|
| Status |
Public on Nov 20, 2018 |
| Title |
eCtrl_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SH-SY5Y
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
cell line: SH-SY5Y
cell type: neuroblastoma
genotype: empty control vector
differentiation day: 3day differentiation
|
| Treatment protocol |
Differentiation medium: Neurobasal®-A medium supplemented with 1x GlutaMAX, 1x B-27 supplement (all Life Technologies), 10µM RA, 2mM cAMP (both Sigma Aldrich), 50ng/ml hBDNF (Immunotools), 1% Penicillin/Streptomycin (PAA) and 20mM KCl.
|
| Growth protocol |
WT, del268T, ins395A and eCtrl were seeded with a density of 2x10^4 cells/cm2 and harvested after 3 days of differentiation without media changes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA of three biological replicates was extracted using the GeneJet RNA Purification Kit (Thermo Fisher Scientific) including DNase treatment. RNA integrity number (RIN) was analyzed using the LabChip GX system and only samples with RINs above 9.7 underwent further analysis.
MACE-Seq libraries were prepared by GenXPro GmbH Frankfurt am Main, Germany, using the “MACE-Seq Kit” and the provided software tool (http://tools.genxpro.net). Briefly, mRNA was captured by modified poly-T primers, cDNA was generated and fragmented to an average size of 350 bps. Adapters were ligated and the 3’ Ends amplified by PCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
leer_2b
Protocol: MACE-seq
|
| Data processing |
Sequencing on Illumina NextSeq 500, basecalling pipeline: bcl2fastq2 Conversion Software v2.19
Sequences were cleaned from duplicates (TrueQuant/UMI), bases with low sequencing quality and sequencing adapters were removed
The trimmed reads were mapped to ENSEMBL genome version Homo_sapiens.GRCh38.89 using Bowtie 2 version 2.2.4 with standard parameters
Expression analysis was performed by in-house scripts and DESeq2 (R package)
Genome_build: Homo_sapiens.GRCh38.89
Supplementary_files_format_and_content: csv with raw read counts
|
| |
|
| Submission date |
Apr 26, 2018 |
| Last update date |
Nov 20, 2018 |
| Contact name |
Denise Haslinger |
| E-mail(s) |
denise.haslinger@kgu.de
|
| Organization name |
University Hospital Frankfurt
|
| Street address |
Theodor-Stern-Kai 7
|
| City |
Frankfurt am Main |
| ZIP/Postal code |
60596 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE113734 |
Loss of the Chr16p11.2 candidate gene QPRT leads to aberrant neuronal differentiation |
|
| Relations |
| BioSample |
SAMN08990369 |
| SRA |
SRX4002035 |
