title: pre_rearranged_Vk5_37_Jk1_Vk18_36_pro_del_vAbl_gro_seq_rep1
organism: Mus musculus
description: Protocols: Briefly, 10 million cells were permeabilized with permeabilization buffer (10 mM Tris-HCl, pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, one tablet of protease inhibitors per 50 ml and 4 units Rnase inhibitor per ml) and resuspended in 100 ul storage buffer (10 mM Tris-HCl, pHHH 8.0, 25% (vol/vol) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT). Permeabilized cells were subjected to nuclear run-on (2xRun-on mix: 5 mM Tris-Cl, PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, 10 units of RNase inhibitor, 1% sarkosyl) at 37o for 5 min, followed by Trizol-based RNA extraction. v-Abl cell lines were cultured in RPMI1640 media with 15% FBS G1-arrest was performed by treating v-Abl cell lines with 3uM STI for 4 days Briefly, 10 million cells were permeabilized with permeabilization buffer (10 mM Tris-HCl, pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, one tablet of protease inhibitors per 50 ml and 4 units Rnase inhibitor per ml) and resuspended in 100 ul storage buffer (10 mM Tris-HCl, pHHH 8.0, 25% (vol/vol) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT). Permeabilized cells were subjected to nuclear run-on (2xRun-on mix: 5 mM Tris-Cl, PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, 10 units of RNase inhibitor, 1% sarkosyl) at 37o for 5 min, followed by Trizol-based RNA extraction. Illumina adapters were ligated to RNA followed by cDNA generation with reverse transcriptase.  Libraries were PCR-amplified with Illumina primers and subjected to sequencing.
attributes.tag: ENA first public
attributes.value: 2026-02-24
attributes.tag: INSDC center name
attributes.value: BCH
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-16014:pre_rearranged_Vk5_37_Jk1_Vk18_36_pro_del_vAbl_gro_seq_rep1
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell line
attributes.value: v-Abl transformed pro-B cell line
attributes.tag: collection date
attributes.value: not collected
attributes.tag: common name
attributes.value: house mouse
attributes.tag: genotype
attributes.value: Rag2-/-, Emu-Bcl2, single Igk allele, pre-rearranged Vk5-37/Jk1_Vk18-36 pro del
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: sample name
attributes.value: E-MTAB-16014:pre_rearranged_Vk5_37_Jk1_Vk18_36_pro_del_vAbl_gro_seq_rep1
attributes.tag: scientific_name
attributes.value: Mus musculus