|
| Status |
Public on Jul 31, 2018 |
| Title |
H3 MTF2 knockdown shRNA 3 healthy sample 2 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: H3
type: MTF2 knockdown
cell sorting: CD34+/CD38-
status: Healthy
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were sheared using a Covaris sonicator until DNA reached a final size of 100-300bp. 750ng of drosophila spike in chromatin (Active Motif) was added to each sonicated sample. 4ug of anti-H3K27me3 antibody (Cell Signaling, c36B11) or H3 (Abcam, ab1791) was bound to pre-blocked Protein A7 magnetic beads (Millipore) in combination with 2ug of Spike-in antibody (Active Motif) for 12 hours. The beads were then combined with sonicated sample containing Drosophila spike in chromatin and incubated overnight. After incubation, beads were collected and DNA-antibody complexes were eluted at 65 o C. Crosslinks were reversedovernight at 65 o C. Samples were treated with Proteinase K (Fisher Scientific) and RNaseA (Fisher Scientific) and DNA was purified using phenol-chloroform. All ChIP-seq experiments were cell number normalized and 150,000 cells per biological sample were used for each H3 and H3K27me3 ChIP experiment.
For sequencing total ChIP DNA was used for library preparation (NextFlex Illumina Chip-seq kit).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped separately to the reference human (hg19) and Drosophila melanogaster (BDGP6.0) genome assemblies using Bowtie 2.2.6. Reads were mapped separately to the reference human (hg19) and Drosophila melanogaster (BDGP6.0) genome assemblies using Bowtie 2.2.6
Genome_build: hg19, Ensembl 67
Supplementary_files_format_and_content: peak, bigwig
|
| |
|
| Submission date |
May 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
William Stanford |
| E-mail(s) |
wstanford@ohri.ca
|
| Phone |
613-737-8899
|
| Organization name |
Ottawa Hospital Research Institute
|
| Lab |
Stanford
|
| Street address |
501 Smyth Road
|
| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1H 8L6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE98378 |
Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy [ChIP-Seq] |
| GSE98380 |
Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy |
|
| Relations |
| BioSample |
SAMN06854454 |
| SRA |
SRX2771335 |
