|
| Status |
Public on Sep 07, 2021 |
| Title |
WT_Ikaros_frozen_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wildtype
cell type: splenic B cells
cell state: frozen
target: Ikaros
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Spleens were harvested from C57BL/6 mice and B cells were isolataed by MACS. Cells were used immediated for CUT&RUN (fresh) or cell pellets were resuspended in 90%FBS/10% DMSO and frozen overnight.
Libraries were prepared using the NEBnext Ultra II DNA Library Prep Kit (Illumina)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Library strategy: CUT&RUN
File processing was carried out using CUT&RUNTools (Zhu et al., 2019)
Trimmomatic-0.36 was used to trim TruSeq adapters
Bowtie 2 2.2.9 was used with "--dovetail" option indicated
Picard 2.8.0 MarkDuplicates was used to mark PCR duplicates
MACS2 was used to callpeaks with options " -f BAMPE -q 0.01 -B --SPMR" indicated
Genome_build: mm10
Supplementary_files_format_and_content: peak files
|
| |
|
| Submission date |
Apr 15, 2021 |
| Last update date |
Sep 07, 2021 |
| Contact name |
Princess Rodriguez |
| E-mail(s) |
pdrodrig@uvm.edu
|
| Organization name |
University of Vermont
|
| Department |
Microbiology and Molecular Genetics
|
| Lab |
Given Courtyard S453
|
| Street address |
89 Beaumont Avenue
|
| City |
Burlington |
| State/province |
Vermont |
| ZIP/Postal code |
05405 |
| Country |
USA |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE172130 |
An integrated CUT&RUN quality control workflow for histone modifications and transcription factors |
|
| Relations |
| BioSample |
SAMN18747087 |
| SRA |
SRX10605820 |
