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Sample GSM3790175 Query DataSets for GSM3790175
Status Public on Apr 07, 2020
Title RNA_CMP_nonBMT_WT_rep3
Sample type SRA
 
Source name bone marrow cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: bone marrow
cell type: CMP
genotype: WT
Extracted molecule total RNA
Extraction protocol RNA-seq experiments were performed using LSK or CMP cells obtained from WT-, SKO-, RKO-, or DKO-transplanted mice.
RNA was extracted using RNeasy Mini Kit (QIAGEN) or NucleoSpin RNA XS (Macherey-Nagel). Libraries for RNA-seq were prepared using the NEBNext Ultra RNA Library Prep kit for Illumina (New England BioLabs) and were subjected to sequencing using HiSeq 2500 instrument (Illumina) with a standard 125-bp paired-end protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description RNA_CMP_nonBMT_cpm.txt
Data processing RNA-seq experiments were performed in three or more biological replicates. The sequencing reads were aligned to the mouse reference genome (mm9) using STAR7 (v2.5.3).
Reads on each gene were counted with featureCounts (v1.5.3) from Subread package, and edgeR package in R was used to identify the differentially expressed genes with FDR threshold of 0.05 and to generate the multidimensional scaling (MDS) plot.
The analysis was performed in genes expressed at >1 count per million (CPM) in two or more samples, and generalized linear models were used to compare gene expression data.
Genome_build: mm9
Supplementary_files_format_and_content: Reads on each gene were counted with featureCounts (v1.5.3) from Subread package, and edgeR package in R was used.
 
Submission date May 21, 2019
Last update date Apr 07, 2020
Contact name Yotaro Ochi
Organization name Kyoto Univiersity
Department Department of Pathology and Tumor Biology
Street address Yoshida-Konoe-cho
City Kyoto
ZIP/Postal code 606-8501
Country Japan
 
Platform ID GPL17021
Series (2)
GSE131581 Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes [RNA-seq]
GSE131583 Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes
Relations
BioSample SAMN11808176
SRA SRX5877931

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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