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Sample GSM495982 Query DataSets for GSM495982
Status Public on Feb 25, 2010
Title P19(Lin28)-day4b
Sample type RNA
 
Channel 1
Source name transfected P19 EC cells
Organism Mus musculus
Characteristics cell line: mouse P19 cells, stably transfected with plasmid constitutively expressing human LIN28
Treatment protocol P19 and P19+Lin28A cells differentiated to 5 days with Retinoic acid/aggregation to induce neurogenesis by standard methods.
Growth protocol P19 cells were grown in maintained in alpha-MEM supplemented with 2.5% fetal bovine serum, 7.5% bovine serum, and 50 units/mL of penicillin/streptomycin. P19_Lin28 cells were maintained in the same medium with 2 microg/mL puromycin .
Extracted molecule total RNA
Extraction protocol Total RNA was purified using the miRNA isolation kit (Ambion, Austin, TX, USA).
Label Hy3
Label protocol One µg total RNA from sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
 
Channel 2
Source name common reference pool
Organism Mus musculus
Characteristics cell line: mouse P19 cells
Extracted molecule total RNA
Extraction protocol Total RNA was purified using the miRNA isolation kit (Ambion, Austin, TX, USA).
Label Hy5
Label protocol One µg total RNA from sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
 
 
Hybridization protocol The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 13.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).
Scan protocol The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 7.0 software (BioDiscovery, Inc., USA)
Description biological replicate 2 of 2
Data processing The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
 
Submission date Jan 12, 2010
Last update date Feb 25, 2010
Contact name Eric Moss
E-mail(s) mosseg@umdnj.edu
Phone 8565662896
Fax 8565662691
Organization name UMDNJ
Department Molecular Biology
Street address 2 Medical Center Dr.
City Stratford
State/province NJ
ZIP/Postal code 08084
Country USA
 
Platform ID GPL7722
Series (1)
GSE19858 Effect of LIN28 on miRNA profile at day 5 of neurogliogenesis in vitro

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (test/reference)

Data table
ID_REF VALUE
33401 -1.133094986
42463 -1.187702151
3320 -1.051174204
10914 -1.06692702
17748 -1.082114995
27838 -0.693684037
17676 -0.279997774
42904 -0.77095532
19004 -0.496655099
42868 -0.115543057
42471 -0.117642621
42707 0.287948538
13149 -0.499155124
10978 0.286715518
19600 0.131678771
42878 -0.365216934
17489 -0.611376559
11077 -0.355003018
11020 0.038517314
42540 -0.161276542

Total number of rows: 619

Table truncated, full table size 6 Kbytes.




Supplementary file Size Download File type/resource
GSM495982_0_Exiqon_13837108_S01_Cropped.txt.gz 473.2 Kb (ftp)(http) TXT
GSM495982_1_Exiqon_13837108_S01_Cropped.txt.gz 518.4 Kb (ftp)(http) TXT
Processed data included within Sample table

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