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Sample GSM1224582 Query DataSets for GSM1224582
Status Public on Sep 06, 2013
Title 24h_shh+arrest_replicate_1_chip_B
Sample type RNA
 
Source name PN4-5 cerebellar culture_24h_shh+arrest
Organism Mus musculus
Characteristics strain: Swiss-Webster B
age: postnatal day 4-5 (PN4-5)
cell type: primary cerebellar culture (pooled from litter mates)
treated with: shh+arrest for 24h
microarray hybridization date: 2001-10-11
Treatment protocol Described in PMID:11960025
Growth protocol Described in PMID:11960025
Extracted molecule total RNA
Extraction protocol 20 micrograms of total RNA was used to generate target cRNA for hybridization to Affymetrix Mu11K chipset subA and subB oligonucleotide microarrays. A single chip set was used for each time-point. Before target generation, individual RNA samples were pooled so that each target was derived from a minimum of 3 individual cerebella. This step was performed to minimize both biologic variability and the number of microarrays necessary to generate informative data. After pooling, RNA was re-purified using Qiagen purification kits (Valencia, CA). Target cRNA was synthesized according to manufacturer's protocol. Briefly, total RNA was reverse transcribed into a complete cDNA library (SuperScript Choice kit; Invitrogen) using a T7/T24 primer (Genset Corp., La Jolla, CA). This cDNA was subsequently in vitro transcribed into biotin-labeled cRNA (High Yield RNA Transcript Labeling kit; Enzo Diagnostics, Farmingdale, NY). The resulting cRNA was fragmented and assessed for quality by gel electrophoresis. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols.
Label Biotin
Label protocol In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
 
Hybridization protocol 25 micrograms of each biotin-labeled cRNA was hybridized to an Affymetrix Mu11K sub A and B chip according to the manufacturer's protocol. Four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) were included in each hybridization reaction to verify consistent hybridization efficiency. Hybridization is carried out according the Affymetrix GeneChip® Manual. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
Scan protocol Standard Affymetrix protocol.
Description 24h_shh_arrest_1_chipB__CL2001011012AA
PN4-5 cerebellar culture, 24h, shh+arrest, chip_B
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
 
Submission date Sep 05, 2013
Last update date Sep 06, 2013
Contact name Alvin T. Kho
E-mail(s) alvin_kho@hms.harvard.edu
Phone 617-919-2182
Organization name Boston Children's Hospital
Department Informatics Program
Street address 320 Longwood Avenue
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL76
Series (1)
GSE50606 Identification of genes expressed with temporal-spatial restriction to developing cerebellar neuron precursors by a functional genomic approach perspective of human cancers.

Data table header descriptions
ID_REF
VALUE MAS 5.0-calculated Signal intensity.
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
AFFX-18SRNAMur/X00686_3_at 651.3 A
AFFX-18SRNAMur/X00686_5_at 931.4 P
AFFX-18SRNAMur/X00686_M_at 842 P
AFFX-b-ActinMur/M12481_3_at 54052.7 P
AFFX-b-ActinMur/M12481_3_st 250.1 A
AFFX-b-ActinMur/M12481_5_at 27374.3 P
AFFX-b-ActinMur/M12481_5_st 166.8 A
AFFX-b-ActinMur/M12481_M_at 29880.5 P
AFFX-b-ActinMur/M12481_M_st 543.9 P
AFFX-BioB-3_at 61.5 A
AFFX-BioB-3_st 173.8 A
AFFX-BioB-5_at 192.2 A
AFFX-BioB-5_st 596 A
AFFX-BioB-M_at 23.9 A
AFFX-BioB-M_st 56.4 A
AFFX-BioC-3_at 45.3 A
AFFX-BioC-3_st 22.7 A
AFFX-BioC-5_at 313.2 A
AFFX-BioC-5_st 69.3 A
AFFX-BioDn-3_at 154.5 A

Total number of rows: 6595

Table truncated, full table size 145 Kbytes.




Supplementary file Size Download File type/resource
GSM1224582_24h_shh_arrest_1_chipB_CL2001011012AA.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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