|
| Status |
Public on Apr 02, 2021 |
| Title |
U937 cells, Control_3 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Monocytic cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: genetically modified U937
genetic modification: Control plasmids
genotype: control
|
| Treatment protocol |
N/A
|
| Growth protocol |
U937 cells were cultured in RPMI1640 (Gibco) supplemented with 10% fetal bovine serum (ATCC), glutamine (Gibco), and penicillin/streptomycin and selected with 500ug/ml geneticin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
U937 cells RNA was prepared using the Rneasy Plus mini kit (Qiagen) following the manufacture’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Control plasmid transduced U937 cell line 3
|
| Data processing |
Assessment of FASTQ quality was performed using FASTQC. All included data passed QC checks.
Reads from FASTQ files were aligned to the human genome (GRCh38) using HISAT2 (v. 2.0.0) with default settings.
Aligned BAM files were sorted by position and indexed using samtools (v.1.5.9)
Gene-level counts were generated with HTSeq-Count (v.0.11.1) using the Ensembl GrCh38.p12 GTF file for gene coordinates with the following options: --stranded=yes --order=pos --mode=union --type=exon --idattr=gene_id. Genes with >= 10 counts total (summed across controls and ΔNSPs replicates were retained for downstream analysis)
Genome_build: GRCh38
Supplementary_files_format_and_content: counts_raw.csv contains the compiled HTSeq-Count gene-level counts. The first column contains the Ensembl gene id and the subsequent columns represent each sample.
|
| |
|
| Submission date |
Dec 27, 2019 |
| Last update date |
Apr 02, 2021 |
| Contact name |
Purvesh Khatri |
| Organization name |
Stanford University
|
| Department |
BMIR
|
| Street address |
279 Campus Dr. Beckman Center B235A
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE142662 |
Transcriptomic analysis by RNA-seq unveils distinct gene expression profile of U397 cells depleted of NSPs |
|
| Relations |
| BioSample |
SAMN13690920 |
| SRA |
SRX7450586 |
