Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA sequencing of young versus aged endothelial cells

ABSTRACT: Freshly dissected Thymus, Kidney, and Spleen from young and aged mice were subjected to collagenase digestion to prepare single-cell suspension for the isolation of endothelial cells. Endothelial cells form the single-cell suspension was isolated using a magnetic bead-based separation method using CD144 and Endomucin antibody. RNA from 150,000 cells from each group was isolated using the RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s instructions. The library preparation was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina.

INSTRUMENT(S): Illumina HiSeq 2500, FACS Aria 3

ORGANISM(S): Mus musculus

SUBMITTER: Amit Singh

PROVIDER: E-MTAB-8941 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Spheroids, near spherical multicellular aggregates, are one of the most common types of threedimensional (3D) cell cultures. Despite decades of implementation of spheroid technology in various fields of life science and medical research, no minimal information (MI) guidelines are available to cope with heterogeneity and to stimulate transparency. To cope with this unmet need, we assembled an international consortium to develop the MISpheroID knowledgebase (https://www.mispheroid.org) and interrogation revealed heterogeneity and lack of transparency in published spheroid-related experiments. This steered us to empirically evaluate the impact of cell line, culture medium type, spheroid formation method and spheroid size on complementary spheroid metrics (RNA fingerprints, presence of cell death, ATP content, glucose to lactate conversion, secreted protein signatures, circularity, size and cancer therapy response). We measured media-induced transcriptional variation in lung cancer (A549), colorectal cancer (HCT116), ovarium cancer (SKOV3) and glioblastoma (U87MG) spheroids using RNA sequencing (RNA-seq). These spheroids were formed in ultra-low attachment plates and cultured in 6 different media types (DMEM high glucose, DMEM/F12, RPMI1640, DMEM low glucose, EMEM and MEM) for 5 (HCT116) or 7 (A549, SKOV3 and U87MG) days. RNA extraction was performed on 2 spheroids per condition using the miRNeasy micro kit (217084, Qiagen, Hilden, Germany). RNA-sequencing libraries were prepared from purified RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) according to the manufacturer's instructions, using 27.5ng of RNA that was DNase treated using HL-dsDNA (Arcticzymes, TromsØ, Norway). The individual libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche, Pleasanton, CA, US) and equimolarly pooled. The pool concentration was measured with Qubit and 1.4pM with 1% PhiX was sequenced on a NextSeq 500 (Illumina, San Diego, CA, US) using a high-output 1x75 run. Reads were mapped to the human genome using Tophat and gene expression counts were generated using HTSeq. This data was used to perform Principal Component Analysis (PCA) and Gene Set Enrichment Analysis (GSEA).

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RNA sequencing of young versus aged endothelial cells

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