Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

To determine the potential molecular mechanisms by which STAT5 signaling controls colonic crypt homeostasis, we isolated total RNA from ileal intact crypts of STAT5+/+, STAT5DIEC-/- and STAT5DIEC+++ mice and performed RNA sequencing (RNA-seq).

ABSTRACT: Reads were aligned to the mm10 genome with annotations provided by Ensembl. Transcripts were filtered, requiring at least 3 reads in 50% of samples within at least one condition. To identify differentially-regulated transcripts, we performed ANOVA (FDR-corrected p<0.05) and required the fold change to exceed 1.5.

ORGANISM(S): Mus musculus

PROVIDER: GSE112607 | GEO | 2019/04/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

STAT5 activation enhances Paneth cell function by regulated ileal Wnt3a-Tcf4-Sox9 or Gfi1 to sustain niche differentiation.

Project description:To determine the potential molecular mechanisms by which STAT5 signaling control ileal Paneth cell homeostasis, we isolated total RNA from ileal intact crypts of STAT5+/+, STAT5DIEC-/- and STAT5DIEC+++ mice and performed RNA sequencing (RNA-seq). With an average of 22.3 million reads per sample, we observed 27540 transcripts when reads were aligned to the mm10 genome with annotations provided by Ensembl. Transcripts were filtered, requiring at least 3 reads in 50% of samples within at least one condition, leaving 10197 transcripts for analysis. To identify differentially-regulated transcripts, we performed ANOVA (FDR-corrected p<0.05) and required the fold change to exceed 1.5.

2019-03-21 | GSE112166 | GEO

To determine the potential molecular mechanisms by which STAT5 signaling controls colonic crypt homeostasis, we isolated total RNA from ileal intact crypts of STAT5+/+, STAT5DIEC-/- and STAT5DIEC+++ mice and performed RNA sequencing (RNA-seq).

Project description:To determine the potential molecular mechanisms by which STAT5 signaling controls colonic crypt homeostasis, we isolated total RNA from ileal intact crypts of STAT5+/+, STAT5DIEC-/- and STAT5DIEC+++ mice and performed RNA sequencing (RNA-seq).

| PRJNA448447 | ENA

Mus musculus

Project description:MRLxSM eQTL in Liver by RMA on Ensembl transcripts

| PRJNA134845 | ENA

Adenoviral vector transduced in vitro differentiated C57bl6 BMDM cells

Project description:Total mRNA was extracted at 48 hour post transduction using Qiagen RNeasy Kits following the manufacture’s protocol.1 ug ofRNAwas used for cDNA library construction and bulk RNA sequencing were performed by Novogene (Sacramento CA). RNA-seq raw data were analysised using Partek Flow. Briefly, sequencing reads were aligned to the mouse or human genome using Spliced Transcripts Alignment to a Reference (STAR 2.5.3a). Aligned reads were then quantified to transcriptome (mm10; Ensembl Transcripts release 100), and normalized (Median Ratio normalization). Differentiated gene expression analysis (DESeq2) were performed to generate raw counts

2024-04-21 | GSE253342 | GEO

RiboZero Gold paired-end RNA-seq data from postmortem tissue of the dorsolateral prefrontal cortex of autism spectrum disorder samples and healthy control samples

Project description:Purpose: The goals of this study was to compare the expression of histamine related genes in ASD patients and controls. Methods: RNA-Seq was performed using strand-specific Ribosomal RNA depletion (RiboZero) library preparation and the TruSeq RNA Sample Preparation v2 kit from Illumina. One hundred base pair paired-end sequencing was run on the HiSeq 2000. TopHat (v2.0.4) was used to enforce strand specificity and to align the sequencing reads to known transcripts of the Ensembl Build GRCh37.67. FeatureCounts (v1.4.4) was used to count the total number of reads overlapping each gene using the default settings, with paired-end and reverse-stranded counting specified using the Ensembl Build GRCh37.67 gtf file. These counts were merged from both reads of the paired-end sequencing and normalized by library size and coding gene length to form Reads Per Kilobase of Gene per Million mapped reads (RPKM) values. The influence of diagnosis on expression was analyzed with linear regression transcriptome-wide and further evaluated using a gene set analysis. Results: There was no significant diagnosis effect on any of the individual genes but expression of the gene set of HNMT, HRH1, HRH2, and HRH3 was significantly altered. Conclusions: Our study represents the first specific analysis of the expression of histamine related genes in ASD and suggests that these genes may collectively be dysregulated.

2017-08-17 | GSE102741 | GEO

Sox2 suppresses gastric tumorigenesis in mice [RNA-seq]

Project description:Purpose: Sox2 expression marks gastric stem and progenitor cells, raising important questions regarding the genes regulated by Sox2 and the role of Sox2 itself during stomach homeostasis and disease. The goal of this study is to determine the function of and the genes regulated by Sox2 in the stomach. Methods: mRNA profiles of Sox2 WT and Sox2 KO gastric glands were generated by RNA-sequencing, in triplicate, using a Illumina HiSeq 2500 instrument, resulting in 36 million single-end 50bp reads per smaple. Sequencing reads were mapped to the mouse reference genome (mm10/GRCm38) using STAR (Dobin et al., 2013). Read counts over transcripts were calculated using HTSeq v.0.6.0 (Anders et al., 2015) based on a current Ensembl annotation file for mm10/GRCm38 (release 75). Results: Sox2 is dispensiable for gastric stem cell self-renewal and epithelial homeostasis, however modulates the expression of cancer and intestinal related genes. mRNA profiles of stomachs from 10 week old Sox2 WT and Sox2 KO mice were generated by sequencing, in triplicate, using a Illumina HiSeq 2500.

2016-08-04 | E-GEOD-83964 | biostudies-arrayexpress

RNA-seq analysis comparing WT, Rad21 MO and CTCF MO zebrafish embryos at stages (2.5, 3.3, 4.5, 5.3, 10 hpf) pre and post ZGA (zygotic genome activation)

Project description:Methods: Triplicate RNA samples from morphologically stage-matched embryos were sequenced to compare expression profiles over time. Strand-specific libraries were prepared using the TruSeq stranded total RNA-ribozero kit (Illumina) and 100-bp paired-end sequencing was performed to depth of 10 million reads per library on an Illumina HiSeq 2000. Methods: On average, 19 million 100 bp paired-end reads per library were generated. These were then adapter and quality trimmed using cutadapt and SolexaQA. Each sequencing data set was independently mapped to the zebrafish genome with a bowtie2 index generated from Danio_rerio.Zv9.70 (Ensembl) downloaded from Illumina’s iGenomes collection. Zebrafish genome danRer7was used to provide known transcript annotations from Ensembl using TopHat2 (version 2.0.9) with the following options: “tophat2 --GTF genes.gtf --library-type fr-firststrand -p 24 --mate-inner-dist -8 --mate-std-dev 6 zv9” (on average, 75.38% reads mapped uniquely to the genome). Transcriptomes were assembled with Cufflinks (version 2.2.0) using options: ‘cufflinks -p 32 --GTF genes.gtf’ and differential expression analysis between control and knockdown embryos was performed using Cuffdiff. A FDR corrected p-value of 0.05 was applied as the cut off to identify differentially regulated transcripts Results: We could show that MO assisted depletion of Rad21 and CTCF affected the transcriptional profiles of embryos in different ways.

2017-12-01 | GSE84601 | GEO