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Organizing biological data
Streptococcus agalactiae isolate:Alim_agalac_1000
Streptococcus agalactiae isolate:Alim_agalac_1000 Genome sequencing
Expression data from leaves of tomato (Solanum lycopersicum L. cv. MicroTom) plants subjected to 1000 Hz sound vibration (at 90 dB for 2 h for 3 consecutive days) and/or inoculated with Pst DC300.
Salmonella enterica subsp. enterica
1000 genomes Salmonella - Peru
Low pass sequencing of 1000 Genomes samples on the Element AVITI system and the Illumina NovaSeq 6000
1000 16S Sequencing Data of Human Vaginal Microorganisms
1KMPMG
1000 Medicinal Plant Mitochondrial Genome Project (1KMPMG) Genome sequencing and assembly
HiChIP on pooled LCLs from 1000 Genomes Project
Bos sp.
Run9: The 1000 Bull Genomes Project
Homo sapiens
High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios
LCL RNA-seq from African Ancestry Samples in the 1000 Genomes Project
RNA-sequencing of lymphoblastoid cell lines from 731 globally diverse individuals from the 1000 Genomes Project
Aeromonas veronii strain:Alim_AV_1000
Aeromonas veronii strain:Alim_AV_1000 Genome sequencing and assembly
Pasteurella multocida strain:Alim_FC_1000
Pasteurella multocida strain:Alim_FC_1000 Genome sequencing and assembly
Fungal community of mud solarization (MS) in a 1000-year-old marine solar saltern
Bacterial community of mud solarization (MS) in a 1000-year-old marine solar saltern
1000 Mitochondrial Genomes
EMG produced TPA metagenomics assembly of PRJNA377109 data set (Wastewater bioreactor microbial communities from Cape Town, South Africa - Thiocy_cont_1000_plan metagenome).
EMG produced TPA metagenomics assembly of PRJNA377108 data set (Wastewater bioreactor microbial communities from Cape Town, South Africa - Thiocy_cont_1000_biof metagenome).
Dissecting iNKT cell selection and subset differentiation in real-time
To systematically investigate the earliest phases of iNKT cell development and subsequent subset differentiation, we generated a genetic system to induce a timed wave of iNKT cell generation upon 4-hydroxytamoxifen (4-OHT) administration in mice bearing CD4-CreERt2 (Sledzinska et al., 2013) and Vα14iStopF (Vahl et al., 2013) knock-in transgenes. We globally investigated the transcriptional changes that guide early iNKT cell development by bulk 3’-sequencing of poly(A)-RNA of induced developing iNKT cells between 12h and 5d after induction in comparison to DP thymocytes, stage 0 CD24+ iNKT cells as well as NKT1, NKT2 and NKT17 mature subsets. Briefly, CD4-CreERt2 Vα14iStopF (± Traj18KO) mice were administered with 4-OHT and sacrificed at different timepoints after administration (between 12h and 120h). 1000 cells of the following samples were FACS purified for RNA-seq analyses: 9 timepoints of induced iNKT cells (from 12h to 120h) (gated as mCD1d-PBS57- Tetramer+ CD44low NK1.1−); DP = DP thymocytes (TCRβ− mCD1d-PBS57-Tetramer− CD4+ CD8+ CD69−); CD24+ = early wildtype iNKT cells (mCD1d-PBS57-Tetramer+ CD44− CD24+); NKT1 (mCD1d-PBS57-Tetramer+ CD44+ NK1.1+ CD27+ CD138−); NKT2 (mCD1d- PBS57-Tetramer+, NK1.1− PLZFeGFP+ ICOS+ IL17RB+ CD138−); NKT17 (mCD1d- PBS57-Tetramer+ CD19− ICOS+ CD138+). For each condition, four biological replicates were sequenced (except for 96h timepoint, where two samples of the same mouse where sequenced). For the NKT17 samples and two NKT2 samples, 2 mice were pooled. For CD24+ samples, 4-6 mice were pooled. Library preparation for bulk 3’-sequencing of poly(A)-RNA was done as described previously (Parekh et al., 2016). The library was sequenced on a NextSeq 500 (Illumina) with 16 cycles for the barcodes and UMIs and 50 cycles for the cDNA.
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