|
| Status |
Public on May 22, 2023 |
| Title |
shNTC1_1 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
cell line: IMR-90
cell type: Human lung fibroblasts cell line
genotype: Non-target control
treatment: non-targeting shRNA control (NTC) HRAS G12V-induced senescent IMR90 cells
|
| Treatment protocol |
non-target control, and shTHBD knock down in IMR-90 cells,shTHBD knock down in Palbocilcib-induced senescent Huh7 cells
|
| Growth protocol |
IMR-90 cells were cultured in Eagle’s Minimum Essential Medium (EMEM) supplemented with 10% FBS, 1X glutamine, 1X non-essential amino acids (NEAA), 1X sodium pyruvate, and 1X penicillin streptomycin. To establish replicative senescence, IMR90 cells were passaged for 90 days. Huh7 cells were cultured Dulbecco’s modified eagle medium (DMEM) supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using an RNAeasy kit (Qiagen) and dissolved in RNase-free water. RNA samples were sequenced by Novogene Corporation. In brief, RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using a NanoPhotometer Spectrophotometer (IMPLEN). RNA integrity and quantity were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies).
Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Clustering of index-coded samples was performed on an Illumina NovaSeq sequencer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
non-targeting shRNA control
Chris_THBD_featurecount_matrix.txt
|
| Data processing |
RNA-seq data were processed using the fastp toolkit to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads with default parameter. Only reads that were ≥20nt after trimming were kept for further analysis.
Reads were mapped to human genome reference combining the GRCh38. STAR software was used to align reads to reference genome. Reads were kept for subsequent analysis if they mapped to a single genomic location. Gene counts were measured using the featureCounts.
Assembly: GRCh38
Supplementary files format and content: Chris_THBD_featurecount_matrix.txt: Reads mapped to human GRCh38, featurecount was used to count reads per gene per sample, tab-delimited txt file
Supplementary files format and content: Chris_Palbo_featurecount_matrix.txt: Reads mapped to human GRCh38, featurecount was used to count reads per gene per sample, tab-delimited txt file
|
| |
|
| Submission date |
Apr 04, 2023 |
| Last update date |
May 22, 2023 |
| Contact name |
Liuyang Wang |
| Organization name |
Duke University
|
| Street address |
213 Research Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE228941 |
Antagonizing the irreversible thrombomodulin-initiated proteolytic signaling alleviates age-related liver fibrosis via senescent cell killing |
|
| Relations |
| BioSample |
SAMN34069155 |
| SRA |
SRX19866503 |
