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Sample GSM460416 Query DataSets for GSM460416
Status Public on Dec 31, 2013
Title Liver_F
Sample type RNA
 
Source name pooled Human liver total RNA
Organism Homo sapiens
Characteristics tissue: liver
race: caucasian
Extracted molecule total RNA
Extraction protocol Samples of total RNA from Human tissues were purchased from several companies (Clontech, Ambion, Stratagene, Cell Applications). HeLa and SH-SY5Y cells were cultured in standard DMEM / 10% FBS medium. Total RNA was extracted from cells with TRIzol regent (Invitrogen). Additionally, total RNA was purified with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.
Label biotin
Label protocol Reverse transcription, amplification, fragmentation and labeling steps were performed according to Affymetrix protocol using WT Amplified Double-Strand cDNA Synthesis Kit (Affymetrix) and WT Double-Strand DNA Terminal Labeling Kit (Affymetrix).
 
Hybridization protocol Approximately 6.0μg of DNA was hybridized per array using the Affymetrix hybridization kit. For these 14 array sets, 7 arrays were hybridized for 16 hours at 45°C at 60rpm using an Affymetrix hybridization oven. The hybridized solution was removed from these arrays and reused to hybridize the remaining seven arrays.
Scan protocol Arrays were scanned on an Affymetrix Scanner 3000 7G. Images were quantified using GCOS software (Affymetrix). Signal values ware exported to text files using GCOS Manager software (Affymetrix).
Description liver Human Tiling 1.0R chip F
Data processing The ".CEL" files are raw data. The "normalized.txt" files (supplementary data linked to GSE18490) are data normalized as follows.

1) To exclude potential low quality probes, we excluded probes that corresponded to the following conditions: A) probes for which either the Perfect Match (PM) or Miss Match (MM) probe perfectly match more than once in the genome, B) probes which contain SNPs, C) probes located on sex chromosomes.
2) To reduce inter-chip differences, we equalized the mean and variance of probe intensities among all chips in each tissue. Note that the intensities were converted to a logarithmic scale (base 2).
3) To reduce background noise, we subtracted the intensity of each MM probe from the PM probe in each probe set. If the value was negative, zero was assigned as the value.
4) To adjust for GC content of probes, we calculated normalized intensities by each GC content.
5) To equalize the distribution of signals in each chip, we performed quantile normalization for each chip
6) To smooth the probe intensities with neighboring probes, we calculated Hodges-Lehmann statistics. The size of each sliding window was 101bp.
7) All probes that ranked higher than the top 15% signal threshold were selected and those with an inter-probe distance less than a maximum gap threshold of 25bp were concatenated. Then, the concatenated probes with length longer than a minimum run threshold of 101bp were defined as transfrags. Finally, we performed BLAST to exclude probes that mapped to multiple locations.
 
Submission date Oct 09, 2009
Last update date Dec 31, 2013
Contact name Fuyuki Miya
E-mail(s) fmiya@keio.jp
Phone +81-3-5363-3890
Organization name Keio University
Department School of Medicine
Lab Center for Medical Genetics
Street address 35 Shinanomachi, Shinjuku-ku
City Tokyo
State/province Tokyo
ZIP/Postal code 160-8582
Country Japan
 
Platform ID GPL6161
Series (2)
GSE18490 Whole genome transcriptional profile of human tissues and cells
GSE18676 Whole genome expression in human tissues

Supplementary file Size Download File type/resource
GSM460416_Liver_F.CEL.gz 37.3 Mb (ftp)(http) CEL
Processed data are available on Series record
Processed data included within Sample table

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