation) and 24 hrs of recovery after watering water-stressed plants. Besides, a two-condition experiment where WT vs AhDOF OE plant leaves were compared. The experimental conditions were: normal growth conditions and plants watered with 40mL of 400mM NaCl solution for three straight days to produce salt stress.
Project description:Transcriptional profiling of Arabidopsis rossette leaves comparing WT Col-0 with a transgenic line overexpressing Ah24 gene from Amaranthus hypochondriacus. One-condition experiment WT vs Ah24 OE plant leaves.
Project description:Experiment was designed to study the effect of Hippo pathway on osimertinib resistance in non-small cell lung cancer cell lines. The specific comparisons investigated were: PC-9: NTC vs NF2 KO, EV vs YAP1 OE, EV vs WWTR1 OE, EV DMSO treated vs EV osimertinib treated HCC827: NTC vs NF2 KO, EV vs YAP1 OE, EV vs WWTR1 OE,EV DMSO treated vs EV osimertinib treated HCC4006: NTC vs NF2 KO, EV vs YAP1 OE, EV vs WWTR1 OE, EV DMSO treated vs EV osimertinib treated
