Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: EGAD00001008763 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

fe4e3260-5455-4100-a11b-32a9426a70c5 - samples

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

| EGAD00001009854 | EGA

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

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

Molecular profiling of stem cell-like female germ line cells in Drosophila delineates networks important for stemness and differentiation

Project description:We characterize the transcriptome of germline stem cell (GSC)-like cells isolated from bag of marbles (bam) mutant Drosophila ovaries by next generation RNA sequencing (RNA-seq) and compare it to the transcriptome of germline cells isolated from wild type ovaries. We further refine this dataset by utilizing an RNA-immunoprecipitation strategy to identify transcripts bound to the master differentiation factor Bam.

2019-10-31 | GSE138987 | 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

Unique Patients from the Genomics of Pediatric SIRS and Septic Shock Investigators (GPSSSI)

Project description:This dataset is composed of the unique patients (276; at the Day 1 timepoint) that are present in the six other GEO datasets published by Hector Wong and the Genomics of Pediatric SIRS and Septic Shock Investigators. This dataset thus includes all unique patients from GSE4607, GSE8121, GSE9692, GSE13904, GSE26378, and GSE26440. These are only from the Day 1 timepoint. The original studies examined pediatric patients admitted to the ICU, who were later classified as either SIRS (non-infectious) or Sepsis or Septic Shock (infectious). There is also a group of healthy controls. Although the original studies examine patients at both ICU day 1 and ICU day 3, here we have only aggregated ICU day 1 patients. All samples here were downloaded as .CEL files and re-normalized together using gcRMA using R package 'affy'. The normalized data can be found on the series record and contains the gcRMA normalized expression values.

2015-05-12 | E-GEOD-66099 | biostudies-arrayexpress

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