Browse
Submit Data
Databases
API
Help

Dataset Information

35 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of murine bone marrow-derived macrophages (mBMDM) of the wild type (WT) group versus the RBP-J conditionally knockout (CKO) group at 36 hours post HTNV (Hantaan orthohantavirus) infection

ABSTRACT: Total RNA was extracted from WT and RBP-JCKO mBMDMs at 36 hpi (HTMV, MOI=1), using TRIzol (Invitrogen). Ribosomal RNA was removed using the Ribo-Zero™ kit (Epicentre Biotechnologies). Fragmented RNA (the average length was approximately 200 bp) was subjected to first-strand and second-strand cDNA synthesis followed by adaptor ligation and enrichment with a low cycle according to the instructions of the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0 (Life Technologies). The libraries were paired-end sequenced (PE150, sequencing reads were 150 bp) at Guangzhou Ribo Biotechnology (Guangzhou, China) using the Illumina HiSeq 3000 platform. Transgenic mice type: RBP-JCKO (Lyz2-Cre+ RBP-Jfloxed) C57BL/6J Mice.

INSTRUMENT(S): Illumina HiSeq 3000

ORGANISM(S): Mus musculus

SUBMITTER: Hongwei Ma

PROVIDER: E-MTAB-11926 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of HTNV-infected murine bone marrow-derived macrophages (mBMDM) from 0 to 36 hours

Project description:The murine bone marrow-derived macrophages (mBMDMs) were infected with Hantaan viruses (HTNV) with an MOI of 1, or mock-infected with Co60-inactivated HTNV. The mBMDM RNAs were extracted for RNA sequencing (RNA-seq) at 0 (mock-infected), 12, 24, and 36 hours post-infection (hpi). Each group contained three repeats (mBMDM from three different C57/6L mice). The data of 0 hpi group (labeled as A) were shown as A1, A2 and A3.The data of 12 hpi group (labeled as B) were shown as B1, B2 and B3. The data of 24 hpi group (labeled as C) were shown as C1, C2 and C3. The data of 36 hpi group (labeled as D) were shown as D1, D2 and D3.

2022-02-05 | E-MTAB-11353 | biostudies-arrayexpress

Identification of transcripts bound by an RNA binding protein (RBP) in early erythroid progenitor using RNA-binding protein immunoprecipitation-microarray (RIP-Chip) experiment

Project description:Early erythroid progenitors were isolated from mouse E14.5 fetal liver. After cell lysing, control IgG or RBP specific antibody were incubated with cell lysis. Immunoprecipitation followed by microarray experiments were carried out to identify transcripts that are immunoprecipitated by either control IgG or RBP specific antibody. Examination of transcripts that are immunoprecipitated by either control IgG or RBP specific antibody in primary mouse early erythroid progenitor

2013-06-14 | E-GEOD-46108 | biostudies-arrayexpress

Stable expression of intracellular Notch suppresses v-Src-induced transformation in avian neural cells

Project description:We reported that stable expression of constitutively active intra cellular Notch (ICN), in quail neuroretina (QNR) cells transformed by a conditional v-Src mutant (QNR/v-src cells), resulted in the suppression of their transformed properties. Acquisition of a normal phenotype coincided with a major switch in cell identity, as these undifferentiated QNR/v-src cells acquired characteristics of glial differentiation. Similar loss of transformation and gene reprogramming can be achieved in QNR/v-src cells, stably expressing the human CBF protein, RBP-Jk, whose activity was rendered ligand independent by fusion to the VP16 transactivator. These major phenotypic changed are correlated with a dominant interference with signaling effectors, regulating cell morphology and cytoskeleton organization. To understand the mechanisms by which Notch signaling activation suppressed v-Src induced cell transformation and induced differentiation, we compared the transcription profile of QNR cells transformed by a v-Src mutant encoding a temperature sensitive oncoprotein (QNR/v-src), with that of cells stably expressing ICN (QNR/v-src/ICN) or RBP-Jk-VP16 (QNR/v-src/RBP-Jk-VP16). Total RNA was extracted from QNR/v-src, QNR/v-src/ICN or QNR/v-src/RBP-Jk-VP16 cells maintained at permissive (37°C) or restrictive (41°C) temperature. cDNA from QNR/v-src cells was probed with that of QNR/v-src/ICN or QNR/v-src/RBP-Jk-VP16 at both temperature on microarrays spotted with 13,000 cDNA from chicken EST collections designed by the genomic facility of the Fred Hutchinson Cancer Research Center (Seattle). For two sets of sample, dye swap experiments were performed.

2010-12-01 | E-GEOD-22054 | biostudies-arrayexpress

Ribo-seq of human colorectal cancer cell line HCT116/L-OHP against HCT116

Project description:Oxaliplatin (L-OHP) serves as a standard chemotherapy for colorectal cancer, while the drug resistance is still a considerable challenge. Dysregulation of lncRNA is involved in cancer and recent translatomics has found some alleged lncRNA actually contained small open reading frames and could encode short peptides. This ribosome footprint profiling (Ribo-seq) was a paired-end sequencing and aimed to investigate whether lncRNA could regulate oxaliplatin resistance in colorectal cancer by encoding short peptides.

2021-11-12 | E-MTAB-10805 | biostudies-arrayexpress

Serial interactome capture of the human cell nucleus

Project description:Novel RNA-guided cellular functions are paralleled by an increasing number of RNA binding proteins (RBPs). We present “serial interactome capture” (serIC), a multiple purification procedure of UV-crosslinked poly(A)-RNA-protein complexes that enables global RBP detection with maximal specificity. We apply serIC to nuclei of proliferating K562 cells to obtain the first human nuclear interactome. The domain composition of the 382 identified nuclear RBPs markedly differs from previous IC experiments, including fewer factors without known RNA binding domains that are in better agreement with computationally predicted RNA binding. serIC extends the number of DNA-RNA binding proteins (DRBPs), and reveals a network of RBPs involved in p53 signaling and double strand break repair. serIC is an effective tool to couple global RBP capture with additional selection or labelling steps for specific detection of highly purified RBPs. The nuclear interactome presented here is a stepping-stone towards deciphering of the functional RNA-protein network in the mammalian nucleus.

2016-03-31 | PXD003664 | Pride

RNA-seq of mouse myeloma cell line SP 2/0 overexpressed with Gm614 against vector control

Project description:We found that a novel gene Gm614 mRNA significantly changed in plasma cells. Because of plasmablast-like, Mus musculus myeloma SP 2/0 cell line was selected to test the effect of Gm614 overexpression on plasmablast/plasma cells. Gm614 cDNA (General Biosystems, Anhui, China) was cloned into lentiviral vector LV201 (Fugene Corp., Guangzhou, China) to generate Gm614 protein. Gm614-expressing LV201 was then transfected into SP 2/0 cells, and stable transfectants were identified by drug selection (Puromycin, Sigma, 10 μg/ml). To identify the effect of Gm614 overexpression on gene expression, we determined mRNA profiles in Gm614-overexpressed and vector-transduced SP 2/0 cells by RNA-seq. RNA-seq was done with an Illumina HiSeq 2500 instrument at GENEWIZ, Suzhou, China.

2020-08-10 | E-MTAB-7135 | biostudies-arrayexpress

RNA-seq of mouse myeloma cell line SP 2/0 cells overexpressed with LOC108168067 against vector control

Project description:We found that a novel gene LOC108168067 mRNA significantly changed in plasma cells. Because of plasmablast-like, mus musculus myeloma SP 2/0 cell line (ATCC® CRL-1581™, https://www.atcc.org/products/all/CRL-1581.aspx) was selected to test the effect of LOC108168067 overexpression on plasmablast/plasma cells. LOC108168067 cDNA (General Biosystems, Anhui, China) was cloned into lentiviral vector LV201 (Fugene Corp., Guangzhou, China) to generate LOC108168067 protein. LOC108168067-expressing LV201 was then transfected into SP 2/0 cells, and stable transfectants were identified by drug selection (Puromycin, Sigma, 10 μg/ml). To explore the effect of on gene expression, we determined mRNA profiles in LOC108168067-overexpressed and vector-transduced SP 2/0 cells by RNA-seq. RNA-seq was done with an Illumina HiSeq 2500 instrument at GENEWIZ, Suzhou, China.

2019-07-31 | E-MTAB-7111 | biostudies-arrayexpress

Ribosome profiling of NEW1 knock-out as well as the isogenic wild type strain of Saccharomyces cerevisiae. The cultures were grown either at 20°C or 30°C.

Project description:Loss of New1 leads to a cold-sensitive phenotype of yeast Saccharomyces cerevisiae. In this study we investigated the effect of NEW1 knockout on translation using Ribo-Seq and RNA-Seq analyses.

2019-05-31 | E-MTAB-7763 | biostudies-arrayexpress

Ribosome profiling of NEW1 knock-out of budding yeast Saccharomyces cerevisiae

Project description:New1 is not an essential gene but its deletion shows a cold-sensitive phenotype in yeast Saccharomyces cerevisiae. In this study, we compare the NEW1 knockout effect on translation using Ribo-Seq and RNA-Seq analyses.

2018-11-10 | E-MTAB-6963 | biostudies-arrayexpress

Ribosome profiling of budding yeast Saccharomyces cerevisiae in eEF3 depleted conditions

Project description:Ribosome profiling (Ribo-Seq) and RNA-Seq analysis of eEF3 depletion in yeast (Saccharomyces cerevisiae). eEF3 depletion was induced by methionine in a modified strain where the native promoter was replaced by methionine repressible MET25 promoter. Conditional depletion enables us to study global effects of an essential gene.

2018-06-30 | E-MTAB-6938 | biostudies-arrayexpress

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