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| Status |
Public on May 15, 2020 |
| Title |
si-CLOCK ZT44 |
| Sample type |
SRA |
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| Source name |
NHEK_CLOCK siRNAs
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| Organism |
Homo sapiens |
| Characteristics |
cell line: NHEK
cell type: Human epidermal keratinocytes, neonatal
passages: 3
transfected with: CLOCK siRNAs for 8 h
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| Treatment protocol |
The cells were transfected with either scrambled or CLOCK siRNAs for 8 h and incubated overnight in the growth medium. The cells were then synchronized with serum-rich medium for 2 h at ZT 0.
For UV irradiation, the cells were treated with 20 mJ/cm2 UVB using BIO-SUN UV-H (VILBER LOURMAT, France) at ZT 20, and the cells were cultured back in fresh KBM. The cells were harvested at ZT 32 and 44.
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| Growth protocol |
Human epidermal keratinocytes, neonatal (NHEKs), were purchased from Lonza (Clonetics Lonza, Walkersville, MD) and maintained in Keratinocyte Growth Medium (KGM)-Gold supplemented with BulletKit (Lonza). The cells were cultured at 37°C in a humidified incubator containing 5% CO2.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were extracted using the TRIzol reagent (Invitrogen)), and poly-A containing mRNAs were purified and converted into a cDNA library.
Subsequent cluster generation and DNA sequencing following the instructions of the illumina® TruSeq RNA sample preparation kit (Illumina, San Diego, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
data column (in the'FPKM_all_samples.xlsx'): 4_FPKM
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| Data processing |
Sequence reads were mapped to hg19 by TopHat (v2.0.11) using Bowtie2 (v2.1.0)
FPKM abundances were estimated by Cufflink (v2.1.1) with -G option
Genome_build: hg19
Supplementary_files_format_and_content: Microsoft Excel file include FPKM values of 4 samples
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| Submission date |
May 15, 2017 |
| Last update date |
May 15, 2020 |
| Contact name |
Sunyoung Park |
| E-mail(s) |
ivysy@hanmail.net
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| Organization name |
Amorepacific corporation
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| Street address |
1920, Yonggu-daero
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| City |
Yongin-si |
| State/province |
Gyeonggi-do |
| ZIP/Postal code |
17074 |
| Country |
South Korea |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE98900 |
TIMP3, a CLOCK-controlled gene, determines cell susceptibility to UV-induced expression of inflammatory factors in human keratinocytes. |
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| Relations |
| BioSample |
SAMN07109651 |
| SRA |
SRX2821735 |
| 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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