run_metadata: 33013
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 33013 | SRR29632275 | SRX25138327 | SRS21830411 | SRP516621 | PRJNA1129168 | in vitro construction of an embryonic caudal organizer | GSE270989 | Other | Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq. | Bmp4 explant 6h | GSM8366750 | source name:embryonic|tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell|geo loc name:missing|collection date:missing | Bmp4 explant 6h | Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline | embryonic | To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 μl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development. | Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery. | Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation. | tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell | GSM8366750 | GSM8366750: Bmp4 explant 6h; Danio rerio; RNA Seq | GSM8366750 r1 | GSM8366750 | 1 | Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP516621 | Bmp4_6h_S1_L001_R1_001.fastq.gz Bmp4_6h_S1_L001_R2_001.fastq.gz | fastq fastq | 52586645972.0 | 441904588.0 | GSM8366750 r1 | 0:28 1:91 | A:14755432217;C:11271293276;G:11858476334;T:14700289448;N:1154697 | 28 | 91 | 14755432217 | 11271293276 | 11858476334 | 14700289448 | 1154697 | SRX25138327 | SRS21830411 | SRA1911917 | Institute of genetics, Zhejiang University | Institute of genetics, Zhejiang University | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2024-06-27 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures |