|
| Status |
Public on Jan 22, 2018 |
| Title |
HSV-1 w/Dro #2 |
| Sample type |
SRA |
| |
|
| Source name |
HEP-2 Cells and Drosophila S2 Cells
|
| Organisms |
Drosophila melanogaster; Homo sapiens |
| Characteristics |
cell line: HEp-2
cell line: S2
cell type: lung epithelial cells from a carcinoma
infection: HSV-1
cell type: epithelial, late stage embryo
processing: nuclei isolation
|
| Treatment protocol |
Hep-2 cells were infected with HSV-1 F strain at an MOI of 5. S2 cells were left untreated before nuclei isolation, and spiked-in to isolated Hep-2 nuclei (1 drosophila nuclei/10,000 Hep-2 nuclei)
|
| Growth protocol |
Hep-2 cells--grown at 37 degrees C in 5% CO2 in DMEM 10% Newborn calf serum supplemented with Penn/Strep
Drosophila S2 cells--grown at 20 degrees C on bench top in Schneider's Drosophila Medium with 10% FBS and Penn/Strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei isolation followed by Nuclear Run-on in the presence of biotinylated nucleotides (A, U, G, C). Biotinylated transcripts were isolated using streptavadin coated magnetic beads
Libraries were constructed following the protocol outlined by Mahat et al. 2016. "Base-pair-resolution genome-wide mapping of active RNA Polymerases using precision nuclear run-on (PRO-seq). Nature Protocols. Aug 11(8):1455-76 doi:10.1038/nprot.2016.086
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Library strategy: PRO-seq
All processing steps were done using the Danko lab template for PRO-seq alignment/QC found at https://github.com/Danko-Lab/utils/tree/master/proseq with instructions at https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md
Pre-processing reads and sequence adapter trimming are done with cutadapt
Reads are mapped to the bwa index reference genome using bowtie
BAM files are converted to BigWig using Kentsource
BigWig can be viewed using IGV, and BAM files analyzed with DESeq2 statistics using SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/. SeqMonk data is reported in Xcel files as supporting/supplemental information in the publication
Genome_build: hg 38 (Samples 1-12), and dm3 (Samples 7-12)
Supplementary_files_format_and_content: big wig
|
| |
|
| Submission date |
Oct 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Joel D Baines |
| E-mail(s) |
jdb11@cornell.edu
|
| Organization name |
Cornell University
|
| Street address |
235 Hungerfordhill Rd
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL22339 |
| Series (1) |
| GSE106126 |
Herpes Simplex Virus 1 dramatically alters loading and positioning of RNA Polymerase II on host genes early in infection |
|
| Relations |
| BioSample |
SAMN07834023 |
| SRA |
SRX3325374 |
