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Sample GSM2212051 Query DataSets for GSM2212051
Status Public on Jul 15, 2016
Title AML-DMSO (PRO-seq)
Sample type SRA
Source name primary acute myeloid leukemia patient cells
Organism Homo sapiens
Characteristics cell type: primary acute myeloid leukemia patient cells
treatment: DMSO, 1hr
Treatment protocol DMSO, 1hr
Growth protocol IMDM supplemented with 20% BIT 9500 Serum Substitute, 50 ng/ml SCF, 10 ng/ml IL-6, and 10 ng/ml IL-3.
Extracted molecule nuclear RNA
Extraction protocol Nuclei isolation by douncing in isotonic buffer with 0.1% Triton X-100
Nuclear run-on assays were performed with ATP, UTP, GTP, and biotin-11-CTP or with all 4 biotin-11-NTPs. Nuclei were lyzed with TRIzol, nuclear RNA was extracted and fragmented, and biotinylated RNA was purified with strepavidin magnetic beads, which was followed by 3' adaptor ligation, 5' repair, 5' adaptor ligation, reverse transcription, and PCR full-scale amplification.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
Data processing Library strategy: PRO-seq
Base-calling, filtering, and demultiplexing were performed using Illumina CASAVA 1.8.2 with default settings.
Raw reads were processed to trim adaptor and low quality sequences using Trimmomatic (version 0.32) with parameters: -phred33 input.txt.gz output.txt.gz ILLUMINACLIP:adaptor.txt:2:30:7 TRAILING:15.
For PRO-seq, reverse complements of the trimmed reads were generated using “fastx_reverse_complement” (version 0.0.13) with default settings, and the reverse complement sequences were aligned to the human genome hg19 using bowtie2 (version 2.2.4) with default settings. For ChIP-exo, pre-processed reads were aligned to hg19 using bowtie2 with default settings. For RNA-seq, pre-processed reads were aligned to hg19 using TopHat (version 2.0.10) with default settings.
H3K27ac peak calling was performed using MACS2 (version 2.0.10) with parameters: MACS2 callpeak -t H3K27ac.bam -c Input.bam --nomodel -f BAM -g hs -n -B.
Genome_build: hg19
Supplementary_files_format_and_content: Genome coverage was normalized and calculated for each strand separately and reported in bedGraph format. The ChIP-exo peak file reports genome coordinates, peak length, read counts, and enrichment significance for each called H3K27ac peak. RNA-seq count files contain gene RefSeq IDs and their normalized read counts in reads per kilobase of transcript per million mapped reads (RPKM).
Submission date Jun 23, 2016
Last update date May 15, 2019
Contact name Scott W Hiebert
Phone 615-936-3582
Organization name Vanderbilt University
Department Biochemistry
Lab Hiebert Lab
Street address 2220 Pierce Ave
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
Platform ID GPL11154
Series (1)
GSE83660 High Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML
BioSample SAMN05290367
SRA SRX1873252

Supplementary file Size Download File type/resource
GSM2212051_PRO-AML-DMSO.minus.bedGraph.gz 38.4 Mb (ftp)(http) BEDGRAPH 40.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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