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Sample GSM1040697 Query DataSets for GSM1040697
Status Public on Dec 20, 2012
Title Day6_Thy+ M2 [miRNA]
Sample type RNA
 
Channel 1
Source name Sorted cells
Organism Mus musculus
Characteristics strain: C57BL6/129
time after induction [days]: 6
cell stage: Intermediates
thy1: POS
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 RNA was isolated using the miRNeasy Mini Kit (QIAGEN)
Label Cy5
Label protocol Each sample was labeled using the miRCURY™ Hy3™/Hy5™ power labelling kit
 
Channel 2
Source name a pool of all the samples
Organism Mus musculus
Characteristics strain: C57BL6/129
sample type: reference
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 RNA was isolated using the miRNeasy Mini Kit (QIAGEN)
Label Cy3
Label protocol Each sample was labeled using the miRCURY™ Hy3™/Hy5™ power labelling kit
 
 
Hybridization protocol Each hybridized on Exiqon BWA 0.5.9 arrays against a pool of all the samples.
Scan protocol Samples were scanned as a service by Exiqon using their inhouse protocol
Description Sample 6
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.
Data processing Samples were loess normalized and probes with more than 3 missing values were removed from further consideration. Other missing data were imputed using a KNN method
 
Submission date Nov 23, 2012
Last update date Dec 20, 2012
Contact name Ben S. Wittner
E-mail(s) wittner.ben@mgh.harvard.edu
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 GPL14957
Series (2)
GSE42475 Defining a molecular roadmap of cellular reprogramming into iPS cells [miRNA profiling]
GSE42478 Defining a molecular roadmap of cellular reprogramming into iPS cells

Data table header descriptions
ID_REF
VALUE log2 (Cy5/Cy3) ratio

Data table
ID_REF VALUE
9064 -4.31
8421 0.96
9013 1.16
8665 0.82
7609 1.13
7767 0.99
7028 -2.42
9199 1.01
7474 0.95
8561 0.87
7613 -2.56
8642 1.16
8442 0.85
7892 1.04
7855 0.31
9337 0.99
7277 0.76
8228 0.82
7680 -2.24
7387 0.7

Total number of rows: 272

Table truncated, full table size 2 Kbytes.




Supplementary file Size Download File type/resource
GSM1040697_0_Exiqon_14238665_S01.txt.gz 805.4 Kb (ftp)(http) TXT
GSM1040697_1_Exiqon_14238665_S01.txt.gz 894.8 Kb (ftp)(http) TXT
Processed data included within Sample table

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