3792 results for "RNA AND sequencing OR transcriptome"

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• RNA sequencing of NK cells in human lung

  The dataset contains RNAseq data from 5 subsets of NK cells isolated from human lung: 1) CD69+CD49a+CD103+CD16-CD56bright NK cells 2) CD69+CD49a+CD103-CD16-CD56bright NK cells 3) CD69+CD49a-CD103-CD16-CD56bright NK cells 4) CD69-CD49a-CD103-CD16-CD56bright NK cells 5) CD56dimCD16+NKG2A+CD57- NK cells The dataset contains paired data for the subsets from 2 donors with 2 biological replicates/donor and subset.

  Dataset EGAD00001004850

• RNA-seq of cells cultured in vitro

  This dataset includes 90 samples profiled by high-throughput Illumina sequencing, in bam format, aligned to GRCh37. Normal human CD34+ cord blood (CB), bone marrow (BM), or post-natal thymus (PNT) cells were transduced with various combinations of T-ALL oncogenes and cultured in vitro.

  Dataset EGAD00001009750

• Genomic Data for Integrative Profiling of T790M Negative EGFR Mutated NSCLC

  Contains WES and RNA-seq for the 59 patients with first- and second-generation EGFR TKI-resistant metastatic EGFR-mutated NSCLC.

  Dataset EGAD00001010272

• TRACERx NSCLC - Multiregion RNA sequencing data from the 421 cohort

  RNAseq data from the TRACERx 421 cohort

  Dataset EGAD00001009862

• Smartseq2 data of single immune cells in hepatocellular carcinoma

  The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites. This dataset is part of Smartseq2 data

  Dataset EGAD00001005960

• Prognostic and immunomodulatory consequences of ERV expression in ovarian cancer

  The dataset contains transcriptional data obtained using total RNA sequencing on a Illumina machin. 59 samples are from the Hammersmith Hospital (HH) cohort of human primary ovarian tumours and 20 samples are from ovarian cancer cell lines Kuramochi (3 replicates) and Ovsaho (2 replicates) treated with 1 uM DNMTi guadecitabine or vehicle, at an early (day 5) or late (day 8) timepoint.

  Dataset EGAD00001006589

• The BNT162b2 mRNA COVID-19 vaccine induces long-term effects on both adaptive and innate immune responses

  This dataset contains bulk RNA sequencing at different timepoints post-BNT162b2 mRNA COVID-19 vaccination. Stimulation experiments were performed at each of the timepoints (RPMI, Influenza, R848 and Influenza stimuli), resulting in 242 libraries distributed over 4 stimulations and 4 timepoints. Libraries were sequenced on the DBNSEQ platform.

  Dataset EGAD00001011042

• Single-cell RNA and TCR sequencing of 37 PBMC pools of advanced HCC patients.

  scRNAseq and scTCRseq of serial peripheral blood mononuclear cell (PBMC) samples (n=72) taken at various timepoints before and during treatment (Week 0 (W0), Week 3 (W3), Week 6 (W6)). PBMC samples were pooled together into 37 pools, loading 2 or three samples per lane in the 10X Genomics chip, in equal proportions, according to a pre-designed pooling matrix.

  Dataset EGAD00001011345

• SCA1 and control cerebral organoids

  3' RNA-sequencing data of cerebral organoids from controls and individuals with SCA1 was performed at day 31 and day 60 of organoid formation. Matched case-control cerebral organoids were used (Ctrl A+SCA1 A and Ctrl B+SCA1 B) as well as isogenic cerebral organoids, CRISPR/Cas9 gene-edited from Ctrl A (SCA1-/CAG and SCA1CAG/CAG). Biological triplicates were assessed for all lines at both time points.

  Dataset EGAD50000002473

• mRNA profiling of CAFs and cancer cells in response to TGF-β and BMP signaling

  TGF-β and BMP signalings are important signaling pathways in the tumor microenvironment during cancer progression. This RNA-sequencing (62 fastq pairs) analysis explored how cancer-associated fibroblasts (CAFs) from human (19TT) and mice (Balbc A/B) respond to TGF-β, BMP2, or Gremlin antibody, as well as how cancer cells (66cl4) respond to Gremlin antibodies.

  Dataset EGAD50000001351

• Genetic investigation of 12q-amplified osteosarcomas

  Further investigation and characterisation of 12q-amplified low- and high-grade osteosarcomas with MDM2 and/or CDK4 amplification focusing on SV, copy number and gene fusion analyses. In total, 25 cases (33 samples total due to multi-sampling) were included, with some form of sequencing data available for 27 samples. Mate-pair whole genome sequencing (Illumina) is available for 19 samples, longread whole genome sequencing (PacBio HiFi) on 10 samples and RNA-sequencing (Illumina Truseq) on 21 samples. Data is available as BAM files.

  Dataset EGAD50000000707

• Counts: Brain transcriptome of hereditary cerebral haemorrhage with amyloidosis–Dutch type (HCHWA-D)

  These are the log2CPM (log2 counts per million) fragments per gene counts associated with the BAM files in EGAD00001003806, in tab separated format. Counts for 36 postmortem brain samples from 9 non-demented control subjects and 9 Hereditary cerebral hemorrhage with amyloidosis-Dutch type subjects are included (1 Frontal cortex sample and 1 Occipital cortex sample per subject). RNA samples were depleted for ribosomal RNA with the Ribo Zero Gold Human kit (Illumina) and strand specific RNA-Seq libraries were generated. Paired-end sequencing was performed on a HiSeq2500 Illumina system (2x50bp reads). Alignments were performed using GSNAP v2014-12-23 with setting "--npaths 1" on GRCh38 reference genome without the alternative contigs. Fragment per gene counting was performed using HTSeq-count v0.6.1p1 with setting "--stranded reverse". The gene annotation used for quantification were UCSC RefSeq genes for GRCh38 downloaded on 2015-07-13.

  Dataset EGAD00010001457

• RNA-Seq of human longitudinal whole blood samples from PCR-positive and PCR-negative recent household contacts of COVID-19 index cases.

  Little is known about the transcriptomic profile of individuals who are exposed to SARS-CoV-2 yet resist becoming PCR positive. To investigate this, longitudinal whole-blood samples were taken (0, 7, 14, and 28 days after enrolment) from PCR positive and PCR negative SARS-CoV-2-naïve household contacts who were recently exposed to a COVID-19 index. Samples were also taken from pre- and post-pandemic unexposed controls. Total RNA was extracted from PAXgene tubes before undergoing poly(A) selection followed by globin and rRNA depletion. DNA libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. All samples were then sequenced across 2 flowcells of an Illumina HiSeq 4000.

  Dataset EGAD50000000684

• Single-cell RNA sequence analysis of iPS cell-derived cardiomyocytes treated with S-RBD-sfGFP or GFP

  To determine the transcriptional response in human cardiomyocytes treated with SARS-CoV-2 spike receptor-binding domain (S-RBD-sfGFP), human cardiomyocytes differentiated from induced pluripotent stem cells (iPSC-CMs) were replated on day 21 after differentiation and treated with S-RBD-sfGFP or control-GFP for 48 hours on day 26-28. iPSC-CMs were dissociated and the single cell suspension was analyzed by single cell RNA-sequence.

  Study JGAS000620

• Single cell ATAC seq component of ATAC-RNA multiome analysis of a four weeks post conception embryo head

  Four single-cell ATAC libraries were generated from an unbiased sample of cells of a human four weeks post conception embryo using the 10X Chromium Single-Cell Instrument and NextGEM Single Cell Multiome ATAC+Gene Expression kit (10X Genomics) according to the manufacturer’s protocol.

  Dataset EGAD50000001502

• 4_eCLIP_NOVA1_NOVA2_RBFOX2

  eCLIP of NOVA1, NOVA2 and RBFOX2 from iPSC-derived motor neurons in 2 control lines. Per line and RNA-binding protein input and IP samples and analysis including bigWig files and peak files.

  Dataset EGAD00001008428

• Advanced iPSC-CMs maturation by integrating maturation medium, nanopatterning, and electrical stimulation

  RNA seq of iPSC-derived cardiomyocytes cultured in lipid-enriched maturation medium (MM), in MM on nanopattern-surfaces (NP) and under the influence of MM, NP and electrical Stimulation (ES, 2Hz, 14 days). 9 Samples from 3 Independent batches/differentiations of cardiomyocytes from 2 different iPSC-lines (iWTD2.1 and isWT7.22).

  Dataset EGAD00001011289

• Human tumor single-cell

  We profiled 11 patient tumor samples by single-cell and single-nuclei RNA-seq using 10X Chromium 3'. These include samples from the following entities: WNT-subtype medulloblastoma (N=3), embryonal tumors with multilayered rosettes (N=3), and atypical teratoid-rhabdoid tumors (N=5). The BAM files are provided.

  Dataset EGAD00001005129

• RNAseq in ASD patients and controls

  RNA sequences of a total of 24 samples, including 13 unrelated ASD patients (13 males) and 11 adult individuals of Spanish origin as controls (4 males, 7 females). The RNAseq study was conducted on a HiSeq 4000 (Illumina) and paired-end sequences were obtained (fastq files).

  Dataset EGAD00001008160

• Colon Cancer Organoid Cultures and Tumors RNASeq Data

  Four micrograms of total RNA was used for cDNA library construction using the KAPA Stranded mRNA-Seq Kit (KR0960-v3.15), following manufacturer's protocol. The adaptor-ligated libraries were enriched by 6 cycles of polymerase chain reaction (PCR). Libraries were sequenced using the Novaseq 6000 with paired end 151bp reads.

  Dataset EGAD00001005753

• CITE-seq data of primary acute myeloid leukemia patient samples with complex karyotype

  In this study, we aimed to assess RNA expression and surface antigen expression of acute myeloid leukemia with complex karyotype (CK-AML) at the single-cell level. For this purpose, we performed cellular indexing of transcriptomes and epitopes (CITE-seq) of primary leukemia samples from four CK-AML patients.

  Dataset EGAD00001011171

• Bulk RNA Seq in FAP Adenoma

  Bulk RNASeq data of Duodenal organoids, sorted ILC3 and duodenal tissue

  Dataset EGAD00001015488

• Transcriptome alterations underlying metabolic dysfunction and liver disease in myotonic dystrophy type 1

  Myotonic dystrophy type 1 (DM1) is a multisystem disorder affecting various organs, including the skeletal muscles, eyes, heart, central nervous system, and endocrine system. Liver dysfunction and lipid metabolism abnormalities are frequently observed in DM1 but are not fully understood. To explore the molecular basis of these abnormalities, transcriptome analysis was performed on postmortem liver samples from DM1 patients DM1 patients (n = 11) and disease control patients (n = 9) using bulkRNA sequencing (RNA-seq) on the MGI DNBSEQ-G400RS. Differential gene expression and alternative splicing analyses revealed significant transcriptomic changes associated with lipid metabolism, liver fibrosis, and glucose homeostasis. Interestingly, transcriptome changes in DM1 livers also revealed partial resolution of sexual dimorphism in gene expression, along with unique sex-specific pathway alterations. A correlation between serum GGT levels and splicing abnormalities in DM1 patients was identified, suggesting a link between transcriptomic changes and clinical outcomes. This dataset provides valuable insights into the molecular mechanisms underlying DM1-related liver dysfunction and metabolic abnormalities.

  Study JGAS000814

• mRNA capture sequencing and RT-qPCR for the detection of pathognomonic, novel and secondary fusion transcripts in formalin-fixed paraffin-embedded tissue: a sarcoma showcase

  RNA sequencing is widely used to study gene abundance patterns, but less frequently to assess structural alterations such as fusion transcripts. In this study, we assess the performance of messenger RNA (mRNA) capture sequencing to identify fusion transcripts in formalin-fixed paraffin-embedded (FFPE) tissue of different types of sarcoma, followed by orthogonal confirmation using RT-qPCR. To validate our workflow, we used the TruSight RNA Pan-Cancer Panel to analyze a first cohort of 6 positive control tumors for which the diagnostic workup demonstrated the presence of a specific chromosomal rearrangement. Fusion transcript calling by FusionCatcher confirmed all known aberrations and enabled the identification of both fusion gene partners and breakpoints. Next, whole transcriptome TruSeq RNA Exome sequencing was applied to a second cohort of 17 patients, diagnosed with fusion gene-negative alveolar rhabdomyosarcoma (ARMS) or undifferentiated round cell sarcoma (URCS), for whom fluorescence in situ hybridization (FISH) did not identify the classical pathognomonic rearrangements. Remarkably, for 6 out of 17 patients, mRNA capture sequencing readily detected a pathognomonic fusion transcript, i.e. PAX3-FOXO1 in 2 ARMS patients, and EWSR1-FLI1, EWSR1-ERG or EWSR1-NFATC2 in 4 URCS patients. These data show that RNA capture sequencing may enhance the detection rate of pathognomonic fusion genes in sarcoma. For the 11 patients with no known pathognomonic fusion transcript, 11 newly identified fusion transcripts were confirmed by RT-qPCR, including COPS3-TOM1L2, NCOA1-DTNB, WWTR1-LINC01986, PLAA-MOB3B, AP1B1-CHEK2 and BRD4-LEUTX fusion transcripts in ARMS patients. Additionally, recurrently detected secondary fusion transcripts in two patients diagnosed with EWSR1-NFATC2-positive sarcoma were confirmed (COPS4-TBC1D9, PICALM-SYTL2, SMG6-VPS53 and UBE2F-ALS2). Our results provide new insights into the underlying genetic causes of these malignancies.

  Study EGAS00001005202

• ICARUS-BREAST01 Dataset

  A phase II clinical trial (NCT04965766) of patritumab deruxtecan in 99 breast cancer patients. Whole-exome sequencing (WES) is available for 43 tumor samples and 43 blood samples collected at entry into the trial. RNA-squencing is available for 44 samples comprising 22 samples collected at entry into the trial and 22 samples collected during treatment (cycle 1 day 3, cycle 1 day 19, or cycle 2 day 3) from 22 patients.

  Dataset EGAD50000000773