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Sample GSM5570000 Query DataSets for GSM5570000
Status Public on Jun 27, 2022
Title H2AK119ub CUT&RUN wt mESC line 2
Sample type SRA
 
Source name mESC cultured in 2i+LIF medium
Organism Mus musculus
Characteristics development stage: Pluripotent state
genotype: Smchd1[fl/+] (wild-type)
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 SAMN21363743
SRA SRX12118448

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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