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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 10, 2021 |
| Title |
Control mouse MPPs, rep 1 |
| Sample type |
SRA |
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| Source name |
Mouse MPPs
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| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse MPPs
treatment: Control (excipient)
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| Treatment protocol |
Bone marrow cells were incubated in cold flow cytometry buffer with a panel of antibodies against lineage committed cells (CD3, CD45R, CD11b, Ter-119, Gr-1) all biotinylated and from BD Pharmigen. After washing, cells were incubated with streptavidin magnetic beads (Miltenyi) and passed through LS columns (Miltenyi) . Thus, collected cells were stained with Sca-1, c-kit (CD117), CD48, CD150 antibodies and with the viability marker Hoechst 33258 prior to be sorted by FACS Aria II. MPPs were identified as Lin-c-kit+ sca-1+ CD48+ CD150- cells.
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| Growth protocol |
Mice were treated for 2 weeks with 50 µL of MV130 (300 Formazin Turbidity Units [FTU]/mL ~ 1.0E+9 bacteria/mL) or excipient intranasal (4 mice for condition). After one week of resting mice were sacrified in a CO2 chamber to collect femurs and tibia that were subsequently flushed with cold PBS to harvest bone marrow. Red blood cells lysis was performed once for 3 minutes.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Flow sorted mouse MPPs were collected in ice-cold Flow cytometry buffer and 30.000 cells were obtained pooling two biological replicates for every condition. Samples were immediately processed following previously published protocol (Buenrostro et al, 2013). The transposition reaction was started by adding Nextera’s Tn5 Transposase in reaction buffer and maintained by incubation for 30 minutes at 37°C. DNA was purified using a Quiagen MinElute PCR purification kit.
ATAC-seq libraries were generated following Buenrostro et al (2013), purified using a PCR purification MinElute kit (Quiagen) and quantified using a 2100 Bioanalyzer instrument (Agilent). Finally, libraries were sequenced 2x50 in a paired end flowcell (PE) run on Illuminaa NextSeq 2000 System.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Illumina and Nextera adapter contaminations were removed from reads using Cutadapt.
Processed reads were mapped against MM10 whole genome using bowtie2.
Alignments were filtered with samtools to retain only properly mapped, non duplicate reads, with mapping quality above 0, not aligning to unlocalized or unassembled contigs, the mitochondrial genome, or chromosome Y.
Peaks were called with MACS3, using parameters "--nomodel --shift -100 --extsize 200", and "-q 0.05" as the false discovery rate cut-off.
Genome_build: MM10
Supplementary_files_format_and_content: ENCODE narrow peak files (extended bed format) including coordinates, score and qvalue for ATAC-seq peaks, using MACS3.
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| Submission date |
Sep 05, 2021 |
| Last update date |
Nov 10, 2021 |
| Contact name |
Manuel J Gomez |
| E-mail(s) |
[email protected]
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| Organization name |
CNIC
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| Lab |
Bioinformatics Unit
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| Street address |
Melchor Fernández Almagro, 3
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| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
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| Platform ID |
GPL30172 |
| Series (2) |
| GSE183486 |
ATAC-Seq based chromatin accessibilty profile of MPPs from mice treated with MV130 or its excipient |
| GSE183721 |
Trained immunity induction by the inactivated mucosal vaccine MV130 protects against experimental viral respiratory infections |
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| Relations |
| BioSample |
SAMN21239483 |
| SRA |
SRX12020764 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5558278_E1_PBrandi_ATACSeq_S1.mm10_peaks.narrowPeak.gz |
1.5 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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