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| Status |
Public on Feb 17, 2025 |
| Title |
3K M17D cells, transfection with siRNA against TAX1BP1, day 2 post-transfection, biological replicate 1 |
| Sample type |
SRA |
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| Source name |
3K M17D
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| Organism |
Homo sapiens |
| Characteristics |
cell line: 3K M17D
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| Extracted molecule |
total RNA |
| Extraction protocol |
PureLink RNA mini kit (Thermofisher)
NEB Next Ultra RNA library prep
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
TAX1BP1-R1
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| Data processing |
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the groups of samples was performed.
Assembly: GRCh38/hg38
Supplementary files format and content: csv file including TPM values for all samples
Supplementary files format and content: csv file including raw counts for all samples
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| Submission date |
Aug 29, 2024 |
| Last update date |
Feb 17, 2025 |
| Contact name |
Eleanna Kara |
| E-mail(s) |
ek851@rwjms.rutgers.edu
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| Organization name |
Rutgers University
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| Street address |
683 Hoes Lane West
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| City |
Piscataway |
| State/province |
New Jersey |
| ZIP/Postal code |
08901 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE276032 |
Increased burden of rare risk variants across gene expression networks predisposes to sporadic Parkinson’s disease |
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| Relations |
| BioSample |
SAMN43413634 |
| SRA |
SRX25905336 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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