Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

102 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types

ABSTRACT: Most human pre-mRNAs are spliced into linear molecules that retain the exon order defined by the genomic sequence. By deep sequencing of RNA from a variety of normal and malignant human cells, we found RNA transcripts from many human genes in which the exons were arranged in a non-canonical order. Statistical estimates and biochemical assays provided strong evidence that a substantial fraction of the spliced transcripts from hundreds of genes are circular RNAs. Our results suggest that a non-canonical mode of RNA splicing, resulting in a circular RNA isoform, is a widespread and perhaps general feature of the gene expression program in human cells. 3 samples of non-malignant primary human leukocytes, one replicate each

ORGANISM(S): Homo sapiens

SUBMITTER: Julia Salzman

PROVIDER: E-GEOD-33772 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types.

Salzman Julia J Gawad Charles C Wang Peter Lincoln PL Lacayo Norman N Brown Patrick O PO

PloS one 20120201 2

Most human pre-mRNAs are spliced into linear molecules that retain the exon order defined by the genomic sequence. By deep sequencing of RNA from a variety of normal and malignant human cells, we found RNA transcripts from many human genes in which the exons were arranged in a non-canonical order. Statistical estimates and biochemical assays provided strong evidence that a substantial fraction of the spliced transcripts from hundreds of genes are circular RNAs. Our results suggest that a non-can ...[more]

PMID: 22319583

Similar Datasets

Monocyte-derived IL-1 and IL-6 are differentially required for cytokine release syndrome and neurotoxicity by CAR-T cells.

Project description:Single-cell transcriptome profiling using a 3' droplet-based platform (Chromium,10x Genomics) of human CD45+ leukocytes isolated from leukemic HuSGM3 mice infused with CD19.28z CAR-T cells, two days after cytokine release syndrome (CRS) onset and 5 days later.

2018-05-24 | E-MTAB-6505 | biostudies-arrayexpress

Expression data from normal and Malignant hematopoietic cells

Project description:This data was used to determine levels of BRCA1 and BRCA2 in primary human leukemia samples. Samples were determined to be high BRCA1 and/or BRCA2 or low BRCA1 and/or BRAC2. This data was used to determine levels of BRCA1 and BRCA2 in primary human leukemia samples. Samples were determined to be high BRCA1 and/or BRCA2 or low BRCA1 and/or BRAC2. AML cell lines and patient samples, B ALL cell lines and Patient samplest, T ALL cell lines and patient samples, norma B cells, normal granulocytes, normal monocytes, normal T cells and normal CD34+ cells were used for RNA extraction and hybridization on Affymetrix microarrays. All the AML, B ALL, T ALL cell lines were cultured in vitro under appropriate culture conditons and harvested in their log phase growth for RNA extraction. AML, B ALL, and T ALL patient samples were collected...(I assume these are the PBMCs from eitehr peripheral blood or bone marrow from patients, please confirm). Normal B cells, granulocytes, monocytes, and T cells were purified from human peripheral blood of normal healthy donors.

2013-07-06 | E-GEOD-48558 | biostudies-arrayexpress

miRNA expression data from normal and Malignant hematopoietic cells

Project description:This data was used to identify miRNA signatures that can be used to calssify specific leukemia types including AML, precursor B ALL, precursor T ALL, and normal hematopoietic progenitor and mature populations This data was used to identify miRNA signatures that can be used to calssify specific leukemia types including AML, precursor B ALL, precursor T ALL, and normal hematopoietic progenitor and mature populations AML cell lines and patient samples, B ALL cell lines and Patient samplest, T ALL cell lines and patient samples, norma B cells, normal granulocytes, normal monocytes, normal T cells and normal CD34+ cells were used for RNA extraction and hybridization on Affymetrix microarrays. All the AML, B ALL, T ALL cell lines were cultured in vitro under appropriate culture conditons and harvested in their log phase growth for RNA extraction. AML, B ALL, and T ALL patient samples were collected...(I assume these are the PBMCs from eitehr peripheral blood or bone marrow from patients, please confirm). Normal B cells, granulocytes, monocytes, and T cells were purified from human peripheral blood of normal healthy donors.

2013-10-31 | E-GEOD-51908 | biostudies-arrayexpress

Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types

Project description:Most human pre-mRNAs are spliced into linear molecules that retain the exon order defined by the genomic sequence. By deep sequencing of RNA from a variety of normal and malignant human cells, we found RNA transcripts from many human genes in which the exons were arranged in a non-canonical order. Statistical estimates and biochemical assays provided strong evidence that a substantial fraction of the spliced transcripts from hundreds of genes are circular RNAs. Our results suggest that a non-canonical mode of RNA splicing, resulting in a circular RNA isoform, is a widespread and perhaps general feature of the gene expression program in human cells.

2012-02-10 | GSE33772 | GEO

Study of circular RNA in Dictyostelium discoideum

Project description:RNA-Seq to discover circular RNA expression in Dictyostelium discoidieum with a shallow RNaseR treated RNA-Seq library; our goal was simply to prove existence of these molecules and hence samples were multiplexed with Neurospora Crassa using the same barcode. RNA-Seq on Rnase R treated RNA

2014-04-01 | E-GEOD-55429 | biostudies-arrayexpress

Identification of common endothelial intronic circular RNAs from different vascular beds

Project description:The study aimed to identify circular RNAs (circRNAs) commonly back-spliced to intronic region of different sets of endothelial cells (human cardiac microvascular endothelial cells (HCMEC), human aortic endothelial cells (HAoEC), human umbilical vein endothelial cells (HUVECs)) and to evaluate their overall expression and their expression compared to their respective host gene. Identified circRNAs were quality controlled by their detection in an additional exonuclease RNase R treated RNA-Seq dataset performed with RNA of HUVECs. CircRNAs were compared for overlapping detection between datasets and filtered by annotation for circRNAs back-spliced to intronic regions. Common endothelial intronic circRNAs candidates were compared to respective murine circRNAs stored in the circATLAS database. The prime candidate cZNF292 was functionally characterized in vivo and in vitro.

2023-11-30 | E-MTAB-11171 | biostudies-arrayexpress

Extracellular vesicles impose quiescence and confer DNA-damage on residual HSC in the AML niche

Project description:To understand the mechanism by which AML-EVs may enforce quiescence, we performed tandem mass tag (TMT) proteomic profiling of in vitro cultured c-Kit+ hematopoietic stem and progenitor cells (HSPC) (to obtain the minimum required amount of protein lysates) treated with extracellular vesicles (EVs) for 48 hours from human HL-60 or Molm-14 cell cultures versus controls.

2019-06-24 | PXD013688 | Pride

Conditional modeling of MLL-AF9 induced leukemia revealed a stem cell derived aggressive disease [RNA-Seq]

Project description:To address the impact of cellular origin on AML, we generated an inducible transgenic mouse model for MLL-AF9 driven leukemia. MLL-AF9 expression in long-term hematopoietic stem cells (LT-HSCs) in vitro resulted in unprecedented clonogenic growth and expression of genes involved in migration and invasion. In vivo, some LT-HSC-derived AMLs were particularly aggressive with extensive tissue infiltration, chemo-resistance and expression of genes related to epithelial-mesenchymal transition (EMT) in solid cancers. Knockdown of the EMT regulators Zeb1 and Tcf4 significantly reduced leukemic blast invasion. By classifying mouse and human leukemia according to Evi1/EVI1and Erg/ERG expression, reflecting aggressiveness and cell-of-origin and performing comparative transcriptomics we identified numerous EMT-related genes that were significantly associated with poor overall survival of AML patients. RNA from FACS sorted bone marrow subpopulations was isolated, RNA-sequencing libraries were prepared and sequenced on an Illumina HiSeq 2000. Reads mapping to RefSeq transcripts were counted.

2016-06-27 | E-GEOD-65383 | biostudies-arrayexpress

Enhancer Transcripts Mark Active Estrogen Receptor Binding Sites

Project description:In this study, we used Global Run-On sequencing (GRO-seq), a method that assays the genome-wide location and orientation of all active RNA polymerases. We generated a global profile of active transcription at ERM-NM-1 binding sites in MCF-7 human breast cancer cells in response to short time course of E2 treatment. This method enabled us to detect active transcription at enhancers and define a class of primary transcripts transcribed uni- or bidirectionally from the ERM-NM-1 binding sites. The raw data used in this study is from GSE27463 but sequenced to a greater depth. Using GRO-seq over a time course (0, 10, 40 min) of estrogen signaling in ER-alpha positive MCF-7 human breast cancer cells.

2013-05-08 | E-GEOD-43835 | biostudies-arrayexpress

Back-spliced RNA from Retrotransposon Binds to Centromere and Regulates Centromeric Chromatin Loops in Maize

Project description:In most plants, centromeric DNA contains highly repetitive sequences, including tandem repeats and retrotransposons; however, the roles of these sequences in the structure and function of the centromere are unclear. Here, we found that retrotransposon-derived back-spliced RNA can bind to the centromere through R-loops and regulate the formation of centromeric chromatin loops. Multiple RNA sequences from centromeric retrotransposons (CRMs) were enriched in maize (Zea mays) centromeres and back spliced RNA from CRM1 were detected. We identified three types of circular CRM1 RNAs with the same back-splicing site based on the back-spliced sequences. These circular RNAs bound to the centromere through R-loops. Two R-loop sites inside a single circular RNA promoted the formation of chromatin loops in CRM1 regions. When RNAi was used to target the back-spliced site of the circular CRM1 RNAs, the levels of R-loops and chromatin loops formed by these circular RNAs decreased, while the levels of R-loops produced by linear RNAs with similar binding sites increased. Linear RNAs with only one R-loop site could not promote chromatin loop formation. Higher levels of R-loops and lower levels of chromatin loops in the CRM1 regions of RNAi plants led to a reduced localization of the centromeric H3 variant (CENH3). Our work reveals that centromeric chromatin organization by circular CRM1 RNAs via R-loops and chromatin loops. R-loops are integral components of centromeric chromatin. Proper centromere structure is essential for CENH3 localization. CRM1 elements may have helped to build a suitable chromatin environment during centromere evolution.

2020-01-01 | GSE137701 | 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