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Sample GSM1677143 Query DataSets for GSM1677143
Status Public on Nov 06, 2015
Title Input_ChIP-seq
Sample type SRA
Source name Mouse_Testis
Organism Mus musculus
Characteristics strain: FVB
tissue: Testis pooled
age: 84 days post partum
genotype: Trim33 +/+
chip antibody: input
Extracted molecule genomic DNA
Extraction protocol Testis were removed and pooled from 3 mice and flash frozen on dry ice. Testis 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 mm9 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 MACS (Version 1.4.2) by first filtering out duplicate reads and reads with a mapping quality of less than 25, then using default parameters and the following options -s 75--bw 200 -m 10 30 –p 0.0000001
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 mm9 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: mm9
Supplementary_files_format_and_content: For processed ChIP-seq data, Bigwig format files showing the fragment density for 32 nucleotide binds along the genome. For processed RNA-seq data, tab-delimited text files include raw read counts for each of the samples
Submission date May 06, 2015
Last update date May 15, 2019
Contact name Luke Thomas Isbel
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)
GSE68617 Trim33 binds and silences a class of young endogenous retroviruses in the mouse testis
BioSample SAMN03610060
SRA SRX1019998

Supplementary file Size Download File type/resource 162.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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