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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 23, 2013 |
| Title |
Control Mouse #5 |
| Sample type |
SRA |
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| Source name |
Whole mouse lung
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/J
gender: Female
schisto exposure: None
disease state: control
treatment: None
tissue: whole lung
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| Treatment protocol |
Control group: no exposure. Schisto-PH group: 240 S. mansoni eggs IP/gram body weight, followed 2 weeks later by 240 S. mansoni eggs IV/gram body weight (tail vein injection), followed 1 week later by tissue harvest. 1D11 treated mice (in both the control and schisto-PH groups) were additionally administered 2 doses of 1D11 at 0.5ug/g body weight IP on the day of IV egg administration and 3 days thereafter (4 days prior to catheterization).
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| Growth protocol |
N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNAeasy kit
Illumina TruSeq RNA Sample Preparation kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Control 5
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| Data processing |
Groomer/Tophat/Bowtie/Cufflinks analysis performed using Galaxy (https://main.g2.bx.psu.edu/)
Groomer: map Illumina reads onto Sanger reads, using NCBI37/mm9 mouse genome database
Bowtie, Single-ended, Mapped to mouse mm9 genome, Maximum number of mismatches: 2, Maximum permitted total of quality values at mismatched read positions: 70, Seed length: 28, Alignment policy: MAQ-like, Alignments per read: 1, Maximum number of backtracks permitted when aligning a read: 125
Tophat v1.2.0, Anchor length: 8, Maximum number of mismatches that can appear in the anchor region of spliced alignment: 0, Minimum intron length: 70, Minimum intron length that may be found during split-segment (default) search: 50, Maximum intron length: 500,000, Max insertion length: 3, Max deletion length: 3, Minimum isoform fraction: 0.15, Maximum number of alignments allowed: 40, Number of mismatches allowed in the initial read mapping: 2, Number of mismatches allowed in each segment alignment for reads mapped independently: 2, Minimum length of read segments: 25, Minimum intron length that may be found during coverage search: 50, Maximum intron length that may be found during coverage search: 20,000
Cufflinks v1.0.3, Max Intron Length: 300,000, Min Isoform Fraction: 0.05, Pre MRNA Fraction: 0.05, Reference Annotation: mouse mm9 genome, Bias Correction: No
Separately, Illumina CASAVA v1.7 was used to generate gene expression data for each sample as well.
Genome_build: NCBI Build 37/mm9
Supplementary_files_format_and_content: Cufflinks output (gene expression data) .tabular files in gtf format
Supplementary_files_format_and_content: CASAVA output (Illumina gene expression data) .txt files. [Column 1] Chromosome number-starting with a c. The chromosome on which the exon resides. [Column 2] Start-The start of the gene. [Column 3] End-The end of the gene. [Column 4] Genes-The gene symbol. [Column 5] Normalized count (RPKM)=(10^9 x raw count)/(feature length x number of mapped bases). [Column 6] Raw count=sum of coverages for each base within the feature.
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| Submission date |
Jul 23, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Graham |
| E-mail(s) |
brian.graham@ucdenver.edu
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| Organization name |
University of Colorado Denver
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| Department |
Medicine
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| Street address |
12700 E 19th Ave, C-272
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| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE49114 |
Murine Schistosoma-Induced Pulmonary Hypertension: RNA-seq Data |
| GSE49116 |
Protective Role of IL6 in Vascular Remodeling in Schistosoma-Pulmonary Hypertension |
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| Relations |
| BioSample |
SAMN02261930 |
| SRA |
SRX327168 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1193939_casava_cntrl5.txt.gz |
592.9 Kb |
(ftp)(http) |
TXT |
| GSM1193939_cufflinks_cntrl5.tabular.txt.gz |
697.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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