|
| Status |
Public on Jan 08, 2024 |
| Title |
HEK293 cells, nuclear fraction, control, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
sirna: control
fraction: nuclear
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells with Quick-RNA MicroPrep kit (Zymo). Polyadenylated RNA was then isolated using Dynabeads™ mRNA Purification Kit. Purification was done twice to increase purity.
Strand-specific libraries were generated using KAPA Stranded RNA-seq Library Preparation Kit (Roche)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using STAR 2.7.9a
Reads counted on GENCODE release 29 gene models using STAR 2.7.9a
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: hg38
Supplementary files format and content: Two-column tab-delimited text file with gene identifier and raw read count columns
Supplementary files format and content: Raw RNA-seq coverage in bigWig format, separate files for plus and minus strands
|
| |
|
| Submission date |
Oct 05, 2023 |
| Last update date |
Jan 09, 2024 |
| Contact name |
IBRAHIM AVSAR ILIK |
| E-mail(s) |
[email protected]
|
| Organization name |
Max-Planck-Institut für molekulare Genetik
|
| Lab |
OWL Aktas
|
| Street address |
Ihnestraße 63-73
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE223263 |
Autonomous transposons tune their sequences to ensure somatic suppression. |
| GSE244711 |
Autonomous transposons tune their sequences to ensure somatic suppression [totalRNA_HEK293_fractionation] |
|
| Relations |
| BioSample |
SAMN37700740 |
| SRA |
SRX22006751 |
