|
| Status |
Public on Jul 31, 2022 |
| Title |
UREΔ/+;Tet2+/-_oxBS5 |
| Sample type |
SRA |
| |
|
| Source name |
UREΔ/+;Tet2+/-
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell type: cKit+ Lymph- Ery- HSPC
disease state: AML
genotype: URE{delta}/+;Tet2+/-
ure: HET
tet2: HET
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total bone marrow cells were isolated from the femurs, tibiae, pelvic bones and spines of mice and were treated with 1x ACK lysing buffer pH 7.4 to lyse the red blood cells. cKit+ Lymph- Ery- cells were FACS-purified and gDNA was extracted using the Puregene Cell and Tissue kit (Qiagen)
oxBS-seq library construction was performed using the Ovation Ultralow Methyl-Seq with TrueMethyl oxBS kit and the M01320 v10 manual (Nugen/Tecan)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
FCH52JCCCX2_L7_CHKPE85219070013
|
| Data processing |
library strategy: OxBS-seq (Oxidative bisulfite sequencing)
adapters were trimmed from fastq files using trim_galore 0.4.0 with default parameters
reads were aligned to the PhiX RTA genome using bowtie2 with parameters: -N 1 Mapped reads were filtered away.
bisulfite mapping was performed with Bismark version 0.14.5 using default parameters.
Duplicate reads were marked with picard-tools 1.92.
number of methylated reads were counted at each loci with mpileup2methylation.py
Genome_build: mm10
Supplementary_files_format_and_content: The output files are in bedGraph-like format with columns: Chromosome, Position of C (0-based), Position of C +1, Percentage reads methylated, Count methylated reads, Total read count, Strand
|
| |
|
| Submission date |
Jan 21, 2022 |
| Last update date |
Jul 31, 2022 |
| Contact name |
Britta Will |
| E-mail(s) |
[email protected]
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Cell Biology
|
| Street address |
1300 Morris Park Avenue, Chanin Bldg., Rm. #401
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE191053 |
PU.1-dependent enhancer inhibition separates Tet2 deficient clonal hematopoiesis from malignant transformation |
| GSE194170 |
PU.1-dependent enhancer inhibition separates clonal hematopoiesis from malignant transformation (oxBS-Seq) |
|
| Relations |
| BioSample |
SAMN25159614 |
| SRA |
SRX13858027 |
