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GEO help: Mouse over screen elements for information. |
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Status |
Public on Aug 26, 2022 |
Title |
Bisulfite-seq_Donor 6.5TCR T cells which were converted to Tregs, rep2 |
Sample type |
SRA |
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Source name |
Lymphocytes
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Organism |
Mus musculus |
Characteristics |
strain: Balb/c cell type: T cell sorting markers: CD45.1-CD45.2+CD3+CD4+CD25+Foxp3+
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Growth protocol |
Mice were housed at UKR central animal facility
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Extracted molecule |
genomic DNA |
Extraction protocol |
T cell subsets were sorted directly into FACS buffer and then lysed with buffer ATL and proteinase K (Qiagen QIAamp DNA Micro Kit #56304) for one hour at 56°C. Buffer ATL and AL with carrier RNA were added and sample stored at -80°C until further processing. To isolate genomic DNA, samples were heated to 90°C for 30 minutes followed by column-based DNA isolation according to manufacturer’s protocol (Qiagen QIAamp DNA Micro Kit #56304). DNA was eluted in 40 µl buffer AE and sodium bisulfite conversion was performed (Qiagen EpiTect Plus DNA Bisulfite Kit #59124). Bisulfite-converted DNA was used to amplify regions of interest56 with the following PCR conditions: 4 µl bisulfite-converted DNA, 0.5 µl forward primer (10 µM), 0.5 µl reverse primer (10 µM), 5 µl 2X PCR buffer, 0.1 µl dNTPs and 0.1 µl hot-start Taq polymerase (PCR buffer, dNTPs and Taq from: ZymoTaq DNA Polymerase Kit #E2002). To detect Foxp3 methylation at the Treg-specific demethylated region, we used a forward primer TGGGTTTTTTTGGTATTTAAGAAAG and a reverse primer AAAAAACAAATAATCTACCCCACAA. To detect Il2ra gene methylation, we used a forward primer TTTTAGAGTTAGAAGATAGAAGGTATGGAA and a reverse primer TCCCAATACTTAACAAAACCACATAT. For Ikzf2 gene methylation, we used a forward primer AGGATGGTTTTTATTGAAGGTGAT and a reverse primer ATACACACCAAACAAACACTACACC. For Ctla4 gene methylation, we used a forward primer TGGTGTTGGTTAGTAGTTATGGTGT and a reverse primer AAATTCCACCTTACAAAAATACAATC. For Tnfrsf18 gene methylation, we used a forward primer GAGGTGTAGTTGTTAGTTGAGGATGT and a reverse primer AACCCCTACTCTCACCAAAAATATAA. PCR was initiated with 95°C for 10 minutes, followed by 40 cycles with denaturation (95°C-30sec), annealing (56°C-30sec) and elongation (72°C-30sec) completed with a final elongation step (72°C for 7 minutes). PCR products were combined, pre-purified with AMPure XP beads (Beckman Coulter #463881) and indexed for Illumina-based sequencing (NEBNext Ultra II DNA Library Prep Kit for Illumina #E7645S with NEBNext Multiplex Oligos for Illumina #E7335S). Samples were pooled in an equimolar ratio and supplemented with an unindexed PhiX spike-in (50% spike-in, Illumina FC-110-3001). Sequencing was performed on an Illumina MiSeq with a reagent nano kit v2 and 500 cycles of PCR.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
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Description |
BM Treg R2
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Data processing |
Library strategy: Targeted Bisulfite-seq Indexed reads were aligned to the respective gene region and the mouse mm10 genome, followed by CG methylation calling and raw data table exporting using a customized code. For Foxp3, following CG dinucleotides were analyzed and plotted CG1 X:7,583,950; CG2 X:7,583,986; CG3 X:7,584,002; CG4 X:7,584,036; CG5 X:7,584,063; CG6 X:7,584,068. For Il2ra, following CG dinucleotides were analyzed and plotted CG1 2:11,645,653; CG2 2:11,645,705; CG3 2:11,645,718; CG4 2:11,645,738. For Ikzf2, following CG dinucleotides were analyzed and plotted CG1 1:69,670,284; CG2 1:69,670,291; CG3 1:69,670,370; CG4 1:69,670,377; CG5 1:69,670,385. For Tnfrsf18, following CG dinucleotides were analyzed: CG1 4:156,028,566; CG2 4:156,028,568; CG3 4:156,028,605; CG4 4:156,028,648; For Ctla4, following CG dinucleotides were analyzed: CG1 1:60,912,472; CG2 1:60,912,521; CG3 1:60,912,536; CG4 1:60,912,573; CG5 1:60,912,684. Genome_build: mouse mm10 Supplementary_files_format_and_content: txt
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Submission date |
Sep 04, 2019 |
Last update date |
Aug 26, 2022 |
Contact name |
Philipp Beckhove |
E-mail(s) |
philipp.beckhove@rcii.de
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Organization name |
Regensburg Center for Interventional Immunology
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Street address |
Franz-Josef-Strauss-Allee 11
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City |
Regensburg |
ZIP/Postal code |
93053 |
Country |
Germany |
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Platform ID |
GPL16417 |
Series (2) |
GSE136650 |
Induction of autoreactive regulatory T cells through promiscuous gene expression by bone marrow-resident Aire+ antigen-presenting cells |
GSE136875 |
Assessment of the stabilty of Treg cell subsets in the bone marrow [targeted Bisulfite-seq] |
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Relations |
BioSample |
SAMN12692333 |
SRA |
SRX6801360 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4060092_Run2_Index3_panel_extracted.txt.gz |
736 b |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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