Dataset features

Specifications


Application: ChIP-on-chip analysis
Number of samples: 6
Release date: Mar 3 2011
Last update date: Jan 17 2013
Access: Public
Diseases: Amyotrophic Lateral Sclerosis, Neurodegenerative Diseases
Dataset link Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (Affymetrix)

Experimental Protocol


6 samples of polyA-selected RNA were extracted from control-oligo and Tdp43-targeted oligo mouse striatum, and hybridized to custom splice-junction array. *Addendum Depending on the analysis software used, these CEL files may not load correctly using default parameters. This is due to the custom chip type of MJAY not being used during the array scanning step. There are three workarounds known for this problem so far. 1) If using APT, use multiple --chip-type parameters. Specifically, --chip-type mjay --chip-type MJAY --chip-type MoEx-1_0-st-v1.1sq 2) Edit the CEL file by converting to text using the APT command apt-cel-convert, then replacing the MoEx-1_0-st-v1.1sq in the DatHeader line with MJAY (all caps). 3) Edit the .pgf, .clf, and antigenomics.bmp files to use the MoEx-1_0-st-v1.1sq array instead of MJAY for the chip_type and lib_set_name options. (works on AltAnalyze software)

Repositories


GEO

GSE27371

ArrayExpress

E-GEOD-27371

BioProject

PRJNA141843

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Contact


Gene Yeo

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