|
| Status |
Public on Jun 26, 2018 |
| Title |
m402_p300 |
| Sample type |
SRA |
| |
|
| Source name |
thymus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: NUP214-ABL1 positive, TLX1 positive
chip antibody: p300 (Santa Cruz Biotechnology, SC-585X, AB_2616339)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
all libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
p300 binding in NUP214-ABL1 positive, TLX1 positive cells.
|
| Data processing |
Library strategy: ChIPmentation
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with Bowtie2 / TopHat2
count reads with htseq-count
call peaks with MACS2
normlization with deepTools
Genome_build: Mus musculus (mm10), Homo sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts
Supplementary_files_format_and_content: narrowpeak / bed files with the called peaks (macs2)
Supplementary_files_format_and_content: bedgraph files with normalized signals
|
| |
|
| Submission date |
Aug 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sofie Demeyer |
| E-mail(s) |
sofie.demeyer@kuleuven.vib.be
|
| Organization name |
KULeuven / VIB
|
| Department |
Center for Cancer Biology
|
| Lab |
Laboratory of Molecular Biology of Leukemia
|
| Street address |
Herestraat 49 / bus 912
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE102209 |
Cooperation between TLX1 and the NUP214-ABL1/STAT5 signaling in T-cell acute lymphoblastic leukemia |
|
| Relations |
| BioSample |
SAMN07446167 |
| SRA |
SRX3058106 |
