EXPERIMENT_TITLE: GSM6585558: Hi-C DE biol rep 3; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C: 2 million cells were collected and fixed with 1% formaldehyde. The subsequent steps of Hi-C were then performed using the Arima-HiC kit (Arima; A510008). Hi-C: Libraries for sequencing were prepared with the KAPA Hyper Prep Kit (KAPA; KK8502) following the manufacturer's guidelines. Samples were pooled and sequenced on Illumina HiSeq 4000 platform.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We performed CRISPRi enhancer screens during differentiation of human embryonic stem cells (hESC) to definitive endoderm (DE) in genomic windows surrounding ten lineage-specifying core TFs. We also generated scRNA-seq, ATAC-seq, and TF ChIP-seq data and show that CTCF loops constrain the interactions between enhancers and their promoter targets. Overall design: Single-cell scRNA-seq gene expression profiling of differentiating idCas9-KRAB SOX17eGFP/+ HUES8 hESC line at 7 time points from 0hr to 72hr post-differentiation ATAC-seq chromatin accessibility profiling of differentiating idCas9-KRAB SOX17eGFP/+ HUES8 hESC line at 7 time points from 0hr to 72hr post-differentiation gRNA sequencing data of CRISPRi experiment at 36hr post differentiation in idCas9-KRAB SOX17eGFP/+ HUES8 hESC line Hi-C chromatin interaction profiling in hESC and DE HUES8 hESC cell line. TF ChIP-seq for GATA6, EOMES, SOX17, H3K27ac, and CTCF in HUES8 hESC line
SAMPLE_TITLE: Hi-C DE biol rep 3
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Hues8"}, {"TAG": "cell line", "VALUE": "Hues8"}, {"TAG": "cell type", "VALUE": "hESC"}, {"TAG": "genotype", "VALUE": "idCas9-KRAB SOX17eGFP/+"}, {"TAG": "treatment", "VALUE": "ESC-DE differentiaion"}]
Pool_Member_@attributes_sample_title: Hi-C DE biol rep 3
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