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RNAseq of colorectal cancer cell lines (LS1034/HCT116) cultured with iPSC-derived intestinal stroma, separated by EpCAM expression (MACS). Monocultures of each cell line and co-cultures with LS1034 or HCT116 with stroma.

ABSTRACT: RNAseq of colorectal cancer cell lines (LS1034/HCT116) cultured with iPSC-derived intestinal stroma, separated by EpCAM expression (MACS). Monocultures of each cell line and co-cultures with LS1034 or HCT116 with stroma.

PROVIDER: PRJEB72641 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12654315_1.fastq.gz	Fastqsanger.gz
	ERR12654315_2.fastq.gz	Fastqsanger.gz
	ERR12654316_1.fastq.gz	Fastqsanger.gz
	ERR12654316_2.fastq.gz	Fastqsanger.gz
	ERR12654317_1.fastq.gz	Fastqsanger.gz

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RNAseq of colorectal cancer cell lines (LS1034/HCT116) cultured with iPSC-derived intestinal stroma, separated by EpCAM expression (MACS). Monocultures of each cell line and co-cultures with LS1034 or HCT116 with stroma.

Project description:Colorectal cancer (CRC) cell lines (LS1034 and HCT116, representing different genetic backgrounds of CRC) were co-cultured with iPSC-derived intestinal stroma (described in other protocols). Control conditions were each cell line cultured separately. A dose response for HCT116 on stroma was tested using a varying seeding density. After culture, cells were separated using MACS based on EpCAM expression (EpCAM+: CRC cell line / EpCAM-: stroma) and then measured for reciprocal changes in gene expression by RNAseq (i.e. CRC effect on stromal expression and vice verse on cell lines).

2026-03-02 | E-MTAB-13803 | biostudies-arrayexpress

Comparison of gene expression between MACs and MIL4-MACs

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Comparison of gene expression between MACs and MIL4-MACs

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Bacterial Intestinal Gut Modification Around Cancer Surgery (BIG MACS) Diet

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Diatom monocultures associated bacterial communities

Project description:xenic diatom monocultures 16S rRNA gene sequencing (V4 region)

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Microbiota-driven transcription signatures in lung stroma cells

Project description:Commensal bacteria have been shown to influence the reactivity of immune cells in the gut and in other organs. This study aims to assess the impact of microbiota on transcription signatures in lung stroma cells. Samples were generated from mice that were either left on plain water, on water with antibiotics, or on water with antibiotics followed by faecal transplant to reverse the antibiotics effect. CD45 negative cells were MACS-purified from the lung, and RNA seq was performed on samples.

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NIAID Mulit-Center AIDS Cohort Study (MACS)

Project description:NIAID Mulit-Center AIDS Cohort Study (MACS)

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Comparison of microglial proteomes of MACS and FACS-based purified CD11b+ microglia

Project description:Background Proteomic characterization of microglia has been limited by low yield and contamination by non-microglial proteins by magnetic-activated cell sorting (MACS) enrichment strategies. To determine whether a fluorescent-activated cell sorting (FACS)-based strategy overcomes these limitations, we compared microglial proteomes of MACS and FACS-based purified CD11b+ microglia in order to identify core sets of microglial proteins in adult mouse brain tissue. Results Quantitative multiplex proteomics by tandem mass tag mass spectrometry (TMT-MS) of MACS-enriched (N = 5) and FACS-purified (N = 5) adult wild-type CD11b+ microglia identified 1,791 proteins, of which 953 were differentially expressed indicating significant differences between both approaches. While the FACS-purified microglia proteome was enriched with cytosolic, endoplasmic reticulum and ribosomal proteins involved in protein metabolism and immune system functions, the MACS-enriched microglia proteome was enriched with proteins related to mitochondrial function and synaptic transmission. As compared to MACS, the FACS microglial proteome showed strong enrichment for canonical microglial proteins while neuron, astrocyte, and oligodendrocyte proteins were decreased. Interestingly, we observed enrichment of endothelial specific proteins in the FACS microglia proteome. By comparing FACS-purified microglia proteomes with transcriptomes, we observed highly concordant as well as highly discordant proteins that were abundant at the protein level but low at the transcript level. Conclusions We demonstrate that TMT-MS proteomics of FACS-purified adult microglia is superior to column-based enrichment approaches, resulting in purer and highly-enriched microglial proteomes. We also define core sets of highly-abundant adult microglial proteins including Moesin (Msn) that can guide future studies.

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