Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Lepidothrix manakins

ABSTRACT: RADseq data for development of custom sequence capture baits

PROVIDER: PRJNA787238 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17237500_1.fastq.gz	Fastqsanger.gz
	SRR17237500_2.fastq.gz	Fastqsanger.gz
	SRR17237501_1.fastq.gz	Fastqsanger.gz
	SRR17237501_2.fastq.gz	Fastqsanger.gz
	SRR17237502_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 192

Similar Datasets

Targeted resequencing of phenology genes in a diverse panel of barley varieties

Project description:We provide raw gene sequences of 174 flowering time regulatory genes and gene othologs across a large barley population (895 barley lines) selected from a collection of landrace, cultivated barley, and research varieties of diverse origin. This set represents the whole variety of cultivated barley lifeforms, namely two- and six-row genotypes with winter, spring, and facultative growth habits. We applied a target capture method based on in-solution hybridization using the myBaits® technology (Arbor Biosciences, Ann Arbour, MI, USA) which is based on in-solution biotinylated RNA probes. Baits were designed for flowering time regulatory genes and gene othologs, and used for production of 80mer capture oligonucleotides for hybridization. Genomic DNA was extracted from leaves of a single two-week old barley plant per variety using the cetyl-trimethyl-ammonium bromide (CTAB) method. Physical shearing of genomic DNA was performed with an average size of 275 bp. Library preparation was conducted with KAPA Hyper Prep Kit (KAPA Biosystems, Wilmington, MA). Hybridization of customised RNA baits with capture pools was performed at 65°C for 24 hours. Each pooled sequence capture library was sequenced on an Illumina HiSeq3000 instrument using three lanes to generate paired-end reads per sample. Genome sequencing was conducted at AgriBio, (Centre for AgriBioscience, Bundoora, VIC, Australia).

2019-02-15 | E-MTAB-7362 | biostudies-arrayexpress

Targeted capture DNA-seq for HPV16-human breakpoint junctions in HPV16 infected W12 cervical cell lines

Project description:HPV integrated site capture (HISC) protocol used to detect HPV16 integration breakpoints in the genomes of W12 cell lines. Biotinylated HPV16-specific RNA baits were used to capture HPV16-human breakpoint junctions in genomic DNA.

2021-06-18 | E-MTAB-10154 | biostudies-arrayexpress

Runx1 Circular Chromosome Conformation Capture Sequencing in Mouse Hematopoietic Progenitor Cells

Project description:We have performed circular chromosome conformation capture sequencing (4C-seq) with six baits located at the Runx1 locus in the mouse hematopoietic progenitor cell line HPC-7. 4C baits were designed to the P1 and P2 promoters and to the previously characterised +24 hematopoietic enhancer (P1, P2 and 24), with secondary baits located at nearby cohesin/CTCF (cc) binding sites (P1cc, 24cc, P2cc).

2017-10-22 | GSE86994 | GEO

Hi-C and capture Hi-C for HPV16 infected human W12 cervical cell lines and normal cervical tissue

Project description:Two biological replicates Hi-C and HPV16-specific Region Capture Hi-C libraries were prepared for each of the W12 cell lines. Capture Hi-C was performed using HPV16-specific RNA baits. Hi-C libraries alone were prepared from normal cervix tissue (Ncx).

2021-06-18 | E-MTAB-10152 | biostudies-arrayexpress

Project description:Hybridization Capture Baits for Antimicrobial Resistance

| PRJNA746311 | ENA

RADseq for tumour mutation burden estimation and mutation signature analysis.

Project description:The utility of RADseq in an experimental setting is also demonstrated, based on our chasacterisation of an APOBEC mutation signature in an APOBEC3A transfected mouse cell line. 0D5 cells, derived from SSM3 cells, were co-transfected with a mixture containing pcDNA3.1 vectors expressing either APOBEC3A or APOBEC3B (kindly donated by Vincent Caval), pcDNA3.1 construct expressing deaminase null APOBEC3A linked to a uracil deglycosylase construct and a plasmid encoding mutant GFP and WT mCherry that is a reporter for APOBEC mutagenesis. Cells were grown, and gDNA extracted, prior to preparation of RADseq libraries using a PstI- MspI double-digest. Libraries underwent a Pippin Prep to select fragments in the size range of 220-520 bp (genomic sequence plus 148 bp of adapters). Single-end sequencing (1x101bp) was performed on an Illumina NovaSeq6000 utilizing v1.5 chemistry. Reads were aligned to mm10 using bwa mem and variants called using the GATK4 pipeline.

2023-06-30 | GSE234146 | GEO

Expression data from embryonic mouse pleuroperitoneal folds and diaphragms

Project description:Microarray data from this study represent the first global transcriptional survey of gene expression during early compared to late diaphragm formation. Based on the assumption that Congenital diaphragmatic hernia (CDH) candidate genes will have similar temporal expression trends and will be part of the same biological pathways as those already implicated in CDH, we used known CDH-associated genes as “baits” to filter expression microarray data sets (GSEA and STEM) to identify a list of novel CDH candidate genes. Laser-capture microdissected C57BL/6J mouse embryonic diaphragm tissues were studied at three key time-points during normal development. We studied the primordial diaphragm’s pleuroperitoneal folds at E11.5 and E12.5, and the muscularized mature diaphragm at E16.5 to identify genes and pathways that characterize important stages in diaphragm morphogenesis.

2012-02-10 | E-GEOD-35243 | biostudies-arrayexpress

Lepidothrix coronata

Project description:Lepidothrix coronata Raw sequence reads

| PRJNA321179 | ENA

Project description:Genome-wide target capture baits for endangered shark species

| PRJNA990973 | ENA

Project description:Todiramphus RADseq data

| PRJNA992577 | ENA