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Sample GSM1313525 Query DataSets for GSM1313525
Status Public on Mar 01, 2015
Title H3K79me2_HSPC-MA9cells_ChIPseq
Sample type SRA
 
Source name umbilical cord blood
Organism Homo sapiens
Characteristics cell type: CD34+ cells
transduction: HSPC-MA9
chip antibody: H3K79me2 (Millipore 04-835)
Growth protocol Umbilical cord blood CD34+ cells were selected using immunomagnetic beads (Miltenyi Biotech) and stably transduced with retrovirus expressing empty vectors (HSPC control) or the MLL-AF9 (HSPC-MA9) fusion protein. Cells were cultured as described elsewhere (Wei et al., cell 2008).
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
9 ng of ChIP DNA as quantitated by fluorometry was used. Electrophoretic fraction of 150 bp was processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (12 cycles). The resulting purified DNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Data processing Alignment was performed with BWA (Burrorws-Wheeler aligner software package) versus the human sequence assembly GRCh37/hg19 (Feb 2009)
MLL and AF9 peaks: Findpeaks was used to analyze the identified ChIP-seq MLL and AF9 binding regions. Calibration using input control was used, and peaks with a confidence less than 99.9 % for MLL and 99.0% for histone samples were rejected. Subpeaks (0.7) and trim (0.95) were enabled. The maximum number of genes associated to a peak is two (one in sense and the other in antisense)
MLL and AF9 peaks: A custom program was run to search Ensembl database and to find the first gene that lays in sense and antisense direction taking as reference point the defined peaks.a window of 5000 nt upstream and 200 nt downstream of the origin of transcription for each gene was defined
chromatin modifications: The SICER 1.1 was used following developer’s technical recommendations for histone modifications (200-bp window/ FDR≤ 0.01).
chromatin modifications: The software pipeline for finding differential peaks in pair-wise comparisons (HSPC-MA9 vs HSPC) was applied and significant ChIP-seq peaks were filtered at FC<1.5 and FDR ≤ 0.001.
Genome_build: hg19
 
Submission date Jan 23, 2014
Last update date May 15, 2019
Contact name Sara Alvarez
E-mail(s) salvarez@nimgenetics.com
Phone +34 672 05 98 89
Organization name NIMGenetics
Street address C/Faraday 7
City Madrid
State/province Madrid
ZIP/Postal code 28049
Country Spain
 
Platform ID GPL10999
Series (2)
GSE54344 Aberrant chromatin acetylation in MLL-AF9 leukemia mediates the response to HDAC inhibition (ChIP-Seq)
GSE54348 Aberrant chromatin acetylation in MLL-AF9 leukemia mediates the response to HDAC inhibition
Relations
BioSample SAMN02595457
SRA SRX447431

Supplementary file Size Download File type/resource
GSM1313525_HSPC-MA9-K79_hg19.wig.gz 2.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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