run_metadata: 34547
This data as json
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| 34547 | SRR32092978 | SRX27440700 | SRS23867512 | SRP559408 | PRJNA1214750 | Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [scRNA seq] | GSE287811 | Other | During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: mcherry+ cells from 16 somite stage zebrafish embryos migratory cardiac neural crest stage were FAC sorted from Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP and analyzed using 10X Chromium Single Cell three prime v3.1 sequencing. | mch+ CdNC cells from 16ss zebrafish embryos | GSM8751763 | source name:midbrain hindbrain boundary to somite 6|tissue:midbrain hindbrain boundary to somite 6|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|cell type:Cardiac Neural Crest|age:16 somite stage|geo loc name:missing|collection date:missing | mch+ CdNC cells from 16ss zebrafish embryos | Reads were mapped to GRCz11 and initial quality control was performed using Cell Ranger v7.20. Scanpy was used for further quality control filtering clustering and downstream analysis. Assembly: GRCz11 Supplementary files format and content: tab separated barcodes and features files as well as matrix file. | midbrain hindbrain boundary to somite 6 | mch+ CdNC cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. Single cell libraries were prepared using the Chromium Single Cell 3’ v3.1 reagent kit 10X Genomics PN 1000075 according to manufacturer's protocol. | tissue:midbrain hindbrain boundary to somite 6|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|cell type:Cardiac Neural Crest|age:16 somite stage | GSM8751763 | GSM8751763: mch+ CdNC cells from 16ss zebrafish embryos; Danio rerio; RNA Seq | GSM8751763 r1 | GSM8751763 | 1 | mch+ CdNC cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. Single cell libraries were prepared using the Chromium Single Cell three prime v3.1 reagent kit 10X Genomics PN 1000075 according to manufacturer's protocol. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP559408 | SE6898_SA80357_S1_L001_R1_001.fastq.gz SE6898_SA80357_S1_L001_R2_001.fastq.gz | fastq fastq | 71160584348.0 | 235631074.0 | GSM8751763 r1 | 0:151 1:151 | A:17520054424;C:13126677931;G:14006245844;T:26493745251;N:13860898 | 151 | 151 | 17520054424 | 13126677931 | 14006245844 | 26493745251 | 13860898 | SRX27440700 | SRS23867512 | SRA2058075 | Martik Lab, Molecular and Cell Biology, University of California Berkeley | Martik Lab, Molecular and Cell Biology, University of California Berkeley | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2025-01-23 | Segmentation | Embryo | Brain | Nervous System |