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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.
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|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
|
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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.
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|
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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 |