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| Status |
Public on Oct 01, 2017 |
| Title |
KO_Oil Brep2 Trep2 |
| Sample type |
SRA |
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| Source name |
HSC
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
age: 3 months
genotype: Esr1fl/fl;Mx1-Cre
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| Treatment protocol |
2 month old male mice (Esr1fl/fl and Esr1fl/fl;Mx1-Cre) were treated with Poly(I:C ) intraperitoneally every other day for a total of 6 treatments. Upon reaching 3 months of age, Poly(I:C) treated mice were then treated injected with 100 microliters of corn oil containing 2 micrograms of oestradiol.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly isolated HSCs were sorted into Trizol and total RNA was extracted per manufacturers instructions.
Ion Torrent Libraries were constructed using cDNA generated with NuGEN Ovation 2 protocol. After Covaris shearing, Ion Torrent libraries were made with the KAPA Library Preparation Kit (KK8301) per manufacturers instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Description |
KO Oil
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| Data processing |
Basecalls were provided by Torrent Suite (version 4.0.2)
Reads were mapped to mm10 using STAR (version 2.5.1b), with an mm10-derived index, and the following parameters: outFilterType (BySJout), outFilterMultimapNmax (20), alignSJoverhangMin (8), alignSJDBoverhandMin (1), outFilterMismatchNmax (999), alignIntronMin (20), alignIntronMax (1000000), alignMatesGapMax (1000000), twopassMode (Basic), sjdboverhang (100)
Overlap with genes was determined using the function “summarizeOverlaps” from the R package “GenomicAlignments” (version 1.8.4), with Ensembl release 84 as a reference.
FPKM (fragments per kilobase of exon per million reads) values were derived from the gene overlap data, using the function “fpkm” from the R package “DESeq2” (version 1.12.4).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated file containing FPKM values generated using DESeq2 (version 1.12.4) and Ensembl release 84
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| Submission date |
May 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Daisuke Nakada |
| E-mail(s) |
nakada@bcm.edu
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| Organization name |
Baylor College of Medicine
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| Department |
Molecular and Human Genetics
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| Street address |
One Baylor Plaza
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL18635 |
| Series (1) |
| GSE99120 |
RNA-Seq of hematopoietic stem cells from vehicle and estrogen-treated mice |
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| Relations |
| BioSample |
SAMN07150500 |
| SRA |
SRX2839540 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2633770_KO_Oil_Brep2_Trep2.tsv.gz |
261.8 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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