GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2024998 Query DataSets for GSM2024998
Status Public on Jun 13, 2016
Title A5_4
Sample type SRA
Source name RNA from SH-SY5Y FUS KO cells. A5 clone.
Organism Homo sapiens
Characteristics cell type: neuroblastoma cell line
cell line: SH-SY5Y
Treatment protocol Three wells of a six well plate containing 80 % confluent SH-SY5Y neuroblastoma cells were each transfected with 2.7 μg FUS knockout ZeoR matrix (GeneArt, Life Technologies) and 1.3 μg of plasmid coding for the Cas9 endonuclease and the guide RNAs which target the first intron of FUS
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from biological replicates.
PolyA transcripts were selected. Stranded Illumina library kit was employed.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Description RNA from SH-SY5Y FUS KO cells. A5 clone.
Data processing Mapping: TopHat v2.0.9
Counting: HTSeq-count, –r name –s reverse –a 0 –m union
Genome_build: GRCh38.81
Supplementary_files_format_and_content: Counts: Ensembl gene id, reads count
Submission date Dec 31, 2015
Last update date May 15, 2019
Contact name Oliver Muehlemann
Organization name University of Bern
Street address Freiestrasse 6
City Bern
ZIP/Postal code 3012
Country Switzerland
Platform ID GPL21290
Series (1)
GSE71812 FUS KO mRNA sequencing and anti-FUS RNA immunoprecipitation sequencing
BioSample SAMN04378681
SRA SRX1510920

Supplementary file Size Download File type/resource
GSM2024998_A5_4_counts.txt.gz 222.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap