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Sample GSM1269943 Query DataSets for GSM1269943
Status Public on Nov 21, 2013
Title n2a-pax6_control-R1
Sample type RNA
 
Source name N2A_non-targeting vector
Organism Mus musculus
Characteristics cell line: neuro 2A (N2A)
cell type: neuroblastoma
transiently transfected with: non-targeting control vector
Treatment protocol Approximately 2x10^5 cells were plated per well in a 6 well plate. 16-24 hrs later cells were transfected with 1.5 ug shRNA expression construct using FuGENE 6 (Promega) according to the manufacturer’s instructions. Total RNA was extracted from the cells 3 days later.
Growth protocol N2A mouse neuroblastoma cells were grown in DMEM supplemented with 10% fetal bovine serum.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Qiagen Mini RNeasy kit following the manufacturer’s instructions and RNA integrity assessed on a BioAnalyzer (Agilent Technologies).
Label biotin
Label protocol 200 ng RNA was used to generate labelled sense single stranded DNA (ssDNA) for hybridization with the Ambion WT Expression Kit, the Affymetrix WT Terminal Labelling and Controls Kit and the Affymetrix Hybridization, Wash, and Stain Kit as described by the manufacturer. Sense ssDNA was fragmented and the distribution of fragment lengths was measured on a BioAnalyzer.
 
Hybridization protocol Fragmented ssDNA was then labelled and hybridized to the Affymetrix GeneChip Mouse Gene 1.0 ST Array (Affymetrix). Chips were processed on an Affymetrix GeneChip Fluidics Station 450.
Scan protocol Chips were scanned on an Affymetrix Scanner 3000.
Description control1
Data processing Affymetrix CEL files were analysed using the Limma, oligo, and genefilter R Bioconductor packages. Arrays were RMA background corrected, quantile normalised and summary expression values calculated for Refseq and full length mRNAs. Before differential expression analysis, genes changing upon Pax6 knockdown were filtered to remove genes genes with consistently low expression.
 
Submission date Nov 20, 2013
Last update date Nov 21, 2013
Contact name Stephen Sansom
E-mail(s) stephen.sansom@kennedy.ox.ac.uk
Organization name Kennedy Institute of Rheumatology
Department NDORMS
Lab Sansom
Street address Roosevelt Drive
City Oxford
State/province Oxfordshire
ZIP/Postal code OX3 7FY
Country United Kingdom
 
Platform ID GPL6246
Series (2)
GSE52568 The long non-coding RNA Paupar regulates the expression of both local and distal genes [Pax6 KD]
GSE52571 The long non-coding RNA Paupar regulates the expression of both local and distal genes

Data table header descriptions
ID_REF
VALUE log2 RMA (Oligo package)

Data table
ID_REF VALUE
10338001 12.48166415
10338002 8.143504865
10338003 10.67285148
10338004 7.685388322
10338005 3.842566213
10338006 4.13791048
10338007 4.645091584
10338008 5.727112199
10338009 9.763328369
10338010 3.876101495
10338011 7.641423105
10338012 4.003050922
10338013 3.732598805
10338014 3.788701035
10338015 3.748592192
10338016 9.31321608
10338017 13.4535689
10338018 8.602297936
10338019 7.103565566
10338020 9.751253577

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM1269943_n2a-pax6_control-R1.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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