|
| Status |
Public on Jan 18, 2024 |
| Title |
OCI_Ly7_shZNF587-417v1_D6_RNA_Rep2_2 |
| Sample type |
SRA |
| |
|
| Source name |
OCI_Ly7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OCI_Ly7
cell type: Diffuse large B cell lymphoma
genotype: ZNF587,ZNF417 knockdown
treatment: Lentiviral transduction
time: Day 6
|
| Treatment protocol |
Lentiviral transduction
|
| Growth protocol |
U2932 = RPMI 1640 + 10% FCS + 1% Pen-Strep / OCI-Ly7 = IMDM + 20% FCS + 1% Pen-Strep
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA extraction was performed using the NucleoSpin RNA plus kit (Machery-Nagel) according to the manufacturer’s recommendations. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
OCI_Ly7_U2932_D6_RNA.tab
OCI_Ly7_U2932_D6_RNA_TEs.tab
|
| Data processing |
RNA-seq reads were mapped to the hg19 using hisat v2.1.0
Mapped reads were filtered for uniquely mapping reads (MAPQ > 10)
Read counts on genes and repetitive sequence integrants was performed with featureCounts v2
Assembly: hg19
Supplementary files format and content: OCI_Ly7_U2932_D6_RNA.tab: coma-separated table containing raw read counts on genes
Supplementary files format and content: OCI_Ly7_U2932_D6_RNA_TEs.tab: coma-separated table containing raw read counts on TEs
|
| |
|
| Submission date |
Apr 12, 2023 |
| Last update date |
Jan 18, 2024 |
| Contact name |
Filipe Martins |
| E-mail(s) |
[email protected]
|
| Organization name |
Epfl
|
| Street address |
Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE229468 |
KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation [RNA_D6] |
| GSE229471 |
KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation. |
|
| Relations |
| SRA |
SRX19940407 |
| BioSample |
SAMN34154175 |
