Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Low-pass sequencing of cattle F1 crosses

PROVIDER: PRJNA930154 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23597900_1.fastq.gz	Fastqsanger.gz
	SRR23597900_2.fastq.gz	Fastqsanger.gz
	SRR23598000_1.fastq.gz	Fastqsanger.gz
	SRR23598000_2.fastq.gz	Fastqsanger.gz
	SRR23598100_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 644

Similar Datasets

Whole-genome bisulphite sequencing of met1-3/+

Project description:14 F1 individuals that resulted from crosses between a 420-CEN3 reporter line and met1-3/+ plants were subject to whole-genome bisulphite sequencing alongside Col wild-type and met1-3/+ controls

2015-10-10 | E-MTAB-3927 | biostudies-arrayexpress

Gene expression analysis of mouse F1 hybrids to study cis regulatory variations

Project description:To analyze the difference in gene expression between alleles of F1 hybrids of mouse C57BL6/J (B6) and MSM/Ms (MSM) strains, we sequenced these F1 hybrids of reciprocal crosses. While most genes did show allelic bias, a small number of genes showed either B6- or MSM-biaed expression in both crosses. These allelic differences were associated with the allelic differences in histone acetylation in promoter regions determined by another experiments.

2024-05-31 | GSE246401 | GEO

Allelome.PRO A pipeline to define allele-specific genome features

Project description:We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. Defining allele-specific genome features from F1 E12.5 mouse embryonic fibroblasts

2015-08-03 | E-GEOD-69168 | biostudies-arrayexpress

RNA-seq on DGRP lines and F1 crosses

Project description:We performed mRNA sequencing of reciprocal F1 female hybrids from two crosses (362/765 and 517/765) and the parental DGRP lines (362, 517 and 765). Specifically, we aimed to identify whether transcripts predicted to be regulated by cis-eQTLs exhibit a significant allele-specific bias in gene expression. Since both alleles act in the cross in the same trans environment, differential expression in the F1 is a direct measure of cis-regulatory activity.

2012-08-28 | E-MTAB-1266 | biostudies-arrayexpress

Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays

Project description:Low-pass sequencing (sequencing a genome to an average depth less than 1× coverage) combined with genotype imputation has been proposed as an alternative to genotyping arrays for trait mapping and calculation of polygenic scores. To empirically assess the relative performance of these technologies for different applications, we performed low-pass sequencing (targeting coverage levels of 0.5× and 1×) and array genotyping (using the Illumina Global Screening Array (GSA)) on 120 DNA samples derived from African and European-ancestry individuals that are part of the 1000 Genomes Project. We then imputed both the sequencing data and the genotyping array data to the 1000 Genomes Phase 3 haplotype reference panel using a leave- one-out design. We evaluated overall imputation accuracy from these different assays as well as overall power for GWAS from imputed data, and computed polygenic risk scores for coronary artery disease and breast cancer using previously derived weights. We conclude that low-pass sequencing plus imputation, in addition to providing a substantial increase in statistical power for genome wide association studies, provides increased accuracy for polygenic risk prediction at effective coverages of ∼ 0.5× and higher compared to the Illumina GSA.

2021-01-31 | GSE165845 | GEO

Cissus quadrangularis

Project description:Cissus quandrangularis Genome low-pass sequencing

| PRJNA521517 | ENA

ChIP-seq data of HNF4A, CEBPA, FOXA1, H3K27ac,

Project description:We profiled the genome-wide occupancy of three tissue-specific transcription factors, HNF4A, CEBPA and FOXA1, as well as the genome-wide occurrence of the histone mark, H3K4me3 in the livers of two inbred parental mouse strains (C57BL/6J and CAST/EiJ) and their F1 crosses. We also included H3K27ac data generated from F1 hybrids as well as the profiling of HNF4A, CEBPA and FOXA1 in both CEBPA and HNF4a heterozygous knock-outs.

2016-06-30 | E-MTAB-4089 | biostudies-arrayexpress

Site-specific silencing of regulatory elements as a mechanism of X-inactivation

Project description:The inactive X chromosome’s (Xi) physical territory is microscopically devoid of transcriptional hallmarks and enriched in silencing-associated modifications. How these microscopic signatures relate to specific Xi sequence is unknown. This study reports the profiling of Xi gene expression and chromatin states at high-resolution via allele-specific sequencing in F1 hybrid mouse trophoblast stem cells (TSCs). Datasets provided include those generated from strand-specific RNA-Seq, ChIP-Seq, FAIRE-Seq, and DNase-Seq protocols. Included for each dataset are FASTQ files, BED alignments and WIG files with coordinates relative to UCSC genome build mm9, and _snp files that report the location of all SNP-overlapping reads. The F1 TSC lines profiled were generated from crosses between CAST/EiJ (Cast) and C57BL/6J (B6) mice. C/B denotes a Cast mother and B6 father, and B/C denotes a B6 mother and Cast father.

2012-11-21 | E-GEOD-39406 | biostudies-arrayexpress

Homo sapiens

Project description:Homo sapiens low-pass whole genome sequencing

| PRJNA309109 | ENA

Project description:Low pass sequencing of Hawaiian native plants

| PRJNA911344 | ENA