ABSTRACT: The Samples were collected from Saint James's Hospital, Dublin and after informed consent Extracted Genomic DNA samples were prepared and sequenced using the Automated Illumina TruSeq PCR-free methodology.
Project description:The Samples were collected from Saint James's Hospital, Dublin and after informed consent Extracted Genomic DNA samples were prepared and sequenced using the Automated Illumina TruSeq PCR-free methodology.
Project description:The Samples were collected from Saint James's Hospital, Dublin and after informed consent Extracted Genomic DNA samples were prepared and sequenced using the Automated Illumina TruSeq PCR-free methodology. The raw reads aligned with GRCh38 human genome and variant calling has been accomplished by GATK. The resulted GVCF and vcf has been submitted as variant analysis.
Project description:The Samples were collected from Saint James's Hospital, Dublin and after informed consent. RNA-Sequencing library preparation was performed using the Illumina TruSeq Stranded Total RNA Library Prep Globin kit (20020612) with an input amount of 100 – 1000 ng. Library preparation was automated and processed using a Hamilton NGS Star. Library quality was assessed using the Roche KAPA Library Quantification Kit (7960298001) and GX Caliper HS Assay (CLS760672, 760517), run on Roche Lightcycler 480 II and Perkin Elmer LabChip GX Touch analyser respectively. Libraries were pooled and sequenced (75bp PE) on an Illumina NovaSeq 6000 instrument using NovaSeq 6000 S2 Reagent Kit v1.5 (20028314) targeting 50M paired reads. Raw data (BCL format) were demultiplexed and converted to FASTQ format using BCL2FastQ (Illumina). Adapters were trimmed using Skewer (PMID: 24925680) and QC assessed using FASTQC. STAR (PMID: 23104886) was used to align reads to the reference genome (GRCh38/hg38) as well as to the transcriptome (GENCODE v. 25). Quality of the RNA alignment was assessed using Picard QC. Gene and isoform quantification was performed using RSEM (PMID: 21816040). The study shares expression data (gene.results) and chimeric.junction.out.
Project description:Hepatocellular carcinoma samples were obtained after patients provided written informed consent and with the approval of the institutional research ethics board at the Liver Cancer Institute of Zhongshan Hospital, Fudan University (Shanghai, China). Fresh tumor tissues were implanted in NOD/SCID mice. Tumor lines were successfully maintained through multiple rounds of serial transplantation. We used microarrays to evaluate the genotype similarity between patient tumor and patient-derived xenograft (PDX).
Project description:Hepatocellular carcinoma samples were obtained after patients provided written informed consent and with the approval of the institutional research ethics board at the Liver Cancer Institute of Zhongshan Hospital, Fudan University (Shanghai, China). Fresh tumor tissues were implanted in NOD/SCID mice. Tumor lines were successfully maintained through multiple rounds of serial transplantation. We used microarrays to evaluate the expression similarity between patient tumor and patient-derived xenograft (PDX).
Project description:In this study, we collected 10 normal oral mucosa samples and 10 OLP samples separately from Huashan Hospital, Fudan University. This study was approved by the Institutional Research Ethics Committee of Huashan Hospital, Fudan University (Approval No.KY2019-589, KY2022-1000), and every patient has signed an informed consent form.
Project description:To studied how transcript expression was distributed in heterogenous colorectal tumor tissues, we performed spatial transcriptome analysis of 12 CRC tumor samples. The OrgaRES consortium study includes tissues samples from patients at the university hospital of Lille (CHU Lille, France) obtained with the approval of the institutional review board and the Lille ALLIANCE-CANCER biobank. All patients gave their informed consent and signed a non-opposition statement to research use of a biological sample.
Project description:We searched for three NSCLC patients with brain metastases in the First Affiliated Hospital of Nanjing Medical University. After obtaining informed consent, the lung cancer brain metastasis surgical specimens and lung carcinoma in situ puncture specimens were collected from the three patients. The histopathological characteristics were examined using hematoxylin and eosin (H&E) staining. We searched for three pairs of differentially expressed RNAs in brain metastasis tissues and lung carcinoma in situ tissues by ceRNA microarray.
Project description:In this study, a total of 10 patients who received rt-PA were enrolled. Plasma samples were collected before and 1 hour after the rt-PA infusion for proteomic analysis. Blood sample collection has been approved by Tianjin Medical University General Hospital Ethics Committee, and collection was conducted according to the Declaration of Helsinki. Informed consent was obtained from all participants, and all experiments were conducted in accordance with Chinese laws and institutional guidelines.
