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| Status |
Public on Apr 04, 2018 |
| Title |
SP8_Mouse302_SeqID_73451 |
| Sample type |
SRA |
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| Source name |
CD8 SP thymocytes
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| Organism |
Mus musculus |
| Characteristics |
cell type: CD8 SP thymocytes
strain: C57BL/6J
age: 9 weeks old
genotype: wild type
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| Treatment protocol |
Single-cell suspension isolated from thymus were stained for cell surface marker, and then each stage of thymoctytes were isolated by flow cytometer
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared following Buenrostro et al, 2013 Nat Methods 10:1213-1218.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
In order to account for sequencing depth differences between each library, we down-sampled reads (keeping read pairs intact) to the median depth of all libraries after the pruning steps. This ensures that sequencing depth does not confound this analysis.
After this step, we combined all replicates from each stage into a single BAM file to increase sequencing depth (ranging from 120 to 134 million reads per stage) and called peaks using macs2 with options --nomodel --shift -50 --extsize 100 -B --keep-dup all.
macs2 analyses. Files with .fdr0.05.noBlackList.bed extension are the coordinates of the peak calls for each sample. Additionally, we removed peaks with FDR < 0.05 and in non-mappable regions (blacklisted) to generate a more stringent peak set.
We used CENTIPEDE to generate the posterior probability of each motif instance being bound. We subsequently selected motifs that had a posterior >= 0.99 and fully intersected an ATAC-seq peak in their sample of origin to be considered as bound motifs (footprints).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, bed
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| Submission date |
Nov 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tomonori Hosoya |
| Organization name |
University of Michigan
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| Department |
CDB
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| Lab |
Engel
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| Street address |
109 Zina Pitcher Place
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE107076 |
Global dynamics of stage-specific transcription factor binding during thymocyte development |
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| Relations |
| SRA |
SRX3405629 |
| BioSample |
SAMN08044946 |
| 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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