EXPERIMENT_TITLE: GSM5665773: DND41ResCas9_bioRep2_EBF1g7_Arima_HiC_rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: 1-2x10^6 cells were washed with 1xPBS containing 3% BSA and fixed with 2% formaldehyde and proceeded with Arima-HiC Kit per manufacturer's instructions. Samples passing Arima-QC1 were used for library construction with Accel-NGS 2S Plus DNA Library Kit (Swift cat# 21024) and 2S SET A INDEXING KIT (Swift cat# 26148) and assessed with Arima-QC2. Samples passing Arima-QC2 were subsequently PCR amplified based on Arima-QC2 calculations, quantified with TapeStation 4150 (Agilent) and KAPA Library Quantification Kit (Roche cat# KK4824) and paired-end (38bp+38bp) sequenced on Illumina NextSeq 550.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Purpose: To investigate the mechanisms of 3D genome organization in drug-resistant T-ALL Methods: We used multiple epigenomics, chromatin conformation, and transcriptomic assays to study the mechanisms of chromatin adaptation in GSI-sensitive and GSI-resistant T-ALL Results: We report here that T/B cell lineage determining transcription factors are differentially expressed in GSI-resistant T-ALL cells, driving enhancer switching and genome folding reorganization events to promote GSI-resistance. Conclusions: These observations suggest a general mechanism that diffenrential activity of pioneering factors can be exploited to evade addiction to oncogenic signals. Overall design: In situ HiC was performed in parental and GSI-resistant DND41 cells, and DND41-Res-Cas9 control and LRmCherry2.1-EBF1-g7 cells sorted 6 days post transduction.
SAMPLE_TITLE: DND41ResCas9_bioRep2_EBF1g7_Arima_HiC_rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "DND41 cell line"}, {"TAG": "cell line", "VALUE": "DND41 cell line"}, {"TAG": "cell type", "VALUE": "T-ALL cell line"}, {"TAG": "lentiviral transduction", "VALUE": "Cas9 and EBF1-targeting sgRNA"}, {"TAG": "drug treatment", "VALUE": "GSI"}]
Pool_Member_@attributes_sample_title: DND41ResCas9_bioRep2_EBF1g7_Arima_HiC_rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: DND41ResCas9_bioRep2_EBF1g7_Arima_HiC_rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR16701052.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR016/16701/SRR16701052/SRR16701052.lite.1", "size": "32264406785", "date": "2022-09-26 17:28:35", "md5": "f8c79f2d2ecbb5551a8a3d3a122569b1", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR16701052", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16701052/SRR16701052", "size": "40338911949", "date": "2021-11-05 15:52:19", "md5": "1720da39639fe90e5af578e7b92a0180", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "s02_210714_DND41yzshCas9_EBF1g7_ArimaHiC_nova_S2_R2_001.fastq.gz", "size": "37220399765", "date": "2021-11-05 15:33:40", "md5": "7123e02d9a146954f99541a6e725c1fa", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "s02_210714_DND41yzshCas9_EBF1g7_ArimaHiC_nova_S2_R1_001.fastq.gz", "size": "35607878079", "date": "2021-11-05 15:14:07", "md5": "532af06fd3ad9a86aae042b699a691ad", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]