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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 22, 2022 |
| Title |
HA_restingBcells_rep1 |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Mus |
| Characteristics |
tissue: Spleen
cell type: resting B cells
genotype: Ago2HA/HA
chip antibody: HA (CST #3724)
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| 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). Cells were used immediately after isolation.
libraries were generated using Thruplex DNA-seq Kit from Takara according to manufactures’ instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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-discordant --no-unal --phred33’. 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
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| Submission date |
Jul 19, 2022 |
| Last update date |
Jul 22, 2022 |
| Contact name |
Joana A Vidigal |
| E-mail(s) |
joana.vidigal@nih.gov
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| Phone |
240-760-6691
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| Organization name |
NIH/NCI
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| Department |
LBMB
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| Lab |
Vidigal
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| Street address |
37 Convent Dr, Room 6056
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-0001 |
| Country |
USA |
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| Platform ID |
GPL31136 |
| 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 |
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| Relations |
| BioSample |
SAMN29831165 |
| SRA |
SRX16346897 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6351518_HA1_sorted_q30_nodup_ext.bw |
152.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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