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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 14, 2023 |
| Title |
GFP+ ILC2, post-transplant, rep2, snATAC-Seq |
| Sample type |
SRA |
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| Source name |
lamina propria
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| Organism |
Mus musculus |
| Characteristics |
tissue: lamina propria
strain: C57BL/6
age: 8-16 weeks old
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
(in vitro) ILC2 + pcILC2: Lineage negative, ST2+ cells from the peritoneum and mesenteric lymph nodes were isolated and expanded in culture for 2 days in the presence of recombinant IL-7 and IL-33. ILC2s were expanded in IL-7 and IL-33 for 4 additional days, while the pcILC2 cells were treated with IL-12, IL-1b, and IL-18 (pcILC2). (ex vivo) GFP+ exILC2 post-BMT: Animals were euthanized with CO2 and the small intestine lamina propria (LP) was excised. LP lymphocytes were isolated using the Miltenyi LP dissociation kit (catalog 130-097-410) as per the manufacturer’s instructions. Livers and lungs were digested in a solution of 1 mg/ml collagenase A (Roche) and 75 U DNase I (Sigma-Aldrich) in RPMI 1640 with 5% newborn calf serum. Digested tissues were treated with ACK lysis buffer to remove RBCs and were passed through 100 μm cell strainers. Leukocytes were collected at the interface of a 40%:80% Percoll (Sigma-Aldrich) gradient in RPMI 1640 with 5% NCS. The pelleted cells were washed in 1x DPBS with 2% FBS. Spleens and MLN were teased apart, treated with ACK lysis buffer, and washed in 1 x DPBS with 2% FBS.
For all experiments, library preparation was performed according to the manufacturer’s instructions (see Single Cell Chromium Next GEM Multiome ATAC+GEX, 10x Genomics, CG000338, Rev D). Nuclei were isolated from sorted GFP+ cells following the ‘Low Cell Input Nuclei Isolation’ protocol (CG000365, Rev C) where lysis buffer was used at 1x and lysis proceeded for 4 minutes.
10X Multiome
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| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Tn5 cut DNA
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0.0. Addiitonal analyses were performed using Seruat v.4.3.0.
Assembly: mm10
Supplementary files format and content: h5 (count matrix), ATAC fragment file, fragment index file, bed/csv files (cellRanger_atac_peakcalls).
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| Submission date |
May 08, 2023 |
| Last update date |
May 30, 2024 |
| Contact name |
SONIA LAURIE |
| E-mail(s) |
sonia.laurie@gmail.com
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| Organization name |
UNC CHAPEL HILL
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| Street address |
125 Mason Farm Road
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| City |
CHAPEL HILL |
| State/province |
NC |
| ZIP/Postal code |
27514 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE232001 |
Multiomic Single Cell Evaluation Reveals Inflammatory Cytokines Affect Innate Lymphoid Cell Fate After Allogeneic Stem Cell Transplantation [10X Multiome] |
| GSE232003 |
Multiomic Single Cell Evaluation Reveals Inflammatory Cytokines Affect Innate Lymphoid Cell Fate After Allogeneic Stem Cell Transplantation |
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| Relations |
| BioSample |
SAMN35004328 |
| SRA |
SRX20260881 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7308298_ILC2_post-transplant_rep2_atac_fragments.tsv.gz |
1.0 Gb |
(ftp)(http) |
TSV |
| GSM7308298_ILC2_post-transplant_rep2_atac_fragments.tsv.gz.tbi.gz |
736.6 Kb |
(ftp)(http) |
TBI |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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