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Sample GSM6579020 Query DataSets for GSM6579020
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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