 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 03, 2015 |
| Title |
HDAC1_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
antibody vendor/catalog: Abcam, ab7028
ChIP: HDAC1
|
| 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 II and HiSeq 2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-seq reads were aligned to the HG19 genome assembly with pipeline CASAVA 1.7 using ELANDv2 or CASAVA-1.8.2 using ELANDv2e. For H3K4me3 and H3K27me3 ChIP-seq data, the bed files are made from a BAM file created from the CASAVA pipeline, which contains uniquely mapping reads as described above. The FASTQ under this pipeline is Phred33 or Phred64.
BED files (applied for SISSRS) were converted directly from the original ELAND export files; they were filtered to exclude tags that do not align uniquely to the hg19 genome, tags that do not pass filter, tags that contain Ns, and tags that contain more than 2 mismatches.
ALN files (used for CisGenome) were also converted directly from the ELAND export files using the program tool built-in CisGenome.
Cisgenome 2.0 was used for peak calling of Ikaros, HDAC1, H3K4me3 and H3K27me3. Parameters lpcut = 3 and c = 2 were selected for Ikaros, lpcut = 3 and w = 5 for HDAC1, and w = 5 for H3K4me3 and H3K27me3 datasets, respectively. Other parameters remain in default to run the program. Peaks with FDR ≤ 0.05 and Log2FC ≥ 1 were selected for further analysis.
SISSRS 1.4 was applied to find peaks of histone modification markers H3K9ac, H3K9me3 and H3K36me3 with parameter P-value ≤ 0.05 and other parameters remain in default. The output peaks with FC ≥ 2 were kept for further data analysis.
Genome_build: hg19
Supplementary_files_format_and_content: The final processed files are all in COD format. Each file contains peaks for a sample.
|
| |
|
| Submission date |
Feb 11, 2013 |
| 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 |
| SRA |
SRX235031 |
| BioSample |
SAMN01919575 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1080932_Nalm6-WT-HDAC1_peak.cod.gz |
412.2 Kb |
(ftp)(http) |
COD |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
|
|
|
|
 |
