Cajal body - OmicsDI

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Tissue

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Mass Spectrometry (6)
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Mass spectrometry (1)
Mass spectrometry assay (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (64)
NextSeq 500 (21)
NextSeq 550 (12)
Illumina HiSeq 4000 (12)
Illumina NovaSeq X (11)
Illumina HiSeq 2500 (4)
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)
Chromium Controller (2)
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N/A (2)
NextSeq 2000 (2)
Illumina HiSeq 2000 (2)
Chromium X instrument (10x Genomics); GEM-X FX Chips (10x Genomics); Agilent TapeStation D1000; qPCR (library quantification kit for Illumina platforms) (1)
Chromium X instrument (10x Genomics); GEM-X Flex Sample Preparation v2 Kit (10x Genomics; 1000781); Human Gene Expression Probe Set v1.0.1 (10x Genomics) (1)
Countess 3 FL Automated Cell Counter (Thermo Fisher Scientific; AMQAF2000); GEM-X Flex Sample Preparation v2 Kit (10x Genomics; 1000781) (1)
Scanpy (hash 98de5d1a) (1)
Chromium Next GEM Single Cell 5' Reagent Kits (10x Genomics) (1)
10xGenomics Chromium 3'v3 (1)
CryoStor® CS10 Freezing Medium (Cat. No. 100-1061; StemCell Technologies) (1)
Basic laboratory equipment (1)
10x Genomics Chromium Controller, PCR thermocycler, Agilent 2100 Bioanalyzer with High Sensitivity DNA chip (for quality control) (1)
Water bath (for enzymatic dissociation), cell strainer (70-μm), benchtop centrifuge, automated cell counter/hemocytometer, biological safety cabinet (1)
Sterile surgical instrument set (scalpels, tissue forceps, dissection scissors), animal operating table, biological safety cabinet (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Cell culture (1)
NaN (1)
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10x Genomics Chromium controller (GEM generation on Chromium Next GEM Chip G) (1)

Publication Date

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CHEBI ID

CHEBI:17822 (2)
CHEBI:22660 (2)
CHEBI:26986 (2)
CHEBI:28044 (2)
CHEBI:27266 (2)
CHEBI:18237 (2)
CHEBI:16449 (2)
CHEBI:28742 (1)
CHEBI:29083 (1)
CHEBI:22860 (1)
CHEBI:229981 (1)
CHEBI:57642 (1)
CHEBI:133038 (1)
CHEBI:183886 (1)
CHEBI:229203 (1)
CHEBI:228843 (1)
CHEBI:132284 (1)
CHEBI:43295 (1)
CHEBI:17907 (1)
CHEBI:16003 (1)
CHEBI:83718 (1)
CHEBI:140506 (1)
CHEBI:143241 (1)
CHEBI:156019 (1)
CHEBI:157877 (1)
CHEBI:46202 (1)
CHEBI:88768 (1)
CHEBI:88755 (1)
CHEBI:4608 (1)
CHEBI:45956 (1)

Metabolite Name

Pentanedioic acid (1)
N-METHYL-GLUTAMATE (1)
METHYLTHIOADENOSINE (1)
Homothreonine (1)
5,6-DIHYDROURACIL (1)
5-O-methylvisammioside (1)
CARNITINE (1)
Dioctylamine (1)
METHIONINE (1)
ALANINE (1)
DEOXYCARNITINE (1)
TRIGONELLINE (1)
4-AMINOBUTANOATE (1)
ALPHA-AMINOADIPATE (1)
Dihydroxyacetone phosphate (1)
Oxoproline (1)
Myristic acid (1)
Glucose-6-phosphate (1)
Tributylamine (1)
Coniine (1)
DEOXYCYTIDINE (1)
N-Acetylarginine (1)
2-Methylpyrrolidine (1)
Alanine betaine (1)
Glutamylphenylalanine (1)
DEOXYGUANOSINE (1)
GUANOSINE (1)
THYMIDINE (1)
SUCROSE (1)
TREHALOSE (1)

First Public Date

2024 (7)
2014 (5)
2025 (3)
2021 (3)
2016 (3)
2026 (2)
2022 (2)
2019 (2)
2013 (2)
2020 (1)
2018 (1)

Study type

RNA-seq of coding RNA from single cells (107)
Transcription profiling by array (23)
RNA-seq of coding RNA (8)
Single nucleus RNA sequencing (5)
Differential (4)
Cell line - Single-cell sequencing (3)
Animal - Single-cell sequencing (3)
ChIP-seq (3)
ScATAC-seq (2)
RNA-seq of non coding RNA from single cells (1)
Methylation profiling by array (1)
RNA-seq of total RNA (1)

Release Date

2025 (58)
2022 (48)
2026 (41)
2021 (41)
2024 (40)
2023 (30)
2020 (20)
2018 (16)
2016 (16)
2019 (15)
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2014 (13)
2012 (12)
2010 (12)
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2011 (10)
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2009 (7)
2006 (6)
2007 (5)
2008 (4)
2004 (3)
2003 (3)
2000 (2)
2005 (2)
2002 (2)
2001 (1)

Lab affiliation

Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University, D-72076 Tübingen, Germany (1)
Institute of Molecular Biology (IMB) (1)
Institute of Plant and Microbial Biology, Academia Sinica (1)
Investigador Ramon y Cajal, grupo Bionanosurf, Instituto de nanociencia y materiales de ARagón (Zaragoza, España) (1)
Max-Planck-Institute for Multidisciplinary Sciences Bioanalytical Mass Spectrometry Group Am Fassberg 11 D-37077 Goettingen, Germany University Medical Center Goettingen Bioanalytics Institute for Clinical Chemistry Robert Koch Strasse 40 D-37075 Goettingen, Germany (1)
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. (1)

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A plant Cajal body proteome reveals kingdom-specific components

Cajal bodies from Nicotiana benthamiana were isolated using fluorescence-activated particle sorting (FAPS) and subjected to LC-MS/MS for comprehensive proteomic profiling. In parallel, TurboID-based proximity labeling was performed using Cajal body-resident proteins to identify their proximal proteo...

ORGANISM(S): Nicotiana benthamiana

2026-09-21 | PXD065938 | Pride

Transcription profiling of mouse small intestine interstitial cells of Cajal (ICC) from deep muscular plexus and myenteric plexus

Interstitial cells of Cajal (ICC) have important functions in regulation of motor activity in the gastrointestinal tract. In murine small intestine ICC are gathered in the region of the myenteric plexus (ICC-MY) and within the deep-muscular plexus near the submucosal surface of the circular muscle ...

ORGANISM(S): Mus musculus

2008-06-15 | E-GEOD-7809 | biostudies-arrayexpress

Small nucleolar RNAs and small Cajal body-specific RNAs show distinct transcriptional profiles in the context of the molecular heterogeneity of multiple myeloma.

Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs) are non-coding RNAs involved in the maturation of other RNA molecules and generally located in the introns of host genes. It is now emerging that altered sno/scaRNAs expression may play a pathological role in cancer. This st...

ORGANISM(S): Homo sapiens

2013-06-25 | E-GEOD-39683 | biostudies-arrayexpress

Identification of coilin interactors reveals coordinated control of Cajal body number and substructure

The cell nucleus contains distinct biomolecular condensates that form at specific genetic loci, organize chromosomes in 3D space, and regulate RNA processing. Among these, Cajal bodies (CBs) require key “scaffolding” proteins for their assembly, which is not fully understood. Here we employ proximit...

ORGANISM(S): Homo sapiens (Human)

2024-11-10 | PXD042406 | Pride

Lc-ms/ms

A point mutation in human coilin prevents Cajal body formation.

Not available

S-EPMC9080554 | biostudies-literature

Disruption of ZC3H15 Compromises Telomere Length Maintenance by Sequestering Telomerase within Cajal bodies

Telomere homeostasis, crucial for various biological processes, relies on telomerase activity. We identified ZC3H15 as a novel telomerase-interacting protein. Its deletion unexpectedly increased telomerase activity but led to shortened telomeres and cellular senescence. ZC3H15 interacts with telomer...

ORGANISM(S): Homo Sapiens

2024-05-06 | PXD052036 |

WRAP53 is essential for Cajal body formation and for targeting the survival of motor neuron complex to Cajal bodies.

Not available

S-EPMC2970535 | biostudies-literature

A Cajal body-independent pathway for telomerase trafficking in mice.

Not available

S-EPMC2945411 | biostudies-literature

Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs.

Not available

S-EPMC126017 | biostudies-literature

In vivo analysis of Cajal body movement, separation, and joining in live human cells.