|
Status |
Public on Jun 07, 2023 |
Title |
H1_KO_2 |
Sample type |
SRA |
|
|
Source name |
H1 hESC
|
Organism |
Homo sapiens |
Characteristics |
cell line: H1 hESC genotype: WT treatment: UBR5 siRNA
|
Growth protocol |
HEK 293T cells were maintained in DMEM/GlutaMAX + 10% FBS in humidified atmosphere with 5% CO2 at 37C
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was harvested using the Macherey-Nagel NucleoSpin Mini Kit RNA libraries for RNA-seq were prepared by Novogene
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
Mapping to reference was performed with hisat2 (Version 2.0.5) using default parameters Quantification was performed with featureCounts (Version 1.5.0-p3) Differential analysis was performed using DESeq2 (Version 1.20.0) and edgeR (Version 0.22.0) Assembly: GRCm38/mm10 Supplementary files format and content: Tab-delimited text file includes FPKM values for each Sample
|
|
|
Submission date |
Jun 05, 2023 |
Last update date |
Jun 07, 2023 |
Contact name |
Michael Rapé |
E-mail(s) |
mrape@berkeley.edu
|
Organization name |
University of California Berkeley
|
Department |
Molecular and Cell Biology
|
Street address |
330F Li Ka Shing Center
|
City |
Berkeley |
State/province |
CA |
ZIP/Postal code |
94720 |
Country |
USA |
|
|
Platform ID |
GPL24676 |
Series (1) |
GSE234200 |
Orphan quality control shapes network dynamics and gene expression |
|
Relations |
BioSample |
SAMN35639515 |
SRA |
SRX20599677 |