|
| Status |
Public on Mar 04, 2017 |
| Title |
H3K27me3_suppl_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Nalm6 ALL leukemia cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: pre-B ALL leukemia cells
culture condition: 10% FBS RPMI1640 in 5% CO2, 37°C
chip antibodies: Millipore, 07-449
|
| Growth protocol |
10% FBS RPMI1640 + A/P + b-ME in 5% CO2, 37°C, change media every 2-3 days, cell density in 2x10^5 to 1x10^6
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the ChIP-seq DNA Sample Kit . 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 18 cycles and library fragments of 200-400bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The resulted library was validated by using Agilent Technologies 2100 Bioanalyzer. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer (Illumina GA2) following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were aligned using bowtie2 v.2.2.4
Alignment was sorted using samtools v.0.1.19
Peaks were called using MACS2 v.2.1.0.20151222 with the --broad parameter
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 broadPeaks in bed format
|
| |
|
| Submission date |
Mar 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
chunhua song |
| E-mail(s) |
csong@hmc.psu.edu
|
| Phone |
717-531-1841
|
| Organization name |
Pennsyvania State University College of Medicine
|
| Department |
Pediatrics
|
| Street address |
500 University Drive
|
| City |
Hershey |
| State/province |
PA |
| ZIP/Postal code |
17033 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE44217 |
Mechanisms of Ikaros Tumor Suppression with HDAC1 through distinct histone markers in Pre-B ALL Leukemia |
| GSE44218 |
Mechanism of Ikaros tumor suppression in Leukemia |
|
| Relations |
| BioSample |
SAMN06477653 |
| SRA |
SRX2612175 |
