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Genome-wide map of PCL2 (Polycomb-like 2) enrichment in undifferentiated mouse embryonic stem cells (ESCs)

ABSTRACT: In total 8,736,191 reads from IP fraction and 9,958,984 reads from Wash fraction uniquely mapped to the mouse genome (mm9). Settings for enrichment analysis: maxSpacing=500; minHits=20; minPeakHits=6; minRatio=3. 4,701 regions have been identified as enriched in the IP fraction. In order to get a rough idea of false discovery rate (FDR), enrichment analysis using Wash fraction as test and IP fraction as control was performed, 15 regions was found. This suggests that the FDR likely is around 0.3%. Keywords: Epigenetics

ORGANISM(S): Mus musculus

PROVIDER: GSE16526 | GEO | 2010/02/05

SECONDARY ACCESSION(S): PRJNA116091

REPOSITORIES: GEO

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Genome-wide map of PCL2 (Polycomb-like 2) enrichment in undifferentiated mouse embryonic stem cells (ESCs)

Project description:In total 8,736,191 reads from IP fraction and 9,958,984 reads from Wash fraction uniquely mapped to the mouse genome (mm9). Settings for enrichment analysis: maxSpacing=500; minHits=20; minPeakHits=6; minRatio=3. 4,701 regions have been identified as enriched in the IP fraction. In order to get a rough idea of false discovery rate (FDR), enrichment analysis using Wash fraction as test and IP fraction as control was performed, 15 regions was found. This suggests that the FDR likely is around 0.3%. Keywords: Epigenetics Examination of PCL2 enrichment in mouse ESCs.

2010-02-05 | E-GEOD-16526 | biostudies-arrayexpress

Transcripts enriched in microsome fraction in ribosome-independent manner

Project description:To identify the transcripts fractionated into microsome fraction in ribosome-independent manner, we isolate rough microsome fraction by sucrose density gradient ultracengrifugation, then the rough microsome fraction is centrifugated following treatment with puromycine and EDTA in high-salt buffer to remove ribosomes. The pellet and surpernatant are named naked microsome fraction (NM) and stripped ribosome fraction (SR), respectively. By calculating the ratio of the level of each mRNA in NM and SR, we identify the enriched transcripts in NM.

2016-12-25 | GSE85768 | GEO

Differentially expressed genes in rough and smooth colony isolates of Clostridioides difficile

Project description:Purpose: to determine the differentially expressed genes in the phase-variable rough and smooth colony isolates of C. difficile Methods: C. difficile R20291 was grown on BHIS agar to obtain distinct colonies. Individual rough and smooth colonies were chosen for propagation on BHIS-agar for 24 hours as described in Garrett, et al., PLoS Biology, 2019. Growth was collected from n = 2 biological replicates. RNA was purified using TriSure and chloroform, beadbeating, and isopropanol/ethanol precipitation. Quality was verified with Bioanalyzer Assay. Samples were submitted to Genewiz for depletion of rRNA using the TruSeq RiboZero Gold Kit, library preparation, and single-end sequencing on the Illumina HiSeq 2500 platform. RNA sequencing analysis was done using CLC Genomic Workbench v20. Reads were mapped to C. difficile R20291 genome using the software's default menalties for mismatch, deletion, and insertion differences from the reference genome. Transcript reads were normalized as RPKM. Results: 88 genes were differentially expressed between bacteria from rough versus smooth colonies, with equal to or greater than a 2-fold change and p < 0.05 with FDR correction.

2020-09-27 | GSE158225 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Macrophage (RAW264.7) with and without arctigenin treatment

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore the mechanism and target of arctigenin affecting macrophages (RAW264.7) Methods: Total mRNA was extracted from cells using an RNA extraction kit (Qiagen K.K., Tokyo, Japan). RNA-Seq was performed using HiSeq X Ten for next-generation sequencing by OE Biotech. Co., Ltd. (Shanghai, China). Sequenced reads were mapped to the mm9 genome using hisat2.The RNA-Seq reads that were aligned against the exon regions of genes were quantified with HTSeq-Count in the RefSeq mm9 annotation. GSEA was performed on mRNA expression datasets using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Gene signatures were considered enriched if the false discovery rate (FDR) q-values and the family-wise error rate (FWER) p-values show significant difference. Result: The GSEA from the KEGG database indicated that AG-induced biological processes involved several inflammatory process. GSEA methods on immunologic gene sets of Molecular Signatures Database show that the gene set of NFAT5 knockout passed the filtering criteria (p<0.01) Conclusion: NFAT5 was the target of arctigenin

2019-03-07 | GSE127902 | GEO

ChIP-seq facilitates the quantitative analysis of Rvb proteins' enrichment on the genome during stress

Project description:The goals of this study are to quantitatively analyze the enrichment of Rvb1/Rvb2 on the yeast genome during glucose starvation. The ChIP-seq files were generated from 2 biological replicates of Rvb1’s immunoprecipitation (IP), Rvb2-IP, and Pgk1-IP in 10-min glucose starved yeast cells, respectively, using NextSeq 500 SR 75. The sequence reads that passed quality filters were analyzed by calculation of the read counts on 2 regions: -500 bp to TSS and TSS to +500 bp. Using an optimized data analysis workflow, we found Rvb1/Rvb2’s enrichment peaks and that they are significantly more enriched on the Class II alternative glucose metabolism promoters than Class I heat shock promoters.

2021-09-22 | GSE184473 | GEO

Global identification of Arabidopsis thaliana ARGONAUTE1-associated small RNA.

Project description:Small RNA from total RNA (input fraction) and immunoprecipitated HA-AGO1-complexes (IP fraction) were identified using high-throughput sequencing-by-synthesis. Two replicate input fraction samples were used as controls for two replicate IP fraction samples. Total RNA from input fractions and small RNA that co-immunoprecipitated with HA-AGO1 complexes were size fractionated by polyacrylamide gel electrophoresis to recover 18-24 nucleotide small RNA. 3' and then 5' adaptors were serially ligated on to each small RNA followed by PAGE purification. RT-PCR was used to convert RNA to DNA amplicons. Amplicons were sequenced using the Illumina GAIIx platform. Resulting reads were parsed and mapped to the A. thaliana genome (TAIR9) using the CASHX pipeline.

2010-06-21 | E-GEOD-22252 | biostudies-arrayexpress

Ago2 associated gene transcripts in two Hodgkin lymphoma cell lines

Project description:The aim of the study is to identify miRNA targets in Hodgkin lymphoma cell lines. By immunoprecipitation of wild type Ago2, it is expected to pull down the Ago2 associated gene transcripts. Through microarray analysis, the Ago2 associated gene transcripts identified are expected to be miRNA targets. Keywords: Ribonucleoprotein Immunoprecipitation - Gene Chip (RIP-Chip) RNA isolated from the Ago2 immunoprecipitated (IP) fraction is hybridized against the RNA from total cell lysate (T) fraction. The experiment is performed in two independent Hodgkin lymphoma cell lines, L1236 and L428. In addition, RNA of flow through (FT) fraction of L1236 is hybridized against RNA of total cell lysate (T) fraction of L1236 to demonstrate the specificity/enrichment seen in the IP fraction and not in the FT fraction. All hybridizations is done with a dye swap design.

2010-04-08 | E-GEOD-14409 | biostudies-arrayexpress

To detect CENP-A enrichment on Chromosome 1,5 &7 in C. albicans centromere deleted clones

Project description:ChIP Seq revealed presence of unique CEN-proximal neocentromere peaks in CEN deleted clones. Using 10 million reads generated from ChIP-seq for each sample, chromosome wide maps for CENP-A enrichment were generated . Examination of CENP-A enrichment in Input/IP samples of various CEN deleted C. albicans clones

2012-12-21 | E-GEOD-42907 | biostudies-arrayexpress

Global analysis of m6A mRNA methylation in human cells

Project description:m6A RNA immunoprecipitation was performed according to published procedure (Dominissini et al., 2012). Human m6A-seq data from DTSC2 HeLa cells were aligned to the hg19 transcriptome. To locate m6A peaks, the hg19 transcriptome was divided into 25 nucleotide-wide tiles. The number of reads in the m6A immunoprecipitation (IP) and non-IP (control) sample was counted in each tile, and a p-value was calculated using Fisher’s exact test and adjusted for multiple testing. Tiles with significant enrichment of the m6A signal (adjust-P value < = 0.05) were merged into larger regions. Regions lesser than 100 bp were discarded, and regions over 200 bp were separated into 100 to 200 bp sub-regions; the m6A signal from rapamycin-treated cells compared to control (DMSO) was calculated for each region; and regions with at least a two-fold enrichment in all replicates were identified as m6A peaks. The distributions of m6A peaks and m6A marked genes were identified by overlapping all m6A peaks with the hg19 RefGene annotation (Meng et al., 2014).

2021-02-17 | GSE165690 | GEO

Hepatic gene expression in male fetuses from maternal nutrient restriction in mice

Project description:The aim of this study was to identify fetal adaptations to gene expression in our mouse model of intrauterine growth restriction (IUGR). Starting at E6.5, pregnant CD-1 mice received either control (ad libitum) or 70% of ad libitum food (maternal nutrient restriction [MNR]). At E18.5, fetal right liver lobes were collected from 2 pups/litter in litters with 11-15 pups. Frozen liver was homogenized for RNA isolations. Isolated RNA was sequenced on a HiSeq2500 with an average read depth of 23M reads and a range of 17-31M reads per sample. Reads were aligned to the mm9 transcriptome with Bowtie2. Normalization and differential expression was done with DESeq2, ALDex2 and EdgeR, and genes were considered in the study if they were consistent in 2 or more tools (FDR <0.1).

2019-12-17 | GSE124006 | GEO

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