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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 05, 2024 |
| Title |
wt_fl_36_Input_1 |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
cell type: resting B cells
genotype: Ago2+/flx
treatment: 4OHT, 36h
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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). 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.
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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 |
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
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| Submission date |
Jun 04, 2024 |
| Last update date |
Jun 05, 2024 |
| 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 |
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 |
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| Relations |
| BioSample |
SAMN41672958 |
| SRA |
SRX24794259 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8305334_wt_fl_36_Input_1_sorted_q0_nodup.bw |
84.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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