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Sample GSM2212042 Query DataSets for GSM2212042
Status Public on Jul 15, 2016
Title DMSO-3hr (RNA-seq)
Sample type SRA
 
Source name t(8;21)-containing acute myeloid leukemia cell line
Organism Homo sapiens
Characteristics cell line: Kasumi-1 cells
treatment: DMSO, 3 hr
Treatment protocol DMSO, 3 hr
Growth protocol RPMI 1640 supplemented with 10% FetalPlex and 2 mM L-Glutamine
Extracted molecule polyA RNA
Extraction protocol TRIzol extraction
PolyA enriched RNA was used to build library using TruSeq RNA Library Preparation Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing 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
E-mail(s) scott.hiebert@vanderbilt.edu
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
Relations
BioSample SAMN05290358
SRA SRX1873243

Supplementary file Size Download File type/resource
GSM2212042_RNAseq-Kasumi1-DMSO-3hr-normalized-count.txt.gz 77.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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