|
| Status |
Public on Feb 15, 2016 |
| Title |
01-31_V1 |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs
|
| Organism |
Homo sapiens |
| Characteristics |
individual: patient 01-31
disease state: Lyme disease
time: acute Lyme pre-treatment (V1)
cell type: PBMC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PBMCs were isolated from fresh whole blood using Ficoll (Ficoll-Paque Plus, GE Healthcre) and total RNA was extracted from 10e7 PBMCs using TRIzol reagent (Life Technologies). Messenger RNA was isolated with Oligotex mRNA mini kit (Qiagen)
Scriptseq RNA-seq library preparation kit (Epicentre) was used to generate the RNA-seq libraries according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
reads were mapped to hg19 Refseq annotation using Bowtie 2 version 2.2.2 as part of Tophat 2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Nov 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles Chiu |
| E-mail(s) |
charles.chiu@ucsf.edu
|
| Organization name |
University of California, San Francisco
|
| Department |
Laboratory Medicine
|
| Lab |
Chiu Laboratory
|
| Street address |
185 Berry Street, Box 0134
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143-0134 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE63085 |
Identification of a Molecular Signature for Acute Lyme Disease by Human Transcriptome Profiling |
|
| Relations |
| Reanalyzed by |
GSE122515 |
| BioSample |
SAMN03167878 |
| SRA |
SRX753408 |
