|
| Status |
Public on Feb 02, 2018 |
| Title |
H46 24h IL3+ [28_C4EANACXX_TGACCA_L007] |
| Sample type |
SRA |
| |
|
| Source name |
RNA from lysed whole blood cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
donor: H46
age: 27
gender: Female
ancestry: Indian
disease status: Healthy
treatment: IL3
time point: 24h
|
| Treatment protocol |
RNA was extracted with an RNA Protect Cell Mini Kit (Qiagen, Catalog number 74624).
|
| Growth protocol |
Cell pellets were suspended in RNAprotect Cell Reagent (Qiagen, Catalog number 76526) and frozen at -80 degrees Celsius until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from pDCs using an RNeasy pus micro kit (Qiagen, catalog number 74034).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
28_C4EANACXX_TGACCA_L007
H46 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt
|
| Data processing |
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.58 and Real Time Analysis (RTA) v1.18.64, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Reads were mapped to Homo sapiens GRCh37.p10 genome, using TopHat (TopHat v2.0.8, bowtie v2.1.0; Trapnell et al.,2009).
Mapped reads were summarized on a gene level using Ensembl ID gene annotation (Ensembl Release 70 based on GRCh37.p10 genome build) and HTSeq (v0.5.3p9; Anders et al., 2014) software.
Summarised read counts in this submission were NOT normalised nor filtered. We recommend using Bioconductor edgeR package functions: i) calcNormFactors (TMM method) to normalise between samples based on library sizes, and ii) rpkm function to normalise between genes within a sample based on gene lengths.
Genome_build: GRCh37.p10
Supplementary_files_format_and_content: *txt: All processed data files are in a tab-delimited file format. They contain raw read counts summarised on a gene level according to Ensembl Release 70 annotation.
|
| |
|
| Submission date |
Feb 01, 2018 |
| Last update date |
Nov 19, 2018 |
| Contact name |
CSL Research |
| Organization name |
CSL Limited / bio21 Institute
|
| Street address |
30 Flemington Rd
|
| City |
Parkville |
| State/province |
VIC |
| ZIP/Postal code |
3010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE110041 |
In-vitro stimulation of healthy donor blood with IL-3 cytokine |
|
| Relations |
| BioSample |
SAMN08455681 |
| SRA |
SRX3641450 |
