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| Status |
Public on Jul 24, 2024 |
| Title |
rifampicin 10uM 24h, rep3 |
| Sample type |
SRA |
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| Source name |
ShP51 (HepG2 derived)
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| Organism |
Homo sapiens |
| Characteristics |
cell line: ShP51 (HepG2 derived)
cell type: hepatocellular carcinoma
treatment: rifampicin 10uM
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| Treatment protocol |
Cells were treated with dimethyl sulfoxide (DMSO), or with 10µM or 100µM rifampicin dissolved in DMSO (Sigma-Aldrich, Burlington, MA, USA) for 24 h.
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| Growth protocol |
ShP51 cell lines were cultured in Dulbecco’s modified Eagle’s medium (high glucose) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, Waltham, MA, USA), 1× MEM Non-Essential Amino Acids Solution (Thermo Fisher Scientific), 100 U/mL penicillin, and 100 μg/mL streptomycin (Thermo Fisher Scientific). Cells were maintained in a humidified incubator, which provided an atmosphere of 5% CO2 and 95% air at a constant temperature of 37°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using a miRNeasy Mini Kit (Qiagen, Venlo, Netherlands).
CAGE libraries were prepared using a CAGE Library preparation kit (DNAform, Kanagawa, Japan). Briefly, cDNA was synthesized from total RNA using random primers. The ribose diols in the 5′ cap structures of RNA were oxidized and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (a process known as cap-trapping). RNA was digested with RNaseONE/H, adaptors were ligated to both ends of cDNA, and CAGE libraries of double-stranded cDNA were constructed.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
S06
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| Data processing |
Obtained reads were aligned with the reference human genome GRCh38 by using STAR (v2.7.5a), taking splice junctions of Gencode transcripts (v37) to improve the alignment accuracy. The first position of each uniquely mapped read was counted as the transcription initiation with CREate (https://github.com/hkawaji/CREate), bedtools (v2.29.2), and the utility programs of the UCSC Genome Browser Database (v425).
Assembly: GRCh38 (hg38)
Supplementary files format and content: The observed counts of transcription starting sites (CAGE tag starting site, CTSS) are included in BED format.
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| Submission date |
Jul 12, 2024 |
| Last update date |
Jul 24, 2024 |
| Contact name |
Hideya Kawaji |
| Organization name |
Tokyo Metropolitan Institute of Medical Science
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| Department |
Research Center for Genome & Medical Sciences
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| Street address |
2-1-6 Kamikitazawa
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| City |
Setagaya-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
156-8506 |
| Country |
Japan |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE272109 |
Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with drug efficacy and adverse reactions |
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| Relations |
| BioSample |
SAMN42466615 |
| SRA |
SRX25304308 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8393385_S06.10uM.Rif.24h.ctss.bed.gz |
11.9 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
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