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Sample GSM900205 Query DataSets for GSM900205
Status Public on Sep 12, 2012
Title Shef1, DFNB
Sample type RNA
 
Source name hESCs differentiating with basal DFNB medium
Organism Homo sapiens
Characteristics time: Day 14
cell line: Shef1
treatment: DFNB
Treatment protocol Undifferentiated hESCs were dissociated with Trypsin -EDTA (Sigma) and the cell suspension passed through a 100-micrometer cell strainer (BD Labware). Cells were plated onto laminin-coated plastic and incubated with DFNB medium (DMEM/high glucose: F12 mixed as 1:1, with N2 and B27) supplemented with FGF3 (50ng/ml) and FGF10 (50ng/ml) or with DFNB alone, without FGFs. Cells were allowed to differentiate for 14 days.
Growth protocol hESC lines H14, Shef1 and Shef3 were maintained on inactivated mouse embryonic fibroblast (MEF) feeder cells in medium comprised of knockout Dulbecco’s modified Eagle’s medium supplemented with 20% knockout serum replacement (KOSR), 1% nonessential amino acids, 2mM L-glutamine, (all from Invitrogen), 0.1mM ß-mercaptoethanol (Sigma), and 4ng/ml of basic fibroblast growth factor (bFGF; R&D systems).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNAeasy Kit (Qiagen) following the manufacturer's instructions
Label Biotin
Label protocol 200ng of total RNA was amplified using the 3' IVT method and biotinylation of antisense RNA carried out according to Affymetrix protocol
 
Hybridization protocol 12.5µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus 2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
Scan protocol the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
Data processing Normalization and initial analysis were done using puma (www.bioconductor.org) that estimates gene expression levels using probabilistic models
 
Submission date Mar 23, 2012
Last update date Sep 12, 2012
Contact name Marcelo Nicolas Rivolta
E-mail(s) m.n.rivolta@shef.ac.uk
Phone 44-114-222 2385
Fax 44-114-222 2360
Organization name University of Sheffield
Department Biomedical Science
Street address Western Bank
City Sheffield
State/province Yorkshire
ZIP/Postal code S10 2TN
Country United Kingdom
 
Platform ID GPL570
Series (1)
GSE36754 Gene expression of differentiating hESCs into otic progenitors

Data table header descriptions
ID_REF
VALUE Puma multi-mgMOS log2 of gene expression levels

Data table
ID_REF VALUE
1007_s_at 8.660203449
1053_at 8.205210453
117_at 3.478169269
121_at 6.382868487
1255_g_at 6.1904837
1294_at 3.589113489
1316_at 3.948671452
1320_at 3.440494168
1405_i_at -3.969281545
1431_at 1.916064079
1438_at 1.287708081
1487_at 5.159680405
1494_f_at 3.398356361
1552256_a_at 6.159124415
1552257_a_at 8.30260746
1552258_at 2.272356726
1552261_at 2.750452085
1552263_at 5.939301688
1552264_a_at 6.377317845
1552266_at 1.802452339

Total number of rows: 54675

Table truncated, full table size 1224 Kbytes.




Supplementary file Size Download File type/resource
GSM900205_Shef1_DFNB.CEL.gz 5.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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