|
| Status |
Public on Sep 28, 2017 |
| Title |
WI-38 cells, unstranded polyA RNA-seq, 4h HSV-1 infection, Replicate 2, unlabeled RNA |
| Sample type |
SRA |
| |
|
| Source name |
WI-38 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WI-38
4su treatment: 1h before harvesting
hsv-1 infection: Infected 4h before harvesting
rna isolation: unlabeled RNA (flowthrough)
adapter sequence: GATCGGAAGAGCACACGT
barcode: ACGTCCC
|
| Treatment protocol |
For RNA labeling, 4SU at a concentration of 500 µM was added one hour before harvesting. Cells were infected with Herpes simplex virus 1 as indicated.
|
| Growth protocol |
WI38 fibroblasts were cultured in Minimal Essential Medium (MEM) supplemented with 10% Fetal Bovine Serum (FBS) and with 100 units/ml penicillin, 100 µg/ml streptomycin. HeLa cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS) and with 100 units/ml penicillin, 100 µg/ml streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Illumina TruSeq RNA Library Prep Kit v2
Cells were resuspended in Trizol and, following Chloroform-mediate phase separation, RNA extracted from the aqueous phase using the CC-25 kit (Zymo).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
no processed data due to technical reasons
UnStranded RNA-seq
|
| Data processing |
Data was mapped onto the hg19 reference using Tophat2 (Kim et al. 2013).
Antisense transcripts were defined on the coverage tracks using a custom running sum algorithm, followed by extensive filtering.
Antisense transcripts were classified into divergent, convergent and intal, based on the location of the TSS in respect to the sense transcript.
Expression values for the different samples (columns X-X) are presented as log(2) transformed RPKM values of averages from biological replicates.
Expression values are shown for the stranded RNA-sequencing data provided here (columns X-X). In addition, published RNA-sequencing data was reanalyzed the same way (columns X-X, as indicated by first author name and GSM identifiers).
The following datasets were reanalyzed: HSV-1 infected HFF cells (Rutkowski et al. 2015, PMID: 25989971, GEO: GSE59717), RNA-sequencing from VZV keratinocytes (Jones et al. 2014, PMID: 24497829, SRA: E-MTAB-1717) and CMV infected fibroblast (Tirosh et al. 2015, PMID: 26599541, GEO: GSE69906), and NET-seq data from HeLa cells (Schlackow et al. 2017, PMID: 28017589, GEO: GSE81662)
Column names contain first author name, SRA identifiers for VZV data and GEO identifiers for all others. Several identifiers indicate that replicates were available and averaged.
Nearest FANTOM transcripts (Hon et al. 2017) are provided.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated text
|
| |
|
| Submission date |
Mar 24, 2017 |
| Last update date |
May 15, 2019 |
| 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 |
GPL11154 |
| Series (1) |
| GSE97009 |
Widespread activation of antisense transcription of the host genome during Herpes simplex virus 1 infection |
|
| Relations |
| BioSample |
SAMN06642096 |
| SRA |
SRX2671624 |
