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| Status |
Public on Apr 04, 2016 |
| Title |
RNA-seq of human differentiated keratinocytes (DK) rep1 |
| Sample type |
SRA |
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| Source name |
DK
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Differentiated Keratinocytes
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| Treatment protocol |
None
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| Growth protocol |
KP cells were obtained from foreskin biopsies of healthy neonatal donors and expanded by cultivation onto lethally irradiated 3T3-J2 cells in growth FAD medium, a DMEM and Ham’s F12 media mixture (2:1) containing FCS (10%), penicillin-streptomycin (1%), glutamine (2%), insulin(5ug/ml), adenine (24.3ug/ml), hydrocortisone (0.4ug/ml), cholera toxin (50ug/ml), triiodotyronine (2nM). DKs were cultivated in KGM serum-free medium (Invitrogen), penicillin-streptomycin (1%) and glutamine (2%).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen, Grand Island, NY) and treated sequentially with the RNeasy Mini Kit (Qiagen, Valencia, CA) and Turbo DNA Free (Ambion, Grand Island, NY).
RNA-seq libraries were prepared from 300 ng RNA using the TruSeq RNA Sample Preparation kit (Illumina) and 75-bp single-end sequences were obtained on a NextSeq 500 Instrument (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Sequence tags were mapped to reference genome Hg19 using TopHat v2.0.6 and transcript levels in triplicate samples were calculated as fragments per kb per 106 mapped reads (FPKM) using Cufflinks v2.0.2.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM were obtained using Cufflinks
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| Submission date |
Feb 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Luca Petiti |
| E-mail(s) |
luca.petiti@itb.cnr.it
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| Organization name |
ITB-CNR
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| Street address |
Via Fratelli Cervi, 93
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| City |
Segrate |
| State/province |
Milan |
| ZIP/Postal code |
20090 |
| Country |
Italy |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE64328 |
Transcriptional Regulationand Chromatin Dynamics inHuman Epithelial Cell Differentiation |
| GSE78725 |
Transcriptional Regulationand Chromatin Dynamics inHuman Epithelial Cell Differentiation (RNA-seq) |
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| Relations |
| BioSample |
SAMN04519516 |
| SRA |
SRX1603683 |
| 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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