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Sample GSM2221113 Query DataSets for GSM2221113
Status Public on Oct 01, 2016
Title Wild-type_integrase_HepG2_DNA_rep1
Sample type SRA
Source name hepatocellular carcinoma cell line
Organism Homo sapiens
Characteristics cell line: HepG2
cell type: hepatocellular carcinoma cell line
Treatment protocol For the lentiMPRA, 2.4 million HepG2 cells were plated on a 10 cm dish and cultured for 24 hours. The cells were infected with integrating or non-integrating lentivirus libraries along with 8 ug/ml polybrene, and incubated for 4 and 3 days, when they have an estimated 50 and 100 viral particles/cell, respectively. Three independent replicate cultures were infected.
Growth protocol HepG2 cells (ATCC) were maintained in DMEM supplemented with 10% FCS, glutamine (2 mM), penicillin (100 U/ml) and streptomycin (50 μg/ml)
Extracted molecule genomic DNA
Extraction protocol The cells were washed with PBS three times, and genomic DNA and total RNA was extracted using AllPrep DNA/RNA mini kit (Qiagen). Messenger RNA (mRNA) was purified from the total RNA using Oligotex mRNA mini kit (Qiagen) and treated with Turbo DNase to remove contaminating DNA.
For each RNA replicate, 3x500ng was reverse transcribed with SuperscriptII (Invitrogen 18064-014) using a primer downstream of the barcode, which contained a sample index and a P7 Illumina adaptor sequence. The resulting cDNA was pooled and split into 24 reactions, amplified with Kapa Robust polymerase for 3 cycles using this same reverse primer paired with a forward primer complementary to the 3’ end of EGFP with a P5 adaptor sequence (BARCODE_lentiF_v4.1, Table S3). The implemented two-round PCR set-up is supposed to reduce PCR jack-potting effects and allows for incorporating unique molecular identifiers (UMIs), which could be used to correct for other PCR biases in future experiments. PCR products are then cleaned up with AMPure XP beads (Beckman Coulter) to remove the primers and concentrate the products. These products underwent a second round of amplification in 8 reactions per replicate for 15 cycles, with a reverse primer containing only P7. All reactions were pooled at this point, run on an agarose gel for size-selection, and submitted for sequencing. For the DNA replicates, 16x500ng of each replicate was amplified for 3 cycles just as the RNA. First round products were cleaned up with AMPure XP beads, and amplified for another 16 reactions, each for 20 cycles. Reactions were pooled, gel-purified, and sequenced.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Description Targeted barcode amplification from DNA
Data processing Library strategy: lentivirus-based massively parallel reporter assay (lentiMPRA)
Libraries were sequenced on MiSeq or NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis softwarre. Multiplexed paired end (PE) Illumina sequencing data was split based on sample barcodes allowing up to one substitution in the barcode sequence.
Paired-end reads shorter or equal to read length were consensus called and adapter trimmed.
For oligo validation, consensus sequences were aligned to all designed oligo sequences using BWA MEM (Li and Durbin 2009) with parameters penalizing soft-clipping of alignment ends (-L 80). For RNA/DNA counts, sequences were matched against the designed barcode sequences.
To normalize RNA and DNA for different sequencing depths in each sample, we divided reads by the sum of observed counts and reported them as counts per million. Only barcodes observed in RNA and DNA of the same sample were considered.
To determine the RNA/DNA ratios per insert, we summed up the counts of all barcodes contributing and determined the ratio of the average normalized counts.
Genome_build: GRCh37
Supplementary_files_format_and_content: All processed data files are in gzip-compressed tab-separated text file format. DNA.tsv and RNA.tsv files contain assigned RNA and DNA barcode counts. ActivityRatios.tsv is contains RNA/DNA ratios as well as all annotation values explored in the study. ColumnDescriptionActivityRatios.tsv provides a description for the short column labels used in ActivityRatios.tsv. validationExpDesignBarcodes.tsv contains the barcode counts observed in the design validation experiment. liverEnhancer_design.tsv contains all designed oligo sequences.
Submission date Jun 30, 2016
Last update date May 15, 2019
Contact name Jay Shendure
Organization name University of Washington
Department Genome Sciences
Lab Shendure
Street address 3720 15th Ave NE
City Seattle
State/province WA
ZIP/Postal code 98195-5065
Country USA
Platform ID GPL18573
Series (1)
GSE83894 A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity
BioSample SAMN05330274
SRA SRX1888127

Supplementary file Size Download File type/resource
GSM2221113_WT1-DNA.tsv.gz 3.7 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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