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| Status |
Public on Apr 07, 2020 |
| Title |
RNA_HL60_KO_DKO_5 |
| Sample type |
SRA |
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| Source name |
HL-60
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HL-60
genotype: STAG2/RUNX1 KO
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
HL60_DKO_48
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| 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.
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| Submission date |
Feb 28, 2020 |
| Last update date |
Apr 07, 2020 |
| Contact name |
Yotaro Ochi |
| Organization name |
Kyoto Univiersity
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| Department |
Department of Pathology and Tumor Biology
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| Street address |
Yoshida-Konoe-cho
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| City |
Kyoto |
| ZIP/Postal code |
606-8501 |
| Country |
Japan |
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| 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 |
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| Relations |
| BioSample |
SAMN14247795 |
| SRA |
SRX7820355 |
| 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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