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Sample GSM5743512 Query DataSets for GSM5743512
Status Public on Dec 01, 2023
Title D3IFNa5
Sample type SRA
 
Source name PBMC
Organism Homo sapiens
Characteristics cell type: PBMC
subject: Donor 3
Treatment protocol Mock treated with PBS or ISRE activity normalized doses of IFNa1, IFNa2, IFNa4, IFNa5, IFNa8, IFNa14, or IFNb for 18 hrs.
Growth protocol RPMI 1640 + 10% FBS + 1% PSG
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy Plus kit according to the manufacturer’s instruction.
Lexogen QuantSeq 3’ mRNA-Seq Library (FWD) Prep kit according to the manufacturer’s instruction.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Donor 3_IFNa5
Data processing Illumina Casava1.7 software used for basecalling.
Quality screened and adapter removal using cutadapt (v1.15).
Mapped to GRch38 human genome using HiSat2 (v2.1.0).
Raw gene counts were extracted using featureCounts (v1.6.5, the Subread package).
Gene Raw count matrix and Transcript per Million (TPM) table for samples was generated using custom Perl scripts.
Genome_build: Human GRch38
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: gene_counts_TPM_matrix.txt: Matrix table with TPM normalized counts.
Supplementary_files_format_and_content: *_geneCounts.txt: Tab-delimited text files include abundance measurements.
 
Submission date Dec 20, 2021
Last update date Dec 01, 2023
Contact name Kejun Guo
E-mail(s) Kejun.guo@cuanschutz.edu
Phone 3037245291
Organization name University of Colorado Anschutz Medical Campus
Department Division of Infectious Diseases
Street address 12700 E 19th Ave, Rm 11420D
City Aurora
State/province Colorado
ZIP/Postal code 80045
Country USA
 
Platform ID GPL24676
Series (1)
GSE191317 Type-I interferome in human peripheral blood mononuclear cells (PBMC)
Relations
SRA SRX13419477
BioSample SAMN24103257

Supplementary file Size Download File type/resource
GSM5743512_D3a5_geneCounts.txt.gz 305.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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