|
| Status |
Public on May 15, 2018 |
| Title |
WT ctrl rep3 |
| Sample type |
SRA |
| |
|
| Source name |
primary cultured neuron
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
day in vitro: Div 4
genotype/variation: WT
treatment: vechicle
|
| Treatment protocol |
WT neurons were treated with vehicle control, poly IC and CL075, while Tlr7-/- neurons were treated with vehicle control and CL075/poly dT ( for 6hr
|
| Growth protocol |
Mouse cortical and hippocampal mixed neurons were cultured in Neurobasal medium/DMEM (1:1) with B27 supplement
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was using Trizol reagent according to the manufacturer’s instructions (Invitrogen).
2 ug of total RNA was used for RNA-seq library preparation using the TruSeq Stranded mRNA LT set A Sample Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina bcl2fastq2.17 was used to generate fastqs from bcl files
Sequenced reads were trimmed for adaptor sequence,low quality sequences, then mapped to mm10 whole genome using CLC Genomics Workbench with parameters: mismatches=2, minimum fraction length =0.9, minimum fraction similarity=0.9, and maximum hits per read = 5.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample .
Supplementary_files_format_and_content: Txt files include "Name" "Chromosome" "Region" "TPM" "RPKM" "Total exon reads"
|
| |
|
| Submission date |
Nov 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yi-Ping Hsueh |
| E-mail(s) |
yph@gate.sinica.edu.tw
|
| Phone |
886-2-27899311
|
| Organization name |
Academia Sinica
|
| Department |
Institute of Molecular Biology
|
| Lab |
N514
|
| Street address |
128 Academia Road, Section 2, Nankang
|
| City |
Taipei |
| ZIP/Postal code |
11529 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE107199 |
Next Generation Sequencing for Quantitative Transcriptomic Profiling of TLR3, TLR7 and TLR8 Activation in Neurons |
|
| Relations |
| BioSample |
SAMN08048993 |
| SRA |
SRX3412396 |
