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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 02, 2012 |
| Title |
Stat5-null rep2 in P6 |
| Sample type |
SRA |
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| Source name |
Mammary gland
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| Organism |
Mus musculus |
| Characteristics |
sample tag: #1217
strain: 129SV::FVB/N::C57BL/6
tissue: Mammary gland
developmental stage: Day 6 of pregnancy
genotype: Stat5abfl/fl;MMTV-Cre
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| Growth protocol |
Animals were handled and housed in accordance with the guidelines of NIH and all experiments were approved by the Animal Care and Use Committee of NIDDK. By mating Stat5ab+/- mice (Cui et al., 2004) with Stat5a-/- mice (Liu et al., 1997) and Stat5b-/- mice (Udy et al., 1997), we generated mice carrying a null allele of the Stat5ab locus and one functional allele of either Stat5a (Stat5ab-/Stat5b-) or Stat5b (Stat5ab-/Stat5a-). Stat5abf/f mice (Cui et al., 2004) were mated with the MMTV-Cre transgenic mouse line A (Wagner et al., 1997) in order to generate Stat5abf/f;MMTV-Cre mice (Yamaji et al., 2009).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mammary tissues without lymph nodes from two mice of each genotype were collected, frozen in liquid nitrogen, and stored at -80 °C. Total RNA was extracted using TRIzol reagent, followed by a cleanup step using the RNeasy Plus Mini Kit (QIAGEN). Poly(A) RNA was purified twice from 1 mg total RNA and cDNA was synthesized using SuperScript II (Invitrogen) and TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA), and sequenced using HiSeq 2000 (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls performed using the CASAVA software
Sequenced reads were aligned to the mm9 genome assembly using the TopHat program (Trapnell et al., Bioinformatics, 2009)
Fragment Per Kilobase of exon per million fragments mapped (FPKM) were calculated using a protocol (Mortazavi et al., Nat. Methods, 2008). 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.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files (P6 and L1) include FPKM values for each Sample
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| Submission date |
Apr 29, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Keunsoo Kang |
| E-mail(s) |
[email protected]
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| Phone |
82-41-550-3456
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| Organization name |
Dankook University
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| Department |
Microbiology
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| Lab |
Computational Biology Lab
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| Street address |
Dandae-ro 119
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| City |
Cheonan |
| State/province |
Chungnam |
| ZIP/Postal code |
31116 |
| Country |
South Korea |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE37646 |
Distinct STAT5 concentrations uniquely control establishment and differentiation of mammary epithelium during pregnancy |
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| Relations |
| SRA |
SRX145296 |
| BioSample |
SAMN00990427 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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