Comment[GEAAccession]	E-GEAD-547
MAGE-TAB Version	1.1
Investigation Title	Expression profile (Illumina Human-6 v2 chip) of THP-1 knocked down by siRNA
Experiment Description	We analyzed expression profiles of THP-1 cells which knocked down with siRNAs, and used 3 biological replicas for each analysis.
Experimental Design	development or differentiation design
Experimental Factor Name	treatment
Experimental Factor Type	treatment
Person Last Name	Kasukawa
Person First Name	Takeya
Person Affiliation	RIKEN
Person Roles	submitter
Public Release Date	2022-09-29
PubMed ID	19377474
Protocol Name	P-GEAD-1462	P-GEAD-1463	P-GEAD-1464	P-GEAD-1465	P-GEAD-1466	P-GEAD-1467	P-GEAD-1468	P-GEAD-1469
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol	growth protocol	treatment protocol
Protocol Description	missing	Total RNAs were extracted with FastPure RNA kit (TAKARA bIO, Ohtsu, Shiga, Japan) at 48 hr after transfection.	RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion).	Add Hybridization mix to the labeled cRNA, the samples were applied to the arrays. The beadChip was hybridized at 55degree C for 16-20 hours. Then, beadChip was washed and detected signal with streptavidin-Cy3. All steps were done according to the manufacturer's instructions.	The beadChip was scanned on the Illumina beadArray Reader. After scanning, the images were analyzed using Illumina beadStudio Software version 3.1.7	missing	THP-1 cells were maintained in RPMI1640, 1 mM sodium pyruvate, 10 mM HEPES supplemented with 0.001%(v/v) 2-mercaptoethanol, 10 microg/ml Penicillin/Streptomycin (Invitrogen) and 10% fetal bovine serum at 37degree C in a 5% CO2 and 95% atmosphere.	THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth  MYb siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth MYbL2 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth CbFb siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth TCFL5 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth FOxD1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth FOxP1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth FOxJ3 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth MxI1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth RUNx1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth GFI1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth PCGF4(bMI1) siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth CEbPA siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth CEbPG siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth CEbPD siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth ZNF238 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth UHRF1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth IRF8 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth IRx3 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth YY1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth LMO2 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth CEbPb siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth SPI1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth SP1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth NFKb1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth GATA2 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth NFYA siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth NRAS siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of  Stealth RNAi Negative Control Duplexes (Cat. No. 12935-300, Invitrogen) THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth E2F1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth EGR1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth SREbP1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth bCL6 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth CTCF siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth CR595356(anti-GATA2) siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth ETS1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth ETS2 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth FLI1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth HOxA9 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth HOxA10 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth HOxA11 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth HOxA13 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth ID1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth IRF7 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth MAFb siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth NFE2L1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth NOTCH1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth PTTG1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth SbAI1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth SNAI3 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth STAT1 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth TRIM28 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth MLL siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth MLLT3 siRNA. THP-1 cells were seeded in 6 cm dishes at a density of 1 ~ 106 cells/dish for transfection. Transfection was performed with 1.6 microg/ml (final concentration) of Lipofectamine 2000 (Invitrogen) and 20 microM (final concentration) of stealth MYC siRNA.
SDRF File	E-GEAD-547.sdrf.txt
Comment[Number of channel]	single-channel
Comment[CIBEX Submitter]	Mutsumi Kanamori-Katayama, Yoshihide Hayashizaki, Harukazu Suzuki, Yasuhiro Tomaru, Christophe Simon, Asami Hirakiyama, Ai Kaiho, Fumi Hori, Jun Kawai, Katharine Irvine, Kate Schroder, David Hume
Comment[Array Design REF]	A-MEXP-930
Comment[AEExperimentType]	transcription profiling by array
Comment[SecondaryAccession]	CBX47
Comment[BioProject]	PRJDB14411
Comment[CIBEX Accept Date]	2010-01-01
Comment[CIBEX Public Release Date]	2009-04-17
Comment[Last Update Date]	2022-09-30