Rock D L DL - OmicsDI

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Transcriptomics (1648)
Genomics (220)
Unknown (60)
Proteomics (58)
Metabolomics (9)
Other (1)

Organisms

Mus musculus (364)
Homo sapiens (354)
Drosophila melanogaster (135)
Saccharomyces cerevisiae (129)
Rattus norvegicus (79)
Arabidopsis thaliana (55)
Escherichia coli (47)
Caenorhabditis elegans (34)
Rhizobium leguminosarum (30)
Escherichia coli str. K-12 substr. MG1655 (26)
Mycobacterium tuberculosis (23)
Schizosaccharomyces pombe (21)
Pseudomonas putida (19)
Bacillus subtilis (15)
Danio rerio (15)
Staphylococcus aureus (14)
Bos taurus (13)
Listeria monocytogenes (12)
Escherichia coli K-12 (12)
Triticum aestivum (12)
Plasmodium falciparum (11)
Clostridium acetobutylicum (8)
Streptococcus pneumoniae (8)
Hordeum vulgare (8)
Shewanella piezotolerans WP3 (7)
Bacillus subtilis subsp. subtilis str. 168 (7)
Corynebacterium glutamicum (7)
Oryza sativa (7)
Salmonella enterica subsp. enterica serovar Typhimurium (7)
Candida albicans (7)

Repository

biostudies-arrayexpress (1889)
MassIVE (29)
jPOST (22)
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Disease

Normal (9)
Porphyria NOS (2)
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Blumeria graminis hordei (powdery mildew) inoculation (1)
Squamous cell carcinoma has accession C0007137 in DiseaseStateDatabase NCI_Thesaurus (1)
Uncomplicated gonorrhoea (1)
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Plasmodium berghei CTRP knockout strain (Dessens et al., 1999) infection (1)
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Technology Type

Mass spectrometry (7)
Mass spectrometry assay (2)

Instrument Platform

NextSeq 500 (76)
Illumina HiSeq 2000 (41)
Illumina NovaSeq 6000 (39)
Illumina HiSeq 2500 (26)
Illumina HiSeq 4000 (24)
NextSeq 550 (18)
Illumina MiSeq (13)
NextSeq 2000 (10)
Axon GenePix 4000B scanning hardware (9)
Axon- GenePix4000B (7)
418 [Affymetrix] (6)
Illumina NovaSeq X (6)
Axon GenePix 4000A scanning hardware (5)
Illumina HiSeq 1000 (5)
Illumina HiSeq 1500 (5)
GenePix 4000A [Axon Instruments] (4)
Illumina Genome Analyzer IIx (4)
Generation III Array Scanner [Amersham] (4)
Vortex (4)
GenePix 4000B [Axon Instruments] (3)
Illumina Genome Analyzer II (3)
Scanning hardware (3)
Affymetrix (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)
Manual (2)
10x Genomics Chromium (2)
Infors HT Multitron shaker (2)
Sony SH800 (2)
Anaerobic workstation with airlock (2)
Nanodrop N1000 spectrophotometer (2)

Publication Date

2010 (255)
2013 (187)
2014 (171)
2012 (170)
2015 (162)
2011 (153)
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2008 (109)
2009 (90)
2007 (81)
2005 (66)
2006 (54)
2018 (44)
2022 (41)
2023 (37)
2024 (36)
2021 (36)
2020 (35)
2025 (28)
2017 (25)
2019 (23)
2026 (22)
2004 (13)
2003 (2)
2002 (1)

UNIPROT ID/AC

1FEH1_WHEAT (1)
4565.Traes_1BL_55033DAE8.2 (1)
4565.Traes_2DL_36E87BA3F.1 (1)
4565.Traes_2DL_49B44D5E3.1 (1)
4565.Traes_2DS_A32E0CCF5.1 (1)
4565.Traes_2DS_FA532168A.2 (1)
4565.Traes_3DL_613DF9009.1 (1)
4565.Traes_3DL_CB9CA6DF6.1 (1)
4565.Traes_3DS_AB85A8D36.2 (1)
4565.Traes_4AL_45CFFFB35.1 (1)
4565.Traes_4AS_254B6D654.4 (1)
4565.Traes_4BL_518630DDF.1 (1)
4565.Traes_4DL_C4877C20D.1 (1)
4565.Traes_4DS_2ABE97FD8.1 (1)
4565.Traes_4DS_2F98108D7.1 (1)
4565.Traes_4DS_88B2B1D0C.1 (1)
4565.Traes_4DS_9C71814E9.1 (1)
4565.Traes_4DS_CB4EF3DEB.1 (1)
4565.Traes_5AS_B16145290.1 (1)
4565.Traes_5BS_C64E893BD.1 (1)
4565.Traes_5DL_24E161E8F.1 (1)
4565.Traes_5DL_4211ABEC3.1 (1)
4565.Traes_6AL_67ED9DB4D.1 (1)
4565.Traes_6BS_7D98E1A6D.2 (1)
4565.Traes_6DL_B3AD4834A.1 (1)
4565.Traes_7AL_0A92A2224.1 (1)
4565.Traes_7BL_82850CC15.1 (1)
4565.Traes_7DL_5320E59A61.1 (1)
4565.Traes_7DL_62F01AA40.1 (1)
4565.Traes_7DL_84549CB3E.1 (1)

CHEBI ID

CHEBI:25017 (4)
CHEBI:28044 (4)
CHEBI:15428 (3)
CHEBI:15741 (3)
CHEBI:15978 (3)
CHEBI:16449 (3)
CHEBI:16765 (3)
CHEBI:16811 (3)
CHEBI:16865 (3)
CHEBI:17509 (3)
CHEBI:17822 (3)
CHEBI:18012 (3)
CHEBI:18186 (3)
CHEBI:22653 (3)
CHEBI:26271 (3)
CHEBI:27266 (3)
CHEBI:27897 (3)
CHEBI:30769 (3)
CHEBI:4170 (3)
CHEBI:6650 (3)
CHEBI:15318 (2)
CHEBI:15356 (2)
CHEBI:15725 (2)
CHEBI:16027 (2)
CHEBI:16235 (2)
CHEBI:16335 (2)
CHEBI:16551 (2)
CHEBI:16610 (2)
CHEBI:16680 (2)
CHEBI:16691 (2)

Metabolite Name

Guanine (2)
Leucine (2)
Methionine (2)
Phenylalanine (2)
Proline (2)
Tryptophan (2)
1,3,5-Triazin-2(1H)-one, 4,6-bis((1-methylethyl)amino)- (1)
1,3-diaminopropane (1)
1,5-Anhydroglucitol (1)
2' deoxyuridine (1)
2'-deoxycytidine (1)
2,3-Dihydroxypropane-1-sulfonate (1)
2,3-dihydroxybenzoic acid (1)
2,3-dihydroxypropane-1-sulfonate (1)
2-Deoxy-D-galactose (1)
2-Keto-3-deoxy-6-phosphogluconate (1)
2-Monoolein (1)
2-hydroxypyridine (1)
2-phenylacetamide (1)
3-Hydroxypropionic acid (1)
3-Methylamino-1,2-propanediol (1)
3-hydroxy-3-methylglutaric acid (1)
3-mercaptopropionic acid (1)
3-methyl-2-oxobutanoic acid (1)
3-methyl-2-oxopentanoic acid (1)
3-phenylcatechol (1)
4-Acetamidobutyric acid (1)
4-Aminobenzoic acid (1)
4-Cholesten-3-one (1)
4-Hydroxybenzoic acid (1)

Study type

Transcription profiling by array (905)
RNA-seq of coding RNA (217)
ChIP-seq (183)
Other (77)
ChIP-chip by tiling array (76)
ChIP-chip by array (68)
RNA-seq of non coding RNA (66)
Comparative genomic hybridization by array (45)
RNA-seq of coding RNA from single cells (31)
Methylation profiling by high throughput sequencing (25)
Methylation profiling by array (18)
Transcription profiling by tiling array (15)
Unknown experiment type (14)
DNA-seq (12)
High-throughput sequencing (11)
Ribo-seq (11)
CUT&RUN (9)
RNAi profiling by array (7)
CLIP-seq (7)
RIP-seq (7)
MicroRNA profiling by array (7)
Cell line - High-throughput sequencing (6)
RNA-seq of total RNA (6)
Translation profiling (5)
Animal - High-throughput sequencing (5)
ATAC-seq (5)
Proteomic profiling by array (4)
GRO-seq (3)
Transcription profiling by SAGE (3)
MNase-seq (3)

Release Date

2010 (257)
2013 (190)
2014 (171)
2012 (171)
2015 (168)
2011 (156)
2008 (110)
2016 (108)
2009 (91)
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2005 (66)
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2023 (34)
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2017 (29)
2024 (28)
2026 (22)
2025 (21)
2019 (21)
2004 (14)
2003 (2)
2002 (1)
1998 (1)

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Transcription profiling of yeast under conditions of ammonium, L-alanine or L-glutamine limitation

Response of Saccharomyces cerevisiae to Ammonium, L-alanine, or L-glutamine Limitation. The protrotophic laboratory strain CEN.PK113-7D (MAT a) was grown in laboratory fermentors with a working volume of 1 litre at dilution rate (D) of 0.20 per hour (in triplicate for each nitrogen limited condition...

ORGANISM(S): Saccharomyces cerevisiae

2006-06-13 | E-MEXP-724 | biostudies-arrayexpress

L-Glutamine metabolism and its regulation in C. glutamicum

Corynebacterium glutamicum, a gram-positive soil bacterium used for the industrial production of amino acids such as L-glutamate and L-lysine, is able to use a number of different nitrogen sources, such as ammonium, urea, or creatinine. In this communication, we show that L-glutamine serves as an ex...

ORGANISM(S): Corynebacterium glutamicum ATCC 13032

2010-10-05 | E-GEOD-19779 | biostudies-arrayexpress

Chromatin immunoprecipitation of Drosophila melanogaster transcription factors BCD, HB, KR, KNI, GT, CAD, HKB, TLL, D, FTZ, HRY, PRD, RUN, SLP1, DA, DL, MAD, MED, SHN, SNA, TWI, TFIIB and RNA polII

ChIP-chip was performed using chromatin isolated from formaldehyde crosslinked, staged embryos, and affinity purified antibodies against 21 transcription factors (including: BCD, HB, KR, KNI, GT, CAD, HKB, TLL, D, FTZ, HRY, PRD, RUN, SLP1, DA, DL, MAD, MED, SHN, SNA, TWI) that belong to 11 DNA bind...

ORGANISM(S): Drosophila melanogaster

2009-07-27 | E-TABM-736 | biostudies-arrayexpress

Engineering Corynebacterium glutamicum for fast production of lysine and pipecolic acid

The Gram-positive soil bacterium Corynebacterium glutamicum is widely used in industrial fermentative processes for the production of amino acids. The world production of L-lysine has surpassed 2 million tons per year. Glucose is taken up into the C. glutamicum cell by the phosphotransferase system ...

ORGANISM(S): Corynebacterium glutamicum

2016-03-30 | E-GEOD-79690 | biostudies-arrayexpress

Transcription profiling of mouse fibroblasts to examine the cellular transformation induced by Rho subfamily GTPases

We have used microarray technology to identify the transcriptional targets of Rho subfamily GTPases. This analysis indicated that murine fibroblasts transformed by these proteins show similar transcriptomal profiles. Functional annotation of the regulated genes indicate that Rho subfamily GTPases ...

ORGANISM(S): Mus musculus

2008-06-14 | E-GEOD-5913 | biostudies-arrayexpress

Metabolomic analysis of alfalfa (Medicago sativa L.) root-symbiotic rhizobia responses under alkali stress

Alkaline salts (e.g., NaHCO3 and Na2CO3) causes more severe morphological and physiological damage to plants than neutral salts (e.g., NaCl and Na2SO4) due to differences in pH. The mechanism by which plants respond to alkali stress is not fully understood, especially in plants having symbotic relat...

2018-07-27 | MTBLS481 | MetaboLights

A nonessential African swine fever virus gene UK is a significant virulence determinant in domestic swine.

Not available

S-EPMC124574 | biostudies-literature

LINT - a novel dL(3)mbt containing complex represses malignant brain tumour signature genes - sequencing data

dLint1 (CG1908) was ChIPseq`d in Drosophila melanogaster KC cells and S2 cells

ORGANISM(S): Drosophila melanogaster

2012-06-27 | E-MTAB-855 | biostudies-arrayexpress

pH stress in Desulfovibrio vulgaris Hildenborough

Using data from microarray experiments, we investigated the effects of excess NaCl on D. vulgaris. Keywords: stress response, time course Comparison of cells treated with pH10 pH to untreated cells at times of 0,120,240,30,60 min.

ORGANISM(S): Desulfovibrio vulgaris str. Hildenborough

2007-08-31 | E-GEOD-8197 | biostudies-arrayexpress

Inhibition of Antiviral Innate Immunity by Foot-and-Mouth Disease Virus L^pro through Interaction with the N-Terminal Domain of Swine RNase L.