|
| Status |
Public on Sep 28, 2022 |
| Title |
THAP1+/- SP1-/- SHSY5Y Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
SHSY5Y cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SHSY5Y cells
genotype: THAP1+/-, SP1-/-
|
| Growth protocol |
SH-SY5Y cells were cultured in DMEM medium with 10% FBS and 1% Glutmax at 37℃ in a humidified atmosphere containing 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy mini kit (Qiagen)
Libraries were generated using NEBNext Ultra II Directional RNA library Preparation Kit for Illumina (NEB, #E7760L)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calling performed using Illumina bcl2fastq2 version 2.19.1
Reads qualities of RNA-seq data in fastq files were assessed using QoRTs (v1.2.37) to identify sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification.
Reads were aligned using HISAT2 (v2.2.1) allowing gapped alignments to account for splicing against a custom-built genome composed of the Ensembl Homo Sapiens GRCh37 (hg19) and Alignment quality was analyzed using samtools (v1.12) and visually inspected in the Integrative Genome Viewer (v2.4.19).
Normalized read counts for all genes were obtained using DESeq (V1.22.1).
Genome_build: hg19
Supplementary_files_format_and_content: tabular files counted mapped reads of each gene
|
| |
|
| Submission date |
Oct 19, 2021 |
| Last update date |
Sep 28, 2022 |
| Contact name |
Fubo Cheng |
| E-mail(s) |
fubo.cheng@med.uni-tuebingen.de
|
| Organization name |
University of Tuebingen
|
| Department |
Institute of Medical Genetics and Applied Genomics
|
| Street address |
Calwerstrasse 7
|
| City |
Tuebingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE184958 |
THAP1 is cell type dependent regulator of SP1 family crucial for dystonic syndromes in human and rat [SHSY5Y_RNA-seq] |
| GSE184961 |
THAP1 is cell type dependent regulator of SP1 family crucial for dystonic syndromes in human and rat |
|
| Relations |
| BioSample |
SAMN22405565 |
| SRA |
SRX12685141 |
