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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 09, 2024 |
| Title |
Spleen, WT, ATAC |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
age: P21
genotype: Cdca7+/+
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
In brief, single cell suspensions were prepared by squeezing the tissues through a 35-μm nylon cell strainer (352235, Corning). 50,000 mouse splenic cells were resuspended in 50 µL transposition mix (Nextera) and incubated for 30 min at 37 °C
ATAC-seq libraries were prepared as previously described (Buenrostro et al, 2013). Libraries were amplified by PCR with barcoded Nextera primers.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
After preprocessing with TrimGalore to remove low quality reads, reads were aligned to the mouse genome (mm10) using bowtie2 v2.3.4.2 (Langmead and Salzberg, 2012) with parameters -very sensitive.
Peaks were called using SICER (Xu et al, 2014) for H3K9me3 (parameters - W200, G600) and H3K27me3 (parameters – W 1000, G 4000). For ChIP-seq peaks were called using input fractions as control.
bigWig files were generated using deepTools version 3.1.3 (Ramirez et al., 2016). Score represents the normalized coverage of DNA fragments at a given genomic coordinate
Assembly: mm10
Supplementary files format and content: bigWig, ATAC_P21_spleen.xlsx
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| Submission date |
Aug 24, 2022 |
| Last update date |
Feb 09, 2024 |
| Contact name |
Lucia Daxinger |
| E-mail(s) |
L.Clemens-Daxinger@lumc.nl
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| Organization name |
Leiden Univeristy Medica Center
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| Street address |
Albinusdreef 2
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| City |
Leiden |
| ZIP/Postal code |
2333ZA |
| Country |
Netherlands |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE211941 |
CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses [ATAC-seq] |
| GSE212007 |
CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses |
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| Relations |
| BioSample |
SAMN30473843 |
| SRA |
SRX17242905 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6505953_1882-80_2months.bw |
149.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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