|
| Status |
Public on Nov 03, 2021 |
| Title |
TET2KO_H3Kme1_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Lin- bone marrow cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Tet2 Knockout
cell type: Lin- bone marrow cells
chip antibody: Diagenode Cat#15410194 lot#A1862D
|
| Growth protocol |
25 million mouse bone marrow Lin- cells (purity >80%) obtained using the Direct Lineage Cell depletion kit (Miltenyi Biotec, 140-110-470) were crosslinked and processed with the ChIP-IT High Sensitivity kit (Active Motif 53040) following manufacturer’s instructions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
5 ug of chromatin from Lin- cells and 1 ug of antibody were combined with 10 ng of chromatin from Drosophila melanogaster S2 cells (Active Motif 53083) as spike-in control.
Libraries were generated using NEBNExt Ultra II DNA library prep kit for Illumina
Libraries were sequenced single-end in an Illumina Nextseq 500
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base calling using Illumina RTA 2.4.11
Reads were trimmed for adapters using Cutadapt (v1.15 –nextseq-trim=20 –m 18).
Fastq files were aligned to mouse mm10 using BWA (v0.7.13 aln -q 5 -l 32 -k 2).
Aligned files were deduplicated using Picard Mark Duplicates (v2.10.6).
Genome_build: mm10_no_alt_analysis_set (ENCSR425FOI)
Supplementary_files_format_and_content: Bigwig fold enrichment signal files were generated using Macs2 (v2.1.1.20160309) using H3 as control.
Supplementary_files_format_and_content: narrowPeaks were called using Macs2 for H3K27ac, H3K4me1 and H3K4me3 using H3 as a control.
|
| |
|
| Submission date |
Jul 15, 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 |
GPL19057 |
| Series (2) |
| GSE145876 |
p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia [ChIP-seq] |
| GSE145878 |
p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN15543784 |
| SRA |
SRX8737402 |
