15138 results for "cancer studies using rna-seq"

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• Whole-exome sequencing of MDS and related myeloid neoplasms

  Myelodysplastic syndromes(MDS) and related myeloid neoplasms (myelodysplasia) are heterogenous group of myeloid neoplasms characterized by deregulated blood cell production with evidence of myeloid dysplasia. Previously, frequent mutations in genes on RNA splicing machinery and DNA methylation pathway have been identified. However, comprehensive analysis of genetic alterations have not performed on a large cohort of these diseases. Therefore, in this study, we performed whole-exome sequencing of MDS and related myeloid neoplasms.

  Study JGAS000023

• RNaseq of mantle cell lymphoma patient samples

  This study presents bulk RNA sequencing data from 78 clinical mantle cell lymphoma (MCL) samples. Following rigorous quality control and batch effect correction to account for sample type and redundancy, 62 samples from 59 patients were included in the final analysis. The transcriptomic profiles capture the molecular diversity across both solid and liquid tumor contexts and support investigations into the phenotypic plasticity and metabolic states of drug-tolerant persister (DTP) cells.

  Study EGAS50000001086

• Comprehensive miRNA Sequence Analysis Reveals Survival Differences in Diffuse Large B-cell Lymphoma Patients

  Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30-40% of patients failing to achieve complete responses to standard therapy. miRNAs are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 benign centroblast fresh frozen samples and from 140 DLBCL formalin-fixed, paraffin-embedded tissue (FFPET) samples for validation.

  Study EGAS00001001025

• Investigation of the keratinocytic gene expression pattern in Hidradenitis suppurativa

  The underlying pathogenetic factors generating the innate immune signal necessary for T cell activation, initiation and chronification of Hidradenitis suppurativa (HS, also known as Acne inversa) are still poorly understood. Emerging evidence suggests that defective keratinocyte function critically contributes to HS disease development and progression. To elucidate the role of keratinocytes in HS lesion formation, we compared the transcriptomes of isolated lesional and perilesional HS epidermis by RNA sequencing.

  Study EGAS00001005544

• Cell types of the human retina and its organoids at single-cell resolution. Cowan et al

  Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers, and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas.

  Study EGAS00001004561

• glioblastoma single cell RNAseq

  Understanding the cellular origin and differentiation status of glioblastoma is critical to resolve the etiology of the disease. we profile 18 patient glioblastomas by single cell RNA sequencing (scRNAseq). From this, we uncovered two principal cell-of-origin relations. Each lineage displays unique directional differentiation trajectories and transcriptional cores from the naïve cell populations. Thus, glioblastoma is defined by robust cell lineage features which may provide insights into the cell origin of the diseases.

  Study EGAS00001006236

• Induction of trained immunity by influenza vaccine: impact on COVID-19

  Cryopreserved PBMCs from 10 individuals before and after vaccination were used to perform single cell RNA sequencing. Equal number of cells per individual were pooled together (5 individuals per pool) and single-cell RNA sequencing was performed in paired-end mode on NovaSeq 6000 (Illumina) with a depth of 50,000 reads per cell. DNA was isolated from PBMCs and then used for genotyping by Illumina GSA Beadchip. This dataset contains the fastq sequence files, genotypes of the donors used for demultiplexing the pools and files indicating the linkages between individuals, pools and fastq files. The number of samples listed by EGA does not match the actual number of samples due to limitations on the upload scheme used.

  Dataset EGAD00001007827

• RNAseq data

  RNAseq FASTq files from 797 tumors from AVANT. Sequencing libraries were generated with the TruSeq Stranded Total RNA kit (Illumina) following ribosomal RNA (rRNA) depletion with the Ribo-Zero Gold kit (Illumina). The libraries were sequenced on the HiSeq4000 (Illumina) with a sequencing protocol of 75 bp paired-end sequencing. Note: 10 samples used in the original publication were excluded from this upload due to regulations from the Human Genetics Resources Administration of China (HGRAC).

  Dataset EGAD00001009728

• Bulk-tissue RNA-sequencing paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen tissues from 4 post-mortem neuropathologically-confirmed control individuals ( anterior prefrontal cortex & cerebellar cortex – 4 individuals, putamen- 3 individuals)

  Profiling of paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen samples by bulk-tissue RNA-sequencing. Samples were derived from 4 post-mortem neuropathologically-confirmed control individuals ( anterior prefrontal cortex – 4 individuals, cerebellar cortex – 4 individuals, putamen- 3 individuals). Paired-end FASTQ files for each of the human samples are provided. Fastp (v 0.20.0), a fast all-in-one FASTQ pre-processor, was used for adapter trimming, read filtering and base correction. Fastp default settings were used for quality filtering and base correction. Further details on parameters used are available here: https://github.com/RHReynolds/RNAseqProcessing .

  Dataset EGAD00001009264

• RNA stability controlled by m6A methylation contributes to X-to-autosome dosage compensation in mamals

  In mammals, X-chromosomal genes are expressed from a single copy since males (XY) possess a single X chromosome, while females (XX) undergo X inactivation. To compensate for this reduction in dosage compared to two active copies of autosomes, it has been proposed that genes from the active X chromosome exhibit dosage compensation. However, the existence and mechanism of X-to-autosome dosage compensation are still under debate. Here, we show that X-chromosomal transcripts are reduced in m6A modifications and more stable compared to their autosomal counterparts. Acute depletion of m6A selectively stabilises autosomal transcripts, resulting in perturbed dosage compensation in mouse embryonic stem cells. We propose that higher stability of X-chromosomal transcripts is directed by lower levels of m6A, indicating that mammalian dosage compensation is partly regulated by epitranscriptomic RNA modifications.

  Dataset EGAD00001010194

• ATAC-Seq on OCIAML-22 Fractions

  The donor AML patient (unsorted) that was used to generate OCI-AML22 was expanded for 3-4 months, then sorted for the indicated fraction (CD34p: CD34+; CD34m: CD34-)

  Study EGAS00001006511

• Low-pass whole-genome DNA sequencing of cohesin-mutated and wildtype adult AMLs

  Low-pass whole-genome DNA sequencing of cohesin-mutated (STAG2 or RAD21 mutations) and wildtype (CTRL-AML) adult AMLs generated generated from ultrasound-fragmented genomic DNA. Samples were only sequenced shallow (20-40 Mio reads) Used for digital karyotyping and ChIP-seq background/copy-nuber normalization/correction.

  Dataset EGAD00001011207

• Mixture of 2

  Mixture of 2 unrelated individuals sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.

  Dataset EGAD00001008726

• AML-PMP miRNA-Seq

  miRNA libraries of the AML-PMP project were sequenced on the Illumina HiSeq 2000 instrument, approximately 16 samples per HiSeq lane, to a median depth of 5.7 million reads per library.

  Dataset EGAD00001009772

• HiC-sequencing in human monocyte differentiation

  This dataset consists of in situ HiC-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, the data set includes 42 samples.

  Dataset EGAD00001007955

• scRNA-seq of nonhematopoietic cells in human lymph nodes and lymphoma

  Single-cell count data generated by the Cellranger (10X Genomics).

  Dataset EGAD00001008311

• High Density SNP Association Analysis of Lung Cancer

  This research builds upon an extensive resource of a case-control study that has been ongoing at the UT MD Anderson Cancer Center since 1991. To identify risk variants for lung cancer, we conducted a genome-wide association study. Cases are newly diagnosed, histologically-confirmed patients presenting at MD Anderson Cancer and who had not previously received treatment other than surgery. Controls are healthy individuals seen for routine care at Kelsey-Seybold Clinics, the largest physician group-practice plan in the Houston Metropolitan area. This lung GWAS led to the identification of a susceptibility locus for lung cancer at 15q25.1. We used data from 315,450 tagging SNPs in 1,154 current and former (ever) smoking cases of European ancestry and 1,137 frequency-matched, ever-smoking controls from Houston, Texas in the discovery followed by the replication of the ten SNPs most significantly associated with lung cancer in an additional 711 cases and 632 controls from Texas and 2,013 cases and 3,062 controls from the UK. Two SNPs, rs1051730 and rs8034191, were significantly associated with risk of lung cancer with combined analysis yielded odds ratios of 1.32 (P < 1X10-17) for both SNPs. These two SNPs mapped to a region of strong linkage disequilibrium within 15q25.1 containing PSMA4 and the nicotinic acetylcholine receptor subunit genes CHRNA3 and CHRNA5. (Nat Genet. 2008 May;40(5):616-22. PMID:18385676)

  Study phs000753

• OICR PANCREATIC CANCER DATASET 2

  OICR PANCREATIC CANCER DATASET 2

  Dataset EGAD00001000276

• Colorectal cancer cells possess an equipotent capacity to enter a developmental pausing-like state to survive chemotherapy

  Study EGAS00001004773

• Patient-derived organoids identify tailored therapeutic options and determinants of plasticity in sarcomatoid urothelial bladder cancer

  Study EGAS00001007430