22959 results for "ega"

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• Exome_pituitary_adenoma

  Whole‐exome sequencing was performed using NimbleGen MedExome capture (Roche NimbleGen, Madison, WI, USA) from 1 μg of high quality genomic DNA, followed by sequencing of libraries using paired-end mode (2x 75bp) on a Nextseq 500 platform (Illumina, San Diego, CA, USA), at the Genomics Platform of the Cochin Institute. Reads were aligned on hg19 (GRCh37) using BWA V0.7.17.

  Dataset EGAD00001004997

• Survival Benefit and Genetic Profile of Pemetrexed as Initial Chemotherapy in Selected Chinese Patients with Advanced Lung Adenocarcinoma

  NGS data of 12 patients enrolled in the Chinese Patient Assistance Program from multiple centers who received pemetrexed alone or combined with platinum as initial chemotherapy and continued pemetrexed maintenance therapy for advanced lung adenocarcinoma from November 2014 to June 2017.

  Dataset EGAD00001006287

• Single-cell RNA sequencing of acute myeloid leukemia patients

  Single-cell RNA sequencing was performed on bone marrow mononuclear cells from 8 acute myeloid leukemia patients at diagnosis. The profiling was performed using 10x Genomics 3' (5 samples) and 5' (3 samples) platforms. The raw data are available as fastq files.

  Dataset EGAD00001006173

• Sequencing of Plasma DNA from breast cancer patients

  Dataset contains plasma DNA whole genome sequencing on 4 breast cancer patients. It also includes matched germline and tumour whole genome sequencing data. Two benign cancer patients were also sequenced and their plasma DNA and matched germline whole genome sequencing data are included in the dataset. Samples were sequenced on Illumina HiSeqX Ten.

  Dataset EGAD00001006869

• DNA repair knockouts

  We generated HPRT-only knockout lines as well as the combination of HPRT with MSH2, UNG and XPC. Whole genome sequencing was performed on generated clones and subclones. By subtracting variants present in the clones from those in the subclones, the somatic mutations, that accumulated in between the clonal steps, were determined.

  Dataset EGAD00001006777

• RNA-seq of iPSC-derived microglia treated with miRNA mimics and inhibitors

  Microglia were derived from iPSCs and treated with mimics and inhibitors of the miRNAs hsa-miR-150-5p, hsa-miR-193a-3p and hsa-miR-19b-3p. RNA-sequencing was then performed to examine the effects of up- and down-regulation of the respective miRNAs.

  Dataset EGAD00001006842

• Single cell mRNA sequencing of primary GBM - SF 10282

  We collected fresh tissue from an untreated GBM (SF10282) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002270

• Single cell mRNA sequencing of primary GBM - SF 10360

  We collected fresh tissue from an untreated GBM (SF10360) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002272

• Single-Cell Mitochondrial Variant Profiling via TAMITO-seq

  This dataset focuses on mitochondrial variant detection using the TAMITO-seq protocol. A pre-designed mitochondrial panel (https://designer.missionbio.com/catalogpanels/Virtual-mtDNA) was spiked into the scTAMseq workflow targeting 200 CpGs and 167 genotyping loci. Data were generated from a peripheral blood sample of a healthy donor, donor X.2, multiplexed with data from another donor.

  Dataset EGAD00001015494

• Dataset for melanoma-WHOLE_GENOME

  Rare cancer sequencing data of 22 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008889

• WGBS analysis corresponding to representative cases of iBCP-ALL patients

  This dataset was conceived to characterize the epigenomic landscape of representative iBCP-ALL subtypes. To do so, we performed Whole Genome DNA bisulfite-sequencing on 2 MLL-AF4, 2 MLL-AF9 and 2 non-MLL rearranged leukemias, and also 2 pools of BCPs obtained from fetal liver.

  Dataset EGAD00001005010

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10592i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003109

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW20_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW20_F

  Dataset EGAD00001001797

• Dataset for Direct Detection of Early-Stage Cancers using Circulating Tumor DNA

  The dataset for Direct Detection of Early-Stage Cancers using Circulating Tumor DNA includes 602 bam files from next-generation sequencing on the Illumina HiSeq2500 or MiSeq. The samples analyzed include cancer cell lines as well as plasma and tissue specimens from healthy individuals and patients with cancer.

  Dataset EGAD00001003601

• WGS of multi-centric liver cancers and intra-haptatic metastasis of liver cancer.

  RIKEN collection of WGS read of 59 multi-centric liver cancers or intra-haptatic metastasis and matched blood samples from 19 donors.

  Dataset EGAD00001001643

• SF11136 scRNA-Seq Primary astrocytoma IDH mutant

  Single cell RNA-Seq Primary diffuse astrocytoma G2. IDH mutant, ATRX mutant. Gender Male Age 34. Single Cell RNA seq from primary astrocytoma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

  Dataset EGAD00001005394

• Mixture of 4

  Mixture of 4 unrelated individuals sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.

  Dataset EGAD00001008724

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96213A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 522 samples; filetype=bam

  Dataset EGAD00001004771

• Alveolar Rhabdomyosarcoma sequencing data

  This dataset contains samples from 9 patients with alveolar rhabdomyosarcoma. 9 samples have whole exome data (one has multiple). 6 samples have RNAseq data (one has multiple). 6 samples have matched normals dna sequence data

  Dataset EGAD00001007778

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10679iA

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003110

• A95732B

  Whole genome sequencing for single cells for library A95732B 655 samples; filetype=bam

  Dataset EGAD00001008231

• 20191008_EGA_MELA_Acral_WGS+RNASeq

  Illumina platform sequencing of whole genome libraries prepared from paired tumour/normal samples from 87 cases of melanoma Acral subtype. 63 cases also have RNASeq sequencing from the tumour sample.

  Dataset EGAD00001005500

• Pre-neoadjuvant treatment biopsy RNAseq breast cancer dataset

  This dataset contains RNAseq data of n=87 pre-treatment biopsies of triple negative and luminal- type breast cancer patients, all scheduled to receive neoadjuvant chemotherapy. Gene expression data is linked with treatment response and survival.

  Dataset EGAD00001008433

• BLUEPRINT release August 2016, ChIP-Seq for macrophage - T=6days untreated, on genome GRCh38

  ChIP-Seq data for 2 macrophage - T=6days untreated sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002458