422aa293-1afb-4095-88ff-47754cd940fc - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001005463 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:BAM files corresponding to sequencing of 18 circulating tumor DNA and matched tumor samples from SCLC patients. Each ctDNA sample was sequenced twice.
| EGAD00001005460 | EGA
Project description:BAM files corresponding to sequencing of 28 circulating tumor DNA and matched tumor samples from SCC patients. Each ctDNA sample was sequenced twice.
| EGAD00001005462 | EGA
Project description:In this study we have sequenced the TP53 gene (exons) from circulating-tumor DNA of 125 controls samples. Each ctDNA samples was sequenced independently twice.
| EGAS00001003989 | EGA
Project description:Purpose: A method for identifying genome-wide DNA binding sites for Fosb. Methods: Alive cells were sorted from retro-Fosb-OE(over-expression) organoids. The samples were incubated with anti-Fosb antibody (Abcam, ab184938). Purified DNA was subjected to Tru-seq library construction using NEBNext Ultra II DNA Library Prep Kit and sequenced as paired-end with Illumina Novaseq 6000. HISAT2 was used to align the sequences to the mouse genome and generate bam files. bamCoverage (CPM normalized and extended reads) was used to generate bigwig files from bam files. MACS2 was used for peak calling and to generate bed files from aligned reads. HOMER annotatePeaks.pl was used to annotate the peaks. Conclusions: Target genes of Fosb through ChIP assay were consistent with predicted target genes. Thus, we concluded that Fosb, which is a key TF could regulate most of ISC signature genes to maintain Lgr5+ ISCs.
2023-04-13 | GSE186915 | GEO
Project description:Liquid biopsy profile which can screen for early CRC. We aimed to depict the profile of early stage CRC as well as for advanced adenomas by combination of current molecular knowledge with microarray technology, using efficient circulating free RNA purification from blood and RNA amplification technologies. Circulating free RNA profile of plasma from colorectal cancer patients, advanced adenomas and healthy colonoscopia subjects. Plasma was drawn from 3 healthy colonoscopia subjects, 4 adanced adenomas subjects and 3 colorectal cancer patients. Circulating free RNA was purified from plasma samples and applied on GeneChip human 1.0 ST Arrays. The 'HuGene_1_0_green_yelow_red_DATASET.xlsx' and 'probe_level_expression_matrix.txt' files contain the primary data that was used to draw the conclusions of the current study. Please note that exon-level' analysis was performed but NO probe summarization to probeset was performed, therefore both data matrices contains non-unique identifiers.
2016-06-15 | E-GEOD-83353 | biostudies-arrayexpress
Project description:Overview: RNA-seq was used to profile the whole-transcriptome gene expression of highly replicated schizont-stage cultures of W2mef and Dd2 grown under static and suspended conditions. Methods: Transcript profiles of schizont stages of static and suspended W2mef and Dd2 were generated by RNA sequencing. Two to eight replicates were sequenced per sample. Illumina stranded TruSeq libraries were sequenced using an Illumina MiSeq. Hisat2 was used to align paired-end fastQ files and indexed bam files generated with samtools. Bam files were filtered to exclude reads with MAPQ scores below 60, reads counted using the SummarizeOverlaps feature of the GenomicAlignments package in R and differential expression analysis conducted using DESeq2 in R. Results: We show that in addition to invasion-related genes, parasites that have been induced to switch invasion phenotype upon culturing in suspension increase the expression of a number of genes most of which belong to gene families that code for exported proteins. Conclusions: Our data suggest that in addition to invasion phenotype switch, suspension cultures may select for other parasite properties that may be essential for parasite survival in vivo.
2019-04-18 | GSE129949 | GEO
Project description:Purpose: A method for mapping chromatin accessibility genome-wide, to reveal chromatin accessibility in Intestinal stem cells. Methods: Intestinal stem cells(Lgr5-high cells) were sorted by flow cytometry from wild type mice. The samples were prepared in duplicate. HISAT2 was used to align the sequences to the mouse genome and generate bam files. bamCoverage was used to generate bigwig files from bam files. MACS2 (v2.2.5) was used for peak calling and to generate bed files from aligned reads. Conclusions: ATAC-seq analysis confirmed that Fosb binding sites in Chip-seq assay were correlated with the chromatin accessibility .
2023-04-13 | GSE186916 | GEO
Project description:This dataset provides the transcriptome of the central cell of the female gametophyte from Arabidopsis thaliana. We sequenced two biological replicates. Each replicate started with a pool of 450 central cells collected using laser-assisted microdissection (LAM). Libraries were prepared as described in DOI:10.1038/NMETH.1315. Each library was sequenced on one eight of a slide on the AB SOLiD platform (version 3). IMPORTANT: In the alignment files (.bam), we named the mitochondrial and the chloroplastidial chromosomes ChrM and ChrC. This is different from the "chloroplast" and "mitochondrium" names in the whole genome fasta file available on TAIR.
2012-01-26 | E-GEOD-29719 | biostudies-arrayexpress