Table 1 List of accessions. For the ENCODE RNA-seq libraries, the control and target depletion samples are listed under separate accessions
From: Quantitative analysis of cryptic splicing associated with TDP-43 depletion
Assay | Accession Code | Downloaded from | Target | Cell-Tissue | Pubmed ID |
|---|---|---|---|---|---|
RNA-seq | PRJNA282887 | ncbi.nlm.nih.gov/sra | TDP-43 | Mouse ES | 26250685 |
RNA-seq | PRJNA282692 | ncbi.nlm.nih.gov/sra | TDP-43 | Human Hela | 26250685 |
RNA seq | PRJNA127211 | ncbi.nlm.nih.gov/sra | TDP-43 | Mouse ES | 20660762 |
RNA-seq | PRJNA141971 | ncbi.nlm.nih.gov/sra | TDP-43 | Mouse adult brain | 21358643 |
RNA-seq | ENCSR129RWD | encodeproject.com | control | K562 mRNA | NA |
RNA-seq | ENCSR134JRE | encodeproject.com | TDP-43 | K562 mRNA | NA |
RNA-seq | ENCSR372DZW | encodeproject.com | control | K562 total RNA | NA |
RNA seq | ENCSR455TNF | encodeproject.com | TDP-43 | K562 total RNA | NA |
RNA-seq | PRJNA174534 | ncbi.nlm.nih.gov/sra | FUS | Mouse adult brain | 23023293 |
RNA-seq | ENCSR084SCN | encodeproject.com | control | K562 mRNA | NA |
RNA-seq | ENCSR32500M | encodeproject.com | FUS | K562 mRNA | NA |
RNA-seq | PRJEB3048 | ncbi.nlm.nih.gov/sra | hnRNP C | HeLa | 23374342 |
iCLIP | 20100222_LUjt3 | icount.biolab.si | TDP-43 | Mouse embryonic brain 1 | 22934129 |
iCLIP | 20091102_LUjt5 | icount.biolab.si | TDP-43 | Mouse embryonic brain 2 | 22934129 |
iCLIP | 20100222_LUjt3 | icount.biolab.si | TDP-43 | Human neural stem cells | 21358640 |
iCLIP | 20101125_LUjt8 | icount.biolab.si | TDP-43 | Human SH-SY5Y 1 | 21358640 |
iCLIP | 20091102_LUjt5 | icount.biolab.si | TDP-43 | Human SH-SY5Y 2 | 21358640 |
eCLIP | Multiple | encodeproject.com | Multiple | HepG2/K562 | NA |