|
| Status |
Public on Oct 01, 2021 |
| Title |
THP1_IFNyLPS_PANOBINOSTAT_2 |
| Sample type |
SRA |
| |
|
| Source name |
THP-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: peripheral blood monocyte
cell line: THP-1
|
| Treatment protocol |
Primed THP-1 cells with PMA 50 nM were pre-treated with panobinostat (0.0034 μM, HDACs inhibitor) for one hour and then treated with either BSA (control), IL-4 (20 ng/ml, M2 polarization) or IFNγ (20 ng/ml) and LPS (10 ng/ml, M1 polarization) for 24 hours.
|
| Growth protocol |
THP-1 cells were obtained from ATCC (ATCC Cat# TIB-202, RRID:CVCL_0006) and cultured in RPMI1640+10% FBS+1% Anti-Anti (Life technologies, 15240).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
0.5X10^6 cells were harvested for mRNA using mRNeasy Mini Kit (Qiagen, No. 217004).
We used 0.4 μg total RNA for RNA-seq library preparation by TruSeq Ribo Profile Mammalian Kit (Illumina, RPHMR12126).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
We followed the nf-core/rnaseq workflow version 1.3 (https://github.com/nf-core/rnaseq) for all rna-seq data, with default parameters. The detail includes as following:
low-quality reads were eliminated using FastQC and trim_galory software, remaining only high quality reads.
The remaining clean reads were aligned against the iGenome Ensembl human referenece genome GRCh37 using by STAR. STAR is a read aligner designed for RNA sequencing.
Next, we generated counts relative to genes by featureCounts and StringTie with default parameters.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Nov 12, 2019 |
| Last update date |
Oct 01, 2021 |
| Contact name |
Alexander G Marneros |
| E-mail(s) |
[email protected]
|
| Organization name |
Massachusetts General Hospital, Harvard Medical School
|
| Department |
Department of Dermatology, Cutaneous Biology Research Center
|
| Street address |
13th Street
|
| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE140235 |
Identification of pharmacologic inhibitors and activators of IL-4-induced macrophage polarization |
|
| Relations |
| BioSample |
SAMN13264018 |
| SRA |
SRX7130029 |
