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Series GSE78747 Query DataSets for GSE78747
Status Public on Jul 06, 2017
Title GRN knockout, sorted brain cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 1 year old mice were perfused and brains were dissociated. Cells were fixed, immunolabeled and FACS sorted. RNA was extracted from neuron, astrocyte, and microglial cell populations. Typical RIN=4-5 for neurons, 6-8 for astrocytes, and 5-7 for microglia. Typical RNA yields ~100ng for neurons, ~20ng for microglia, and ~10ng for astrocytes.
cDNA was generated from up to 25 ng of total RNA using Nugen’s RNA-Seq method for low-input RNA samples, Ovation RNA-Seq System V2 (NuGEN). (Per manufacturers instructions, total RNA was neither depleted of rRNA nor polyA-selected.) 1 μg of sheared cDNA was taken into further processing, starting at end repair step, using Illumina’s TruSeq RNA Sample Preparation Kit v2 (Illumina).
The "SAMID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0007717
 
Overall design Astrocytes, microglia and neurons were sorted from PGRN heterozygous or knockout mice.
 
Contributor(s) Friedman B, Chang M, Sheng M
Citation(s) 28778989
Submission date Feb 29, 2016
Last update date May 15, 2019
Contact name Brad A Friedman
E-mail(s) friedmab@gene.com
Organization name Genentech, Inc.
Department Bioinformatics
Street address 1 DNA Way
City South San Francisco
State/province CA
ZIP/Postal code 94133
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (29)
GSM2075519 5641-385 GFAP
GSM2075520 5641-352 NeuN
GSM2075521 5641-337 NeuN
Relations
BioProject PRJNA313425
SRA SRP070944

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE78747_RAW.tar 8.6 Mb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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