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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 19, 2019 |
| Title |
SH-SY-Y5_S2_R1_001 |
| Sample type |
SRA |
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| Source name |
human neuroblastoma
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SH-SY-Y5
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| Treatment protocol |
n/a
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| Growth protocol |
n/a
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cell line samples were stabilized in RNAlater (Qiagen, Germany) and stored at room temperature. RNA extraction was performed immediately before the preparation of sequencing libraries using QIAGEN RNeasy Kit (Qiagen) or Direct-zol RNA MiniPrep (Zymo Research, USA), followed by an additional purification step by TRI Reagent (MRC, USA) for cell lines in RNAlater and RecoverAll Total Nucleic Acid Isolation Kit (Invitrogen, USA) for FFPE, according to the manufacturers’ protocols. RNA was quantified using Nanodrop (Thermo Fisher Scientific, USA), ethanol-precipitated, and stored in liquid nitrogen until sequencing.
RNA Integrity Number (RIN) was measured using Agilent 2100 bioanalyzer (Agilent, USA). Agilent RNA 6000 Nano or Qubit RNA Assay (Thermo Fisher Scientific) kits were used to measure RNA concentration. KAPA RNA Hyper with RiboErase Kit (KAPA Biosystems, USA) was used for further depletion of ribosomal RNA and library preparation. Different adaptors were used for multiplexing samples in one sequencing run. Library concentration and quality were measured using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and Agilent TapeStation system (Agilent). Single-end RNA sequencing was performed using Illumina HiSeq 3000 system (Illumina, USA), 50 bp read length, for approx. 30 million raw reads per sample. Data quality check was conducted using Illumina SAV. De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 software.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Runing STAR aligner in "Gene_counts" mode
Merging STAR output ("ReadPerGene.out" files) with Python into a single table
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw gene counts for each sample
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| Submission date |
Dec 18, 2019 |
| Last update date |
Mar 25, 2020 |
| Contact name |
Maria Vladimirovna Suntsova |
| E-mail(s) |
suntsova86@mail.ru
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| Phone |
+79261076626
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| Fax |
+7 (495) 330-65-38
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| Organization name |
M.M. Shemyakin and Yu.A. Ovchinnikov Institute of bioorganic chemistry of the Russian Academy of Sciences
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| Department |
Department of Genetics and Postgenomic Technologies
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| Lab |
Group for Genomic Regulation of Cell Signaling Systems
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| Street address |
Miklukho-Maklaya, 16/10
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| City |
Moscow |
| ZIP/Postal code |
117997 |
| Country |
Russia |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE142293 |
NGS based identification of GD2-positive tumor-specific phenotype for cancer diagnostics and therapy |
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| Relations |
| BioSample |
SAMN13624648 |
| SRA |
SRX7410057 |
| 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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