|
| Status |
Public on Apr 23, 2023 |
| Title |
AT_30_RC17_hGPC_IFN_gamma_S39 |
| Sample type |
SRA |
| |
|
| Source name |
hGPC IFN gamma
|
| Organism |
Homo sapiens |
| Characteristics |
condition: IFN gamma +
cell type: hGPC
treatment: IFN gamma
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RC17-derived glial progenitor cells were plated on laminin 521 (2μg/cm2) coated plates in a terminal differentiation medium. Cells were matured for 14 days and stimulated with IFN-g (5ng/ml) for 48hrs in the culture medium. Post stimulation, cells were washed twice with 1XPBS and detached with accutase and pellets were frozen down on dry ice for bulk-RNA seq.
Total RNA was isolated using the Rneasy Mini Kit (Qiagen).
Libraries were generated using Illumina TruSeq Stranded mRNA library prep kit (poly-A selection) and were sequenced on an Illumina NextSeq500 machine (paired-end 2×150bp).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Illumina Truseq
ERV_count_matrix_2.csv
|
| Data processing |
Unique mapping using STAR aligner (--outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.03)
ERV predictions from RetroTector (https://github.com/PatricJernLab/RetroTector) were quantified using featureCounts (Subread version 1.6.3), forcing matching strandness of the reads to the features being quantified (-s 2).
BAM files were indexed using samtools (version 1.12) and converted to bigwig files using deeptools bamCompare (version 2.5.4) (--normalizeUsingRPKM)
Assembly: GRCh38
Supplementary files format and content: Bulk RNAseq bigwigs for genome browser visualization
Supplementary files format and content: Bulk RNAseq ERV quantification read count matrix
|
| |
|
| Submission date |
Apr 21, 2023 |
| Last update date |
Apr 24, 2023 |
| Contact name |
Johan Jakobsson |
| E-mail(s) |
johan.jakobsson@med.lu.se
|
| Organization name |
Lund University
|
| Department |
Wallenberg Neuroscience Center
|
| Lab |
Molecular Neurogenetics
|
| Street address |
Sölvegatan 17
|
| City |
Lund |
| ZIP/Postal code |
22362 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE209552 |
Single-cell transcriptomics of resected human traumatic brain injury tissues reveals acute activation of endogenous retroviruses in oligodendroglia |
|
| Relations |
| BioSample |
SAMN34277608 |
| SRA |
SRX20032647 |
