|
| Status |
Public on Nov 03, 2021 |
| Title |
P300KO_TET2KO_Input_DIPseq_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HSPCs
|
| Organism |
Mus musculus |
| Characteristics |
genotype: p300 Tet2 KO
cell type: HSPCs
dip antibody: input
|
| Growth protocol |
Genomic DNA from sorted HSPCs was isolated using the AllPrep DNA/RNA Plus micro kit (Qiagen)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 200 ng of genomic DNA was sonicated followed by end-repair, A-tailing and adaptor ligation using standard Illumina protocols. 10% of the volume was retained for Input.
Immunoprecipitation with anti-5- hmC antibodies (1 μg/ml, Active Motif) was performed at 4°C overnight and immunoprecipitated DNA was recovered using protein G magnetic beads (Invitrogen). After proteinase K digestion, DNA was purified from all input and immunoprecipitated samples, and amplified by PCR for library preparation.
Single-End, 100bp sequenced on an Illumina HiSeq 2500.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base calling using Illumina RTA 2.4.11
Reads were trimmed using cutadapt (–m25), aligned using bowtie2 (v2.0.5) to the mouse mm10 genome build, quality filtered (mapq > 30), and deduplicated using Picard Markduplicates.
Peaks were called using macs2 (-g mm --nomodel --extsize 200 –B) and differential peaks were determined using macs2 bdgdiff from the intermediate lambda and pileup bedgraphs generated from macs2 callpeaks.
Genome_build: Encode: mm10_no_alt_analysis_set (ENCSR425FOI)
Supplementary_files_format_and_content: Bigwig files contain fold change signal over input generated from macs2.
|
| |
|
| Submission date |
Feb 25, 2020 |
| Last update date |
Nov 03, 2021 |
| Contact name |
Stephen Nimer |
| Organization name |
University of Miami
|
| Department |
Sylvester Comprehensive Cancer Center
|
| Street address |
1120 NW 14th ST
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE145877 |
p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia [DIP-seq] |
| GSE145878 |
p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN14180088 |
| SRA |
SRX7798339 |
