EXPERIMENT_TITLE: GSM6050304: UPN3550_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Five million cells for each cell line were cross-linked with 1% formaldehyde for 10 mins at room temperature and then then quenched with 0.2M Glycine. Cell pellets were washed with cold PBS and lysed with lysis buffer to get nuclei pellets. MB004 (G3 MB) and UPN3550 (G4 MB) cells were processed for Hi-C library construction using the Arima Hi-C Kit following the manual (Arima Genomics). Briefly,  nuclei were permeabilized and in situ digested. KAPA Hyper Prep kit was used for library amplification (KAPA, KK2802).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We report the application of single-molecule-based sequencing technology for high-throughput profiling of chromosome occupation and single cell gene expression or single nuclei chromatin accessibility in medulloblastoma tissues or cells. To further define the cellular identity at the single cell level, we characterized 26 MB tissues including 18 newly diagnosed MB tumor tissues by single cell scRNA-seq and scATAC-seq (the assay for transposase-accessible chromatin-sequencing) together with 8 previously reported MB single cell transcriptomics. The newly diagnosed MB tumors included four SHH-MBs (45,731 cells), nine G3-MBs (82,834 cells), thirteen G4 MBs (77,521 cells) with a median of 7,926 cells for scRNA-seq and 9,342 cells for scATAC-seq per MB tumor, respectively. To decipher how dynamic accessibility at the cis-regulatory elements (CREs) relates to the gene regulatory program in TCP-like cells from G3- and G4- MBs, we performed single nuclei ATAC-seq (snATAC-seq) to determine the single-cell chromatin accessibility landscape using high-quality nuclei from a set of fresh G3 and G4 MB tumors that matched with scRNA-seq. Finally, we show that gene expression with chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. Our studies identified a human-specific intermediate progenitor population important for cerebellar neural lineage development and the growth and metastasis of aggressive MBs, highlighting potential therapeutic targets. Overall design: Examination of single cell transcriptional and ATAC profiling in 3 human medulloblastoma tissues. Cut&run of 4 antibody for 2 cells To comprehensively explore the 3D genome architecture of human aggressive medulloblastomas and to assess the contributions of genome architecture to transcriptional regulation across subgroups, we performed comparative analyses of high-throughput chromosome conformation capture (Hi-C) in medulloblastoma patient derived tumor cells, including Group 3 MB cells MB-004 and Group 4 MB cells UPN3550. We performed the Hi-C experiments in these 2 cells Please note that the processed data file (along with the data processing description) has been updated for the GSM5952337 sample on April 26, 2023.
SAMPLE_TITLE: UPN3550_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Brain"}, {"TAG": "tissue", "VALUE": "Brain"}, {"TAG": "cell line", "VALUE": "UPN3550"}, {"TAG": "cell type", "VALUE": "medulloblastoma cells"}, {"TAG": "genotype", "VALUE": "wt"}, {"TAG": "treatment", "VALUE": "no"}]
Pool_Member_@attributes_sample_title: UPN3550_HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: UPN3550_HiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR18825717.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR018/18825/SRR18825717/SRR18825717.lite.1", "size": "176034631930", "date": "2022-10-09 10:10:12", "md5": "51aac27c00d6f5d065d609e9b99a2faf", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR18825717", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR18825717/SRR18825717", "size": "222238991814", "date": "2022-05-08 00:26:10", "md5": "8d744b80ccc4c9700ebf583674001f0d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "UPN3550_Hic38_CKDL210001540-1a_HWM5WDSXY_L4_2.fq.gz", "size": "177929945938", "date": "2022-05-07 23:28:20", "md5": "0aecdd3cc836ff8e0f61d5d721ceadba", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "UPN3550_Hic38_CKDL210001540-1a_HWM5WDSXY_L4_1.fq.gz", "size": "169023294900", "date": "2022-05-07 23:39:56", "md5": "377f1e5a0cc38f652d40836a556a87a3", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]