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Sample GSM1559600 Query DataSets for GSM1559600
Status Public on Dec 21, 2015
Title UD, biological rep1 (AS level)
Sample type RNA
Source name Undifferentiated CESCs
Organism Homo sapiens
Characteristics cell type: Undifferentiated CESCs
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Fragmented single-stranded DNA was labeled using DNA labeling reagent according to standard Affymetrix protocol.
Hybridization protocol After fragmentation, 5 ug cDNA were hybridized for 16hr at 45C in 60rpm of spanning on Human Transcriptome Array 2.0. The microarray was washed and stained using Affymetrix GeneChip Command Console (AGCC) software.
Scan protocol The microarray was scanned using AGCC software.
Description Alternative splicing data from human CESCs
Data processing We used Expression Console software to pre-treat .CEL files through Robust Multichip Analysis (RMA) algorithm (3), including background correction, probeset signal integration, quantile normalization. After pretreatment, the obtained chp files were analyzed by Transcriptome Analysis Console software to identify differentially expressed genes (DEGs) and alternatively spliced genes (ASGs).
Submission date Dec 05, 2014
Last update date Dec 21, 2015
Contact name Jin Shang
Organization name Third Military Medical University
Street address No. 183, Xinqiao Main Street
City Chongqing
ZIP/Postal code 400038
Country China
Platform ID GPL17585
Series (1)
GSE63897 Gene expression and alternative splicing data from human cartilage endplate-derived stem cells
Alternative to GSM1559599 (gene level analysis)

Data table header descriptions
VALUE RMA signal

Data table
JUC01000001.hg.1 6.08027 0.0310529
JUC01000002.hg.1 4.15655 0.305654
JUC01000003.hg.1 6.26244 0.00126467
JUC01000004.hg.1 4.81148 0.1123
JUC01000005.hg.1 7.19918 0.00268084
JUC01000006.hg.1 6.93874 0.00561508
JUC01000007.hg.1 3.50218 0.453934
JUC01000008.hg.1 6.46003 0.000195091
JUC01000009.hg.1 3.14509 0.0487673
JUC01000010.hg.1 3.21958 0.00824668
JUC01000011.hg.1 12.3644 4.90787e-09
JUC01000012.hg.1 8.7281 0.00227848
JUC01000013.hg.1 11.8379 4.63897e-09
JUC01000014.hg.1 9.69667 4.49409e-09
JUC01000015.hg.1 5.41923 0.00715005
JUC01000016.hg.1 7.36972 9.93272e-05
JUC01000017.hg.1 7.63112 2.45973e-07
JUC01000018.hg.1 8.32115 0.00414273
JUC01000019.hg.1 7.67634 0.000386059
JUC01000020.hg.1 7.67634 0.000386059

Total number of rows: 914585

Table truncated, full table size 32089 Kbytes.

Supplementary file Size Download File type/resource
GSM1559600_UD.CEL.gz 24.5 Mb (ftp)(http) CEL
GSM1559600_UD_AS_level.chp.gz 9.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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