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| Status |
Public on Apr 09, 2017 |
| Title |
RB1-/- B-derived Teratoma (2) |
| Sample type |
SRA |
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| Source name |
Teratoma
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| Organism |
Homo sapiens |
| Characteristics |
group: RB1-null
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Teratoma_RB1.txt
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| 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
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| Submission date |
Jul 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yishai Avior |
| Phone |
+972-2-6584803
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| Organization name |
Hebrew University of Jeursalem
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| Department |
Genetics
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| Lab |
Nissim Benvenisty
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| Street address |
Edmond J. Safra Campus, Givat Ram
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| City |
Jerusalem |
| State/province |
Israel |
| ZIP/Postal code |
91904 |
| Country |
Israel |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE84504 |
Modeling Trilateral Retinoblastoma using Human Embryonic Stem Cells |
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| Relations |
| BioSample |
SAMN05413968 |
| SRA |
SRX1958699 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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