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| Status |
Public on Jul 15, 2016 |
| Title |
DMSO-1hr (PRO-seq) |
| Sample type |
SRA |
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| Source name |
t(8;21)-containing acute myeloid leukemia cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Kasumi-1 cells
treatment: DMSO, 1 hr
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| Treatment protocol |
DMSO, 1 hr
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| Growth protocol |
RPMI 1640 supplemented with 10% FetalPlex and 2 mM L-Glutamine
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| 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.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| 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).
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| Submission date |
Jun 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Scott W Hiebert |
| E-mail(s) |
scott.hiebert@vanderbilt.edu
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| Phone |
615-936-3582
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| Organization name |
Vanderbilt University
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| Department |
Biochemistry
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| Lab |
Hiebert Lab
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| Street address |
2220 Pierce Ave
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| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN05290349 |
| SRA |
SRX1873235 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2212033_PRO-Kasumi1-DMSO-1hr.minus.bedGraph.gz |
35.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM2212033_PRO-Kasumi1-DMSO-1hr.plus.bedGraph.gz |
35.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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