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Sample GSM495527 Query DataSets for GSM495527
Status Public on Dec 06, 2010
Title Snf1lk ES clone at T0, biological rep3
Sample type RNA
 
Source name inducible ES cell clone
Organism Mus musculus
Characteristics inducible gene: Snf1lk
cell type: ES cell
Treatment protocol Clones were grown in medium deprived of Tc to perform a time course of induction (24, 39 or 48hrs depending on experiment). In presence of Tc (0 hrs), the expression of each mRNA was indicative of the basal expression level in mES cells.
Growth protocol ES cells were grown in mES media + LIF and supplemented with 1ug/ml tetracycline (Tc) at 37°C in an atmosphere of 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA samples at various times of induction were purified by QIAshredder and extracted with RNeasy Protect Mini Kit using standard conditions. Total RNA were reverse transcribed to single stranded cDNA with a special oligo (dT)24 primer containing a T7 RNA promoter site prior to second strand synthesis (One cycle cDNA synthesis kit by Affymetrix).
Label biotin
Label protocol Biotinylated cRNA were prepared using the GeneChip IVT labelling kit (Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse 430_2 Array (430A_2 in case of Runx1).
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description Gene expression data from ES clone before induction of gene overexpression.
Data processing The data were analyzed using the RMA function of the Affy package of the Bioconductor tool. RMA analysis was performed separately on each set of six arrays relative to a same gene overexpression experiment.
 
Submission date Jan 11, 2010
Last update date Dec 06, 2010
Contact name Mario Lauria
E-mail(s) lauria@tigem.it
Phone +39 081 6132 339
Organization name TIGEM
Street address via P. Castellino 111
City Napoli
ZIP/Postal code 80131
Country Italy
 
Platform ID GPL1261
Series (1)
GSE19836 A mouse Embryonic Stem Cell Bank for inducible overexpression of human chromosome 21 genes

Data table header descriptions
ID_REF
VALUE Base 2 logarithm of RMA signal intensity

Data table
ID_REF VALUE
1415670_at 9.819416541
1415671_at 10.16510486
1415672_at 11.23494657
1415673_at 10.87826437
1415674_a_at 9.822518734
1415675_at 8.391015507
1415676_a_at 11.96598251
1415677_at 7.998528947
1415678_at 10.84967816
1415679_at 10.28969125
1415680_at 9.517051704
1415681_at 10.65391131
1415682_at 9.248114989
1415683_at 11.67411638
1415684_at 8.681854862
1415685_at 9.582391318
1415686_at 8.759767049
1415687_a_at 9.796611903
1415688_at 10.40959708
1415689_s_at 6.899797296

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM495527_hSNF1LK_B3_T0.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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