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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 09, 2008 |
| Title |
BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse ES cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
We used BAF250b-/- ES cells, two independently derived clones, at 18 and 72 hr in culture and compared them with parental cell line (wild-type) at the same time in culture (two replications each). Total RNAs were extracted using Trizol (Invitrogen) according to manufacturer protocol. 2.5 ug of total RNA samples were labeled with Cy3-CTP using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent). A reference target (Cy5-CTP-labeled) was prepared from the Universal Mouse Reference RNA (Stratagene). Labeled targets were purified using an RNeasy Mini Kit (Qiagen) according to the Agilent's protocol, quantitated by a NanoDrop scanning spectrophotometer (NanoDrop Technologies), and hybridized to the NIA Mouse 44K Microarray v2.2 (whole genome 60-mer oligo; manufactured by Agilent Technologies, #014117) (Carter et al. 2005) according to the Agilent protocol (G4140-90030; Agilent 60-mer oligo microarray processing protocol - SSC Wash, v1.0). All hybridizations were carried out in the two color protocol by combining one Cy3-CTP-labeled experimental target and Cy5-CTP-labeled reference target. Microarrays were scanned on an Agilent DNA Microarray Scanner, using standard settings, including automatic PMT adjustment.
Keywords: genetic modification design,time series design
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| Overall design |
Biological replications were performed on BAF250b-/- ES cells with their parental line (wild-type) at 18 and 72 hrs after passaging, as well as with 12 other pluripotent cells (ES and EG cells from strains C57BL/6 and 129 data from Sharova et al., 2007) using whole-genome mouse microarrays (NIA 44k V2.2 with 60-mer synthesized oligos).
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| Contributor(s) |
Yan Z, Wang Z, Sharova L, Sharov AA, Ling C, Piao Y, Aiba K, Matoba R, Wang W, Ko MS |
| Citation(s) |
18323406 |
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| Submission date |
Sep 10, 2007 |
| Last update date |
Jan 17, 2013 |
| Contact name |
Minoru S.H. Ko |
| E-mail(s) |
[email protected]
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| Phone |
410-558-8359
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| Organization name |
NIH
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| Department |
National Institute on Aging
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| Lab |
Lab of Genetics
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| Street address |
251 Bayview Blvd, Suite 100, 10C
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
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| Platforms (1) |
| GPL4358 |
NIA Mouse 44K Microarray v2.2 (Whole Genome 60-mer Oligo) |
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| Samples (12)
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| GSM228402 |
BAF250b WT #3A (18 hrs) Repl#1 (251411710234) |
| GSM228403 |
BAF250b WT #3A (18 hrs) Repl#2 (251411710235) |
| GSM228404 |
BAF250b WT #3A(72 hrs) Repl#1 (251411710236) |
| GSM228405 |
BAF250b WT #3B(72 hrs) Repl#2 (251411710237) |
| GSM228406 |
BAF250b-/- #4A(18 hrs) Repl#1 (251411710238) |
| GSM228407 |
BAF250b-/- #4B(18 hrs) Repl#2 (251411710239) |
| GSM228408 |
BAF250b-/- #4A(72hrs) Repl#1 (251411710240) |
| GSM228409 |
BAF250b-/- #4B(72hrs) Repl#2 (251411710241) |
| GSM228410 |
BAF250b-/- #7A(18hrs) Repl#1 (251411710243) |
| GSM228411 |
BAF250b-/- #7B(18hrs) Repl#2 (251411710244) |
| GSM228412 |
BAF250b-/- #7A(72hrs) Repl#1 (251411710245) |
| GSM228413 |
BAF250b-/- #7B(72hrs) Repl#2 (251411710246) |
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| Relations |
| BioProject |
PRJNA102469 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE8996_RAW.tar |
411.8 Mb |
(http)(custom) |
TAR (of TIFF, TXT) |
| Processed data included within Sample table |
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