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Sample GSM1846257 Query DataSets for GSM1846257
Status Public on Jun 13, 2016
Title FUS RIP 1
Sample type SRA
 
Source name neuroblastoma cell line
Organism Homo sapiens
Characteristics cell type: neuroblastoma cell line
cell line: SH-SY5Y
Extracted molecule total RNA
Extraction protocol Total extracts from SH-SY5Y cells were prepared and subjected to FUS-Immunoprecpitation. After subsequent washes of the beads RNA was eluted with TRIreagent.
Subsequently, RNA was isolated, strand specific paired-end RNA libraries were prepared and sequenced on the Illumina HiSeq2000 platform.
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing Base calling: Casava 1.8.2
Mapping: TopHat with default options against GRCh37, aided by Ensembl transcriptome gtf file (GRCh37.75)
Counting: HTSeq -s reverse -a 0 -m union
Genome_build: GRCh37
Supplementary_files_format_and_content: raw counts
 
Submission date Aug 06, 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 GPL11154
Series (1)
GSE71812 FUS KO mRNA sequencing and anti-FUS RNA immunoprecipitation sequencing
Relations
SRA SRX1135838
BioSample SAMN03979386

Supplementary file Size Download File type/resource
GSM1846257_RIP1_rawCounts.txt.gz 183.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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