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| Status |
Public on Sep 14, 2017 |
| Title |
TC32_YK_RNAseq |
| Sample type |
SRA |
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| Source name |
TC32_YK_RNAseq
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| Organism |
Homo sapiens |
| Characteristics |
cell line: TC32 Ewing sarcoma cell line
genotype/variation: treatment with YK-4-279
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| Treatment protocol |
In treatment conditions, cells were treated with 3uM YK-4-279 (DMSO vehicle) for 15h
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| Growth protocol |
TC32 cells were grown in RPMI supplemented with 10% FBS at 37C in 5% CO2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a Qiagen RNeasy Mini Kit (Qiagen), and submitted to Otogenetics Corporation (Norcross, GA USA) for RNA-Seq assays. Briefly, the integrity and purity of total RNA were assessed using Agilent Bioanalyzer or Tapestation and OD260/280. cDNA was generated from high quality total RNA using SMARTer PCR cDNA Synthesis kit (Clontech Laboratories, Inc., Mountain View, CA USA, catalog# 634926).
The resulting cDNA was fragmented using Bioruptor (Diagenode, Inc., Denville, NJ USA), profiled using Agilent Tapestation, and subjected to Beckman Biomek FXp (Biomek 6000, Beckman Coulter) fully automatic workstation and a Beckman HT library kit (SPRIworks HT, Beckman Coulter, Inc. CA USA; PN B09855AA) to generate fragment libraries. The instructions were strictly followed to perform library construction. Briefly, after fragmentation the ends were repaired and 'A' bases were added to the 3' end of the fragments. Adapters were then ligated to both ends. The adaptor-ligated templates were further purified using Agencourt AMPure SPRI beads (Beckman Coulter, Inc. CA USA). The adaptor-ligated library was amplified by ligation-mediated PCR which consisted of 11 cycles of amplification, and the PCR product was purified using Agencourt AMPure SPRI beads again. After the library construction procedure was completed, QC was performed using Nanodrop 2000 (Thermo Scientific, USA) and an Agilent TapeStation (Agilent, USA) to ensure the library quality and quantity.
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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 |
Sequencing was performed on the Illumina HiSeq 2500 (Rapid run, Illumina, CA USA) with chemistry v1.0 and using the 2×106bp paired-end read mode and original chemistry from Illumina according to the manufacturer's instructions.
The initial data analysis was HiSeq 2500. The HiSeq Control Software 2.0.5 in combination with RTA 1.17.20.0 (real time analysis) performed the initial image analysis and base calling.
CASAVA-1.8.2 generated and reported run statistics and the final FASTQ files. Sequences were de-multiplexed according to the 6bp index code with 1 mismatch allowed.
FASTQ output was aligned with TopHat and quantified/normalized to the RefSeq GRCh37/hg19 transcriptome using the Cufflinks (v2.2.1) pipeline (with frag bias correction)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Gene-level FPKM
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| Submission date |
Sep 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Garrett Thomas Graham |
| E-mail(s) |
gtg9@georgetown.edu
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| Phone |
8148822017
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| Organization name |
Georgetown University Medical Center
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| Department |
Oncology
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| Street address |
3970 Reservoir Rd NW
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| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20007 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE103837 |
Inhibition of the oncogenic fusion protein EWS-FLI1 causes G2/M cell cycle arrest and enhanced vincristine sensitivity in Ewing sarcoma |
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| Relations |
| BioSample |
SAMN07638846 |
| SRA |
SRX3183026 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2782707_TC32_YK.fpkm.txt.gz |
648.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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