Dataset Information

Proteomes of chromatin fractions derived from SU-DHL-5 cells

ABSTRACT: SU-DHL-5 cells display limited expression of the SUMO isopeptidase SENP6. In this experiment, the chromatin associated fraction of SU-DHL-5 cells was analysed by mass spectrometry. SU-DHL-5 cells were either stably transfected with an empty vector or with a SENP6 expression construct. Changes in protein levels were compared between these two cell lines in triplicate experiments.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Lymph Node

DISEASE(S): Lymphoma

SUBMITTER: Stefan Müller

LAB HEAD: Stefan Müller

PROVIDER: PXD027355 | Pride | 2022-02-17

REPOSITORIES: Pride

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Publications

Genetic alterations of the SUMO isopeptidase SENP6 drive lymphomagenesis and genetic instability in diffuse large B-cell lymphoma.

Schick Markus M Zhang Le L Maurer Sabine S Maurer Hans Carlo HC Isaakaidis Konstandina K Schneider Lara L Patra Upayan U Schunck Kathrin K Rohleder Elena E Hofstetter Julia J Baluapuri Apoorva A Scherger Anna Katharina AK Slotta-Huspenina Julia J Hettler Franziska F Weber Julia J Engleitner Thomas T Maresch Roman R Slawska Jolanta J Lewis Richard R Istvanffy Rouzanna R Habringer Stefan S Steiger Katja K Baiker Armin A Oostendorp Robert A J RAJ Miething Cornelius C Lenhof Hans-Peter HP Bassermann Florian F Chapuy Björn B Wirth Matthias M Wolf Elmar E Rad Roland R Müller Stefan S Keller Ulrich U

Nature communications 20220112 1

SUMOylation is a post-translational modification of proteins that regulates these proteins' localization, turnover or function. Aberrant SUMOylation is frequently found in cancers but its origin remains elusive. Using a genome-wide transposon mutagenesis screen in a MYC-driven B-cell lymphoma model, we here identify the SUMO isopeptidase (or deconjugase) SENP6 as a tumor suppressor that links unrestricted SUMOylation to tumor development and progression. Notably, SENP6 is recurrently deleted in ...[more]

PMID: 35022408

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Project description:This is a dataset generated by the modENCODE Project. It contains both the pair-end and single-end sequencing data of genomic DNA, chromatin input and the ChIP of the factors Su(Hw) and H3K36me3 from Drosophila S2 cells and it was generated on Illumina Genome Analyzer. The goal was to sequence ~120M tags of each sample and used this ultra-deep dataset to systematically evaluate both experimental and computational factors that influence the results of ChIP-seq experiments. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf S2 cells from the modENCODE batch were amplified before transferring to the plates. 15 plates were put in culture until the cells reached the appropriate concentration. Cells were harvested from 2 plates to extract the genomic DNA. The remaining 13 plates were then treated with formaldehyde at the same time and the chromatin were extracted. 3 plates were used to produce an Input sample corresponding to the chromatin DNA of the treated cells. Each plate corresponding to an eppendorff tube of chromatin, ChIP experiments were performed on 5 tubes for H3K36me3 and on 5 tubes for Su(Hw). ChIP and DNA extraction were performed independently on each tube. After the purification of the DNA, the tubes corresponding to the same sample (Su(Hw), H3K36me3, Input and gDNA) were pooled together. After mixing, each sample was aliquoted again into 5 tubes. 1 aliquot of each was used for ChIP-chip on Affymetrix tiling arrays for quality control, 1 aliquot was used for single-end sequencing at the University of Chicago HGAC, 1 aliquot was used for single-end sequencing at UNC, 1 aliquot was used for paired-end sequencing at UNC and the remaining aliquot was kept as a back-up of the original samples. For each sample, >100M single-end tags were produced (~5 runs), along with the tags from 1 lane of paired-end sequencing experiment. Besides several experimental factors, the performance of multiple peak callers were evaluated at different sequencing depths.

Dataset Information

Proteomes of chromatin fractions derived from SU-DHL-5 cells

Publications

Genetic alterations of the SUMO isopeptidase SENP6 drive lymphomagenesis and genetic instability in diffuse large B-cell lymphoma.

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