|
| Status |
Public on Jul 01, 2024 |
| Title |
IonCode_0105 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
cell type: Embryonic Kidney Cells
genotype: Wild-type receptors
treatment: High-affinity INFL3 (H11) treated
time: 24hr
|
| Treatment protocol |
Cells were treated with 100nM of indicated interferons for 15 minutes in humidified atomosphere with 5% CO2 at 37C
|
| Growth protocol |
HEK293 cells were maintained in Free-style Media supplemented with antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Monarch Total RNA miniprep kit (NEB). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ion Torrent Ion 540 or 550 Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 XL |
| |
|
| Description |
biol rep1
|
| Data processing |
Ion Torrent S5 with ampliSeqRNA plugin v 5.16.1
Trimed sequence reads were mapped to hg19 AmpliSeq Transcriptome ERCC v1 using Ion Torrent S5 software
Read count extraction and normalization were performed using Ion Torrent S5 software
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts of sequencing reads
|
| |
|
| Submission date |
Jul 15, 2022 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Juan L Mendoza |
| E-mail(s) |
jlmendoza@uchicago.edu
|
| Phone |
6507220233
|
| Organization name |
The University of Chicago
|
| Street address |
920 E 58th Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL24014 |
| Series (1) |
| GSE208288 |
Effect of JAK-JAK Geometry on Gene Expression Levels in Cells Treated with Type I and III Interferons |
|
| Relations |
| BioSample |
SAMN29767446 |
| SRA |
SRX16264739 |
