Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
Home Datasets Genes
Metadata
Species Projects Samples Publications
Tools
Online Analysis GEN Toolkit
Statistics Documentation Download Contact
Home Projects
PRJNA554601

PRJNA554601: Electrical and synaptic integration of glioma into neural circuits

Source: NCBI / GSE134269
Submission Date: Jul 15 2019
Release Date: Oct 02 2019
Update Date: Oct 02 2019

Summary: We report single cell RNA-seq data from patient-derived xenografts that were dissociated, FACS sorted into 96-well plates and profiled by Smart-seq2 and sequencing on an Illumina NextSeq500

Overall Design: Individual cells from two DIPG cell cultures derived by the Monje lab (DIPG VI and DIPG XIII-FL) were isolated by enzymatic and mechanical digestion followed by FACS sorting. cDNA libraries were generated using Smart-seq2 and Nextera XT with dual unique indexes. Libraries were sequenced on an Illumina NextSeq500, reads aligned by Bowtie and quantified by RSEM and alayses performed using Seurat.

GEN Datasets:
GEND000209
Strategy:
Species:
Healthy Condition:
Cell Type:
Cell Line:
Protocol
Growth Protocol: Cells were lentivirally transduced to constitutively express GFP protein and firefly luciferase.
Treatment Protocol: -
Extract Protocol: Cells were extracted from the brain using mechanical and enzymatic dissociation (Brain Tumor Dissociation Kit, Miltenyi)
Library Construction Protocol: Libraries were constructed following Illumina Nextera XT protocol and a dual-unique indexing strategy.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina NextSeq 500
Strand-Specific: Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Electrical and synaptic integration of glioma into neural circuits.
Nature . 2019-09-18 [PMID: 31534222]