 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 06, 2015 |
| Title |
lib245 |
| Sample type |
SRA |
| |
|
| Source name |
Whole Blood
|
| Organism |
Homo sapiens |
| Characteristics |
age: 24
cellcount: 2000000
celltype: CD4
collectiondate: May 23 2012
diseasestatus: Type 1 Diabetes
donorid: 34
gender: F
index: 15
race: White
samplename: 34_CD4T
smoker: --
time since last flare (months): --
time since steroid dose: --
time since symptom onset (yrs): --
years since diagnosis: 7
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh blood samples were collected from healthy subjects and subjects diagnosed type 1 diabetes, amyotrophic lateral sclerosis, and sepsis, as well as multiple sclerosis patients before and 24 hours after the first treatment with IFN-beta. At the time of blood draw, an aliquot of whole blood was collected into a Tempus tube (Invitrogen), while the remainder of the primary fresh blood sample was processed to highly pure populations of neutrophils, monocytes, B cells, CD4 T cells, CD8 T cells, and natural killer cells. RNA was extracted from each of these cell subsets, as well as the whole blood samples, and processed into RNA sequencing (RNAseq) libraries (Illumina TruSeq). Sequencing libraries were analyzed on an Illumina HiScan, with a target read depth of ~20M reads. Reads were demultiplexed, mapped to human gene models (ENSEMBL), and tabulated using HTSeq. Read count data were normalized by the TMM procedure (edgeR package).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
fastq files were created from .bcl files via Illumina's CASAVA 1.8.2
reads were aligned to Hg19 via Omicsoft sequence aligner (OSA) version 2.0.1
gene counts were generated by HTSeq version 0.5.4p3
TMMs were generated with Bioconductor package EdgeR
Genome_build: Hg19
Supplementary_files_format_and_content: tab delimited file contains TMM normalized counts
|
| |
|
| Submission date |
Aug 14, 2014 |
| Last update date |
Jan 04, 2024 |
| Contact name |
Stephanie Osmond |
| E-mail(s) |
sosmond@benaroyaresearch.org
|
| Organization name |
Benaroya Research Institute
|
| Street address |
1201 9th Ave
|
| City |
Seattle, |
| State/province |
WA |
| ZIP/Postal code |
98101 |
| Country |
USA |
| |
|
| Platform ID |
GPL15456 |
| Series (1) |
| GSE60424 |
Next generation sequencing of human immune cell subsets across diseases |
|
| Relations |
| BioSample |
SAMN02990341 |
| SRA |
SRX680565 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
