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Sample GSM6175607 Query DataSets for GSM6175607
Status Public on Jun 27, 2022
Title H2AK119ub CUT&RUN wt mESC day 2 line 1 rep 1
Sample type SRA
 
Source name primary mouse embryonic stem cell line
Organism Mus musculus
Characteristics cell line: primary mouse embryonic stem cell line
cell type: mouse embryonic stem cells in a differentiation time course to neural mesodermal progenitors
genotype: Smchd1[fl/+] (wild-type)
time: day 2 differentation
antibody: H2AK119ub (Cell Signalling Technologies, D27C40)
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 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 male
Data processing 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 and library size using Seqmonk.
FPKM reads were called over defined MACS2 peaks (determined by calling peaks between all H3K27me3 sample libraries and all input (no Ab) libraries) using the features over probes pipeline in Seqmonk
FPKM reads were calculated over genes +/- 10kb using the features over probes pipeline in Seqmonk, then were normalised to the geometric average of FPKM reads over MACS peaks in Microsoft Excel
Differential genome-wide peaks were called using the csaw v1.24.3 package between wt and maternal null samples at each day, as well as between days each for wt and maternal null
Assembly: GRCm38.p6
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_diff_FPKM_over_MACS_peaks.txt: tab-delimited text file containing FPKM reads over defined MACS2 peaks (determined by calling peaks between all H2AK119ub sample libraries and all input (no Ab) libraries)
Supplementary files format and content: benetti_CUT_RUN_diff_FPKM_values_for_probes_over_Hox.txt: tab-delimited text file containing FPKM reads calculated over genes +/- 10kb, and normalised to the geometric average of FPKM reads over MACS peaks (in benetti_H2AK119ub_CUT_RUN_diff_FPKM_over_MACS_peaks.txt). Note that this file is contained in the H3K27me3 CUT&RUN folder.
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_d2_wt_vs_matdel.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw at day 2 of differentiation between Smchd1 wildtype and maternal null samples
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_d2.5_wt_vs_matdel.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw at day 2.5 of differentiation between wt and maternal null samples
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_d3_wt_vs_matdel.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw at day 3 of differentiation between Smchd1 wildtype and maternal null samples
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_matdel_d2_vs_d2.5.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw in Smchd1 maternal null samples between days 2 and 2.5 of differentiation
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_matdel_d2_vs_d3.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw in Smchd1 maternal null samples between days 2 and 3 of differentiation
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_matdel_d2.5_vs_d3.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw in Smchd1 maternal null samples between days 2.5 and 3 of differentiation
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_wt_d2_vs_d2.5.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw in Smchd1 wildtype samples between days 2 and 2.5 of differentiation
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_wt_d2_vs_d3.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw in Smchd1 wildtype samples between days 2 and 3 of differentiation
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_wt_d2.5_vs_d3.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw in Smchd1 wildtype samples between days 2.5 and 3 of differentiation
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_2i_wt_vs_matdel.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw ain mESCs grown in 2i + LIF medium between Smchd1 wildtype and maternal null samples.
Library strategy: CUT&RUN
 
Submission date May 21, 2022
Last update date Nov 29, 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 SAMN28577357
SRA SRX15406120

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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