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ProteomicsComparative proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies
Clinical proteomics research is in part limited by the availability of clinical samples. However, large biobanks exist worldwide containing formalin-fixed and paraffin embedded samples and samples stored in RNAlater. The extraction of proteins for proteome analysis from samples prepared by either me...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-04-01 | MSV000080863 | MassIVE
ProteomicsSTXBP5 prevents reannealing of autophagic cis-SNARE disassembled by NSF/αSNAP
We generated a HEK293 cell line expressing ZZ-TEV-FLAG-bait protein by Lipofectamine 3000 transfection. The expression level of bait protein is controlled to endogenous level by addition of 2 ng/mL doxycycline. Note the combined treatment of Torin1 and CQ was applied for STX17. The tandem affinity p...
ORGANISM(S): Homo sapiens (Human) 
2023-09-18 | PXD043048 | Pride
Stxbp5 Alphasnap Autophagy Disassemble Snare Nsf 
GenomicsSingle-nucleotide resolution mapping of DNA abasic sites by snAP-seq
Abasic (AP) sites are one of the most common forms of DNA damage which can lead to polymerase stalling, strand breaks and mutations. We developed snA-seq, a mapping method that reveals the location of abasic sites at base-resolution. Using synthetic DNA, we show that high selectivity for AP DNA is a...
ORGANISM(S): Leishmania major 
2019-06-12 | E-MTAB-7152 | biostudies-arrayexpress
GenomicsEdU-seq and H3 variant SNAP capture-seq in HIRA KO HeLa cells rescued with HIRA
Our previous work on the histone H3.3 chaperone HIRA revealed its importance for maintaining the targeting of H3.3 to its pre-existing sites. In concert with replication fork-coupled deposition of the replicative H3.1 variant, this establishes boundaries of H3.3/H3.1, which define early replication ...
ORGANISM(S): Homo sapiens 
2025-08-07 | E-MTAB-14419 | biostudies-arrayexpress
ProteomicsHuman colon biopsies (healthy and Ulcerative Colitis) LC-MS/MS
The etiology of the inflammatory bowel diseases, including ulcerative colitis, remains incomplete, but recent findings points to the involvement of complex host-microbial interactions. We hypothesized that an analysis of the proteins on the host-microbial interacting surface, the intestinal mucosa, ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-31 | MSV000080833 | MassIVE
MetabolomicsResearch on the Molecular Mechanism of Fiber Formation in the Suture of Snap Bean (Phaseolus vulgaris L.) Pods

The tender pod is the primary edible part of the snap bean (Phaseolus vulgaris L.), and the level of suture fiber content is one of the key factors affecting its edible quality. To elucidate the key regulatory mechanisms and metabolic basis underlying suture fiber formation in pods, this study em...

2026-01-30 | MTBLS13805 | MetaboLights
TranscriptomicsThe C. elegans SNAP complex component SNPC-4 coats piRNA domains and globally affects piRNA abundance
Remarkably, tens of thousands of piwi-interacting RNAs (piRNAs) arise from a minimal number of discrete clustered regions in many organisms. However, it remains unclear if organization into these domains contributes to the highly coordinated, germline-specific expression of these small RNAs. Here, w...
ORGANISM(S): Caenorhabditis elegans 
2014-11-17 | E-GEOD-53412 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of patients with four neurodegenerative disorders distinguishes tauopathies and identifies shared molecular pathways
We have constructed genome wide expression profiles from snap frozen post-mortem tissue from the medial temporal lobe of patients with four neurodegenerative disorders (5 AD, 5 PSP, 5 PiD and 5 FTD patients) and 5 control subjects. All patients were matched for age, gender, ApoE-epsilon and MAPT (ta...
ORGANISM(S): Homo sapiens 
2010-01-14 | E-MEXP-2280 | biostudies-arrayexpress
GenomicsGenomic Study of RNA Polymerase II and III SNAPc-Bound Promoters Reveals a Gene Transcribed by both Enzymes and a Broad Use of Common Activators
SNAPc-dependent promoters are unique among cellular promoters in being very similar to each other, even though some of them recruit RNA polymerase II and other RNA polymerase III. We have examined all SNAPc-bound promoters present in the human genome. We find that there is a surprisingly small numbe...
ORGANISM(S): Homo sapiens 
2012-11-22 | E-GEOD-38303 | biostudies-arrayexpress
TranscriptomicsStudy for evaluating the effect of cold ischemic time and RNA stabilization method on RNA integrity and gene expression measurements
Time series of eleven breast cancer samples subjected to different cold ischemic stress of up to 3 hr post tumor excision. A different 2x2 factorial within this study evaluated the effect of stabilization method (RNAlater vs snap freezing) and stablization delay (0 and 40 min) at room temperature. T...
ORGANISM(S): Homo sapiens 
2011-11-02 | E-GEOD-25011 | biostudies-arrayexpress
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