|
| Status |
Public on Jul 14, 2015 |
| Title |
PBMCs sample_TR105 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood mononuclear cells (PBMCs)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PBMC
gender: Male
age: 38
time: PRE
location: Cali
individual: 306N
|
| Growth protocol |
Peripheral blood mononuclear cells (PBMCs)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood mRNA was extracted using TempusTM Blood RNA Tube isolation kits provided by the manufacturer Applied Biosystems, and the quality was determined based on the Agilent Bioanalyzer 2100 RNA Integrity score (RIN).
Illumina RNA seq kit was used for sequence library preparation using the Illumina TruSeq RNA Sample Prep Guide: Low Throughput (LT) Protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The raw RNA-Seq reads for each sample were aligned to the reference human genome (hg19) using Bowtie as the short read aligner, and splice junctions were identified using TopHat
Raw sequence read depths were converted to estimated transcript abundance measures as fragments per kilobase of exons per million (FPKM) values using Cufflinks
All genes with an FPKM greater than 2.5 averaged across all 24 samples were retained, representing 6,154 genes
FPKM values were transformed to logarithm base 2 and normalized using the supervised normalization of microarray (SNM) procedure with the R package from Bioconductor
Supplementary_files_format_and_content: excel file include normalize expession values matrix for all samples
|
| |
|
| Submission date |
Mar 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Monica L. Rojas-Peña |
| E-mail(s) |
monica.rojas@gatech.edu
|
| Organization name |
Georgia Institute of Technology
|
| Department |
School of Biology
|
| Lab |
Center for Integrative Genomics (CIG)
|
| Street address |
310 Ferst Dr.
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30332 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE67184 |
Transcription Profiling of Malaria-Naïve and Semi-Immune Colombian Volunteers in a Plasmodium vivax Sporozoite Challenge [RNA-Seq] |
| GSE67470 |
Transcription Profiling of Malaria-Naïve and Semi-Immune Colombian Volunteers in a Plasmodium vivax Sporozoite Challenge |
|
| Relations |
| Reanalyzed by |
GSE122515 |
| BioSample |
SAMN03437995 |
| SRA |
SRX965517 |
