|
| Status |
Public on Nov 30, 2020 |
| Title |
U937 lot2 PMA |
| Sample type |
SRA |
| |
|
| Source name |
U937 cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: with PMA for 72 hours
cell line: U937
|
| Treatment protocol |
For the differentiation to macrophage-like cells, cells were cultured onto the culture dish at 6 x 104 cells /cm2 in 10 nM PMA for 72 hours.
|
| Growth protocol |
U937 cells were maintained in RPMI1640 Medium (Thermo Fisher Scientific) supplemented with 10 % (v/v) fetal bovine serum and 1 % Penicillin-Streptomycin (Thermo Fisher Scientific). Cells were cultured at 37 °C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed by PBS(-) and peletted by centrifugation. Total RNA were extracted by RNeasy Plus Mini Kit (QIAGEN) and polyA(+) RNA were concentrated by Dynabeas mRNA DIRECT Micro kit (Thermo fisher scientific).
Whole transcriptome library was prepared by Ion Total RNA-Seq Kit for the AB Library builder System (Thermo fisher Scientific) and whole transcriptome library was amplified and barcoded by IonXpress RNA-Seq Barcode 1-16 Kit (Thermo Fisher Scientific).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
IonXpressRNA_002
|
| Data processing |
Torrent suite software (version5.0.5) were used for basecalling and creation of fastq file.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Torrent suite software (version 5.0.5).
Sequence reads were mapped by HISAT2 version 2.1.0 (Kim et al., 2015) against GRCh.38 p13 release version 33.
Mapped reads were assembled and merged by StringTie version 2.1.1 (Pertea et al., 2015).
Merged transcript count data were normalized by TCC version 1.26.0 (Sun et al., 2013).
Genome_build: GRCh.38 p13 release version 33
Supplementary_files_format_and_content: Matrix table of raw gene reads counts is "gene_count_re.tsv".
Supplementary_files_format_and_content: "tcc_result_gene.txt" is the tab-delimited text files include normalized read counts.
|
| |
|
| Submission date |
Jul 30, 2020 |
| Last update date |
Nov 30, 2020 |
| Contact name |
Kensuke Ohse |
| E-mail(s) |
[email protected]
|
| Organization name |
Tokyo Metropolitan Institute of Gerontology
|
| Street address |
Sakaecho
|
| City |
Itabashi-ku |
| ZIP/Postal code |
173-0015 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE155459 |
Gene expression analysis of U937 cells during the differentiation by phorbol 12-myristate 13-acetate (PMA) |
|
| Relations |
| BioSample |
SAMN15680893 |
| SRA |
SRX8854930 |
