|
Status |
Public on Jun 07, 2023 |
Title |
HCT116.WT.UT.rep1 |
Sample type |
SRA |
|
|
Source name |
HCT116wt uninfected cells
|
Organism |
Homo sapiens |
Characteristics |
biomaterial provider: Korean Collection for Type Cultures (KCTC) cell line: HCT116 genotype: wt infection: Uninfected cells
|
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 |
|
|
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) |
GSE218187 |
Contribution of 6mer seed toxicity to HIV-1 induced cytotoxicity [DISE-19] |
GSE218195 |
Contribution of 6mer seed toxicity to HIV-1 induced cytotoxicity |
|
Relations |
BioSample |
SAMN31769810 |
SRA |
SRX18292928 |