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AP-MS MudPIT run of Swr1 complex

ABSTRACT: File name explanation: Sc_Swr1_TAP_V2_P1_Ti_101: Sc = Saccharomyces cerevisiae (specie) Swr1 = bait protein TAP = tag V2 = lab instrument name(Velos_Elite2) P1 = biological replicate 1 Ti = LysC+Trypsin digestion 101 = MudPIT run 1 from 1st technical replicate

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932)

SUBMITTER: Michael P. Washburn, Craig L. Peterson, Thomas Walz

PROVIDER: MSV000079019 | MassIVE | Wed Jan 28 10:51:00 GMT 2015

SECONDARY ACCESSION(S): PXD001743

REPOSITORIES: MassIVE

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Publications

Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C.

Watanabe Shinya S Tan Dongyan D Lakshminarasimhan Mahadevan M Washburn Michael P MP Hong Eun-Jin Erica EJ Walz Thomas T Peterson Craig L CL

Nature communications 20150512

INO80-C and SWR-C are conserved members of a subfamily of ATP-dependent chromatin remodelling enzymes that function in transcription and genome-maintenance pathways. A crucial role for these enzymes is to control chromosomal distribution of the H2A.Z histone variant. Here we use electron microscopy (EM) and two-dimensional class averaging to demonstrate that these remodelling enzymes have similar overall architectures. Each enzyme is characterized by a dynamic 'tail' domain and a compact 'head' ...[more]

PMID: 25964121

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AP-MS MudPIT run of yeast R2TP complex

Project description:File name explanation: Sc_Rvb1_TAP_P1_Ti_101: Sc = Saccharomyces cerevisiae (specie) Rvb1 = bait protein TAP = tag L1 = lab instrument name(LTQ1) P1 = biological replicate 1 Ti = LysC+Trypsin digestion 101 = MudPIT run 1 from 1st technical replicate rvb1_his_sf21_E1_P1_Ti_101: Sf21 = Spodoptera frugiperda rvb1 = protein with tag his = 6x HIS tag E1 = elution number 1 L1 = lab instrument name(LTQ1) P1 = biological replicate 1 Ti = LysC+Trypsin digestion 101 = MudPIT run 1 from 1st technical replicate rvb2 = rvb2 protein hsc82 = hsp90 protein

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CLIP-seq of S. cerevisiae Drn1-TAP and Dbr1-TAP

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Mus musculus strain:C57BL/6J

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[E-TABM-828] ChIP-Seq in human MCF7 and HEPG2 cells

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Genome-wide maps of nucleosome positioning in asynchronously growing yeast cells

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Single cell transcriptomic analysis of P8 and P15 mouse cochlea (control and three overexpression conditions) and simultaneous single cell transcriptomic and accessible chromatin analysis of P1 and P8 mouse cochlea (wildtype)

Project description:Purpose - To determine transcriptomic variations in the mouse cochlea in response to three different transcription factor overexpression conditions and no induction control and to determine transcriptomic and accessible chromatin variations in the mouse cochlea between postnatal day 1 (P1) and postnatal day 8 (P8) stages of development. Methods - SC RNA seq performed on FACS enriched cells obtained from experimental animals (Sox9CreER; Rosa26A/GA/GAP/+; Rosa26 tdtomato). Same samples at two timepoints 1 week (P8) and 2 week (P15) ages. scMultiome ATAC + Gene Expression (10x Genomics) experiments on enzymatically dissociated and unenriched cochlear nuclei from wildtype mice in a mixed background of CD1 and FVB/NJ, and C57BL/6. Samples were collected at P1 and P8. Gene expression data was used to annotate clusters. Chromatin accessibility determined by ATAC was compared between P1 and P8 stages. Results - The SC RNA seq highlighted differential transcriptomic changes between the two ages and the three overexpression conditions. Hair cell loci become less epigenetically accessible in supporting cells and GER cells between P1 and P8. Conclusions - Our study highlights the variability in transcriptomic response to three transcription factor combination mediated reprogramming cues at two different ages. The SC RNA seq confirmed a variety of our biological observations with regard to the hair cell reprogramming process in the mouse cochlea. We also demonstrate variability in chromatin accessibility between P1 and P8, which may explain why GER and supporting cells of the cochlea become more resistant to transcription factor reprogramming into hair cells during the first postnatal week.

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