20160404_e13
Mus musculus
Protocols: 3 µg of RNA was treated with TURBO DNase according to manufacturer's instructions followed by RNeasy Minelute RNA cleanup kit and RNA quality was confirmed using Agilent 2100 Bioanalyzer with RNA Pico 6000 kit (RIN values >8). Per RNA-seq library, 1 µg of DNAse-treated RNA was treated with RiboZero Gold (Human/Mouse/Rat) kit to remove rRNAs, followed by RNA cleanup using the RNeasy Minelute RNA cleanup kit. Sequencing libraries were prepared using TruSeq Stranded total RNA LT kit according to manufacturer's instructions using 11 cycles of PCR followed by purification with Agencourt Ampure XP beads. Libraries were evaluated on an Agilent 2100 Bioanalyzer using the DNA 1000 kit and DNA concentration was measured using a Qubit dsDNA HS Assay Kit. Samples were sequenced using a HiSeq2500 instrument to generate 50-nt single-end reads, sequencing depth was 20-40 Mio reads per library. Mouse ESCs were maintained on gelatin-coated plates in serum free N2B27 added to equal ratio of neurobasal medium and DMEM, supplemented with MEK inhibitor PD0325901 (1 μM), GSK3 inhibitor CHIR99021 (3 μM), 1,000 U/ml LIF (in-house production), 1% Glutamax, 0.1mM 2-mercaptoethanol , 1% nonessential amino acids. To induce TDP-43 KO, mESCs were treated with tamoxifen and harvested upon trypsinization ~60hours later. Lexogen 3'-end QuandSeq Reverse
ENA first public
2019-02-25
ENA last update
2016-09-20
External Id
SAMEA4444201
INSDC center alias
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics
INSDC center name
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics
INSDC first public
2019-02-25T17:03:10Z
INSDC last update
2016-09-20T14:39:20Z
INSDC status
public
Submitter Id
E-MTAB-5091:20160404_e13
broker name
ArrayExpress
cell type
mouse embryonic stem cell
common name
house mouse
phenotype
control
sample name
E-MTAB-5091:20160404_e13