Affymetrix GeneChip Human Genome HG-U133A [HG-U133A]

Hypoxia modifies the transcriptome of primary human monocytes: modulation of novel immune-related genes and identification of CC-chemokine ligand 20 as a new hypoxia-inducible gene

HypoxiaDB: a database of hypoxia-regulated proteins.

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Experiment with 6 hybridizations, using 30 samples of species [Homo sapiens], using 6 arrays of array design [Affymetrix GeneChip Human Genome HG-U133A [HG-U133A]], producing 6 raw data files and 6 transformed and/or normalized data files.

growth condition

Transcription profiling by array of human primary monocytes grown in hypoxia

Transcription profiling of effect of hypoxia in human primary monocytes

Experiment with 6 hybridizations, using 30 samples of species [Homo sapiens], using 6 arrays of array design [Affymetrix GeneChip Human Genome HG-U133A [HG-U133A]], producing 6 raw data files and 6 transformed and/or normalized data files.


Affymetrix:Protocol:ExpressionStat

Title: Affymetrix CHP Analysis (ExpressionStat). Description:

Affymetrix:Protocol:Hybridization-EukGE-WS2v4

Title: Fluidics Station Protocol. Description:

Affymetrix:Protocol:Hybridization-Unknown

P-AFFY-2

Labeling of samples was carried out according to the manufacturer’s standard protocol

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-MEXP-12910

Total RNA was purified from different donor-derived Mn using the RNeasy Mini Kit from Qiagen (Milano, Italy). The physical quality control of RNA integrity was carried out by electrophoresis with an Agilent Bioanalyzer 2100 (Agilent Technologies Europe, Waldbroon, Germany). 10 mg RNA from five Mn preparations were pooled, and the RNA pools used for probe synthesis. Briefly, 20 mg of total RNA were reverse transcribed into double-stranded cDNA on a GeneAmp PCR System 2700 thermal cycler (Applied Biosystems, Milano, Italy),  using the SuperScript Double-Stranded cDNA synthesis kit (Invitrogen Life Technologies, Milano, Italy) according to the manufacturer's instructions, except that a T7-(dT)24 primer (HPSF purified) (MWG Biotech, Firenze, Italy) was used in place of the oligo provided with the kit. cDNA was purified and used for in vitro transcription with the BioArray High Efficiency RNA Transcript Labeling kit (Enzo Life Sciences, DBA, Milano, Italy) in the presence of biotin-11-CTP and biotin-16-UTP. 

P-MEXP-12911

10 mg RNA from five Mn preparations were pooled, and the RNA pools used for probe synthesis. 

P-MEXP-12991

Mn were plated in Costar plates (Celbio, Milano, Italy) in RPMI 1640 (Euroclone, Celbio) supplemented with 10% heat-inactivated FCS (HyClone, Celbio), 2 mM L-glutamine, 100 U/ml penicillin, and 100 mg/ml streptomycin (Celbio) and maintained at 37°C in a humidified incubator containing 20% O2, 5% CO2, and 75% N2.

P-MEXP-12992

Mn were plated in Costar plates (Celbio, Milano, Italy) in RPMI 1640 (Euroclone, Celbio) supplemented with 10% heat-inactivated FCS (HyClone, Celbio), 2 mM L-glutamine, 100 U/ml penicillin, and 100 mg/ml streptomycin (Celbio) and maintained at 37 C in a humidified incubator containing 20% O2, 5% CO2, and 75% N2, referred to as normoxic conditions. 

P-MEXP-12993

Hypoxic conditions were achieved by incubating and handling the cells in an humidified anaerobic work station incubator (BUG BOX, ALC International, Cologno Monzese, Milano, Italy) flushed with a mixture of 94% N2, 5% CO2 and 1% O2 (corresponding to a pO2 of 7,6 mm Hg, equivalent to hypoxia which ranges betwen 0-20 mm Hg9-12,16) at 37 C. Culture medium was allowed to equilibrate for 3 hr in a loosely capped flask in the hypoxic incubator before cell exposure. A portable trace oxygen analyzer (Oxi 315i/set, WTW, Germany) was used to monitor O2 tension in culture medium.

Hypoxia modifies the transcriptome of primary human monocytes: modulation of novel immune-related genes and identification of CC-chemokine ligand 20 as a new hypoxia-inducible gene.

Transcription profiling by array of human primary monocytes grown in hypoxia

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