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Sample GSM1193944 Query DataSets for GSM1193944
Status Public on Jul 23, 2013
Title Schisto-PH Mouse #5
Sample type SRA
Source name Whole mouse lung
Organism Mus musculus
Characteristics strain: C57BL6/J
gender: Female
schisto exposure: IP/IV eggs
disease state: experimental Schistosoma-induced pulmonary hypertension
treatment: None
tissue: whole lung
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).
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Qiagen RNAeasy kit
Illumina TruSeq RNA Sample Preparation kit
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Schisto-PH 5
Data processing Groomer/Tophat/Bowtie/Cufflinks analysis performed using Galaxy (
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.
Submission date Jul 23, 2013
Last update date May 15, 2019
Contact name Brian Graham
Organization name University of Colorado Denver
Department Medicine
Street address 12700 E 19th Ave, C-272
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
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
BioSample SAMN02261936
SRA SRX327173

Supplementary file Size Download File type/resource
GSM1193944_casava_schistoPH5.txt.gz 593.0 Kb (ftp)(http) TXT
GSM1193944_cufflinks_schistoPH5.tabular.txt.gz 697.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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