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| Status |
Public on Jun 01, 2023 |
| Title |
IRF8KO_3m_rep2 [RNA-seq] |
| Sample type |
SRA |
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| Source name |
FACS-sorted microglia
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 3-month-old
genotype: IRF8KO
gender: female
treatment: N.A.
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| Treatment protocol |
N.A.
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| Growth protocol |
In vivo microglia from each brain were non-enzymatically isolated.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Microglia were FACS-sorted directly in TRIzol and stored until usage. Total RNA was purified by phase extraction.
The cDNA was synthesized using SMART-Seq v4 Ultra Low Input RNA Kit (Takara bio USA, CA) with 15-cycle amplification. Adaptors were added to 1ng cDNA using the Nextera XT library prep kit (Illumina, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
2x55 paired-end sequence reads
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| Data processing |
Basecalls performed using bcl2fastq without the acceptance of index mismatch
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.5.2b.
Sequence duplicates were removed using Picard v2.17.11. Aligned tags were counted with Subread featureCounts. All steps are packaged in CCBR/Pipeliner.
Assembly: mm10
Supplementary files format and content: raw counts
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| Submission date |
May 01, 2023 |
| Last update date |
Jun 01, 2023 |
| Contact name |
Keita Saeki |
| E-mail(s) |
keita.saeki@nih.gov
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| Organization name |
NIH/NICHD
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| Street address |
6 Center Drive
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE231403 |
Transcriptome profiles of wild-type, IRF8KO, IRF8cKO, Batf3KO, 5xFAD, and 5xFAD/IRF8KO microglia [RNA-seq] |
| GSE231406 |
IRF8 configures enhancer landscape in postnatal microglia and directs microglia specific transcriptional programs |
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| Relations |
| BioSample |
SAMN34507504 |
| SRA |
SRX20177785 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7273525_9726_KOP2.p2.ReadsPerGene.out.tab.gz |
299.2 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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