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The effect of cold ischemia time on hypoxia, EMT, and apoptosis pathways in normal colon mucosa

https://doi.org/10.1101/2025.03.09.642255

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Prelude to malignancy: A gene expression signature in normal mammary gland from breast cancer patients suggests pre‐tumorous alterations and is associated with adverse outcomes

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RNA Quality in Fresh-Frozen Gastrointestinal Tumor Specimens—Experiences from the Tumor and Healthy Tissue Bank TU Dresden

inferredcites →https://doi.org/10.1007/s10561-012-9313-5openalex-snapshot

The interference of cold ischemia time in the quality of total RNA from frozen tumor samples

inferredcites →https://doi.org/10.1016/j.ab.2012.02.003openalex-snapshot

Impact of warm ischemia on gene expression analysis in surgically removed biosamples

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The procurement, storage, and quality assurance of frozen blood and tissue biospecimens in pathology, biorepository, and biobank settings

inferredcites →https://doi.org/10.1016/j.molonc.2011.08.004openalex-snapshot

Ischemia caused by time to freezing induces systematic microRNA and mRNA responses in cancer tissue

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Global gene expression changes induced by prolonged cold ischemic stress and preservation method of breast cancer tissue

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The transcription factor Snail controls epithelial–mesenchymal transitions by repressing E-cadherin expression

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Biobanking of fresh frozen tissue: RNA is stable in nonfixed surgical specimens

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Enabling personalized cancer medicine through analysis of gene-expression patterns

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EMTome: a resource for pan-cancer analysis of epithelial-mesenchymal transition genes and signatures

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UK Biobank: a globally important resource for cancer research

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Tumor specimen cold ischemia time impacts molecular cancer drug target discovery

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Immunophenotyping and transcriptional profiling of in vitro cultured human adipose tissue derived stem cells

inferredcites →https://doi.org/10.1089/bio.2016.0013openalex-snapshot

Effects of Cold Ischemia on Gene Expression: A Review and Commentary

inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot

STAR: ultrafast universal RNA-seq aligner

inferredcites →https://doi.org/10.1093/nar/gkv007openalex-snapshot

limma powers differential expression analyses for RNA-sequencing and microarray studies

inferredcites →https://doi.org/10.1093/nar/gkz401openalex-snapshot

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

inferredcites →https://doi.org/10.1093/nargab/lqaa078openalex-snapshot

ComBat-seq: batch effect adjustment for RNA-seq count data

inferredcites →https://doi.org/10.1111/j.1365-2559.2009.03470.xopenalex-snapshot

Gene expression in colorectal neoplasia: modifications induced by tissue ischaemic time and tissue handling protocol

inferredcites →https://doi.org/10.1155/2020/9349132openalex-snapshot

DV200 Index for Assessing RNA Integrity in Next‐Generation Sequencing

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Impact of Ischemia and Procurement Conditions on Gene Expression in Renal Cell Carcinoma

inferredcites →https://doi.org/10.1177/20543581231178960openalex-snapshot

The Impact of Combined Warm and Cold Ischemia Time on Post-transplant Outcomes

inferredcites →https://doi.org/10.1186/1471-2105-9-559openalex-snapshot

WGCNA: an R package for weighted correlation network analysis

inferredcites →https://doi.org/10.1186/gb-2010-11-3-r25openalex-snapshot

A scaling normalization method for differential expression analysis of RNA-seq data

inferredcites →https://doi.org/10.1186/s10020-018-0058-xopenalex-snapshot

Differential effect of surgical manipulation on gene expression in normal breast tissue and breast tumor tissue

inferredcites →https://doi.org/10.1186/s12920-023-01525-8openalex-snapshot

Apoptosis related genes mediated molecular subtypes depict the hallmarks of the tumor microenvironment and guide immunotherapy in bladder cancer

inferredcites →https://doi.org/10.1186/s13045-022-01347-8openalex-snapshot

The molecular mechanisms and therapeutic strategies of EMT in tumor progression and metastasis

inferredcites →https://doi.org/10.1245/s10434-012-2440-1openalex-snapshot

Biobanking of Fresh-frozen Human Colon Tissues: Impact of Tissue Ex-vivo Ischemia Times and Storage Periods on RNA Quality

inferredcites →https://doi.org/10.1371/journal.pone.0053406openalex-snapshot

Effects of Warm Ischemic Time on Gene Expression Profiling in Colorectal Cancer Tissues and Normal Mucosa

inferredcites →https://doi.org/10.1371/journal.pone.0154326openalex-snapshot

Biobanking of Fresh-Frozen Human Adenocarcinomatous and Normal Colon Tissues: Which Parameters Influence RNA Quality?

inferredcites →https://doi.org/10.1371/journal.pone.0266111openalex-snapshot

Comprehensive cancer-oriented biobanking resource of human samples for studies of post-zygotic genetic variation involved in cancer predisposition

inferredcites →https://doi.org/10.18637/jss.v025.i01openalex-snapshot

FactoMineR : An R Package for Multivariate Analysis

inferredcites →https://doi.org/10.21037/atm-20-681openalex-snapshot

Prognostic values of SNAI family members in breast cancer patients

inferredcites →https://doi.org/10.2144/04366rr04openalex-snapshot

Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision

inferredcites →https://doi.org/10.3389/fmolb.2022.967310openalex-snapshot

Standard operating procedures for biobank in oncology

inferredcites →https://doi.org/10.3389/fonc.2020.00486openalex-snapshot

Hypoxia-Induced Epithelial-Mesenchymal Transition in Cancers: HIF-1α and Beyond

inferredcites →https://doi.org/10.3748/wjg.v21.i12.3499openalex-snapshot

Degradation of intestinal mRNA: A matter of treatment

inferredcites →https://doi.org/10.5858/2007-131-1805-thfgeaopenalex-snapshot

Tissue Handling for Genome-Wide Expression Analysis: A Review of the Issues, Evidence, and Opportunities

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