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| Status |
Public on Nov 06, 2015 |
| Title |
Input_ChIP-seq |
| Sample type |
SRA |
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| Source name |
Mouse_Testis
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| Organism |
Mus musculus |
| Characteristics |
strain: FVB
tissue: Testis pooled
age: 84 days post partum
genotype: Trim33 +/+
chip antibody: input
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| 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
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
May 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Luke Thomas Isbel |
| E-mail(s) |
luke.isbel@adelaide.edu.au
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| Organization name |
SAiGENCI
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| Lab |
Isbel
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| Street address |
4 North Terrace, AHMS, Lvl 9
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| City |
Adelaide |
| State/province |
South Australia |
| ZIP/Postal code |
5000 |
| Country |
Australia |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE68617 |
Trim33 binds and silences a class of young endogenous retroviruses in the mouse testis |
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| Relations |
| BioSample |
SAMN03610060 |
| SRA |
SRX1019998 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1677143_Input_ChIP-seq.bw |
162.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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