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Sample GSM1082435 Query DataSets for GSM1082435
Status Public on Feb 13, 2013
Title Oct4_shutdown_Day3
Sample type RNA
 
Channel 1
Source name Oct4_shutdown_Day3
Organism Mus musculus
Characteristics cell type: V6.5 embryonic stem cells
background strain: C57BL/6-129
treatment: shRNA knockdown of Oct4
Growth protocol V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy5
Label protocol Cy-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 1 µg total RNA. Briefly, first and second strand cDNA are generated using MMLV-RT enzyme and an oligo-dT based primer. In vitro transcription is performed using T7 RNA polymerase and either cyanine 3-CTP or cyanine 5-CTP, creating a direct incorporation of dye into the cRNA.
 
Channel 2
Source name Embyonic stem cells
Organism Mus musculus
Characteristics cell type: V6.5 embryonic stem cells
background strain: C57BL/6-129
treatment: none
Growth protocol V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy3
Label protocol Cy-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 1 µg total RNA. Briefly, first and second strand cDNA are generated using MMLV-RT enzyme and an oligo-dT based primer. In vitro transcription is performed using T7 RNA polymerase and either cyanine 3-CTP or cyanine 5-CTP, creating a direct incorporation of dye into the cRNA.
 
 
Hybridization protocol Agilent (mouse 4x44k) expression arrays were hybridized according to our lab’s method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail consisted of 825 ng / 1.65 ug cy-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 60°C in an Agilent rotor oven set to maximum speed.
Scan protocol Arrays were scanned using an Agilent scanner G2565BA and the data was extracted using Agilent’s Feature Extraction software v10.1.1.1.
Data processing Data was extracted using Agilent’s Feature Extraction software v10.1.1.1 set to the default two-color gene expression protocol.
 
Submission date Feb 13, 2013
Last update date Feb 13, 2013
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL4134
Series (2)
GSE44287 Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes [gene expression]
GSE44288 Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

Data table header descriptions
ID_REF
VALUE normalized log10 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
1 1.26E-01
2 0.00E+00
3 0.00E+00
4 0.00E+00
5 0.00E+00
6 0.00E+00
7 0.00E+00
8 0.00E+00
9 0.00E+00
10 0.00E+00
11 0.00E+00
12 0.00E+00
13 8.45E-02
14 2.16E-02
15 5.34E-01
16 3.72E-03
18 2.71E-02
19 0.00E+00
20 0.00E+00
21 -3.71E-01

Total number of rows: 45018

Table truncated, full table size 664 Kbytes.




Supplementary file Size Download File type/resource
GSM1082435_Oct4_Day3_agilent.txt.gz 14.4 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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