|
| Status |
Public on Oct 21, 2020 |
| Title |
AML cells, Hi-FLAG |
| Sample type |
SRA |
| |
|
| Source name |
Hoxa9- and Trib1-expressing murine AML cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: AML cell line
genotype: Hoxa9 and Trib1
strain: C57Bl/6
chip antibody: FLAG (Sigma, F7425, lot 011M4789)
|
| Treatment protocol |
Trib1 cDNA was introduced by retrovirus-mediated gene transfer
|
| Growth protocol |
AML cells are maintained in IMDM supplemented with 10% FBS and 10 ng/ml IL3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and immunoprecipitated with each antibodies
Libraries were prepared according to Illumina's instructions accompanying the ThruPLEX DNA-seq 6S (12) Kit (R400523). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Base calls were performed using Bowtie 1.1.1.
ChIP-seq reads were aligned to the mm9 genome assembly using samtools 1.2.
Peak call was performed using MACS1.4.
For every 300 bp window, the mapped tag count for ChIP, Cc and that for Input, Ci were used for calculation. Ec and Ei indicates the estimate count for 300 bp window for ChIP and Input. Signal ratio of ‘target TF’ was calculated as, Cc/Ec + 1 ÷ Max(1, Ci/Ei + 1).
Genome_build: mm9
Supplementary_files_format_and_content: tdf
|
| |
|
| Submission date |
Nov 13, 2019 |
| Last update date |
Oct 21, 2020 |
| Contact name |
Takuro Nakamura |
| E-mail(s) |
takuro-ind@umin.net
|
| Phone |
81-3-3570-0462
|
| Organization name |
Japanese Foundation for Cancer Research
|
| Department |
The Cancer Institute
|
| Lab |
Carcinogenesis
|
| Street address |
3-8-31 Ariake, Koto-ku
|
| City |
Tokyo |
| ZIP/Postal code |
135-8550 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE140313 |
Trib1 promotes acute myeloid leukemia progression by modulating transcriptional programs of Hoxa9 [ChIP-seq] |
| GSE140315 |
Trib1 promotes acute myeloid leukemia progression by modulating transcriptional programs of Hoxa9 |
|
| Relations |
| BioSample |
SAMN13279551 |
| SRA |
SRX7135170 |
