Whole transcriptome sequence data of 5-FU sensitive and 5-FU resistant tumors generated in a mouse model of de novo carcinogenesis

We have performed whole transcriptome sequencing of 5-FU resistant and 5-FU sensitive tumors generated in a mouse model of de novo carcinogenesis that closely recapitulates tumor initiation, progression and maintenance in vivo. Tumors were generated using the DMBA/TPA model of chemically induced carcinogenesis [1], tumor-bearing mice were subsequently treated with 5-FU, and tumor growth as well as response to treatment was monitored by measuring tumor volume twice a week. Based on these measurements, we selected two 5-FU resistant and two 5-FU sensitive tumors and performed whole transcriptome sequencing and in order to identify differentially expressed transcripts between the two sets. Data obtained is deposited and available through NCBI SRA (reference number SRP155180 – https://www.ncbi.nlm.nih.gov/sra/?term=SRP155180).


a b s t r a c t
We have performed whole transcriptome sequencing of 5-FU resistant and 5-FU sensitive tumors generated in a mouse model of de novo carcinogenesis that closely recapitulates tumor initiation, progression and maintenance in vivo. Tumors were generated using the DMBA/TPA model of chemically induced carcinogenesis [1], tumor-bearing mice were subsequently treated with 5-FU, and tumor growth as well as response to treatment was monitored by measuring tumor volume twice a week. Based on these measurements, we selected two 5-FU resistant and two 5-FU sensitive tumors and performed whole transcriptome sequencing and in order to identify differentially expressed transcripts between the two sets. Data obtained is deposited and available through NCBI SRA (reference number SRP155180https://www.ncbi.nlm.nih. gov/sra/?term ¼SRP155180 Value of the data Data in this article can be used to identify differentially expressed genes between tumors that are sensitive or resistant to treatment with 5-FU.
These transcripts represent potential markers of response to treatment with 5-FU. Thus, data presented herein could facilitate the development of clinically meaningful biomarker signatures of response to 5-FU and contribute towards personalized cancer treatment.

Data
Eight raw sequence read data files are shared. Two 5-FU sensitive (S1 and S2) and two 5-FU resistant (NR1 and NR2) tumors were sequenced, and each tumor is represented with two technical replicates (A and B) (Figs. 1 and 2).

DMBA/TPA treatment
Treatment with 200 μl of 0.03 μmol/μl DMBA (Sigma-Aldrich, cat. # D3254) was administered once on the back of 7-8 weeks old mice previously shaved at the area. Two weeks after DMBA administration, we initiated treatment with 2.5 μg TPA diluted in 200 μl acetone twice a week (Sigma-Aldrich, cat. #P8139) until a mouse was sacrificed.

Treatment with 5-Fluorouracil
Treatment with 50 mg/kg of 5-FU was initiated when the first tumor on a mouse reached 3-4 mm in size. The drug was administered intraperitonially (5-FU; Sigma-Aldrich, cat. # F6627) once a week, until any tumor on the animal reached $ 1 cm in diameter, at which point the mouse was sacrificed.

Tumor measurements
Measurements of tumor volume on a mouse were recorded twice a week during treatment with 5-FU, as previously described [5]. As tumors generated here had an ellipsoid shape, tumor volume (V) was calculated using the formula: where x and y denote the length and width of the tumor respectively [6].
In order to determine sensitivity and resistance to 5-FU treatment, we compared tumor volume measurements obtained right before commencing treatment with 5-FU with volumes of the same tumors just right before sacrificing the animal. Sensitive tumors were selected based on at least 50% reduction in tumor size, and resistant tumors were selected as those with at least 2-fold growth in volume despite treatment with 5-FU. One sensitive and one resistant tumor were selected from each animal for sequencing.
Magnetic beads with Oligo (dT) were subsequently used to isolate mRNA which was then fragmented into short fragments, purified and resolved for end reparation and single nucleotide A (adenine) addition. The short mRNA fragments were connected with adapters, subjected to agarose gel electrophoresis, and cDNA was subsequently synthesized using the mRNA fragments as templates through PCR amplification. Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System were used for quantification and qualification of the sample library, and the library was then sequenced using Illumina HiSeq™ 2000. Sequence alignment and quantification analysis of gene expression was done using SOAPaligner/SOAP2 [7]. Transcript reads were assembled using Cufflink [8]. KEGG [9] was used to perform pathway enrichment analysis of differentially expressed genes (DEGs), and expression pattern analysis was performed using Cluster [10] and JavaTreeView [11]. Gene expression levels were measured and normalized using the RPKM method [12]. For each pair of sensitive and resistant tumor samples, we then calculated the log2-ratio of each gene's corresponding RPKM value, and subsequently calculated the p-value for the test that the expression levels between the two samples for a specific gene are different. Since multiple comparisons were performed, we corrected these p-values using the Benjamini and Yekutieli method [13]. We consider significant DEGs those with adjusted p values less than 1e À 4 .