title: 20160404_e10
organism: Mus musculus
description: 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
attributes.tag: ENA first public
attributes.value: 2019-02-25
attributes.tag: ENA last update
attributes.value: 2016-09-20
attributes.tag: External Id
attributes.value: SAMEA4444198
attributes.tag: INSDC center alias
attributes.value: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics
attributes.tag: INSDC center name
attributes.value: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics
attributes.tag: INSDC first public
attributes.value: 2019-02-25T17:03:10Z
attributes.tag: INSDC last update
attributes.value: 2016-09-20T14:39:20Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-5091:20160404_e10
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell type
attributes.value: mouse embryonic stem cell
attributes.tag: common name
attributes.value: house mouse
attributes.tag: phenotype
attributes.value: TDP-43 inducible knock out
attributes.tag: sample name
attributes.value: E-MTAB-5091:20160404_e10