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| Status |
Public on Dec 10, 2020 |
| Title |
LPS 30 minutes 3 |
| Sample type |
SRA |
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| Source name |
Cerebral Vessels
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| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
strain: C57BL6
treatment: 10mg/kg LPS for 30 min
Sex: pooled male and female
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from mouse cerebral vessels after trizol homogenization, and then using QIAGEN miRNeasy micro Kit. Samples were later DNAse treated and cleaned up using RNEasy minelute clean up kit, finally eluted in RNAse free water from Qiagen.
Isolated RNA sample quality was determined using High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and concentration was measured using Qubit 2.0 RNA High Sensitivity assay (ThermoFisher, Massachusetts, USA). Libraries were then constructed following manufacturer’s instructions for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio USA Inc., California, USA) followed by Nextera® XT DNA Library Prep Kit (Illumina, California, USA). Final library quantities were measured by KAPA SYBR® FAST qPCR and quality was assessed using TapeStation D1000 ScreenTape (Agilent Technologies, CA, USA). Resulting final library size was about 430bp with an insert size of about 200bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed basing on QC values and sequencing was performed on an Illumina® NovaSeq 6000 (Illumina, California, USA). The read length configuration was 150 PE for 20M PE reads per sample (10M in each direction).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
one male and one female pooled together
DESeq2_normalized_counts.txt
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| Data processing |
Transcript abundance from RNA-seq reads was quantified using Salmon, and gene-level counts were obtained using tximport, against the C57BL/6J mouse genome annotation Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6), obtained from the National Center for Biotechnology Information. Subsequently, raw counts were processed with DESeq2 to determine differentially expressed genes.
salmon version 1.2.1
Genome_build: Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: DESeq2 normalized count matrix
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| Submission date |
Jul 31, 2020 |
| Last update date |
Dec 11, 2020 |
| Contact name |
Mahesh Chandra Kodali |
| Organization name |
Massachusetts General Hospital / Harvard Medical School
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| Department |
Neurology
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| Lab |
Steven E. Arnold
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| Street address |
114 16th St, Room 2300
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| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE155516 |
Effect of acute systemic inflammation on the Cerebral Vasculature in mice |
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| Relations |
| BioSample |
SAMN15690474 |
| SRA |
SRX8862337 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4705620_S9_quant.sf.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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