NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1162383 Query DataSets for GSM1162383
Status Public on Jun 01, 2015
Title HS306 line cells at initial passage 25
Sample type genomic
 
Source name hESC at initial passage
Organism Homo sapiens
Characteristics cell line source gender: female
cell line: HS306
passage number: p25
Treatment protocol Mechanical passaging was carried out under an inverted microscope under the hood using scalpels (Assou et al., 2009; Bai et al., 2011). For enzymatic single cell passaging, the cells were pre-treated with Y-27632 for 1h and dissociated with TrypLE™ Select (Invitrogen) for 10 mn at 37ºC. The reaction was stopped by hESC culture media and single hESC were released by pipetting and passed through a 20 µm strainer to eliminate hFF feeders, then counted and seeded on newly prepared feeder in density of 20 000 cells/cm2 at beginning and progressively to 3 000 cells/cm2 when cells were adaptated to enzymatic passaging. Both mechanic and enzymatic passaging were performed weekly. Experiments on HD291, HD129 and HS306 lines were initiated at p13, p16 and p25 respectively (termed initiating passages) and maintained independently using mechanic passaging (+MP) or enzyamatic passaging (+EP). All cell cultures were regularly checked for mycoplasma contamination and remained negative throughout the experiments.
Growth protocol These lines were maintained in culture media consisting of 80% KO-DMEM, 20% KOSR, 2 mM L-glutamine, 1% non-essential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and complemented with 10 ng/mL bFGF (Abcys, Paris, France). These cells were maintained in 35-mm dishes with pre-coated irradiated (40 Gy) human foreskin fibroblast (hFF) feeders and were either enzymatically or mechanically passaged every week.
Extracted molecule genomic DNA
Extraction protocol In mechanically passaged culture, the hESC colonies were exscinded carefully using a scalpel. In enzymatic-passaged culture, the singles cells were released as described above. As SSEA4 is one of most obstinate pluripotence markers (Ramirez et al., 2011), hESC cells were purified and enriched using the magnetic beads Dynabeads® SSEA-4 (Invitrogen) and the manufacture’s instructions were rigorously followed. The quality control of the purification showed high efficiency and no over-selection of SSEA4+ sub-population. Genomic DNA was purified from cell culture using the QIAamp DNA Mini Kit (Qiagen, Courtaboeuf, France) following manufacture’s instructions. We added an RNsae A treatment in DNA extraction to eliminate residual DNA.
Label biotin
Label protocol Affymetrix standard procedure
 
Hybridization protocol Affymetrix standard procedure
Scan protocol Affymetrix standard procedure
Description HS306_p25
Data processing The genotyping and copy number variation result were processed with Genotype Console (Affymetrix);
affymetrix-algorithm-name/version = CN5 v.5.0.0,
affymetrix-algorithm-param-ArraySet = GenomeWideSNP_6,
program-name = Genotyping Console v.4.0.3566.17491
CNCHP files were results for copy number variation data.
 
Submission date Jun 13, 2013
Last update date Jun 01, 2015
Contact name Qiang BAI
E-mail(s) qiang.bai@inserm.fr
Phone +33 (0)4 67 41 52 08
Organization name PhyMedExp INSERM U1046
Lab Maladies respiratoires et environnement
Street address 371 Avenue du Doyen Gaston Giraud
City Montpellier
ZIP/Postal code 34295
Country France
 
Platform ID GPL6801
Series (2)
GSE47914 Genomic instability of human embryonic stem cells in mechanic and enzymatic passaging culture
GSE47917 Genome alterations in human pluripotent stem cells as very early events highly dependent on cell passaging conditions

Data table header descriptions
ID_REF
VALUE CN STATE
CHROMOSOME
POSITION
LOG2 RATIO
SMOOTH SIGNAL
LOH
ALLELE DIFFERENCE

Data table
ID_REF VALUE CHROMOSOME POSITION LOG2 RATIO SMOOTH SIGNAL LOH ALLELE DIFFERENCE
CN_473963 1.000000 1 61723 -1.186109 0.557062 nan nan
CN_473964 1.000000 1 61796 -1.070804 0.557133 nan nan
CN_473965 1.000000 1 61811 -1.422314 0.557148 nan nan
CN_473981 1.000000 1 62908 -1.823666 0.558225 nan nan
CN_473982 1.000000 1 62925 -0.987022 0.558241 nan nan
CN_497981 1.000000 1 72764 -0.685763 0.568149 nan nan
CN_502615 1.000000 1 85924 0.546901 0.582096 nan nan
CN_502613 1.000000 1 85986 0.095859 0.582163 nan nan
CN_502614 0.000000 1 86312 -1.625971 0.582519 nan nan
CN_502616 0.000000 1 86329 -2.786053 0.582537 nan nan
CN_502843 4.000000 1 98590 -0.064296 0.596257 nan nan
CN_466171 4.000000 1 228694 0.924811 4.847472 nan nan
CN_468414 4.000000 1 229063 -0.171561 4.846927 nan nan
CN_468412 4.000000 1 229146 1.232514 4.846805 nan nan
CN_468413 4.000000 1 229161 0.749557 4.846783 nan nan
CN_470565 4.000000 1 229607 1.517193 4.846124 nan nan
CN_468424 4.000000 1 235658 0.543105 4.837160 nan nan
CN_468425 4.000000 1 235716 0.166956 4.837074 nan nan
CN_460512 2.000000 1 356431 -0.353731 1.912651 nan nan
CN_460513 2.000000 1 356530 0.282113 1.912652 nan nan

Total number of rows: 1813281

Table truncated, full table size 114228 Kbytes.




Supplementary file Size Download File type/resource
GSM1162383_HS306p25_20120601_GenomeWideSNP_6_.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM1162383_HS306p25_20120601_GenomeWideSNP_6_.CN5.CNCHP.gz 35.0 Mb (ftp)(http) CNCHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap