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Organizing biological data
S_1 S_2 S_3 S_4 S_5 S_6 FE_1 FE_2 FE_3 FE_4 FE_5 FE_6 M_1 M_2 M_3
S_1 S_2 S_3 S_4 S_5 S_6 FE_1 FE_2 FE_3 FE_4 FE_5 FE_6 M_1 M_2 M_3 Raw sequence reads
Guppy life-history F2 QTL (RAD-seq markers)
Using an F2 QTL breeding cross design, we examine the genetic basis of seven life history traits in guppies: female age (1) and size (2) at first brood, first brood size (3), interbrood period (4), average dry offspring weight in the first brood (5), and male age (6) and size (7) at maturity.
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.
NCD_1 NCD_2 NCD_3 NCD_4 NCD_5 NCD_6 NCD_7 NCD_8 NCD_9 NCD_10 HFD_1 HFD_2 HFD_3 HFD_4 HFD_5 HFD_6 HFD_7 HFD_8 HFD_9 HFD_10 AO_1 AO_2 AO_3 AO_4 AO_5 AO_6 AO_7 AO_8 AO_9 AO_10
Aspergillus niger strain:DeltagalX DeltaxlnR
Aspergillus niger DeltagalX DeltaxlnR Gene Expression - 6.3.2.1 transcriptome
Aspergillus niger DeltagalX DeltaxlnR Gene Expression - 6.1.2.3 transcriptome
Methanospirillum sp. J.3.6.1-F.2.7.3
Methanospirillum sp. J.3.6.1-F.2.7.3 Genome sequencing
Transposon random mutagenesis of Mycoplasma pneumoniae M129. Samples sequenced for passage numbers 1, 2, 3, 4, 6, 8 and 10, two biological replicates per passage and two technical replicates for passages 2-4.
ESBL-producing E. coli from Children and Domestic Animals in Ecuador
Environmental Spread of Extended Spectrum Beta-lactamase (ESBL) Producing E. coli and ESBL Genes Among Children and Domestic Animals in Ecuador
Sulfolobus acidocaldarius strain:98-3 | isolate:DSM 639
Sulfolobus acidocaldarius 98-3 transcriptome - 65_1.6_stat_C.2
Sulfolobus acidocaldarius 98-3 transcriptome - 65_1.6_stat_B.2
Cyprinus carpio 'koi'
Cyprinus carpio 'koi' Raw sequence reads
Connexin 30 deficiency attenuates A2 astrocyte responses and induces severe neurodegeneration in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine hydrochloride Parkinson’s disease animal model
Gene expression data obtained from Oryza sativa adventitious roots (2-6 cm behind the root tip) grown in nutrient solution with (30 mgL-1) and without (3 mgL-1) Si
wood decay metagenome
1) Aquatic; 2) Marine; 3) Submerged Wood; 4) Fungi; 5) Bacteria; 6) Archaea Targeted loci
Tetrahymena thermophila
mRNA sequencing of WT and e2fl-1∆ cells in conjugation 2, 3, 4, 5, 6 and 7 (C2, C3, C4, C5, C6 and C7) hours of Tetrahymena thermophila
Homo sapiens
Expression data from Huh7 cells after 1,2,3,4,6-penta-O-galloyl-beta-D-glucopyranoside (PGG) treatment
soil metagenome
1)S; 2)SC; 3)SB; 4)SBC; 5)SBced; 6)SBCing Raw sequence reads
aquatic metagenome
1) BD; 2) BN; 3) GD; 4) GN; 5) MD; 6) MN; 7) RD; 8) RN; 9) SD; 10) SN; 11) XD; 12) XN. Metagenome
Mesotoga sp. BH458_6_3_2_1
Mesotoga sp. BH458_6_3_2_1 Genome sequencing and assembly
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