Mrna maturation

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Organisms

Mus musculus (289)
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ILLUMINA, Illumina HiSeq 2000 (1)
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Instrument Platform

Illumina NovaSeq 6000 (36)
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NextSeq 550 (4)
Illumina HiSeq 3000 (4)
PromethION (3)
HiSeq X Ten (3)
Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (2)
Axon GenePix 4000B scanning hardware (2)
Illumina NovaSeq X (2)
DNBSEQ-G400 (2)
Illumina MiSeq (2)
IPK PhenoSphere (1)
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Arcturus PicoPure (1)
Miltenyi Biotec (cat no. 130-096-730) ,Fortessa X-20 flow cytometer (BD Biosciences) (1)
MA900, Sony (1)
Cutadapt, STAR (1)

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2004 (4)
2003 (3)

UNIPROT ID/AC

P26599 (1)
O75400 (1)
P26368 (1)
Q0ZAI8 (1)
P49960 (1)
O43290 (1)
Q8TDC3 (1)
Q8WVK2 (1)
P52298 (1)
Q09161 (1)
P31483 (1)
P38852 (1)
O43447 (1)
Q5CU80 (1)
Q13435 (1)
B7PBN4 (1)
Q15393 (1)
O75533 (1)
Q15459 (1)
Q15428 (1)
Q01130 (1)
Q06819 (1)
Q12874 (1)
O94906 (1)
Q15637 (1)
O43143 (1)
Q9Y3B4 (1)
P08621 (1)
Q15427 (1)
P09012 (1)

CHEBI ID

CHEBI:16761 (4)
CHEBI:17553 (2)
CHEBI:17858 (2)
CHEBI:16856 (2)
CHEBI:16732 (2)
CHEBI:17562 (2)
CHEBI:16977 (2)
CHEBI:17196 (2)
CHEBI:7916 (2)
CHEBI:18050 (2)
CHEBI:17053 (2)
CHEBI:16015 (2)
CHEBI:30887 (2)
CHEBI:16027 (2)
CHEBI:17345 (2)
CHEBI:44897 (2)
CHEBI:16347 (2)
CHEBI:17191 (2)
CHEBI:15603 (2)
CHEBI:17895 (2)
CHEBI:30769 (2)
CHEBI:84596 (1)
CHEBI:15996 (1)
CHEBI:17552 (1)
CHEBI:15422 (1)
CHEBI:59020 (1)
CHEBI:141393 (1)
CHEBI:79968 (1)
CHEBI:31580 (1)
CHEBI:183886 (1)

Metabolite Name

L-Glutamine (4)
Uracil (3)
Betaine (3)
Thymine (3)
O-Phosphoethanolamine (3)
L-Proline (3)
Erucic acid (3)
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L-Glutamic acid (3)
Indole (3)
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N-Acetylneuraminic acid (3)
Adenosine (3)
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L-Tryptophan (3)
Creatinine (3)
L-Methionine (3)
L-Phenylalanine (3)
Alpha-Methyltryptamine (2)
Glu-Pro (2)
N6-Methyl-L-lysine (2)
Pristanic acid (2)
N-Acetyllactosamine (2)
25-Hydroxycholesterol (2)
Ethyl glucuronide (2)
7-Dehydrocholesterol (2)
N6,N6,N6-Trimethyl-L-lysine (2)
Hypotaurine (2)
3,4-Methylenedioxyamphetamine (2)
N-Acetyl-D-glucosamine (2)

First Public Date

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Modelling Approach

Petri net (1)

Lab affiliation

EDyP (3)
Protein Biogenesis Laboratory, Francis Crick Institute, London, UK (3)
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain (2)
Max Planck Unit for the Science of Pathogens Charitéplatz 1,D-10117 Berlin, Germany (2)
1 Institute of Marine Sciences, Spanish National Research Council (CSIC), 08003 Barcelona, Spain 2 Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Spain (1)
1-Tyrolean Cancer Research Institute (TKFI), Innrain 66, A-6020 Innsbruck, Austria 2-Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria. (1)
1Natural Sciences and Engineering, University of South Carolina Upstate, Spartanburg, SC 29303 (1)
Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Germany Bioanalytics, Institute for Clinical Chemistry, University Medical Center Goettingen, Germany (1)
Boston Children's Hospital (1)
Carnegie MS Facility (1)
Cell Signal unit, OIST Graduate University, Okinawa, Japan (1)
Center for Reproductive Medicine, Shandong University (1)
Centre for Addiction and Mental Health (1)
Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece (1)
Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada; Department of Physiology and Pharmacology, University of Calgary, Alberta, Canada; The Hotchkiss Brain Institute, University of Calgary, Alberta, Canada; McCaig Institute for Bone and Joint Health, University of Calgary, Alberta, Canada. (1)
Department of Biochemistry, University of Oxford (1)
Department of Biology, AG Stengel, University of Konstanz, Germany (1)
Department of Biology, Cellular Proteostasis and Mass Sepectrometry, University of Konstanz (1)
Department of Chemistry and Biochemistry, California State University Fullerton (1)
Department of Comparative Biosciences, University of Illinois at Urbana-Champaign (1)
Department of Computational, Cellular, Integrative Biology (DeCIBIO), University of Trento 38123, TN, Italy (1)
Department of Genetics, Cell Bioliogy, & Anatomy Buckley Lab University of Nebraska Medical Center Omaha, Nebraska United States of America (1)
Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden. Max Planck Institute for Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17165, Sweden. (1)
Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences; Göttingen, Germany (1)
Department of Molecular and Cellular Hemostasis Plasma Proteins, Sanquin Research, Amsterdam, The Netherlands (1)
Department of Neurobiology and Developmental Science, University of Arkansas for Medical Sciences, Little Rock, AR (1)
Department of Neurology, Nagoya University Graduate School of Medicine (1)
Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic (1)
Department of Pharmaceutical Sciences Oregon State University College of Pharmacy Portland, OR 97301 USA (1)
Deputy head of department at Department of Translational Medicine. Lund University. Principal investigator at CEBMMS PI. Professor at Clinical Chemistry, Malmö Professor at Clinical Protein Science and Imaging Professor at Department of Clinical Sciences, Lund (1)

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Classification

bacteria (10)
fungi (4)
viruses (3)
protozoa (1)

Study type

Transcription profiling by array (702)
RNA-seq of coding RNA (294)
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Other (24)
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Unknown experiment type (21)
RNA-seq of coding RNA from single cells (14)
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Cell line - High-throughput sequencing (8)
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Methylation profiling by array (7)
ChIP-chip by array (6)
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Baseline (1)
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2000 (13)
2002 (9)
1999 (9)
2003 (7)
2001 (7)
1997 (4)
1998 (3)

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Polysome-bound mRNA during oocyte maturation

Oocyte maturation, fertilization, and early embryonic development occur in the absence of gene transcription. Therefore, it is critical to understand at a global level the post-transcriptional events that are driving these transitions. Here, we have used a systems approach by combining polysome mRNA...

ORGANISM(S): Mus musculus

2012-01-14 | E-GEOD-35106 | biostudies-arrayexpress

Identification of mRNA processing complexes bound to histone H2A.2 3’ untranslated region

Processing of 3’ untranslated region (3’-UTR) of precursor messenger RNAs (pre-mRNA) is a fundamental step in mRNA maturation, where the mRNA transcript is cleaved at a specific site, located downstream the open reading frame of the encoded gene. The position of the cleavage site is determined by ci...

ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse)

2022-12-09 | PXD034984 | Pride

Effects of Dcp1a and Dcp2 knockdown during mouse oocyte maturation

Oocyte maturation is accompanied by a transition from mRNA stability to instability. We investigated the role of DCP1A and DCP2, proteins responsible for mRNA decapping, in mRNA destabilization during mouse oocyte maturation. siRNA-mediated knockdown of both Dcp1a and Dcp2 transcripts prior to ini...

ORGANISM(S): Mus musculus

2013-02-06 | E-GEOD-27049 | biostudies-arrayexpress

Effects of in vitro maturation on oocyte gene expression

In vitro oocyte maturation (IVM) holds great promise as a tool for enhancing clinical treatment of infertility, enhancing availability of non human primates for development of disease models, and facilitating endangered species preservation. However, IVM outcomes have remained significantly below s...

ORGANISM(S): Macaca mulatta

2009-05-20 | E-GEOD-11895 | biostudies-arrayexpress

SAGE in Cultured Murine COC During Early Maturation

In cultured cumulus oocyte complexes (COC) FSH induces gene transcription required for germinal vesicle breakdown (GVBD). Experiments were performed to determine the critical period when gene transcription is required for GVBD and identify candidate mRNAs involved. Experiment I: murine COC were cult...

ORGANISM(S): Mus musculus

2006-08-31 | E-GEOD-5568 | biostudies-arrayexpress

Integrated small RNA, mRNA and protein omics reveal a miRNA network orchestrating metabolic maturation of the developing human heart

As the fetal heart develops, cardiomyocyte proliferation potential decreases while fatty acid oxidative capacity increases, a highly regulated transition known as cardiac maturation. Small noncoding RNAs, such as microRNAs (miRNAs), contribute to the establishment and control of tissue-specific tran...

ORGANISM(S): Homo sapiens (Human)

2024-01-26 | PXD044936 | Pride

Lc-msms Human fetal heart

MicroRNAs regulate DC maturation via M-CSFR

We identify a panel of microRNAs that are differentially expressed during both spontaneous and LPS-induced DC maturation and show the M-CSF receptor (M-CSFR) as a key target for microRNA-mediated regulation. MicroRNA-22, -34a and -155 are up-regulated in mature GM-CSF-generated DC and mediate M-CSFR...

ORGANISM(S): Mus musculus

2013-11-04 | E-MEXP-3311 | biostudies-arrayexpress

Long non-coding RNAs and microRNAs involved in integrated co-regulation of neuronal maturation [mRNA and lncRNA expression]

Neurogenesis is a pro-survival process that comprises of dendritic and axonal growth, synaptogenesis, synaptic and neuronal pruning. These complex processes are determined by temporal gene expression during development, which is in turn tightly regulated by long non-coding RNAs and microRNAs. In thi...

ORGANISM(S): Mus musculus

2014-10-24 | E-GEOD-44833 | biostudies-arrayexpress

Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals (single embryo)

Parental dietary conditions can influence the metabolic traits of offspring. In mice, paternal consumption of low protein diet alters cholesterol and lipid metabolism of progeny. Here, we examine RNA species expressed in male reproductive tissues of mice. Protein restriction leads to altered levels ...

ORGANISM(S): Mus musculus

2015-12-31 | E-GEOD-75765 | biostudies-arrayexpress

Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals

ORGANISM(S): Mus musculus

2016-01-04 | E-GEOD-74537 | biostudies-arrayexpress

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