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Sample GSM6736332 Query DataSets for GSM6736332
Status Public on Jun 07, 2023
Title Jurkat.parental.UT.rep2
Sample type SRA
 
Source name Jurkat wt uninfected cells
Organism Homo sapiens
Characteristics biomaterial provider: ATCC
cell line: Jurkat
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
 
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)
GSE218192 Contribution of 6mer seed toxicity to HIV-1 induced cytotoxicity (DISE-45)
GSE218195 Contribution of 6mer seed toxicity to HIV-1 induced cytotoxicity
Relations
BioSample SAMN31769908
SRA SRX18292991

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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