|
| Status |
Public on Apr 09, 2017 |
| Title |
Control B (CSES7, Cas9 No guide) |
| Sample type |
SRA |
| |
|
| Source name |
Human embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
group: Control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using NucleoSpin RNA Plus kit (Macherey-Nageland). For RNA sequencing analysis, poly(A) pull-down was used to enrich mRNAs from total RNA samples (200 ng–1 µg per sample, RIN > 9)
Libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
hESC_RB1.txt
|
| Data processing |
Reads were mapped to the human reference genome (GRCh38/hg38) using Tophat (version 2.0.4)
Human embryonic stem cell expression values were obtained and normalized using HTSeq (Anders et al., 2015) and DESeq2 (Love et al., 2014). Batch-effect removal was performed using SVseq2.
In the teratoma-derived data, fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks (version 2.0.2)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: hESC data: Tab-delimited text file includes FPKM values for each sample; Teratoma data: Tab-delimited text file includes relative expression values for each sample
|
| |
|
| Submission date |
Jul 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yishai Avior |
| Phone |
+972-2-6584803
|
| Organization name |
Hebrew University of Jeursalem
|
| Department |
Genetics
|
| Lab |
Nissim Benvenisty
|
| Street address |
Edmond J. Safra Campus, Givat Ram
|
| City |
Jerusalem |
| State/province |
Israel |
| ZIP/Postal code |
91904 |
| Country |
Israel |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE84504 |
Modeling Trilateral Retinoblastoma using Human Embryonic Stem Cells |
|
| Relations |
| BioSample |
SAMN05413960 |
| SRA |
SRX1958691 |
