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| Status |
Public on Mar 16, 2015 |
| Title |
RNASeq_Resistance1 |
| Sample type |
SRA |
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| Source name |
resistant basal cell cancers
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| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
cell type: basal cell carcinomas (BCCs)
response to smoothened (smo) inhibitors: Resistance
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| Extracted molecule |
total RNA |
| Extraction protocol |
2ug of total RNA was extracted from tissue samples stored in RNA later using the RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. RNA integrity was confirmed with the Agilent 2001 bioanalyzer.
cDNA were prepared using the Ovation RNA- Seq System V2 (NuGen) per the manufacturer’s protocol. cDNA libraries were sheared by sonication (Covaris model S1) and purified using the Qiagen Minelute Kit. End repair was performed with T4 DNA Polymerase, T4 Polynucleotide Kinase, and Klenow DNA polymerase (New England Biolabs) at 20 ̊C for 30 min and purified using the Qiagen Minelute Kit. dA-tailing was performed with Klenow fragment 3’ to 5’ exonuclease (New England Biolabs) at 37 ̊C for 30 min and purified using the Qiagen Minelute Kit. Adapter ligation was performed with Illumina adapters and T4 DNA Ligase (New England Biolabs), purified with Qiagen Minelute Kit, and 150-400 basepair fragments were gel purified on a 3% GTG low melting point agarose gel. RNA-Seq libraries were PCR amplified 18 cycles with Phusion DNA polymerase (New England Biolabs), purified with Qiagen Minelute Kit, and size-selected on a 3% GTG low melting point agarose gel. RNA-Seq libraries were analyzed with the Agilent 2001 bioanalyzer and were sequenced paired-end at 100bp using an Illumina HiSeq 2500.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
RNA-Seq reads were aligned to the human reference genome sequence (hg19) with TopHat. Expression in FPKM was calculated by cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: RPKM values. Each column represents an independent sample and each row represents a gene.
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| Submission date |
Jun 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiang Li |
| E-mail(s) |
jiangli@stanford.edu
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| Phone |
6507258839
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| Organization name |
Stanford University
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| Department |
Dermatology
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| Lab |
Tony Oro
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| Street address |
269 Campus Drive, Stanford University
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE58375 |
SMO variants explain the majority of drug resistance in basal cell carcinoma [RNA-Seq] |
| GSE58377 |
SMO variants explain the majority of drug resistance in basal cell carcinoma |
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| Relations |
| BioSample |
SAMN02849613 |
| SRA |
SRX588237 |
| 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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