Low-cell input - OmicsDI

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Transcriptomics (2983)
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Methylation profiling (18)
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Organisms

Homo sapiens (1340)
Mus musculus (1159)
Drosophila melanogaster (216)
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Escherichia coli str. K-12 substr. MG1655 (8)
Ciona intestinalis (6)
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Mammalia (1)

Organisms

Mus musculus (308)
Homo sapiens (254)
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Danio rerio (11)
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Arabidopsis thaliana (9)
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synthetic construct (2)
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Repository

biostudies-arrayexpress (3381)
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Inoculated with P. syringae pv. tomato strain DC3000 + avrRps4 (1)
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IV (1)
Infected (1)
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Technology Type

Mass Spectrometry (141)
Bottom-up proteomics (55)
Shotgun proteomics (55)
Data-independent acquisition (31)
Affinity purification coupled with mass spectrometry proteomics (21)
Data-dependent acquisition (19)
Mass spectrometry (9)
SWATH MS (9)
DiaPASEF (5)
Gel-based experiment (5)
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All-ion fragmentation (2)
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ILLUMINA, NextSeq 500 (1)
NMR spectroscopy (1)
Affinity proteomics (1)
Immunopeptidomics (1)
Top-down proteomics (1)

Instrument Platform

NextSeq 500 (95)
Illumina NovaSeq 6000 (94)
Illumina HiSeq 2500 (75)
Illumina HiSeq 4000 (71)
Illumina HiSeq 2000 (51)
NextSeq 550 (17)
NextSeq 2000 (14)
Illumina MiSeq (13)
Illumina HiSeq 3000 (11)
DNA Microarray Scanner BA [Agilent Technologies] (10)
G2565BA DNA microarray scanner [Agilent] (9)
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Axon GenePix 4000B scanning hardware (6)
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Agilent G2565AA and G2565BA Microarray Scanner (4)
G2565AA DNA microarray scanner [Agilent] (4)
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Qubit (3)
Agilent Scanner G2505B (3)
GenePix 4000B [Axon Instruments] (3)
Scanning hardware (3)
NA (3)
DNBSEQ-G400 (3)
HiSeq X Ten (3)
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C1 Single-Cell Auto Prep System, Fluidigm (2)
AB 5500 Genetic Analyzer (2)
Agilent G2505B (2)
Illumina Genome Analyzer (2)

Publication Date

2013 (489)
2014 (441)
2015 (432)
2012 (337)
2010 (298)
2016 (268)
2011 (258)
2008 (142)
2009 (130)
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2022 (112)
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2020 (98)
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2018 (77)
2017 (65)
2007 (42)
2006 (29)
2005 (12)
2004 (3)
2002 (1)

UNIPROT ID/AC

P62755 (3)
Q63484 (3)
Q9WTS1 (2)
P07522 (2)
P35739 (1)
P25427 (1)

CHEBI ID

CHEBI:30831 (3)
CHEBI:15414 (3)
CHEBI:17858 (3)
CHEBI:16750 (3)
CHEBI:16865 (3)
CHEBI:17115 (3)
CHEBI:16335 (3)
CHEBI:17750 (3)
CHEBI:17203 (3)
CHEBI:18050 (3)
CHEBI:16704 (3)
CHEBI:16857 (3)
CHEBI:17053 (3)
CHEBI:16015 (3)
CHEBI:30915 (3)
CHEBI:16414 (3)
CHEBI:15354 (3)
CHEBI:15603 (3)
CHEBI:16643 (3)
CHEBI:17895 (3)
CHEBI:17295 (3)
CHEBI:17596 (3)
CHEBI:17837 (2)
CHEBI:133083 (2)
CHEBI:16039 (2)
CHEBI:37480 (2)
CHEBI:68566 (2)
CHEBI:31969 (2)
CHEBI:27993 (2)
CHEBI:49603 (1)

Metabolite Name

L-Proline (4)
L-Threonine (4)
Choline (4)
L-Glutamine (4)
L-Serine (4)
L-Valine (4)
L-Leucine (4)
L-Methionine (4)
L-Phenylalanine (4)
4-Aminobutanoate (3)
L-Alanine (3)
Betaine (3)
L-Arginine (3)
L-Asparagine (3)
L-Histidine (3)
Adenosine (3)
Guanosine (3)
L-Isoleucine (3)
L-Tyrosine (3)
Inosine (3)
D-Galactose 1-phosphate (2)
3-Aminoisobutyric acid (2)
2-Oxobutanoate (2)
D-Glucosamine (2)
D-Glucose 1-phosphate (2)
D-Tagatose 6-phosphate (2)
3-Methylglutaconic acid (2)
Anthranilate (2)
D-Glucuronic acid (2)
L-Aspartate (2)

First Public Date

2024 (94)
2025 (87)
2026 (74)
2019 (73)
2014 (73)
2021 (71)
2022 (65)
2023 (63)
2020 (58)
2018 (41)
2017 (32)
2013 (18)
2016 (14)
2015 (14)

Modelling Approach

Ordinary differential equation model (7)
Differential equation model (2)

Lab affiliation

1 German Cancer Research Center (DKFZ), Heidelberg, Germany 2 Heidelberg University, Medical Faculty, Heidelberg, Germany (lab head) (3)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (3)
1 German Cancer Research Center (DKFZ), Heidelberg, Germany 2 Heidelberg University, Medical Faculty, Heidelberg, Germany (2)
BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea (2)
Department of Chemistry and Biochemistry University of Bern Switzerland (2)
Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA (2)
1 Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia. Department of Medicine, School of Clinical Sciences, Monash University, Clayton, Australia. 2 Department of Medicine, School of Clinical Sciences, Monash University, Clayton, Australia. 3 Monash Proteomics and Metabolomics Platform, Clinical Proteomics Node, School of Clinical Sciences, Monash University, Clayton, Australia (1)
1 VIB Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium 2 Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium (1)
Assistant Professor, Pediatrics-Heme/Onc and Bone Marrow Transplantation (1)
Attending Physician Medical Director, Brain Tumor Institute Principal Investigator, Center for Cancer and Immunology Research, Children Research Institute Associate Professor of Pediatrics - The George Washington University School of Medicine and Health Sciences Executive co-Chair, Childrens Brain Tumor Network www.CBTN.org (1)
Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Biophysical Chemistry Department of Clinical Chemistry, University Medical Center Goettingen (1)
Biological Mass Spectrometry Lab, Department of Translational Medicine, University of Piemonte Orientale (1)
Biological Mass Spectrometry Lab,Department of Translational Medicine (DiMeT),Center for Translational Research on Autoimmune & Allergic Diseases - CAAD, University of Piemonte Orientale, Novara (NO),Italy. (1)
Biotechnology, Applied Sciences, Delft University of Technology, The Netherlands (1)
CCB, LUMC, Netherlands (1)
CECAD Excellence Center, University of Cologne, Germany, D-50931 Center for Physiology and Pathophysiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany, D-50931 (1)
CRG,UPF (1)
CSIC/UAB Proteomics Laboratory, IIBB-CSIC, Barcelona, Spain (1)
Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom. (1)
Cardiovascular Proteomics Laboratory & Proteomics Unit Centro Nacional de Investigaciones Cardiovasculares Madrid, Spain (1)
Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, The Netherlands (1)
Center for Integrative Genomics University of Lausanne Quartier Sorge 1015 Lausanne Switzerland (1)
Center for theragnosis, Korea Institute of Science and Technology (1)
Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool,L69 7ZB (1)
Centre for Proteome Research, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, U.K (1)
Centre for medicines discovery, University of Oxford (1)
Charité - Universitätsmedizin Berlin Research group Biochemistry and Systems Biology of the Metabolism Institute of Biochemistry Germany (1)
Chemical Cell Biology Leiden Univerity Medical Center Einthovenweg 20 2333ZC Leiden, The Netherlands (1)
College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea (1)
DTU Bioengineering (1)

IsPrivate

False (9)

Classification

bacteria (3)
viruses (1)
protozoa (1)

Modification

2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)
N6 (1)

Study type

Transcription profiling by array (1779)
ChIP-seq (486)
RNA-seq of coding RNA (359)
ChIP-chip by tiling array (250)
ChIP-chip by array (98)
Methylation profiling by array (70)
Other (45)
Comparative genomic hybridization by array (33)
Methylation profiling by high throughput sequencing (28)
Animal - High-throughput sequencing (25)
RNA-seq of coding RNA from single cells (23)
RNA-seq of non coding RNA (17)
Cell line - High-throughput sequencing (16)
Unknown experiment type (14)
DNA-seq (13)
RNA-seq of total RNA (13)
Human - High-throughput sequencing (12)
RIP-seq (9)
High-throughput sequencing (7)
Transcription profiling by RT-PCR (7)
Transcription profiling by tiling array (6)
Cell line - One-color microarray (5)
ATAC-seq (5)
CUT&RUN (5)
Baseline (4)
RNAi profiling by array (4)
Hi-C (4)
MicroRNA profiling by array (4)
Plant - One-color microarray (3)
MNase-seq (2)

Release Date

2013 (494)
2014 (450)
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2010 (301)
2016 (291)
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2005 (9)
2004 (5)
1998 (2)
2003 (1)
2001 (1)
2000 (1)

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Limitations and possibilities of low cell number ChIP-seq

ChIP-seq experiments using low numbers of input cells, scaled down to the point where data quality is unnacceptably compromised, reveals limits of the technique. Two-part ChIPseq study using native chromatin (non-crosslinked) generated with MNase from human CD4+ cells. Part 1: Previously published p...

ORGANISM(S): Homo sapiens

2012-12-03 | E-GEOD-42147 | biostudies-arrayexpress

Seq-Well: A portable, low-cost platform for single-cell RNA-seq of low-input samples

PRJNA374551 | ENA

Low-input proteomics using lauryl maltose neopentyl glycol

We developed a sample preparation method for low-input proteomics using lauryl maltose neopentyl glycol. Using the developed method, we performed proteome analysis of 100ng of HEK293T proteins, coIP samples, and serum extracellular vesicles, and further challenged label-free single-cell proteomics o...

ORGANISM(S): Homo Sapiens (human) Bos Taurus

2024-03-06 | PXD044605 | JPOST Repository

Low input Hi-C datasets for a diffuse large B-cell lymphoma sample, healthy control human B-cells and mouse embryonic stem cells

In this experiment, we've examined chromatin conformation of OG2 (B6; CBA-Tg(Pou5f1-EGFP)2Mnn/J; stock number 004654) mouse stem cells cultured as described in (Shi et al., 2008), using different amounts of starting cells. We performed a modified in situ Hi-C protocol for 6 samples digested with Mbo...

ORGANISM(S): Mus musculus

2018-11-30 | E-MTAB-5875 | biostudies-arrayexpress

Low-input ATAC-seq of mouse EPCR+ and EPCR– hematopoietic stem cell and multipotent progenitor cell populations

PRJEB120972 | ENA

CoBATCH for high-throughput single-cell epigenomic profiling [low input in situ ChIP]

PRJNA531012 | ENA

Ultra-low-input native ChIP-seq data of four germ-cell types during mouse spermatogenesis

PRJNA566429 | ENA

Evaluation of ultra-low input RNA sequencing for the study of human T cell transcriptome

PRJNA541904 | ENA

Cell-free DNA methylome profiling by MBD-seq with ultra-low input

PRJNA677900 | ENA

Simple in-cell processing enables deep proteome analysis of low-number Caenorhabditis elegans

Caenorhabditis elegans is a widely used genetic model organism, however, the worm cuticle complicates extraction of intracellular proteins, a prerequisite for typical bottom-up proteomics. Conventional physical disruption procedures are not only time-consuming, but can also cause significant sample ...

ORGANISM(S): Caenorhabditis Elegans (ncbitaxon:6239)

2025-01-02 | MSV000096763 | MassIVE

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