Search Results - EGA European Genome-phenome Archive

FASTQ files of total RNA-Seq data from the POPS SGA (Small for Gestational Age) samples

All the samples were obtained from the Pregnancy Outcome Prediction–a prospective cohort study of nulliparous women attending the Rosie Hospital, Cambridge (UK) for their dating ultrasound scan between January 14, 2008, and July 31, 2012. Ethical approval for the study was given by the Cambridgeshire 2 Research Ethics Committee (reference number 07/H0308/163) and all participants provided written informed consent. Cases of preeclampsia (PET) were defined on the basis of the 2013 ACOG criteria and cases of small for gestational age (SGA)infants were confined to severe SGA, i.e. a customized birth weight <5th percentile. Chorionic villi from the corresponding placentas (free from decidua, visible infarction, calcification, hematoma, or damage) were collected and processed within 30 minutes of separation from the uterus. After repeated washes in chilled phosphate buffered saline, the samples were placed in RNA later (Applied Biosystems) and stored at -80°C. Total placental RNA was extracted using mirVana Isolation Kit (Ambion). For each placenta, approximately 5 mg of tissue were homogenized in the Lysis/Binding solution for 20 sec at 6 m/s using a bead beater (FastPrep24) and Lysing Matrix D Tubes (MP Biomedicals). The samples were then spun at 13,000 rpm for 5 min at 4°C and the supernatants recovered. Afterwards, the manufacturer's instructions were followed. Immediately after the RNA extraction, placental RNA samples were DNase-treated using DNA-free DNA Removal Kit (Ambion), aliquoted, and stored in -80°C. Quantity and quality of the RNA samples were assessed using the Agilent 2100 Bioanalyzer, the Agilent RNA 6000 Nano Kit (Agilent Technologies), and Qubit fluorometer. Libraries were prepared starting with 300-500 ng of good quality total RNA (RIN ≥7.5) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina), according to the manufacturer's instructions. The kit contains 96 uniquely indexed adapter combinations in order to allow pooling of multiple samples prior to sequencing. After determining their size (with the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA Kit by Agilent Technologies) and concentration (by qPCR with the KAPA Illumina ABI Prism Library Quantification Kit, Kapa Biosystems), libraries have been pooled and sequenced (single-end, 125 bp) using a Single End V4 Cluster Kit and an Illumina HiSeq2500 or HiSeq4000 instrument.

Dataset EGAD00001003507

FASTQ files of total RNA-Seq data from the POPS PET (pre-eclamptic) samples

All the samples were obtained from the Pregnancy Outcome Prediction–a prospective cohort study of nulliparous women attending the Rosie Hospital, Cambridge (UK) for their dating ultrasound scan between January 14, 2008, and July 31, 2012. Ethical approval for the study was given by the Cambridgeshire 2 Research Ethics Committee (reference number 07/H0308/163) and all participants provided written informed consent. Cases of preeclampsia (PET) were defined on the basis of the 2013 ACOG criteria and cases of small for gestational age (SGA)infants were confined to severe SGA, i.e. a customized birth weight <5th percentile. Chorionic villi from the corresponding placentas (free from decidua, visible infarction, calcification, hematoma, or damage) were collected and processed within 30 minutes of separation from the uterus. After repeated washes in chilled phosphate buffered saline, the samples were placed in RNA later (Applied Biosystems) and stored at -80°C. Total placental RNA was extracted using mirVana Isolation Kit (Ambion). For each placenta, approximately 5 mg of tissue were homogenized in the Lysis/Binding solution for 20 sec at 6 m/s using a bead beater (FastPrep24) and Lysing Matrix D Tubes (MP Biomedicals). The samples were then spun at 13,000 rpm for 5 min at 4°C and the supernatants recovered. Afterwards, the manufacturer's instructions were followed. Immediately after the RNA extraction, placental RNA samples were DNase-treated using DNA-free DNA Removal Kit (Ambion), aliquoted, and stored in -80°C. Quantity and quality of the RNA samples were assessed using the Agilent 2100 Bioanalyzer, the Agilent RNA 6000 Nano Kit (Agilent Technologies), and Qubit fluorometer. Libraries were prepared starting with 300-500 ng of good quality total RNA (RIN ≥7.5) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina), according to the manufacturer's instructions. The kit contains 96 uniquely indexed adapter combinations in order to allow pooling of multiple samples prior to sequencing. After determining their size (with the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA Kit by Agilent Technologies) and concentration (by qPCR with the KAPA Illumina ABI Prism Library Quantification Kit, Kapa Biosystems), libraries have been pooled and sequenced (single-end, 125 bp) using a Single End V4 Cluster Kit and an Illumina HiSeq2500 or HiSeq4000 instrument.

Dataset EGAD00001003508

BCL2 Break NegativeFollicular Lymphoma

Whole Exome Sequencing reads consisting of BAM paired end reads from Follicular Lymphoma samples.

Dataset EGAD00001003509

The genomic landscape of cutaneous squamous cell carcinoma based on 40 paired normal and tumour whole-exome sequencing samples

40 paired normal and tumour whole-exome sequencing samples was used to investigate the genomic landscape of cutaneous squamous cell carcinoma

Dataset EGAD00001003555

3794 results for "*oma"

in 31.75 milliseconds.

FASTQ files of total RNA-Seq data from the POPS SGA (Small for Gestational Age) samples

FASTQ files of total RNA-Seq data from the POPS PET (pre-eclamptic) samples

BCL2 Break NegativeFollicular Lymphoma

The genomic landscape of cutaneous squamous cell carcinoma based on 40 paired normal and tumour whole-exome sequencing samples

STJUDE_450k

Whole exome sequencing of SU- DIPG-XIII from different sites

ICGC_450k

Genome and transcriptome sequence data from a solitary fibrous tumors (sarcoma) patient

Promoter capture HiC on KMS11 (multiple myeloma)

Genome and transcriptome sequence data from a thymoma carcinoma patient

Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic paraganglioma patient

Genome and transcriptome sequence data from a radiation-induced pleomorphic sarcoma patient

Genome and transcriptome sequence data from a salivary duct carcinoma patient

Genome and transcriptome sequence data from a metastatic melanoma patient

Genome and transcriptome sequence data from a metastatic colonic adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma of the rectum patient

Genome and transcriptome sequence data from a mullerian mixed tumor with carcinosarcoma of the ovaries patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma of the lung patient

Genome and transcriptome sequence data from a mesothelioma patient

Genome and transcriptome sequence data from a metastatic non-small cell lung carcinoma patient

Genome and transcriptome sequence data from a metastatic small cell carcinoma patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma of appendiceal origin patient

Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient

Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient