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Sample GSM1327313 Query DataSets for GSM1327313
Status Public on May 15, 2015
Title H1-Day8 shAlien
Sample type RNA
Source name Differentiated H1 ESCs
Organism Homo sapiens
Characteristics shRNA: stable Alien (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 late vascular progenitor cells with stable Alien (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 6.723357214
7892502 5.355674938
7892503 4.83726744
7892504 9.804186412
7892505 4.97894705
7892506 6.440619433
7892507 7.160723651
7892508 8.50511529
7892509 12.39780671
7892510 5.712531924
7892511 6.793026102
7892512 8.444520967
7892513 4.760498884
7892514 12.10535682
7892515 10.06730839
7892516 4.121794002
7892517 8.62400151
7892518 3.793784243
7892519 5.815877048
7892520 9.850063535

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.

Supplementary file Size Download File type/resource
GSM1327313_H1_D8_shAlien_KD.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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