GSE262745 Predictive biomarkers and maternal immune alterations in postpartum preeclampsia reveal an immune-driven pathology
Contributors : Camille Couture ; Marie-Eve Brien ; Jade Rechtzigel ; SuYun Ling ; Cecilia Ledezma-Soto ; Gilberto D Bishop ; Ines Boufaied ; Doroth ée Dal Soglio ; Evelyne Rey ; Serge McGraw ; Charles H Graham ; Sylvie GirardSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPostpartum preeclampsia (PPPE) is an under-diagnosed condition, developing within 48 hours to 6 weeks following an uncomplicated pregnancy. The etiology of PPPE is still unknown, leaving patients vulnerable and making the identification and treatment of patients requiring postpartum care an unmet need. We ...
Source: GEO: Gene Expression Omnibus - March 29, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE115917 RNAseq of human primary T cell lymphoma
Contributors : Karthik Ganapathi ; Huimin GengSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNAseq of 14 samples of human primary T cell lymphoma (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE189735 Influenza A virus replicates productively in primary human kidney cells and induces factors and mechanisms related to regulated cell death and renal pathology observed in virus-infected patients
Contributors : Benjamin F Koch ; Stephan PleschkaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensInfluenza A virus (IAV) infection can cause the often-lethal acute respiratory distress syndrome (ARDS) of the lung. Concomitantly, acute kidney injury (AKI) is frequently noticed during IAV infection, correlating with an increased mortality. The aim of this study was to elucidate the interaction of IAV with human kidney cells and, thereby, to assess the mechanisms underlying IAV-mediated AKI. We demonstrate productive replication of low and highly pathogenic IAV strains on primary and im...
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE196786 Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk promoting immunosuppression and immunotherapy resistance [RNAseq_meta_analysis]
Contributor : Massimiliano MazzoneSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe project aims to identify metabolic genes and pathways associated with immunotherapy resistance.Methods: 4x10e6 Panc02, 1x10e6 MC38 or 2x10e6 CT26 cells were injected subcutaneously (s.c.) in the right flank of the mouse in a final suspension of 200 μl PBS. Tumor volumes were measured at least three times per week. At the indicated time points, mice were randomized and treated intraperitoneally (i.p.) with 10 mg/kg α-PD-1 (BioXcell) or α-CTLA4 or control IgG from rat serum (Sigma-Aldrich). At end-...
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE196787 Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk promoting immunosuppression and immunotherapy resistance [RNAseq_Panc02_sgNT_sgCda_invitro]
Contributor : Massimiliano MazzoneSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: To study the effects of CDA depletion on PancO2 cell line. Here, we used RNA sequencing to understand if sgCda can alter cancer cell immunogenicity by looking at mutational burden.Methods: PancO2 cancer cells were transduced with a doxycycline-inducible Cas9 nuclease (Edit-R Inducible Lentiviral Cas9, Dharmacom) and selected with blasticidin (Bio-Connect). Cells expressing the doxycycline-inducible Cas9 nuclease were transduced with a target specific gRNA for CDA and a control non-targeting NT...
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE196788 Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk promoting immunosuppression and immunotherapy resistance [RNAseq_Panc02_sgNT_sgCda_tumor]
Contributor : Massimiliano MazzoneSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: Here we use Here, we used RNA sequencing to identify trascriptictomic profile of sgNT and sgCda PancO2 tumor bearing-mice.Methods: 4x10e6 sgNT and sgCda Panc02 cells were injected subcutaneously (s.c.) in the right flank of the C57BL/6J mouse in a final suspension of 200 μL PBS. Tumor volumes were measured at least three times per week. At day 16 after injection, tumor-bearing mice were sacrificed by cervical dislocation and RNA was isolated from tumor tissue using TRIzol (Life Technologies). ...
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE196790 Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk promoting immunosuppression and immunotherapy resistance
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE200176 Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function [ATAC-Seq]
Contributors : Matthew C Pahl ; Rajan M Thomas ; Andrew D WellsSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusWe investigated the role of Ikaros in regulatory Tcell identity and function during stimulation using RNA-seq, ATAC-seq, and H3K27ac/Foxp3/Ikzf1 ChIP-seq (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE200177 Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function [ChIP-Seq]
Contributors : Matthew C Pahl ; Rajan Thomas ; Andrew D WellsSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusWe investigated the role of Ikaros in regulatory Tcell identity and function during stimulation using RNA-seq, ATAC-seq, and H3K27ac/Foxp3/Ikzf1 ChIP-seq (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE200178 Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function [RNA-Seq]
Contributors : Matthew C Pahl ; Rajan Thomas ; Andrew D WellsSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe investigated the role of Ikaros in regulatory Tcell identity and function during stimulation using RNA-seq, ATAC-seq, and H3K27ac/Foxp3/Ikzf1 ChIP-seq (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE200179 Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE207166 The long non-coding RNA Meg3 mediates imprinted gene expression during stem cell differentiation
Contributors : Benoit Moindrot ; Daan NoordermeerSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe imprinted Dlk1-Dio3 domain comprises the developmental genes Dlk1 and Rtl1, which are silenced on the maternal chromosome in different cell types. On this parental chromosome, the domain ’s imprinting control region activates a polycistron that produces the lncRNA Meg3 and many miRNAs (Mirg) and C/D-box snoRNAs (Rian). Although Meg3 lncRNA is nuclear and associates with the maternal chromosome, it is unknown whether it controls gene repression in cis. We created mouse...
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

Gse226936 environment modulates protein heterogeneity through transcriptional and translational stop codon miscoding
Contributors : Maria L Romero-Romero ; Anastasiia Kirilenko ; Jonas Poehls ; Doris Richter ; Tobias Jumel ; Anna Shevchenko ; Agnes Toth-PetroczySeries Type : OtherOrganism : Escherichia coli str. K-12 substr. MG1655In order to systematically assess the frequency and origin of stop codon miscoding events, we designed a library of reporters. We introduced premature stop codons into mScarlet that enabled high-throughput quantification of protein synthesis termination errors in E. coli using fluorescent microscopy. We found that under stress conditions, stop codon miscoding may occur with a rate as high as 80%, dependin...
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Other Escherichia coli str. K-12 substr. MG1655 Source Type: research

GSE227087 Transfer learning enables identification of multiple types of RNA modification using nanopore direct RNA sequencing
Contributors : You Wu ; Wenna Shao ; Mengxiao Yan ; Hongxia Wang ; Xiang YuSeries Type : Expression profiling by high throughput sequencingOrganism : Oryza sativa ; synthetic constructRNA internal modifications play critical role in development of multicellular organisms and their response to environmental cues. Using nanopore direct RNA sequencing (DRS), we constructed a large in vitro epitranscriptome (IVET) resource from plant cDNA library labeled with m6A, m1A and m5C respectively. Furthermore, after transfer learning, the pre-trained model was used to detect additional RNA internal modification such as m1A, hm5C,...
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Oryza sativa synthetic construct Source Type: research

GSE227420 An innate immunity against Xanthomonas oryzae activated by ATM-mediated host DSB damage response in rice
We examined the transcriptional data in rice leaves of TOP6A3 overexpressed line (TOP6A3-OE1) with WT (K3) plants under normal growth. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 28, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Oryza sativa Source Type: research