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CITE-seq of SUMOi treated C57Bl6 mice

ABSTRACT: CITE-seq of SUMOi treated C57Bl6 mice

PROVIDER: PRJNA795953 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17524939.fastq.gz	Fastqsanger.gz
	SRR17524940.fastq.gz	Fastqsanger.gz
	SRR17524941.fastq.gz	Fastqsanger.gz
	SRR17524942.fastq.gz	Fastqsanger.gz
	SRR17524943.fastq.gz	Fastqsanger.gz

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CITE-seq of SUMOi treated C57Bl6 mice

Project description:In our study, we investigated the effect of inhibition of SUMOylation on murine splenocytes. Mice were treated with 7,5 mg/kg SUMOi (TAK-981) on day 1 and day 4 and analysed on day5.

2022-01-15 | GSE193359 | GEO

Transcriptional profiling of hepatic stellate cells (HSCs) isolated from Western diet/high fructose-fed C57BL6/J mice, carbon tretrachloride (CCl4)-treated C57BL6/J mice, and of murine HSCs differentiated in vitro

Project description:Hepatic stellate cells are involved in the development of hepatic fibrosis. We here perform transcriptional profiling of hepatic stellate cells (HSCs) isolated from Western diet/high fructose-fed C57BL6/J mice, carbon tretrachloride (CCl4)-treated C57BL6/J mice, and of murine HSCs differentiated in vitro. Specifically, gene expression profiles are obtained from hepatic stellate cells isolated from C57BL6 mice fed a Western Diet supplemented with high fructose for 12, 16 or 24 weeks or normal chow. From hepatic stellate cells isolated from C57BL6 mice treated CCl4 for 1, 4 or 8 weeks or treated with vehicle. From hepatic stellate cells isolated from healthy C57BL6 mice and seeded on normal plastic cell culture dishes for 1, 4, 8, or 12 days. And from hepatic stellate cells isolated from healthy C57BL6 mice and seeded on normal plastic cell culture dishes for 6 days in the presence of 10uM U0126 or DMSO.

2019-04-07 | E-MTAB-7054 | biostudies-arrayexpress

Single Cell RNA-Seq of Ear Epithelial Cells from i) steady state C57BL6/N & Tcrd-GDL mice, ii) untreated and TPA-treated C57BL6/J mice, and iii) IL13Ra1-knockdown CD1 mice

Project description:This dataset contains three experiments, designed for interrogating the effect of DETC on epithelial keratinocytes: Dataset 1) steady state ear epithelial cells (live, CD45-) from C57BL6/N (n=3) and Tcrd-GDL (n=3), after DETC deletion. Dataset 2) untreated and topical TPA-treated ear epithelial cells (live, CD45-, Vg5-) from C57BL6/J (n=3 untreated ears, n=3 treated ears). Dataset 3) steady state ear epithelial cells (GFP+) from CD1 (n=6) mice at age p8 weeks, following transduction with IL13Ra1-shRNA-GFP at e9.5.

2022-12-31 | E-MTAB-10441 | biostudies-arrayexpress

RNAseq in C57Bl6 and congenic Atf3-/- mice

Project description:RNA expression from whole pancreatic tissue was assessed by RNA-seq following 4 hours into cerulein-induced pancreatitis in mice lacking the transcription factor ATF3 or congenic C57Bl6 mice. Three mice were used for each group and sequncing performed by Toronto Genomics Centre.

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CITE-seq reveals inhibition of NF-kB pathway in B cells from vitamin D-treated multiple sclerosis patients

Project description:Vitamin D deficiency is a risk factor for multiple sclerosis (MS) and is correlated with disease activity and progression. Vitamin D treatment has emerged as potentially protective, even though results from randomized controlled trials are conflicting. Here, we used single-cell RNA-seq (scRNA-seq) coupled with barcoded antibodies targeting surface markers (CITE-seq) to discover candidate genes and pathways regulated in PBMC subpopulations from MS patients treated with high-dose vitamin D (n=5) or placebo (n=5). Best candidates were combined with genes involved in immune function and vitamin D metabolism for validation in a new cohort (n=8 in each group) by high-throughput qPCR (HT-qPCR) in naive CD4, Th1, Th17, Treg, naive CD8, memory and naive B cells, and MAIT cells, sorted by FACS. CITE-seq showed no significant changes in the proportions of these subpopulations in vitamin D-treated patients. Of the 92 candidate genes revealed by CITE-seq, differential expression of five genes (UXT, SNRPN, SUB1, GNLY and KLF6) was validated by HT-qPCR. CITE-seq also revealed the regulation of several pathways by vitamin D in naive and memory B cells, including MAPK, TLR and interleukin pathways, that contribute to counteract EBV-induced resistance to apoptosis through inhibition of the NF-kB pathway.

2023-10-05 | GSE239626 | GEO

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Project description:Proteomic dataset of 15 murine kidneys of 14-week-old male C57Bl6 mice. Mice were divided into 3 treatment groups four weeks prior to nephrectomy and 5 mice had ad libitum access to food and water, while another 10 mice received 30% food restriction. Calorically restricted mice either received intraperitoneal supplementation of 20-HETE or vehicle (EtOH in sodiumchloride 0.9%) for 8 days on a daily basis prior to nephrectomy. Ad libitum fed mice received vehicle injections for 8 days on a daily basis prior to nephrectomy.

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Single cell 5’ transcript, TCRαβ enriched, and Cell hashing/CITE-seq library preparation on the 10x chromium, and sequencing

Project description:Single cells from human colorectal cancer and normal adjacent colon of 16 patients were used for single-cell RNA-seq, TCR-seq, CITE-seq and Cell hashing. In brief, single cells were incubated for 3h with or without PMA/Ionomycin, and were treated with Cell hashing and CITE-seq antibodies to distinguish samples, stimulation/non-stimulation, and cell surface proteins. Sorted viable CD3+TCRαβ+ single cells were loaded into 10x genomics ChromiumTM controller to make nanoliter-scale droplets with uniquely barcoded 5’ gel beads called GEMs. After GEM-RT and the following some cDNA amplification steps, cDNAs derived from cellular mRNA were pooled for downstream processing and library preparation according to the manufacturer’s instructions. The 5’ transcript library was sequenced with Illumina Novaseq. The single cell TCR enriched library was sequenced with Illumina Miseq using 150 paired-end reads. HTO/ADTs from Cell hashing or CITE-seq were amplified using specific primers that append P5 and P7 sequences for illumina sequencing (Miseq or Nextseq). All fastq files were demultiplexed. Cell hashing and CITE-seq barcodes are available in attached text files. Fastq files from RNA-seq and TCR-seq can be processed through cellranger and vdjranger by 10xgenomics. The datasets include the data of independent experiments at May 29, June 16, June 23, and Aug 13, 2019. Details are available in Masuda et al., bioRxiv, 2020, The functional and phenotypic diversity of single T-cell infiltrates in human colorectal cancer as correlated with clinical outcome.

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Single Cell RNA-Seq of Ear Epithelial Cells from i) steady state C57BL6/N & Tcrd-GDL mice, ii) untreated and TPA-treated C57BL6/J mice, and iii) IL13Ra1-knockdown CD1 mice

Project description:Single Cell RNA-Seq of Ear Epithelial Cells from i) steady state C57BL6/N & Tcrd-GDL mice, ii) untreated and TPA-treated C57BL6/J mice, and iii) IL13Ra1-knockdown CD1 mice

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Transcriptome profiling of bladders of CYP-treated C57BL6/J mice (male and female)

Project description:Transcriptome profiling of bladders of CYP-treated C57BL6/J mice (male and female)

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CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) of paired diagnosis and relapse specimens from acute myeloid leukemia (AML) patients treated with venetoclax plus azacitidine

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