|
| Status |
Public on Apr 27, 2023 |
| Title |
MGD1551F |
| Sample type |
SRA |
| |
|
| Source name |
Patient-Derived
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Patient-Derived
cell type: Fibroblast
genotype: Control
|
| Growth protocol |
Patient- derived fibroblast cell lines were grown in DMEM (Gibco™, #11-995-073), 10% FBS, 1% Non-essential Amino Acid (100X, Gibco™, 11140-050) and 1% PenStrep at 37℃ in 5% CO2 incubators.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy Plus Mini Kit (Qiagen, #74136). 1ug of. NA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QIAseq FastSelect −rRNA HMR (Qiagen, #334386) and lllumina Truseq® Stranded Total RNA Library Prep Gold (Illumina, 20020599)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Arboleda Lab Pipeline
Samples were demultiplexed after sequencing.
Raw reads were then aligned against the Gencode human genome version hg38 (GR38) version 31 using STAR 2.7.0e with default parameters.
Gene counts from raw reads were generated using featureCounts 1.6.5 from the Subread package. Only reads that uniquely mapped to exons of a gene were counted per gene. Differential expression analysis was completed using DESeq2 v1.24.0, adjusting for sample gender.
Assembly: GR38
Supplementary files format and content: Text files include raw count values for each sample, csv files include DESeq normalized counts per sample
|
| |
|
| Submission date |
Apr 26, 2023 |
| Last update date |
Apr 27, 2023 |
| Contact name |
Valerie Arboleda |
| E-mail(s) |
VArboleda@mednet.ucla.edu
|
| Organization name |
UCLA
|
| Street address |
615 Charles E. Young Drive South
|
| City |
Los Angeles |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE230686 |
Multi-omics of Bohring-Opitz syndrome truncating ASXL1 mutations identify canonical and non-canonical Wnt signaling dysregulation [RNA-seq Fibro] |
| GSE230696 |
Multi-omics of Bohring-Opitz syndrome truncating ASXL1 mutations identify canonical and non-canonical Wnt signaling dysregulation |
|
| Relations |
| BioSample |
SAMN34386303 |
| SRA |
SRX20111133 |
