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| Status |
Public on May 06, 2013 |
| Title |
Sample_8_180 |
| Sample type |
SRA |
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| Source name |
Sample_8_180
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| Organism |
Homo sapiens |
| Characteristics |
time: 180 days post LVAD
tissue: whole blood
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction from whole blood was carried out per the manufacturer’s instructions using the PreAnalytiX PAXgene Blood RNA Kit, Version 2 from Qiagen.
Libraries were created using the 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 |
TCA_T4
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| Data processing |
Libraries were sequenced to 100 nucleotide lengths on Illumina HiSeq2000 using RTA (real-time analysis) for image analysis, base calling, and data filtering.
Casava 1.8.0 was used to demultiplex and generate fastq files for each patient index.
Image analysis, base calling, and base call quality calibration were done using the Real Time Analysis software (Illumina).
Alignment and transcript abundance estimates generated with Tophat and Cufflinks software suite.
Genome_build: Ensembl GRCh37.66
Supplementary_files_format_and_content: bed file format of Tophat alignments
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| Submission date |
May 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Rod A. Staggs |
| E-mail(s) |
stagg004@umn.edu
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| Phone |
612-384-6451
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| Organization name |
Minnesota Informatics
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| Street address |
20040 Cottagewood Ave
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| City |
Excelsior |
| State/province |
MN |
| ZIP/Postal code |
55331 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE46665 |
Identification of differentially expressed transcripts and pathways one week and six months following implant of left ventricular devices |
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| Relations |
| BioSample |
SAMN02117510 |
| SRA |
SRX275453 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1133681_TCA_T4.alignedreads.bed.gz |
387.3 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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