Homo sapiens
Protocols: We used GM12878 cells (LCL) The lymphoblastoid cell line GM12878 was cultured using RPMI 1640 medium supplemented with 10% fetal bovine serum and 1x penicillin/streptomycin. One million cells were treated with DMSO (Applichem #A3672,0250) or 3 µM BAY11-7082 (SignalChem, # C51-900) during 24 hours prior to harvesting for RNA isolation Cells were treated with either DMSO or IKK inhibitor (BAY 11-7082) to induce gene expression differences. Total RNA was isolated using TRI Reagent (Molecular Research Center, #TR118) followed by double precipitation with ethanol. The RNA concentration was determined using the Qubit RNA HS Assay Kit (Invitrogen, #Q32852) and integrity was assessed using a Fragment Analyzer (Advanced Analytical). The RNA from each differentiation time point was used in two technical replicates, resulting in four samples pooled per library. Libraries were prepared with the BRB-seq protocol using total RNA amounts ranging from 1 ng to 2 µg per sample. RNA fragmentation was done using the NEBNext Magnesium RNA Fragmentation Module (NEB, #E6150S) with incubation time at 94°C for one or two minutes. This resulted in RNA with a variable extent of degradation and corresponding RQN values. TruSeq libraries were prepared with 1 µg of total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina, #RS-122-2101) and following the manufacturer's instructions. Four libraries were paired-end sequenced (75 nt each) with the NextSeq 500 using the Mid Output v2 kit (150 cycles) (Illumina, #FC-404-2001).
ENA-FIRST-PUBLIC
2018-07-07T17:02:47Z
ENA-LAST-UPDATE
2018-07-06T11:21:57Z
External Id
SAMEA4778530
INSDC center name
Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
INSDC first public
2018-07-07T17:02:47Z
INSDC last update
2018-07-06T11:21:57Z
INSDC status
public
Submitter Id
E-MTAB-6984:SCRB-Seq (DMSO, rep 1)
broker name
ArrayExpress
cell line
GM12878
cell type
B cell
common name
human
disease
normal
organism part
blood
sample name
E-MTAB-6984:SCRB-Seq (DMSO, rep 1)
scientific_name
Homo sapiens