|
| Status |
Public on Dec 21, 2021 |
| Title |
P18_CUT&RUN_IgG_Ino80cKO_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
spermatogenic cells from Testes
|
| Organism |
Mus musculus |
| Characteristics |
age: P18
genotype: Ino80cKO
strain: Mixed background
cell type: Spermatogenic cells
tissue: Testis
antibody: Rabbit-IgG, Sigma (I5006)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Seminiferous tubules from P18 testes were digested with collagenase and trypsin to obtain spermatogenic cells followed by filtration through 40 micron filter. Cells were prepared for CUT&RUN library by previously published protocol (Skene et al., 2018; Meers et al., 2019).
Libraries were generated using Kapa hyperprep DNA library kit for Illumina sequencing with modifications from CUT&RUN protocol (Skene et al., 2018; Meers et al., 2019).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
IgG_Ino80cKO.bw
|
| Data processing |
Library strategy: CUT&RUN
CUT&RUN reads were aligned to the reference genome mm10 using Bowtie2 with very-sensitive setting allowing dovetail alignment.
Duplicates were marked by Picard and replicates were merged using Samtools.
Bigwig files were prepared from merged files with 1X normalization using Deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files for genomic tracks.
|
| |
|
| Submission date |
Jul 06, 2021 |
| Last update date |
Dec 21, 2021 |
| Contact name |
Prabuddha Chakraborty |
| E-mail(s) |
pchakrab@email.unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Genetics
|
| Lab |
Terry Magnuson
|
| Street address |
120 Mason Farm Road5023 B, Genetic Medicine Building, CB#7264
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7264 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE179580 |
INO80 requires a polycomb subunit to regulate the establishment of poised chromatin in murine spermatocytes [CUT&RUN] |
| GSE179584 |
INO80 requires a polycomb subunit to regulate the establishment of poised chromatin in murine spermatocytes |
|
| Relations |
| BioSample |
SAMN20084425 |
| SRA |
SRX11364728 |
