|
| Status |
Public on Dec 01, 2023 |
| Title |
D20IFNa14 |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PBMC
subject: Donor 20
|
| 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 20_IFNa14
|
| 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 |
SRX13419467 |
| BioSample |
SAMN24103283 |
