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Sample GSM2813928

Query DataSets for GSM2813928

Status

Public on Feb 09, 2018

Title

DEW059_f1

Sample type

SRA

Source name

zebrafish brain

Organism

Danio rerio

Characteristics

tissue: brain
developmental stage: 23-25dpf

Treatment protocol

Growth protocol

Extracted molecule

total RNA

Extraction protocol

Single-cell suspensions were processed through inDrops to generate single-cell cDNA libraries. cDNAs were in vitro transcribed and fragmented. The 3' fragments were reverse transcribed and prepared for sequencing
Libraries were prepared as described in Zilionis et al., 2017, Nature Protocols (PMID = 27929523)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

inDrops Transcriptome libraries DEW058-DEW063, Fish1
GSTLT_f1.noQ.genes.csv.gz

Data processing

Single-cell RNA Sequencing data (FASTQ files) were processed using the inDrops.py bioinformatics pipeline available at https://github.com/indrops/indrops.
Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 (release-86) genome assembly.
Bowtie version1.1.1 was used with parameter –e 200; UMI quantification was used with parameter –u 2 (counts were ignored from UMIs split between more than 2 genes).
genomic DNA GESTALT and scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping
Genome_build: GRCz10
CSV files for transcriptome data were generated using the inDrops pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for genes. Txt files for genomic DNA GESTALT libraries (*allReadCounts) contain lineage barcode sequences (HMID column) for each cell and their proportion in the sequenced libraries. scGESTALT data (*GestMaster.txt) contains the inDrops cell identifiers (CellBarcode and BarcodeKey) that were used to match barcodes to transcriptomes. They also contain lineage barcode sequences (HMID column) for each cell with a corresponding inDrops single-cell gene expression profile, as well as the the t-SNE cluster membership number (ClusterIdent column)
Txt files ending in *stats.txt contain information about the each individually captured UMI or cell per sample. 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.
inDropsExpMatrix_noQ txt file is the gene expression matrix for the full dataset. Columns are individual cells from different batches of whole brains (f1_, f2_, f3_, f4_, f5_, f6_) or brain regions (fore_, mid_, hind_). fall.inDrops.Robj is the processed Seurat R object, which can be loaded into R and explored.

Submission date

Oct 16, 2017

Last update date

May 15, 2019

Contact name

Bushra Raj

E-mail(s)

bushra.raj@pennmedicine.upenn.edu

Organization name

University of Pennsylvania

Street address

421 Curie Boulevard