2024-08-13
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA113902832
External Id
Berlin Institute for Medical Systems Biology
INSDC center name
2023-06-20T13:30:29Z
INSDC last update
public
INSDC status
ERS15897001
SRA accession
E-MTAB-13096:PANC1_3x8Gy_72h_br3
Submitter Id
ArrayExpress
broker name
PANC1
cell_line
not collected
collection date
human
common name
Protocols: The pancreatic cancer cell lines PANC-1, MIA Paca-2 and BxPc-3 were purchased from ATCC. PANC-1 and MIA Paca-2 were in cultured in Dulbecco’s Modified Eagle Medium (DMEM) medium, supplemented with 10% fetal bovine serum (FCS) and 1% penicillin/streptomycin (P/S). BxPC-3 were cultured in Roswell Park Memorial Institute (RPMI) 1640 Medium, supplemented with 10% FCS, 1% P/S and 1% L-Glutamine. All cells were maintained at at 37 °C in a humidified atmosphere with 95% air and 5% CO2. Cells were grown to 70-80% of confluency at time or irradiation. Prior to irradiation, cell culture flasks were filled air-bubble free with unsupplemented medium, which was replaced immediately after irradiation with fresh, supplemented medium. RNA-seq samples were prepared in three biological replicates. Cells were harvested and counted, 20% Drosophila S2 cells were added as a spike-in control. Cell pellets were resuspended in 1 mL TRI reagent (Sigma). 200 µL Chloroform (Applichem) were added, samples were mixed and centrifuged at 4°C, max. speed for 15 min. The upper phase was transferred to a new tube and subjected to isopropanol precipitation. 20 µg of RNA were treated with 40 U DNase I (Roche) at 37°C for 30 min and purified by phenol-chloroform extraction and Ethanol precipitation. rRNA was depleted and RNA-seq libraries were prepared with NEBNext rRNA depletion kit v2 (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions.
description
adult
developmental stage
pancreatic carcinoma
disease
not collected
geographic location (country and/or sea)
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
pancreatic duct
organism part
Homo sapiens
scientific_name
PANC1_3x8Gy_72h_br3
title