Transcriptomics

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Expression study of the Hodgkin’s lymphoma cell line L-1236 upon CRISPR Cas9-mediated knockout of lymphotoxin alpha (LTA) compared to control


ABSTRACT: Persistent activation of canonical and non-canonical NF-κB pathways is a hallmark of the malignant Hodgkin and Reed-Sternberg cells in classical Hodgkin lymphoma (cHL). We identified lymphotoxin alpha (LTA), which is secreted by the cHL cell line L-1236 in high concentrations. This cytokine contributes to the constitutive activation of the canonical and non-canonical NF-κB pathways. L-1236 cells were purchased from the DSMZ (Braunschweig, Germany) and cultured in RPMI (Gibco) with 10% heat-inactivated fetal calf serum (FCS; Gibco). Cells were transducted with the lentiCRIPSPR v2 vector containing gRNAs which target the second (g2) and the fourth exon (g3) of LTA. Following single cell clonal selection, L-1236 control cells (v2) and two LTA knockout (KO) clones g2_1 and g3_4 were cultured in normal culture medium for 72 h. The RNA was extracted using the RNeasy kit (Qiagen) according to manufacturer’s instructions. Preparation of cDNA, fragmentation and labeling was performed with the GeneChIPTM WT PLUS reagent kit (ThermoFisher Scientific). Samples were hybridized to the human Clariom™ S Assay (ThermoFisher Scientific).

ORGANISM(S): Homo sapiens  

DISEASE(S): Hodgkins Lymphoma

SUBMITTER: Claus Scheidereit   Eva Kaergel  

PROVIDER: E-MTAB-6896 | ArrayExpress | 2019-01-24

REPOSITORIES: ArrayExpress

Dataset's files

Source:
Action DRS
E-MTAB-6896.idf.txt Idf
E-MTAB-6896.idf.txt_original Idf
E-MTAB-6896.processed.1.zip Processed
E-MTAB-6896.raw.1.zip Raw
E-MTAB-6896.sdrf.txt Txt
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Publications


Persistent NF-κB activation is a hallmark of the malignant Hodgkin/Reed-Sternberg (HRS) cells in classical Hodgkin lymphoma (cHL). Genomic lesions, Epstein-Barr virus infection, soluble factors, and tumor-microenvironment interactions contribute to this activation. Here, in an unbiased approach to identify the cHL cell-secreted key factors for NF-κB activation, we have dissected the secretome of cultured cHL cells by chromatography and subsequent mass spectrometry. We identified lymphotoxin-α (L  ...[more]

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