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Sample GSM2040558 Query DataSets for GSM2040558
Status Public on Jul 14, 2016
Title Wiz.Female_Het2.E13.5Brain.RNAseq
Sample type SRA
 
Source name Mouse_E13.5_Whole_Brain
Organism Mus musculus
Characteristics strain: FVB
tissue: Embryonic Whole Brain
age: 13.5 days post coitum
genotype: Wiz MommeD30/+
Extracted molecule polyA RNA
Extraction protocol Brains were dissected from embryos into 1xPBS and flash frozen on dry ice, RNA was harvested using Trizol reagent. Libraries were constructed using the illumina TruSeq RNA Sample Preparation kit (cat Num RS-122-2201).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing For ChIP-seq, sequenced reads were provided by the sequencing service provider (Active Motif) in a .fastq.gz format. Reads were mapped to the mouse mm10 genome by the service provider, using the BWA program using default settings.
For ChIP-seq, peak calling was done by the service provider (Active Motif) using MACS2 (Version 2.1.0) by first filtering out duplicate reads then using default parameters and the following options -s 75 --bw 200 -m 10 30 –p 0.0000001. Peaks were considered significant if they had a p value of equal or less than 1E-20
For RNA-seq, sequenced reads were provided by the sequencing service provider (Australian Genome Research Facility) in a .fastq.gz format. Reads were mapped to the mouse mm10 genome using the program Tophat (version 2.0.11) with the following parameters: -I 100000 --library-type=fr-unstranded --read-edit-dist 3 --no-coverage-search --read-mismatches 3
For RNA-seq, read counts for gene exons were extracted using the program htseq-count (version 0.6.1) with the options -s no -m intersection-strict. Normalization and differnetial gene expression was assessed using the R-package DEseq, with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: For processed ChIP-seq data, Bigwig format files showing the mapped read density across the genome. For processed RNA-seq data, tab-delimited text files include raw read counts for each of the samples
 
Submission date Jan 15, 2016
Last update date May 15, 2019
Contact name Luke Thomas Isbel
E-mail(s) luke.isbel@adelaide.edu.au
Organization name SAiGENCI
Lab Isbel
Street address 4 North Terrace, AHMS, Lvl 9
City Adelaide
State/province South Australia
ZIP/Postal code 5000
Country Australia
 
Platform ID GPL13112
Series (1)
GSE76909 Widely Interspaced Zinc Finger Motifs, Wiz, binds active promoters and CTCF-binding sites and is required for normal neural function in the mouse
Relations
BioSample SAMN04417566
SRA SRX1532009

Supplementary file Size Download File type/resource
GSM2040558_Wiz.Female_Het2.E13.5Brain.RNAseq.txt.gz 159.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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