|
Status |
Public on Feb 24, 2021 |
Title |
ATP8 Dead - Rep 2 [X-2] |
Sample type |
SRA |
|
|
Source name |
ATP8 Dead
|
Organism |
Homo sapiens |
Characteristics |
cell line/type: ARPE-19 treatment: Transfected - WT mtDNA source molecule: total cellular RNA
|
Treatment protocol |
Transfection of plasmid DNA with Lipofectamine 3000 (Thermo Fischer Scientific)
|
Extracted molecule |
polyA RNA |
Extraction protocol |
RNAeasy Mini Kit, Qiagen NEBNext Ultra RNA Library Prep kit, New England Biolabs
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
processed data file: DEADvsNT.xlsx ATP8vsDEAD.xlsx DLOOPvsDEAD.xlsx ARPE19_mtDSB_normalizedCounts.txt ARPE19_mtDSB_rawCounts.txt
|
Data processing |
Read quality check, FASTQC Alignment to reference genome, STAR Transcript quantification, HTSeq Normalization and DE Analysis, DeSeq2 Genome_build: hg19 Supplementary_files_format_and_content: Differentially Expressed genes from DeSeq2, Excel Format. Raw reads count, normalized counts.
|
|
|
Submission date |
Jan 17, 2021 |
Last update date |
Feb 24, 2021 |
Contact name |
Marco Tigano |
E-mail(s) |
marco.tigano@med.nyu.edu
|
Organization name |
NYU Grossman School of Medicine
|
Street address |
540 First Avenue
|
City |
New York City |
ZIP/Postal code |
10016 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE164979 |
Gene expression profile of human ARPE-19 cells subjected to mitochondrial DNA double stranded breaks through expression of mitochondrial TALENs |
|
Relations |
BioSample |
SAMN17367725 |
SRA |
SRX9863240 |