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Sample GSM67129 Query DataSets for GSM67129
Status Public on Jun 30, 2006
Title Unstaged Head Hair Follicles Plucked from woman (27F)
Sample type RNA
 
Source name Human Unstaged Head Hair Follicles
Organism Homo sapiens
Characteristics Individual hairs were grasped as near to the scalp as possible and then yanked quickly out. The bottom centimeter of each hair, containing the hair follicle, was trimmed off into a 5ml specimen jar filled to the top with RNALater (Ambion, Austin, Texas). Samples were stored at ambient temperature until reaching the analytical laboratory, a period of 1-4 hr.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted on the day of collection or following storage at 4oC for 1-9 days in RNAlater. The hair follicle samples from each individual were removed from RNALater and, without verifying their stage, placed directly into a 2 ml microcentrifuge tube containing 1 ml Trizol™. RNA extraction was then conducted according to manufacturer’s instructions (Invitrogen Life Technologies, CA); a handheld homogenizer (Fisher Scientific, Hampton NH) was used to break up the samples. At the isopropanol precipitation step, RNA was pelleted either immediately or following storage at -80oC for up to seven months. After centrifugation, the pellet was washed with 70% ethanol, air dried and resuspended in 10 µl RNA free water (Gibco-BRL, Gaithersburg, MD). Concentration of the eluted RNA was quantified using GeneQuant spectrophotometer (Pharmacia Biotech, now Amersham Pharmacia Biotech, Piscataway, NJ) by absorbance readings at 260 and 280nm.
Label biotin: double amplication using MessageAmp aRNA Kit (Ambion)
Label protocol Briefly, first and second strand cDNA were synthesized. Unlabelled aRNA was generated by in vitro transcription with unbiotinylated NTPs. For probe preparation, aRNA was reverse transcribed with second round primers. Second-strand cDNA was synthesized with T7 Oligo(dT) primer and purified. Biotin-labeled cRNA was generated by in vitro synthesis transcription, and purified with Qiagen RNeasy kit.
 
Hybridization protocol Each labeled cRNA was then fragmented, added to a hybridization solution, and hybridized for 16 hours to a HG-Focus genechip (Affymetrix, Santa Clara, CA) in an Affymetrix Fluidics Station 400.
Scan protocol The chips were washed, stained with phycoerythrin-conjugated streptavidin and amplified by biotinylated anti-streptavidin. After a final wash the arrays were scanned in a GCS3000 (Affymetrix, Santa Clara, CA).
Description Healthy adult female
Data processing Affymetrix Microarray Suite version 5.0
 
Submission date Aug 04, 2005
Last update date Dec 27, 2005
Contact name David J Dix
E-mail(s) [email protected]
Phone 919-541-2701
Fax 919-541-4017
Organization name US EPA
Department NHEERL
Lab RTD
Street address E. HWY54 US EPA
City RTP
State/province NC
ZIP/Postal code 27711
Country USA
 
Platform ID GPL201
Series (1)
GSE3058 Gene Expression in Unstaged Head Hair Follicles Plucked from Men and Women

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-5_at 4873.5 P
AFFX-BioB-M_at 8012.8 P
AFFX-BioB-3_at 6478.4 P
AFFX-BioC-5_at 16588.6 P
AFFX-BioC-3_at 12499 P
AFFX-BioDn-5_at 28236.8 P
AFFX-BioDn-3_at 53347.7 P
AFFX-CreX-5_at 132338.4 P
AFFX-CreX-3_at 166346.3 P
AFFX-HUMISGF3A/M97935_5_at 16.3 A
AFFX-HUMISGF3A/M97935_MA_at 35.1 A
AFFX-HUMISGF3A/M97935_MB_at 8.4 A
AFFX-HUMISGF3A/M97935_3_at 361.6 P
AFFX-HUMRGE/M10098_5_at 190.9 A
AFFX-HUMRGE/M10098_M_at 127.3 A
AFFX-HUMRGE/M10098_3_at 300.3 A
AFFX-HUMGAPDH/M33197_5_at 539.6 P
AFFX-HUMGAPDH/M33197_M_at 2246.4 P
AFFX-HUMGAPDH/M33197_3_at 6778.6 P
AFFX-HSAC07/X00351_5_at 345.3 P

Total number of rows: 8793

Table truncated, full table size 158 Kbytes.




Supplementary file Size Download File type/resource
GSM67129.CEL.gz 1.2 Mb (ftp)(http) CEL
GSM67129.EXP.gz 496 b (ftp)(http) EXP

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