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Bulk data release notes 39 (July 2023) #42

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#### Data statistics

- Ensembl **104** / Ensembl Genomes **51** / WormBase ParaSite **15** gene annotations.
array design probe set mappings.
- This release contains **4424** datasets (**158401** assays), in particular:
- **1406** RNA-seq and **93** proteomics datasets, of which **340** report
[baseline](https://www.ebi.ac.uk/gxa/baseline/experiments) gene expression, across a total of **47** different
organisms;
- **1007** datasets reporting expression in [plants](https://www.ebi.ac.uk/gxa/plant/experiments);
- **4084** datasets studying samples in **14283**
[differential](https://www.ebi.ac.uk/gxa/experiments?experimentType=Differential) comparisons across **51**
different organisms.
- **66** overall species count

#### Selected new experiments

**New species!**
- [Drosophila pseudoobscura](https://www.ebi.ac.uk/gxa/experiments?species=%22drosophila%20pseudoobscura%22)

**New featured collection! - with data arising from the DIAMONDS project**
- [European Diagnostic Transcriptomic Library (EDTL)](https://www.ebi.ac.uk/gxa/edtl/experiments)

#### Selected differential experiments

- [Molecular Response of Chorioretinal Endothelial Cells to Complement Injury: Implications for Macular Degeneration](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-70806)
- [Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes for Wild Type and Mutants including opaque2, PbfRNAi and PbfRNAi;o2 in Maize (Zea mays)](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-79513)
- [RNA-seq to investigate dual role of lesion simulating disease 1 as a condition-dependent scaffold protein and transcription regulator in Arabidopsis thaliana](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-83262)
- [Germinal Center B-Cell gene expression comparison between Wiskott-Aldrich syndrome protein KO mice and WT mice](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10056)
- [RNA-Seq of zebrafish whole-eye comparing wild-type and mab21l1 c.107delA p.(Lys36Argfs*7) embryos at 5 days post fertilization](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10068)
- [RNA-seq of mouse embryonic fibroblasts(MEFs) with knock-out of SERF2 compared to control MEFs](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10083)
- [RNA-seq: STAT1 and STAT3 transcription factors sense and interpret changes in inflammation through engagement of specific enhancers](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10087)
- [Mutant FUS triggers age-dependent synaptic impairment in presymptomatic ALS-FUS mice (RNA-seq part2)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10104)
- [RNA-Seq analysis of the Oryza sativa Dongjin wild type and far1-1 mutant anthers](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10106)
- [RNA-seq to investigate gene expression after HCV eradication with IFN therapy in HIV/HCV-coinfected patients](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10232)
- [RNA-seq of oocytes and zygotes from pabpn1l ko and wt female mice](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10233)
- [Intestinal ulcers from biopsy-wounded wild-type and Bmp4-overexpressing mice](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10238)
- [RNA-seq of mouse sciatic peripheral nerve of injured mouse with implant: control (untreated) vs local delivery of MCC950 (NLRP3inh) vs standard FBR treatment dexamethasone (Dex). .](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10293)
- [RNA-seq of human oesophageal adenocarcinoma OE19 cell line treated with lapatinib](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10304)
- [RNA-seq following shRNA-mediated knock-down of ETV6-RUNX1 in the B-ALL cell line Reh](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10308)
- [RNA-seq of C. elegans reared on experimental microbiome (EM) and EM cell-free media against OP50-fed controls](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10693)
- [RNA-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-11866)
- [RNA-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR) and with or without prior TNFa treatment (IR_TNF)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-11867)
- [Rhizogenic Agrobacterium protein RolB interacts with the TOPLESS and NINJA repressor proteins to reprogram plant jasmonate signaling (GUS overexpression)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-11876)
- [Rhizogenic Agrobacterium protein RolB interacts with the TOPLESS and NINJA repressor proteins to reprogram plant jasmonate signaling (rolB overexpression)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-11880)
- [RNA-seq of definitive endoderm and pancreatic progenitor cells derived in vitro from human pluripotent stem cells in order to study the role of transcription factor GATA6 in human pancreas development](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-5958)
- [Gene expression ATLAS of Brachypodium distachyon (cv. BD21) during photomorphogenesis (transition from dark to light)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-6445)
- [Transcriptome analysis of HSPC, THP1 and K562 cells under IFNɑ treatment](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-6598)
- [RNA-seq of PBMC derived macrophages derived from healthy donors in response to lipid A or TNF alpha (Dataset_170630_SysmedIBD_RNA_HEngland)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-6607)
- [RNA sequencing analysis for differentially expressed genes in neonatal rat cardiomyocytes following knockdown of transcription factor Vezf1](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-7124)
- [RNA-seq analysis of C. elegans mina-1 mutants](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-7389)
- [RNA-seq from cortex and hippocampus of mice harboring heterozygous and homozygous deletion of Kctd13, as well as wild-type controls.](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-7398)
- [Comprehensive RNA-Seq Profiling of the Lung Transcriptome of Bashbay Sheep in Response to Experimental Mycoplasma ovipneumoniae Infection](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-7408)
- [RNA-seq of Drosophila melanogaster testes upon knock-down of dCoREST, dLSD1 and controls](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-7439)
- [RNAseq of proneural glioblastoma stem-like cells 72 hours after infection with human cytomegalovirus (CMV) Towne strain](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-7613)
- [RNA-seq analysis of the most basal half centimeter (dividing cells) of the fourth leaf of maize RIL89 plants, profiled at different time points after leaf appearance and with different watering conditions](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-7749)
- [Pro-inflammatory cytokines drive functional deregulation of potassium channels in primary synovial fibroblasts](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-7798)
- [RNASeq of human mesenchymal stem cells (6 donors) with and without treatment with 1 hour of cyclic tensile strain (2.6 – 6.2% strain, 5.0 Hz).](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-7925)
- [An integrated approach to profile lung tumor endothelial cell heterogeneity across species and models and to identify angiogenic candidates](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-8031)
- [Thyroid deficiency before birth modifies adipose transcriptome to promote overgrowth of white adipose tissue and impair thermogenic capacity](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-8396)
- [RNA-Seq profiling of ERCC1-XPF DNA repair defect (Er1F/-) versus wild type (Er1F/+) macrophages](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-8439)
- [RNA-Seq of SOX4 and HOXD3 CRISPR KO SupT1 cells against wildtype SupT1 cells during HIV-1 infection](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-8444)
- [Transcriptomic analysis of cocoa (Theobroma cacao L.) response to water deficit.](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-8525)
- [RNA-seq of RS4:11 cell line populations that are unedited (SPI1 +/+), mono (SPI1 +/-) and biallelicaly edited (SPI1 -/-)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-8677)
- [RNA-seq of blood samples from patients diagnosed with visceral leishmaniasis and asymptomatic individuals (Brazil)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-8818)
- [RNA-seq of whole tissue of 3 days post fertilization atp6v1e1b-deficient zebrafish larvae and wild-type controls](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-8824)
- [A natural variant of the sole pyruvate kinase of fission yeast lowers glycolytic flux triggering increased respiration and oxidative-stress resistance but decreased growth](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-8847)
- [RNA-Seq of BEAS-2B cells treated with low doses of Ni and NiO nanoparticles as well as NiCl2 for 6 weeks](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-8903)
- [Zebrafish il-4 il-10 regulated immunity in gills](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-8958)
- [RNA-seq experiment of developing mouse forelimbs, comparing Bcl9/9l mutant with control littermates.](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9000)
- [RNA-Seq of wild type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate (DSS)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9018)
- [RNA-seq of wild type and mutant Drosophila flies with a deletion of the gene CG16717 (dMPPED)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9081)
- [RNA-seq of sfpq-/- zebrafish embryos and siblings at 24 hpf](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9113)
- [RNA-Seq of transgenic rice (Oryza sativa spp. japonica cultivar Kitaake) plants containing a single construct that over-expresses C4 metabolic pathway components CA, PEPC, MDH, ME and PPDK](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9129)
- [RNAseq of small intestinal organoids from mice treated with the cytokines IFNG, IL-13 and IL-22 for 24 hours](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9182)
- [RNAseq of small intestinal epithelium extracted from mice infected with Nippostrongylus brasiliensis](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9183)
- [RNAseq of colon intestinal epithelium extracted from mice infected with Citrobacter rodentium](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9184)
- [RNA-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9194)
- [RNA-Seq of Arabidopsis thaliana plants primed by insect eggs from Pieris brassicae and triggered by insect herbivory against untreated controls in two different developmental phases (vegetative vs. reproductive)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9196)
- [Role of Macrophage migration inhibitory factor (MIF) in pancreatic stellate cells (PSCs)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9392)
- [RNA-seq of Zbtb10 Knockdown and Control cDC1 dendritic cells (Cd8+)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9495)
- [Transcriptome analysis in the old Brazilian wheat variety Toropi in response to infection with Puccinia triticina, the causal pathogen of leaf rust](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9791)
- [mRNA-Seq of zebrafish embryos (96hpf) exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9852)
- [mRNA-Seq of zebrafish embryos (96hpf) exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9853)
- [RNA sequencing of GPRC5C-Knockdown (GPRC5C-KD) and control CD34+ human bone marrow](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9863)
- [RNA sequencing of control and GPRC5C-Overexpression (GPRC5C-OE) in human mobilized peripheral blood (mPB)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9874)
- [3' mRNA-seq of sfpq-/- zebrafish embryos and siblings at 24 hpf](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9899)
- [RNA-seq profiling of three distinct cell populations in a murine model of epilepsia with and without drug treatment](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9943)
- [Influence of SUMOylation on transcriptional signature of hIPSCs (ChiPS4) assessed by time-resolved RNA-seq in response to ML792 treatment](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9962)
- [Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from single dose studies: compounds starting with A.](https://www.ebi.ac.uk/gxa/experiments/E-CURD-50)
- [Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from single dose studies: compounds starting with B.](https://www.ebi.ac.uk/gxa/experiments/E-CURD-51)
- [Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from repeat dosing studies: compounds starting with F to I.](https://www.ebi.ac.uk/gxa/experiments/E-CURD-63)
- [Profiling of human bronchial epithelial BEAS-2B infected with influenza A and treated with succinate to study the anti-influenza activity of succinate](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10031)
- [Transcriptomic analysis investigating the role of TNC in tumor progression using the MMTV-NeuNT mouse model](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10149)
- [Microarray analysis of MRC-5 cells infected with Zika virus strains](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10292)
- [Transcriptional profiling by array of U2OS cells overexpressing the BRCT domain of PARP1 after UV radiation](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-3619)
- [Neurog3-independant role of Notch signaling in pancreas explants. Microarray of pancreata of Wildtype or Neurog3tTA/tTA (Neurog3-Null) background at E12.5, explanted for 3d + treatment 24h with DAPT/vehicle.](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-6898)
- [Expression profiles of Hif1a mutant and wild type mouse livers subjected to cycles of fasting and re-feeding](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-7040)
- [Transcriptomic analyses of 11.5 dpc female germ cell (mouse) exposed or not to Bisphenol A analogues (BPAF and BADGE)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9344)

#### Selected baseline experiments

- [RNA-seq from gastrocnemius muscles from rats aged 6](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10583)
- [RNA-seq from tibialis muscles from rats aged 15 months (adult) and 27 months (old)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10582)
- [RNA-seq of Zbtb20-expressing Tregs against activated (CD62Llo) and naive (CD62Lhi) Tregs that do not express Zbtb20](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-11442)
- [RNA-seq analysis of quiescent human splenic B cell populations](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-11622)
- [Global gene expression differences between blood- and lymphatic-specific human dermal microvascular endothelial cells](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-74322)
- [A genetic](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-116969)
- [Temporal analysis of mRNA from panicle tissue from field grown rice](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-92302)
- [Transcriptome dynamics during the onset of conceptus elongation and between female and male porcine embryos](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-113366)
- [RNA-Sequencing of whole blood samples from children with a range of acute febrile illnesses](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-11671)
- [Genome-wide expression profiling and phenotypic evaluation of European maize inbreds at seedling stage in response to heat stress](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-88917)
- [RNA-Seq of hippocampus in Diversity Outbred mice](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-7637)
- [Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-89233)
- [The role of cis regulatory evolution in Zea Mays domestication](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-61810)
- [RNA-seq data of Arabidopsis thaliana germination](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-94457)
- [RNA-seq of human neuroblastoma cell lines](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-2690)
- [Genome-wide gene expression profile in inner stem tissue of V2 seedlings and husks (maize B73) [RNA-Seq]](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-94252)
- [Transcriptional analysis of tendons from rat](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-138540)
- [Gene expression in B73 maize aleurone and starchy endosperm at 18 and 22 day after pollination](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-95678)
- [Transcript profile analyses of maize silk strands during silk senescence](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-10847)
- [Distinct small RNA populations act antagonistically in formation of heterosis](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-51662)
- [RNA-Seq of various rice tissues (Root hair](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-11005)
- [RNAseq of murine brown fat](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-7175)
- [modENCODE: RNA-seq of gonads and carcasses in Drosophila pseudoobscura](https://www.ebi.ac.uk/gxa/experiments/E-CURD-23)
- [RNA-Seq of cultivated (i) bulk human thymic epithelial cells (hTECs) (ii) cortical hTECs (iii) medullary hTECs (iv) human thymic interstitial cells (hTICs)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-9641)
- [Transcriptome profiling of various organs at different developmental stages in rice (single-end)](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-56463)
- [Transcriptome profiling of various organs at different developmental stages in rice (paired-end)](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-56462)
- [RNA-sequencing of maize tissues at different developmental stages (comparative transcriptome study)](https://www.ebi.ac.uk/gxa/experiments/E-MTAB-5915)
- [High-resolution gene expression datasets of ontogenetic zones in the root apical meristem](https://www.ebi.ac.uk/gxa/experiments/E-GEOD-98097)\

**New proteomics experiments**
- [Secretome analysis of colorectal cancer cell linesSW620](https://www.ebi.ac.uk/gxa/experiments/E-PROT-110)
- [Proteomics of whole cell lysate vs. extracellular vesicles](https://www.ebi.ac.uk/gxa/experiments/E-PROT-102)
- [Proteome analysis of formalin-fixed paraffin-embedded colorectal adenomas](https://www.ebi.ac.uk/gxa/experiments/E-PROT-105)
- [Biomarkers discovery for Colorectal cancer liver metastasis](https://www.ebi.ac.uk/gxa/experiments/E-PROT-100)
- [Biomarkers discovery for Colorectal cancer](https://www.ebi.ac.uk/gxa/experiments/E-PROT-101)
- [Tissue-exudative extracellular vesicles of colorectal cancer](https://www.ebi.ac.uk/gxa/experiments/E-PROT-108)
- [Identification and validation of stage-associated serum biomarkers in colorectal cancer stages.](https://www.ebi.ac.uk/gxa/experiments/E-PROT-107)
- [Quantitative proteomics analysis of paired colorectal cancer and non-tumorigenic tissues](https://www.ebi.ac.uk/gxa/experiments/E-PROT-103)
- [Global proteome analysis of paired colorectal cancer sample using LC-MS/MS](https://www.ebi.ac.uk/gxa/experiments/E-PROT-106)
- [Proteome Landscapes of the Human Colorectal Mucosa](https://www.ebi.ac.uk/gxa/experiments/E-PROT-104)
- [Molecular composition of serum exosomes](https://www.ebi.ac.uk/gxa/experiments/E-PROT-109)