D2f1a98a-f6ff-4ee0-8a38-370234684438 - samples
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ABSTRACT:
PROVIDER: EGAD00001009757 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:E15.5 embryos were micro-disscted from Gata4 G295S mutant mice and littermate controls, RNA was isolated using Norgen total RNA isolation, and libraries were generated with the RNA TruSeq Stranded Total RNA kit. 50 base pair paired end reads were obtained on an illumina high seq 2500. Fastq files were aligned to the mouse genome using STAR aligner. QC was performed using RNASeQC and RSeQC. BAM files were processed using cufflinks pipeline.
2019-05-17 | GSE117621 | GEO
Project description:<p>The purpose of this study was to obtain tissue specimens derived from patients with melanoma to generate research tools to advance our understanding of the genetics, pathogenesis, and therapeutics of melanoma. Briefly, tissue was obtained from metastatic lesions and used to generate clonal primary cell lines from melanoma cells and fibroblasts from the tumor microenvironment. RNA was extracted from low passage cell lines using Trizol reagent. cDNA libraries were prepared using the TruSeq mRNA sample preparation kit, v2 (Illumina) and sequenced on the HiSeq 2000 platform (Illumina). The submitted files are bam files that contain both unaligned and aligned reads (human genome, build hg19). </p>
| phs001115 | dbGaP
Project description:Purpose:The goal of this study was to evalute gene expression patterns of equine chorioallantoic membrane during different stages of the pregnancy Method: mRNA profile of equine chorioallantoic membrane (CAM) from 45days, 4months, 6months and 10months (4 samples for each time points) generated by RNA-sequencing,using a Illumina HiSeq 4000 ( HiSeq 4000 sequencing kit version 1). The sequence reads were trimmed for adapters and quality using TrimGalore Version 0.4.4,and then mapped to EquCab2.0 using STAR-2.5.2b. Final quantification at the gen level was performed by analyzing the BAM files in cufflinks using the Equus_caballus_ENSEMBL_88 gtf file as Guide.
2018-11-19 | GSE108279 | GEO
Project description:Purpose: Quiescence is a state of reversible cell cycle exit. Levels of polyadenylation factors decreases when proliferating cells become quiescent. The goals of this study are to determine the differential use of polyadenylation sites (changes in alternative polyadenylation) in quiescent vs. proliferating cells and also upon knockdown of polyadenylation factors. Methods: Two biological replicates of human dermal fibroblasts (12-1 and 12-3) were used for polyadeylation-site enriched RNA-seq on an Illumina HiSeq 2500 to compare quiescent vs. proliferating cells and polyadenylation factor knockdown vs. control cells. The reads were aligned to the human genome (hg19) uisng Tophat (2.0.14). The resulting bam files were used as an input to a python script provided by Gruber et al. (PMID: 27382025) to determine the counts for each polyadenylation site. Results: We observed a shift toward greater use of distal polyadenylation sites when the fibroblasts entered quiescence. We observed significant overlap between the genes that shift to greater distal site use with quiescence and CstF-64 or CPSF73 knockdown. Conclusions: The shift to greater distal site use with quiescence may reflect in part the reduced levels of cleavage and polyadenylation factors.
2018-08-28 | GSE117033 | GEO
Project description:Tumors and control of nodal B-cell lymphoma of one patient. WES sequencing on Illumina HiSeq 4000 with Agilent SureSelect V5+UTRs. Bam files were aligned with bwa mem to hg19.
| EGAD00001006059 | EGA
Project description:In this study, we performed chromatin immunoprecipitation-coupled massive parallel DNA sequencing (ChIP-seq) to analyze the genome-wide transcriptional profile of ING5 in hepatocytes. ChIP was performed first in HepG2 cells with antibodies against ING5. Following ChIP, ING5-associated DNAs were amplified using non-biased conditions, labeled, and sequenced with HiSeq 2500. The raw sequencing image data were examined by the Illumina analysis pipeline, aligned to the unmasked human reference genome (GRCh37, hg19) using Bowtie2, and further analyzed by MACS (Model-based Analysis for ChIP-Seq).
2021-02-09 | GSE160192 | GEO
Project description:Introduction: HGFL-Ron signaling is augmented in human breast cancer and is associated with poor overall prognosis. Here, we investigate the role of HGFL-Ron signaling in RON-modulated human luminal A breast cancer cells T47D through RNA-sequencing, focusing on the impact of Ron knockdown through a short hairpin construct. Methods: non-targeting shRNA (shNT) and RON-targeting shRNA (shRON) were submitted for transcriptomic characterization on the Illumina HiSeq 2500. High quality reads were aligned to the hg19 genome and quantified to generate RPKM
2020-12-03 | GSE162532 | GEO
Project description:Purpose: RNase Y is a major enzyme responsible for mRNA degradation in Streptococcus pyogenes. The goals of this study are to understand whether RNase Y plays a role in operon transcription of S. pyogenes NZ131 by using RNA-seq analysis. Methods: S. pyogenes mRNA profiles of wild type (WT) and RNase Y mutant (∆rny) were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000. The sequence reads were aligned to the S. pyogenes genome using Bowtie2. The aligned files were sorted to BAM format and indexed using Samtools. The read depth of each base was derived from BAM files using BEDtools. Operon organization of S. pyogenes WT and ∆rny strains were predicted based on base reads. Results: A total of 11 to 12 billion reads were obtained from each sample. More than 99% of these reads were mapped to the S. pyogenes genome. Predictions of operon organization using WT and ∆rny samples showed little difference between the two strains. Conclusions: Our result shows that the mutation of RNase Y does not affect the operon organization of S. pyogenes NZ131.
2017-06-02 | GSE99533 | GEO
Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Florencia Pauli mailto:fpauli@hudsonalpha.org). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track is produced as part of the ENCODE Project. RNA-seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly (Mortazavi et al., 2008). Biological replicates of ENCODE cell lines were grown on separate culture plates, total RNA was purified and polyA selected two times. mRNA was then fragmented by magnesium-catalyzed hydrolysis, reverse transcribed to cDNA by random priming and amplified. The cDNA was sequenced on an Illumina Genome Analyzer (GAI or GAIIx). The DNA sequences were aligned to the NCBI Build37 (hg19) version of the human genome using the sequence alignment programs ELAND (Illumina) or Bowtie (Langmead et al., 2009). The first 10 residues of sequencing have a weak characteristic nucleotide bias of unknown origin. This RNA-seq protocol does not specify the coding strand. As a result, there will be ambiguity at loci where both strands are transcribed. This is the first NCBI Build37 (hg19) release of this track (Jan 2012). This release includes the 3 datasets (Jurkat, A549/DEX100nm, and A549/EtOH2pct) previously released on NCBI Build36 (hg18) and adds data for several more cell types and growth conditions in replicate. Four types of download files are available for each replicate including the Raw Data (fastq), Transcripts GencodeV7 (gtf), Raw Signal (bigwig), and Alignments (bam). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Experimental Procedures Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell) except for H1-hESC for which frozen cell pellets were purchased from Cellular Dynamics. Cells were lysed in RLT buffer (Qiagen RNEasy kit) and processed on RNEasy midi columns according to the manufacturer's protocol, with the inclusion of the "on-column" DNase digestion step to remove residual genomic DNA. mRNA was isolated from at least 10 ug of total RNA with oligo(dT) two times (Dynabeads mRNA PurificationgKit, Invitrogen). Alternatively, cells were lysed and mRNA was purified directly two times with oligo(dT) (Dynabeads mRNA DIRECT Kit, Invitrogen). 100 ng of mRNA was fragmented by magnesium-catalyzed hydrolysis and reverse transcribed to cDNA by random priming according to the protocol in Mortazavi et al. (2008). cDNA was prepared for sequencing on the Genome Analyzer flowcell according to the protocol for the ChIPSeq DNA genomic DNA kit (Illumina). The sequencing libraries were size-selected around 225 bp and amplified with 15 rounds of PCR. Libraries were sequenced with an Illumina Genome Analyzer I or an Illumina Genome Analyzer IIx according to the manufacturer's recommendations. Single end reads of 36 nt in length were obtained. Data Processing and Analysis Fastq files were made from qseq files generated by the Illumina pipeline (Casava 1.7). The Raw Signal files (bigWig) were generated from bedgraph files and the score was calculated as the number of reads at that position divided by the total number of reads divided by one million. Casava export files were aligned to the NCBI Build37 (hg19) version of the human genome with ELAND (Illumina), generating SAM files. Fastq files of experiments that were previously aligned to NCBI Build36 (hg18) were aligned to NCBI Build37 (hg19) using Bowtie (Langmead et al., 2009; parameters: -S -n 2 -k 11 -m 10 --best), also generating SAM files. SAM files were converted to BAM with SAMtools (Li et al., 2009). Gene expression within Gencode.v7 (Harrow et al., 2006) gene models was estimated using Cufflinks v0.9.3 (Roberts et al., 2011). Estimates of transcript abundance were reported in Fragments Per Kilobase of exon per Million fragments mapped (FPKM). FPKM is calculated by dividing the total number of fragments that align to the gene model by the size of the spliced transcript (exons) in kilobases. This number is then divided by the total number of reads in millions for the experiment. FPKM is reported in the last column of the gtf (TranscriptGencV7) files. Raw Data (fastq), Raw Signal (bigWig), Alignments (bam) and Transcript Gencode V7 (gtf) files are available from the Downloads (http://hgwdev.cse.ucsc.edu/cgi-bin/hgFileUi?g=wgEncodeHaibRnaSeq) page.
2012-04-27 | E-GEOD-35584 | biostudies-arrayexpress