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| Status |
Public on Jan 07, 2022 |
| Title |
Radial glia cells - Dam-only_Rep2 |
| Sample type |
SRA |
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| Source name |
Radial glia cells E13-14
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| Organism |
Mus musculus |
| Characteristics |
tissue: mouse embryonic cortex
stage of electroporation-dissection: E13.5-E14.5
dam-fusion protein: Dam-only
cell type: RGC
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
After dissection of electroporated cortex, gDNA was extracted using the QiAmp DNA Micro kit. The gDNA was digested with DpnI, adaptors were ligated and then digested with DpnII and amplified by PCR (Marshall et al, Nat Protoc, 2016).
After gDNA extraction and DamID, DNA was sonicated to an average size of 300bp using a Diagenode Bioruptor and DamID adaptors removed with AlwI digestion. Sonicated material was end-repaired, A-tailed, sequencing adaptors ligated and PCR amplified (see Marshall et al., Nat Protoc, 2016).
DamID-seq
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
pHes5_iDam.bedgraph
pHes5_iDam.bedgraph.bw
pHes5_Notch_unlog.bedgraph
pHes5_RBPJ_unlog.bedgraph
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| Data processing |
Fastq-files were processed with the damidseq_pipeline (Marshall and Brand, Bioinformatics, 2015), with bins=300, RPM normalization and otherwise default parameters.
For transcripton factor data, each Dam-fusion sample was normalized to each Dam-only sample from the same cell-type, resulting in a matrix of n1 Dam-fusion x n2 Dam-only. All normalizations were then averaged and backtransformed ("unlog") to generate a final average .bedgraph file.
For chromatin accessibility data, Dam-only files from a each experimental condition were averaged and provided as .bedgraph files.
Peaks were called using MACS2 (broad peaks), and only peaks present in all replicates at FDR<10^-5 were considered.
Peaks from all samples were merged and then k-means clustered to generate pHespTa1_NotchRbpj_clus8_FDR5.allPeak.bed
Genome_build: mm10
Supplementary_files_format_and_content: .bedgraph files are tracks at gatc-fragment resolution, of averaged transcription factor or chromatin accessibility DamID. Scores represent normalised fold enrichment of transcription factor DamID vs Dam-only; for chromatin accessibility scores represent read density.
Supplementary_files_format_and_content: .bw files are browser-readable versions of the .bedgraph files
Supplementary_files_format_and_content: .bed files contain peak coordinates
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| Submission date |
Jun 10, 2020 |
| Last update date |
Jan 07, 2022 |
| Contact name |
Andrea Brand |
| Organization name |
The Gurdon Institute
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| Street address |
Tennis Court Rd
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| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE152207 |
Reduced chromatin accessibility correlates with resistance to Notch activation |
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| Relations |
| BioSample |
SAMN15198625 |
| SRA |
SRX8520838 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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