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Sample GSM1229965 Query DataSets for GSM1229965
Status Public on Dec 01, 2013
Title ABAH_4h
Sample type RNA
 
Source name HL-60 cells, ABAH exposed, 4h
Organism Homo sapiens
Characteristics cell line: HL-60
Treatment protocol 1, 2, 4-benzenetriol (BT) exposure: For control or BT exposure sample, HL-60 cells suspended in RPMI 1640 supplemented with 10% heat-inactivated FBS at 4×10^5/mL were exposed to BT (0 or 50μM) at 37℃ in 5% CO2 for 1 hour or 4 hours. For 4-aminobenzoic acid hydrazine (ABAH, MPO inhibitor) treatment sample, HL-60 cells suspended in RPMI 1640 supplemented with 10% heat-inactivated FBS at 4×10^5/mL were treated with ABAH (100μM) and preincubated at 37℃ in 5% CO2 for 24 hours. After the pretreatment of ABAH, media was then replaced with new media containing the reagent plus 50μM of BT.
Growth protocol HL-60, a human promyelocytic cell line, was cultured in RPMI-1640 medium (SIGMA-Aldrich, St. Louis, MO) with 10 % of heat-inactivated fetal bovine serum (FBS) (Nichirei Bioscience, Tokyo, Japan) at 37℃ in a humidified atmosphere with 5 % CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)
Label Cy3
Label protocol cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).
 
Hybridization protocol cRNA was hybridized to a 44K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8×60K v2; Agilent Technologies) according to the manufacturer's instructions.
Scan protocol The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).
Data processing The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities were normalized by the quantile algorithm with the Bioconductor.
 
Submission date Sep 12, 2013
Last update date Dec 01, 2013
Contact name Takuro Nishikawa
E-mail(s) adu44150@ams.odn.ne.jp
Organization name Kagoshima University
Department Pediatrics
Street address Sakuragaoka 8-35-1
City Kagoshima
ZIP/Postal code 890-8520
Country Japan
 
Platform ID GPL17077
Series (1)
GSE50805 The effect of MPO inhibitor on the gene expression profiles in HL-60 cell lines exposed to 1, 2, 4,-benzenetriol

Data table header descriptions
ID_REF
VALUE quantile normalized signal, non-log scaled
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
A_19_P00315452 7.346473125 A
A_19_P00315459 154.3893125 P
A_19_P00315482 15.92113 P
A_19_P00315492 11.66512538 A
A_19_P00315493 4.542386875 A
A_19_P00315502 2.4515655 A
A_19_P00315506 14.25438375 P
A_19_P00315518 2.604159125 A
A_19_P00315519 2.664096375 A
A_19_P00315524 11.4017565 A
A_19_P00315528 42.3983425 P
A_19_P00315529 35.94249902 P
A_19_P00315538 2.548728375 A
A_19_P00315541 17.4978825 P
A_19_P00315543 25.8202575 P
A_19_P00315550 116.4255213 P
A_19_P00315551 228.3438125 P
A_19_P00315554 6.065928191 A
A_19_P00315581 2151.922 P
A_19_P00315583 27.44503375 P

Total number of rows: 50599

Table truncated, full table size 1323 Kbytes.




Supplementary file Size Download File type/resource
GSM1229965_253949414986_S01_GE1_107_Sep09_2_3.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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