|
| Status |
Public on Jul 25, 2022 |
| Title |
HepG2_RNASeq_siHNF4a_1_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HepG2 pSLIK YAPs127a cells transfected with siRNA HNF4a (#1)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Liver
cell line: HepG2
treatment: transfected with siHNF4a_1
|
| Treatment protocol |
Doxycycline 2µg/ml for 48h. siRNA transfection with Lipofectamine RNAi-MAX in antibiotics-free medium according to manufacturer instructions (Life Technologies)
|
| Growth protocol |
RPMI, 10% FBS. Medium renewal: twice per week
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Quick RNA miniprep kit following manufacturer instructions (Zymo Research).
Libraries were prepared with QuantSeq 3‘ mRNA-Seq Library Prep Kit for Illumina (FWD) following manufacturer instructions (Lexogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Assembly: hg19
Supplementary files format and content: differential expression results (DESeq2) and eRPKM after 48h YAP overexpression and after knock-down of HNF4a using two different siRNAs (siHNF4a_1 and 2)
|
| |
|
| Submission date |
Mar 21, 2022 |
| Last update date |
Jul 25, 2022 |
| Contact name |
stefano campaner |
| E-mail(s) |
stefano.campaner@iit.it
|
| Organization name |
fondazione Istituto italiano di tecnologia
|
| Department |
Center for Genomic Science
|
| Lab |
Cancer Biology
|
| Street address |
via adamello 16
|
| City |
milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE138191 |
Genome-wide chromatin analyses and RNA-seq of liver cells upon YAP induction |
| GSE199068 |
Decoding YAP dependent transcription in the liver [HepG2_RNASeq] |
|
| Relations |
| BioSample |
SAMN26850503 |
| SRA |
SRX14531830 |
