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ProteomicsStructural basis of the interaction between SETD2 methyltransferase and hnRNP L paralogs for governing co-transcriptional splicing
Protein samples were analyzed by Multidimensional Protein Identification Technology (MudPIT), as described previously. Briefly, precipitated proteins were resuspended in 30uL of 100mM Tris pH 8.5 with 8M urea to denature proteins. Cysteines were reduced and alkylated prior to digestion with recombi...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2021-05-11 | MSV000087403 | MassIVE
TranscriptomicsThe MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila
Active genes on the X chromosome of Drosophila males are upregulated by the Male-specific lethal (MSL) complex containing five MSL proteins and two non-coding roX RNAs. To probe the targeting mechanism, we have solved the structure of the MSL3 chromodomain, designed point mutations in key residues t...
ORGANISM(S): Drosophila melanogaster 
2008-11-18 | E-GEOD-11817 | biostudies-arrayexpress
TranscriptomicsMicroarray analysis of gene expression changes in human A549 lung cancer cells upon siRNA knockdown of FAM60A and SDS3
The Sin3 histone deacetylase (HDAC) complex is a 1.2 MDa chromatin modifying complex that can repress transcription by binding to gene promoters and deacetylating histones. The Sin3/HDAC complex can affect cell cycle progression through multiple mechanisms and is among the targets of anticancer dru...
ORGANISM(S): Homo sapiens 
2012-09-15 | E-GEOD-39733 | biostudies-arrayexpress
GenomicsPost-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation (ChIP-seq)
SAGA is a highly conserved transcriptional co-activator complex involved in multiple steps of transcription with activities that function both pre and post initiation. Loss of individual subunits results in developmental defects, suggesting a role in development. To better understand the roles of SA...
ORGANISM(S): Drosophila melanogaster 
2011-08-22 | E-GEOD-29513 | biostudies-arrayexpress
ProteomicsMudPIT analyses of the proteins co-purified with Ada2b-PB-FLAG-HA FLAG-affinity purified from Drosophila melanogaster S2 cells
Protein Complexes Purification- Stable S2 cell lines expressing Ada2b (isoform B; NP_001027151.1) in the pRmHa3-CHA2FL2 (Ada2b-PBH2F2) were maintained at 1-2 e6 cells/mL in SFX medium (HyQ SFX-Insect). Cells stably transfected with empty vector served as negative controls. Protein complexes containi...
ORGANISM(S): Drosophila Melanogaster (ncbitaxon:7227) 
2018-11-20 | MSV000083153 | MassIVE
ProteomicsMudPIT analyses of the proteins associated with Human SETD2 deletion mutants
N-terminally Halo-tagged deletions of human SETD2 were constructed such as SETD2 ABCN1, A, B, C, CN, and CC consisted of amino acids 1-1692, 1-503, 504-1403, 1404-2564, 1404-1963, and 1964-2564, respectively. Deletion mutants were expressed in HEK293T cells and affinity purified, each in biological ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2021-06-08 | MSV000087587 | MassIVE
GenomicsA role for Snf2 related nucleosome spacing enzymes in genome-wide nucleosome organization
The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here we show that the combined action of Isw1 and Chd1 nucleos...
ORGANISM(S): Saccharomyces cerevisiae 
2011-09-16 | E-GEOD-31015 | biostudies-arrayexpress
ProteomicsMudPIT analyses of the pyruvate dehydrogenase complex (PDC) isolated from Saccharomyces cerevisiae by FLAG-affinity purification and Size Exclusion Chromatography
Yeast protein extractions and subcellular fractionation Yeast cells expressing FLAG tagged proteins were grown in YPD medium at 30oC to OD600 of 0.8. 12 Liters YPD culture of cells were pelleted and washed in SB buffer. The pellet was resuspended in SB buffer and treated with 2 mg/ml Zymolyase 20T ...
ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932) 
2020-03-20 | MSV000085126 | MassIVE
ProteomicsMudPIT analyses of the pyruvate dehydrogenase complex (PDC) isolated from human
Mammalian protein extraction and Halo purification For Halo purification, HEK293T cells at 40% confluency in a 100 mm plate were transfected with 10ug of plasmid containing ORF of PDHA1-HA-Halo in 1X BBS with 125 mM CaCl2. Cells were harvested by scraping in PBS following PBS wash after 24 hours fro...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-03-20 | MSV000085125 | MassIVE
ProteomicsThe nuclear granule Paraspeckles interacts with the chromatin remodeling SWI/SNF complex to regulate alternative splicing
Protein samples were analyzed by Multidimensional Protein Identification Technology (MudPIT), as described previously. Briefly, precipitated proteins were resuspended in 30uL of 100mM Tris pH 8.5 with 8M urea to denature proteins. Cysteines were reduced and alkylated prior to digestion with recombi...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2022-04-04 | MSV000089198 | MassIVE
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