Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Small RNA sequencing of healthy and osteoarthritis diseased anterior cruciate ligament

ABSTRACT: Comparison of differential expression of small-noncoding RNAs between healthy and osteoarthritis diseased anterior cruciate ligament

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Yongxiang Fang

PROVIDER: E-MTAB-9106 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of Wister Rat blood serum to investigate small non-coding RNAs in serum as biomarkers of tendon injury

Project description:Injury was induced in the left Achilles tendon by needle puncture. Rats were sacrificed 4 and 21 days post injury. Shams, in which the tendon was isolated but not punctured, were included as controls. Serum was collected post-mortem and RNAseq used to identify differentially expressed ncRNAs.

2021-03-31 | E-MTAB-9509 | biostudies-arrayexpress

Small RNAseq between young and old normal equine chondrocytes

Project description:This project aims to identify differentially expressed small non coding RNAs between young and old normal chondrocytes isolated from the metacarpophalangeal joint of 10 horses; 5 young and 5 old.

2021-04-30 | E-MTAB-8112 | biostudies-arrayexpress

Small non-coding RNAs in early equine osteoarthritis synovial fluid

Project description:Small RNA isolated from synovial fluid of the metacarpophalangeal joints of horses. Horses either had minimal signs of osteoarthritis based on macroscopic and microscopic joint scoring or early (mild) osteoarthritis. Differential expression of small non-coding RNAs was undertaken.

2020-06-30 | E-MTAB-8409 | biostudies-arrayexpress

Widespread N6-methyladenosine-dependent RNA Structural Switches Regulate RNA-Protein Interactions

Project description:We show that N6-methyladenosine (m6A), the most abundant internal modification in mRNA/lncRNA with still poorly characterized function, alters RNA structure to facilitate the access of RBM for heterogeneous nuclear ribonucleoprotein C (hnRNP C). We term this mechanism m6A-switch. Through combining PAR-CLIP with Me-RIP, we identify 39,060 m6A-switches among hnRNP C binding sites transcriptome-wide. We show that m6A-methyltransferases METTL3 or METTL14 knockdown decreases hnRNP C binding at 16,582 m6A-switches. Taken together, 2,798 m6A-switches of high confidence are identified to mediate RNA-hnRNP C interactions and affect diverse biological processes including cell cycle regulation. These findings reveal the biological importance of m6A and provide insights into the sophisticated regulation of RNA-RBP interactions through m6A-induced RNA structural remodeling. Measure the m6A methylated hnRNP C binding sites transcriptome-wide by PARCLIP-MeRIP; measure the differential hnRNP C occupancies upon METTL3/METTL14 knockdown by PAR-CLIP; measure RNA abundance and splicing level changes upon HNRNPC, METTL3 and METTL14 knockdown

2015-02-27 | E-GEOD-56010 | biostudies-arrayexpress

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

Project description:Background: In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequenced long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins. Results: Analysis of these data sets revealed that many loci in the human genome reproducibly give rise to C/D box-like snoRNAs, whose expression and evolutionary conservation are typically less pronounced relative to the snoRNAs that are currently catalogued. We further found that virtually all C/D box snoRNAs are specifically processed inside the regions of terminal complementarity, retaining in the mature form only 4-5 nucleotides upstream of the C box and 2-5 nucleotides downstream of the D box. Sequencing of the total and Argonaute 2-associated populations of small RNAs revealed that despite their cellular abundance, C/D box-derived small RNAs are not efficiently incorporated into the Ago2 protein. Conclusions: We conclude that the human genome encodes a large number of snoRNAs that are processed along the canonical pathway and expressed at relatively low levels. Generation of snoRNA-derived processing products with alternative, particularly miRNA-like, functions appears to be uncommon. PAR-CLIP profiling for snoRNP core proteins NOP56, NOP58, Fibrillarin, and Dyskerin in HEK293 cells. Small RNA profiling using RNA-seq in HEK293 and HeLa cells, small RNA profiling using IP-seq of Ago2 associated small RNAs.

2013-05-08 | E-GEOD-43666 | biostudies-arrayexpress

Small RNA sequencing of healthy and osteoarthritis diseased anterior cruciate ligament

Project description:Small RNA sequencing of healthy and osteoarthritis diseased anterior cruciate ligament

| PRJEB38433 | ENA

High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection

Project description:Small RNA deep sequencing analysis was conducted on primary human fibroblasts infected with human cytomegalovirus (HCMV). HCMV-encoded miRNAs accumulated to ~20% of the total smRNA population at late stages of infection, and our analysis led to improvements in viral miRNA annotations and identification of novel HCMV miRNAs. Through crosslinking and immunoprecipitation of Argonaute-bound RNAs from infected cells, followed by high-throughput sequencing (Ago CLIP-seq), we obtained direct evidence for incorporation of all HCMV miRNAs into the endogenous host silencing machinery. Additionally, significant upregulation was observed during infection for a host miRNA cluster containing miR-96, miR-182 and miR-183. We also identified novel non-miRNA forms of virus-derived smRNAs, revealing greater complexity within the smRNA population during HCMV infection. High-throughput profiling of smRNAs, Ago1-, and Ago2-associated miRNAs from HCMV-infected fibroblast cells. Wild-type HCMV Towne (Genbank FJ616285.1) was used for these studies.

2011-11-10 | E-GEOD-33584 | biostudies-arrayexpress

Comparison of the myometrial transcriptome from singleton and twin pregnancies by high throughput RNA-Seq

Project description:We performed high-throughput RNA sequencing (RNA-Seq) of human myometrium from singleton and twin pregnancies at term (> 37+0 weeks) and preterm (< 37+0 weeks), collected during pre-labour Caesarean Section.

2020-01-08 | E-MTAB-8233 | biostudies-arrayexpress

Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-11-20 | E-GEOD-55333 | biostudies-arrayexpress

RNA-Seq of full-length RNA from worker and royal jelly of honey bees (Apis mellifera)

Project description:Characterization of naturally-occurring RNAs (up to 200nt) in the honey bee worker and royal jelly

2018-11-29 | E-MTAB-6557 | biostudies-arrayexpress