|
| Status |
Public on Aug 21, 2017 |
| Title |
HL60-0-hrs-1-hMeDIP |
| Sample type |
SRA |
| |
|
| Source name |
Myeloid leukemia cells, vitamin C, 0h, hMeDIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HL60
cell type: Human myeloid cells
cancer type: Leukemia
treatment: Vitamin C
time: 0h
antibody: 5-hydroxymethylcytosine
sample type: hMeDIP enrichment
|
| Treatment protocol |
Human cell lines were treated with vitamin C in culture for 0 and 72hrs.
|
| Growth protocol |
Human cell lines were grown in RPMI media with 10-20% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated by proteinase K digestion, phenol chloroform extraction and ethanol precipitation.
Libraries were prepared according to Illumina standard protocols. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: hMeDIP-Seq
Base calling and demultiplexing were performed using Illumina bcl2fastq software.
The reads were aligned to the human genome (build hg19/GRCh37) using Bowtie2 aligner with local alignment.
Poorly mapped reads (mapping quality <30) were removed using samtools.
Duplicate reads were removed using Picard.
Peaks were called using MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: *bed: Bed files include peaks.
|
| |
|
| Submission date |
Jun 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Igor Dolgalev |
| Organization name |
NYU Grossman School of Medicine
|
| Street address |
550 1st Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE97442 |
Genetic and pharmacological restoration of TET2 function blocks stem cell self-renewal and progression of leukemia |
| GSE99953 |
hMeDIP sequencing of human leukemia cells |
|
| Relations |
| BioSample |
SAMN07223290 |
| SRA |
SRX2912108 |
