|
| Status |
Public on Jun 06, 2019 |
| Title |
CD4_w0__R104_K8115: CD4 before treatment 3 |
| Sample type |
SRA |
| |
|
| Source name |
CD4 T cell
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: rheumatoid arthritis
tissue: CD4 T cell
gender: F
age: 65
|
| Treatment protocol |
Frozen peripheral mononuclear cells were thawed, and CD4 and CD8 T cell were purified using FACS Aria Ⅲ.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from were extracted using RNeasy Micro kit (Qiagen).
0.2 ng of total RNA from each dose and biological replicate were reverse transcribed to cDNA with SuperScript® VILO™ cDNA Synthesis Kit. Then cDNA is amplified using Ion AmpliSeq™ technology. After primer digestion, adapters and molecular barcodes were ligated to the amplicons followed by magnetic bead purification. Libraries were then diluted to 75 pM and pooled equally, with eighteen individual samples per pool.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Base calling was performed using software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.0.4.0).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Count data were calculated using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (read count) for each sample.
|
| |
|
| Submission date |
Apr 16, 2018 |
| Last update date |
Jun 06, 2019 |
| Contact name |
Masaru Takeshita |
| Organization name |
Keio University
|
| Department |
Division of Rheumatology
|
| Lab |
research park 6S8
|
| Street address |
35 shinanomachi
|
| City |
sinjuku-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE113156 |
Transcriptome change after tocilizumab therapy in rheumatoid arthritis patients |
|
| Relations |
| BioSample |
SAMN08934977 |
| SRA |
SRX3939819 |
