GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM4086428 Query DataSets for GSM4086428
Status Public on Jul 17, 2020
Title thy1 Input
Sample type SRA
Source name testis
Organism Mus musculus
Characteristics tissue: testis
cell type: undifferentiated spermatogonia cells
development stage: 6-8 days post-natal
chip antibody: H3K9me3 (Active Motif, 39161)
strain: C57BL/6
Extracted molecule genomic DNA
Extraction protocol All sorted cells and H3K9me3 antibody incubated by magnetic beads were immunoprecipitated and DNA was finally isolated. The amount of DNA used for the ChIP: 6pg.
The sequence libraries were generated using the KAPA Hyper Prep Kit for the Illumina platform (kk8504), following the manufacturer's instructions. Paired-end 150-bp sequencing was performed on Illumina HiSeq X10.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
Description marker: thy1
THY1-antibody manufacturer : Biolegend lot number:B284489
Data processing Sequenced reads were trimmed for adaptor sequence, low quality. The processed reads were then aligned to the mouse genome (mm9) with bowtie2 (version 2.2.9) with default settings.
Peaks were called using macs14(v1.4.2) with the parameters "macs14 -g mm --nomodel --nolambda --shiftsize=73" relative to input samples.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using macs2 callpeak function and normlized to one million eads per sample using --SPMR option. Scores represent normalized tag counts per million reads.
Submission date Sep 19, 2019
Last update date Jul 17, 2020
Contact name liu ying dong
Phone 18729187605
Organization name Northwest University of Agriculture and Forestry Science and Technology
Department College of Animal Science and Technology
Lab Zeng wenxian
Street address Shaanxi
City Xi'an, Shaanxi
ZIP/Postal code 710000
Country China
Platform ID GPL21273
Series (2)
GSE137742 Ultra-low-input native ChIP-seq data of four germ-cell types during mouse spermatogenesis
GSE137744 ltra-low-input native ChIP-seq and Whole genome bisulfite Sequencing data of four types mouse spermatogenesis
BioSample SAMN12788965
SRA SRX6874365

Supplementary data files not provided
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