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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 05, 2024 |
| Title |
IP_HA1_R |
| 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: Ago2HA/HA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Resting primary B cells were isolated from mouse spleens by negative selection using Mouse CD43 (Untouched™ B Cells; Invitrogen). Cells were activated in vitro to induce proliferation. AGO2 was immunopercipitated using an antibody against its HA epitope after which RNA was extracted and small RNA libraries prepared. The experiment was also performed in cells from animals not expressing the HA epitope, but no RNA was recovered. Therefore, libraries from those experiments were not prepared.
8 microRNA-Seq samples were pooled and sequenced on NextSeq 2000 P2 using QIAseq miRNA Library Prep and single-end sequencing
small RNA seq
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Description |
R_countTable
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| Data processing |
Processed reads were mapped to the mm10 genome with STAR v2.7.9a with the parameters ‘STAR –readFilesIn Processed_sample.fastq.gz –genomeDir mm10 –runThreadN 12 –genomeLoad LoadAndRemove –limitBAMsortRAM 20000000000 –readFilesCommand zcat –outSAMtype BAM SortedByCoordinate –outReadsUnmapped Fastx –outFilterMismatchNmax 1 –outFilterMismatchNoverLmax 1 –outFilterMismatchNoverReadLmax 1 –outFilterMatchNmin 16 –outFilterMatchNminOverLread 0 –outFilterScoreMinOverLread 0 –outFilterMultimapNmax 5000 –winAnchorMultimapNmax 5000 –seedSearchStartLmax 30 –alignTranscriptsPerReadNmax 30000 –alignWindowsPerReadNmax 30000 –alignTranscriptsPerWindowNmax 300 –seedPerReadNmax 3000 –seedPerWindowNmax 300 –seedNoneLociPerWindow 1000 –outFilterMultimapScoreRange 0 –alignIntronMax 1 –alignSJDBoverhangMin 999999999999,’ as previously described for transposons119. Duplicates of mapped reads were removed on the basis of the UMI sequence using umitools, and fastq files were generated from deduplicated mapped reads using samtools v1.15 (ref.120). Subsequently, fastq files from deduplicated reads were re-mapped. Initially, they were mapped to known noncoding RNA sequences annotated in Ensemble (including miRNAs, rRNAs, small nucleolar RNAs, small nuclear RNAs, and tRNAs). Reads that did not map to these elements were then re-mapped against the consensus sequence of mouse retrotransposon elements, as described above. These consensus sequences were downloaded from the SalmonTE github repository
Assembly: mm10
Supplementary files format and content: count table
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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 |
GPL30172 |
| Series (2) |
| GSE203049 |
AGO2 silences mobile transposons in the nucleus of quiescent cells |
| GSE269033 |
AGO2 silences mobile transposons in the nucleus of quiescent cells [RIP-seq] |
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| Relations |
| BioSample |
SAMN41673178 |
| SRA |
SRX24794897 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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