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Sample GSM1269954 Query DataSets for GSM1269954
Status Public on Nov 21, 2013
Title n2a-paupar_knockdown-R3
Sample type RNA
 
Source name N2A_Paupar knockdown construct
Organism Mus musculus
Characteristics cell line: neuro 2A (N2A)
cell type: neuroblastoma
transiently transfected with: Paupar knockdown construct
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 2.5 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 pauparkd3
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 Paupar knockdown were filtered to remove genes showing little variation in expression (variance cut off of 0.5).
 
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)
GSE52569 The long non-coding RNA Paupar regulates the expression of both local and distal genes [Paupar 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 12.44613782
10338002 7.678230606
10338003 10.80896187
10338004 9.855323794
10338005 2.695870643
10338006 3.116682442
10338007 3.864475856
10338008 5.181030119
10338009 9.25117329
10338010 2.739585731
10338011 7.175819706
10338012 2.86040191
10338013 2.416556585
10338014 2.576471771
10338015 2.495684789
10338016 8.935124765
10338017 13.54227058
10338018 8.175700998
10338019 6.622809284
10338020 9.368195657

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM1269954_n2a-paupar_knockdown-R3.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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