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Sample GSM2027279 Query DataSets for GSM2027279
Status Public on Jan 21, 2016
Title Bdh2 morphant expressing ectopic Bdh2, rep 1
Sample type RNA
 
Source name Bdh2 morphant zebrafish embryos expressing ectopic Bdh2 at 72 hpf
Organism Danio rerio
Characteristics developmental stage: embryo
Treatment protocol Fertilized 1- to 2-cell embryos were microinjected with morpholinos (MOs; 1 to 2 nL of 130 micromol/L in water; Gene Tools). Rescue experiments were performed by co-injecting 1 to 2 nL of a synthetic capped mRNA (50 microgram/ml in water) synthesized from a full-length mouse bdh2 cDNA cloned into pCS2+MT vector as described in Cell 141:1006-1017.
Growth protocol Wild-type Danio rerio (zebrafish) were bred and raised following the procedures approved by the Case Western Reserve University Institutional Animal Care and Use Committee. The embryos were collected from natural spawnings, cultured, and staged as described in Cell 141:1006-1017.
Extracted molecule total RNA
Extraction protocol Extraction of total RNAs were performed using RNeasy Mini kit (Qiagen) per manufacturer's protocol.
Label biotin
Label protocol Per manufacturer’s instructions (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA, USA) at Case Comprehensive Cancer Center Microarray Core Facility.
 
Hybridization protocol Per manufacturer’s instructions (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA, USA) at Case Comprehensive Cancer Center Microarray Core Facility.
Scan protocol Per manufacturer’s instructions (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA, USA) at Case Comprehensive Cancer Center Microarray Core Facility.
Data processing The data were analyzed with Affymetrix Expression Console Software using Affymetrix default analysis settings and global scaling as normalization method.
 
Submission date Jan 04, 2016
Last update date Jan 21, 2016
Contact name Zhuoming Liu
Organization name Case Western Reserve University
Street address 2103 Cornell Road
City Cleveland
State/province OH
ZIP/Postal code 44106
Country USA
 
Platform ID GPL1319
Series (1)
GSE76509 Comparison of expression data between control and Bdh2 morphant zebrafish embryos, as well as Bdh2 morphant zebrafish embryos expressing ectopic Bdh2

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 240.336 P 0.0032123
AFFX-BioB-M_at 235.412 P 0.000146581
AFFX-BioB-3_at 208.73 P 0.00255552
AFFX-BioC-5_at 672.916 P 5.16732e-05
AFFX-BioC-3_at 538.39 P 0.000581214
AFFX-BioDn-5_at 1378.98 P 4.42873e-05
AFFX-BioDn-3_at 2988.8 P 8.14279e-05
AFFX-CreX-5_at 10537.7 P 5.16732e-05
AFFX-CreX-3_at 14050 P 4.42873e-05
AFFX-DapX-5_at 11.8736 A 0.544587
AFFX-DapX-M_at 73.9607 P 0.0113844
AFFX-DapX-3_at 193.823 P 0.00255552
AFFX-LysX-5_at 15.3188 A 0.52976
AFFX-LysX-M_at 30.6791 A 0.645547
AFFX-LysX-3_at 44.4463 P 0.00933744
AFFX-PheX-5_at 5.4821 A 0.843268
AFFX-PheX-M_at 4.93823 A 0.852061
AFFX-PheX-3_at 78.8591 A 0.131361
AFFX-ThrX-5_at 7.76844 A 0.891021
AFFX-ThrX-M_at 9.42885 A 0.455413

Total number of rows: 15617

Table truncated, full table size 569 Kbytes.




Supplementary file Size Download File type/resource
GSM2027279_69Dev22.CEL.gz 2.0 Mb (ftp)(http) CEL
GSM2027279_69Dev22.Zebrafish.mas5.CHP.gz 173.9 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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