|
| Status |
Public on Jun 27, 2022 |
| Title |
H2AK119ub CUT&RUN mat del mESC line 1 |
| Sample type |
SRA |
| |
|
| Source name |
mESC cultured in 2i+LIF medium
|
| Organism |
Mus musculus |
| Characteristics |
development stage: Pluripotent state
genotype: Smchd1[del/+] (maternally deleted)
strain: C57BL/6/Cast F1
Sex: M
cell type: mESC
|
| Growth protocol |
mESCs derived, and cultured as described in Jansz et al., Nature Structural Molecular Biology 2018 DOI:10.1038/s41594-018-0111-z
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fresh cells were subject to CUT&RUN for H2AK119ub. DNA was extracted with phenol/chloroform/isoamyl alcohol
NEBNext Ultra II DNA Library Prep Kit for Illumina
CUT&RUN was performed as described in Skene and Henikoff eLife 2017;6:e21856 DOI: 10.7554/eLife.21856 DNA was purified by phenol/chloroform/isoamylalcohol extraction followed by glycogen/ethanol precipitation
NEBNext Ultra II DNA Library Prep Kit for Illumina
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Maternal deletion with Zp3-Cre
|
| Data processing |
Library strategy: CUT&RUN
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using Bowtie2 v2.3.4.1 with default parameters after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth library size using Seqmonk.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited txt file containing log2-transformed read counts normalized by library size within bins created ±2.5kb centered on a list of MACS peaks determined using SeqMonk's MACS-like functionality for each genotype separately. MACS peaks were called between H2AK119ub ChIP and input samples from Fursova et al., 2021 (Genes Dev . 2021 May 1;35(9-10):749-770. doi: 10.1101/gad.347005.120. Epub 2021 Apr 22) . Peak lists from biological replicates were merged before peak calculation.
|
| |
|
| Submission date |
Sep 08, 2021 |
| Last update date |
Jun 27, 2022 |
| Contact name |
Natalia Benetti |
| E-mail(s) |
nataliabenetti17@gmail.com
|
| Organization name |
WEHI
|
| Street address |
1G Royal Parade
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE183739 |
Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo [H2AK119ub CUT&RUN] |
| GSE183740 |
Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo |
|
| Relations |
| BioSample |
SAMN21363745 |
| SRA |
SRX12118450 |
