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Sample GSM2212271 Query DataSets for GSM2212271
Status Public on Jan 12, 2017
Title SEM_1umEPZ5676_Rep3
Sample type SRA
Source name Leukemia cell line (SEM)
Organism Homo sapiens
Characteristics cell line: Leukemia cell line; SEM
cell type: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation
treated with: 1┬ÁM EPZ-5676 for 7 days
molecule subtype: nascent RNA
Growth protocol 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.
Extracted molecule total RNA
Extraction protocol 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).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description processed data file: EPZ5676_rpkm.txt
Data processing 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)
Genome_build: hg18
Supplementary_files_format_and_content: bed files were generated from text files outputted directly from SeqMonk; Rpkm tables (.txt) were generated using edgeR
Submission date Jun 23, 2016
Last update date May 15, 2019
Contact name Thomas Milne
Organization name Weatherall Institute of Molecular Medicine
Department Molecular Haematology Unit
Street address John Radcliffe Hospital
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
Platform ID GPL18573
Series (1)
GSE83671 MLL-AF4 Spreading Identifies Binding Sites that Are Distinct from Super-Enhancers and that Govern Sensitivity to DOT1L Inhibition in Leukemia.
BioSample SAMN05290495
SRA SRX1873483

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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