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

Journal: Acta Neuropathologica Communications

Article Title: Metabolic and transcriptomic profiles of glioblastoma invasion revealed by comparisons between patients and corresponding orthotopic xenografts in mice

doi: 10.1186/s40478-021-01232-4

Figure Lengend Snippet: Baseline information of patients and PDOX

Article Snippet: Preprocessing of RNA sequencing (RNAseq) data was performed following the standard pipeline and recommendations from bcbio-nextgen (version 1.0.4, http://bcbio-nextgen.readthedocs.org/en/latest/ ).

Techniques: