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Sample GSM6726662 Query DataSets for GSM6726662
Status Public on Jul 15, 2024
Title A2_ENeg_2_S2
Sample type SRA
 
Source name mouse embryonic fibroblasts, control, day 3
Organism Mus musculus
Characteristics cell type: mouse embryonic fibroblasts
genotype: C57/B16 background
treatment: scrambled control
time: Day 3
Treatment protocol We transduced mouse embryonic fibroblasts with a CRISPRa-VPR–mCherry construct and assessed more immediate and longer term effects of Fra2 over-expression by performing OMNI-ATACseq on FACS purifed mCherry+/THY1+ cells 3 and 10 days following lentiviral infection with Fra2 gRNAs or scrambled control
Extracted molecule genomic DNA
Extraction protocol Omni ATAC-seq
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model NextSeq 2000
 
Data processing ATAC-seq: Peak calling was performed using the MACS2 callpeak command with the following parameters “-g mm –shift -100 –extsize 200 –nomodel –call-summits –nolambda –keep-dup all -p 0.01” [34], [35]. Then, peak summits were extended by 250 bp on both sides to a final width of 501 bp. Peaks were filtered for mm10 blacklisted regions [36] (https://www.encodeproject.org/annotations/ENCSR636HFF/).
As in Corces et al. 2020 per sample overlapping peaks were handled using an iterative removal approach. That is in case of two overlapping peaks the most significant peak is kept and the other removed. This process is performed in an iterative manner, so all peaks have been kept or removed based on their overlap and significance score. This method results in a set of fixed-width peaks per sample.
Next, significance peak scores “(-log10(p-value))” were converted to a score per million value by dividing each individual peak score by the sum of all of the peak scores in the given sample divided by 1 million. This normalized score per million value corrects the original peak calling scores for sample sequencing depth and quality, as higher quality samples yield higher number of peaks and higher significance scores overall. Thus, scores per million allow the direct comparison of peaks across biological replicates.
Next, we compiled a condition - MEF, mESC- and sequencer specific - BGI, Illumina - peak set containing reproducible peaks observed in a particular cell type and sequencing platform. For that, we generated a cumulative peak set per cell type and sequencing platform and performed the same iterative approach as mentioned above. Therefore, maintaining the peak with the highest significance or score per million. Only peaks with a score per million value >=3 observed in at least two samples (minimal overlap 50%) were further considered.
Assembly: mm10
Supplementary files format and content: Matrix table with counts per peaks in (.txt) format, samples mapping in bigwig format (.bw) and peaks called per individual sample as (.txt) format.
 
Submission date Nov 11, 2022
Last update date Jul 15, 2024
Contact name Christian Nefzger
Organization name The University of Queensland
Department Institute for Molecular Biology
Lab Cellular Reprogramming and Ageing
Street address 306 Carmody Road
City Brisbane
State/province Queensland
ZIP/Postal code 4067
Country Australia
 
Platform ID GPL30172
Series (1)
GSE217780 Fosl2 overexpression and Ezh2 inhibition in mouse embryonic fibroblasts
Relations
BioSample SAMN31693467
SRA SRX18238693

Supplementary file Size Download File type/resource
GSM6726662_A2_ENeg_2_S2.bw 399.2 Mb (ftp)(http) BW
GSM6726662_A2_ENeg_2_S2.narrowPeak.txt.gz 2.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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