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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 01, 2013 |
| Title |
Hoxd9,10,11-/- vas deferens, pooled from n=3 |
| Sample type |
SRA |
| |
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| Source name |
Hoxd9,10,11-/- vas deferens
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| Organism |
Mus musculus |
| Characteristics |
strain background: CD1/129
genotype/variation: Hoxd9,10,11-/-
tissue: vas deferens
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fresh tissue using the Qiagen RNeasy Mini kit
RNA libraries were prepared for sequencing using Illumina TruSeq reagents and protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
VasDKO
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| Data processing |
Tophat version April 2012 was used for basecalling and Bam files were generated
Avadis NGS version 1.3.1 was used to analyze Bam files and generate nRPKM values for each sample
Avadis NGS NewGene finding option was used
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include nRPKM values for each sample
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| Submission date |
Nov 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Steve Potter |
| E-mail(s) |
[email protected]
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| Organization name |
Cincinnati Children's Hospital Medical Center
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| Department |
Developmental Biology
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| Street address |
3333 Burnet Ave.
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE42339 |
RNA-Seq expression data from the reproductive tracts of WT, Hoxa91011, and Hoxd91011 mutant mice |
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| Relations |
| SRA |
SRX204864 |
| BioSample |
SAMN01815881 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1038113_VasDKO.txt.gz |
607.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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