|
| Status |
Public on Aug 10, 2019 |
| Title |
PBS1nuc bulk RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
sampletype: Microglia nuclei
sequencing protocol: 3’ Quantseq
tissue type: fresh
treatment: PBS
|
| Treatment protocol |
I.p. PBS or LPS injection, 1mg/kg for 3 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation with Rneasy Plus Micro Kit (Qiagen)
Quant Seq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen) and Chromium Single Cell 3’ v2 kit from 10x Genomics
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
BE180802_Lexogen_082_S76_R1_001
|
| Data processing |
QC with FASTQC
Trimming with TrimGalore v0.4.5
Alignment with HiSat v2.1
Counting with FeatureCounts
Supplementary_files_format_and_content: Raw count file
|
| |
|
| Submission date |
Aug 09, 2019 |
| Last update date |
Aug 10, 2019 |
| Contact name |
Emma Gerrits |
| E-mail(s) |
e.gerrits@rug.nl, e.gerrits@umcg.nl
|
| Organization name |
UMCG
|
| Department |
BSCS
|
| Lab |
Molecular Neurobiology
|
| Street address |
Antonius Deusinglaan 1
|
| City |
Groningen |
| State/province |
Groningen |
| ZIP/Postal code |
9713AV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE135618 |
Transcriptional profiling of microglia; current state of the art and future perspectives |
|
| Relations |
| BioSample |
SAMN12542160 |
| SRA |
SRX6686192 |
