15028 results for "cancer studies using rna-seq"

in 16.86 milliseconds.

• Understanding human fetal pancreas development using subpopulation sorting and RNA sequencing

  To decipher the populations of cells present in the human fetal pancreas and their lineage relationships, we developed strategies to isolate pancreatic progenitors, endocrine progenitors and endocrine cells. Transcriptome analysis of the individual populationsrevealed a large degree of conservation among vertebrates in the drivers of gene expression changes occurring at different steps of differentiation, althoughnotably, sometimes, different members of the same gene family are expressed. The transcriptome analysis establishes a resource to identify novel genes and pathways involved in human pancreas development. Single cell profiling further captured intermediate stages ofdifferentiation and enabled us to decipher the sequence of transcriptional events occurring during human endocrine differentiation. Furthermore, we evaluate how well individual pancreatic cells derived in vitro from human pluripotent stem cells mirror the natural processoccurring in human fetuses. This comparison uncovers a few differences at the progenitor steps, a convergence at the steps of endocrine induction and the current inability to fully resolve endocrine cell subtypes in vitro.

  Study EGAS00001003127

• Spatially resolved single-nucleus RNA sequencing of Choroid Plexus Tumours reveals clinically relevant hypoxia- and stress-driven dedifferentiation programs that sculpt an immunosuppressive and pro-angiogenic microenvironment

  Our study leverages single-nucleus RNA sequencing (~124,500 nuclei) and spatial transcriptomics (~40,650 spots) to dissect the molecular architecture of CPTs. We generated a comprehensive transcriptomic atlas of 45 CPT samples spanning all three methylation groups and a reference cohort of 16 non-neoplastic choroid plexus (ChP) samples, spanning foetal, paediatric and adult specimens. Key discoveries from this investigation include that paediatric B tumorus exhibit a dedifferentiated state and enrichment of stress-related metaprograms, including hypoxia, TGFß signaling, Interferon I signaling and early stress response, that correlate with poor clinical outcome and antagonise multiciliogenesis. On a spatial level, these stress-linked programs co-localise with immunosuppressive, pro-angiogenic microenvironment, suggesting a link between developmental arrest, microenvironmental remodelling and aggressive behaviour.

  Study EGAS50000001617

• INVADE cohort

  Cohort of bulk RNAseq data from DCIS, invasive and microinvasive breast cancer at diagnosis. This dataset covers 18 DCIS cases, 17 microinvasive and 20 primary invasive breast cancer.

  Study EGAS50000000219

• DAC for "Cancer-associated fibroblasts promote drug resistance in ALK-driven lung adenocarcinoma cells by upregulating lipid biosynthesis"

  DAC for the data of "Cancer-associated fibroblasts promote drug resistance in ALK-driven lung adenocarcinoma cells by upregulating lipid biosynthesis" with: • Holger Sültmann • h.sueltmann@dkfz.de • German Cancer Research Center (DKFZ) • Ann-Kathrin Daum • a.daum@dkfz.de • German Cancer Research Center (DKFZ)

  Dac EGAC50000000076

• Organoid_Derivation_Project___GRCh38___RNAseq

  Generation of normal and cancer organoids for sequencing as part of the WTSI-CRUK international collaboration with NCI (in HCMI) to generate the next generation of cancer cell lines.

  Study EGAS00001004677

• Organoid_Derivation_Project___GRCh38___WGS

  Generation of normal and cancer organoids for sequencing as part of the WTSI-CRUK international collaboration with NCI (in HCMI) to generate the next generation of cancer cell lines

  Study EGAS00001004712

• Organoid_Derivation_Project___GRCh38___TGS

  Generation of normal and cancer organoids for sequencing as part of the WTSI-CRUK international collaboration with NCI (in HCMI) to generate the next generation of cancer cell lines.

  Study EGAS00001007349

• Test Study for EGA using data from 1000 Genomes Project - Big CRAM, BAM, VCF and BCF files used for testing

  This is a test study for EGA using data from 1000 Genomes Project, specifically created to add more diversity to the existing dataset EGAD00001003338. This Test Study should NOT be confused with the real study of 1000 Genomes Project - Phase 3. Specifically, this study encompasses 4 CRAM, 4 BAM, 2 VCF and 2 BCF files, of different sizes (all above 1 GB), used for testing downloads and monitoring services. It also contains their respective indexes: crai for crams, bai for bams, tbi for vcfs and csi for bcfs.

  Study EGAS00001006718

• Gut 16S rRNA/FINRISK 2002

  Gut microbiome 16S rRNA raw data for N=7174 FINRISK 2002 participants. FINRISK fecal samples were mailed to the Knight laboratory at the University of California (San Diego, CA), for microbiota sequencing using the standard Earth Microbiome Project protocols (https://earthmicrobiome.org/protocols-and-standards/). DNA was extracted using a magnetic bead-based DNA extraction protocol. Amplicon sequence data for the V4 region of the 16S rRNA gene was generated using 515F (Parada) and 806R (Apprill) primers. For a total of 25μl reaction volume, 13 µl PCR-grade water was combined with 10 µl PCR master mix (Platinum Hot Start PCR Master Mix, 2x, ThermoFisher), 0.5 µl forward primer (10 µM), 0.5 µl reverse primer (10 µM), and 1 µl template DNA. Amplification was performed in triplicate reactions, and triplicate PCR reactions were pooled afterwards. Expected products were visualized on agarose gels (300–350 bp) and quantified with Quant-iT PicoGreen dsDNA kit (Invitrogen). Equal amounts (240 ng) of amplicon were combined for each sample and cleaned (MoBio UltraClean PCR Clean-Up Kit). Cleaned amplicon pools were sequenced with 515F and 806R primers.

  Dataset EGAD50000000287

• PopCol 16S gut microbiome sequencing

  PopCol is a cohort study in Stockholm, Sweden that includes a data-rich set of individuals with data available from bowel symptoms questionnaires, gastroenterology visits and biospecimens (genotype and 16S sequencing from blood and stool samples, respectively). Genotyping was carried out using the Illumina HumanOmniExpressExome-8v1 arrays at the SciLifeLab NGI facility in Uppsala, Sweden. Fecal DNA was extracted from samples kept at -80°C using Qiagen 5 QIAamp DNA Stool Mini Kits and analyzed using 16S rRNA gene amplicon sequencing (in the V1-V2 hypervariable region). This was performed on the Illumina MiSeq platform at the Institute of Clinical Molecular Biology (IKMB) in Kiel, Germany. Of these, six PopCol participants were PPI users and 12 used antibiotics. The study was approved by the local Committee of Research Ethics (Forskningskommitté Syd) at Karolinska Institutet, Stockholm, in November 2001. Written informed consent was obtained from all participants

  Dataset EGAD00001007071