|
| Status |
Public on Mar 01, 2015 |
| Title |
H4ac_HSPCcells_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
umbilical cord blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD34+ cells
transduction: control
chip antibody: H4ac (Millipore 06-598)
|
| 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 |
SAMN02595456 |
| SRA |
SRX447435 |
