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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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SnATAC-seq data from single cell multiomics (paired snRNA-seq+snATAC-seq) of human colorectal cancer liver metastatic samples

ABSTRACT: These samples are part of a study investigating cancer cell plasticity in colorectal cancer metastasis. Tumour microenvironment cell types and cancer cell states were identified using 10x Genomics Multiome (paired snRNA-seq + snATAC-seq). snATAC-seq data is uploaded here.

INSTRUMENT(S): 10x Chromium, NextSeq 550

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-13652 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): E-MTAB-13651

REPOSITORIES: biostudies-arrayexpress

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snRNA-seq data from single cell multiomics (paired snRNA-seq+snATAC-seq) of human colorectal cancer liver metastatic samples

Project description:These samples are part of a study investigating cancer cell plasticity in colorectal cancer metastasis. Tumour microenvironment cell types and cancer cell states were identified using 10x Genomics Multiome (paired snRNA-seq + snATAC-seq). snRNA-seq data is uploaded here.

2025-04-22 | E-MTAB-13651 | biostudies-arrayexpress

snATAC-seq of the developing mouse cerebellum across eleven stages

Project description:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 91,922 nuclei in the mouse cerebellum across eleven developmental stages, from the beginning of neurogenesis (e10.5) till adulthood (P63). The study included two biological replicates per stage, one from each sex. Cerebelli were dissected as whole or in two halves, nuclei were extracted and profiled using 10x single-cell ATAC reagent kit (v1.0) and a Chromium controller. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).

2021-09-07 | E-MTAB-9765 | biostudies-arrayexpress

snATAC-seq of the gray short-tailed opossum cerebellum in two developmental stages

Project description:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 19,204 nuclei in the opossum (Monodelphis domestical) cerebellum across two developmental stages (postnatal day 21 and adult). The study included two biological replicates per stage, one from each sex, and an additional adult sample enriched for white matter. Cerebelli were dissected in two halves, nuclei were extracted from one half and profiled using 10x single-cell ATAC reagent kit (v1.1) and a Chromium controller. The white matter enriched sample was dissected from coronal cerebellum slices. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).

2021-09-07 | E-MTAB-10533 | biostudies-arrayexpress

Multiomic (Joint snRNA/snATAC) sequencing data of intestinal crypts and epithelial only organoids derived from human fetal duodenum

Project description:Here, we used joint single-nuclei RNA-sequencing (snRNA-seq) and single-nuclei ATAC sequencing (scATAC) to profile freshly isolated crypts from the human fetal intestine and matched intestinal epithelial only organoids (also known as enteroids) derived from these crypts after one passage of in vitro growth. Organoids were grown in the standard 25% LWRN media with either 100 ng/ml of EGF or 1 ng/ml of EREG added. Fresh crypts were not placed in culture but rather immediately frozen for multiomic processing.

2022-07-16 | E-MTAB-11908 | biostudies-arrayexpress

Multiome scRNA- and scATAC-seq of healthy and trisomy 21 (Down's syndrome) foetal liver

Project description:Here, we performed multiome sequencing (snRNA-seq + snATAC-seq) of human fetal liver samples from 3 trisomy 21 (Ts21) and 3 healthy foetuses (median age 14 post-conception weeks). The data set is composed of approximately 60,000 CD45+ foetal liver cells.

2024-07-17 | E-MTAB-13070 | biostudies-arrayexpress

Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation

Project description:We present high quality deep read-depth single cell RNA sequencing for 91 cells from five mouse tissues and 18 cells from two rat tissues, along with 30 control samples of bulk RNA diluted to single-cell levels. We find that transcriptomes differ globally across tissues with regard to the number of genes expressed, the average expression patterns, and within cell-type variation patterns. We develop methods to filter genes for reliable quantification and to calibrate biological variation. All cell types include genes with high variability in expression, in a tissue-specific manner. We also find evidence that single cell variability of neuronal genes in mice is correlated with that in rats consistent with the hypothesis that levels of variation may be conserved. From an initial 143 cells we identified 107 high quality samples with deep genic coverage, including 13 brown adipocytes, 19 cardiomyocytes, 19 cortical pyramidal neurons and 18 hippocampal pyramidal neurons from embryonic mouse, 8 cortical pyramidal neurons and 8 hippocampal pyramidal neurons from embryonic rat, and 22 serotonergic neurons from adult mouse. While mouse data is collected from three strains of mice at different ages, each cell type dataset is internally consistent. There are no technical replicates of single-cell samples. We additionally prepared 30 control samples, amplifications of bulk total cardiomyocyte RNA diluted to single cell quantities.

2015-05-21 | E-GEOD-56638 | biostudies-arrayexpress

GRO-seq in HeLa cells

Project description:Mapping the nascent RNA transcriptome of HeLa cells with GRO-seq Standard GRO-seq assay from two replicates in HeLa cells

2014-10-04 | E-GEOD-62046 | biostudies-arrayexpress

snATAC-seq from stomach (ENCSR549JEQ)

Project description:snATAC-seq of human stomach For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2025-01-14 | GSE286753 | GEO

snATAC-seq from stomach (ENCSR848EID)

2025-01-14 | GSE286835 | GEO

snATAC-seq from forebrain (ENCSR836VNN)

Project description:snATAC-seq of mouse forebrain For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2025-01-14 | GSE286832 | GEO

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