|
| Status |
Public on Jun 13, 2024 |
| Title |
Vehicle Control treated ZMEL1 Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
ZMEL1 Cells
|
| Organism |
Danio rerio |
| Characteristics |
cell line: ZMEL1 Cells
treatment: Vehicle
|
| Treatment protocol |
Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.
|
| Growth protocol |
ZMEL1 were grown in filter sterilized DMEM, 10% FBS, 1% PenStrep, 1% Glutamine at 28°C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit (Qiagen #74134).
One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit (NEB #E6310). Ribodepleted RNA was fragmented, reverse transcribed, and library prepped (NEB #E7530, NEB #E7335).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to Ensembl GRCz11 whole genome using tophat 2.1
Transcript abundance were calculated with Htseq-count
Assembly: GRCz11
Supplementary files format and content: raw count file
|
| |
|
| Submission date |
Sep 14, 2022 |
| Last update date |
Jun 13, 2024 |
| Contact name |
Leonard Zon |
| E-mail(s) |
zon@enders.tch.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Department |
Oncology/Hematology
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21741 |
| Series (2) |
| GSE213328 |
A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA-seq, ZMEL] |
| GSE213360 |
A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma |
|
| Relations |
| BioSample |
SAMN30852718 |
| SRA |
SRX17566317 |
