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Sample GSM4367009 Query DataSets for GSM4367009
Status Public on Apr 07, 2020
Title RNA_HL60_KO_WT_4
Sample type SRA
 
Source name HL-60
Organism Homo sapiens
Characteristics cell line: HL-60
genotype: WT
Extracted molecule total RNA
Extraction protocol RNA-seq experiments were performed using WT-, SKO-, RKO-, or DKO-cells.
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 or NovaSeq 6000 instrument (Illumina) with a 100-150 bp paired-end protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description HL60_WT_D
Data processing RNA-seq experiments were performed in two or more biological replicates. The sequencing reads were aligned to the reference genome (hg19 or 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: hg19, 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 Feb 28, 2020
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 GPL24676
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 SAMN14247789
SRA SRX7820360

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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