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Sample GSM1038597 Query DataSets for GSM1038597
Status Public on Dec 20, 2012
Title Day3_Thy- M3 [mRNA]
Sample type RNA
Source name Sorted cells
Organism Mus musculus
Characteristics strain: C57BL6/129
time after induction [days]: 3
cell stage: Intermediates
thy1: NEG
ssea1: NEG
gfp: NEG
Treatment protocol Harvested cells were incubated with antibodies against Thy1.2 (PE conjugated, 53-2.1, eBiosciences) and SSEA-1 (mouse IgM, MC-480, Developmental Hybridoma Bank) for 20 minutes. Cells were washed in PBS and then incubated for 20 minutes with APC conjugated anti mouse IgM, (eBioscience) and Pacific Blue-conjugated streptavidin (Invitrogen). The cells were washed in PBS, resuspended in propidium iodide 5% FBS/PBS solution and passed through a 40mm cell strainer to achieve single cell suspension. Cells were sorted on a FACSAria (BD Biosciences ) and/or analysed in a LSRII (BD Bioscience). For analysis and/or sorting of intermediates, cells were stained with Thy1.2 and SSEA1 antibodies and sorted or analyzed as indicated.
Growth protocol Mouse Embryonic fibroblast (MEFF) cultures were established from E13.5 embryos from a reprogrammable mice strain carrying one copy of the OKSM cassette and Rosa26-M2rtTA allele (het/het) or carrying two copies of the OKSM cassette and Rosa26-M2rtTA allele (ho/ho). Reprogramming was performed in ESC medium (KODMEM with 15% FBS, L-Glutamin, penicillin-streptomycin, non-essential amino acids, b-mercaptoethanol and 1000 U/ml LIF) in the presence of doxycycline.
Extracted molecule total RNA
Extraction protocol iPSCs were harvested when they reached about 50% confluency and preplated on non-gelatinized T25 flasks for 45 minutes to remove feeder cells. Intermidiates cell types were harvest after FACS sorting. Cells were then spun down and the pellet used for isolation of total RNA using the miRNeasy Mini Kit (QIAGEN) without DNase digestion. RNA was eluted from the columns using 50 ml RNase-free water or TE buffer, pH7.5 (10 mM Tris-HCl and 0.1 mM EDTA) and quantified using a Nanodrop (Nanodrop Technologies).
Label biotin
Label protocol Samples were labeled with biotin in the standard way
Hybridization protocol Samples were hybridized to affymetrix MOE430A arrays using the protocol provided by the supplier
Scan protocol Arrays were scanned on an affymetrix scanner in according to the manufacturers protocol
Description Sample name: KH183
Data processing Data were normalized using robust multi array averaging (RMA) and converted to log2 scale
Submission date Nov 19, 2012
Last update date Dec 20, 2012
Contact name Ben S. Wittner
Organization name Massachusetts General Hospital
Department Center for Cancer Research
Lab Lawrence
Street address 149 13th Street
City Boston
State/province MA
ZIP/Postal code 02129
Country USA
Platform ID GPL8759
Series (2)
GSE42379 Defining a molecular roadmap of cellular reprogramming into iPS cells [mRNA profiling]
GSE42478 Defining a molecular roadmap of cellular reprogramming into iPS cells

Data table header descriptions
VALUE log2 RMA signal

Data table
1415670_at 10.64144368
1415671_at 9.596925833
1415672_at 10.30779452
1415673_at 8.51239782
1415674_a_at 9.25074811
1415675_at 9.893877719
1415676_a_at 11.264283
1415677_at 9.157069419
1415678_at 11.47288989
1415679_at 9.947977925
1415680_at 9.901711008
1415681_at 9.17935836
1415682_at 9.04989041
1415683_at 10.75029496
1415684_at 7.73449001
1415685_at 8.978314013
1415686_at 10.77545281
1415687_a_at 10.84991883
1415688_at 10.03250957
1415689_s_at 7.362449128

Total number of rows: 22716

Table truncated, full table size 522 Kbytes.

Supplementary file Size Download File type/resource
GSM1038597_CGCLG_092909_HT_MG-430A_PHY09290901B10_1.CEL.gz 2.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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