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Sample GSM6509811 Query DataSets for GSM6509811
Status Public on Jan 03, 2024
Title Short-1
Sample type RNA
 
Source name Lymphoblastoid cell line RNA
Organism Homo sapiens
Characteristics gender: Female
Extracted molecule total RNA
Extraction protocol For mRNA extraction, 75 µl LCL suspension containing approximately 5x10^6 cells was taken through the QIAGEN RNeasy Mini Kit protocol following the manufacturer’s instructions, with total RNA eluted in 40μL RNase-free water
Label biotin
Label protocol 300 ng of extracted RNA was processed using the Ambion Whole Transcript (WT) Expression Kit (Thermo Fisher Scientific, UK) producing fragmented biotin-labelled sense-stranded copy DNA that was hybridised onto Human Exon 1.0ST GeneChip microarrays
 
Hybridization protocol Post-hybridisation array washing, and staining were performed in the GeneChip Fluidics station and arrays scanned using the GeneChip 3000 7G scanner.
Scan protocol standard Affymetrix protocol
Data processing Individual sample .CEL files quantifying gene transcripts were uploaded into Expression Console (Thermo Fisher Scientific, UK) and several quality control (QC) parameters were checked for each sample including poly-A RNA labelling controls, hybridisation controls, positive vs. negative area under the curve (AUC) and signal intensity. Qlucore Omics Explorer (Qlucore, Lund, Switzerland) was used to identify differentially expressed genes between successfully QC’d samples with long vs. short disease duration (FC ≥ ±1.20, p-value 0.05). Both Metascape (http://metascape.org) 14 and Ingenuity Pathway Analysis (IPA) (Qiagen, UK) were used to interrogate the data further.
 
Submission date Aug 26, 2022
Last update date Jan 03, 2024
Contact name Rachel Waller
E-mail(s) r.waller@sheffield.ac.uk
Organization name The University of Sheffield
Department Neuroscience
Street address SITraN, 385A Glossop Road
City SHEFFIELD
State/province South Yorkshire
ZIP/Postal code S102HQ
Country United Kingdom
 
Platform ID GPL5175
Series (2)
GSE212131 Establishing mRNA and miRNA interactions driving disease heterogeneity in ALS patient survival (microarray)
GSE212134 Establishing mRNA and microRNA interactions driving disease heterogeneity in Amyotrophic lateral sclerosis

Data table header descriptions
ID_REF
VALUE Quantification

Data table
ID_REF VALUE
3948543 8.64471
3063807 7.64026
3096575 7.56393
2949118 7.84903
3227645 9.22882
4014076 5.32604
2637819 2.80998
3850234 8.4825
3719161 8.71261
2916345 7.71022
2342904 6.49768
3817464 7.57158
2408437 7.01984
3932148 7.72788
3375091 8.58561
3653619 8.37434
2818035 5.58336
3063795 7.15532
2359282 8.629
2981874 8.08117

Total number of rows: 22011

Table truncated, full table size 341 Kbytes.




Supplementary file Size Download File type/resource
GSM6509811_JO_S79.CEL.gz 21.7 Mb (ftp)(http) CEL
GSM6509811_JO_S79.rma-gene-core.chp.gz 178.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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