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Sample GSM5710062 Query DataSets for GSM5710062
Status Public on Nov 01, 2022
Title LSCs, cxcl12_WT4_2
Sample type SRA
 
Source name Bone marrow
Organism Mus musculus
Characteristics strain: C57BL/6JRj
tissue: Bone marrow
cell type: Leukemia stem cells (LSCs)
genotype: Prx1-Cxcl12-wild type
Extracted molecule polyA RNA
Extraction protocol Bone marrow cells were harvested from bones and LSCs were sorted by Fluorescence-activated cell sorting according to the manuscript methods description. Low input 3´end RNA-Seq was performed following Massively Parallel RNA sequencing (MARS-Seq) protocol adapted for bulk RNA-Seq and sequenced using Illumina NextSeq 500.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The quality of the samples was verified using FASTQC software. FASTQ files were mapped to mouse genome assembly version GRCm38, UCSC version M25, using Salmon version 1.3 using default parameters.
Gene expression quantification were then imported to R using tximport package
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file including Matrix table with raw count values for each gene
 
Submission date Dec 01, 2021
Last update date Nov 01, 2022
Contact name Itziar Cenzano
E-mail(s) icenzano@unav.es
Organization name CIMA Universidad de Navarra
Street address Avenida de Pio XII, 55
City Pamplona
State/province Navarra
ZIP/Postal code 31008
Country Spain
 
Platform ID GPL19057
Series (1)
GSE189928 The bone marrow niche regulates redox and energy balance in leukemia stem cells
Relations
BioSample SAMN23532311
SRA SRX13273095

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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