organism: Mus musculus
description: Protocols: The iCLIP protocol was performed as described previously (Tollervey, 2011, Nature Neuroscience), with the following modifications. Cells were UV irradiated once with 160 mJ/cm2 in a Stratlinker 2400 at 254 nm. TDP-43 was immunoprecipitated with protein A Dynabeads conjugated to rabbit-anti TDP-43 (Sigma, SAB4200006). The region corresponding to 55-100kDa complexes was excised from the membrane to isolate the RNA, and sequenced using Illumina HiSeq, instrument to generate 50-nt single-end reads, sequencing depth was 15- 20 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. Human ESCs (line H9) were maintained in mTeSR1 medium (05850, STEMCELL Technologies) on Matrigel-coated plates (356234, Corning) prepared by 1:100 dilution, and 5 ml coating of 10 cm plates for 1 h at 37 °C. Colonies were passaged using the gentle cell dissociation reagent (07174, StemCell Technologies). mouse ESCs and human ESCs were not treated and grown as described above in pluripotency medium. iCLIP
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2019-03-31T17:02:02Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-03-21T11:43:40Z
attributes.tag: External Id
attributes.value: SAMEA5523788
attributes.tag: INSDC center name
attributes.value: The Francis Crick Institute
attributes.tag: INSDC first public
attributes.value: 2019-03-31T17:02:02Z
attributes.tag: INSDC last update
attributes.value: 2019-03-21T11:43:40Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-5100:Sample 3
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell type
attributes.value: embryonic stem cell
attributes.tag: common name
attributes.value: house mouse
attributes.tag: sample name
attributes.value: E-MTAB-5100:Sample 3
attributes.tag: scientific_name
attributes.value: Mus musculus