Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: HiC Capture Imprinted Gene Panel

PROVIDER: PRJNA926951 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23199639_1.fastq.gz	Fastqsanger.gz
	SRR23199639_2.fastq.gz	Fastqsanger.gz
	SRR23199640_1.fastq.gz	Fastqsanger.gz
	SRR23199640_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

HiC Capture Imprinted Gene Panel

Project description:Region Capture HiC Imprinted Gene Panel

| PRJEB59120 | ENA

Promoter capture GM12878 CD34

2015-03-01 | E-MTAB-2323 | biostudies-arrayexpress

Chromosomal loop engineering in human beta globin locus (CUT & RUN)

Project description:We have engineered the 3 prime HS1 CTCF binding site at the human beta globin gene locus in HUDEP-2 cells and performed RNA-seq/ChIP-seq/ATAC-seq as well as HiC and capture HiC to dissect its potential in regulating gene expression

2020-10-30 | GSE160424 | GEO

Chromosomal loop engineering in human beta globin locus (ChIP-Seq)

2020-10-30 | GSE160423 | GEO

Chromosomal loop engineering in human beta globin locus (ATAC-Seq)

2020-10-30 | GSE160421 | GEO

Promoter Capture-HiC in Ring1a KO and Ring1a/b dKO mouse ES cells

2015-08-01 | E-MTAB-3109 | biostudies-arrayexpress

Chromosomal loop engineering in human beta globin locus (Hi-C)

2020-10-30 | GSE160422 | GEO

Chromosomal loop engineering in human beta globin locus (RNA-Seq)

2020-10-30 | GSE160420 | GEO

A survey of imprinted gene expression in mouse trophoblast stem cells

Project description:Several hundred mammalian genes are expressed preferentially from one parental allele due to a process called genomic imprinting. Genomic imprinting is particularly prevalent in extra-embryonic tissue, where it plays an essential role during development. Here, we profiled imprinted gene expression via RNA-Seq in a panel of six mouse trophoblast stem (TSC) lines, which are ex vivo derivatives of a progenitor population that gives rise to the placental tissue of the mouse. We found evidence of imprinted expression for 48 genes, 31 of which had previously been described as imprinted and 17 of which we suggest as candidate imprinted genes. An equal number of maternally and paternally biased genes were detected. Several genes showed variability in imprinted expression between the six TSC lines. Sixteen of the 48 known and candidate imprinted genes were previously or newly annotated noncoding RNAs, and six encoded for a total of 60 annotated microRNAs. Pyrosequencing across a panel of six TSC lines returned levels of imprinted expression that were concordant with RNA-Seq measurements for eight genes examined in all six independently derived TSC lines. Our results solidify TSCs as a cell culture-based experimental model to study genomic imprinting, and provide a quantitative foundation upon which to delineate mechanisms by which the process is maintained in the mouse. RNA-Seq from F1 hybrid TSC lines generated from crosses between Cast and B6 mice.

2015-02-24 | E-GEOD-63968 | biostudies-arrayexpress

Promoter capture mESC and fetal liver

Project description:Genome organization influences transcriptional regulation by facilitating interactions between gene promoters and distal regulatory elements. To analyse distal promoter contacts we used Capture Hi-C (CHi-C) to enrich for promoter-interactions in HiC libraries from mouse ESC and E14.5 fetal liver. Please note additional files included. These files were created using the following protocol: Significantly interacting regions were called using the GOTHiC BioConductor package (http://www.bioconductor.org/packages/devel/bioc/html/GOTHiC.html) as described in (Mifsud et al.).<br>Update on December 2015: the original additional file E-MTAB-2414.additional.1.zip contained an earlier iteration of processed data and not the one that was used for the published paper. The file now contains the correct list of interactions.

2015-02-01 | E-MTAB-2414 | 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