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Sample GSM1327325 Query DataSets for GSM1327325
Status Public on May 15, 2015
Title H1-Day8 shCtrl
Sample type genomic
Source name Differentiated H1 ESCs
Organism Homo sapiens
Characteristics shRNA: stable control (scramble) shRNA
Treatment protocol Pluripotent stem cells were differentiated as previously described (Kurian et al, 2012). Briefly, undifferentiated human ES/iPS cells were freshly split on to matrigel-coated plates, making sure the sub-colonies were of small size (~300-500 cells /colony). Cells were differentiated using the chemically defined mesodermal induction media (MIM) (DMEM:F12, 15mg/ml stem cell grade BSA (MP biomedicals), 17.5µg/ml Human Insulin, (SAFC bioscience), 275 µg/ml Human holo transferrin (Sigma Aldrich), 20ng/ml bFGF (Hymanzyme), 50ng/ml Human VEGF-165 aa (Humanzyme), 25ng/ml human BMP4 (Stemgent), 450µM monothioglycerol (Sigma Aldrich), 2.25mM each L-Glutamine and Nonn-essential amino acids (Invitrogen).
Growth protocol Human ES cells, H1 (WA1, WiCell), (passage 25-40) were cultured in chemically defined hES/hiPS growth media, mTeSR on growth factor reduced matrigel (BD biosciences) coated plates. Briefly, 70-80% confluent hES/hiPS cells were treated with dispase (Invitrogen) for 7 minutes at 37¡C and the colonies were dispersed to small clusters and lifted carefully using a 5ml glass pipette, at a ratio of ~1:6. Human Umbilical Vein Endothelial Cells (HUVEC) were purchased from Promocell and cultivated in EBM medium supplemented with EGM singlequots (Lonza). iPS/ES-derived endothelial cells were cultivated in EGM-2 bullet kit (Lonza). All the endothelial cells were grown on collagen I coated plates (BD biosciences). All cell lines were maintained in an incubator (37¡C, 5% CO2) with media changes every day (hES/hiPS) or every second day (HUVEC).
Extracted molecule genomic DNA
Extraction protocol genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina 450K Infinium Methylation Arrays using standard Illumina protocol
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
Description late vascular progenitor cells with stable control (scramble) shRNA
Data processing Illumina GenomeStudio
Submission date Feb 13, 2014
Last update date May 15, 2015
Contact name Christopher Benner
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
Platform ID GPL13534
Series (2)
GSE54966 Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development [Illumina]
GSE54969 Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development

Data table header descriptions
VALUE Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.75333 0
cg00000108 0.88061 0
cg00000109 0.75659 0
cg00000165 0.1456 0
cg00000236 0.73506 0
cg00000289 0.58579 0
cg00000292 0.81616 0
cg00000321 0.26168 0
cg00000363 0.24905 0
cg00000622 0.03147 0
cg00000658 0.71968 0
cg00000714 0.23094 0
cg00000721 0.80233 0
cg00000734 0.07636 0
cg00000769 0.09445 0
cg00000807 0.79412 0
cg00000884 0.66516 0
cg00000905 0.09901 0
cg00000924 0.4223 0
cg00000948 0.80705 0

Total number of rows: 485577

Table truncated, full table size 9909 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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