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Sample GSM493410 Query DataSets for GSM493410
Status Public on Mar 30, 2010
Title zMNCs, day 14, replicate B, batch 2
Sample type RNA
 
Source name zebrafish mononuclear myogenic cells from day 14 differentiation
Organism Danio rerio
Characteristics tissue: dorsal muscle
cell type: mononuclear myogenic cells
time point: day 14
microarray hybridization date: 08/15/07
microarray data quality: good
microarray scanning scale factor: 6.50
microarray scanning target intensity: 1500
microarray batch: 2
Treatment protocol Zebrafish mononuclear myogenic cells were differentiated in Differentiation media, Promocell human differentiation media, supplemented with 2% horse serum, 1x antibiotics/antimyocotics, 1x Glutamax.
Growth protocol Zebrafish mononuclear myogenic cells were expanded in Promocell growth media, supplemented with 20% FBS, 1x antibiotics/antimycotics, 1x Glutamax, 3 ng/ml rhFGF.
Extracted molecule total RNA
Extraction protocol Zebrafish mononuclear myogenic cells were isolated with Tripure (Roche Applied Sciences) following the manufacturer's protocol.
Label biotin
Label protocol cRNA was biotin-labeled by the Children's Hospital Boston Molecular Genetics Core Facility.
 
Hybridization protocol Affymetrix hybridization protocol for the Zebrafish Whole Genome Arrays, 1 µg of cRNA.
Scan protocol Scanning was carried out on an Affymetrix GeneChip® Scanner 3000 7G with autoloader. The scanner settings are included in the 'characteristics' field. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
Description Zebrafish mononuclear myogenic cells from dorsal muscle from day 14 differentiation.
14_B_081507
Data processing CEL files were inputted into Bioconductor/R to derive Affymetrix Microarray Suite version 5.0 (MAS 5.0)-normalized output.
 
Submission date Jan 05, 2010
Last update date Jan 08, 2010
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 GPL1319
Series (1)
GSE19754 Transcriptome analysis of zebrafish mononuclear myogenic cells (zMNCs) during myogenic differentiation

Data table header descriptions
ID_REF
VALUE MAS5-calculated signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M)

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-3_at 131.958088452147 P
AFFX-BioB-5_at 203.223176025805 P
AFFX-BioB-M_at 246.887960839656 P
AFFX-BioC-3_at 245.596341701112 P
AFFX-BioC-5_at 214.614202395794 P
AFFX-BioDn-3_at 2436.71350396075 P
AFFX-BioDn-5_at 1471.49958424931 P
AFFX-CreX-3_at 13884.5783577500 P
AFFX-CreX-5_at 8464.91223728693 P
AFFX-DapX-3_at 672.58300288393 P
AFFX-DapX-5_at 21.2179122921398 A
AFFX-DapX-M_at 195.877986513042 P
AFFX-Dr-AB076373-1_at 3.93346922991812 A
AFFX-Dr-AF292559-1_at 16.5525542820735 A
AFFX-Dr-AF292559-2_s_at 5.89337751560469 A
AFFX-Dr-AF292559-3_s_at 0.627649682475565 A
AFFX-Dr-AF292559-4_s_at 20.6411119610646 A
AFFX-Dr-AF292560-1_s_at 321.423383547911 P
AFFX-Dr-AF298789-1_at 6.59760781557671 A
AFFX-Dr-AF323980-1_at 10.4639279249372 A

Total number of rows: 15617

Table truncated, full table size 544 Kbytes.




Supplementary file Size Download File type/resource
GSM493410.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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