|
| 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 |
|
| Relations |
| BioSample |
SAMN04378681 |
| SRA |
SRX1510920 |
