 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 20, 2013 |
| Title |
HEB ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
HEB ChIP-seq
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Hematopoietic
tumor stage: Acute myeloid leukemia
cell line: Kasumi-1 cells
chip antibody: anti-HEB (Santa Cruz; sc-357)
|
| Growth protocol |
Kasumi-1 cells were grown with RPMI 1640 medium (Invitrogen) plus 10% fetal bovine serum (FBS; Gemini Bio-Products) and penicillin-streptomycin (Invitrogen) at 37°C in a humidified atmosphere with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Kasumi-1 cells were first dual cross-linked with 2 mM disuccinimidyl glutarate and 1% formaldehyde and then lysed with buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA and 1% SDS). Cell lysates were subjected to sonication, dilution with buffer (16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS and 1.1% Triton X-100) and then immunoprecipitation using the indicated antibodies. After extensive washing, ChIP DNA samples were purified with QIAquick PCR Purification Kit (Qiagen).
ChIP-Seq libraries were constructed following the Illumina protocol. Briefly, end-repair, “A” addition, and adaptor ligation steps were performed on 10 ng ChIP or Input DNA. Adaptor-ligated DNA with a size between 200 to 300 bp was selected and amplified to generate a sequencing library. 8 pM of sequencing library was applied to Illumina Single-Read flowcell for cluster generation on cBot. Finally, clusters were sequenced on the Illumina Genome Analyzer II to generate 36-bp short sequence reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Sequence reads were aligned to the human reference genome (hg18) using ELAND.
After filtering clonal reads, uniquely aligned reads were then used to perform peak-calling and flowing analyses by ChIPseeqer (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml).
Genome_build: hg18
|
| |
|
| Submission date |
Feb 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yanwen Jiang |
| E-mail(s) |
yaj2001@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Street address |
413 E. 69th St. BB1462
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE43834 |
A Stable Transcription Factor Complex Nucleated by Dimeric AML1-ETO Controls Leukaemogenesis |
|
| Relations |
| SRA |
SRX236114 |
| BioSample |
SAMN01919793 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1082308_HEB_ChIP_Read_Density.wig.gz |
177.0 Mb |
(ftp)(http) |
WIG |
| GSM1082308_Kasumi_HEB_T15F2_Enrichment.txt.gz |
246.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
