F8e15ed5-9d1a-49ab-82b8-bc335c43f5e6 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009815 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Concatenated long-read single-cell RNA sequencing samples prepared using 10X and the HIT-scIsoSeq protocol. The sequencing was performed on Sequel II Pacbio machine.
3 ovarian cancer patients, 5 omentum biopsies samples: 3 metastasis samples (one per patient), 2 healthy samples (one per patient except Patient2). 4 bam files per metastasis sample, 2 bam files per healthy sample.
| EGAD00001009814 | EGA
Project description:Colorectal cancer (CRC) is one of the most prevalent cancers, with over one million new cases per year. Overall, prognosis of CRC largely depends on the disease stage and metastatic status. As precision oncology for patients with CRC continues to improve, this study aimed to integrate genomic, transcriptomic, and proteomic analyses to identify significant differences in expression during CRC progression using a unique set of paired patient samples while considering tumour heterogeneity.We analysed fresh-frozen tissue samples prepared under strict cryogenic conditions of matched healthy colon mucosa, colorectal carcinoma, and liver metastasis from the same patients. Somatic mutations of known cancer-related genes were analysed using Illumina's TruSeq Amplicon Cancer Panel; the transcriptome was assessed comprehensively using Clariom D microarrays. The global proteome was evaluated by liquid chromatography-coupled mass spectrometry (LC‒MS/MS) and validated by two-dimensional difference in-gel electrophoresis. Subsequent unsupervised principal component clustering, statistical comparisons, and gene set enrichment analyses were calculated based on differential expression results.Although panomics revealed low RNA and protein expression of CA1, CLCA1, MATN2, AHCYL2, and FCGBP in malignant tissues compared to healthy colon mucosa, no differentially expressed RNA or protein targets were detected between tumour and metastatic tissues. Subsequent intra-patient comparisons revealed highly specific expression differences (e.g., SRSF3, OLFM4, and CEACAM5) associated with patient-specific transcriptomes and proteomes.Our research results highlight the importance of inter- and intra-tumour heterogeneity as well as individual, patient-paired evaluations for clinical studies. In addition to changes among groups reflecting CRC progression, we identified significant expression differences between normal colon mucosa, primary tumour, and liver metastasis samples from individuals, which might accelerate implementation of precision oncology in the future.
2023-03-11 | PXD036434 | Pride
Project description:Purpose: The goals of this study are to compare RNA-seq profiles of Col-0, acd6-1, flk-1, flk-5, acd6-1flk-1, and acd6-1flk-5 to identify genes affected by FLK. Methods: Total RNA was extracted from 25-d old plants. A total amount of 1 μg RNA per sample was used to generate cDNA libraries, using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Deep sequencing was performed using Illumina NovaSeq 6000 (Novogene Corporation Inc.). Triplicate biological samples were used for all genotypes except acd6-1flk-5, which had duplicate samples because one sample failed to pass quality control. The samples were multiplexed and sequenced with the standard paired-end sequencing that has a read length of 150bp per end and 20M reads per end per sample. Results: We found that over 8000 genes are differentially affected by FLK based on the RNAseq analysis. GO analysis revealed that FLK-affected genes are enchriched for genes involved in primary metabolism and in response to abiotic and biotic stimuli. Conclusions: The RNAseq analysis support a role of FLK in regulation of plant development and defense.
2023-04-12 | GSE164424 | GEO
Project description:Whole-cell patch-clamp electrophysiology was performed on cholinergic interneurons of the mouse dorsal striatum. Cells were classified as active or silent based on spontaneous activity at the onset of recordings. Nuclei and surrounding cytoplasm were then collected using the patch pipette, and RNA-seq libraries were prepared using the SMART-Seq mRNA Single Cell LP kit (Takara, 634787). Paired-end 100-cycle sequencing was carried out on a NovaSeq X+ (Illumina) in the St. Jude Hartwell Center Genome Sequencing Core. At least 100 million reads were obtained per cell. Samples were collected and sequenced in two independent batches.
2026-07-07 | GSE328896 | GEO
Project description:The goal of this study was to compare transcription profiles of high grade serous ovarian cancer (HGSOC) patients at Day 0 and Day 15 of a single course Prexasertib treatment at 105mg/m2 intravenously over 1 hour. HGSOC patients recruited for this study were women aged 18 and older with most (79%) showing platinum resistant or refractory disease. Total RNA from patients before (Day 0, n=18) and 2 weeks after Prexasertib treatment (Day15, n=11) were prepared from frozen biopsies, and analysed using HiSeq4000 using Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing. Data is shown as quartile normalized CPM-TMM values. Patient survival and response was monitored till end of study. Our study show that prexasertib has clinical benefit in HGSOC patients.
2020-05-02 | GSE149723 | GEO
Project description:Membrane-initiated estrogen receptor alpha (mERα) signaling plays an important role in bone metabolism, but its contribution in the brain remains unclear. In this study, we performed RNA sequencing of hypothalamic tissue from 16-week-old female mice with selective inactivation of mERα signaling in POMC neurons (POMC-C451Af/f) and wild-type littermate controls. Total RNA was isolated from hypothalamus, and samples were pooled (two animals per sample) resulting in four biological replicates per genotype. Libraries were prepared using poly(A) selection and sequenced on an Illumina NovaSeq 6000 platform with paired-end 150 bp reads. Transcript abundance was quantified using Salmon and summarized to gene-level counts. Differential expression analysis was performed using DESeq2. This dataset provides insight into transcriptional changes associated with disrupted mERα signaling in hypothalamic neurons.
2026-04-27 | GSE328990 | GEO
Project description:To uncover transcriptional alterations associated with lenvatinib resistance in papillary thyroid carcinoma, we performed paired-end RNA-Seq (2 × 150 bp, NovaSeq 6000) on parental TPC-1 cells and an in-house generated lenvatinib-resistant sub-line (TPC-1-Len). Total RNA from three biological replicates per group was extracted with TRIzol, libraries were prepared with poly(A) selection, and sequencing was carried out at OE Biotech (Shanghai, China). Differential gene expression was analysed using DESeq2 (Q < 0.05)
2026-06-18 | GSE300132 | GEO
Project description:MKN-45 gastric cancer cells were subjected to NNMT knockdown or negative control treatment and cultured in three independent biological replicates per group. Total RNA was extracted using TRIzol reagent, and RNA integrity was confirmed with RIN > 8.0. RNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads. Differential gene expression analysis was performed to identify transcriptomic changes induced by NNMT knockdown.
2026-06-08 | GSE315562 | GEO
Project description:This dataset contains glomerulus-enriched RNA sequencing (RNA-seq) data from two BALB/c mouse substrains, BALB/cAjcl (Ajcl) and BALB/cByJcl (ByJcl). Glomeruli were isolated using a Dynabeads-based perfusion method. Samples were collected from untreated (baseline) mice and from mice on Day 5 after a single intravenous administration of adriamycin (doxorubicin hydrochloride; 10 mg/kg; retro-orbital injection under isoflurane anesthesia). Total RNA was extracted from isolated glomeruli, and only samples with RNA integrity number (RIN) ≥ 7.0 were used. RNA-seq libraries were prepared using poly(A) selection for strand-specific sequencing and sequenced on an Illumina NovaSeq 6000 platform to generate 2 × 150 bp paired-end reads (approximately 6 Gb per sample). Primary processing included quality control (FastQC), trimming (Trimmomatic), alignment to the Mus musculus reference genome (GRCm39) with STAR, and gene-level read summarization with featureCounts. Gene-level raw count matrices (tab-delimited) are provided as processed data files.
2026-03-02 | GSE320498 | GEO
Project description:This RNA-seq dataset contains whole blood transcriptome profiles from individuals with X-linked familial Kallmann syndrome associated with a new variant in the ANOS1 gene (c.452G>C). Samples were collected from two affected male siblings, their mother, and controls. Total RNA was extracted from whole blood, and ribosomal RNA was depleted prior to library preparation using the KAPA RNA HyperPrep Kit with RiboErase. Paired-end RNA sequencing was performed on the Illumina NovaSeq X Plus platform, generating approximately 100 million paired-end reads per sample. Sequencing utilized 1% of a 10B, 300-cycle flow cell, which produces up to 20 billion paired-end reads per flow cell. This dataset enables a comprehensive analysis of gene expression and splicing patterns associated with ANOS1-related Kallmann syndrome, providing a valuable resource for studying transcriptomic alterations in hypogonadotropic hypogonadism.
2026-02-16 | GSE318901 | GEO