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| Status |
Public on Oct 15, 2018 |
| Title |
Control 1 |
| Sample type |
SRA |
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| Source name |
Foxo1f/f, uterus
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| Organism |
Mus musculus |
| Characteristics |
age: 8 weeks
strain: C57BL/6J
genotype/variation: Foxo1f/f
developmental stage: Pseudo pregnancy day 4.5
tissue: uterus
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| Treatment protocol |
Control Foxo1f/f and conditional knock out PgrCre/+ Foxo1f/f female mated with vasectomized males. Uteri harvest at day 4.5 of pseudopregnancy. Serum progesterone levels used to confirm stage of pregnancy.
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| Growth protocol |
standard chow
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the Qiagen RNeasy Kit
Illumina TruSeq RNA Sample Preparation Protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
FD41834
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| Data processing |
In order to increase the mappability, we trimmed 11 low-quality nucleotides from the 5’ ends of the reads.
The resulting 90-nucleotide pair-ended reads were mapped to the mouse genome (UCSC mm9) using STAR (Dobin et al., 2013) with NCBI RefSeq genes as the reference.
In order to reduce possible PCR biases, we removed the read duplicates using picard tools (http://broadinstitute.github.io/picard/)
HTseq (http://www-huber.embl.de/users/anders/HTSeq) was used to determine the number of reads falling in the known genes.
EdgeR (Robinson et al., 2010) was used to analyze the gene-based read counts to detect differentially expressed genes between the control and treatment groups.
Genome_build: mm9
Supplementary_files_format_and_content: EdgeR_KO.vs.WT_DE.txt reports Symbol, rawMeanCount_WT, rawMeanCount_KO, FC_edgeR, log2CPM_edgeR, PV_edgeR, FDR_edgeR, EntrezGene, geneName2.
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| Submission date |
Sep 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Rainer B Lanz |
| E-mail(s) |
[email protected]
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| Phone |
7137986478
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| Organization name |
Baylor College of Medicine
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| Department |
Molecular and Cellular biology
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| Street address |
One Baylor Plaza
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| City |
Houaton |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE72895 |
FOXO1 Regulates Uterine Epithelial Integrity and Progesterone Receptor Expression Critical for Embryo Implantation [RNA-seq] |
| GSE72896 |
FOXO1 Regulates Attachment of the Implanting Blastocyst to the Endometrium at the Window of Receptivity |
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| Relations |
| BioSample |
SAMN04045418 |
| SRA |
SRX1219627 |
| 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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