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Sample GSM1421111 Query DataSets for GSM1421111
Status Public on Sep 02, 2014
Title PD-His-1
Sample type RNA
 
Source name Human Heptoma (HepG2)
Organism Homo sapiens
Characteristics cell line: HepG2
treatment: 2.5M PD98059-depleted for Histidine
Treatment protocol The MEK inhibitor PD98059 (Sigma-Aldrich, St. Louis, MO) was diluted in dimethyl sulfoxide (DMSO). Cells were pre-treated with an equal volume of DMSO (control) or PD98059 for 1 h prior to activation of the AAR for the indicated times in the continued presence of inhibitor
Growth protocol All of the cell lines used in these studies were cultured in Dulbecco’s modified Eagle’s medium (DMEM, pH 7.4, Mediatech, Herndon, VA), supplemented with 1X non-essential AA, 2 mM glutamine, 100 μg/ml streptomycin sulfate, 100 U/ml penicillin G, 0.25 μg/ml amphotericin B, and 10% v/v fetal bovine serum.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Qiagen RNeasy kit (Qiagen), including DNase I treatment before the final elution to eliminate any DNA contamination, following the manufacturer’s directions.
Label biotin
Label protocol A 100 ng aliquot of total RNA from four independent incubations for each of four conditions (DMEM vs DMEM lacking histidine, each with or without 2.5 uM PD98059) was amplified using the GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) following the manufacturer’s instructions and then 5.5 ug of cDNA was fragmented and terminally labeled.
 
Hybridization protocol Labeled targets were hybridized to Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA 2.0) for 16 h at 45°C and washed according to Affymetrix standard protocols.
Scan protocol The Genechips were scanned with an Affymetrix G7 scanner.
Description 2.5M PD98059-depleted for Histidine
Data processing For gene expression analysis, arrays were normalized using RMA as implemented in Partek Genomics Suite 6.6 (Partek Incorporated, St Louis MO).
probe group file:HTA-2_0.r1.pgf
meta-probeset_file: HTA-2_0.na33.1.hg19.transcript.csv
 
Submission date Jun 26, 2014
Last update date Sep 02, 2014
Contact name Michael Kilberg
E-mail(s) mkilberg@ufl.edu
Organization name University of Florida
Department Biochemistry & Molecular Biology
Lab Kilberg
Street address 1600 SW Archer Road
City Gainesville
State/province Florida
ZIP/Postal code 32610
Country USA
 
Platform ID GPL17586
Series (1)
GSE58869 HepG2-MEK Inhibition with PD98059

Data table header descriptions
ID_REF
VALUE RMA signal with quantile normalization from Partek Genomics Suite 6.6

Data table
ID_REF VALUE
2824546_st 13.249
2824549_st 12.5054
2824551_st 13.1661
2824554_st 12.9913
2827992_st 12.3179
2827995_st 12.2161
2827996_st 12.3968
2828010_st 10.4451
2828012_st 11.1051
2835442_st 11.5995
2835447_st 9.99758
2835453_st 11.6388
2835456_st 13.5907
2835459_st 12.4916
2835461_st 11.6127
2839509_st 13.3645
2839511_st 12.7667
2839513_st 13.1111
2839515_st 11.9282
2839517_st 13.1742

Total number of rows: 70459

Table truncated, full table size 1653 Kbytes.




Supplementary file Size Download File type/resource
GSM1421111_7097_2d5H1_HTA-2_0_.CEL.gz 27.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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