 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 08, 2016 |
| Title |
SH-SY5Y cell line undifferentiated replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
SH-SY5Y cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 5% FBS
cell line: SH-SY5Y
|
| Treatment protocol |
For neuronal differentiation, we set up a 9 days long paradigm (hereafter referred as RA-NBM treatment) including a 6 days pre-differentiation step in DMEM/HIGH supplemented with 5% FBS and 10 μM all trans Retinoic Acid (RA, Sigma-Aldrich, Milan, Italy) followed by a 3 days differentiation step in neurobasal medium (GIBCO, Life Technologies) enriched with 50 ng ml-1 recombinant human BDNF (rhBDNF, Peprotech, Rocky Hill, NJ, USA), 2 mM dibutyryl-cyclic AMP (db-cAMP, Sigma-Aldrich), 20 mM KCl, B27 and 1% GlutaMAX (both purchased form GIBCO, Life Technologies, Monza, Italy). Control (not treated, NT) cells were grown under basal conditions at low FBS concentration (5%) for comparison with RA-NBM treated cells.
|
| Growth protocol |
Human neuroblastoma SH-SY5Y cells (catalogue number #94030304, purchased by European Collection of Cell Cultures) were cultured in DMEM-High glucose medium (DMEM/HIGH) supplemented with 15% Foetal Bovine Serum (FBS), 2 mM L-glutamine and 1% non-essential aminoacids (all purchased from Euroclone, Pero, Italy) at 37°C and 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were collected in three independent experiments and total RNA was isolated using TRI Reagent.
Indexed directional cDNA libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to manufacturer's instructions. Adapter-ligated cDNA libraries with an insert size of 200-250 bp were size selected on 1.5% agarose gel cassettes using Pippin Prep instrument (Sage Science, Beverly, MA, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
SH-SY5Y_Undiff_3
|
| Data processing |
CASAVA 1.8.2
Reads with more than 10% of undetermined bases or more than 50 bases with a quality score < 7 were discarded
Reads were then clipped from adapter sequences using Scythe software (https://github.com/vsbuffalo/scythe), and low quality ends (Q score < 20 on a 10 nt window) were trimmed with Sickle (https://github.com/vsbuffalo/sickle).
Alignment of reads to reference human genome (hg19) was performed using TopHat 2 (http://tophat.cbcb.umd.edu/)
Normalized expression values expressed as Fragments per Kilobase per Million Mapped Reads (FPKM) for each transcript were calculated using Cufflinks 2 with default parameters (http://cole-trapnell-lab.github.io/cufflinks/) using Ensemble GRCh37 annotation as reference
Genome_build: hg19
Supplementary_files_format_and_content: expression data matrix (expression_matrix.txt) contains expression values expressed as Fragments per Kilobase per Million Mapped Reads (FPKM)
|
| |
|
| Submission date |
Jan 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alberto Ferrarini |
| E-mail(s) |
alberto.ferrarini@univr.it
|
| Phone |
+39-045-802-7058
|
| Organization name |
University of Verona
|
| Department |
Scientific and Technological Department
|
| Lab |
Plant Functional Genomics Centre
|
| Street address |
Strada le Grazie, 15
|
| City |
Verona |
| State/province |
Veneto |
| ZIP/Postal code |
37134 |
| Country |
Italy |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE77383 |
Transcriptomic profiling discloses molecular and cellular events related to neuronal differentiation in SH-SY5Y cells |
|
| Relations |
| BioSample |
SAMN04448170 |
| SRA |
SRX1553127 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
|
|
|
|
 |
