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TranscriptomicsFormalin Fixation at Low Temperature Better Preserves Nucleic Acid Integrity
INTRODUCTION. Fixation with formalin, a widely adopted procedure to preserve tissue samples, leads to extensive degradation of nucleic acids and thereby compromises procedures like microarray-based gene expression profiling. We hypothesized that RNA fragmentation is caused by activation of RNAses du...
ORGANISM(S): Homo sapiens 
2011-09-04 | E-GEOD-27175 | biostudies-arrayexpress
MetabolomicsSpatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies

Recent developments in spatially resolved -omics have enabled the joint study of gene expression, metabolite levels and tissue morphology, offering greater insights into biological pathways. Integrating these modalities from matched tissue sections to probe spatially-coordinated processes, howeve...

2025-12-03 | MTBLS13445 | MetaboLights
ProteomicsFixated rat liver tissue - Cleavable crosslinkers as tissue fixation reagents for proteomic analysis
Formaldehyde fixation is widely used for long-term maintenance of tissue. However, due to formaldehyde-induced cross-links, fixated tissue proteins are difficult to extract hampering the performance of mass spectrometry (MS)-proteomic analysis on formaldehyde-fixated tissue. Recent years saw the use...
ORGANISM(S): Rattus norvegicus (Rat) 
2018-01-29 | PXD002169 | Pride
Rat liver Tissue fixation Cleavable crosslinkers Reversible crosslinking 
TranscriptomicsRhizobium etli CFN42 wild type transcriptional profiling was compared between free living and symbiosis conditions
Rhizobium etli is a bacteria that fix nitrogen in symbiotic activity with Phaseolus vulgaris, the common bean plant. In order to accomplish this nitrogen reduction a especial environment is induced in nodules such that gene expression of bacteroid suffer a significant change with respect to its wild...
ORGANISM(S): Rhizobium etli CFN 42 
2014-02-03 | E-GEOD-21638 | biostudies-arrayexpress
MetabolomicsMetabolomic profiling of Sophora flavescens under different tissue types using LC–MS-based untargeted metabolomics

Sophora flavescens (Kushen) is a traditional medicinal plant widely used in East Asia for its anti-inflammatory, antimicrobial, and antitumor properties. Its pharmacological activities are mainly attributed to diverse secondary metabolites, including alkaloids, flavonoids, and phenolic compounds....

2026-03-24 | MTBLS13994 | MetaboLights
TranscriptomicsTranscription profiling of femoral fracture healing in Rattus norvegicus subjects comparing intramedullary nailing, screw and plate fixation, and sham surgery
This is a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery. The sham surgery group received a surgical exposure of the femur, but no fracture, no plate, and no nail. Samples were collected at 1 d...
ORGANISM(S): Rattus norvegicus 
2007-11-03 | E-GEOD-1685 | biostudies-arrayexpress
ProteomicsNon-reversible tissue fixation by EDC carbodiimide allows for imaging extracellular vesicles in situ
Extracellular vesicles (EVs) are secreted nanosized particles with many biological functions and a broad range of pathological associations. A major technical limitation to understanding the role of EVs in normal and diseased specimens has been the inability to visualize the spatial localization ...
ORGANISM(S): Bos taurus (Bovine) 
2019-11-18 | PXD015234 | Pride
Imaging extracellular vesicles fixation tissue 
ProteomicsHOPE-fixation of lung tissue allows retrospective proteome and phosphoproteome studies
Hepes-glutamic acid buffer mediated Organic solvent Protection Effect (HOPE)-fixation has been introduced as an alternative to formalin fixation of clinical samples. Beyond preservation of morphological structures for histology, HOPE-fixation was demonstrated to be compatible with recent methods for...
ORGANISM(S): Homo sapiens (Human) 
2014-05-22 | PXD000836 | Pride
Post-translational modifications Hope-fixation technique Phosphorylation Biobank Proteome Lung tissues Lc-ms/ms 
TranscriptomicsCell- and tissue-specific transcriptome analyses of Medicago truncatula root nodules
We used laser-capture microdissection (LCM) to isolate specific cells from the Medicago truncatula nodule meristem (M), the distal infection (DIZ), the proximal infection zone (PIZ), infected cells (IC) and uninfected cells (UIC) from the fixation zone. Based on Medicago GeneChips, we identified the...
ORGANISM(S): Medicago truncatula 
2013-05-29 | E-GEOD-43354 | biostudies-arrayexpress
GenomicsDirect Formalin Fixation Induces Widespread Transcriptomic Effects in Archival Tissue Samples
Direct Formalin Fixation Induces Widespread Transcriptomic Effects in Archival Tissue Samples
PRJNA643500 | ENA
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