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Status |
Public on Jun 23, 2022 |
Title |
SUM159 SHP2 sh2 3 |
Sample type |
RNA |
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Source name |
SUM159 SHP2 sh2
|
Organism |
Homo sapiens |
Characteristics |
cell line: SUM159 transfection: SHP2 miR2
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Treatment protocol |
Doxycycline, added the day after seeding the cells in cultures and refreshed every 2 days
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Growth protocol |
Cultures of SUM159 cells expressing inducible CTRL miR, SHP2 miR1 or SHP2 miR2 for 15 days. Cells were grown in Nutrient Mixture F-12 (Sigma #N6658-500mL), 5% FCS (Sigma #F7524), 1% Pen/Strep (Gibco #15140-122), Normocin (InvivoGen #ant-nr-1), Insulin 10µg/mL (Sigma #I5500-50mg), Hydrocortisone 500ng/mL (Sigma #H0888-1g).
|
Extracted molecule |
total RNA |
Extraction protocol |
After 15 days cultures, RNA was extracted with Qiagen RNeasy Kits to obtain total RNA from SUM159 cells in the presence or absence of SHP2
|
Label |
biotin
|
Label protocol |
100ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).
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Hybridization protocol |
Affymetrix Human Gene 1.0 st v1 GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.
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Scan protocol |
Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.
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Description |
SHP2miR2_3
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Data processing |
All gene arrays were processed in R (http://www.r-project.org/) using Bioconductor package oligo. Robust multi-array mean was performed using the following command: expr <- rma(read.celfiles(filenames)). Probes with the largest interquartile range were selected as representative for corresponding genes (using array annotation from Bioconductor package hugene10sttranscriptcluster.db).
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Submission date |
Aug 13, 2021 |
Last update date |
Jun 23, 2022 |
Contact name |
Mohamed Bentires-Alj |
E-mail(s) |
bentireslab.data@gmail.com
|
Organization name |
University Hospital Basel
|
Department |
DBM
|
Lab |
THMR
|
Street address |
Hebelstrasse 20
|
City |
Basel |
ZIP/Postal code |
4031 |
Country |
Switzerland |
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|
Platform ID |
GPL6244 |
Series (1) |
GSE182033 |
SUM159 cells grown in 2D cultures in the presence or absence of SHP2 |
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