4731 results for "RNA AND sequencing OR transcriptome"

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• Human Blastocyst 10X Single Cell RNA Sequencing

  Recent advances in human blastoids have opened new avenues for modeling early human development and implantation. One limitation of our first protocol for human blastoid generation was relatively low efficiency. We now report an optimized protocol for the efficient generation of large quantities of high-fidelity human blastoids from naive pluripotent stem cells. This enabled proteomics analysis that identified phosphosite-specific signatures potentially involved in the derivation and/or maintenance of the signaling states in human blastoids. Additionally, we uncovered endometrial stromal effects in promoting trophoblast cell survival, proliferation, and syncytialization during co-culture with blastoids and blastocysts. Side-by-side single-cell RNA sequencing revealed similarities and differences in transcriptome profiles between pre-implantation blastoids and blastocysts, as well as post-implantation cultures, and uncovered a population resembling early migratory trophoblasts during co-culture with endometrial stromal cells. Our optimized protocol will facilitate broader use of human blastoids as an accessible, perturbable, scalable, and tractable model for human blastocysts. In addition, this study is the first to use the 10X Genomics platform for human blastocysts, and we anticipate this resource will be widely used by the community as a reference for future studies.

  Study phs003122

• Transcriptome and TCR Sequencing of T Cells from Metastectomies

  T cells were sorted from metastatic tumors (colon, rectal, breast, anal, melanoma primary histologies) following tumor dissociation and single-cell sequencing was performed (RNAseq and TCRseq). For samples from tumors that had been previously studied, cells were analyzed comparing known neoantigen-reactive TCR-expressing cells to other T cells. For samples without previously identified neoantigen reactivity, TCRs were predicted on the basis of T cell transcriptomic states. To determine candidate neoantigen screening, exome and RNA sequencing were performed on fragments of matched tumors from which T cells were sequenced   

  Study phs002748

• Recurrent CLTC::SYK fusions and CSF1R mutations in juvenile xanthogranuloma of soft tissue

  In this study, the genomic landscape of extracutaneous juvenile xanthogranuloma (JXG) was analyzed. By leveraging the Dutch Nationwide Pathology Databank (Palga), tumor samples were obtained from different academic medical centers in the Netherlands. The study was approved by the Palga Scientific Council and Privacy Committee (LZV-2016-183) and the Institutional Review Board of Leiden University Medical Center (B19.074). In addition, the study was approved by the Biobank and Data Access Committee of the Princess Máxima Center for Pediatric Oncology (PMCLAB2024.0512). Provided are whole transcriptome sequencing (WTS) data of 3 histiocytic tumors with CLTC::SYK fusions. WTS was performed in the routine workflow of the Princess Máxima Center for Pediatric Oncology (as described in Hehir-Kwa, et al. JCO Precis Oncol 2022). RNA was derived from formalin-fixed paraffin-embedded tumor tissue (n=1) or from frozen tumor tissue (n=2).

  Study EGAS50000000584

• WTS and WES of Renal Cell Carcinoma Tumors From a Phase III Anti-Angiogenic Adjuvant Therapy Trial

  Archival de-identified formalin-fixed paraffin-embedded RCC tumor tissue blocks from nephrectomy or tumor biopsy were processed as per below and the same sections were used for both DNA and RNA extractions. For WES (ACE version 3; Illumina NovaSeq), samples were profiled using Personalis ACE Cancer Exome (Personalis, Inc, Menlo Park, CA) Whole-transcriptome profiles were generated by RNA-seq (Accuracy and Content Enhanced (ACE) version 3; Illumina NovaSeq) using Personalis ACE Cancer Transcriptome (Personalis, Inc, Menlo Park, CA ) Of the 615 patients in the intent-to-treat population in S-TRAC trial, 193 individual specimens were available for molecular profiling, of which 171 (27.8%) (sunitinib, n = 91; placebo, n = 80) returned results for the WES analysis, and 133 (21.6%) (sunitinib, n = 72; placebo, n = 61) returned results for the GES analysis. Of the 138 WTS samples with data, replicates for two patients were summarized by median expression, and three samples were excluded from the final analysis due to low counts.

  Dataset EGAD00001009294

• Laser Capture Microscopy (LCM)-RNAseq for Topological Mapping of Synovial Pathology during Rheumatoid Arthritis

  Synovial tissue from the hip or knee was collected from rheumatoid arthritis (RA) and osteoarthritis (OA) patients at the time of joint replacement surgery. Samples were analyzed using laser capture microdissection (LCM) followed by RNA-seq to evaluate the transcriptome in distinct synovial compartments. Results indicated that synovial compartments have both shared and distinct transcriptional signatures that correspond to key pathways relevant to RA pathogenesis.

  Study phs003587

• This dataset includes FASTQ for single-nucleus RNA-seq of normal controls, and multiple system atrophy (MSA) or Parkinson's disease (PD) patients.

  The dataset includes more than 130k nuclei isolated using 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1. In total, 30 samples are included from 10 controls, 8 MSA (including one sample that was omitted during QC), or 12 PD patients. Samples were sequenced on Illumina Novaseq 6000 or NextSeq 550 instruments.

  Dataset EGAD50000002041

• scRNA-seq data set for 13 AML patients

  This dataset includes single cell (sc)RNA-seq of N=13 AML patients. The dataset includes bam files that have been purged of reads mapping to cells where a majority of the reads from that cell mapped to the human genome. All scRNA-seq data were generated using the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) from 10X Genomics.

  Dataset EGAD50000001346

• miRNAseq of paired FL and tFL samples

  This dataset contains miRNA-seq of paired FL and tFL samples (n=10 pairs) sequenced by Illumina NextSeq500. Libraries used in this miRNA-seq dataset were prepared with NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB,Catalog number: E7560S). RNAs used for library preparation were isolated from FFPE tissues using High Pure miRNA Isolation Kit (Roche,Catalog number: 05080576001). Data are uploaded as FASTQ format.

  Dataset EGAD50000001385

• RNASEQ_TALL_t_14_16_translocation

  RNA-seq results of sequenced data of patients with t(14;16) translocated T-ALL.

  Dataset EGAD50000001781

• Bulk RNASeq on CD8+CD69+CD103+ and CD8+CD69+CD103- T cells form breast cancer.

  CD8+CD69+CD103+ and CD8+CD69+CD103- T cells were flow sorted from 1 primary triple negative breast cancer, 1 primary HER2 amplified breast cancer, and 1 triple negative liver metastasis. Prior to flow sorting, fresh tumor samples were digested to produce single cell homogenates on the day of surgery. Following RNA extraction, RNASeq was performed using polyA selection.

  Dataset EGAD00001003964