RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata: 74108

This data as json

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
74108 SRR23380803 SRX19321396 SRS16719695 SRP422528 PRJNA934545 A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq] GSE224918 Other During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates parent bioproject:PRJNA933118 pubmed:37131717;pubmed:38600066   zebrafish embryo 50% epiboly IAA replicate A scRNAseq GSM7035741   source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:IAA|geo loc name:missing|collection date:missing zebrafish embryo 50% epiboly IAA replicate A scRNAseq Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files zebrafish embryo 20mM 4sUTP injection at 1 cell stage Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:IAA GSM7035741 GSM7035741: zebrafish embryo 50% epiboly IAA replicate A scRNAseq; Danio rerio; RNA Seq GSM7035741 r1 GSM7035741 1 Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32°C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP422528   loader:fastq load.py B04_S4_R1_001.fastq.gz B04_S4_R2_001.fastq.gz B04_S4_I1_001.fastq.gz fastq fastq fastq 18799793040.0 111903530.0 GSM7035741 r1 0:8 1:20 2:140 A:5320607436;C:2779767285;G:3920270375;T:3644700536;N:1148568 8 20 140   5320607436 2779767285 3920270375 3644700536 1148568 SRX19321396 SRS16719695 SRA1590430 Hebrew University of Jerusalem Hebrew University of Jerusalem 1 0.64644   0.0354   0.85886   0.48293   140   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   Israel 2023-02-09 Gastrula Embryo Embryo Imprecise All anatomical structures