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Sample GSM4404074 Query DataSets for GSM4404074
Status Public on Mar 10, 2020
Title 1502_IRN_144h_3
Sample type SRA
 
Source name Ewing sarcoma
Organism Homo sapiens
Characteristics tissue: Ewing sarcoma
tumor: ES4 xenograft
treatment: irinotecan, 2.5mg/kg
harvest time: 144 hour
Treatment protocol Mice were randomized into groups of 10, and treatment was started when tumors were 200-400 mm^3. Eribulin was dissolved in sterile water and administered days 1 and 8, and irinotecan was dissolved in saline and administered days 1-5, with the cycle repeated at day 21. Eribulin was dosed at 1 mg/kg and irinotecan at 2.5 mg/kg. Both drugs were administered by intraperitoneal injection.
Growth protocol C.B.17SC scid−/− (C.B-Igh-1b/IcrTac-Prkdcscid) female mice (Taconic Farms, Germantown NY) were used to propagate subcutaneously implanted tumors. All mice were maintained under barrier conditions and experiments were carried out using protocols and conditions approved by the institutional animal care and use committee of UTHSA.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from snap-frozen xenografts chilled under liquid nitrogen to prevent thawing. RNA was extracted with TRIzol reagent and purified on an RNeasy mini column (Qiagen). On-column DNase digestion was performed with Qiagen RNase-free DNase kit.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. To remove RNA species from host (mouse RNA), a custom-designed algorithm was performed to align reads using TopHat2 to both host genome (mm9) and graft genome (hg19). We kept reads as human-specific or human/mouse-common based on number of mis-match bases, number of gaps and alignment QC scores. The human RNA sequence reads (unique to human + common human/mouse) were then re-aligned to graft genome hg19 using TopHat2, and the BAM files obtained after alignment were processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
 
Submission date Mar 09, 2020
Last update date Mar 10, 2020
Contact name Yidong Chen
E-mail(s) cheny8@uthscsa.edu
Phone 2105629163
Organization name UT Health Science Center at San Antonio
Department Population Health Sciences
Street address 8403 Floyd Curl Drive, MSC 7784
City San Antonio
State/province Texas
ZIP/Postal code 78229
Country USA
 
Platform ID GPL21290
Series (1)
GSE146687 Evaluation of Eribulin Combined with Irinotecan for Treatment of Pediatric Cancer Xenografts
Relations
BioSample SAMN14341530
SRA SRX7883580

Supplementary file Size Download File type/resource
GSM4404074_Sample_ES_4_1502_IRN_144h_3_Genes_ReadCount.txt.gz 98.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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