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| Status |
Public on Aug 18, 2019 |
| Title |
C646-rep1 |
| Sample type |
SRA |
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| Source name |
Mammary tumor tissue
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| Organism |
Mus musculus |
| Characteristics |
strain: MMTV-PyVT
tissue: Mammary tumor tissue
treatment: 1mg/kg C646 injection
age: 12 weeks old
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| Extracted molecule |
total RNA |
| Extraction protocol |
For both normal mammary gland and tumor samples, 20 mg tissue was used for RNA extraction. Total RNA was extracted by using EASYspin RNA Mini Kit (Aidlab RN07).
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat v2.1.1 with default parameters.
The gene expression level was calculated by Cufflinks (v 2.2.1).
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.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.
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| Submission date |
Aug 20, 2018 |
| Last update date |
Aug 19, 2019 |
| Contact name |
Qinglan Li |
| E-mail(s) |
liqinglan@whu.edu.cn
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| Organization name |
Wuhan University
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| Street address |
Room 5005, Life Science College, Wuhan University
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| City |
Wuhan City |
| State/province |
Hubei Province |
| ZIP/Postal code |
430062 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE118802 |
The genome-wide enhancer profiling of breast cancer in the MMTV-PyVT mice [RNA-seq] |
| GSE118812 |
The genome-wide enhancer profiling of breast cancer in the MMTV-PyVT mice |
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| Relations |
| BioSample |
SAMN09866097 |
| SRA |
SRX4580510 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3348000_C646-rep1.txt.gz |
164.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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