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Sample GSM527046 Query DataSets for GSM527046
Status Public on Oct 22, 2021
Title only LPS (4μg/ml) treatment biol rep 3 tech rep 1
Sample type RNA
 
Source name U937 cell line (human histiocytic lymphoma cell)
Organism Homo sapiens
Characteristics cell line: U937
treatment: only LPS (4μg/ml)
Treatment protocol Human macrophage cells were untreatment, LPS (4μg/ml) only, preteated PBD150 inhibitor (10μM) for 2 hrs before the addition LPS (4μg/ml) treatment, the incubation time of the culture was 48 hours.
Growth protocol The U937 cells were maintained at 2-3 × 106 cells/ml in a RPMI 1640 medium supplemented with 10% FBS, the incubation time of the culture was 48 hours.
Extracted molecule total RNA
Extraction protocol RNA extraction by column based extraction kit (RiboPure-Blood, Ambion). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN>8).
Label Cy5
Label protocol 2.5 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion). Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).
 
Hybridization protocol HOA v4.3 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer.
Scan protocol The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 600~630 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.
Description Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1095 control probes, spotted onto glass slides using a proprietary non-contact printing method.
Data processing The raw data were adjust by Rosetta Resolver® error model calculation. The statistic values were calculated after the replicated probes queezing and median scaling normalization.
 
Submission date Mar 26, 2010
Last update date Oct 22, 2021
Contact name Chen Yi Ling
Organization name Academia Sinica
Department Institute of Biological Chemistry
Lab 501
Street address 128 Academia Road, Section 2
City Taipei
ZIP/Postal code 11529
Country Taiwan
 
Platform ID GPL6254
Series (1)
GSE21082 Glutaminyl cyclase (QC) activity affects gene expression in macrophages during inflammation

Data table header descriptions
ID_REF
VALUE Rosetta software computed normalized signal intensity

Data table
ID_REF VALUE
PH_hs_0000002 1447.47021
PH_hs_0000003 -3.82928634
PH_hs_0000004 120.62252
PH_hs_0000005 10.5305376
PH_hs_0000006 53788.0703
PH_hs_0000007 2027.60706
PH_hs_0000008 304.428253
PH_hs_0000009 768.729248
PH_hs_0000010 17287.3125
PH_hs_0000011 246.031647
PH_hs_0000012 8080.75146
PH_hs_0000013 756.284058
PH_hs_0000014 312.086823
PH_hs_0000015 147.427521
PH_hs_0000016 100.518768
PH_hs_0000017 28.7196484
PH_hs_0000018 21.0610752
PH_hs_0000019 3.82928634
PH_hs_0000020 5780.30762
PH_hs_0000021 215.397354

Total number of rows: 30968

Table truncated, full table size 753 Kbytes.




Supplementary file Size Download File type/resource
GSM527046_H46-0607008417.gpr.gz 2.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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