ArticleBMC genomics2007
Microarray amplification bias: loss of 30% differentially expressed genes due to long probe - poly(A)-tail distances.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
10 citing papers in PubMed, 22 citations in OpenAlex.
- Robust transcriptional signatures for low-input RNA samples based on relative expression orderings.BMC genomics · 2017Article
- Microarray experiments and factors which affect their reliability.Biology direct · 2015Review
- Laser capture microdissection in Ectocarpus siliculosus: the pathway to cell-specific transcriptomics in brown algae.Frontiers in plant science · 2015Article
- Adjustment method for microarray data generated using two-cycle RNA labeling protocol.BMC genomics · 2013Article
- The neural crest and cancer: a developmental spin on melanoma.Cells, tissues, organs · 2013Article
- Article
- Distinctions in gastric cancer gene expression signatures derived from laser capture microdissection versus histologic macrodissection.BMC medical genomics · 2011Article
- Sporadic ALS has compartment-specific aberrant exon splicing and altered cell-matrix adhesion biology.Human molecular genetics · 2010Article
- A roadmap for zinc trafficking in the developing barley grain based on laser capture microdissection and gene expression profiling.Journal of experimental botany · 2009Article
- The cerebral microvasculature in schizophrenia: a laser capture microdissection study.PloS one · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLaser microdissection microscopy has become a rising tool to assess gene expression profiles of pure cell populations. Given the low yield of RNA, a second round of amplification is usually mandatory to yield sufficient amplified-RNA for microarray approaches. Since amplification induces truncation of RNA molecules, we studied the impact of a second round of amplification on identification of differentially expressed genes in relation to the probe - poly(A)-tail distances.
resultsDisagreement was observed between gene expression profiles acquired after a second round of amplification compared to a single round. Thirty percent of the differentially expressed genes identified after one round of amplification were not detected after two rounds. These inconsistent genes have a significant longer probe - poly(A)-tail distance. qRT-PCR on unamplified RNA confirmed differential expression of genes with a probe - poly(A)-tail distance >500 nucleotides appearing only after one round of amplification.
conclusionOur data demonstrate a marked loss of 30% of truly differentially expressed genes after a second round of amplification. Therefore, we strongly recommend improvement of amplification procedures and importance of microarray probe design to allow detection of all differentially expressed genes in case of limited amounts of RNA.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.