Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fe4e3260-5455-4100-a11b-32a9426a70c5 - samples

ABSTRACT: This data set includes bam files (aligned to hg38) from the germline of children who have pathogenic mutations in cancer predisposing genes

PROVIDER: EGAD00001009854 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

5646733a-be6e-48d2-b09c-2e9978032b99 - samples

Project description:This data set includes bam files (aligned to hg38) from the germline of parents whose children have CHEK2 germline mutations.

| EGAD00001009516 | EGA

8eb84834-450d-420a-969d-42bb3248eed7 - samples

Project description:This dataset includes bam files (aligned to hg38) from the germline of pediatric cancer patients.

| EGAD00001008763 | EGA

iBET JMJD6

Project description:Aligned BAM files for PCa cell lines (iBET treated and JMJD6 siRNA)

| PRJEB49820 | ENA

m6A modification segregates the stemness program from proliferation in ISCs [ATAC-seq]

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

Hungarian BAM files

Project description:Hungarian BAM files

| PRJEB20905 | ENA

Project description:HIV Bam Files

| PRJNA321053 | ENA

Smart-seq2 analysis of P17 FACS sorted retinal cells from the Kcng4-cre;stop-YFP X Thy1-stop-YFP Line#1 mice

Project description:Four Kcng4-cre;stop-YFP mouse retinas from two mice were dissected, dissociated and FACS sorted, and single cell RNA-seq libraries were generated for 384 single cells using Smart-seq2. Aligned bam files are generated for 383 samples as one failed to align.

2016-08-25 | GSE81903 | GEO

Identification of BSF RNA targets using RIPSeq

Project description:Stroma extracts were isolated from 2-week-old WT plants and incubated with either BSF-specific antibodies or with the pre-immune serum. IgGs were captured with SiMAG-Protein G beads (Chemicell) and recovered RNA was used for generation of libraries with the ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre). Primary reads were aligned to the Arabidopsis chloroplast genome (accession number NC_000932.1) using CLC Genomics Workbench. BAM files were extracted and sorted in Galaxy . Sorted BAM files were converted into RPKM-normalized bigwig files and displayed in IGB. The differential enrichment of BSF/control of the two replicates was displayed across the entire chloroplast genome to identify the RNA targets of BSF.

2019-04-06 | GSE129411 | GEO

Differential expression data between E15.5 outflow tracts of Gata4 G295S mutant embryos and littermate controls

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

m6A modification segregates the stemness program from proliferation in ISCs [ChIP-seq]

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data