|
| Status |
Public on Oct 18, 2018 |
| Title |
INPUT_C12-TAF15_CHA |
| Sample type |
SRA |
| |
|
| Source name |
INPUT_C12-TAF15_CHA
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pre-B cells Arf-/-
strain: C57BL/6
passages: TAF15-ZNF384 Fusion
chip antibody: none
|
| Growth protocol |
Cells were derived from C57BL/6 Arf-/- BM cells as described (Randle et al, PNAS, 2001). Cells were transduced with lentiviral supernatants of ZNF384-HA, TAF15-ZNF384-HA, or TCF3-ZNF384-HA.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was prepared as described (Zhang et.al, Nature Genetics, 2016). Breifly, 20 X 10^6 cells were crosslinked with 1% formaldehyde for 10 minutes. Cells were washed 3 times with PBS and lysed on ice for 10 minutes with lysis buffer. Chromatin was washed twice in wash buffer and once in shearing buffer before resuspending in 1ml of shearing buffer. Chromatin was sonicated with a Covaris E210 instrument and resuspended in dilution buffer. Finally, immunoprecipiation was performed with anti-HA antibody.
To prepare ChIP-seq libraries, 10 ng of ChIP DNA was end repaired and adaptor ligation was performed using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (New England BioLabs). Libraries were purified after 14 rounds of PCR amplification with Q5 DNA Hot-Start polymerase (New England BioLabs). Each ChIP-seq library underwent 50-cycle single-end sequencing using TruSeq SBS kit v3 on an Illumina HiSeq 2000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
TAF15-ZNF384 Fusion
|
| Data processing |
we mapped 50bp single-end reads to mouse genome mm9(MGSCv37) with BWA (version 0.7.12-r1039),
marked duplicated reads with Picard and only unique mapped reads extracted by Samtools (version 1.2) were kept for analysis.
We extend each read to estimated fragment size by SPP (version 1.1) and generated bigwig files scaled the track normalized to 15M unique mapped reads.
Review each sample find they have clear peaks by IGV (3.0.beta) and consistent between anti-HA samples and anti-ZNF384 samples.
Later we performed analysis only used the anti-HA samples since their peaks are stronger and most have ZNF384 motif where anti-ZNF384 samples were weak.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Mar 30, 2018 |
| Last update date |
Oct 18, 2018 |
| Contact name |
Beisi Xu |
| E-mail(s) |
beisi.xu@stjude.org
|
| Organization name |
St Jude Children's Research Hosipital
|
| Department |
Center for Applied Bioinformatics
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE112560 |
ChIP-sequencing to investigate occupancy of wild-type and fusion ZNF384 proteins in murine pre-B cells |
| GSE112561 |
Genomic classification and identification of the cell of origin of pediatric mixed phenotype acute leukemia |
|
| Relations |
| BioSample |
SAMN08824635 |
| SRA |
SRX3868854 |
