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| Status |
Public on Jul 15, 2020 |
| Title |
KW239S20T |
| Sample type |
SRA |
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| Source name |
mammary tumor
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| Organism |
Mus musculus |
| Characteristics |
time of collection: tumor ~10% body weight
strain: FVB
diet: 20% (200g/kg) isolated soy protein
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| Treatment protocol |
mating mice were fed 20% ISP, 1% ISP, 20% casein or Teklad 2018 diets and mother's were maintained on this diet during lactation and pups were maintained on this diet after weaning and until the end of the study. At PND100, MTB-IGFIR mice fed the 20% ISP, 1%ISP and 20% casein diets were switched to the appropriate ISP or casein diet containing 100mg/kg of doxycycline until the end of the study.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted using mirVana miRNA Isolation Kit following the manufacturer's protocol
Library construction was performed by Novogene. rRNA was removed using the Riob-Zero kit that leaves mRNA. mRNA is randomly fragmented and cDNA synthesized using mRNA template and random hexamer primers and custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase were added to initiated second strand synthesis. After a series of terminal repair, A ligation and sequencing adaptor ligation, the double stranded DNA library was completed through size selection and PCR enrichment
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
remove reads containing adapters
remove reads containing N>10% (N represents the base cannot be determined)
remove reads containing low quality (Qscore<=5) base which is over 50% of the total base
RNA-seq data were processed and interpreted with Genialis platform. An automated data analysis pipeline run in the Genilais platform consisted of the following: Sequence quality checks were performed on raw and trimmed reads with FastQC. Trimmomatic was used to trim adapters and filter out poor quality reads. Trimmed reads were then mapped to the reference genome (UCSC GRCm 38) using the HISAT2 aligner. Gene expression levels were quantified with HTSeq-count , and differential gene expression analyses were performed with DESeq2. Lowly-expressed genes, which have expression count summed over all samples below 10, were filtered out from the differential expression analysis input matrix.
Genome_build: GRCm 38
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| Submission date |
Nov 07, 2018 |
| Last update date |
Jul 15, 2020 |
| Contact name |
Roger Moorehead |
| E-mail(s) |
rmoorehe@uoguelph.ca
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| Organization name |
University of Guelph
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| Department |
Biomedical Sciences
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| Street address |
50 Stone Rd E
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| City |
Guelph |
| ZIP/Postal code |
N1G2W1 |
| Country |
Canada |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE122294 |
RNA sequencing of mammary tumors induced in MTB-IGFIR transgenic mice fed 20% ISP, 1% ISP, or 20% Casein |
| GSE122316 |
RNA sequencing of pubertal mammary glands and mammary tumors from MTB-IGFIR transgenic mice fed diets containing different levels of isolated soy protein |
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| Relations |
| BioSample |
SAMN10393078 |
| SRA |
SRX4993739 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3463550_KW239S20T_paired_filtered_rc.tab.gz |
102.0 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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