|
| Status |
Public on Apr 19, 2019 |
| Title |
OCI-Ly1 + sc siRNA rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
OCI-Ly1 + scramble siRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OCI-Ly1
cell type: Diffuse large B-cell lymphoma (DLBCL) cell line
sirna: Scramble Control
|
| Treatment protocol |
Two different sequences targeting the 3’UTR region of hFOXP1 were used (siFOXP1#1: 5’-CAACTTAGCCAGCGCAATA-3’ and siFOXP1#2: 5’-GCCAAGGCCTTCTGACAATT-3’) to effectively knock-down FOXP1 expression in OCI-Ly10 compared to scramble siRNA. All siRNAs were transiently transfected into cells by nucleofection with Amaxa (Lonza) and harvested 48h later for RNA extraction and transcriptional analysis. Data collected from three replicates of each siRNA was averaged and normalized to the siRNA control group.
|
| Growth protocol |
Human DLBCL OCI-Ly1 cells were grown in IMDM media containing 20% of human serum, 50microM Beta-mercaptoethanol and 2% penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from sorted cells using TRIzol (Invitrogen) as described in manufacturer´s protocol and quality control of extracted RNA was measured using Agilent Bioanalyzer.
|
| Label |
Cy5
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Channel 2 |
| Source name |
Untransfected reference OCI-Ly1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OCI-Ly1
cell type: Diffuse large B-cell lymphoma (DLBCL) cell line
sirna: None
|
| Treatment protocol |
Two different sequences targeting the 3’UTR region of hFOXP1 were used (siFOXP1#1: 5’-CAACTTAGCCAGCGCAATA-3’ and siFOXP1#2: 5’-GCCAAGGCCTTCTGACAATT-3’) to effectively knock-down FOXP1 expression in OCI-Ly10 compared to scramble siRNA. All siRNAs were transiently transfected into cells by nucleofection with Amaxa (Lonza) and harvested 48h later for RNA extraction and transcriptional analysis. Data collected from three replicates of each siRNA was averaged and normalized to the siRNA control group.
|
| Growth protocol |
Human DLBCL OCI-Ly1 cells were grown in IMDM media containing 20% of human serum, 50microM Beta-mercaptoethanol and 2% penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from sorted cells using TRIzol (Invitrogen) as described in manufacturer´s protocol and quality control of extracted RNA was measured using Agilent Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
sc_rep2
|
| Data processing |
For analysis of microarray expression data, R and Bioconductor were used to perform preprocessing (quality control and extraction of intensity data from NimbleScan files) and log2 transformation of two-color array intensity signals, background correction, estimation of relative expression as log-Ratios, average between biological replicates, subtraction of averages from the negative (scramble siRNA) control and comparative t-tests.
|
| |
|
| Submission date |
Jun 26, 2018 |
| Last update date |
Apr 19, 2019 |
| Contact name |
SERGIO ROA |
| E-mail(s) |
sroa@unav.es
|
| Organization name |
University of Navarra
|
| Department |
Biochemistry and Genetics
|
| Lab |
Immunogenetics lab
|
| Street address |
Irunlarrea, 1
|
| City |
Pamplona |
| ZIP/Postal code |
31008 |
| Country |
Spain |
| |
|
| Platform ID |
GPL15088 |
| Series (2) |
| GSE116289 |
Transcriptional profiling of human OCI-Ly1 DLBCL cells after siRNA-mediated silencing of FOXP1 [array] |
| GSE116290 |
PD-1/PD-L1 immune checkpoint and p53 loss facilitate tumor progression in activated B cell diffuse large B-cell lymphomas |
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