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Sample GSM1397832 Query DataSets for GSM1397832
Status Public on Jun 21, 2014
Title MCF-7_siSMRT_24h_E2_rep2
Sample type RNA
 
Source name SMRT-depleted MCF-7_Estradiol treated for 24 h
Organism Homo sapiens
Characteristics cell line: MCF-7
cell type: breast cancer cell line
transfected with: SMRT-targeting siRNA
treated with: 1 nM estradiol (E2) for 24hrs
Treatment protocol Cells were plated DME supplemented with 10% FBS 24 h prior to transfection. The transfection was conducted in Opti-MEM using oligofectamine. Media was changed after transfection to phenol red-free DME medium supplemented with 10% charcoal stripped fetal bovine serum and 1% L-Glutamine. After 48 h cells were treated with vehicle (0.1% EtOH) or 1 nM E2 for an additional 4 or 24 h.
Growth protocol We routinely grow MCF-7 cells in Dublecco's Modified Eagle Medium (DME) supplemented with 10% fetal bovine serum (FBS).
Extracted molecule total RNA
Extraction protocol RNA was isolated using the RNeasy kit from Qiagen.
Label biotin
Label protocol Fragmentation of single-stranded cDNA used UDG and APE 1 enzymes, this breaks DNA at points at which dUTP was added during the second cycle of reverse transcription. Followed by terminal labeling with terminal deoxyucleotidyl transferase and Affymetrix proprietary DNA Labeling Reagent.
 
Hybridization protocol Arrays were hybridized for 17 h at 45°C at 60rpm rotation in Affymetrix GeneChip Hybridization Oven 640. Arrays were washed using fluidics script FS450_00070 and stained with streptavidin, R-phycoerythrin conjugate stain using Affymetrix GeneChip Fluidics Station 450. Signal amplification was done using biotinylated anti-streptavidin.
Scan protocol Arrays were scanned on Affymetrix GeneChip Scanner 300 and analyzed using Affymetrix GeneChip Operating System.
Description SMRT_KD_24h_E2_rep2
Data processing Data analysis was performed using GeneChip Operating Software (GCOS) with the RMA alogrithm.
 
Submission date May 23, 2014
Last update date Jun 21, 2014
Contact name Carolyn L Smith
E-mail(s) carolyns@bcm.edu
Organization name Baylor College of Medicine
Department Molecular and Cellular Biology
Street address One Baylor Plaza
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
 
Platform ID GPL6244
Series (1)
GSE57935 Expression data for Control and SMRT-Depleted MCF-7 Cells

Data table header descriptions
ID_REF
VALUE RMA scores

Data table
ID_REF VALUE
7892501 201.0313931
7892502 32.47559381
7892503 18.38423195
7892504 1008.280967
7892505 11.46355812
7892506 22.72219023
7892507 21.65582156
7892508 57.19701689
7892509 5119.900295
7892510 16.48122988
7892511 10.25953188
7892512 169.8273491
7892513 17.47363676
7892514 2224.815522
7892515 684.0580742
7892516 48.09229936
7892517 48.94097711
7892518 9.372377083
7892519 72.87413758
7892520 789.8456817

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM1397832_siSMRT_24h_E2_rep2.cel.gz 6.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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