1171a52b-74fb-4e74-8303-e4b75ca8b0ef - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001010173 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Genomic DNA from IDH1 mutant and WT tumors were used to detect genome wide methylation using Agilent SureSelect XT Mouse Methyl-Seq Enrichment System capture kit following manufacturer’s recommendations.
2018-12-01 | GSE107614 | GEO
Project description:The study included 15 patients (7 males, 8 females) with JMML. Peripheral blood and/or bone marrow aspirates were collected on EDTA at diagnosis. Non-hematopoietic tissues (fibroblasts) was derived from skin biopsy for each patient. Exome sequencing was performed in several distinct series between 2012 and 2017, which explains the differences in capture kit versions and reference genome version.Targeted enrichment and massive parallel sequencing were performed on paired genomic DNA from leukocytes and fibroblasts. Exome capture was carried out using the SureSelect Human All Exon V4+UTRs or V5 or V5+UTRs or SureSelect Clinical Research (Agilent Technologies, Santa Clara, CA, USA) according to manufacturer’s instruction and protocols by IntegraGen (Evry, France). Paired-end 75 bases sequencing was performed on a HiSeq2000 or HiSeq4000 instrument (Illumina, San Diego, CA, USA). Image analysis and base calling were performed using the Real Time Analysis (RTA) pipeline v. 1.14 (Illumina) with default parameters. The alignment of paired-end reads to the reference human genome (UCSC GRCh37/hg19 or UCSC GRCh38), variant calling and generation of Quality variants scores were carried out using the CASAVA v.1.8 pipeline (Illumina).
2018-03-14 | E-MTAB-6461 | biostudies-arrayexpress
Project description:Sequencing libraries were constructed according to standard procedures from 600 ng
of tumor and paired constitutional DNA. WES was captured using Agilent SureSelect V5 (50
Mb), Clinical Research Exome (54 Mb) kit, SureSelect XT human All exon CRE version 1 or
2, or Twist Human Core Exome Enrichment System. Sequencing of subsequent libraries was
performed using Illumina sequencers (Next-Seq 500 or Hiseq 2000/2500/4000) in 75 bp
paired-end mode, aiming for a mean depth of coverage of 100x.
| EGAD00001010928 | EGA
Project description:Whole genome, exome and RNA sequencing of TFCP2-rearranged rhabdomyosarcoma, 86 samples of paired fastq files, sequenced on:
Illumina HiSeq 2500 using Agilent SureSelect WGS,
Illumina HiSeq 2500 using Illumina TruSeq RNA,
Illumina HiSeq 2500 using Agilent SureSelect v5 WES (+UTRs),
Illumina HiSeq 4000 using Agilent SureSelect WGS,
Illumina HiSeq 4000 using Illumina TruSeq stranded mRNA Kit,
Illumina HiSeq 4000 using Agilent SureSelect v5 WES stranded mRNA Kit,
Illumina NovaSeq 6000 using Illumina TruSeq Stranded mRNA,
Illumina NovaSeq 6000 using Illumina TruSeq Nano DNA,
Illumina HiSeq X Ten using TruSeq Nano DNA.
| EGAD00001010108 | EGA
Project description:Non-coding regions of the genome contain cis-regulatory elements (CREs) that govern transcriptional activity critical for development and physiologic functions of major metabolic tissues, such as islets, adipose, liver, and skeletal muscle. Moreover, they contain the majority of genetic variants associated with risk of type 2 diabetes and quantitative alterations in related metabolic phenotypes. Here, we defined comprehensive, representative CRE maps of these major metabolic tissues in mice of both sexes using ATAC and pcHiC data and incorporating genetic variation of the 8 major Collaborative Cross founders and diet-response. Cross-species comparison of these representative maps with those from corresponding human tissues revealed conservation and functional preservation of ~28% of CREs in one or more major metabolic tissues. Importantly, this included an average of 700 (1.8%) cross-species concordant peaks that harbored genetic variants associated with T2D and related metabolic traits, including variants in the CAMK1D/CDC123, C2CD4A/B, and ADCY5 loci. Germline knock-out of the cross-species concordant CRE in ADCY5 yielded mice with impaired fasting glucose, demonstrating the importance of these functionally preserved CREs to glucose homeostasis and genetic risk of type 2 diabetes and progression. Together, the creation and cross-species comparison of comprehensive CRE maps in major metabolic tissues provides a critical resource for variant-to-function studies of type 2 diabetes and an array of related metabolic and cardiovascular traits and demonstrates the power of these mapping strategies to identify conserved metabolic cis-regulatory networks and enable data-driven creation of new preclinical models of diabetes and related metabolic diseases. Sample preparation: Promotor capture libraries were constructed via the following method. Crosslinked cells were lysed, digested with DpnII, ends filled in using biotin-14-dATP followed by overnight proximity ligation. Ligated samples underwent crosslink reversal, DNA extraction with proteinase K, and biotin removal from unligated fragments. DNA was fragmented to 500-600 bp, column purified, and biotinylated fragments pulled down. Biotinylated fragments were converted into Illumina compatible libraries using the SureSelect XT HS2 DNA System and a custom SureSelect probe set (design ID S3346176) (Agilent Technologies) according to the manufacture’s protocol with the following exception: pre-capture PCR was performed as four 50 ul reactions that were recombined during clean-up. The quality and concentration of the libraries were assessed using the High Sensitivity D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. Libraries were sequenced 150 bp paired end on an Illumina NovaSeq 6000.
2023-12-31 | GSE214107 | GEO
Project description:The mutational status of 112 recurrently mutated genes in B-cell lymphoma was examined by targeted next-generation sequencing (NGS). Libraries were performed with 15-30 ng of cfDNA obtained from plasma using molecular-barcoded library adapters (ThruPLEX Tag-seq kit; Takara) coupled with a custom hybridization capture based method (SureSelect XT Target Enrichment System Capture strategy, Agilent Technologies Inc.) and sequenced in a MiSeq instrument (Illumina, 2x150bp).
| EGAD00001006566 | EGA
Project description:Here is mostly paired WGS data of RRMM, 45 samples (tumors and controls) in 86 runs. This data was produced by using Illumina TruSeq Nano DNA and NovaSeq6000 or HiSeq X Ten for sequencing. One tumor/control pair is WES data using Agilent SureSelect V5+UTRs and NovaSeq6000 for sequencing.
| EGAD00001009682 | EGA
Project description:We used RNA-sequencing technology for high-throughput profiling of tumor-derived astrocytes. Laser capture microdissection of individual cells was performed on an ArcturusXT LCM system (Applied Biosystems) with an infrared laser using CapSure HS LCM caps after optimization of laser power and duration. For each sample, 250 cells were microdissected per LCM cap and split into five 50-cell technical replicates (as a control, one replicate did not undergo reverse transcription) after elution from the cap. Reamplified cDNA (~500 bp 3’ ends) was purified away from primer concatemers by two rounds of purification with 0.7x volume of AMPure XP beads (Beckman) according to the manufacturer’s recommendations, and purified cDNA was quantified by Qubit assay (Life Technologies). For each sample, 1 ng was tagmented with the Nextera XT kit (Illumina) and sequenced as 75 bp paired-end reads on a NextSeq instrument using v2 reagents (Illumina). 14–22 million reads per sample were filtered for signal to noise (chastity filtered), assessed for overall quality with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and then mapped with STAR (Dobin et al., 2013) against the mouse genome build mm10.
2020-01-08 | GSE111734 | GEO
Project description:In the process of searching for tumor-specific mutations to predict neoantigens for cancer immunotherapy in a Lynch Syndrome mouse model, tumorigenesis was induced with 1% DSS in drinking water. DNA was isolated from tumors and colon tissue separately from 4 MLH1-KO mice using the DNeasy Qiagen kit according to the manufacturer's protocol. Purity of the DNA was confirmed to be very high with the NanoDrop before sending samples to Illumina for next generation sequencing with the Agilent SureSelect XT Mouse All Exon kit. Finally, an analysis was performed in which common tumor-specific mutations were processed through in silico antigen prediction software in NetMHC.
2021-10-02 | E-MTAB-10962 | biostudies-arrayexpress
Project description:This dataset contains panel sequencing data from 33 samples.
Targeted sequencing was performed by creating libraries using
the Agilent SureSelect XT technology. Libraries were sequenced
using molecular barcode-indexed ligation-based sequencing using
a NextSeq500 (Illumina) instrument. Between three and six lanes
per sample have been sequenced resulting in 262 Fastq files (paired end).
| EGAD00001006208 | EGA