Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA Sequencing Facilitates Quantitative Analysis of differentially expressed genes after UCA1 knockdown in human erythroid cells

ABSTRACT: Purpose: The goals of this study are to determine possible downstream targets of UCA1 on day8 of erythroid differentiation with or without UCA1 knockdown. Methods:gene expression profiling with or without UCA1 knockdown in differentiated erythroblasts at day8 were generated by deep sequencing, induplicate, using Illumina GAIIx.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Conclusions: heme metabolism genes were down-regulated after UCA1 knockdown during erythroid differentiation

ORGANISM(S): Homo sapiens

PROVIDER: GSE106537 | GEO | 2018/10/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA Sequencing Facilitates Quantitative Analysis of differentially expressed genes after PTBP1 knockdown in human erythroid cells

Project description:Purpose: The goals of this study are to determine possible downstream targets of PTBP1 on day8 of erythroid differentiation with or without PTBP1 knockdown. Methods:gene expression profiling with or without PTBP1 knockdown in differentiated erythroblasts at day8 were generated by deep sequencing, induplicate, using Illumina GAIIx.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Conclusions: heme metabolism genes were down-regulated after PTBP1 knockdown during erythroid differentiation

2018-10-30 | GSE106566 | GEO

RNA Sequencing Facilitates Quantitative Analysis of differentially expressed genes after Twist1 knockout in mouse bone marrow stromal cells

Project description:Purpose: The goals of this study are to determine possible downstream targets of Twist1 in bone marrow stromal cells with or without Twist1 knockout. Methods: gene expression profiling with or without Twist1 knockout in bone marrow stromal cells were generated by deep sequencing, using Illumina Hiseq.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays. Conclusions: Notch signaling were activated after Twist1 knockout.

2021-05-26 | GSE107814 | GEO

Next Generation Sequencing Facilitates Analysis of Wild Type and glioma Transcriptomes

Project description:Methods: Brain mRNA profiles of 90-day-old wild-type (WT) and glioma were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2021-03-16 | GSE129899 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Retinoblastoma Transcriptomes

Project description:Methods: mRNA profiles of retinoblastoma samples and para-tumor were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

2018-02-28 | GSE111168 | GEO

Quantitative Analysis of Wild Type and Pich-KO fetal liver LSK Transcriptomes

Project description:mRNA profiles of embryonic day 14.5 wild-type (WT) and Pich-KO mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2022-03-09 | GSE188359 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of HePG2i cell line with and without DOX induced GATA4 expression Transcriptomes

Project description:HePG2i cell line mRNA profiles of DOX induced GATA4 expression and non-DOX induced were generated by deep sequencing, in triplicate, using Illumina HiSeq 10000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2019-08-09 | GSE135579 | GEO

Transcriptome profiling (RNA-seq) of wild type and MYOCD Knockdown in human lung cancer cell line A549.

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) of wild type and MYOCD Knockdown in human lung cancer cell line A549. Methods: mRNA profiles of wild type（WT） and Dox inducible MYOCD Knockdown (MYOCD−/−) human lung cancer cell line A549 were generated by deep sequencing, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR.

2019-03-30 | GSE128918 | GEO

miRNA-seq analysis of RNA-binding protein knock-down HNSCC cell-line UMSCC74B

Project description:Purpose: The goals of this study is to compare NGS-derived miRNA profiling (miRNA-seq) of WT and FXR1 KD UMSCC74B cell-line Methods: miRNA profiles of UMSCC74B HNSCC cells treated with shControl(WT) and shFXR1 (KD), in duplicate, using Illumina hiseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks

2020-01-06 | GSE117031 | GEO

Gene expression analysis in fly ovaries from wuho mutant

Project description:Purpose: The goal of this study is to analyze genes affected by wuho mutation in Drosophila ovary Ovarian mRNA prolife of 7 day old control flies and flies bearing wuho mutation, in duplicate, using Illumina NextSeq 500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2020-01-03 | GSE142829 | GEO

Gene expression analysis in fly ovaries carrying Sco homozgyous clones

Project description:Purpose: The goal of this study is to analyze genes affected by Sco mutation using RNA-seq. Ovarian mRNA prolife of 7-day-old control flies and flies carring Sco mutant follicle cell clones were generated by deep sequence, in duplicate. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2017-11-22 | GSE106484 | 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