Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome profiling of two purebred cattle and their crossbreds

ABSTRACT: Purpose: The aim of this study is to determine the absolute and relative expresson levels of mRNA transcripts across two purbred (Angus and Brahman) cattle and their receipicalcross. Methods: Total RNA was extracted and purified from five tissues using the RiboZero Gold kit. Sequencing libraries were prepared with a KAPA Stranded RNA-Seq Library Preparation Kit following the Illumina paired-end library preparation protocol. Completed libraries were sequenced on HiSeq 2000 as 100 bp paired-end reads at the Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility, Adelaide, Australia and USDA-ARS-US Meat Animal Research Center, Clay Center, USA. Approximately 60 million 100 bp single-end reads were obtained for each sample. Reads were aligned to the cattle reference genome UOA_brahman_1/UOA_angus_1 and mapped to known genomic features at the gene level using the Hisat2. Single reads were then summarized into gene-level counts using FeatureCounts.

ORGANISM(S): Bos taurus

PROVIDER: GSE148909 | GEO | 2021/06/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Vascular fate in misidentified pluripotent-derived blood-brain-barrier endothelial cells rescued by transcriptional reprogramming

Project description:Total RNA, greater than 100ng, from cultured cells was isolated in TRIzol L and purified using Qiagen RNeasy Mini Kit per manufacturer’s protocols. Agilent Technologies 2100 Bioanalyzer was used to assess the RNA quality. RNA libraries were prepared and multiplexed using Illumina TruSeq RNA Library Preparation Kit v2 (non-stranded and poly-A selection) and 10 nM of cDNA was used as the input for high-throughput sequencing via Illumina’s HiSeq 2500 platform, producing 50 bp paired end reads.

2021-03-02 | GSE167959 | GEO

Single cell RNA-seq of 444 epithelial cells from the mammary glands of pubescent and adult mice

Project description:Mammary glands were collected from 8 pubescent (4.7-4.9 week-old) female mice and 8 adult (10 week old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads.

2017-11-20 | GSE95445 | GEO

Single cell RNA-seq of 312 basal epithelial cells from the mammary glands of pregnant and adult mice

Project description:Mammary glands were collected from 8 pregnant (12.5 day) mice and 8 adult (10 week old) female mice. Basal epithelial cells were FACS sorted. Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads.

2017-11-20 | GSE95448 | GEO

Single cell RNA-seq of 346 epithelial cells from the mammary glands of pre-pubescent, pubescent and adult mice

Project description:Mammary glands were collected from pre-pubescent (2 weeks old), pubescent (4.7- 4.9 weeks old) and adult (10 week-old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under a microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100 bp paired-end reads.

2017-11-20 | GSE95434 | GEO

Genome-wide binding and mechanistic analyses of Smchd1 mediated epigenetic regulation [RNA-Seq]

Project description:Purpose: The aim of this study is to identify genes that are under the transcriptional control of the epigenetic regulator Smchd1 in neural stem cells (NSCs) derived from E14.5 mouse brain Methods: Total RNA was extracted using an AllPrep DNA/RNA Mini Kit (Qiagen) from cultured neural stem cells derived from male mouse E14.5 brains either wild-type or null for Smchd1. 1 µg total RNA was used to generate sequencing libraries for whole transcriptome analysis with Illumina’s TruSeq RNA Sample Preparation Kit v2 as per standard protocols. Libraries were sequenced on HiSeq 2000 with Illumina TruSeq SBS Kit v3-HS reagents as either 100 bp single-end or paired-end reads at the Australian Genome Research Facility (AGRF), Melbourne. Reads were aligned to the mouse reference genome mm10 and mapped to known genomic features at the gene level using the Rsubread package (version 1.10.5) (Liao et al. 2013). Mapped reads were then summarized into gene-level counts using FeatureCounts (Liao et al. 2014).

2015-06-11 | GSE65747 | GEO

The effect of signal inhibitors on human induced pluripotent stem cells in suspension culture conditions

Project description:To examine the effect of the effects of PKCbeta and Wnt inhibitors on global gene expression of iPSCs in suspension conditions, RNA-seq experiments were performed. Total RNA was extracted with a FastGene RNA premium kit (Nippon Genetics, Co., Ltd, Tokyo, Japan) and strand-specific library preparation was performed. The prepared library was sequenced by a NovaSeq6000 (Illumina, Inc, CA, USA). Sequencing was performed in a 150 bp x2 paired-end configuration with a data output of about 6 Gb per sample (equivalent to about 20 million paired reads). Library preparation and its sequencing were performed in GENEWIZ (Azenta, MA, USA). The sequencing data were analyzed with a CLC Genomics Workbench (QIAGEN, Hulsterweg, the Neterlands) and the R package edgeR (v3.30.3) to identify differentially regulated genes.

2023-01-17 | GSE222833 | GEO

Transcriptome profiling for genes transcriptionally regulated by Smchd1 in lymphoma cell lines.

Project description:Purpose: The aim of this study is to identify genes that are under the transcriptional control of the epigenetic modifier Smchd1 in mouse lymphoma cell lines. Methods: Total RNA was extracted using QIAGEN RNeasy Minikit from sorted lymphoma cell lines derived from mice either wild-type or null for Smchd1. 1µg total RNA was used to generate sequencing libraries for whole transcriptome analysis with Illumina’s TruSeq RNA Sample Preparation Kit v2 as per standard protocols. Libraries were sequenced on HiSeq 2000 with Illumina TruSeq SBS Kit v3-HS reagents as either 100 bp single-end or paired-end reads at the Australian Genome Research Facility (AGRF), Melbourne. Reads were aligned to the mouse reference genome mm10 and mapped to known genomic features at the gene level using the Rsubread package (version 1.10.5) (Liao et al. 2013). Mapped reads were then summarized into gene-level counts using FeatureCounts (Liao et al. 2014).

2015-03-13 | GSE64099 | GEO

RNA-seq of control and Lmna -/- mice heart samples

Project description:RNA-sequencing analysis from whole heart ribosome depleted RNA from the 2-week old WT and Lmna-/- mice (N=5) . Strand specific RNA seq libraries where prepared form ribosome-depleted cardiac RNA samples using the Illumina TruSeq stranded total RNA library preparation kit. The samples weresequenced on the Illumina HiSeq 4000 instrument using the paired-end sequencing reagents to generate100 base paired end reads.

2019-02-08 | GSE110341 | GEO

Gene Expression in COP1-ETV1-ETV5-cJun deficient mouse brain

Project description:Total RNA was extracted from E18.5 brains with the olfactory bulbs removed using the MirVana miRNA isolation kit (Invitrogen). RNA concentration was determined in a NanoDrop 8000 (ThermoFisher) and RNA integrity using both 2100 Bioanalyzer and 2200 TapeStation (Agilent). Libraries were prepared from 1 μg of total RNA with TruSeq RNA Sample Preparation Kit v2 (Illumina). Library size was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent) and concentration was determined by Library quantification kit (KAPA). Libraries were multiplexed five per lane and then sequenced in a HiSeq2500 (Illumina) to generate 50 million paired end 75 bp reads. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0013017

2018-11-14 | GSE111564 | GEO

ChIP-seq profiling of H3K27 tri-methylation in Ezh2-deficient and control murine lung epithelium at day E16.5

Project description:Epithelial (CD31-CD45-EpCAM+) lung cells were derived by FACS from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ mouse embryos at day E16.5 (2 biological replicates per genotype). Chromatin from each of the replicates was immunoprecipitated with H3K27me3 antibody (Millipore #07-449) and subjected to NGS library preparation using TruSeq Nano DNA Sample Preparation Kit (Illumina). Completed libraries from different samples were sequenced on HiSeq 2500 TruSeq with SBS Kit v3 - HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility.

2015-05-11 | GSE57392 | 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