22992 results for "ega"

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• Genome and transcriptome sequence data from a metastatic adenocarcinoma of unknown primary (upper GI?) patient

  Genome and transcriptome sequence data from a metastatic adenocarcinoma of unknown primary (upper GI?) patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005837

• Summary statistics of meta-analysis using two genome-wide association study of inflammatory bowel disease in Koreans.

  We combined samples from 1,469 inflammatory bowel disease (IBD) patients consisted of 896 Crohn’s disease (CD) and 573 ulcerative colitis (UC) and 4,041 controls used in our previously published GWAS with 1,726 additional IBD patients (725 CD and 1,001 UC) and 378 additional controls genotyped using the Asian Screening Array (ASA). We uploaded summary statistics of three meta-analyses in text files.

  Dataset EGAD00001006983

• CITE-seq of early breast cancer

  CITE-seq of early breast cancer samples.

  Dataset EGAD00001007058

• IGPP Consortium GWSS Summary Results Data

  The data are the aggregate results from an IGPP Consortium genome-wide survival study, showing overall risk for Parkinson disease progression associated with each variant in a longitudinal cohort study. 11.2 million deeply imputed variants in 3,821 PD patients who were prospectively tracked with 36,123 visits over a median of 6.7 years from disease onset (inter-quartile range, 4.2 years) were analyzed. Data include hazard ratio, SNP ID, and P value.

  Dataset EGAD00001007060

• UROMOL 2020 - RNA-seq data

  For this project about non-muscle invasive bladder cancer (NMIBC), we analysed total RNA-seq data from 535 patients. Sequencing of total RNA was performed using ScriptSeq-v2 RNA-Seq Library Preparation Kit (Illumina) and KAPA RNA HyperPrep Kit with RiboErase HMR (Roche). RNA input was 500 ng for both kits. The dataset is composed of 1,596 fastq files.

  Dataset EGAD00001006656

• Longitudinal ctDNA in Uveal Melanoma

  This dataset contains data from 11 uveal melanoma patients. Plasma samples were collected at baseline, 2-weeks, 3-, 6-, and 12-months post treatment (surgery/radiation). Samples underwent targeted panel, shallow whole genome, and cfMeDIP sequencing. A total of 46 plasma samples, 7 tumours, 11 buffy coats, and 10 healthy controls are included.

  Dataset EGAD00001008998

• He et al. WES data

  This dataset are the bam files of WES data from the paper by He et al.

  Dataset EGAD00001007134

• Assessment of cannabidiol and Δ9-tetrahydrocannabiol in mouse models of medulloblastoma

  These data were used in the following publication: Andradas, C.; Byrne, J.; Kuchibhotla, M.; Ancliffe, M.; Jones, A.C.; Carline, B.; Hii, H.; Truong, A.; Storer, L.C.D.; Ritzmann, T.A.; et al. Assessment of Cannabidiol and delta9-Tetrahydrocannabiol in Mouse Models of Medulloblastoma and Ependymoma. Cancers 2021, 13, 330. https://doi.org/10.3390/cancers13020330 There are 4 paired-end RNA-seq samples from paediatric brain cancer cell lines.

  Dataset EGAD00001006923

• Omics data of advanced bladder cancer

  To identify the therapeutic targets in a treatment-refractory cancer patient, we performed single-cell RNA sequencing for 3,115 cells from primary bladder cancer (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib). Matched time-series bulk tumor tissues were also sequenced using whole exome target probe (WES) and whole transcriptome target probe (WTS).

  Dataset EGAD00001005978

• Phenotype 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 clinical phenotype data.

  Dataset EGAD00001006200

• RNA-seq from PDAC samples

  Bam and fastq files from RNA-seq of PDAC samples described in Transcription phenotypes of pancreatic cancer are driven by genomic events events during tumour evolution

  Dataset EGAD00001005799

• Targeted Deep Sequencing of Shwachman-Diamond syndrome bone marrow samples

  This dataset includes amplicon based sequencing of myeloid malignancy associated genes as well as EIF6 in 99 patients with Shwachman-Diamond syndrome and 11 patients who are "SDS-like". SDS-like patients are those that have clinical features of the disease but do not have a confirmed disease-causing mutation. There are 421 samples from serial timepoints, denoted alphabetically or numerically. For each timepoint, there is a single BAM file.

  Dataset EGAD00001006800

• Genome and transcriptome sequence data from a tongue squamous cell carcinoma (head and neck) patient

  Genome and transcriptome sequence data from a tongue squamous cell carcinoma (head and neck) patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005865

• RNA-seq of atypical 3q26 samples

  RNA was isolated using phenol-chloroform extraction followed by DNase digestion or using the Qiagen Allprep DNA/RNA kit and protocol (Qiagen, #80204). cDNA synthesis was done using the SuperScript II Reverse Transcriptase kit (Invitrogen). Quantitative real-time PCR was performed by using primers as described previously13,21 on the 7500 Fast Real-time PCR System (Applied Biosystems). Relative levels of gene expression were calculated using the ΔΔCt method

  Dataset EGAD00001006106

• FIT interval CRCs versus Screen-detected CRCs

  Formalin-fixed, paraffin-embedded samples from 27 FIT interval CRC and 54 screen-detected CRCs collected in a pilot-program of FIT-based CRC screening in the southwest and northwest regions in the Netherlands, were used in this study. DNA was extracted for 1) Shallow Sequencing (copy number analysis) and 2) TSACP Amplicon Cancer Gene Panel (mutations) of 22 FIT Interval CRCs and 45 screen-detected CRCs.

  Dataset EGAD00001006409

• Genome and transcriptome sequence data from a metastatic squamous cell carcinoma of the lung patient

  Genome and transcriptome sequence data from a metastatic squamous cell carcinoma of the lung patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005850

• European Roma whole genomes sequences

  Pair end fastq file of 40 Roma whole genome sequence data. This dataset contains the fastq files obtained using illumina hiseq X generated reads, ~30X coverage. 10 Makedonian Roma - Balkan Roma 10 Spanish Roma - North/Western Roma 10 Hungarian Roma - Vlax and Romungro Roma 5 Lithuanian Roma - North/Western Roma 5 Ukranian Roma - Romungro Roma.

  Dataset EGAD00001006024

• RNASeq of OvCa

  RNAseq data relative to 56 primary and treatment-naive ovarian carcinomas, from independent donors.

  Dataset EGAD00001008547

• FASTQ files for Recommendations to mitigate FFPE-associated problems in NGS

  42 NGS libraries of a 13y/o FFPE sample, a tissue-and-patient-matched FF sample, and a GIAB sample (NA12878). In technical replicates (untreated DNA, treated DNA, two different library types, at least library duplicates for each case). Illumina NextSeq, HiSeq and NovaSeq paired-end sequencing.

  Dataset EGAD00001008399

• Data for the study "Plasma ctDNA is a tumor tissue surrogate and enables clinical-genomic stratification of metastatic bladder cancer"

  Sequencing data from patients with bladder cancer. BAM files from targeted DNA sequencing of bladder cancer driver genes in 344 circulating tumor DNA and tumor tissue samples. BAM files from whole exome sequencing of 49 circulating tumor DNA and tumor tissue samples. Paired FASTQ files from RNA sequencing of 86 tumor tissue samples.

  Dataset EGAD00001006362

• RNA-seq data from the MESOMICS project (French project of molecular characterization of malignant pleural mesothelioma)

  The dataset includes fastq files from 109 tumor samples as well as RNA-seq gene expression R data, RNA-seq transcript expression R data, RNA-seq gene counts matrix, RNA-seq transcript counts matrix, RNA-seq gene FPKM matrix RNA-seq transcript FPKM matrix for the 109 samples. The sequencing was done with HiSeq 2000 instrument.

  Dataset EGAD00001007024

• RNA-Seq of response to Tozinameran vaccination in individuals with KTx/dialysis or healthy controls.

  Low-input RNA-Seq (~200 cells per sample) of CD4+ T cells in patients with kidney transplants, dialysis, or healthy controls after the second dose of Tozinameran COVID-19 vaccine. RNA-Seq was performed using the Smart-Seq v4 ultra-low input protocol. The dataset includes 4 healthy control samples, 3 kidney transplant recipients, and 4 patients undergoing dialysis.

  Dataset EGAD00001007689

• RNA-seq from time-course experiment treating cells for 72h

  RNA sequencing from MSTO-211H cell line cultures treated for 72h with vehicle solution, palbociclib 250nM, or abemaciclib 250nM (N = 3, each). RNA-seq prepared using TruSeq Stranded mRNA libraries and sequenced with Illumina HiSeq 4000. Data is in raw fastq format, paired end. Some samples have been split in two lanes, with a final count of 24 fastq files.

  Dataset EGAD00001007737

• Single-cell reduced-representation bisulfite sequencing generated from 11 glioma patient samples

  This dataset includes 914 BAM files from 6 IDH-mutant, 5 IDH-wild-type glioma patient samples of unmatched initial and recurrent timepoints profiled using single-cell reduced-representation bisulfite sequencing.

  Dataset EGAD00001007769

• SG Peranakan Project dataset

  This dataset contains the genotypes jointly-called from whole genome sequencing data of 177 self-reported Peranakans in Singapore. Reads were aligned to GRCh37 reference genome and jointly-called with other WGS samples. Basic quality control measures and population phasing without reference were performed on the called genotypes. The data are stored in VCF v 4.3 format, and one .vcf.gz file stored the genotypes from one of the 23 chromosomes (22 autosomes+X chromosome).

  Dataset EGAD00001007786