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Sample GSM1193947 Query DataSets for GSM1193947
Status Public on Jul 23, 2013
Title 1D11 Control Mouse #3
Sample type SRA
 
Source name Whole mouse lung
Organism Mus musculus
Characteristics strain: C57BL6/J
gender: Female
schisto exposure: None
disease state: control
treatment: 1D11
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 1D11 Control 3
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.
 
Submission date Jul 23, 2013
Last update date May 15, 2019
Contact name Brian Graham
E-mail(s) brian.graham@ucdenver.edu
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
Relations
BioSample SAMN02261938
SRA SRX327176

Supplementary file Size Download File type/resource
GSM1193947_casava_1d11_cntrl3.txt.gz 594.4 Kb (ftp)(http) TXT
GSM1193947_cufflinks_1d11_cntrl3.tabular.txt.gz 695.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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