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| Status |
Public on Jun 23, 2020 |
| Title |
LungMF E18.5 WT-1 |
| Sample type |
SRA |
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| Source name |
fetal lung immature alveolar macrophage (preAM)
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| Organism |
Mus musculus |
| Characteristics |
strain: FVB/NJ backcross to C57BL/6 over 10 generations
tissue: lung
cell type: fetal lung immature alveolar macrophage (preAM)
age: embryonic day 18.5
genotype: wild-type
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| Extracted molecule |
total RNA |
| Extraction protocol |
The CD45+F4/80loCD11blo lung preAMs were sorted by FACS Aria II flow cytometer. Total RNA was extracted from the sorted cells with miRCURY RNA Isolation Kit - Cell & Plant (Exiqon). cDNA library was generated using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech).
cDNA was pre-amplified by a thermal cycler (Applied Biosystem) using 12-14 cycles and sheered into 150-400 bp fragments using Bioruptor Pico sonicator (Diagenode). The DNA ends were repaired using End-It™ DNA End-Repair Kit (Epicentre). The end repaired DNA fragments were ligated to adaptors by T4 ligase (NEB) after a single “A” was added at 3’ by Klenow Fragment (3’→5’ Exo-) (NEB). MinElute Reaction Cleanup Kit (Qiagen) was used for DNA cleanup after each step. Illumina P5 and P7 primers with individual adaptors were used for final library amplification. The 150-400 bp final product was purified on a 2% E-gel (Thermo Fisher Scientific).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
LG MF E18.5 Expression Browser Raw.xlsx
80330
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| Data processing |
bcl2fastq v2.17.1.14 conversion software used for basecalling.
The RNA-Seq reads were aligned to the mouse GRCm38/mm10 reference genome using Biomedical Genomics Workbench 4 (QIAGEN).
The expression levels for each sample were quantified and normalized usingBiomedical Genomics Workbench 4 (QIAGEN).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes gene name, chromosome, region, identifier, KO vs. WT-Max group means, KO vs. WT-Fold change, KO vs. WT-Log fold change, KO vs. WT-P-value, KO vs. WT-FDR p-value, KO vs. WT- FDR-Bonferroni, Total counts and RPKM values for each Sample
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| Submission date |
Nov 09, 2018 |
| Last update date |
Jun 23, 2020 |
| Contact name |
Qing-Sheng Mi |
| E-mail(s) |
qmi1@HFHS.ORG
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| Organization name |
Henry Ford Health System
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| Department |
Dermatology
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| Lab |
Immunology Program
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| Street address |
One Ford Place
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| City |
Detroit |
| State/province |
Michigan |
| ZIP/Postal code |
48202 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE122393 |
The epigenetic regulator Histone Deacetylase 3 regulates the ontogeny and maintenance of tissue-resident macrophage [RNA-Seq] |
| GSE122533 |
The epigenetic regulator Histone Deacetylase 3 regulates the ontogeny and maintenance of tissue-resident macrophage |
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| Relations |
| BioSample |
SAMN10407072 |
| SRA |
SRX5000381 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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