A9cebac5-7d4b-4300-b9a9-54880b155382 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001006036 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This is the PacBio long read data used for performing de novo assembly of the EGYPT individual (mapped against GRCh38).
| EGAD00001006034 | EGA
Project description:10x Genomics linked read data used in variant phasing and de novo assembly scaffolding for the EGYPT individual (mapped against GRCh38).
| EGAD00001006035 | EGA
Project description:Prostate cancer DU145 tumors were subcutaneously established in male nude mice. In nude mice, Zelnorm were orally administrated. Tumor volume and body weight were assessed (tumor volume=1/2 (length×width2)). Tumors were excised and weighted. Tumor samples were profiled by RNA-seq analysis. Respectively, to differentiate the gene expression originated from human (cancer cells) or mouse (tumor TME part), data were mapped against human (GRCh38) and mouse (GRCm38) genomes separately.
2023-12-31 | GSE198765 | GEO
Project description:To better understand the mechanism by which MAGEA3 contributes to HCC progression, we conducted RNA sequencing in the PLC5 HCC cell line after 72 hours of treatment with scramble or sh8375 in triplicate. RNA-sequencing was conducted on poly-A enriched RNA, 100 bp single reads using an Illumina HiSeq2500 instrument. Libraries were constructed using the TruSeq RNA Library Prep Kit v2. Raw sequencing reads were mapped to the GRCh38 reference genome (USCS) using STAR (2.4.2g1). Aligned reads were mapped to GRCh38 genetic features using featureCounts from the subRead package with default settings. Data analysis included differential gene expression between conditions and gene set enrichment analysis.
2021-05-19 | E-MTAB-8860 | biostudies-arrayexpress
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc
Project description:Purpose: Evaluate the molecular changes associated with Cfz -induced cardiotoxicity Methods: RNA-Seq analysis was performed to analyze global transcriptome profiles of hiPSC-CMs treated with DMSO (Control group), 1 µM Carfilzomib ( Cfz group). The Illumina TruSeq technology was used to prepare RNA-Seq libraries, and next-generation sequencing was done via an Illumina HiSeq 2000. RNA sequence reads were aligned to the human reference genome (GRCh38) using STAR v2.5. HTSeq v0.6.1 was used to count the read numbers mapped of each gene, and then Fragments Per Kilobase Million (FPKM) was calculated to estimate gene abundance. Differential expression analysis was performed using the DESeq2 R package (2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg's approach. As detected by RNA-Seq, some differential genes regulated by Cfz were significantly involved in cardiac contraction and extracellular matrix (ECM). Among the top 10 up-regulated genes post Cfz treatment,most of thoese genes was related to the heat shock protein expression( HSPA1B,HSPA6,,HSPH1, BAG3). And among the top 10 down-regulated genes post Cfz treatment, some correlated to contraction and Extra cellular matrix ( ITG11, SLC9A3, TNN1) . Conclusion: Carfilzomib -induced alteration of hiPSC-CM transcriptomic profiles. Enhanced HSPs and down regulate cardiac related contraction gene and extracellular matrix.
2021-10-04 | GSE163102 | GEO
Project description:C2C12 cells were UV-irradiated at 400 mJ, and whole cell lysates were harvested from the cells. tRIP was performed as previously described (Masuda et al). Samples were sequenced on the Illumina NovaSeq6000 with 150 bp paired-end read (Macrogen, Japan) or Miseq with 150 bp single-read at the core facility of the Nagoya University. For paired-end read data, only P5 reads were used for analysis. Briefly, after standard HiSeq demultiplexing, reads were adapter-trimmed and reads less than 18 bp were discarded using cutadapt (v1.10). Mapping was first performed against the mouse repetitive elements in RepBase with STAR (v2.5.2b). Repeat-mapped reads were removed, and all others were then mapped against the mouse genome (mm10) with STAR (v 2.5.2b). Multiply mapped reads were filtered out. Duplicates of reads uniquely mapped to the human or mouse genome were removed by Picard (v2.0.1).
2021-07-20 | GSE161602 | GEO
Project description:We produced an extensive transcript catalog for LCLs of 5 primate species by leveraging isoform sequencing and short-read RNA-seq. The curated transcriptomes were used to assist mass spectrometry protein identifications.
2022-05-31 | PXD031213 | Pride
Project description:<p>Proper spatial differentiation of retinal cell types is necessary for normal human vision. Many retinal diseases, such as Best disease and male germ cell associated kinase (MAK)-associated retinitis pigmentosa, preferentially affect distinct topographic regions of the retina. While much is known about the distribution of cell types in the retina, the distribution of molecular components across the posterior pole of the eye has not been well-studied. To investigate regional difference in molecular composition of ocular tissues, we assessed differential gene expression across the temporal, macular, and nasal retina and retinal pigment epithelium (RPE)/choroid of human eyes using RNA-Seq. RNA from temporal, macular, and nasal retina and RPE/choroid from four human donor eyes was extracted, poly-A selected, fragmented, and sequenced as 100 bp read pairs. Digital read files were mapped to the human genome and analyzed for differential expression using the Tuxedo software suite. Retina and RPE/choroid samples were clearly distinguishable at the transcriptome level. Numerous transcription factors were differentially expressed between regions of the retina and RPE/choroid. Photoreceptor-specific genes were enriched in the peripheral samples, while ganglion cell and amacrine cell genes were enriched in the macula. Within the RPE/choroid, RPE-specific genes were upregulated at the periphery while endothelium associated genes were upregulated in the macula. Consistent with previous studies, BEST1 expression was lower in macular than extramacular regions. The MAK gene was expressed at lower levels in macula than in extramacular regions, but did not exhibit a significant difference between nasal and temporal retina. The regional molecular distinction is greatest between macula and periphery and decreases between different peripheral regions within a tissue. Datasets such as these can be used to prioritize candidate genes for possible involvement in retinal diseases with regional phenotypes. </p> <p>Reprinted from <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=25446321">Whitmore, S.S., Wagner, A.H., DeLuca, A.P., Drack, A.V., Stone, E.M., Tucker, B.A., Zeng, S., Braun, T.A., Mullins, R.F., Scheetz, T.E., 2014. Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq. Experimental Eye Research</a>. Used under <a href="http://creativecommons.org/licenses/by-nc-sa/3.0/">Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported </a>license.</p> <p>Additional RNA sequencing was performed on temporal, macular, nasal, inferior, and superior retina from a fifth subject and is included in this dataset. See original publication for details.</p>
| phs001151 | dbGaP
Project description:Objectives: To perform long-read transcriptome and proteome profiling of pathogen-stimulated peripheral blood mononuclear cells (PBMCs) from healthy donors. We aim to discover new transcripts and protein isoforms expressed during immune responses to diverse pathogens. Methods: PBMCs were exposed to four microbial stimuli for 24 hours: the TLR4 ligand lipopolysaccharide (LPS), the TLR3 ligand Poly(I:C), heat-inactivated Staphylococcus aureus, Candida albicans, and RPMI medium as negative controls. Long-read sequencing (PacBio) of one donor and secretome proteomics and short-read sequencing of five donors were performed. IsoQuant was used for transcriptome construction, Metamorpheus/FlashLFQ for proteome analysis, and Illumina short-read 3’-end mRNA sequencing for transcript quantification. Results: Long-read transcriptome profiling reveals the expression of novel sequences and isoform switching induced upon pathogen stimulation, including transcripts that are difficult to detect using traditional short-read sequencing. We observe widespread loss of intron retention as a common result of all pathogen stimulations. We highlight novel transcripts of NFKB1 and CASP1 that may indicate novel immunological mechanisms. In general, RNA expression differences did not result in differences in the amounts of secreted proteins. Interindividual differences in the proteome were larger than the differences between stimulated and unstimulated PBMCs. Clustering analysis of secreted proteins revealed a correlation between chemokine (receptor) expression on the RNA and protein levels in C. albicans- and Poly(I:C)-stimulated PBMCs. Conclusion: Isoform aware long-read sequencing of pathogen-stimulated immune cells highlights the potential of these methods to identify novel transcripts, revealing a more complex transcriptome landscape than previously appreciated.
2023-09-16 | PXD045237 | Pride