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Sample GSM493398 Query DataSets for GSM493398
Status Public on Mar 30, 2010
Title zMNCs, day 7, replicate A, batch 1
Sample type RNA
 
Source name zebrafish mononuclear myogenic cells from day 7 differentiation
Organism Danio rerio
Characteristics tissue: dorsal muscle
cell type: mononuclear myogenic cells
time point: day 7
initial number of cells plated: 500,000
microarray hybridization date: 8-27-09
microarray data quality: good
microarray scanning scale factor: 4.11
microarray scanning target intensity: 500
microarray batch: 1
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 7 differentiation.
D7A_082709
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 244.696528221816 P
AFFX-BioB-5_at 286.711912828647 P
AFFX-BioB-M_at 411.73459261774 P
AFFX-BioC-3_at 889.762891498975 P
AFFX-BioC-5_at 855.259686139769 P
AFFX-BioDn-3_at 4442.17631458239 P
AFFX-BioDn-5_at 1979.72389161085 P
AFFX-CreX-3_at 15373.7649467251 P
AFFX-CreX-5_at 11060.8789352855 P
AFFX-DapX-3_at 2261.18293618681 P
AFFX-DapX-5_at 1037.80442451493 P
AFFX-DapX-M_at 1887.88746445099 P
AFFX-Dr-AB076373-1_at 12.0399632396506 A
AFFX-Dr-AF292559-1_at 1.23928754053335 A
AFFX-Dr-AF292559-2_s_at 2.27308177840256 A
AFFX-Dr-AF292559-3_s_at 1.44825073517584 A
AFFX-Dr-AF292559-4_s_at 50.7669353654447 M
AFFX-Dr-AF292560-1_s_at 13.0717672307395 A
AFFX-Dr-AF298789-1_at 6.15513451706723 A
AFFX-Dr-AF323980-1_at 14.5602193402996 A

Total number of rows: 15617

Table truncated, full table size 544 Kbytes.




Supplementary file Size Download File type/resource
GSM493398.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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