|
| Status |
Public on May 10, 2024 |
| Title |
CUTNRUN_Zfp574_aV5_AID_cell_line_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mESC
|
| Organism |
Mus musculus |
| Characteristics |
cell line: mESC
genotype: AID-Zfp574; N-terminal in OsTir1 parental cell line (FRT-EF1a-ARF16-HA-P2A-OsTiR1-noXhoI-3xmYC-T2A-mCherry-SV40polyA-F3)
antibody: V5-tag antibody (Thermo Fisher, R960-25)
|
| Growth protocol |
All mouse experiments presented here were carried out in diploid mouse embryonic stem cells (mESCs) that were derived from originally haploid HMSc2 termed AN3-128. The mESCs were cultivated without feeders in high-glucose-DMEM (Sigma-Aldrich) supplemented with 13.5% fetal bovine serum (Sigma-Aldrich), 2 mM L-glutamine (Sigma-Aldrich), 1x Penicillin-Streptomycin (Sigma-Aldrich), 1x MEM non-essential amino acid solution (Gibco), 1mM sodium pyruvate (Sigma-Aldrich), 50 mM β-mercaptoethanol (Merck) and in-house produced recombinant LIF.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each biological replicate, 1x10^6 cells from the AID-Zfp574 cell line or the Tir1 parental cell line were used. The Tir1 parental cell line is used as Input.
The protocol was performed as in Hendy, O. et al. Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers. Mol Cell 82(19), 3598-3612.E7 (2022) with a V5-tag antibody (Thermo Fisher, R960-25) that was added to a final dilution of 1:100.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
CUTNRUN_Zfp574_aV5_AID_cell_line_merged.bw
CUTNRUN_peaks_Zfp574_aV5_AID_cell_line_merged.narrowPeak
|
| Data processing |
Single-end 50-bp long reads were mapped to the mm10 genome using bowtie v.0.12.9, allowing up to 3 mismatches and only uniquely mapping reads were retained.
Peaks were called for each individual replicate, as well as for the combined replicates against their respective input, using Macs2 v.2.1.2.1, with following settings: -f BEDPE -g mm -B --nomodel --extsize 300 --SPMR. The Macs2 generated BedGraph files that contain normalized coverage were converted into BigWig using bedGraphToBigWig. Given the high correlation between two replicates (PCC of 0.613 at a common set of peaks), only the merged sample was used for assigning bound genes if the peak was localized within +- 500 bp around the gene transcription start sites.
Assembly: mm10
Supplementary files format and content: For each condition and each replicate, individual .bw files can be used to visualize CUT&RUN signal using a genome browser (e.g. IGV) or to quantify the signal
Supplementary files format and content: For each condition, merged .bw file corresponds to the merge of the two biological replicates
Supplementary files format and content: For each replicate, individual .narrowPeak files contain MACS2 peaks
Supplementary files format and content: The merged .narrowPeak file contains MACS2 peaks called from merged samples
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Aug 07, 2023 |
| Last update date |
May 10, 2024 |
| Contact name |
Alexander Stark |
| E-mail(s) |
stark@starklab.org
|
| Organization name |
The Research Institute of Molecular Pathology (IMP)
|
| Lab |
Stark Lab
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE225972 |
Proteome-scale tagging and functional screening in mammalian cells by ORFtag |
| GSE240284 |
Proteome-scale tagging and functional screening in mammalian cells by ORFtag [Cut & Run] |
|
| Relations |
| BioSample |
SAMN36877554 |
| SRA |
SRX21286381 |
