|
| Status |
Public on May 29, 2024 |
| Title |
AECs co-stimulated in vitro with IL-4 and IL-13, Subject 2 |
| Sample type |
SRA |
| |
|
| Source name |
Airway epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Airway epithelial cells
subject: D
age: 64
Sex: Male
treatment: IL-4_IL-13
|
| Growth protocol |
Air-liquid interface (ALI) cultures were grown from nasal basal epithelial cells from healthy adult donors. ALIs were allowed to mature for 14 days, then stimulated with 10 ng/mL of IL-4 and 10 ng/mL of IL-13 for an additional 7 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were lysed with TCL buffer (Qiagen 1031576) and lysates were stored at -80C
SmartSeq2 protocol was used to extract low-input bulk RNA-seq and libraries were later submitted to the Broad Insitute for 38bp paired-end sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
FASTQ files were aligned to the human genome using STAR (v2.7.9a) with standard parameters and two-pass mode.
BAM files generated with STAR and counts were calculated using RSEM (v1.3.3).
We normalized the counts by transforming them to their log2(TPM+1) value, where TPM stands for transcripts per million.
Assembly: GRCh38
Supplementary files format and content: Counts.txt contains expected gene counts as calculated by RSEM.
Supplementary files format and content: Log2TPM.txt contains TPM values as calculated by RSEM that were then scaled to log2(tpm+1).
|
| |
|
| Submission date |
May 21, 2024 |
| Last update date |
May 29, 2024 |
| Contact name |
Nora Barrett |
| Organization name |
Brigham and Women’s Hospital
|
| Department |
Allergy and Clinical Immunology
|
| Lab |
Barrett Lab
|
| Street address |
60 Fenwood Rd
|
| City |
Boston |
| State/province |
Massachussetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE268072 |
Human airway epithelial cells co-treated with IL-4 and IL-13 for seven days. |
|
| Relations |
| BioSample |
SAMN41480603 |
| SRA |
SRX24635667 |
