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| Status |
Public on Sep 08, 2017 |
| Title |
Pt9-D15-A |
| Sample type |
SRA |
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| Source name |
tumor biopsy
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| Organism |
Homo sapiens |
| Characteristics |
mapki treatment: on-treatment
mapki type: BRAFi+MEKi
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
mirVana RNA extraction kit
KAPA Stranded mRNA-Seq Kits, stranded
Poly A transcript enrichment, paired end RNAseq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
Patient 9 melanoma, during BRAFi and MEKi treatment, day 15, 1st biopsy
PatientFPKM.batch3.xlsx
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| Data processing |
FASTQ files were mapped by Tophat2
Tophat BAMs were quantified and normalized using Cuffnorm, DGE were called by cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: The normalized expression levels in FPKM called by cuffnorm
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| Submission date |
Sep 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Willy Hugo |
| E-mail(s) |
hwilly@mednet.ucla.edu
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| Organization name |
UCLA
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| Department |
Medicine
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| Street address |
10833 Le Conte Ave, 52-121 CHS, Division of Dermatology
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| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (2) |
| GSE75313 |
Expression changes in Melanomas pre MAPKi treatment vs. on MAPKi treatment |
| GSE103658 |
Expression changes in Melanomas pre MAPKi treatment vs. on MAPKi treatment (RNA-seq_Patient.batch3) |
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| Relations |
| BioSample |
SAMN07625737 |
| SRA |
SRX3173616 |
| 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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