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Status |
Public on Apr 17, 2020 |
Title |
AD2m1M |
Sample type |
SRA |
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Source name |
Brain
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Organism |
Mus musculus |
Characteristics |
strain: APPswe/PS1-delta=E9 age: 2-month-old
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was isolated from flow cytometry-sorted cell populations using RNeasy Micro Kit (74004, Qiagen) A total amount of 10 ng RNA per sample was used as input material for the RNA sample preparations. Libraries were generated using SMART-Seq v4 Ultra Low Input RNA Kit (634892, Takara Bio USA, Mountain View, CA, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, first-strand cDNA synthesis from total RNA is primed by the 3’ SMART-Seq CDS Primer II A and uses the SMART-Seq v4 Oligonucleotide for template switching at the 5’ end of the transcript. PCR Primer II A amplifies cDNA from the SMART sequences introduced by 3’ SMART-Seq CDS Primer II A and the SMART-Seq v4 Oligonucleotide for 8 cycles. LD-PCR amplified cDNA is purified by immobilization on AMPure XP beads and then quantified with Agilent Bioanalyzer 2100 system. Approximately 200 pg was used for Nextera XT DNA Library Preparation Kit (Illumina, Cat. Nos. FC-131-1024 and FC-131-1096, San Diego, CA) to make cDNA libraries suitable for Illumina sequencing. Tagmented fragments were amplified for 12 cycles and dual indexes were added to each well to uniquely label each library. Concentrations were assessed with KAPA Library Quantification Kits (KK4844, KAPA, Biosystems, USA) and samples were diluted to ~2 nM and pooled. Pooled libraries were sequenced on the Illumina Novaseq platform and 150 bp paired-end reads were generated.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Data processing |
Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: mm8 Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...
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Submission date |
Sep 06, 2019 |
Last update date |
Apr 17, 2020 |
Contact name |
jie pan |
E-mail(s) |
panj@bjmu.edu.cn
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Phone |
18666886732
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Organization name |
Shenzhen Peking University – The Hong Kong University of Science and Technology Medical Center
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Street address |
Lian Hua Lu 1120, FuTian District Guangdong
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City |
shenzhen |
ZIP/Postal code |
518000 |
Country |
China |
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Platform ID |
GPL24247 |
Series (1) |
GSE137028 |
Transcriptomic profiling of microglia and astrocytes throughout aging |
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Relations |
BioSample |
SAMN12708602 |
SRA |
SRX6812635 |
Supplementary data files not provided |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data are available on Series record |
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