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| Status |
Public on Oct 16, 2013 |
| Title |
untreated 1 |
| Sample type |
SRA |
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| Source name |
monocytes from healthy volunteers
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| Organism |
Homo sapiens |
| Characteristics |
cell type: monocytes
treatment: untreated
disease status: healthy volunteers
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| Treatment protocol |
isolated from 3 healthy donors, and left unstimulated or stimulated for 4 hours with 20 μg/ml IDR-1018.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cell lysates using the Qiagen RNA Isolation Kit (Qiagen, Valencia, CA), as per the manufacturerâ??s instructions, treated with RNase free DNase (Qiagen, Valencia, CA), and eluted in RNase-free water (Ambion, Austin, TX). The RNA concentration was assessed using a NanoDrop spectrophotometer, while RNA integrity and purity was determined by Agilent 2100 Bioanalyzer using RNA Nano kits (Agilent technologies). 500 ng of total RNA was processed according to the Illumina TruSeq RNA sample preparation guide (Illumina catalogue number FC-122-1002). Briefly, mRNA was purified using poly-dT beads, followed by synthesis of the first and second cDNA strands, end repair addition of an poly-A overhang, and ligation of adapters and unique barcodes, as per the manufacturer’s instructions. DNA enrichment was carried out via a 15-cycle PCR. Following quantification, 8 pM of dsDNA was used for cluster generation on a CBOT instrument (Illumina, San Diego, CA).Â
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
count_2
untreated
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| Data processing |
convert to sequence CASAVA 1.7 (Illumina)
map sequence to genpme with tophat 1.0, bowtie 0.12.7
mapped to genes using R package GenomicRanges 2.12.1
Genome_build: Genome Reference Consortium release GRCh37.rel59
Supplementary_files_format_and_content: Format is three columns tab-delimited, for Ensembl gene ID, gene transcript counts, and normalized counts as rpmkm. First line is a header is ID, count, rpmkm.
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| Submission date |
Aug 15, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Fjell |
| E-mail(s) |
cfjell@mail.ubc.ca
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| Organization name |
University of British Columbia
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| Department |
Medicine
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| Street address |
Room 166 - 1081 Burrard Street
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| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6Z 1Y6 |
| Country |
Canada |
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| Platform ID |
GPL10999 |
| Series (1) |
| GSE40131 |
Synthetic cationic peptide IDR-1018 modulates human macrophage differentiation |
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| Relations |
| SRA |
SRX176907 |
| BioSample |
SAMN01113355 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM986103_counts2.txt.gz |
477.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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