NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6108226 Query DataSets for GSM6108226
Status Public on Mar 01, 2024
Title PYMT_T_1
Sample type SRA
 
Source name tumors
Organism Mus musculus
Characteristics strain: MMTV-PyMT
genotype: without miR-9 knockout
Sex: female
tissue: tumors
Growth protocol All animal experiments strictly complied with protocols approved by the Animal Welfare and Ethics Committee (AWEC) of China Pharmaceutical University. MiR-9-exon 1 knockout heterozygous (miR-9+/-) mice and MMTV-PyMT (stock No. 022974) transgenic mice were obtained from Shanghai Nanfang model Biotechnology Co., Ltd. All mice were on a mixed C57BL/6 background with littermate controls (females) used in all experiments. Tumours were collected and total RNA was extracted.
Extracted molecule total RNA
Extraction protocol Tumours were collected and subjected to RNA extraction and deep sequencing, in parallel, using Illumina NovaSeq 6000.
RNA was harvested using TriZol Up (Cat # ET111-01, TransGen Biotech, Beijing, China).
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Excel files include RPKM values for each Sample.
 
Submission date May 05, 2022
Last update date Mar 01, 2024
Contact name Lufeng Zheng
E-mail(s) zhlf1989513@163.com
Phone +86-02583271047
Organization name China Pharmaceutical University
Department School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention
Street address Tongjia Xiang 24
City Nanjing
State/province Jiangsu
ZIP/Postal code 210009
Country China
 
Platform ID GPL21493
Series (2)
GSE202303 Genome-wide maps in tumors of MMTV-PyMT mice with or without miR-9 knockout
GSE202309 MicroRNA-9 on the tumorigenesis of breast cancer in MMTV-PyMT mice model
Relations
BioSample SAMN28101385
SRA SRX15163902

Supplementary file Size Download File type/resource
GSM6108226_PYMT_T_1.xls.gz 101.3 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap