|Public on Jan 12, 2017
|Leukemia cell line (SEM)
|cell line: Leukemia cell line; SEM
cell type: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation
molecule subtype: nascent RNA
|SEM cells were continuously grown in IMDM with 10-20% FBS, split when they reached a density of 1-2X10e6 down to 5X10e5; all other cell lines were grown in a similar manner in RPMI 1640.
|ChIP-seq: Fixed cells were lysed in 1% SDS lysis buffer. Samples were sonicated and protein-DNA complexes were isolated with antibody.
Nascent RNA-seq: 108 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
Libraries were prepared according to Illumina's protocol accompanying the DNA Library Prep Master Mix Set (Part# E6040) or Ultra RNA Library Prep Master Mix Set (Part# E7530).
|Illumina HiSeq 2500
|processed data file: SEM_nascent_rpkm_table.txt
|ChIP-seq reads were aligned to the hg18 genome using bowtie version 1.1.2 with following parameters: p1 m2 best strata sam
Peaks were called using SeqMonk version 0.24.1
Nascent RNA-seq reads were aligned to the hg18 genome using STAR
Read counts were determined using featureCounts (Subread package)
Supplementary_files_format_and_content: bed files were generated from text files outputted directly from SeqMonk; Rpkm tables (.txt) were generated using edgeR
|Jun 23, 2016
|Last update date
|May 15, 2019
|Weatherall Institute of Molecular Medicine
|Molecular Haematology Unit
|John Radcliffe Hospital
|MLL-AF4 Spreading Identifies Binding Sites that Are Distinct from Super-Enhancers and that Govern Sensitivity to DOT1L Inhibition in Leukemia.