|
| Status |
Public on Jul 31, 2017 |
| Title |
WT3 |
| Sample type |
SRA |
| |
|
| Source name |
BCR-ABL1 transformed p19 null preB-ALL
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: pre-B cell leukemia
genotype: BCR-ABL1 overexpressed p19 null
|
| Growth protocol |
RPMI-1640 supplemented with 10% FBS, 4mM L-glutamine, 50µM 2-mercaptoethanol, 100U/mL penicillin and 100ug/mL streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
500,000 nuclei were lysed and transposed with the Nextera DNA library preparation kit (Illumina).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
read alignment with bowtie2
ATAC signal peaks were called using macs2
nucleosome signals were called using NucleoATAC
Genome_build: mm9
Supplementary_files_format_and_content: GFF file containing TSS nucleosome signals in 10bp bins, spanning +/-1kb of annotated TSSs
|
| |
|
| Submission date |
May 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Hemann |
| E-mail(s) |
hemann@mit.edu
|
| Phone |
6173240199
|
| Organization name |
Massachusetts Institute of Technology
|
| Department |
Koch Institute
|
| Lab |
Hemann Lab
|
| Street address |
500 Main St, Building 76 Room 301
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE98716 |
PHF6 regulates B-cell identity in acute lymphoblastic leukemia [ATAC-Seq] |
|
| Relations |
| BioSample |
SAMN06921185 |
| SRA |
SRX2793153 |
