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Status |
Public on Nov 01, 2022 |
Title |
LSCs, cxcl12_WT4_2 |
Sample type |
SRA |
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Source name |
Bone marrow
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6JRj tissue: Bone marrow cell type: Leukemia stem cells (LSCs) genotype: Prx1-Cxcl12-wild type
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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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
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Submission date |
Dec 01, 2021 |
Last update date |
Nov 01, 2022 |
Contact name |
Itziar Cenzano |
E-mail(s) |
icenzano@unav.es
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Organization name |
CIMA Universidad de Navarra
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Street address |
Avenida de Pio XII, 55
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City |
Pamplona |
State/province |
Navarra |
ZIP/Postal code |
31008 |
Country |
Spain |
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Platform ID |
GPL19057 |
Series (1) |
GSE189928 |
The bone marrow niche regulates redox and energy balance in leukemia stem cells |
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Relations |
BioSample |
SAMN23532311 |
SRA |
SRX13273095 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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