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rowid run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
51315 SRR8732838 SRX5525691 SRS4492367 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 28 hpf whole zebrafish embryo #2 from anterior to posterior axis GSM3672147   source name:whole embryo|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf Extracted RNA 28 hpf whole zebrafish embryo #2 from anterior to posterior axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. whole embryo   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf GSM3672147 GSM3672147: Extracted RNA 28 hpf whole zebrafish embryo #2 from anterior to posterior axis; Danio rerio; RNA Seq GSM3672147   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672147 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample4_R2_zcat.fastq.gz Sample4_R1_zcat.fastq.gz fastq fastq 5574969530.0 36993436.0 GSM3672147 r1 0:75.32 1:75.38 A:1776560856;C:755982699;G:888659557;T:2151535116;N:2231302 75 75     1776560856 755982699 888659557 2151535116 2231302 SRX5525691 SRS4492367 SRA860716 GEO Hubrecht Institute 2 0.02327 0.77704 0.01701 0.20977 0.99791 0.89873 0.40944 0.50295 75 76 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures