2024-03-30
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA114857215
External Id
(1) Università degli Studi di Napoli Federico II - Dipartimento di Medicina Molecolare e Biotecnologie Mediche (2) CEINGE Biotecnologie Avanzate Franco Salvatore scarl
INSDC center name
2023-12-07T22:36:19Z
INSDC last update
public
INSDC status
ERS17282174
SRA accession
E-MTAB-13616:DR_SP2577_rep1
Submitter Id
ArrayExpress
broker name
primary cell line
cell_line
medulloblastoma GR3
cell_type
not collected
collection date
human
common name
Protocols: Primary Group3 MB cells were plated (3x105 cells) and treated with anti-PRUNE-1 (AA7.1), anti-LSD1 (SP2577), the combination of two or vehicle (0,001% DMSO) as the negative control for the treatment. After 24 hours, the cells were lysed with TRIzol RNA Isolation Reagent (#15596018; Ambion, Thermo Fisher Scientific) and frozen at -80°C. Freshly isolated primary Group3 MB cells were collected by the biopsy after surgery resection of a patient affected by tumour (data deposited at: EVA- EMBL-EBI; project ID: PRJEB42411; analyses: ERZ1700617). These cells were cultured using Dulbecco's modified Eagle's medium (DMEM; 41966-029; Gibco) and Minimum Essential Medium (MEM; 11090081; Gibco) in a ratio 1:1 with 10% fetal bovine serum 10270-106; Gibco), 2 mM L-glutamine (25030-024; Gibco), and 1% penicillin/streptomycin (P0781; Sigma-Aldrich), with the medium changed daily. Primary Group3 MB cells were plated (3x105 cells) and treated with anti-PRUNE-1 (AA7.1), anti-LSD1 (SP2577), the combination of two or vehicle (0,001% DMSO) as the negative control for the treatment. After 24 hours, the cells were lysed, and their RNA were extracted for RNAseq. Total RNA, isolated from human primary medulloblastoma cells by using TRIzol RNA Isolation Reagent (#15596018; Ambion, Thermo Fisher Scientific) was quantified in a NanoDrop™ One/OneC Microvolume UV-Vis Spectrophotometer (Thermo Scientific™), checked for purity and integrity. Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA for Sequencing, Nextera XT DNA Library Preparation Kit according to the protocols recommended by the manufacturer. Library kit: TSMART-Seq v4 Ultra Low Input RNA for Sequencing, Nextera XT DNA Library Preparation Kit; Library protocol: SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing User Manual, Nextera XT DNA Library Prep Kit Reference.
description
medulloblastoma GR3
disease
not collected
geographic location (country and/or sea)
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
cerebellum
organism part
Homo sapiens
scientific_name
DR_SP2577_rep1
title