|
| Status |
Public on Jun 07, 2023 |
| Title |
DicerKO.HIV.rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116 Dicer k.o. VSVg pseudotyped HIV-1 virus infected cells
|
| Organism |
Homo sapiens |
| Characteristics |
biomaterial provider: Korean Collection for Type Cultures (KCTC)
cell line: HCT116
genotype: Dicer k.o.
infection: Cells were infected with HIV-1 for 28hrs
|
| Treatment protocol |
RNA was isolated from cells uninfected or infected with VSVg pseudotyped HIV R9 Env 𝚫iGFP reporter virus after 28hrs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell lysates were subjected to pull down with a GW182 FLAG-GST- T6B peptide isolated using anti-FLAG M2 Magnetic beads. Bound RNA was extracted using Trizol follwing by ethanol precipitation.
Small RNA-SEQ libraries containing library fragments 140-160 bp in size were generated using Illumina TruSeq small RNA adapters the protocol described in Hafner et al. (2012) Methods 58:164. RNA of 19-35 nt in length was size selected by Urea-PAGE gel extraction after adpater ligation. The final library of ~157bp was size selected on an agarose-TBE gel. Quality of final cDNA was assessed by Agilent Bioanalyzer and DNA concentration determined by Qubit.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Single Read
|
| Data processing |
Processing was done with the SPOROS pipeline: https://github.com/ebartom/SPOROS
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed with Trim_galore (4N before pull-down sequence and 2N after). This resulted in the deposited fastq files.
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Reads with hits against artificial and adapter sequences are removed from the table, as well as reads with a summed count < total number of samples
Supplementary files format and content: Tab-delimited file with read, seed (bp 2-7), cell viability based on seed, raw read counts for each sample, and putative source based on blast
|
| |
|
| Submission date |
Nov 17, 2022 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Marcus Peter |
| E-mail(s) |
m-peter@northwestern.edu
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Street address |
303 East Superior Street, Lurie 6-123
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE218189 |
Contribution of 6mer seed toxicity to HIV-1 induced cytotoxicity [DISE-36] |
| GSE218195 |
Contribution of 6mer seed toxicity to HIV-1 induced cytotoxicity |
|
| Relations |
| BioSample |
SAMN31769841 |
| SRA |
SRX18292963 |
