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Sample GSM2786988 Query DataSets for GSM2786988
Status Public on Dec 19, 2018
Title Control_3
Sample type RNA
 
Source name Healthy subject
Organism Homo sapiens
Characteristics cell type: iPS cell-derived neural progenitors
disease state: healthy
Growth protocol Human iPS cell clusters were grown as neurospheres in neuronal differentiation medium. After 6 weeks, neurospheres were plated on poly-D-lysin/laminin coated plates and allowed to differentiate for 1 day. Following day cells were scraped in PBS and the cell pellet was collected.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNA Purification Kit (Norgen Biotek Corp.) according to the manufacturer’s instructions.
Label Biotin
Label protocol Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT Plus reagent Kit, Manual Target Preparation for GeneChip Whole Transcript Expression Arrays, P/N 703174 Rev.5, Affymetrix).
 
Hybridization protocol Following fragmentation, 5.2 ug of cRNA was hybridized for 16 hr at 45oC on Affymetrix Human Clariom D arrays. The Clariom D arrays were washed and stained in the Affymetrix Fluidics Station 450 (GeneChip Expression Wash, Stain and Scan User Manual for Cartridge Arrays, P/N 702731 Rev. 4, Affymetrix).
Scan protocol Clariom D arrays were scanned using the Hewlett-Packard GeneChip Scanner 3000 (GCS3000).
Description SST-RMA expression value derived from Affymetrix Expression Console Software
HEL46.11
Data processing The CEL files were processed and normalized using Expression Console Software using Affymetrix default analysis settings to perform Gene Level Analysis (Gene Level-SST-RMA). Gene level data files (sst-rma-gene-full.chp) were then loaded into Affymetrix’s Transcriptome Analysis Console software to perform gene level analysis.
 
Submission date Sep 18, 2017
Last update date Dec 19, 2018
Contact name Maija L Castrén
E-mail(s) maija.castren@helsinki.fi
Organization name University of Helsinki
Department Faculty of Medicine/Physiology
Street address P.O.BOX 63
City Helsinki
State/province Helsinki
ZIP/Postal code 00014
Country Finland
 
Platform ID GPL23126
Series (1)
GSE103965 Functional changes of AMPA responses in human induced pluripotent stem cell-derived neural progenitors in fragile X syndrome

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 12.9389
AFFX-BkGr-GC04_st 10.0807
AFFX-BkGr-GC05_st 8.0624
AFFX-BkGr-GC06_st 6.48671
AFFX-BkGr-GC07_st 5.42718
AFFX-BkGr-GC08_st 4.5192
AFFX-BkGr-GC09_st 3.67184
AFFX-BkGr-GC10_st 3.28252
AFFX-BkGr-GC11_st 2.88037
AFFX-BkGr-GC12_st 2.65838
AFFX-BkGr-GC13_st 2.35326
AFFX-BkGr-GC14_st 2.18052
AFFX-BkGr-GC15_st 2.06369
AFFX-BkGr-GC16_st 2.08856
AFFX-BkGr-GC17_st 2.05023
AFFX-BkGr-GC18_st 2.11715
AFFX-BkGr-GC19_st 2.2879
AFFX-BkGr-GC20_st 2.30429
AFFX-BkGr-GC21_st 2.41874
AFFX-BkGr-GC22_st 2.67585

Total number of rows: 138745

Table truncated, full table size 3533 Kbytes.




Supplementary file Size Download File type/resource
GSM2786988_HEL46.11_1day_Control_.CEL.gz 22.1 Mb (ftp)(http) CEL
GSM2786988_HEL46.11_1day_Control_.sst-rma-gene-full.chp.gz 887.1 Kb (ftp)(http) CHP
Processed data provided as supplementary file

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