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Sample GSM1327310 Query DataSets for GSM1327310
Status Public on May 15, 2015
Title H1 shCtrl
Sample type RNA
Source name 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 total RNA
Extraction protocol Total RNA from roughly 10x106 cells was isolated using TRIzol reagent (Invitrogen). Intact total RNA samples were treated with DNase1. All the RNA samples met the following RNA quality- OD260/280 = 2-2.2; OD260/230 ³ 2.0; 28S:18S > 1.0, RIN>7.
Label biotin
Label protocol 200 ng of total RNA were amplified using the Ambion WT Expression Kit (Ambion/Applied Biosystems), labeled using the WT Terminal Labeling Kit (Affymetri
Hybridization protocol Samples were hybridized to Human Gene 1.0 ST for 16 h at 45ºC and 60 rpm in a GeneChip® Hybridization Oven 640
Scan protocol Affymetrix GeneChip Scanner 3000 7G
Description H1 cells with stable control (scramble) shRNA
Data processing CEL files were analyzed using the oligo package in R/Bioconductor and normalized using RMA
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 GPL6244
Series (2)
GSE54964 Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development [Affymetrix]
GSE54969 Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development

Data table header descriptions
VALUE RMA normalized log2 intensity values

Data table
7892501 5.772587302
7892502 5.871531442
7892503 5.617265754
7892504 10.50832754
7892505 5.910649141
7892506 7.061138933
7892507 7.106154408
7892508 9.40284589
7892509 13.21770213
7892510 5.870175987
7892511 6.337664958
7892512 9.243453474
7892513 4.649541401
7892514 12.00625683
7892515 10.83661785
7892516 6.738218136
7892517 8.918369172
7892518 4.521129007
7892519 6.356859309
7892520 10.36548324

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.

Supplementary file Size Download File type/resource
GSM1327310_ES4_shCTL.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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