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Sample GSM486831 Query DataSets for GSM486831
Status Public on Mar 30, 2010
Title erStress_60grandparents_GM12760_4_ug_ml_tunicamycin_8_hours_rep1
Sample type RNA
 
Source name Lymphoblastoid cell lines derived from GM12760
Organism Homo sapiens
Characteristics cell line: lymphoblastoid cell line
coriell cell line repository identifier: GM12760
agent: tunicamycin
dose: 4 ug/ml
time: 8 hours
Biomaterial provider Coriell: GM12760
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12760
Treatment protocol 4 ug/ml tunicamycin 8 hours
Growth protocol The cells were grown at a density of 1 million cells/ ml in RPMI 1640 with 15% FBS, 1% penicillin-streptomycin, 2mM L-glutamine at 37°C in a humidified 5% CO2 chamber.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Rneasy Mini-Kit (Qiagen) as per the manufacturer's instructions
Label biotin
Label protocol Biotinylated cRNA were prepared according to the Ambion MessageAmp Premier RNA Amplification Kit protocol from 500 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Description Gene expression data under ER stress from lymphoblastoid cells of individual GM12760 treated with 4 ug/ml tunicamycin 8 hours.
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix print default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Dec 16, 2009
Last update date Mar 30, 2010
Contact name Renuka Nayak
Organization name HHMI, University of Pennsylvania
Street address 3516 Civic Center Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL570
Series (2)
GSE19519 Expression levels in immortalized B cells from unrelated individuals and twins undergoing ER stress
GSE36911 Gene expression levels in immortalized B cells from 131 unrelated CEPH-Utah grandparents treated under ER stress.

Data table header descriptions
ID_REF
VALUE Log2 transformed MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M)

Data table
ID_REF VALUE ABS_CALL
1007_s_at 8.96178999716207 P
1053_at 10.1747334767598 P
117_at 7.53738615505364 P
121_at 9.06882233727291 P
1255_g_at 3.29850098871632 A
1294_at 9.46204781854967 P
1316_at 6.23980586148875 P
1320_at 3.03067561033136 A
1405_i_at 10.8719167853321 P
1431_at 4.72312055349599 P
1438_at 2.4814082246581 A
1487_at 9.82269223209517 P
1494_f_at 6.90590201087657 P
1552256_a_at 11.8793879671635 P
1552257_a_at 9.54411169676724 P
1552258_at 5.38783329769676 A
1552261_at 5.15404603533988 A
1552263_at 9.47447133141396 P
1552264_a_at 9.42351661479223 P
1552266_at 3.20265044610993 A

Total number of rows: 54675

Table truncated, full table size 1588 Kbytes.




Supplementary file Size Download File type/resource
GSM486831.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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