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Sample GSM8305338 Query DataSets for GSM8305338
Status Public on Jun 05, 2024
Title CD_fl_36_H3K9me3 IP_2
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics tissue: Spleen
cell type: resting B cells
genotype: Ago2ADH/flx
treatment: 4OHT, 36h
Extracted molecule genomic DNA
Extraction protocol Resting primary B cells were isolated from mouse spleens by negative selection using Mouse CD43 (Untouched™ B Cells; Invitrogen). Recombination of the floxed allele was achieved by culturing cells in the presence of 4OHT for 36h.
libraries were generated using Thruplex DNA-seq Kit from Takara according to manufacturer's instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing ChIP-seq reads were mapped to the mouse genome (mm10) using bowtie2 (Langmead and Salzberg, 2012) with the options ‘-p 40 --very-sensitive --end-to-end --no-unal --phred33’. For analysis at repetitive elements, multimapping reads where kept but only the best alignment was reported. For reads with multiple equally good alignments, a single alignment was selected for reporting using a pseudo-random number generator. High quality-mapped reads, that we considered as mapping uniquely, were identified with samtools v1.15 (Danecek et al., 2021) using ‘samtools view -q 30’. SAM files containing either all reads or only unique reads were filtered using bedtools v2.30.0 (Quinlan and Hall, 2010) to exclude reads overlapping with the mm10 blacklist (Amemiya et al., 2019; Consortium, 2012). Duplicates were removed with the “Picard Toolkit.” from the Broad Institute (GitHub Repository: https://broadinstitute.github.io/picard/) using ‘java -jar picard.jar MarkDuplicates’. BigWig files were generated using deeptools v3.5.1 (Ramirez et al., 2016) using the RPKM normalization method and visualized on the IGV browser (Robinson et al., 2011).
Assembly: mm10
Supplementary files format and content: bigwig
 
Submission date Jun 04, 2024
Last update date Jun 05, 2024
Contact name Joana A Vidigal
E-mail(s) joana.vidigal@nih.gov
Phone 240-760-6691
Organization name NIH/NCI
Department LBMB
Lab Vidigal
Street address 37 Convent Dr, Room 6056
City Bethesda
State/province MD
ZIP/Postal code 20892-0001
Country USA
 
Platform ID GPL19057
Series (2)
GSE203047 AGO2 silences mobile transposons in the nucleus of quiescent cells [ChIP-seq]
GSE203049 AGO2 silences mobile transposons in the nucleus of quiescent cells
Relations
BioSample SAMN41672954
SRA SRX24794263

Supplementary file Size Download File type/resource
GSM8305338_CD_fl_36_IP_2_sorted_q0_nodup.bw 18.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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