|
Status |
Public on Dec 19, 2023 |
Title |
CML 2 NDC 72 HRS |
Sample type |
SRA |
|
|
Source name |
peripheral blood
|
Organism |
Homo sapiens |
Characteristics |
tissue: peripheral blood cell type: CD34+ stem/progenitor cells disease state: CML chronic phase diagnosis treatment: no drug treatment time: 72 hrs age: 57 Sex: F
|
Treatment protocol |
Primary CD34+ CML cells were treated with nilotinib (3 µM), idasanutlin (166 nM), or a combination for 24 hr or 72 hr.
|
Growth protocol |
CML CD34+ cells were cultured for up to 72 hrs at 37oC in serum free media (20% BIT, 100 μM β-mercaptoethanol, 0.04 mg/mL low density lipoprotein, 2 mM L-glutamine and 1% penicillin-streptomycin in IMDM) containing physiological levels of growth factors (SCF 0.2ng/mL, G-CSF 1ng/mL, GM-CSF 0.2ng/mL, IL-6 1ng/mL, LIF 0.05ng/mL, MIP-α 0.2ng/mL, StemCell Technologies).
|
Extracted molecule |
total RNA |
Extraction protocol |
The cells were pelleted by centrifugation in culture media, washed and then pelleted again in phosphate buffered saline pH 7.4, and total cellular RNA extracted from a minimum of 1 x106 cells in TRIzoLTM Reagent (ThermoFisher). The concentration of the RNA was measured using the Nanodrop 2000, and the quality and RIN value was determined using the Agilent Bioanalyser RNA Nano kit (Agilent). RNA-seq libraries were then prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) with single indexing following the manufacturers’ instructions. Libraries were quantified using the Agilent Bioanalyzer High Sensitivity DNA Kit.
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
Raw sequencing data was pre-processed using the University of Glasgow Galaxy server (https://www.polyomics.gla.ac.uk/galaxy.html) for which quality control was performed by FastQC (0.72) and the reads were trimmed by Trim Galore! (0.4.3.1). Trimmed reads were aligned to human reference genome hg38 using HISAT2 (2.1.0) and assigned by the feature counting tool featureCount (1.6.0.3). Differentially expressed genes between experimental conditions were obtained by DESeq2 (1.32.0) in R. Assembly: human reference genome GRCh38/hg38 Supplementary files format and content: Tab-delimited text files containing raw counts for each sample
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|
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Submission date |
Nov 17, 2022 |
Last update date |
Dec 19, 2023 |
Contact name |
David Vetrie |
E-mail(s) |
David.Vetrie@glasgow.ac.uk
|
Organization name |
Glasgow University
|
Department |
Institute of Cancer Sciences
|
Lab |
Vetrie lab
|
Street address |
Wolfson Wohl Cancer Research Centre
|
City |
Glasgow |
ZIP/Postal code |
G61 1QH |
Country |
United Kingdom |
|
|
Platform ID |
GPL20301 |
Series (1) |
GSE218183 |
Bulk RNA-seq analysis of primary CML CD34+ cells (n=3) treated with idasanutlin alone or in combination with nilotinib in vitro |
|
Relations |
BioSample |
SAMN31769706 |
SRA |
SRX18292895 |