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| Status |
Public on Jul 03, 2015 |
| Title |
CON_7_EOEO2 |
| Sample type |
SRA |
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| Source name |
Whole lung RNA, Baseline Control
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| Organism |
Macaca fascicularis |
| Characteristics |
tissue: lung
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
Truseq RNA with Ribozero rRNA depletion
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Baseline Control
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| Data processing |
Illumina Casava software used for basecalling.
Bowtie (v.0.12.8) was used to build index files from the macaque genome (Ensembl release 69)
The macaque gene transfer format (GTF) file used for alignments was downloaded from Ensembl (ftp://ftp.ensembl.org/pub/release-69/gtf/macaca_mulatta)
Alignments were performed with TopHat (v.2.0.6)
The binary alignment map (BAM) files from TopHat served as input files for the coverageBed command in the BEDTools program (v.2.17.0). A gene-level browser extensible data (BED) file, which defined the start and stop positions of all annotated macaque genes, was downloaded using the Ensembl BioMart tool (http://www.ensembl.org/biomart/martview/).
The coverageBed function assigned reads in the BAM file to genes as defined by the BED file, resulting in an output of counts data representing the number of RNA sequencing reads per gene.
Genome_build: Ensembl release 69
Supplementary_files_format_and_content: Text file with the raw counts data normalized as reads/million total reads
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| Submission date |
Jul 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Raymond J Langley |
| E-mail(s) |
rlangley@lrri.org
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| Phone |
505-348-9614
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| Organization name |
LRRI
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| Department |
immunology
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| Lab |
324
|
| Street address |
2425 Ridgecrest Dr
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| City |
Albuquerque |
| State/province |
New Mexico |
| ZIP/Postal code |
87108 |
| Country |
USA |
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| Platform ID |
GPL18648 |
| Series (1) |
| GSE59075 |
Integrative ‘omic analysis of experimental bacteremia identifies a metabolic signature that distinguishes human sepsis from SIRS |
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| Relations |
| BioSample |
SAMN02902453 |
| SRA |
SRX645386 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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