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| Status |
Public on Jun 13, 2016 |
| Title |
FUS RIP 3 |
| Sample type |
SRA |
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| Source name |
neuroblastoma cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell type: neuroblastoma cell line
cell line: SH-SY5Y
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| 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.
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Aug 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Oliver Muehlemann |
| Organization name |
University of Bern
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| Street address |
Freiestrasse 6
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| City |
Bern |
| ZIP/Postal code |
3012 |
| Country |
Switzerland |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE71812 |
FUS KO mRNA sequencing and anti-FUS RNA immunoprecipitation sequencing |
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| Relations |
| SRA |
SRX1135840 |
| BioSample |
SAMN03979388 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1846259_RIP3_rawCounts.txt.gz |
183.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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