MicroRNA sequencing of BIBINS HIE dried blood spot
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA750768 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15298913.fastq.gz | Fastqsanger.gz | |||
| SRR15298914.fastq.gz | Fastqsanger.gz | |||
| SRR15298915.fastq.gz | Fastqsanger.gz | |||
| SRR15298916.fastq.gz | Fastqsanger.gz | |||
| SRR15298917.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Able to seqence microRNA from 2 x 6 mm dired blood spot chads from the BIBINS study. Samples are from newborns with moderate-severe HIE undergoing therapeutic hypothermia at around 16-24 h post insult, mild HIE without therapeutic hypothermia, and umbilical cord blodd from normal pregnancies.
2021-08-05 | GSE181127 | GEO
Project description:The main purpose of the study is to compare the acceptance and viability of three strategies aimed to screen hepatitis C virus (HCV) infection in a birth cohort by: a) invitation letter offering HCV screening with dried blood spot (DBS) testing at the primary care center, b) invitation letter offering both HCV and colorectal cancer (CCR) screening with faecal occult test (FOT) at the primary care center, and c) invitation letter offering self-collected screening at home for HCV and CCR.
| 2312242 | ecrin-mdr-crc
Project description:Background: Standard Guthrie cards have been widely used to collect blood samples from neonates for newborn screening programs, and to a lesser extent, from normal controls and patients in research studies. Ease of blood collection (small quantity and less pain), transportation, and storage are the advantages of using these cards. It is believed that RNA obtained from these samples is of low quantity and degraded quality. However, we recently discovered that approximately 3,500 expressed genes can be detected from blood spot samples using in-house made, low resolution cDNA microarrays. Here, we established a new and improved methodology to acquire gene expression profiles from blood spot cards using commercially-available high resolution microarrays. We determined the optimal number of blood spot punches required for maximal RNA extraction, eliminated uses of trizol and chloroform for RNA extraction by using a modified protocol of the illustra Mini Spin Kit from GE-Whatm an, concentrated the quantity of RNA templates before amplification, improved amplification efficiency using the new Ribo-SPIA technology in WT-Ovation Pico System (WT-Pico) by NuGEN, before the samples were hybridized onto 4x44K whole human genome gene expression microarrays from Agilent. Nine dried blood spot samples were collected from a control population and stored at ~ -80 °C between 6 months to 2 years. High quality RNA was extracted from the buffy coat of the same individuals as a reference and processed using the standard Agilent microarray procedure. Commercially-available brain RNA was used as a positive control in both standard and new procedures for microarrays. Results: Three 3-mm punches produced the highest yield of total RNA using the non-trizol extraction method. Three to six nanogram per microliter of RNA can be concentrated and is sufficient to be amplified using the WT-Pico. Approximately 9,000 expressed genes can be detected after normalization and background correction of the microarray data. Conclusion: Genome-wide gene expression profile can be obtained from archived dried blood spot samples. Our new and improved methodology will add value to the perception of utilizing archival Guthrie cards eg. neonatal blood spot cards as unique biospecimens for molecular genomics and diagnostic studies of perinatal diseases such as pediatric cancers. Keywords: Gene Expression experiment
2012-12-07 | GSE19919 | GEO
Project description:Background: Standard Guthrie cards have been widely used to collect blood samples from neonates for newborn screening programs, and to a lesser extent, from normal controls and patients in research studies. Ease of blood collection (small quantity and less pain), transportation, and storage are the advantages of using these cards. It is believed that RNA obtained from these samples is of low quantity and degraded quality. However, we recently discovered that approximately 3,500 expressed genes can be detected from blood spot samples using in-house made, low resolution cDNA microarrays. Here, we established a new and improved methodology to acquire gene expression profiles from blood spot cards using commercially-available high resolution microarrays. We determined the optimal number of blood spot punches required for maximal RNA extraction, eliminated uses of trizol and chloroform for RNA extraction by using a modified protocol of the illustra Mini Spin Kit from GE-Whatm an, concentrated the quantity of RNA templates before amplification, improved amplification efficiency using the new Ribo-SPIA technology in WT-Ovation Pico System (WT-Pico) by NuGEN, before the samples were hybridized onto 4x44K whole human genome gene expression microarrays from Agilent. Nine dried blood spot samples were collected from a control population and stored at ~ -80 °C between 6 months to 2 years. High quality RNA was extracted from the buffy coat of the same individuals as a reference and processed using the standard Agilent microarray procedure. Commercially-available brain RNA was used as a positive control in both standard and new procedures for microarrays. Results: Three 3-mm punches produced the highest yield of total RNA using the non-trizol extraction method. Three to six nanogram per microliter of RNA can be concentrated and is sufficient to be amplified using the WT-Pico. Approximately 9,000 expressed genes can be detected after normalization and background correction of the microarray data. Conclusion: Genome-wide gene expression profile can be obtained from archived dried blood spot samples. Our new and improved methodology will add value to the perception of utilizing archival Guthrie cards eg. neonatal blood spot cards as unique biospecimens for molecular genomics and diagnostic studies of perinatal diseases such as pediatric cancers. Keywords: Gene Expression experiment Archival guthrie blood-spot cards may contain valuable data for epidemiological or other studies. Showing microarray data from guthrie blood-spot cards
2012-12-07 | E-GEOD-19919 | biostudies-arrayexpress
Project description:We developed a simple and sensitive analysis method for dried blood spot (DBS) proteins by sodium carbonate precipitation (SCP). We aimed to removing large amounts of hydrophilic blood proteins such as hemoglobin, albumin, fibrinogen and transferrin in DBS using a simple pretreatment with sodium carbonate solution, which concentrates membrane proteins. We evaluated the performance of the SCP method by comparing the LC-MS/MS results obtained for proteins prepared by SCP with those obtained by sodium dodecanate (SoDod) extract as total protein solubilized from DBS.
2020-01-20 | PXD017185 | JPOST Repository
Project description:Dried Blood Spots samples are a rich source of proteins and have therefore great potential for proteomics biomarker discovery studies. Only a few articles have used DBS samples for non-targeted bottom-up protein analysis, probably due to the complexity of the DBS samples. Gas-phase separation by ion mobility spectrometry such as Field Asymmetric Waveform Ion Mobility (FAIMS) could be useful in analysis of DBS samples as FAIMS has previously shown to be advantageous for bottom-up protein analysis of complex samples. The aim of this project was therefore to evaluate FAIMS in non-targeted analysis of Dried Blood Spots.
2018-05-03 | PXD007926 | Pride
Project description:Genome wide DNA methylation profiling of human samples from dried neonatal blood spots taken at birth from a cohort of pregnant people and their infants in Michigan. The Illumina MethylationEPIC Beadchip array was used to obtain DNA methylation profiles across over 850,000 CpGs in dried neonatal blood spot samples. Samples were collected from 166 infants at birth.
2022-01-31 | GSE195595 | GEO
Project description:We investigated the effect of antenatal corticosteroid exposure (ACS) on the DNA methylation patterns in the whole blood of female guinea pig offspring. Guinea pig dams were treated with saline or betamethasone on gestational days 50/51. Whole blood was collected from newborn offspring (post-natal day 1) and dried on blood spot cards. Methylation assessment using genomic DNA was performed with reduced representation bisulfite sequencing techniques.
2024-08-22 | GSE275411 | GEO
Project description:This Dataset goes alongside the 2023 manuscript:
Novel perfluoroalkyl substances (PFAS) discovered in whole blood using automated non-targeted analysis of dried blood spots
by
Jeremy P. Koelmel, Elizabeth Z. Lin, Emily Parry, Paul Stelben, Emma E.Rennie, Krystal J.Godri Pollitt
A small subset of per- and polyfluoroalkyl substances (PFAS) are routinely screened in human blood. These compounds generally explain <50 percent of the total PFAS in human blood. The percentage of known PFAS in human blood has been decreasing as replacement PFAS and more complex PFAS chemistries are introduced to the market. Most of these novel PFAS have not been previous identified. Non-targeted methods are required to characterize this dark matter PFAS. Our objective was to apply non-targeted PFAS analysis to human blood to gain an understanding about the sources, concentrations, and toxicity of these compounds. A high-resolution tandem mass spectrometry (HRMS) and software workflow for PFAS characterization in dried blood spots is reported. Dried blood spots are a less invasive collection technique compared to venous blood draws, allowing collection from vulnerable populations. Biorepositories of archived dried blood spots are available internationally from newborns and present opportunities to study prenatal exposure to PFAS. In this study, dried blood spot cards were analyzed using iterative MS/MS by liquid chromatography HRMS. Data processing was conducted using FluoroMatch Suite including a visualizer tool that presents homologous series, retention time vs m/z plots, MS/MS spectra, feature tables, annotations, and fragments for fragment screening. The researcher performing data-processing and annotation was blinded to the fact that standards were spiked in, and was able to annotated 95 percent of standards spiked on dried blood spot samples, signifying a low false negative rate using FluoroMatch Suite. A total of 28 PFAS (20 standards and 4 exogenous compounds) were detected across five homologous series with Schymanski Level 2 confidence. Of these four, 3 were perfluoroalkyl ether carboxylic acids (PFECA), a chemical class of PFAS which is increasingly being detected in environmental and biological matrices but is not currently screened in most targeted analyses. A further 86 potential PFAS were detected using fragment screening. PFAS are extremely persistent and widespread yet remain largely unregulated. Our findings will contribute to an improved an understanding of exposures. Application of these methods in environmental epidemiology studies have the potential to inform policy with regards to PFAS monitoring, regulation, and individual-level mitigation strategies.
2023-04-24 | MSV000091786 | MassIVE
Project description:Table of gene-level RNA counts from 21 newborn screening dried blood spot (DBS) samples. These DBS samples were obtained from extremely low gestional age newborns, where 10 of them were affected by a fetal inflammatory response (FIR) before birth, and 11 were unaffected. Total RNA was sequenced using an Illumina NextSeq-500 instrument. The sample preparation protocol included the depletion of rRNA and globin mRNA using the Globin Zero Gold rRNA Removal Kit from Illumina. Libraries were prepared using the NebNext Ultra TM II Directionl RNA LIbrary Prep Kit (New England Biolabs). Rows correspond to genes and columns to samples, where there is an additional column (BS13sub), corresponding to sample BS13, which was downsampled to 1/4 of its original depth.
| EGAD00010001707 | EGA