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| Status |
Public on May 08, 2024 |
| Title |
43_MEKi.SPP1.CD44_2 |
| Sample type |
SRA |
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| Source name |
M150543
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| Organism |
Homo sapiens |
| Characteristics |
cell line: M150543
cell type: melanoma
treatment: MEKi.SPP1.CD44
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| Treatment protocol |
M150543 melanoma cells were treated with MEKi for 20 hours alone or in combinatorial treatments: SPP1+MEKi; CD44 blocking antibody +MEKi; or SPP1+CD44 blocking antibody+MEKi. The pre-stimulations with SPP1 or CD44 blocking antibody was performed 2 hours before MEKi treatment.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was collected using the Direct-zol RNA MiniPrep according to manufacturer’s guidelines. The quality of the isolated RNA was determined with a Fragment Analyzer (Agilent, Santa Clara, California, USA). The TruSeq Stranded mRNA (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent, Santa Clara, California, USA). The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20.
Illumina TruSeq mRNA stranded
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X Plus |
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| Description |
150 bp
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| Data processing |
FASTQ files were checked for quality with FastQC (version 0.11.9) and trimmed using Trimmomatic (version 0.39). Trimmed fastq files were aligned to the human genome annotation (retrieved from Ensembl) using STAR algorithm (version 2.7.10a)
Assembly: GRCh38 release 105
Supplementary files format and content: tab delimited text file including raw counts for each sample
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| Submission date |
Mar 29, 2024 |
| Last update date |
May 08, 2024 |
| Contact name |
Lukas Sommer |
| E-mail(s) |
[email protected]
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| Organization name |
University of Zurich
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| Department |
Institute of Anatomy
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| Street address |
Winterthurerstrasse 190
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| City |
Zurich |
| State/province |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
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| Platform ID |
GPL34284 |
| Series (1) |
| GSE262779 |
Monitoring of melanoma patients on treatment reveals a distinct macrophage population driving targeted therapy resistance |
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| Relations |
| BioSample |
SAMN40653652 |
| SRA |
SRX24098448 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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