NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2040542 Query DataSets for GSM2040542
Status Public on Jul 14, 2016
Title Input_ChIP-seq (2)
Sample type SRA
 
Source name Mouse_Cerebellum
Organism Mus musculus
Characteristics strain: FVB
tissue: Cerebellum pooled
age: 56 days post partum
genotype: Wiz +/+
chip antibody: input
Extracted molecule genomic DNA
Extraction protocol Cerebellum were removed and pooled from 2 mice and flash frozen on dry ice. Cerebellum were sent to Active Motif (CA, USA) who then carried out ChIP and library construction as well as Input DNA library construction (Cat No. 25001 and 25046).
ChIP libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
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, using the Bowtie2 program using default settings.
For ChIP-seq, peak calling was done 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 GPL19057
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 SAMN04417550
SRA SRX1531993

Supplementary file Size Download File type/resource
GSM2040542_Wiz_Input.bw 247.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap