Selected Cell
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BAC
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| UID | Name | Scientist | Protocol | Species | Phenotype | Morphology | Culture | Strain | Lab |
| BAC-241118SAS-1 | H37Rv-wildtype | Ryan Finethy | https://fairdomhub.org/sops/796 | Myobacterium tuberculosis | Bacillus | Middlebrook 7h9 media, 0.2% glycerol, 0.05% Tween80, 10% oleic acid-albumin-dextrose-catalase) | H37Rv | Sassetti Lab | |
| BAC-241118SAS-2 | H37Rv::pmCherry | Ryan Finethy | https://fairdomhub.org/sops/796 | Myobacterium tuberculosis | Fluorescence | Bacillus | Middlebrook 7h9 media, 0.2% glycerol, 0.05% Tween80, 10% oleic acid-albumin-dextrose-catalase) | H37Rv | Sassetti Lab |
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| UID | Name | Scientist | Strain | Source | |||||
| MUS-241108SAS-1 | RF-1 | Ryan Finethy | C57BL/6J | Jackson Labs | |||||
| MUS-241108SAS-6 | RF-2 | Ryan Finethy | C57BL/6J | Jackson Labs | |||||
| MUS-241108SAS-11 | RF-3 | Ryan Finethy | C57BL/6J | Jackson Labs | |||||
| MUS-241108SAS-16 | RF-4 | Ryan Finethy | C57BL/6J | Jackson Labs | |||||
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| UID | Name | Protocol | Species | Media | Parent | Scientist | Type | Treatment1 | Treatment1Parent | Treatment2 | Treatment2Dose | Treatment2DoseUnits |
| CEL-241108SAS-1 | RF-BMDM-uninfected-1 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-1 | Ryan Finethy | Bone-marrow derived macrophages | DMSO | ||||
| CEL-241108SAS-2 | RF-BMDM-infected_uninhibited-1 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-1 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | |||
| CEL-241108SAS-3 | RF-BMDM-infected_CeapinA7-1 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-1 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | Ceapin-A7 | 10 | μM |
| CEL-241108SAS-4 | RF-BMDM-infected_GSK-1 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-1 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | GSK2606414 | 1 | μM |
| CEL-241108SAS-5 | RF-BMDM-infected_4u8c-1 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-1 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | 4μ8c | 50 | μM |
| CEL-241108SAS-6 | RF-BMDM-uninfected-2 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-6 | Ryan Finethy | Bone-marrow derived macrophages | DMSO | ||||
| CEL-241108SAS-7 | RF-BMDM-infected_uninhibited-2 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-6 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | |||
| CEL-241108SAS-8 | RF-BMDM-infected_CeapinA7-2 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-6 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | Ceapin-A7 | 10 | μM |
| CEL-241108SAS-9 | RF-BMDM-infected_GSK-2 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-6 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | GSK2606414 | 1 | μM |
| CEL-241108SAS-10 | RF-BMDM-infected_4u8c-3 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-6 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | 4μ8c | 50 | μM |
| CEL-241108SAS-11 | RF-BMDM-uninfected-3 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-11 | Ryan Finethy | Bone-marrow derived macrophages | DMSO | ||||
| CEL-241108SAS-12 | RF-BMDM-infected_uninhibited-3 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-11 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | |||
| CEL-241108SAS-13 | RF-BMDM-infected_CeapinA7-3 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-11 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | Ceapin-A7 | 10 | μM |
| CEL-241108SAS-14 | RF-BMDM-infected_GSK-3 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-11 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | GSK2606414 | 1 | μM |
| CEL-241108SAS-15 | RF-BMDM-infected_4u8c-3 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-11 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | 4μ8c | 50 | μM |
| CEL-241108SAS-16 | RF-BMDM-uninfected-4 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-16 | Ryan Finethy | Bone-marrow derived macrophages | DMSO | ||||
| CEL-241108SAS-17 | RF-BMDM-infected_uninhibited-4 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-16 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | |||
| CEL-241108SAS-18 | RF-BMDM-infected_CeapinA7-4 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-16 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | Ceapin-A7 | 10 | μM |
| CEL-241108SAS-19 | RF-BMDM-infected_GSK-4 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-16 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | GSK2606414 | 1 | μM |
| CEL-241108SAS-20 | RF-BMDM-infected_4u8c-4 | https://fairdomhub.org/sops/797 | Mus musculus | DMEM, 10% FBS, 10mM HEPES, 100 μM sodium pyruvate | MUS-241108SAS-16 | Ryan Finethy | Bone-marrow derived macrophages | H37Rv | BAC-241118SAS-1 | 4μ8c | 50 | μM |
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| UID | Name | Protocol | Scientist | Lab | Parent | Type | |||
| RNA-241112SAS-1 | RF-RNA-uninfected-1 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-1 | Total RNA | |||
| RNA-241112SAS-2 | RF-RNA-infected_uninhibited-1 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-2 | Total RNA | |||
| RNA-241112SAS-3 | RF-RNA-infected_CeapinA7-1 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-3 | Total RNA | |||
| RNA-241112SAS-4 | RF-RNA-infected_GSK-1 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-4 | Total RNA | |||
| RNA-241112SAS-5 | RF-RNA-infected_4u8c-1 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-5 | Total RNA | |||
| RNA-241112SAS-6 | RF-RNA-uninfected-2 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-6 | Total RNA | |||
| RNA-241112SAS-7 | RF-RNA-infected_uninhibited-2 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-7 | Total RNA | |||
| RNA-241112SAS-8 | RF-RNA-infected_CeapinA7-2 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-8 | Total RNA | |||
| RNA-241112SAS-9 | RF-RNA-infected_GSK-2 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-9 | Total RNA | |||
| RNA-241112SAS-10 | RF-RNA-infected_4u8c-3 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-10 | Total RNA | |||
| RNA-241112SAS-11 | RF-RNA-uninfected-3 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-11 | Total RNA | |||
| RNA-241112SAS-12 | RF-RNA-infected_uninhibited-3 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-12 | Total RNA | |||
| RNA-241112SAS-13 | RF-RNA-infected_CeapinA7-3 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-13 | Total RNA | |||
| RNA-241112SAS-14 | RF-RNA-infected_GSK-3 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-14 | Total RNA | |||
| RNA-241112SAS-15 | RF-RNA-infected_4u8c-3 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-15 | Total RNA | |||
| RNA-241112SAS-16 | RF-RNA-uninfected-4 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-16 | Total RNA | |||
| RNA-241112SAS-17 | RF-RNA-infected_uninhibited-4 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-17 | Total RNA | |||
| RNA-241112SAS-18 | RF-RNA-infected_CeapinA7-4 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-18 | Total RNA | |||
| RNA-241112SAS-19 | RF-RNA-infected_GSK-4 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-19 | Total RNA | |||
| RNA-241112SAS-20 | RF-RNA-infected_4u8c-4 | https://fairdomhub.org/sops/798 | Ryan Finethy | Sassetti Lab | CEL-241108SAS-20 | Total RNA | |||
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| UID | Name | Protocol | Scientist | Parent | LibraryType | Lab | |||
| DNA-241112SAS-1 | RF-DNA-uninfected-1 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-1 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-2 | RF-DNA-infected_uninhibited-1 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-2 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-3 | RF-DNA-infected_CeapinA7-1 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-3 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-4 | RF-DNA-infected_GSK-1 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-4 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-5 | RF-DNA-infected_4u8c-1 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-5 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-6 | RF-DNA-uninfected-2 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-6 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-7 | RF-DNA-infected_uninhibited-2 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-7 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-8 | RF-DNA-infected_CeapinA7-2 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-8 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-9 | RF-DNA-infected_GSK-2 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-9 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-10 | RF-DNA-infected_4u8c-3 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-10 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-11 | RF-DNA-uninfected-3 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-11 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-12 | RF-DNA-infected_uninhibited-3 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-12 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-13 | RF-DNA-infected_CeapinA7-3 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-13 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-14 | RF-DNA-infected_GSK-3 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-14 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-15 | RF-DNA-infected_4u8c-3 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-15 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-16 | RF-DNA-uninfected-4 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-16 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-17 | RF-DNA-infected_uninhibited-4 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-17 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-18 | RF-DNA-infected_CeapinA7-4 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-18 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-19 | RF-DNA-infected_GSK-4 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-19 | mRNA | Sassetti Lab | |||
| DNA-241112SAS-20 | RF-DNA-infected_4u8c-4 | https://fairdomhub.org/sops/798 | Ryan Finethy | RNA-241112SAS-20 | mRNA | Sassetti Lab | |||
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| UID | Name | Scientist | Protocol | File_PrimaryData | Link_PrimaryData | File_SecondaryData | Link_SecondaryData | Parent | DataType | SequencingType | Sequencer | LibraryStrategy | LibrarySource | LibrarySelection | ExtractedMolecule | LibraryDesign | Notes |
| D.SEQ-241112SAS-1 | rep_1_uninfected | Ryan Finethy | https://fairdomhub.org/sops/798 | 1_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317088/1_R1_001.fastq.gz.1 | 1_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317088/1_R2_001.fastq.gz.1 | DNA-241112SAS-1 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-2 | rep_1_infected_unhibited | Ryan Finethy | https://fairdomhub.org/sops/798 | 2_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317087/2_R1_001.fastq.gz.1 | 2_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317087/2_R2_001.fastq.gz.1 | DNA-241112SAS-2 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-3 | rep_1_infected+Ceapin-A7 | Ryan Finethy | https://fairdomhub.org/sops/798 | 4_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317086/4_R1_001.fastq.gz.1 | 4_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317086/4_R2_001.fastq.gz.1 | DNA-241112SAS-3 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-4 | rep_1_infected+GSK2606414 | Ryan Finethy | https://fairdomhub.org/sops/798 | 5_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317085/5_R1_001.fastq.gz.1 | 5_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317085/5_R2_001.fastq.gz.1 | DNA-241112SAS-4 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-5 | rep_1_infected+4u8c | Ryan Finethy | https://fairdomhub.org/sops/798 | 6_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317084/6_R1_001.fastq.gz.1 | 6_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317084/6_R2_001.fastq.gz.1 | DNA-241112SAS-5 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-6 | rep_2_uninfected | Ryan Finethy | https://fairdomhub.org/sops/798 | 9_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317083/9_R1_001.fastq.gz.1 | 9_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317083/9_R2_001.fastq.gz.1 | DNA-241112SAS-6 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-7 | rep_2_infected_unhibited | Ryan Finethy | https://fairdomhub.org/sops/798 | 10_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317082/10_R1_001.fastq.gz.1 | 10_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317082/10_R2_001.fastq.gz.1 | DNA-241112SAS-7 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-8 | rep_2_infected+Ceapin-A7 | Ryan Finethy | https://fairdomhub.org/sops/798 | 12_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317081/12_R1_001.fastq.gz.1 | 12_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317081/12_R2_001.fastq.gz.1 | DNA-241112SAS-8 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-9 | rep_2_infected+GSK2606414 | Ryan Finethy | https://fairdomhub.org/sops/798 | 13_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317080/13_R1_001.fastq.gz.1 | 13_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317080/13_R2_001.fastq.gz.1 | DNA-241112SAS-9 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-10 | rep_2_infected+4u8c | Ryan Finethy | https://fairdomhub.org/sops/798 | 14_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317079/14_R1_001.fastq.gz.1 | 14_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317079/14_R2_001.fastq.gz.1 | DNA-241112SAS-10 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-11 | rep_3_uninfected | Ryan Finethy | https://fairdomhub.org/sops/798 | 17_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317078/17_R1_001.fastq.gz.1 | 17_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317078/17_R2_001.fastq.gz.1 | DNA-241112SAS-11 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-12 | rep_3_infected_unhibited | Ryan Finethy | https://fairdomhub.org/sops/798 | 18_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317077/18_R1_001.fastq.gz.1 | 18_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317077/18_R2_001.fastq.gz.1 | DNA-241112SAS-12 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-13 | rep_3_infected+Ceapin-A7 | Ryan Finethy | https://fairdomhub.org/sops/798 | 20_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317076/20_R1_001.fastq.gz.1 | 20_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317076/20_R2_001.fastq.gz.1 | DNA-241112SAS-13 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-14 | rep_3_ infected+GSK2606414 | Ryan Finethy | https://fairdomhub.org/sops/798 | 21_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317075/21_R1_001.fastq.gz.1 | 21_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317075/21_R2_001.fastq.gz.1 | DNA-241112SAS-14 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-15 | rep_3_infected+4u8c | Ryan Finethy | https://fairdomhub.org/sops/798 | 22_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317074/22_R1_001.fastq.gz.1 | 22_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317074/22_R2_001.fastq.gz.1 | DNA-241112SAS-15 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-16 | rep_4_uninfected | Ryan Finethy | https://fairdomhub.org/sops/798 | 25_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317073/25_R1_001.fastq.gz.1 | 25_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317073/25_R2_001.fastq.gz.1 | DNA-241112SAS-16 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-17 | rep_4_infected_unhibited | Ryan Finethy | https://fairdomhub.org/sops/798 | 26_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317072/26_R1_001.fastq.gz.1 | 26_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317072/26_R2_001.fastq.gz.1 | DNA-241112SAS-17 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-18 | rep_4_infected+Ceapin-A7 | Ryan Finethy | https://fairdomhub.org/sops/798 | 28_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317071/28_R1_001.fastq.gz.1 | 28_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317071/28_R2_001.fastq.gz.1 | DNA-241112SAS-18 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-19 | rep_4_infected+GSK2606414 | Ryan Finethy | https://fairdomhub.org/sops/798 | 29_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317070/29_R1_001.fastq.gz.1 | 29_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317070/29_R2_001.fastq.gz.1 | DNA-241112SAS-19 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
| D.SEQ-241112SAS-20 | rep_4_infected+4u8c | Ryan Finethy | https://fairdomhub.org/sops/798 | 30_R1_001.fastq.gz | s3://sra-pub-src-4/SRR31317069/30_R1_001.fastq.gz.1 | 30_R2_001.fastq.gz | s3://sra-pub-src-4/SRR31317069/30_R2_001.fastq.gz.1 | DNA-241112SAS-20 | FASTQ | Single Cell RNA Sequencing | Illumina NovaSeq 6000 | RNA-seq | Transcriptomic | cDNA | total RNA | Paired end | |
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| UID | File_PrimaryData | Link_PrimaryData | Scientist | Parent | Protocol | DataType | Repository | Accession | |
| A.GEX-241119SAS-1 | GSE281697_Normalized_Counts.csv.gz | https://ftp.ncbi.nlm.nih.gov/geo/series/GSE281nnn/GSE281697/suppl/GSE281697%5FNormalized%5FCounts.csv.gz | Ryan Finethy | D.SEQ-241112SAS-1; D.SEQ-241112SAS-2; D.SEQ-241112SAS-3; D.SEQ-241112SAS-4; D.SEQ-241112SAS-5; D.SEQ-241112SAS-6; D.SEQ-241112SAS-7; D.SEQ-241112SAS-8; D.SEQ-241112SAS-9; D.SEQ-241112SAS-10; D.SEQ-241112SAS-11; D.SEQ-241112SAS-12; D.SEQ-241112SAS-13; D.SEQ-241112SAS-14; D.SEQ-241112SAS-15; D.SEQ-241112SAS-16; D.SEQ-241112SAS-17; D.SEQ-241112SAS-18; D.SEQ-241112SAS-19; D.SEQ-241112SAS-20 | https://fairdomhub.org/sops/800 | CSV | Gene Expression Omnibus | GSE281697 | |
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| UID | Name | File_PrimaryData | Link_PrimaryData | Parent | Scientist | Protocol | Type | LightEmission_Plasmid | LightEmission_Reporter | BacterialStrain | InfectedCells | NumberInfectedCells | ExcitationWavelength | EmissionWavelength | ReadingIntervals | Analyzer | Analyzer_Vendor | Dilution |
| D.BSRA-241118SAS-1 | BSRA-H37Rv | 111224_BRSA.xlsx | https://fairdomhub.org/data_files/7660 | BAC-241118SAS-2; CEL-241108SAS-1; CEL-241108SAS-3; CEL-241108SAS-4; CEL-241108SAS-5; CEL-241108SAS-6; CEL-241108SAS-8; CEL-241108SAS-9; CEL-241108SAS-10; CEL-241108SAS-11; CEL-241108SAS-13; CEL-241108SAS-14; CEL-241108SAS-15; CEL-241108SAS-16; CEL-241108SAS-18; CEL-241108SAS-19; CEL-241108SAS-20 | Ryan Finethy | https://fairdomhub.org/sops/801 | Bacteria internalization | pmCherry | mCherry | H37Rv Mtb | Bone marrow derived macrophages (BMDMs) | 50000 | 587 nm | 610 nm | 24 hrs and 48 hrs post-infection | Synergy H4 Hybrid Microplate Reader | BioTek | Dilute based on OD600, then 50µL per well |
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| UID | File_PrimaryData | Link_PrimaryData | Scientist | Type | Parent | Protocol | ExtractionKit | SynthesisKit | Instrument | NormalizationGene | PrimerSequences | QuantificationMethod |
| D.PCR-241118SAS-1 | 111224_PCR.xlsx | https://fairdomhub.org/data_files/7661 | Ryan Finethy | qRT-PCR | RNA-241112SAS-1; RNA-241112SAS-2; RNA-241112SAS-3; RNA-241112SAS-4; RNA-241112SAS-5; RNA-241112SAS-6; RNA-241112SAS-7; RNA-241112SAS-8; RNA-241112SAS-9; RNA-241112SAS-10; RNA-241112SAS-11; RNA-241112SAS-12; RNA-241112SAS-13; RNA-241112SAS-14; RNA-241112SAS-15; RNA-241112SAS-16; RNA-241112SAS-17; RNA-241112SAS-18; RNA-241112SAS-19; RNA-241112SAS-20 | https://fairdomhub.org/sops/799 | Direct-zol RNA Miniprep kit (Zymo Research) | iScript cDNA synthesis kit (Bio-Rad Laboratories) | Applied Biosystems ViiA 7 Real-Time PCR System | Unspliced XBP1; beta-actin | spliced XBP1 F; 5’-ggtctgctgagtccgcagcagg-3’; R; 5’-gaaagggaggctggtaaggaac-3’ 57; unspliced XBP1 F; 5’-cagactatgtgcacctctgc-3’; R; 5’-cagggtccaacttgtccagaat-3’ 58; HSPA5 F; 5’- acttggggaccacctattcct-3’; R; 5’- atcgccaatcagacgctcc-3’ 59; Trib3 F; 5’- gcaaagcggctgatgtctg-3’; R; 5’-agagtcgtggaatgggtatctg-3’ 60–62; β-actin F; 5’- cgcagccactgtcgagtc-3’; R; 5’-ccttctgacccattcccacc-3’ 63. | delta-delta CT method |
