|
| Status |
Public on Mar 21, 2019 |
| Title |
CAL-1 control mock treated at 12hr rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
CAL-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CAL-1
time: 12hr
treatment: mock
replicate: 2
cell line: PH5CH8
|
| Treatment protocol |
CAL-1 pDC cells rested for 6 hours in 0.1% FBS CAL-1 media prior to stimulations with 1,000U/mL recombinant human IFN-β (PBL Interferon Source), 1ug/mL R848 (InvivoGen) with or without 1ug/mL recombinant vaccinia virus B18R protein (Thermo Fisher Scientific), or CpG-B (InvivoGen).
|
| Growth protocol |
CAL-1 cells (1 million cells/mL) were cultured in 0.1% FBS CAL-1 media in triplicate in a 12-well tissue culture plate for 6 hours prior to stimulation with 1,000 U/mL recombinant human IFN-β (PBL Interferon Source) or 1ug/mL R848 (Invitrogen) or 1ug/mL R848 (Invitrogen) + 1ug/mL recombinant vaccinia virus B18R protein (Thermo Fisher Scientific) or mock stimulation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy mini kit (QIAGEN) with on-column DNase treatment.
KAPA Total RNA-seq kit with Ribo Erase
Library quality was evaluated using the Qubit® 3.0 Fluorometer and the Agilent 2100 Bioanalyzer instrument. Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CAL-1 mock treated at 12 hours replicate number 2
X002_SG_Savan_02_2_mock_CAL.1.pDC_12hr_RNA_Total_run03_S1
|
| Data processing |
Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using STAR (version 2.4.0)
Genome_build: Human genome (ENSEMBL, GRCh37)
Supplementary_files_format_and_content: We mapped reads to the human reference genome (GRCh37) from Illumina's igenomes using STAR. After mapping, we assigned aligned read counts from BAM files to exons and genes using the python package HT-Seq. HT-Seq provided the most accurate way of aligning read counts to overlapping exons. Reads that mapped to multiple positions were removed. Raw counts were normalized using the voom function in limma.
Supplementary_files_format_and_content: normalized count matrix
|
| |
|
| Submission date |
Jul 16, 2018 |
| Last update date |
Mar 21, 2019 |
| Contact name |
Michael Gale, Jr |
| E-mail(s) |
uw_galelab_geo@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Immunology
|
| Street address |
750 Republican St. E360, Box 358059
|
| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE117127 |
Long noncoding RNA signatures induced by TLR7 and type I IFN signaling in activated human plasmacytoid dendritic cells |
|
| Relations |
| BioSample |
SAMN09662889 |
| SRA |
SRX4393225 |
