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Sample GSM3209077 Query DataSets for GSM3209077
Status Public on Dec 01, 2018
Title iPSC-NCCs (inflamed condition) 1
Sample type RNA
 
Source name coculture with a mix of PBMCs for 5 days
Organism Homo sapiens
Characteristics cell line: 253G1
cell type: neural crest cell
Growth protocol We induced NCCs from human iPSCs according to the previously described method with some modifications for 3 weeks to complete. After the differentiation, iPSC-NCCs were harvested in a 12-well culture plate. The medium was RPMI 1640 (Nacalai Tesque) containing 10% FBS supplemented with human recombinant interleulin-2 (BD). iPSC-NCCs (normal condition, 1.0 x 10^6 cells/well) were incubated in the absence of the transwell membrane. On the other hand, iPSC-NCCs (inflamed condition, 1.0 x 10^6 cells/well) were incubated in the presence of the transwell membrane. A mix of the human peripheral blood mononuclear cells (PBMCs, 3.0 x 10^6 cells/well) from 5 healthy donors were added to the upper wells of a transwell plate. PBMCs were obtained Lymphoprep (Stemcell technologies) density gradient centrifugation in accordance with the manufacturer’s instructions.
Extracted molecule total RNA
Extraction protocol The total RNA of iPSC-NCCs (normal condition, n=2) and iPSC-NCCs (inflamed condition, n=2) were extracted by High Pure RNA Isolation Kit (Roche) after the cells were incubated for 5 days.
Label biotin
Label protocol We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.
 
Hybridization protocol We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.
Scan protocol We followed manufacturer's protocol, and used GeneChip® Scanner 3000 7G.
Data processing Data acquisition and normalization (SST-RMA) were used Affymetrix® Expression Console™ Software.
 
Submission date Jun 21, 2018
Last update date Dec 02, 2018
Contact name Shota Fujii
Organization name RIKEN Center for Developmental Biology
Department The Laboratory for Retinal Regeneration
Street address 2-2-3 Minatojima-minamimachi, Chuo-ku
City Kobe
ZIP/Postal code 650-0047
Country Japan
 
Platform ID GPL23159
Series (1)
GSE116110 Immunological properties of neural crest cells derived from human induced pluripotent stem cells (normal vs inflammed condition)

Data table header descriptions
ID_REF
VALUE Normalized intensity.

Data table
ID_REF VALUE
TC0100006437.hg.1 18.30636
TC0100006476.hg.1 60.57834
TC0100006479.hg.1 145.6418
TC0100006480.hg.1 42.5623
TC0100006483.hg.1 46.11102
TC0100006486.hg.1 444.4941
TC0100006490.hg.1 39.64101
TC0100006492.hg.1 53.53007
TC0100006494.hg.1 261.9469
TC0100006497.hg.1 29.50273
TC0100006499.hg.1 135.3279
TC0100006501.hg.1 108.1707
TC0100006502.hg.1 22.86162
TC0100006514.hg.1 9.567236
TC0100006516.hg.1 111.1946
TC0100006517.hg.1 17.82343
TC0100006524.hg.1 52.56863
TC0100006540.hg.1 61.2302
TC0100006548.hg.1 11.98427
TC0100006550.hg.1 138.5753

Total number of rows: 24351

Table truncated, full table size 659 Kbytes.




Supplementary file Size Download File type/resource
GSM3209077_neural_crest_cell_inflamed_1.CEL.gz 1.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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