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| Status |
Public on Mar 24, 2022 |
| Title |
Cord blood-CD34+ cells-MA9-ZNF521 transduced-at 58 days-replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Cord blood-CD34+ cells-MA9-ZNF521 transduced-at 58 days-replicate 2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Cord blood-CD34+ cells
transduction: MA9-ZNF521 transduced
time point: 58 days
|
| Treatment protocol |
Lentiviral transformed cells were cultured in MyeloCult™ H5100 (STEMCELL Technologies) supplemented with 1 μM of Hydrocortisone (HC), 10 ng/ml of SCF, FLT3-L and Interleukin 3 (IL3).
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| Growth protocol |
Cord blood (CB)-CD34+ cells were purchased from Lonza and cultured as 0.5-1.0x105 cells/ml in xeno-free StemMACS™ HSC Expansion Media (Miltenyi Biotec) in presence of Thrombopoietin (TPO), FLT3-Ligand (FLT3-L) and Stem Cell Factor (SCF) (100 ng/ml).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from duplicate samples by resuspending in TRI Reagent (Sigma-Aldrich) and freezing at –80°C before processing.
|
| Label |
biotin
|
| Label protocol |
RNA samples were processed using WT PLUS Reagent Kit, according to manifacturer’s protocol (Thermo Fisher Scientific, Waltham, MA, USA)
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| |
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| Hybridization protocol |
The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip ClariomD array, according to the standard protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
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| Scan protocol |
Scanning of the arrays was performed using the GeneChip Scanner 7G
|
| Data processing |
All the following analyses were performed in R Bioconductor (version 3.5.1). Robust Multichip Average (RMA) processing was applied on raw data, based on the platform design (pd.clariom.d.human), allowing background subtraction, quantile normalization and median-polish summarization on core probe sets, by using oligo package.Global expression levels of 138.745 total transcripts were extracted from the ExpressionSet. Following Affymetrix Human Clariom D annotation (clariomdhumantranscriptcluster.db, version 8.7.0, org.Hs.eg.db, version 3.7.0 ) and filtering based on Entrez Gene Identifier and the exclusion of non-coding or uncharacterized protein transcripts (by subtracting microRNA, long non-coding RNA, long intergenic non-coding RNA, small nucleolar RNA, antisense, intronic, uncharachterized protein transcripts), 20.558 total features were further considered.
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| |
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| Submission date |
Jul 28, 2021 |
| Last update date |
Mar 24, 2022 |
| Contact name |
Antonino Neri |
| E-mail(s) |
antonino.neri@policlinico.mi.it
|
| Organization name |
Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico
|
| Lab |
Hematology
|
| Street address |
Via Francesco Sforza, 35
|
| City |
Milan |
| State/province |
Milan |
| ZIP/Postal code |
20122 |
| Country |
Italy |
| |
|
| Platform ID |
GPL23126 |
| Series (1) |
| GSE181006 |
ZNF521 enhances MLL-AF9-dependent hematopoietic stem cell transformation in acute myeloid leukemias by altering the gene expression landscape |
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