23217 results for "ega"

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• BLUEPRINT release August 2016, ChIP-Seq for T-cell Acute Lymphocytic Leukemia, on genome GRCh38

  ChIP-Seq data for 9 T-cell Acute Lymphocytic Leukemia sample(s). 41 run(s), 41 experiment(s), 41 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 EGAD00001002400

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - MC2392, on genome GRCh38

  ChIP-Seq data for 2 Acute Promyelocytic Leukemia - MC2392 sample(s). 14 run(s), 12 experiment(s), 12 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 EGAD00001002406

• BLUEPRINT release August 2016, Bisulfite-Seq for mature neutrophil - G-CSF/Dex. Treatment (16-20 hrs), on genome GRCh38

  Bisulfite-Seq data for 3 mature neutrophil - G-CSF/Dex. Treatment (16-20 hrs) sample(s). 33 run(s), 3 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_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002412

• BLUEPRINT release August 2016, Bisulfite-Seq for CD4-positive, alpha-beta T cell, on genome GRCh38

  Bisulfite-Seq data for 8 CD4-positive, alpha-beta T cell sample(s). 108 run(s), 8 experiment(s), 16 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_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002460

• BLUEPRINT release August 2016, RNA-Seq for Acute Promyelocytic Leukemia - MC2884 (24h), on genome GRCh38

  RNA-Seq data for 1 Acute Promyelocytic Leukemia - MC2884 (24h) sample(s). 1 run(s), 1 experiment(s), 1 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_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002461

• DNA-seq FASTQ files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by HPAH

  Paired-end DNA-seq FASTQ files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by hereditary pulmonary arterial hypertension (HPAH). Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). Each sample was multiplexed across flowcells and lanes, leading to a total number of 86 FASTQ files.

  Dataset EGAD00001005756

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - CTR, on genome GRCh38

  ChIP-Seq data for 3 Acute Promyelocytic Leukemia - CTR sample(s). 22 run(s), 21 experiment(s), 21 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 EGAD00001002490

• Processed RNA-seq data for clinical efficacy and biomarker analysis of neoadjuvant atezolizumab in operable urothelial carcinoma in the ABACUS trial

  ABACUS is a single arm phase 2 study that investigated 2 cycles of atezolizumab (1200mg Q3) prior to cystectomy in 95 patients with muscle invasive transitional cell cancer (T2-4N0M0). Pathological complete response (pCR) occurring in ≥20% of patients was the primary endpoint. Biomarker analysis on sequential tissue was a co-primary endpoint. This dataset includes the TPM and raw counts tables.

  Dataset EGAD00001006199

• BLUEPRINT release August 2016, ChIP-Seq for monocyte - RPMI_T=4hrs, on genome GRCh38

  ChIP-Seq data for 3 monocyte - RPMI_T=4hrs sample(s). 8 run(s), 8 experiment(s), 8 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 EGAD00001002328

• BLUEPRINT release August 2016, RNA-Seq for Acute Promyelocytic Leukemia - CTR, on genome GRCh38

  RNA-Seq data for 3 Acute Promyelocytic Leukemia - CTR sample(s). 3 run(s), 3 experiment(s), 3 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_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002353

• BLUEPRINT release August 2016, RNA-Seq for neutrophilic metamyelocyte, on genome GRCh38

  RNA-Seq data for 3 neutrophilic metamyelocyte sample(s). 3 run(s), 3 experiment(s), 3 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_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002366

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - MC2494, on genome GRCh38

  ChIP-Seq data for 1 Acute Promyelocytic Leukemia - MC2494 sample(s). 2 run(s), 1 experiment(s), 1 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 EGAD00001002516

• Processed bam files for the whole exome sequencing of primary lung adenocarcinoma samples

  We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes. The extensive single cell profiles depicted a complex cellular atlas and dynamics during lung adenocarcinoma progression which includes cancer, stromal, and immune cells in the surrounding tumor microenvironments.

  Dataset EGAD00001010320

• Somatic mutation and clonal evolution in premalignant lung disease

  In this study we aim to characterise the landscape of mutation and clonal selection in normal lung and premalignant lung disease. The study combines targeted sequencing and whole-genome sequencing of microbiopsies of lung and bronchial epithelium. The range of patients studied will include healthy individuals, both smokers and non-smokers, and patients with premalignant lung disease. . This dataset contains all the data available for this study on 2023-03-09.

  Dataset EGAD00001010122

• A living biobank of patient-derived ductal carcinoma in situ Mouse-INtraDuctal xenografts identifies factors associated with risk of invasive progression

  Create a living biobank of patient-derived ductal carcinoma in situ (DCIS) Mouse-INtraDuctal (MIND) xenografts to find factors explaining invasive growth. Samples exist of both primary and pdx samples. Invasive growth was scored in the pdx.

  Dataset EGAD00001009336

• Somatic mutation and clonal evolution in the human bladder WES-NOVASEQ (2020-05-05)

  n this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The study includes targeted sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006117

• Activating AKT1 and PIK3CA mutations in metastatic castration-resistant prostate cancer

  This dataset contains all available targeted exon sequencing bam files from our study, "Activating AKT1 and PIK3CA mutations in metastatic castration-resistant prostate cancer". Patient identifiers are denoted by the first segment of the sample aliases (e.g. "P1"), and additional information is appended to reflect which serial sample is referenced (1st, 2nd, 3rd, etc.), and whether the sample represents cell-free DNA ("cfdna") or paired white-blood cell control ("WBC"). All samples were sequenced using Illumina technology.

  Dataset EGAD00001006122

• DS-ALL RNA-Seq

  RNA-Seq was performed on 249 DS-ALL samples. Library preparation was carried out using TruSeq Stranded Total RNA Library Prep Kit. The libraries were sequenced on a NovaSeq platform with read length of 2×101.

  Dataset EGAD00001009403

• Spatial RNA-sequencing of metastatic melanoma

  We performed RNA sequencing of 48 different regions sub-sampled from a metastatic melanoma biopsy that was treated with anti-PD-1 inhibitor. RNAseq was performed on samples with a minimum RNA integrity number (RIN) of 5.5 except for two cases (6A10 and 8A3) with RINs greater than 3. A minimum of 700ng of RNA were required for all samples undergoing RNAseq. Paired-end transcriptome reads were aligned using TopHat2, to the UCSC hg19 reference genome.

  Dataset EGAD00001005820

• Targeted sequencing of follicular lymphoma tumour samples from the UK's Haematological Malignancy Research Network

  Targeted sequencing was applied to an unselected population-based follicular lymphoma (FL) cohort (n=548) diagnosed in the UK's Haematological Malignancy Research Network catchment population of ~4 million (14 centres). DNA extracted from FL samples was sequenced with a 293-gene panel using the Illumina HiSeq 2500. All data are provided in the CRAM format.

  Dataset EGAD00001007657

• Whole exome sequencing of an alveolar rhabdomyosarcoma patient with RET germline mutation

  Whole exome sequencing of an alveolar rhabdomyosarcoma patient with RET germline mutation and subsequent analysis of potential therapeutic mechanisms associated with the patient's rare germline mutation. Patient sampels were sequenced from an initial biopsy and from a relapse biopsy, in addition to normal blood as the matched normal DNA. RNA sequencing was performed on the relapse sample as initial sample was unable to produce usable RNA for analysis.

  Dataset EGAD00001006125

• Sequencing data for ICGC / OCCAMS samples - Perner et al (WGS, sWGS, WES, mutREAD)

  Data supporting: "The mutREAD method detects mutational signatures from low quantities of cancer DNA." Perner et al. WGS, sWGS, WES, and reduced representation sequencing data tumour and normal samples BAM files

  Dataset EGAD00001006170

• WGS,RNA data of patients with multiple myeloma (MM) refractory to immunomodulatory agents (IMiDs) and proteasome inhibitors (PIs)

  Paired WGS and RNA-Seq data of patients with multiple myeloma (MM) refractory to immunomodulatory agents (IMiDs) and proteasome inhibitors (PIs). We performed whole genome and transcriptome sequencing of 39 heavily pretreated RRMM patients with at least double refractoriness revealing complex structural changes and a high mutational load.

  Dataset EGAD00001006189

• WGS patient 130

  Whole genome sequencing on DNA from snap frozen tumour sample and matched whole blood of patient #130. Analysis used the QIAamp DNA Mini Kit. Libraries were prepared using the Illumina TruSeq Nano library method using 200ng of DNA. Extracted DNA was sheared using the Covaris M220 Focused-ultrasonicator with a target fragment length of 550bp through bead size selection. The libraries were sequenced at depth of 40x for germline DNA and 80-100x for tumour DNA using paired 150bp reads.

  Dataset EGAD00001011271

• Raw RNA-seq data for clinical efficacy and biomarker analysis of neoadjuvant atezolizumab in operable urothelial carcinoma in the ABACUS trial

  ABACUS is a single arm phase 2 study that investigated 2 cycles of atezolizumab (1200mg Q3) prior to cystectomy in 95 patients with muscle invasive transitional cell cancer (T2-4N0M0). Pathological complete response (pCR) occurring in ≥20% of patients was the primary endpoint. Biomarker analysis on sequential tissue was a co-primary endpoint. This dataset includes the raw RNA-seq data.

  Dataset EGAD00001006205