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Sample GSM5239973 Query DataSets for GSM5239973
Status Public on Oct 02, 2023
Title trial number 03, Nonresponder at baseline
Sample type SRA
Source name Peripheral blood
Organism Homo sapiens
Characteristics diagnosis: Myeloproliferative neoplasms
treatment response: non-responder
timepoint: baseline
tissue: Peripheral blood
cell type: CD34+ HSPCs
Extracted molecule polyA RNA
Extraction protocol After ficoll centrifugation of blood, mononuclear cells were subjected to red blood cell lysis and CD34+ HSPCs were immunomagnetically isolated using the Ultrapure CD34 microbead kit suing AUTOMACS. RNA was extracted using Trizol.
Briefly, the Smart-seq2 protocol was implemented with improved reverse transcription, template switching and preamplification to increase both yield and length of cDNA libraries generated from individual cells. The Illumina-compatible cDNA sequencing library was prepared with Nextera XT DNA Library Preparation Kit
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description 03_00
Data processing Sequencing fastq files were demultiplexed using Casava v1.8.2 pipeline.
Reads with adapter contaminations were trimmed using cutadapt.
The alignment of reads to the reference genome was performed using TopHat version v2.1.0; the quantification of expression was performed using RSEM v1.17
Only genes with more than 2 counts per million in at least 2 samples were considered for statistical analysis.
Normalisation and differential expression analysis was performed using DESeq2
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: normalised expression matrix
Submission date Apr 13, 2021
Last update date Oct 02, 2023
Contact name Irina Mohorianu
Organization name University of Cambridge
Department Wellcome-MRC Cambridge Stem Cell Institute
Street address Puddicombe Way
City Cambridge
ZIP/Postal code CB2 0AW
Country United Kingdom
Platform ID GPL24676
Series (2)
GSE172022 Bulk RNAseq of primary CD34+ HSPCs in Myeloproliferative neoplasms patients receiving tamoxifen
GSE172025 RNA-seq of Myeloproliferative neoplasms primary CD34+ HSPCs and cell lines after tamoxifen treatment
BioSample SAMN18736926
SRA SRX10596375

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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