|
| Status |
Public on Jan 28, 2021 |
| Title |
B35_ILC2_CD45RA_il33-tslp |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: FACS-purified lymphocytes
culture conditions: 7 days with IL-2, IL-33 and TSLP
|
| Growth protocol |
Sorted ILC2s were cultured in Yssel's medium with 1% normal human serum. 2000-5000 cells were stimulated for 7 days with IL-2 (10 U/mL), IL-33 (50 ng/mL) and TSLP (both 50 ng/mL). When indicated, dexamethasone was added to the culture medium (10-7 M, Sigma Aldrich) at day 0.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ILC2s were isolatd by FACS as Lineage-CD127+CRTH2+ cells peripheral blood samples (buffy coats) of 4 healthy volunteers.
RNA-Seq: Smart-seq2 library construction (as described in Picelli et al. Nature Methods (2013))
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
rpkm_all_samples.txt
|
| Data processing |
Reads were aligned using HISAT2 v2.0.4. (RNA-seq) with default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization
RPKM generation, sample scaling and statistical analysis were performed using HOMER and its implementation of the R package DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: RPKM expression values
|
| |
|
| Submission date |
Jun 09, 2020 |
| Last update date |
Jan 28, 2021 |
| Contact name |
Ralph Stadhouders |
| E-mail(s) |
stadhoudersralph@gmail.com
|
| Organization name |
Erasmus Medical Center
|
| Department |
Pulmonary Medicine
|
| Street address |
Dr. Molewaterplein 50
|
| City |
Rotterdam |
| ZIP/Postal code |
3015 GE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE152130 |
Steroid-resistant human inflammatory ILC2s are marked by CD45RO and elevated in type 2 respiratory disease |
|
| Relations |
| BioSample |
SAMN15189634 |
| SRA |
SRX8511127 |
