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Sample GSM6736179 Query DataSets for GSM6736179
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.
 
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
 
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

Supplementary file Size Download File type/resource
GSM6736179_s17.tabular.txt.gz 126.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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