|
| Status |
Public on Jul 15, 2016 |
| Title |
Input_for_H3K27ac (ChIP-exo) |
| Sample type |
SRA |
| |
|
| Source name |
t(8;21)-containing acute myeloid leukemia cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Kasumi-1 cells
treatment: none
|
| Treatment protocol |
none
|
| Growth protocol |
RPMI 1640 supplemented with 10% FetalPlex and 2 mM L-Glutamine
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells (50 million) were fixed with 1% formaldehyde for 10 minutes at room temperature and reaction was quenched with 125 mM Glycine. Fragmented chromatin before immunoprecipitation was used to extract DNA as input.
ChIP-exo libraries were prepared according to the published method: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: ChIP-exo
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) |
[email protected]
|
| 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 |
SAMN05290370 |
| SRA |
SRX1873255 |
