|
| Status |
Public on Dec 12, 2022 |
| Title |
HeLa_RNA_Ctr_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa Kyoto
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa Kyoto
cell type: cancer cell
genotype: WT
treatment: siRNA pool Control
|
| Treatment protocol |
si mediated knock down of HMG20A
|
| Growth protocol |
DMEM + 10% FCS
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were transfected (Oligofectamine) with siRNA pools against HMG20A RNA /unspecifc control (Dharmacon). 72 hours post transfection total RNA was harvested using Rneasy mini columns with on-column Dnase digestion (QUIAGEN)
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
RNA-seq
|
| Data processing |
Paired end raw FASTQ files were quality and adaptor trimmed using trimGalore v.1.18
Alignment of the trimmed FASTQ files against the hg19 for HeLa data was performed using hisat2 v.2.2.1 with “--min-intronlen 30 --max-intronlen 3000” parameters
Based on the BAM files and the human hg19 GTF read counts per gene for each sample were calculated using the summarizedOverlaps function of the GenomicAlignments R package
The resulting read counts were normalized using DESeq2 v.1.28.1.
DESeq2 was used for the identification of differentially expressed genes
Assembly: hg19
Supplementary files format and content: CSV of raw sequencing counts per gene
|
| |
|
| Submission date |
May 04, 2022 |
| Last update date |
Dec 12, 2022 |
| Contact name |
Marek Bartkuhn |
| E-mail(s) |
marek.bartkuhn@gen.bio.uni-giessen.de
|
| Organization name |
Justus-Liebig-University Giessen
|
| Department |
Biomedical Informatics and Systems Medicine
|
| Street address |
Aulweg 132
|
| City |
Giessen |
| State/province |
Hessen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE202197 |
The H2A.Z.1/PWWP2A/NuRD-associated protein HMG20A controls early head and heart developmental transcription programs [HeLa_RNA_AH] |
| GSE202199 |
The H2A.Z.1/PWWP2A/NuRD-associated protein HMG20A controls early head and heart developmental transcription programs |
|
| Relations |
| BioSample |
SAMN28088263 |
| SRA |
SRX15148492 |
