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| Status |
Public on Jul 09, 2022 |
| Title |
mTEClo, 3xAireKI,ATAC, rep1 |
| Sample type |
SRA |
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| Source name |
thymus
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| Organism |
Mus musculus |
| Characteristics |
tissue: thymus
strain: NOD
cell type: MHCII-low epitherial cells
genotype: 3xAireKI
age: 8weeks old
Sex: female
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mouse thymus was enzymatically digested and then DAPI-CD45-EpCAM+Ly51-MHCII-high or MHCII-low cells were sorted by FACSAria into 100 uL of BAMBANKER (GC LYMPHOTEC) and kept frozen until library constructions.
ATAC-seq libraries were constructed as previously reported by Corces et al. (Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat. Genet. 2016). Specifically, frozen samples were thawed, split into two tubes, and washed with 1 ml of ice-cold PBS containing protease inhibitors (cOmplete ULTRA, EDTA-free; Merck). Cell pellets were resuspended in 35 uL of Tn5 transposase mixture (10 mM TAPS-NaOH pH 8.5, 5 mM MgCl2, 10% DMF, 0.2 mg/ml digitonin, and in-house Tn5) on ice. Then, the cells were incubated at 37C for 30 min with agitation followed by DNA isolation using the Monarch PCR & DNA Cleanup Kit (New England Biolabs) according to the manufacturer’s instructions. The tagmented DNA was amplified using KAPA HiFi DNA Polymerase (Roche) with a set of primers designed by Buenrostro et al. (Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 2015) with the following thermal cycles: 5 min at 72C, 30 s at 95C followed by 17 cycles (98C for 20 s, 63C for 10 s), and a final extension at 72C for 3 min. The PCR products were purified using a 1.8x volume of AMPure XP beads (Beckman Coulter) and eluted in EB (Qiagen).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
DK20082_03
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| Data processing |
trimming adapter sequences and low-quality reads by fastp
mapping to the mm10 reference genome by bowtie2 with options -X 1000 -fr
filtering nonuniquely mapped reads by samtools view -q 30
removing chrM mapped reads by samtools
removing duplicated reads by samtools
piling up the fragments defined by paired reads using macs2 with the SPMR option
Converting bedgraph into bigwig files using bdg2bw (https://gist.github.com/taoliu/2469050)
Assembly: mm10
Supplementary files format and content: bigWig files: read coverage across the whole genome (fragment pileup per million reads)
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| Submission date |
Jul 07, 2022 |
| Last update date |
Nov 29, 2022 |
| Contact name |
Hideyuki Yoshida |
| E-mail(s) |
[email protected]
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| Organization name |
RIKEN IMS
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| Street address |
1-7-22 Suehiro-cho
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| City |
Tsurumi-ku, Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE155331 |
Transcriptional regulation by Aire in medullary thymic epithelial cells revisited |
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| Relations |
| BioSample |
SAMN29555045 |
| SRA |
SRX16057229 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6304184_DK20082_03.mm10.bw |
83.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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