 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 17, 2013 |
| Title |
Kasumi_RUNX1_2 |
| Sample type |
SRA |
| |
|
| Source name |
Kasumi-1 cell culture
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: AML-patient-derived cell lines t(8;21) Kasumi-1
chip antibody: anti-RUNX1 (c-terminus) [Yoram Groner lab, Weizmann Institute]
|
| Growth protocol |
Kasumi-1 cells were purchased from the ATCC (Manassas, VA) and maintained in RPMI-1640 supplemented with 20% fetal bovine serum (FBS), 2 mM L-glutamine and 1% penicillin–streptomycin at 37°C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cross-linked chromatin from approximately 5-10x107 Kasumi-1 cells was prepared and fragmented to an average size of approximately 200 bp by 30-40 cycles of sonication (30 seconds each) in 15 ml tubes using the Bioruprtor UCD-200 sonicator (Diagenode). For immunoprecipitation, the following antibodies were added to 12 mL of diluted, fragmented chromatin: 32 uL of anti-RUNX1 (Aziz-Aloya, 1998; Levanon, 2011) raised against the protein C-terminal fragment; 320 ul of anti-ETO (PC283; Calbiochem). Non-immunized rabbit serum served as control. DNA was purified using QIAquick spin columns (QIAGEN) and sequencing performed using Illumina genome analyzer IIx, according to the manufacturer’s instructions. For ChIP-seq analysis, Illumina sequencing of short reads (40 bp) was conducted using the GAII system.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Chromain IP against RUNX1 (c-terminus), replicate 2
|
| Data processing |
ChIP-seq short read tags were mapped to the genome using bowtie. Mapped reads were then extended to 120 bp fragments in the appropriate strand and all fragments were piled up to generate a coverage track in 50 bp resolution. We computed the genome-wide distribution of coverage on 50 bp bins for each track, and used it to normalize piled-up chip-seq coverage by transforming coverage values v to log(1-quantile(v), defining the ChIP-seq binding intensity or binding enrichment. We largely preferred using binding intensities directly, and minimized using arbitrarily defined threshold on binding intensity to define binding sites. In cases where a threshold was needed (e.g. to report indicative statistics on binding, or to facilitate motif finding), we searched for genomic bins with normalized coverage > log(1-0.9985) (merging all sites that were within 250 bp of each other). We used a control non-immune serum (NIS) ChIP-seq experiment to filter spurious binding sites (defined as bins with NIS normalized intensity > log(1-0.9985) ).
Genome_build: hg18
Supplementary_files_format_and_content: 50bp-binned profiles were converted to BigWig format.
|
| |
|
| Submission date |
Apr 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yoram Groner |
| E-mail(s) |
yoram.groner@weizmann.ac.il
|
| Organization name |
Weizmann institute
|
| Department |
Molecular Genetics
|
| Street address |
234 Herzl St.
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE45738 |
Addiction of t(8;21) and inv(16) AML to native RUNX1 [ChIP-Seq data] |
| GSE45748 |
Addiction of t(8;21) and inv(16) AML to native RUNX1 |
|
| Relations |
| SRA |
SRX259612 |
| BioSample |
SAMN01997759 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1113428_RUNX1_2.bw |
367.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
