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| Status |
Public on Sep 18, 2020 |
| Title |
zBr8dpf13_S1 |
| Sample type |
SRA |
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| Source name |
zebrafish brain
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| Organism |
Danio rerio |
| Characteristics |
tissue: brain
developmental stage: 8dpf
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| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared as described in manufacturer's protocol for v2 kits
Single-cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single-cell cDNA libraries and prepared for sequencing
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
zf8dpf_cc_filt.cluster4.rds
zf8dpf_cc_filt_MarkRes6v4.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds
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| Data processing |
Single-cell RNA Sequencing data (FASTQ files) were processed using Cell Ranger v2.0.2 to generate count matrices
Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 (release-86) genome assembly. File uploaded as Danio_rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates (marked as *b in raw files) and the processing was done using the combination of all data (processed data files have comb* prefix)
scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping
Genome_build: GRCz10
Supplementary_files_format_and_content: *barcodes.tsv files contain 10X Genomics cell barcodes, *genes.tsv files contain gene names, *matrix.mtx contain transcriptome count data, *web_summary.html contain summary statistics for transcript mapping, .rds files are the processed R objects, .txt files contain marker genes identified for each cluster in the dataset, URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus.
Supplementary_files_format_and_content: scGESTALT data: Gest-zBr15dpf8 and Gest-zBr15dpf9 correspond to two samples from the same zebrafish (ZF1). Gest-zBr15dpf10 and Gest-zBr15dpf11 correspond to two samples from the same zebrafish (ZF2). Gest-zBr15dpf12 and Gest-zBr15dpf13 correspond to two samples from the same zebrafish (ZF3). Gest-zBr15dpf14 and Gest-zBr15dpf15 correspond to two samples from the same zebrafish (ZF4).
Supplementary_files_format_and_content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers (CellBarcode and CellUMI) that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences (HMID column) , the t-SNE cluster membership number (ClusterIdent column), and unique identifier (Readname). zfAllMerge-FILTEREDUSEME.xlsx contains the merged statistics of all samples, filtered to contain high confidence barcodes, the barcode sequence aligned to a reference unedited sequence (mergedRead column), mutations at each target site (target[X] columns) and the edited sequences at each target site (sequence[X] columns) were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping
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| Submission date |
Sep 17, 2020 |
| Last update date |
Sep 20, 2020 |
| Contact name |
Bushra Raj |
| E-mail(s) |
bushra.raj@pennmedicine.upenn.edu
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| Organization name |
University of Pennsylvania
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| Street address |
421 Curie Boulevard
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL20828 |
| Series (1) |
| GSE158142 |
Emergence of neuronal diversity during vertebrate brain development |
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| Relations |
| BioSample |
SAMN16200992 |
| SRA |
SRX9142617 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4793234_comb-zBr8dpf13_S1-barcodes.tsv.gz |
22.7 Kb |
(ftp)(http) |
TSV |
| GSM4793234_comb-zBr8dpf13_S1-genes.tsv.gz |
253.2 Kb |
(ftp)(http) |
TSV |
| GSM4793234_comb-zBr8dpf13_S1-matrix.mtx.gz |
15.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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