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Sample GSM2720077

Query DataSets for GSM2720077

Status

Public on Sep 28, 2017

Title

tg-7

Sample type

SRA

Source name

trigeminal neurons

Organism

Mus musculus

Characteristics

strain: FVB/N
age: 3-6 wks
genotype/variation: wild type
cell type: trigeminal neuron

Extracted molecule

polyA RNA

Extraction protocol

Trigeminal neurons were isolated using the postnatal neural tissue dissociation kit (Miltenyi Biotec), followed by a 12.5%/20% percoll gradient. Glia and other non-neuronal cells were then depleted using the mouse neuron isolation kit (Milteny Biotec).
Libraries construction were performed as described by the Drop-seq protocol from the McCarroll lab

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina MiSeq

Data processing

bcl2fastq (v2.17) was used for basecalling
Sequence reads were processed using the Drop-seq cookbook (v 1.12) from the McCarroll lab (http://mccarrolllab.com/dropseq/)
Reads were aligned using STAR (v 2.5.3a) to mm10 genome
Seurat package (v 1.4.0.16) was used for downstream data analysis in R as described by the Satija lab (http://satijalab.org/seurat/)
Genome_build: mm10
Supplementary_files_format_and_content: csv file with cell barcodes and corresponding gene expression counts; only cells with at least 1000 transcripts are included for analysis

Submission date

Jul 27, 2017

Last update date

May 15, 2019

Contact name

Minh Q Nguyen

Organization name

NIDCR/NIH

Street address

9000, Rockville Pike

City

Bethesda