Search Results - EGA European Genome-Phenome Archive

FASTQ files of total RNA-Seq data of POPS control samples

Placental biopsies (n = 64 female placentas, n = 67 male placentas) were selected from healthy pregnancies from the POPs cohort. These patients had no evidence of hypertension at booking and during pregnancy, did not experience pre-eclampsia, Hemolysis, Elevated Liver enzymes, and Low Platelets (HELLP) syndrome, gestational diabetes, or diabetes mellitus type I or type II and other obstetric complications. They delivered live babies with a birth weight percentile in the normal range (20-80th percentile), with no evidence of slowing in fetal growth trajectory. 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 EGAD00001003457

RNA-SEQ data from 13 CAF (Cancer Associated Fibroblast) samples sorted from fresh high-grade ovarian carcinoma

Dataset EGAD00001003460

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

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4058 results for "*oma"

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FASTQ files of total RNA-Seq data of POPS control samples

RNA-SEQ data from 13 CAF (Cancer Associated Fibroblast) samples sorted from fresh high-grade ovarian carcinoma

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

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

STJUDE_450k

ICGC_450k

Clonal evolution study of Intrahepatic cholangiocarcinoma: 69 PDPCs and 6 tissues.

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 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 metastatic non-small cell lung carcinoma patient

Genome and transcriptome sequence data from a mesothelioma patient

Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient

Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient

Genome and transcriptome sequence data from a retroperitoneal mucinous cystic adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic colon adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic colon adenocarcinoma patient

Genome and transcriptome sequence data from a glioblastoma multiforme patient

Whole exome sequencing data from two patients with isolated myelosarcoma followed by acute myeloid leukemia

Genome and transcriptome sequence data from a squamous cell carcinoma of ge junction patient

Genome and transcriptome sequence data from a metastatic adenoid cystic carcinoma patient

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

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

Genome and transcriptome sequence data from an adenocarcinoma of the lung patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

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

Genome and transcriptome sequence data from a metastatic adrenocortical carcinoma patient

Genome and transcriptome sequence data from a thymoma carcinoma patient

Genome and transcriptome sequence data from a metastatic adenoid cystic carcinoma patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

Genome and transcriptome sequence data from an osterosarcoma patient

Genome and transcriptome sequence data from a metastatic epitheloid angiomyelolipoma patient

Genome sequence data from a metastatic squamous cell carcinoma of the oropharynx patient

Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient

Genome and transcriptome sequence data from a pleomorphic sarcomatoid epithelioid carcinoma patient

Genome and transcriptome sequence data from a peripheral T-cell lymphoma patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient