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Sample GSM874478 Query DataSets for GSM874478
Status Public on Feb 28, 2012
Title HNRPA2B1_KD_2
Sample type RNA
 
Channel 1
Source name MDA-MB-231
Organism Homo sapiens
Characteristics transfection: siRNA transfection (set 2)
Growth protocol MDA-MB-231 cells at 80% confluency were transfected with siRNA (Dharmacon) and control oligo (Invitrogen) using Lipofectamin 2000 reagent (Invitrogen) according to manufacturer’s recommendations. Experiments were performed in duplicates for each set.
Extracted molecule total RNA
Extraction protocol Forty-eight hours post-transfection, total RNA was extracted using Norgen Biotek Total RNA Purification Kit.
Label Cy3
Label protocol 200ng of total RNA were labeled using Low Input Quick Amp Labeling Kits per manufacturer's instructions
 
Channel 2
Source name MDA-MB-231
Organism Homo sapiens
Characteristics transfection: BLOCK-it control transfection
Growth protocol MDA-MB-231 cells at 80% confluency were transfected with siRNA (Dharmacon) and control oligo (Invitrogen) using Lipofectamin 2000 reagent (Invitrogen) according to manufacturer’s recommendations. Experiments were performed in duplicates for each set.
Extracted molecule total RNA
Extraction protocol Forty-eight hours post-transfection, total RNA was extracted using Norgen Biotek Total RNA Purification Kit.
Label Cy5
Label protocol 200ng of total RNA were labeled using Low Input Quick Amp Labeling Kits per manufacturer's instructions
 
 
Hybridization protocol Agilent Gene Expression Hybridization Kit was used to gybridize labeled samples.
Scan protocol Scanned on an Agilent G2505B scanner.
Images were quantified using Agilent Feature Extraction Software (version 9).
Description set 2 of 3.
Data processing Agilent Feature Extraction Software (v 9) was used for background subtraction and LOWESS normalization. In house scripts were then used for downstream processing of the data. GSE35757_HNRNPA2B1_KD_processed.txt: Average LOWESS-normalized log10 ratio (siRNA/BLOCK-it control)
 
Submission date Feb 13, 2012
Last update date Feb 28, 2012
Contact name Hani Goodarzi
Organization name UCSF
Department Biochemistry and Biophysics
Street address 600 16th St, GH S312D
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL4133
Series (2)
GSE35757 siRNA-mediated HNRPA2B1 knock-down in MDA-MB-231 cells
GSE35800 Systematic Discovery of Structural Elements Governing Mammalian mRNA Stability

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 -2.194767339e-001
2 -2.630526561e-001
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 -2.655431072e-002
13 -2.188055433e-001
14 3.156040865e-002
15 -8.711915698e-002
16 1.208136691e-001
17 -2.666284352e-001
18 -1.492657311e-001
19 5.752539626e-002
20 -1.600604328e-001

Total number of rows: 45015

Table truncated, full table size 1019 Kbytes.




Supplementary file Size Download File type/resource
GSM874478_HNRPA2B1_KD_2.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data are available on Series record
Processed data included within Sample table
Processed data provided as supplementary file

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