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SRP070944
Mus musculus
29 Downloadable Samples
Illumina HiSeq 2500
Description
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.
Publication Title
Progranulin deficiency causes impairment of autophagy and TDP-43 accumulation.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Mus musculus
- 15 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA was extracted from cortex of 1 year old wildtype, heterozygous or homozygous PGRN knockout mice. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech''s ExpressionPlot database is PRJ0007808 Overall design: RNA was extracted from cortex of 1 year old wildtype, heterozygous or homozygous PGRN knockout mice.
Publication Title
Progranulin deficiency causes impairment of autophagy and TDP-43 accumulation.
Sample Metadata Fields
Specimen part, Subject
View Samples SRP066728- Mus musculus
- 61 Downloadable Samples
- Illumina HiSeq 2500
Description
Mice of indicated ages and genotypes were perfused and their brains dissected and 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 "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech''s ExpressionPlot database is PRJ0006149 Overall design: Astrocytes, microglia and neurons were sorted from 7- or 13-month old PS2APP or non-transgenic mice, 4 = n = 7 per group.
Publication Title
Untangling the brain's neuroinflammatory and neurodegenerative transcriptional responses.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples SRP066489- Mus musculus
- 27 Downloadable Samples
- Illumina HiSeq 2500
Description
Normal mice were injected i.p. with LPS or saline. 24h later, perfused 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 PRJ0005404 Overall design: Astrocytes, microglia and neurons were sorted from LPS or saline treated mice. n=4 or 5 per group.
Publication Title
Untangling the brain's neuroinflammatory and neurodegenerative transcriptional responses.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples SRP066622- Mus musculus
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA was purified from intact cerebrocortical tissue of female PS2APP or non-transgenic mice, perfused at 7 or 13 months of age. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech''s ExpressionPlot database is PRJ0007648 Overall design: RNA from whole cortex of female PS2APP or non-transgenic mice at 7 or 13 months.
Publication Title
Untangling the brain's neuroinflammatory and neurodegenerative transcriptional responses.
Sample Metadata Fields
Age, Subject
View Samples- Mus musculus
- 15 Downloadable Samples
- Illumina HiSeq 2500
Description
This project defines the microglial gene expression profile in a transgenic mouse model of Alzheimer''s, compared to non-transgenic age-matched controls, at a time when amyloid pathology and microgliosis are rampant. Microglia were sorted live from one hemisphere of cerebral cortex, using GFP expressed from Cx3cr1 locus (mice have one intact copy of Cx3cr1). RNA was isolated from sorted microglia using RNeasy mini. Two groups, PS2APP and non-transgenic, with 9 mice/group, aged 14-15 months. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech''s ExpressionPlot database is PRJ0006715 Overall design: Gene expression in Cx3cr1::GFP+ sorted cells from cortex of wildtype or PS2APP at 14-15 months of age.
Publication Title
Diverse Brain Myeloid Expression Profiles Reveal Distinct Microglial Activation States and Aspects of Alzheimer's Disease Not Evident in Mouse Models.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples GSE62817- Mus musculus
- 14 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Determine gene expression differences between normal, metastatic and non-metastatic mouse lung tissue.
Publication Title
Granulocyte-colony stimulating factor promotes lung metastasis through mobilization of Ly6G+Ly6C+ granulocytes.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 150 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
The systematic characterization of somatic mutations in cancer genomes is essential for understanding the disease and for developing targeted therapeutics. Here we report the identification of 2,576 somatic mutations across approximately 1,800 megabases of DNA representing 1,507 coding genes from 441 tumours comprising breast, lung, ovarian and prostate cancer types and subtypes. Additionally, 373 tumors were assayed for copy number alterations via Agilent 244A CGH arrays and 153 breast, lung, and colon samples were assayed for mRNA abundance with Affymetrix HuEx1 Exon Arrays.
Publication Title
Diverse somatic mutation patterns and pathway alterations in human cancers.
Sample Metadata Fields
Specimen part
View Samples- Danio rerio
- 23 Downloadable Samples
- Affymetrix Zebrafish Genome Array (zebrafish)
Description
Zebrafish (Danio rerio) gutGFP transgenic embryos [Tg(XlEef1a1:GFP)s854] were collected at 4 time points: 2 days post fertilization (dpf), 3, dpf, 4 dpf, 6 dpf. Embryos were dissociated into single cells and sorted by FACS based on GFP expression.
Publication Title
FACS-assisted microarray profiling implicates novel genes and pathways in zebrafish gastrointestinal tract development.
Sample Metadata Fields
Age
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Purpose: To identify the changes in postnatal mouse conjunctival forniceal gene expression and their regulation by Klf4 around eye opening stage when the goblet cells first appear.
Publication Title
Mouse conjunctival forniceal gene expression during postnatal development and its regulation by Kruppel-like factor 4.
Sample Metadata Fields
No sample metadata fields
View Samples