EXPERIMENT_TITLE: GSM3044594: HiC – 1h 110 mM NaCl + recovery (batch 3); Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: HiC: in situ Hi-C was performed according previously described protocol (Rao et al., 2014) with some modifications (Le Dily et al., 2017). RNA-seq: RNA from control or NaCl-treated T47D cells was extracted at the indicated times using the RNeasy Plus Mini Kit (Invitrogen #74134). HiC: Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014). RNA-seq: stranded polyA selected libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) according to the manufacturer's standard protocol.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Osmostress causes chromatin compaction and simultaneously triggers a massive transcriptional response in eukaryotic cells that is required for adaptation and cell survival. However, thus far it was unknown how changes of chromatin organization and ongoing DNA transcription are linked under hyper-osmotic conditions. In this study, we focused on elucidating the extend of chromatin reoganization upon hyper-osmotic shock, its reversibility and its link with active transcription in human T47D cells. Overall design: T47D cells were subjected to 100 mM NaCl for defined periods of time and both total RNA as well as chromatin were collected in several batches. RNA steady state levels between stressed and untreated T47D cells were compared using RNA-seq at 1 h, 3 h and 6 h of exposure to NaCl. Changes of active transcription / Pol II occupation were determined by ChIP-seq of Pol II, again comparing unstressed and stressed cells (1 h stress). We used HiC to study chromatin organization before and after NaCl treatment (1 h) as well as when inhibiting transcription by pre-treating cells with 500 nM of triptolide for 3 h prior to sequencing. In addition, recovery of the initial chromatin interaction profiles was assessed by shifting cells back to isotonic conditions for 1 h after NaCl exposure, both with and without triptolide addition. We also assessed CTCF binding to chromatin after 7.5 min, 30 min and 60 min compared to basal conditions using ChIP-seq. ChIP-seq was also used to evaluate RAD21 binding after 1 h of stress as well as 1 h of stress plus 1 h of recovery (in line with HiC experiments) compared to control.
SAMPLE_TITLE: HiC – 1h 110 mM NaCl + recovery (batch 3)
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "T47D whole cell"}, {"TAG": "cell line", "VALUE": "T47D"}, {"TAG": "batch", "VALUE": "3"}, {"TAG": "pre_treatment", "VALUE": "untreated"}, {"TAG": "pre_treatment_time", "VALUE": "-"}, {"TAG": "treatment", "VALUE": "110 mM NaCl + recovery"}, {"TAG": "treatment_time", "VALUE": "60 min + 60 min"}]
Pool_Member_@attributes_sample_title: HiC – 1h 110 mM NaCl + recovery (batch 3)
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC – 1h 110 mM NaCl + recovery (batch 3)
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