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Sample GSM7698006

Query DataSets for GSM7698006

Status

Public on Aug 14, 2023

Title

HL60_COMBO_2

Sample type

SRA

Source name

hematopoetic

Organism

Homo sapiens

Characteristics

tissue: hematopoetic
cell line: HL-60
cell type: non-adherent
treatment: Decitabine+Simvastatin

Treatment protocol

HL-60 cells in each group (DMSO, DAC 0.5 μM, simvastatin 10 μM, and DAC+simvastatin) were harvested 36 hours after exposure to each treatment

Growth protocol

HL-60 (CCL-240, ATCC) cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% P/S.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using an RNeasy Mini Kit (Qiagen), and RNA integrity and purity were checked using Agilent 2100 Bioanalyzer (Agilent Technologies). 1.0μg of total RNA was used for the construction of sequencing libraries.
After mRNA enrichment using oligo(dT) beads and rRNA depletion using the Ribo-Zero Plus rRNA Depletion Kit (Illumina), cDNA was synthesized using an mRNA template and random primers, second-strand synthesis buffer, dNTPs, RNase H and DNA polymerase I. The double-stranded cDNA library was completed by “A” base ligation and sequencing adaptor ligation. The quality and quantity of these libraries were checked using Qubit 2.0 (Thermo Fisher Scientific), Agilent 2100, and quantitative PCR using the Real-time PCR Systems Step One Plus (Applied Biosystems).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Read quality was confirmed using FastQC.
Sequence reads were trimmed for adaptor sequence/low-quality sequence.
These reads were aligned to the GRCh38 reference genome using the HISAT2 pipeline.
Transcripts per million (TPM) were calculated based on the length of the gene and the number of reads mapped to each gene.
Differential expression analysis among each group was performed using the DESeq2 R package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes TPM counts for each sample.

Submission date

Aug 09, 2023

Last update date

Aug 14, 2023

Contact name

Tomohiro Yabushita

E-mail(s)

[email protected]

Organization name

The University of Tokyo

Street address

7-3-1, Hongou, Bunkyo-ku