title: Vav-Control MPP RNA-seq 1

status: Public on May 06 2010

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

description: To export to gene expression data based on unique gene, we use Sample Gene Profile option of Illumina BeadStudio software.  Therefore, a total of 5553 probe data which have duplicated gene aggregated unique genes from the whole 48701 probes on the Human-6 beadChip ver. 2.

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 2 of the Illumina Human-6 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions.

data_processing:
For RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4
For RNA-seq gene counts were derived with Subread:featureCount v1.4.5 as well as htseq-count v0.8.0
For RNA-seq QC was performed with RSeQC v2.3
For RNA-seq quantification and normalization of gene RPKM was performed using Partek Genomics Suite Software version 6.6
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with raw gene counts

source_name: Multipotent Progenitor Cells (MPPs)

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina’s recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina® TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using RiboGreen were measured (Quant-iTTM RiboGreen® RNA assay kit; Invitrogen-Molecular Probes, ON, Canada) by the Victor3 spectrophotometer (PerkinElmer, CT) and cRNA quality was checked on a 1% agarose gel.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer’s protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide and examined under ultraviolet light.

tag: strain

tag: genotype

value: Wild-type

tag: cre-driver

value: Vav-CRE

value: Multipotent Progenitor Cells (MPPs)

tag: indexes

value: CGTCGCT


title: 3586

status: Public on Sep 05 2014

type: genomic

city: Kelvin Grove

first: Joanne

last: Voisey

state: Queensland

address: 60 Musk Ave

department: IHBI

country: Australia

institute: Queensland University of Technology

description: genomic DNA from frontal cortex

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: standard Illumina scan settings

data_processing: GenomeStudio v2011.1 with Methylation module 1.9.0 softward

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: frontal cortex

label_protocol: Standard Illumina protocol

extract_protocol: genomic DNA was extracted using the Roche MagNa Pure Compact

tag: disease status (1=control, 2=scz patient)

tag: age

tag: pmi (hours)

tag: gender

value: M

tag: sample well

tag: sentrix id

tag: sentrix position


title: 3235

description: genomic DNA from frontal cortex


title: 3540

description: genomic DNA from frontal cortex


title: 3529

description: genomic DNA from frontal cortex


title: 3531

description: genomic DNA from frontal cortex


title: 3504

description: genomic DNA from frontal cortex