{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Qianhui Yu"],"organism":["Pan troglodytes"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15112"],"description":["To study the species difference in developing intestine between human and chimpanzees, we performed scMultiome profiling on developing human intestine tissues and matched intestinal epithelial only organoids (also known as enteroids), and performed scRNA-seq and scATAC-seq measurements on human and chimpanzee pluripotent stem cell derived intestinal multilineage organoids. We have in vitro organoids and organoids that are further transplanted into mice for further maturation. We also performed scSTARR-seq based on developing human enteroids to quantify the enhancer activity of selected regulatory regions at different epithelial cell types or with different genetic variants."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Developing intestinal tissues and organoids samples were enzymatically and mechanically dissociated into single cells using the Neural Tissue Dissociation Kit (Miltenyi Biotec, 130-092-628). For scATAC and multiome, nuclei were isolated with a custom lysis buffer for developing human tissue, while 10x Genomics protocols were followed for all other samples. Specific human and chimpanzee organoid single cell suspensions were pooled at equal amount.","Nucleic Acid Extraction - For all samples, nucleic acids were extracted and processed following the recommendations and standard protocols of 10x Genomics for the corresponding data type.","Library Construction - For all samples, scRNA-seq, scATAC-seq and multiome libraries were generated on a 10x Chromium device following the recommendations and standard protocols of 10x Genomics for the corresponding data type.","Sequencing - Nucleic acid libraries were sequenced on Illumina sequencing platforms by IOB sequencing core, D-BSSE sequencing facility, Roche G&G sequencing core team and the Michigan sequencing facility following the recommendations and standard protocols of Illumina for the corresponding libraries and sequencing platforms.","Sequencing - Nucleic acid libraries were sequenced on Illumina sequencing platforms by Roche G&G sequencing core team and the Michigan sequencing facility following the recommendations and standard protocols of Illumina for the corresponding libraries and sequencing platforms."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - For read alignment of the scRNA-seq data of human pluripotent stem cell-derived intestine organoids, Cell Ranger (10x Genomics, version 4.0.0) with default parameters was used to align reads to the human reference (GRCh38, 10x Genomics, version 3.1.0) to generate the transcript count matrix for cells. For the chimpanzee-induced pluripotent stem cell-derived intestine organoids, we downloaded the panTro6 reference genome and NCBI annotation from the UCSC genome browser and built up the reference packages for Cell Ranger using the cellranger mkref function. To demultiplex the pooled scRNA-seq samples with both human and chimpanzee cells collected from the same 10x run, we first mapped the pooled samples to human-chimp consensus genome. Read alignment coordinate is based on the human genome. The genome alignment between human (hg38) and chimpanzee (panTro6) was downloaded from UCSC Genome Browser. Sites with diverged bases between human and chimpanzee located on human protein-coding genes were obtained based on the genome alignment. Reads covering the species-diverged sites were collected for each reported cell, with the number of bases matching each species counted. Cells with more than 80% reads covering the species-diverged sites matching with one species were assigned as cells from the species (species-specific read assignment). Demultiplexed cell barcodes of each species are provided as lists.  We then ran log-normalization with the function \\\"NormalizeData\\\" in Seurat (version 4.0.0) on the Cell Ranger output gene level count matrix with default settings.  Normalized and annotated chimp data from pooled samples are in Res_inVitro_and_transplanted_CIO_rna_with_refined_cell_type_annotation.rds. Processed human data from pooled samples are in Res_HIO_rna_with_cell_type_annotation.rds.","Data Transformation - For the the scMultiome data of developing human proximal small intestine epithelial stem cell derived enteroids and duodenum primary tissues, Cell Ranger ARC (10x Genomics, version 2.0.1) was used to align reads of both the RNA library and ATAC library to the human reference (GRCh38, 10x Genomics, version 2020-A-2.0.0) to generate both the transcript and peak fragment count matrices. We then normalized the gene expression data using ‘SCTransform’ with default parameters.","Data Transformation - For read alignment of scATAC-seq data of the chimp intestinal organoid samples was aligned to the chimp reference, which was built from panTro6 reference genome and NCBI annotation retrieved from UCSC genome browser using mkref function by Cell Ranger ATAC (10x Genomics, version 1.2.0). For the scATAC-seq data of the human intestinal organoid samples, Cell Ranger ATAC (10x Genomics, version 1.2.0) with default parameters was used to align reads to the human reference (GRCh38, 10x Genomics, version 1.1.0) to generate the peak fragment count matrix for cells. Demultiplexing the scATAC-seq samples is performed with a similar procedure to the scRNA-seq samples, with the differences that human-chimp diverged sites are called within the scATAC-seq peak regions reported by Cell Ranger ATAC. Demultiplexed cell barcodes of each species are provided as lists.  For scATAC-seq data normliazation, to generate a unified peak list to combine the chromatin accessibility profiles in different samples, we used MACS2 to perform peak calling on each sample separately (except for developing human small intestine tissue and epithelial stem cell-derived organoid scMultiome data) and merge (using the Signac-implemented wrapper function CallPeaks in default parameters). Based on the new peak list, the fragment number per peak of cells in the scATAC-seq and multiome data were re-quantified using FeatureMatrix. We then ran \\\"RunTFIDF\\\" function in Signac (version 1.4.0) on the unified open chromatin region list for chromatin accessibility level normalization.  Normalized and annotated human data from the pooled sample are in Res_HIO_atac_annotate_mes_with_low_res_clustering.rds. Processed chimp data from the pooled samples are in Dat_CIO_atac_with_fragment_file.rds."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000","NextSeq 2000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Pan troglodytes"],"pubmed_authors":["Qianhui Yu","Umut Kilik","J. Gray Camp","Stefano Secchia","Jason Spence"],"additional_accession":[]},"is_claimable":false,"name":"Single cell sequencing data of developing human intestine tissue and human and chimpanzee intestine organoids","description":"To study the species difference in developing intestine between human and chimpanzees, we performed scMultiome profiling on developing human intestine tissues and matched intestinal epithelial only organoids (also known as enteroids), and performed scRNA-seq and scATAC-seq measurements on human and chimpanzee pluripotent stem cell derived intestinal multilineage organoids. We have in vitro organoids and organoids that are further transplanted into mice for further maturation. We also performed scSTARR-seq based on developing human enteroids to quantify the enhancer activity of selected regulatory regions at different epithelial cell types or with different genetic variants.","dates":{"release":"2025-08-08T00:00:00Z","modification":"2025-08-08T09:16:09.082Z","creation":"2025-05-02T15:41:41.332Z"},"accession":"E-MTAB-15112","cross_references":{"ENA":["ERP172217"],"Biostudies":["E-MTAB-14972"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}