|
| Status |
Public on Jan 22, 2021 |
| Title |
Xmoo1 line, 3dpi, replicate 1, for FLAM-seq |
| Sample type |
SRA |
| |
|
| Source name |
Brain organoid
|
| Organisms |
Homo sapiens; Human alphaherpesvirus 1 |
| Characteristics |
tissue: Brain organoid
hsv-1 infection status: yes
sampling timepoint: 3dpi
rna population: polyA+ RNA
|
| Treatment protocol |
Organoids were infected using Herpes simplex virus 1, strain 17 containing a GFP gene controlled by an MCMV promoter (Snijder et al. 2012, doi: 10.1038/msb.2012.9)
|
| Growth protocol |
Cerebral organoids were generated according to modified Lancaster protocol (Lancaster et al., 2013, doi: 10.1038/nature12517),
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For isolation of bulk RNA, organoids were dissolved in Trizol. Ribosomal RNA was depleted using Rnase H (Epicentre)
Total bulk RNA-seq libraries were generated using the TruSeq Stranded Total LT Sample Prep Kit (Illumina). FLAMseq libraries were constructed as previously described (Legnini et al. 2019, doi: 10.1038/s41592-019-0503-y)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Sequel |
| |
|
| Description |
NR_AR_ORG_HSV1_4_gene_polyA_length.csv.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
NR_AR_ORG_HSV1_4
FLAMseq (Legnini et al. 2019)
|
| Data processing |
For bulk RNA-sequencing, Illumina base calling, demultiplexing and FASTQ conversion with bcl2fastq v2.20.0 (Illumina)
alignment to GRCh38 genome using STAR v2.7.1a (https://github.com/alexdobin/STAR)
reads counted on GENCODE 27 gene models with htseq-count 0.9.1 (https://htseq.readthedocs.io/)
The HSV1 genome was extended from strain 17 (genbank entry NC_001806) with the GFP and loxP sequences, error-corrected based on the total RNA-sequencing data, and terminal repeats removed to avoid multi-mapping reads
Provided here are the resulting HSV-1 fasta and gtf file used in the data analysis
For FLAM-seq, the CCS reads were then used as input to the FLAManalysis pipeline (https://github.com/rajewsky-lab/FLAMAnalysis), that outputs gene assignment and poly(A) tail length and sequence for each read.
For single-cell RNA-sequencing, data was processed using the pigx pipeline version 1.1.4 (http://bioinformatics.mdc-berlin.de/pigx/, Wurmus et al. 2018 doi: 10.1093/gigascience/giy123) using a combined human/HSV1 genome
Genome_build: Homo sapiens hg38
Genome_build: HSV-1 GFP truncated corrected
Supplementary_files_format_and_content: fasta file
Supplementary_files_format_and_content: gtf file
Supplementary_files_format_and_content: comma-separated values
|
| |
|
| Submission date |
Dec 28, 2020 |
| Last update date |
Jan 22, 2021 |
| Contact name |
Emanuel Wyler |
| E-mail(s) |
emanuel.wyler@mdc-berlin.de
|
| Phone |
+49 30 9406 3009
|
| Organization name |
Max Delbrück Center for Molecular Medicine
|
| Department |
Berlin Institute for Medical Systems Biology
|
| Lab |
RNA Biology and Posttranscriptional Regulation
|
| Street address |
Robert Roessle Str 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL29544 |
| Series (1) |
| GSE163952 |
Neurodegeneration in herpes simplex virus 1 infected human brain organoids |
|
| Relations |
| BioSample |
SAMN17172423 |
| SRA |
SRX9743857 |
