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Sample GSM1411108 Query DataSets for GSM1411108
Status Public on Dec 31, 2015
Title siRNA against Sat III transfection, heat shock treatment followed by recovery, replicate 1
Sample type RNA
 
Source name HEK293T cells, siRNA against Sat III, heat shock followed by recovery
Organism Homo sapiens
Characteristics cell line: HEK293T
sirna: against Sat III
treatment: heat shock followed by recovery
Treatment protocol Heat shocks were performed for 1 h at 42 °C by submersion in a water bath. Recovery was for 6 h.
Growth protocol Human HEK293T cells were cultured in Dulbecco's Modified Eagle's medium. The media were supplemented with 10% fetal calf serum, 2 mM L-glutamine and antibiotics (penicillin and streptomycin), and the cells were cultured in a humidified 5% CO2 atmosphere at 37°C.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from HEK293T cells using the RNeasy kit (Qiagen).
Label Biotin
Label protocol To synthesize the biotinylated cRNA, 300 ng of total RNA was amplified using Ambion's Illumina TotalPrep RNA Amplification kit (cat #AMIL1791).
 
Hybridization protocol From each sample, 750 ng cRNA was hybridized to Illumina's HumanHT-12 Expression BeadChip, version 3 (cat no BD-103-0203) at 58°C overnight (19 h) according to Illumina Whole-Genome Gene Expression Direct Hybridization protocol, revision A.
Scan protocol The chips were scanned with Illumina BeadArray Reader, BeadScan software version 3.5, and numerical results were extracted with Illumina's GenomeStudio v1.0 software without any normalization.
Description siRNA III 1h HS 6hR 1
Replicate 1
Data processing The gene expression microarray data was analyzed using R and Bioconductor softwares. The data was quantile normalized.
The Sample data table and non-normalized data matrix do not include values for the control probes.
 
Submission date Jun 12, 2014
Last update date Dec 31, 2015
Contact name Lea Sistonen
Organization name Åbo Akademi
Department Department of Biosciences
Street address Tykistökatu 6 B
City Turku
ZIP/Postal code 20520
Country Finland
 
Platform ID GPL6947
Series (1)
GSE58439 Long non-coding Satellite III RNAs link the heat shock response and cell proliferation

Data table header descriptions
ID_REF
VALUE Quantile-normalized signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 49.78616182 0.4729908
ILMN_2055271 68.09864909 0.01844532
ILMN_1736007 52.52997364 0.3254282
ILMN_2383229 46.01497409 0.7760211
ILMN_1806310 53.09286 0.28722
ILMN_1779670 57.54465 0.115942
ILMN_2321282 42.16112591 0.9499341
ILMN_1671474 53.57455273 0.2727273
ILMN_1772582 57.14106864 0.1317523
ILMN_1735698 52.18790318 0.342556
ILMN_1653355 63.12269818 0.04347826
ILMN_1717783 44.89859773 0.8432148
ILMN_1705025 54.83189455 0.2068511
ILMN_1814316 48.08654818 0.6113307
ILMN_2359168 52.72759773 0.3109354
ILMN_1731507 50.02167227 0.4611331
ILMN_1787689 45.40410409 0.8115942
ILMN_1745607 40.73276273 0.9749671
ILMN_2136495 50.76687136 0.43083
ILMN_1668111 47.34347227 0.6785244

Total number of rows: 48803

Table truncated, full table size 1585 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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