Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next generation sequencing for patients with hypomyelinating leukodystrophies

ABSTRACT: Targeted enrichment-based next-generation sequencing or whole exome sequencing were taken for patients with hypomyelinating leukodystrophies to reveal genetic aetiologies. All genomic DNA used in the experiments was extracted from the peripheral leukocytes. A complete kit was synthetized using the Agilent SureSelect Target Enrichment technique, capturing the coding regions from 104 candidate genes, including their exons and exon-intron boundaries (11,473 probes, 383.065 kbp in total). The following NGS which included equipment and reagents was performed on an Illumina NEXTSEQ500 platform manufactured by Illumina (San Diego, California, USA) using paired-end sequencing of 110 bp. The clean paired-end reads were aligned to the human reference genome build hg19, which was previously annotated using ANNOVAR, in addition to insertion-deletion (indel) and single-nucleotide polymorphism (SNP) calling.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Ji Haoran

PROVIDER: E-MTAB-6404 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Next generation sequencing for patients with hypomyelinating leukodystrophies

Project description:Targeted enrichment-based next-generation sequencing or whole exome sequencing were taken for patients with hypomyelinating leukodystrophies to reveal genetic aetiologies. All genomic DNA used in the experiments was extracted from the peripheral leukocytes. A complete kit was synthetized using the Agilent SureSelect Target Enrichment technique, capturing the coding regions from 104 candidate genes, including their exons and exon-intron boundaries (11,473 probes, 383.065 kbp in total). The following NGS which included equipment and reagents was performed on an Illumina NEXTSEQ500 platform manufactured by Illumina (San Diego, California, USA) using paired-end sequencing of 110 bp. The clean paired-end reads were aligned to the human reference genome build hg19, which was previously annotated using ANNOVAR, in addition to insertion-deletion (indel) and single-nucleotide polymorphism (SNP) calling.

2018-02-01 | E-MTAB-6054 | biostudies-arrayexpress

Illumina Infinium HumanMethylationEPIC DNA methylation microarray of human donor whole-blood from patients with and without Age-related Macular Degeneration

Project description:DNA methylation microarray analysis was performed on human donor whole blood samples from patients with and without AMD. A total of 30 patient samples including 16 Normal, 3 AREDS grade 2 (early AMD) and 11 AREDS grade 3 (intermediate AMD) (AMD total, n = 14) were selected. Samples were obtained from individuals phenotyped according to the Age-Related Eye Disease Study (AREDS) classification. DNAm levels were measured using the EPIC-array (Illumina Inc., San Diego, CA, USA). Samples run on the EPIC-array were randomized and balanced for disease status and smoking status to minimise chip and row specific effects. The EPIC-array incorporated technical controls into the experimental design. In total, 500 ng (50 ng/μL) total peripheral whole blood-derived gDNA was bisulfite converted using the EZ-96 DNA methylation kit (Zymo Research, Irvine, CA, USA) and hybridised to the EPIC-array according to the manufacturer’s instructions. Quality control analysis was performed using GenomeStudio (v2011.1). Raw IDAT files were then read into R (version 3.31) using the read.metharray.exp function within the minfi package. DNA methylation microarray data was collected in order to assess the estimated DNA methylation age using the Horvath multi-tissue, Hannum and Skin & Blood epigenetic clocks and to identify loci of differential methylation between the experimental groups.

2021-12-31 | E-MTAB-11279 | biostudies-arrayexpress

Chromatin immunoprecipitation of yeast to identify genomic binding locations of yeast transcription machinary factors Reb1, Rpb3, Rpo21, Rsc9, Sua7 and Swr1

Project description:High-resolution genome-wide mapping of the yeast transcription machinery. ChIP-chip was performed to identify the genomic binding locations for each factor. <br><br>Processed data files are also available on the FTP server for this experiment.

2009-02-14 | E-MEXP-1676 | biostudies-arrayexpress

Genome-wide characterization of light-regulated genes in Neurospora crassa

Project description:RNA-seq from Neurospora crassa at 5 time points of light induction, with 2 replicates for each, totalling 10 samples RNA-seq from Neurospora crassa at 5 time points of light induction, with 2 replicates for each, totalling 10 samples

2014-08-01 | E-GEOD-53534 | biostudies-arrayexpress

Characterisation of the mouse megakaryocyte transcriptome

Project description:This study aims to identify all genes expressed in primary mouse megakaryocytes Keywords: Megakaryocyte, SAGE, transcriptome analysis Mouse megakaryocytes were grown in vitro from bone marrow progenitors. Mature, polyploid (approximately 95% 64n and 128n) differentiated megakaryocytes were used to generate RNA for SAGE library construction.

2007-02-02 | E-GEOD-6940 | biostudies-arrayexpress

Chromatin immunoprecipitation of yeast transcription machinary using oligonucleotide arrays

Project description:A canonical organization of the transcription pre-initiation complex and its regulators. High-resolution genome-wide mapping of the yeast transcription machinery was performed for each factor using ChIP-chip.

2009-02-15 | E-MEXP-1677 | biostudies-arrayexpress

The identification of putative circulating miRNA biomarkers of Thioacetamide-induced hepatotoxicity.

Project description:The Thioacetamide-treated rat was first identified as a model of hepatotoxicity by Gupta in 1956 and is now well-established, not least because the histopathogical output closely mimics that seen in humans with chronic liver disease. Acute treatment of rats with Thioacetamide causes pronounced necrosis and inflammation. Animals received intraperitoneal (ip) doses of vehicle-only (0.9% (v/v) saline) (n=3), or 100 mg/kg Thioacetamide (n=3) and were sacrificed after 24 hours. Blood was withdrawn via the descending vena cava and immediately transferred into potassium/EDTA tubes. Following centrifugation (16,100g, 4M-BM-0C, 5 min) the plasma was collected and stored at -80M-BM-0C. miRNA microarray profiling of RNA extracted from the plasma of rats treated with Thioacetamide revealed that a subset of miRNAs were differentially expressed following treatment. These miRNAs appeared to mediate pathways involved in hepatic fibrosis and stellate cell activation, suggesting that they might function as predictive biomarkers following compound-induced hepatotoxicity. The changes correlated well with increases in ALT levels, which are the current gold standard method for determining the extent of liver injury. Furthermore, it is hypothesised that particular aetiologies of liver damage might cause differing expression profiles of miRNAs, thus certain miRNAs could be implemented in a panel-type expression study to distinguish between different types of hepatic injury. Single channel miRNA microarrays were performed on n= 3 samples, 2 treatment groups; control and test. Control animals received vehicle-only (0.9% (v/v) saline) via the ip route. Test animals received 100 mg/kg Thioacetamide dissolved in 0.9% (v/v) saline, via the ip route. 24 h after dosing animals were sacrificed using decapitation under terminal anaesthesia.

2014-03-14 | E-GEOD-55885 | biostudies-arrayexpress

Comparative genomic hybridization of DNA from two recently divergent mouse strains, 12925 and C57BL/6J

Project description:We have performed CGH analysis using 129S5 DNA competitively hybridised with C57BL/6J DNA to RPCI-23 (C57BL/6J) BAC clones spotted at 1Mb resolution (array protocol 7769)

2005-04-01 | E-MEXP-298 | biostudies-arrayexpress

DNA methylation in Breast cancer

Project description:This experiment was performed with an aim to establish an early diagnostic marker for breast cancer based on the DNA methylation patterns. CpG Island were identified and amplified from the breast cancer related genomic loci. These selected loci were amplified using PCR from different human breast tissue samples. The samples included Breast cancer tissues and macroscopically normal tissues (3-5cm away from tumor) from breast cancer patients, benign breast tissues and healthy breast tissues from cancer free patients. All the genomic loci amplified from one particular tissue sample were pooled, biotin labeled and hybridized to a self designed and synthesised oligonucleotide microarray. The obtained signals were statistically analysed and the genomic loci which could differentiate the different kinds of breast tissues used based on their methylation levels are being reported.

2011-12-30 | E-TABM-1171 | biostudies-arrayexpress

shRNA profiling of human cells containing varying concentrations of shRNA expression constructs to determine shRNA abundance using barcodes

Project description:RNAi screens via pooled short hairpin RNAs (shRNAs) have recently become a powerful tool for the identification of essential genes in mammalian cells. We synthesized DNA microarrays with six overlapping 25 nt long tiling probes complementary to each unique 60 nt molecular barcode sequence associated with every shRNA expression construct. By analyzing dilution series of expression constructs we show how our approach allows quantification of shRNA abundance from a pool and how it clearly outperforms the commonly used analysis via the shRNAs half hairpin sequences. In this part of the study one equimolar reference pool and three test pools of varying template concentrations were PCR amplified and hybridized to individual arrays.

2009-12-08 | E-MEXP-2474 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data