External RNA Controls Consortium Beta Version Update.
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ABSTRACT:
SUBMITTER: Lee H
PROVIDER: S-EPMC4978944 | biostudies-literature | 2016
REPOSITORIES: biostudies-literature
Publications
External RNA Controls Consortium Beta Version Update.
Lee Hangnoh H Pine P Scott PS McDaniel Jennifer J Salit Marc M Oliver Brian B
Journal of genomics 20160726
Spike-in RNAs are valuable controls for a variety of gene expression measurements. The External RNA Controls Consortium developed test sets that were used in a number of published reports. Here we provide an authoritative table that summarizes, updates, and corrects errors in the test version that ultimately resulted in the certified Standard Reference Material 2374. We have noted existence of anti-sense RNA controls in the material, corrected sub-pool memberships, and commented on control RNAs ...[more]
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE20555: RNA-Seq on libraries made from serial dilutions of Drosophila melanogaster S2 cell mRNA and ERCC external RNA controls GSE20579: RNA-Seq on libraries made from ERCC external RNA controls, and a mixture of D. melanogaster S2 cell mRNA and ERCC mRNAs Refer to individual Series
2010-04-18 | E-GEOD-20580 | biostudies-arrayexpress
Project description:BackgroundObjective was to determine whether fear for external cephalic version (ECV) and depression are associated with the success rate of ECV in women with a breech presentation at term.MethodsProspective study conducted in the Catharina Hospital Eindhoven between October 2007 and May 2012. Participants fulfilled The Edinburgh Depression Scale (EDS) questionnaire and expressed their degree of fear on a visual analogue scale from one to ten before ECV. Obstetric factors were evaluated as well. Primary outcome was the relation between psychological factors (fear for ECV and depression EDS scores) and ECV success rate. Secondary outcome was a possible relation between fear for ECV and increased abdominal muscle tension.ResultsThe overall success rate was 55% and was significantly lower (p < 0.001) in nulliparous women (44.3%) compared with parous women (78.0%). Fear for ECV and depression EDS-scores were not related with ECV success rate. Parity, placental location, BMI and engagement of the fetal breech were obstetric factors associated with ECV outcome. There was no relation between fear for ECV and abdominal muscle tone.ConclusionFear for ECV and depression were not related with ECV success rate in this study. Engagement of the fetal breech was the most important factor associated with a successful ECV.Trial registration ebisThe Eindhoven Breech Intervention Study, NCT00516555.
| S-EPMC4007643 | biostudies-literature
Project description:BackgroundGene expression profiling is an important approach for detecting diagnostic and prognostic biomarkers, and predicting drug safety. The development of a wide range of technologies and platforms for measuring mRNA expression makes the evaluation and standardization of transcriptomic data problematic due to differences in protocols, data processing and analysis methods. Thus, universal RNA standards, such as those developed by the External RNA Controls Consortium (ERCC), are proposed to aid validation of research findings from diverse platforms such as microarrays and RT-qPCR, and play a role in quality control (QC) processes as transcriptomic profiling becomes more commonplace in the clinical setting.ResultsPanels of ERCC RNA standards were constructed in order to test the utility of these reference materials (RMs) for performance characterization of two selected gene expression platforms, and for discrimination of biomarker profiles between groups. The linear range, limits of detection and reproducibility of microarray and RT-qPCR measurements were evaluated using panels of RNA standards. Transcripts of low abundance (? 10 copies/ng total RNA) showed more than double the technical variability compared to higher copy number transcripts on both platforms. Microarray profiling of two simulated 'normal' and 'disease' panels, each consisting of eight different RNA standards, yielded robust discrimination between the panels and between standards with varying fold change ratios, showing no systematic effects due to different labelling and hybridization runs. Also, comparison of microarray and RT-qPCR data for fold changes showed agreement for the two platforms.ConclusionsERCC RNA standards provide a generic means of evaluating different aspects of platform performance, and can provide information on the technical variation associated with quantification of biomarkers expressed at different levels of physiological abundance. Distinct panels of standards serve as an ideal quality control tool kit for determining the accuracy of fold change cut-off threshold and the impact of experimentally-derived noise on the discrimination of normal and disease profiles.
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Project description:The Primary Immune Deficiency Treatment Consortium (PIDTC) is a collaboration of 41 North American centers studying therapy for rare primary immune deficiency diseases (PIDs), including severe combined immune deficiency (SCID), Wiskott-Aldrich syndrome (WAS), and chronic granulomatous disease (CGD). An additional 3 European centers have partnered with the PIDTC to study CGD. Natural history protocols of the PIDTC analyze outcomes of treatment for rare PIDs in multicenter longitudinal retrospective, prospective, and cross-sectional studies. Since 2009, participating centers have enrolled more than 800 subjects on PIDTC protocols for SCID, and enrollment in the studies on WAS and CGD is underway. Four pilot projects have been funded, and 12 junior investigators have received fellowship awards. Important publications of the consortium describe the outcomes of hematopoietic cell transplantation for SCID during 2000-2009, diagnostic criteria for SCID, and the pilot project of newborn screening for SCID in the Navajo Nation. The PIDTC Annual Scientific Workshops provide an opportunity to strengthen collaborations with junior investigators, patient advocacy groups, and international colleagues. Funded by the National Institute of Allergy and Infectious Diseases and the Office of Rare Diseases Research, National Center for Advancing Translational Sciences, the PIDTC has recently received renewal for another 5 years. Here we review accomplishments of the group, projects underway, highlights of recent workshops, and challenges for the future.
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Project description:Introduction Fetal breech presentation at terms occurs in 3 - 6% of pregnancies. External cephalic version can reduce the number of cesarean sections and vaginal breech deliveries. Different approaches are used to carry out external cephalic version. This study looked at the different approaches used in Germany and compared the approach used with the recommendations given in German and international guidelines. Material and Methods An anonymized online survey of 234 hospitals in Germany was carried out in 2018. In addition to asking about hospital structures, questions also focused on how external version was carried out in practice (preparations, tocolysis, anesthetics, etc.), on relative and absolute contraindications and on the success rate. Results 37.2% of the hospitals approached for the survey participated in the study. Of these, 98.8% performed external version procedures. The majority of participating hospitals were university hospitals (26.4%) and maximum care hospitals (35.6%) with an average number of more than 2000 births per year (60.9%). External cephalic version is the preferred (61.7%) obstetrical procedure to deal with breech presentation, rather than vaginal breech birth or primary cesarean section. 45.8% of respondents carry out external version procedures on an outpatient basis, and 42.1% of hospitals perform the procedure as an inpatient intervention, especially from the 37th week of gestation. Prior to performing an external version procedure, 21.6% of surveyed institutions carry out a vaginal examination to evaluate possible fixation of the fetal rump. 95.5% of institutions used fenoterol for tocolytic therapy; the majority using it for continuous tocolysis (70.2%). 1 - 3 attempts at external version (8.4%) were usually carried out by a specific senior physician. In most cases, no analgesics were administered. The reported rate of emergency cesarean sections was very low. The most common indication for emergency C-section was pathological CTG (56,7%). The assessment of relative and absolute contraindications varied, depending on the surveyed hospital. 67.5% asked patients to empty their bladders before carrying out external version, while 10.8% carried out external version when the bladder was filled. The reported success rate was more than 45%. After successful version, only 14.8% of hospitals arranged for patients to wear an abdominal binder. For 32.4%, the decision to apply an abdominal binder was taken on a case-by-case basis. Conclusion The approach used in Germany to carry out external cephalic version is based on the (expired) German guideline on breech presentation. Based on the evidence obtained, a number of individual recommendations should be re-evaluated. More recent international guidelines could be useful to update the standard procedure.
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Project description:A website (http://www.mcgill.ca/pahdb ) is maintained by the curators for a Consortium (88 investigators, 28 countries) and all other users; it serves a relational database for human locus-specific genetic variation in a defined DNA sequence (GenBank U49897); (100 kb on human chromosome 12q24.1, gene symbol PAH). The intragenic nucleotide variation is both rare (Q< 0.01), extensive (>320 different mutations) and phenotype modifying, causing hyperphenylalaninemia by impairing phenylalanine hydroxylase function (see OMIM 261600), as well as polymorphic and neutral, the latter providing informative locus-specific haplotypes (>1200 different mutation/haplotype associations). The PAH database contains both offline core components (mutations, population associations and data source information) and several accessory online components: (i) relative frequencies of mutations by populations/regions (expanding file); (ii) data on genotype- phenotype correlations both in vitro and in vivo (new file); (iii) polymorphic haplotype structures (new file); (iv) intron sequence data (new file for design of primers); (v) description of mouse homologues (new file for mutations and phenotypes); (vi) the predicted PAH gene mutability profile (improved graphic); (vii) a clinical field for patient use (new interface with database). The website home page has been revised and a counter is recording >15 visits per day. Linkages to other mutation databases and an alliance of mutation database curators (new) are expanding. The primary 'electronic publication' reports now vastly exceed print reports. PAHdb serves as a prototype for obtaining, storing and distributing records of human genetic variation.
| S-EPMC146402 | biostudies-literature
Project description:Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.
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Project description:PURPOSE: To determine the maternal and fetal outcomes of successful external cephalic version (ECV) as well as factors predicting vaginal birth. METHODS: The ECV data over a period of three years at Universiti Kebangsaan Malaysia Medical Centre (UKMMC) between 1 September 2008 and 30 September 2010 was reviewed. Sixty-seven patients who had successful ECV were studied and reviewed for maternal, fetal, and labour outcomes. The control group comprised patients with cephalic singletons of matching parity who delivered following the index cases. RESULTS: The mean gestational age at ECV was 263 ± 6.52 days (37.5 weeks ± 6.52 days). Spontaneous labour and transient cardiotocographic (CTG) changes were the commonest early adverse effects following ECV. The reversion rate was 7.46%. The mean gestational age at delivery of the two groups was significantly different (P = 0.000) with 277.9 ± 8.91 days and 269.9 ± 9.68 days in the study group and control groups, respectively. The study group needed significantly more inductions of labour. They required more operative deliveries, had more blood loss at delivery, a higher incidence of meconium-stained liquor, and more cord around the neck. Previous flexed breeches had a threefold increase in caesarean section rate compared to previous extended breeches (44.1% versus 15.2%, P = 0.010). On the contrary, an amniotic fluid index (AFI) of 13 or more is significantly associated with a higher rate of vaginal birth (86.8% versus 48.3%, P = 0.001). CONCLUSIONS: Patients with successful ECV were at higher risk of carrying the pregnancy beyond 40 weeks and needing induction of labour, with a higher rate of caesarean section and higher rates of obstetrics complications. Extended breech and AFI 13 or more were significantly more likely to deliver vaginally postsuccessful ECV. This additional information may be useful to caution a patient with breech that ECV does not bring them to behave exactly like a normal cephalic, so that they have more realistic expectations. However, these predictive factors needed further confirmation and hopefully, in the future, they would be able to further enhance counselling prior to ECV.
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Project description:We explored the ability of External RNA Control Consortium (ERCC) standards to detect technical biases between batches of sequencing experiments and to set detection thresholds. We compared three normalization methods (FPKM, DESeq2 and RUV) to identify the optimal analysis approach.
2020-05-11 | GSE99081 | GEO
Project description:ObjectiveShame contains external and internal aspects. However, a Japanese language scale for simultaneously assessing both aspects of shame has not been developed to date. This study aimed to standardize the Japanese version of the External and Internal Shame Scale (EISS-J). An online survey was conducted among university students (N = 203) at six universities in Japan (Study 1). A retest questionnaire was sent to the participants by email three weeks after the first survey (Study 2). Study 1 examined the internal consistency, factor structure, and criterion-related validity of the EISS-J, while Study 2 examined its test-retest reliability. Moreover, an additional study was conducted to examine the criterion-related validity of the scale.ResultsStudy 1 demonstrated the high internal consistency of the EISS-J. Moreover, confirmatory factor analysis indicated a two-factor model: external and internal shame. However, exploratory factor analysis indicated a three-factor structure. Study 2 confirmed the test-retest reliability of the scale. Furthermore, both studies indicated correlations between the EISS-J and fear of compassion, anger, humiliation, depression, anxiety, and stress. In addition, the study established the criterion-related validity of the scale. These results confirmed adequate reliability and validity of the EISS-J.
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