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Series GSE111923 Query DataSets for GSE111923
Status Public on Nov 23, 2018
Title Osmostress induced changes of chromatin architecture and transcription in mammalian cells [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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 extent 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 2 h prior stress or no stress, resulting in a total inhibition time of 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. Lastly, both CTCF and RAD21 ChIP-seq with and without stress (1 h) as well as recovery of chromatin binding after 1 h of stress were also performed when inhibiting transcription by triptolide pre-treatment (2 h, 500 nM).
 
Contributor(s) Amat R, Böttcher R, le Dily F, Vidal E, Quilez J, Cuartero Y, de Nadal E, Beato M, Posas F
Citation(s) 30523037
Submission date Mar 15, 2018
Last update date Mar 27, 2019
Contact name Francesc Posas
Organization name Cell Signaling Group, Universitat Pompeu Fabra
Street address Dr. Aiguader 88
City Barcelona
ZIP/Postal code 08003
Country Spain
 
Platforms (3)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (41)
GSM3045107 CTCF - no stress - IP rep1
GSM3045108 CTCF – 7.5min 110 mM NaCl - IP rep1
GSM3045109 CTCF – 1h 110 mM NaCl - IP rep1
This SubSeries is part of SuperSeries:
GSE111924 Osmostress induced changes of chromatin architecture and transcription in mammalian cells
Relations
BioProject PRJNA438548
SRA SRP135831

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Supplementary file Size Download File type/resource
GSE111923_RAW.tar 28.9 Mb (http)(custom) TAR (of BROADPEAK, NARROWPEAK)
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Raw data are available in SRA
Processed data provided as supplementary file

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