Journal: The Journal of Biological Chemistry

Article Title: Transcription factor SOX15 regulates stem cell pluripotency and promotes neural fate during differentiation by activating the neurogenic gene Hes5

doi: 10.1016/j.jbc.2023.102996

Figure Lengend Snippet: Gene expression profile of Sox15 -knockout ESCs . A , RNA-seq analysis identifies differentially expressed genes (DEGs) in Sox15 KO1 ESCs compared to WT, plotted as a function of mean expression (fpkm) and fold changes (log2). Number of genes upregulated (830) and downregulated (589) are indicated. B , gene ontology (GO) analysis on DEGs in Sox15 KO1 ESCs compared with all annotated genes. p -value per GO classification is shown (-log10( p -value)). C , heatmap showing the relative expression levels of indicated genes from three biological replicates each of WT and Sox15 KO ESCs. Scaled values indicate relative downregulation ( red ) or upregulation ( green ) of gene expression. Genes from each category are manually curated. ESC, embryonic stem cell.

Article Snippet: RNA-seq samples were processed using the RNA-seq pipeline implemented in bcbio-nextgen v1.1.3 ( https://bcbio-nextgen.readthedocs.org ).

Techniques: Expressing, Knock-Out, RNA Sequencing Assay

Journal: Scientific Reports

Article Title: Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts

doi: 10.1038/s41598-019-42680-2

Figure Lengend Snippet: Illustration of bioinformatics strategy and workflows for analyzing patient- and PDX-RNAseq. ( a ) Bioinformatics strategy to separate mouse-stroma and human-tumor expression levels from PDX RNAseq data; ( b ) Dotted box indicates patient and PDX Pipelines for processing donor tumors and PDX tumors, respectively; ( c ) Dotted box indicates workflow for examining technical and biological differences.

Article Snippet: A PDX RNAseq analysis pipeline was devised based on Xenome and a standard patient tumor pipeline (Fig. ).

Techniques: Expressing

Journal: Scientific Reports

Article Title: Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts

doi: 10.1038/s41598-019-42680-2

Figure Lengend Snippet: Identification of genes sensitive to patient- versus PDX-RNAseq bioinformatics pipelines. Nine patient donor tumors were processed through patient- and PDX-RNAseq piplines separately; differential expressed genes (DEGs) between the two pipelines are used to determine genes sensitive to pipeline differences. ( a ) MA (M: log ratio, A: Mean average) plot with DEGs highlighted in red; ( b ) Distribution of phast conservation score for all genes and DEGs caused by pipeline differences.

Article Snippet: A PDX RNAseq analysis pipeline was devised based on Xenome and a standard patient tumor pipeline (Fig. ).

Techniques:

Journal: Scientific Reports

Article Title: Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts

doi: 10.1038/s41598-019-42680-2

Figure Lengend Snippet: Expression differences of donor-PDX tumor pairs and impact on transcriptome pair similarity. RNASeq for nine pairs of donor/PDX tumors were processed with patient and PDX pipelines respectively. XDGs indicate differentially expressed genes between paired donor/PDX tumors after excluding previously identified genes that are sensitive to pipeline differences. ( a ) MA plot with XDGs in red; ( b ) Box plot of correlation coefficients of paired PDX-donor tumors before and after removing XDGs; ( c ) Hierarchical clustering of donor/PDX tumor pairs before removing XDGs; ( d ) Hierarchical clustering of donor/PDX tumor pairs after removing XDGs. Patient hetrotransplant (PH) numbers represent a single tumor line and the suffix indicates either the patient donor (P) or corresponding xenograft (PDX).

Article Snippet: A PDX RNAseq analysis pipeline was devised based on Xenome and a standard patient tumor pipeline (Fig. ).

Techniques: Expressing

Journal: Scientific Reports

Article Title: Therapeutic potential of Bifidobacterium breve strain A1 for preventing cognitive impairment in Alzheimer’s disease

doi: 10.1038/s41598-017-13368-2

Figure Lengend Snippet: Change of gene expression profile in hippocampus of AD model mice by Bifidobacterium breve strain A1 treatment using RNA-seq analysis. Transcriptional analysis was performed on hippocampal tissues of sham-operated mice (SH), Aβ25-35 injected mice (AB) and mice treated with Aβ and B breve A1 (ABA). ( a , b ) Venn diagram of shared and unique hippocampal transcripts ( a ) in SH vs AB and/or SH vs ABA, and ( b ) in SH vs AB and/or AB vs ABA, p < 0.05 and FDR < 0.05. RNA-seq data from 5 mice are presented. ( c – e ) GO Term enrichment analysis of differential expressed (DE) genes in AD hippocampus. Enrichment analysis of differential expressed genes ( c ) between Aβ-treated and control mice, ( d ) between groups with or without B. breve A1 administration and ( e ) using DAVID analysis.

Article Snippet: The reads from each sample were aligned to the Mus musculus genome GRCm 38.73 assembly using the RNA-seq pipeline from CLC bio (CLC bio, Tokyo, Japan).

Techniques: Expressing, RNA Sequencing Assay, Injection

Journal: Scientific Reports

Article Title: Identification of TNFAIP3 as relapse biomarker and potential therapeutic target for MOG antibody associated diseases

doi: 10.1038/s41598-020-69182-w

Figure Lengend Snippet: Gene expression analysis in PBMCs from MOG-AAD patients: Single cell RNA sequencing (inDrop) was performed on an untreated MOG-AAD patient#1 with 2 longitudinal samples, (1) Remission (MOG-AAD#1.2) and (2) Pre-relapse (MOG-AAD#1.3) as described in Materials and Methods. cDNA libraries were sequenced using the Illumina NextSeq 500 platform and analyzed following V3 Indrop criteria. After sequencing the raw BCL files were demultiplexed using bcl2fastq software by illumina ( https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html ). Reads obtained from bcl2fastq were further processed using the single-cell RNA-seq pipeline of the bcbio-nextgen ( https://bcbio-nextgen.readthedocs.io/en/latest/contents/pipelines.html#single-cell-rna-seq ) software suite. The scaled data was further clustered using Seurat and visualized using TSNE ( https://www.biorxiv.org/content/early/2018/11/02/460147 ). A Cluster analysis of a relapse and remission sample. B Differential expression of TNFAIP3 in the relapse and remission sample by single cell sequencing. Digital Gene Expression (DGE) sequencing was performed on an untreated MOG-AAD patient#1 with 3 longitudinal samples, (1) Rm (remission, MOG-AA#1.2), (2) PR (pre-relapse, MOG-AAD#1.3), and (3) R (relapse, MOG-AAD#1.4) as described in Materials and Methods. Raw BCL files generated through sequencing were further de-multiplexed using Picard ( https://github.com/broadinstitute/picard ) and the resulting FASTQ files where aligned to the human reference genome (GRCh38) using the STAR v2.4.2a aligner. Further QC was done using the RNA-seQC and transcript counts were produced using feature Counts function of the Subread package . Data was normalized using the DESeq2 package and the graphs were made using GraphPadPrism version 8.4.2 (464). C TNFAIP3 and NFκβ1 expression by DGE sequencing. NanoString Gene Expression Assay was performed on a MOG-AAD patient#2 with 3 longitudinal samples, (1) untreated R (relapse, MOG-AAD#2.1), (2) 8 months Rm/Ct (mycophenolate mofetil treated at remission, MOG-AAD#2.2), and (3) 11 months Rm/Ct (mycophenolate mofetil treated at remission, MOG-AAD#2.3) as described in Materials and Methods. Data were normalized and analyzed using nSolver software via the geometric mean of included housekeeping genes. The graphs were made using GraphPadPrism version 8.4.2 (464). D TNFAIP3 and TNF-α expression by NanoString Gene Expression Assay. qPCR was performed on CD4+ T cells from 7 MOG-AAD patients with longitudinal samples as described in Materials and Methods. It also included MOG-AAD patient#2 with 3 longitudinal samples as previously used for NanoString gene expression assay. The graphs were made using GraphPadPrism version 8.4.2 (464). E TNFAIP3 expression in MOG-AAD patient#2 by qPCR. F Grouped analysis of TNFAIP3 expression in relapse samples, remission samples and samples treated with corticosteroids by qPCR. Relapse n = 5, Remission n = 5, Steroid n = 4, Ordinary 1-way ANOVA; P = 0.0137.

Article Snippet: Reads obtained from bcl2fastq were further processed using the single-cell RNA-seq pipeline of the bcbio-nextgen ( https://bcbio-nextgen.readthedocs.io/en/latest/contents/pipelines.html#single-cell-rna-seq ) software suite.

Techniques: Expressing, RNA Sequencing Assay, Sequencing, Software, Generated, Produced