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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 06, 2023 |
| Title |
Mouse replicate 2 Nur77GFP LO |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
cell line: N/A
cell type: CD4 T cells
genotype: C57BL/6-Tg(Nr4a1-EGFP/cre)820Khog/J
treatment: Mycobacterium tuberculosis infection
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| Growth protocol |
N/A
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mycobacterium tuberculosis-infected Nur77-GFP mice were euthanized with CO2 and lungs were suspended in a digestion buffer containing DMEM, FBS, Collagenase D, DNase, Heparin, CaCl 2 , and MgCl 2 . Lungs were incubated at 37˚C for 30 minutes and dissociated with a gentleMACS dissociator (Miltenyi Biotec), according to the manufacturer’s protocol. To isolate cells, lung suspensions were filtered through a 70 μm cell strainer. Sorting for CD44hi, CD4+, GFP HI and LO cells was performed with a Sony MA900 cell sorter.
Cells FACS sorted (either GFP-HI or -LO) into DMEM with 40% FBS were used for scRNA-Seq sample preparation. After sorting, cell number was confirmed with the Luna II (Logos Biosystems). Approximately 100,000 cells from each population were sorted into DMEM-40 before resuspension in Tri reagent. Samples in TRI Reagent were centrifuged at 1000 x g for 10 minutes. Samples were resuspended in chloroform and incubated for 3 minutes then centrifuged at 12,000 x g for 15 minutes. The supernatant was collected, isopropyl alcohol added, incubated for 10 minutes, then centrifuged at 7,500 x g for 5 minutes. The supernatant was discarded then samples were air dried before resuspension in RNase-free water.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
lo.2
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| Data processing |
RNA was submitted to GeneWiz from Azenta Life Sciences for RNA sequencing and differential gene expression analysis using DeSeq2.
Assembly: mm10
Supplementary files format and content: Tab delimited csv file contains read counts for each sample
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| Submission date |
Jun 22, 2023 |
| Last update date |
Nov 06, 2023 |
| Contact name |
Tyler Bold |
| E-mail(s) |
tbold@umn.edu
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| Organization name |
University of Minnesota
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| Street address |
2101 6th St SE
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| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE235564 |
Activated CD4 T cells in tuberculosis express OX40, a target for host-directed immunotherapy [GFP_HI_LO_BULKRNASeq] |
| GSE235800 |
Activated CD4 T cells in tuberculosis express OX40, a target for host-directed immunotherapy |
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| Relations |
| BioSample |
SAMN35841292 |
| SRA |
SRX20750611 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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