|
Status |
Public on Jan 18, 2024 |
Title |
OCI_Ly7_shZNF587-417v1_D6_RNA_Rep2_1 |
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.
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|
|
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
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|
|
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 |
SRX19940406 |
BioSample |
SAMN34154176 |