|
| Status |
Public on Sep 01, 2022 |
| Title |
sh_WT_2 |
| Sample type |
SRA |
| |
|
| Source name |
mammalian cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
treatment: shLYCHOS + LYCHOS WT
|
| Growth protocol |
Cells were grown in DMEM + 10% FBS, 100 U/mL penicillin, 100 mg/mL streptomycin at 37°C and 5% CO2. Cell were grown for 5days post-lentiviral infection and harvested using RNA lysis buffer from Biorad Aurum total RNA extraction kit.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Biorad Aurum total RNA extraction kit (Cat# 7326820). Libraries were made using NEBNext Ultra II Library prep kit for Illumina (E7770). The construction of sequencing libraries was performed by Novogene Corporation Inc.
RNA libraries were prepared for sequencing using NEBNext Ultra II Library prep kit for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
shLYCHOS + LYCHOS WT_replicate#2
|
| Data processing |
Analysis was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene's wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: Homo sapiens hg19
Supplementary_files_format_and_content: fpkm and read counts
|
| |
|
| Submission date |
Feb 08, 2022 |
| Last update date |
Sep 01, 2022 |
| Contact name |
Roberto Zoncu |
| E-mail(s) |
rzoncu@berkeley.edu
|
| Organization name |
University of California Berkeley
|
| Department |
Molecular Cell Biology
|
| Street address |
Li Ka Shing Center, 1951 Oxford Street, Rm330F
|
| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE196384 |
Genome wide transcriptional change by GPR155/LYCHOS loss |
|
| Relations |
| BioSample |
SAMN25757161 |
| SRA |
SRX14105665 |
