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TranscriptomicsSix in situ Hi-C libraries of control and mESC auxin-inducible degrons for Scc1 and Ring1b.
In this experiment, we've examined chromatin conformation differences of E14 mESC against cohesin and Ring1b degrons. We performed a modified in situ Hi-C protocol from (Rao et al., 2014) that can be found in detail at (Díaz et al., 2018). Samples were digested with MboI restriction enzyme. The aim ...
ORGANISM(S): Mus musculus 
2020-01-23 | E-MTAB-7816 | biostudies-arrayexpress
GenomicsRING1B calibrated ChIP-seq (cChIPseq) datasets for control mESCs and an Scc1-AID auxin-inducible degron.
We examined 3D chromatin structure in the absence of cohesin (Scc1-AID auxin-inducible degron) and a control line (E14-Tir1) and found that PRC1 core promoter component RING1B was one of the most enriched proteins. Hence, we performed calibrated ChIP-seq experiments on the control (E14-Tir1) and the...
ORGANISM(S): Mus musculus 
2020-01-23 | E-MTAB-7817 | biostudies-arrayexpress
TranscriptomicsCapture-C experiments on auxin treated control (E14-Tir) and Scc1-AID, Ring1b-AID, Ring1b-AID-Scc1-AID and CTCF-AID (with and without a 6-hour auxin treatment) cells
The aim of the experiment was to gain a higher resolution for specific regions of interest to complement the Hi-C results. Capture-C experiments were performed on four-inducible degrons for Scc1, Ringb, Ring1b-Scc1 and CTCF, and Tir1 control, always in triplicates (three biological replicates per co...
ORGANISM(S): Mus musculus 
2020-01-23 | E-MTAB-7840 | biostudies-arrayexpress
TranscriptomicsCalibrated total RNAseq (cRNA-seq) of E14_Scc1_AID mESCs mixed with Drosophila SG4 cells with and without a 6-hour auxin treatment
We performed calibrated total RNAseq on mESC (Scc1-AID) for both untreated and treated cells with a 6-hour auxin exposure to assess the effects of cohesin removal on gene expression. For calibration purposes 2x10ˆ6 Drosophila SG4 cells were spiked in.
ORGANISM(S): Mus musculus 
2020-01-23 | E-MTAB-7818 | biostudies-arrayexpress
GenomicsGenome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation
Erythropoiesis is dependent on the activity of transcription factors, including the erythroid-specific erythroid Kruppel-like factor (EKLF). ChIP followed by massively parallel sequencing (ChIP-Seq) is a powerful, unbiased method to map transfactor occupancy. We used ChIP-Seq to study the interactom...
ORGANISM(S): Mus musculus 
2013-06-17 | E-GEOD-48020 | biostudies-arrayexpress
ProteomicsProteome of senescent human lung fibroblasts and Panc-1 cells
Proteomic analysis of proliferating and senescent normal healthy lung fibroblasts (NHLFs) and Panc-1 cells. Senescence was induced using 5 uM Palbociclib for 6 days. Cells were lysed in SDS lysis buffer (2% SDS in 100 mM TEAB), boiled (15 min, 95 °C, 500 rpm) and sonicated in a sonication bath (10 ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2022-10-28 | MSV000090607 | MassIVE
UnknownUsing verbal autopsy to measure causes of death: the comparative performance of existing methods.
Not available
S-EPMC3891983 | biostudies-literature
UnknownElective Cancer Surgery in COVID-19-Free Surgical Pathways During the SARS-CoV-2 Pandemic: An International, Multicenter, Comparative Cohort Study.
Not available
S-EPMC8189635 | biostudies-literature
UnknownDeath following pulmonary complications of surgery before and during the SARS-CoV-2 pandemic.
Not available
S-EPMC10364875 | biostudies-literature
UnknownEffect of COVID-19 pandemic lockdowns on planned cancer surgery for 15 tumour types in 61 countries: an international, prospective, cohort study.
Not available
S-EPMC8492020 | biostudies-literature
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