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Sample GSM4272458 Query DataSets for GSM4272458
Status Public on Apr 29, 2021
Title AOA2-P4_Replicate_3
Sample type RNA
 
Source name Lymphoblastoid Cell Line from AOA2 Patient with SETX Mutation
Organism Homo sapiens
Characteristics cell type: Lymphoblastoid Cell Line transformed by Epstein-Barr Virus
morphology: Lymphoblast
genotype: Homozygous mutation in SETX gene, c.1669C>T
Treatment protocol Cells were harvested by trypsinization followed by two washes with ice-cold PBS.
Growth protocol Lymphoblastoid cell lines (LCLs) from control and AOA2 patients were cultured in RPMI 1640 medium (ThermoFisher) containing 20% FBS (Sigma-Aldrich), 1% Penicillin/Streptomycin (P/S; Sigma-Aldrich), 2 mM L-glutamine (ThermoFisher) and 1% Non-Essential Amino Acids (ThermoFisher). All LCLs were grown at 37°C and in a humidified atmosphere containing 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cultured human and mouse cells using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including an on-column DNase treatment to eliminate any contaminating genomic DNA.
Label Biotin
Label protocol RNA samples were amplified and biotin labeled using the WT-Ovation Pico target prep v1.0 protocol, which was derived from the NuGEN WT-Ovation Pico RNA Amplification system and the NuGEN FL-Ovation cDNA Biotin Module v2.
 
Hybridization protocol All fragmented and biotin labeled cDNA samples were hybridized to Affymetrix GeneChip Human Gene 1.0 ST microarrays for 16 hr at 45C. Arrays were washed using the Affymetrix Fluidics Station 450 according to the manufacturer’s recommendations.
Scan protocol Scanning was performed using the Affymetrix GeneChip 3000 7G scanner with autoloader running Affymetrix GeneChip Command Console (AGCC) software.
Description Gene expression data from AOA2-P4
Data processing Affymetrix gene expression data was analyzed using Bioconductor 2.5 running on R version 2.10.0. Probeset expression measures were calculated using RMA with the oligo package.
 
Submission date Jan 14, 2020
Last update date Apr 29, 2021
Contact name Steve West
E-mail(s) stephen.west@crick.ac.uk
Organization name The Francis Crick Institute
Street address 1 Midland Road
City London
ZIP/Postal code NW1 1AT
Country United Kingdom
 
Platform ID GPL6244
Series (2)
GSE143574 Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2
GSE143680 Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2.

Data table header descriptions
ID_REF
VALUE RMA normalised expression data

Data table
ID_REF VALUE
7892501 3.272154732
7892502 3.015794972
7892503 1.872073625
7892504 7.345812585
7892505 2.14296788
7892506 2.308463271
7892507 3.459344793
7892508 2.342566194
7892509 10.92554621
7892510 1.813978843
7892511 2.241524135
7892512 4.920516677
7892513 3.16995163
7892514 9.008821171
7892515 8.638894104
7892516 4.318502862
7892517 2.051987315
7892518 2.281914576
7892519 3.89654117
7892520 8.440552283

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM4272458_AOA2-P4_Rep_3.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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