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Sample GSM2410330 Query DataSets for GSM2410330
Status Public on Nov 30, 2016
Title SK-N-SH_EBF3_P177L_2
Sample type SRA
Source name SK-N-SH, p.P177L EBF3
Organism Homo sapiens
Characteristics cell line: SK-N-SH (ATCC HTB-11)
stable expression: p.P177L EBF3
Treatment protocol 5 ug of EBF3-WT or EBF3-P177L vector per 1x10e6 cells were transfected into SK-N-SH cell using Nucleofection (Lonza) kit V using manufacturer's instructions. Cells were selected with 400 ug/mL G418 (Invitrogen, 10131035) for two weeks and then with 200 ug/mL for a further 2-3 weeks to generate SK-N-SH cells with stable EBF3-3xFlag expression.
Growth protocol SK-N-SH (ATCC HTB-11) cells were obtained from ATCC and grown under recommended growth conditions.
Extracted molecule total RNA
Extraction protocol Total RNA was harvested using the Norgen Total RNA Preparation Kit (Norgen Biotek). cDNA was prepared using the ThemoFisher High-Capacity RNA-to-cDNA Kit (ThermoFisher).
RNA-seq was performed as previously described (Gertz et al. 2012).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description PolyA RNA
SK-N-SH EBF3 p.P177L transfected RNA-Seq.
Processed data file: SK-N-SH_EBF3_RNA-Seq_Count_Table.txt
Data processing RNA-seq paired-end FASTQ files were aligned to hg19 using STAR 2.5.
RNA-seq counts were merged into a single count table and filtered to remove any gene with no counts in any sample.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: SK-N-SH_EBF3_RNA-Seq_Count_Table.txt: Tab-delimited text file containing raw read counts for all genes with at least one read in any sample.
Submission date Nov 29, 2016
Last update date May 15, 2019
Contact name Richard M Myers
Organization name HudsonAlpha Institute for Biotechnology
Street address 601 Genome Way
City Huntsville
State/province AL
ZIP/Postal code 35806
Country USA
Platform ID GPL16791
Series (1)
GSE90682 Mutations in EBF3 disturb transcriptional profiles and cause intellectual disability, ataxia and facial dysmorphism
BioSample SAMN06074274
SRA SRX2382342

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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