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Sample GSM3208204 Query DataSets for GSM3208204
Status Public on Jun 21, 2018
Title HEK293T_rs199643834_EDIT_HET [11_38]
Sample type SRA
Source name HEK293T_rs199643834_EDIT_HET
Organism Homo sapiens
Characteristics cell line: 293T
rs199643834 genotype: ALT/REF/REF
Treatment protocol For transfection with Cas9- and sgRNA-expressing plasmids as well as ssODN template, cells were harvested for seeding at a log growth phase (approximately 70% confluency). In a 6-well format, 300,000 293T cells were seeded a day prior to transfection. The next day 2 μg of each lentiCRISPR v2 plasmid and 0.5 μg of ssODN HDR template were delivered into the cells using Lipofectamine 3000 reagent (ThermoFisher Scientific, cat. # L3000008). At 24-hours post-transfection selective pressure in the form of 5 μg/ml puromycin was applied for 8 hours to enrich for transfected cells. This population was selected for single-cell sorting in 96-well format on SONY SH800 to obtain monoclonal edited cell lines which were genotyped.
Growth protocol Human 293T cell line (ATCC, cat. # CRL-3216) was adapted to and subsequently routinely grown in Opti-MEM/5% CCS (newborn calf serum), 1% GlutaMAX, 1% Penicillin/Streptomycin and sodium pyruvate. Expanded lines were grown to 70-80% confluency before harvesting.
Extracted molecule total RNA
Extraction protocol RNA was isolated using the Qiagen RNAeasyMini kit.
RNA sequencing libraries were prepared using the TruSeq Stranded mRNA Library Sample Preparation Kit in accordance with manufacturer’s instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description 11_38
Data processing Trimmomatic v0.36 was used to clip Illumina adaptors and quality trim.
Reads were aligned to hg19 using STAR in 2 pass mode.
featureCounts v1.5.3 was used in read counting and strand specific mode (-s 2) with primary alignments only to generate gene level read counts with Gencode v19 annotations used in GTEx v6p.
Genome_build: hg19
Supplementary_files_format_and_content: Expression matrix where lines are genes, columns are samples, and the values are the featureCounts read counts.
Submission date Jun 20, 2018
Last update date Jun 22, 2018
Contact name Stephane Emile Castel
Organization name New York Genome Center
Lab Lappalainen
Street address 101 Avenue of the Americas
City New York
State/province NY
ZIP/Postal code 10013
Country USA
Platform ID GPL24676
Series (1)
GSE116061 Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk
BioSample SAMN09461950
SRA SRX4277125

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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