|
Status |
Public on Jul 25, 2022 |
Title |
HepG2_RNASeq_NT_rep2 |
Sample type |
SRA |
|
|
Source name |
HepG2 pSLIK YAPs127a cells
|
Organism |
Homo sapiens |
Characteristics |
tissue: Liver cell line: HepG2 treatment: not treated
|
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)
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|
|
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)
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|
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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 |
SAMN26850511 |
SRA |
SRX14531822 |