 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 13, 2017 |
| Title |
HLHS_635-333-1-RV |
| Sample type |
SRA |
| |
|
| Source name |
right ventricle, HLHS, E17.5
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
phenotype: hypoplastic left heart syndrome (HLHS)
developmental stage: E17.5
tissue: heart ventricle
side: right
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from mouse embryonic hearts using the miRNeasy micro Kit (QIAGEN) with on-column DNase I digestion method (QIAGEN).
Libraries were constructed using TruSeq RNA Sample Preparation Lit v2 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
HLHS_333-1-RV
Processed data file: counts.txt
Processed data file: deResults.xlsx
|
| Data processing |
Reads were aligned using TopHat2 (v2.0.9) with the following options: --segment-length 25 --segment-mismatches 2 --no-novel-juncs --min-achor=8 --splice-mismatches 0 --max-intron-length 500000 --microexon-search --no-mixed --no-coverage-search and values for the inner mate distance estimated using RSeQC (v2.3.6).
PCR duplicates were removed using the MarkDuplicates utility from the Picard suite of tools (v1.96).
Gene-level counts were calculated by HTSeq-count (v0.5.4p5) using "union" mode and Ensembl GTF file as retrieved from iGenomes (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/README.txt; Ensembl release 66) for mm9.
Differential expression analyses were performed using the R package edgeR (v3.4.2). Genes with low expression (counts-per-million < 1 in all samples) were discarded. Dispersion parameters were estimated accounting for side (LV and RV), stage (E13.5, E14.5, and E17.5), disease (HLHS and control), and their pairwise interactions. For each gene, the maximum of common, trended and tag-wise dispersion estimate was used for subsequent analyses. Linear contrasts were used to compare HLHS to control in LV and RV, respectively, using likelihood ratio tests. Genes with an FDR <=0.05 and a fold-change >= 1.5 were considered significantly differentially expressed.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: counts.txt: Tab-delimited text file with raw gene-level counts for all samples.
Supplementary_files_format_and_content: deResults.xlsx: Excel spreadsheets for results of the differential expression analyses in LV (HLHS vs. Control) and RV (HLHS vs. Control), respectively. These additionally include the counts-per-million (cpm) values (log2 with pseudocount 1) for all analyzed genes.
|
| |
|
| Submission date |
Feb 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Cecilia W Lo |
| E-mail(s) |
cel36@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Department |
Developmental Biology
|
| Street address |
530 45th St., 8120 Rangos Research Center
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15201 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE77798 |
Pathogenesis of Hypoplastic Left Heart Syndrome [RNA-seq] |
| GSE77799 |
The complex genetics of hypoplastic left heart syndrome |
|
| Relations |
| SRA |
SRX1570959 |
| BioSample |
SAMN04501026 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
