NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2090961 Query DataSets for GSM2090961
Status Public on May 25, 2016
Title HBL1 shOCT2_1196 DOX Treated - 2 days - mAdbID:117932
Sample type RNA
 
Channel 1
Source name HBL1 shOCT2_1196 DOX Treated - 2 days
Organism Homo sapiens
Characteristics cell line: HBL1
cell type: ABC DLBCL cells
disease state: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)
Treatment protocol Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_1196. shRNA expression was induced with 50 ng/mL doxycycline for 2 days.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).
Extracted molecule total RNA
Extraction protocol TRIzol Extraction Protocol
Other: Total RNA was prepared by the TRIzol method (Invitrogen) and purified using RNeasy Mini columns (Qiagen).
Label cy3
Label protocol Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
 
Channel 2
Source name HBL1 shControl DOX Treated - 2 days
Organism Homo sapiens
Characteristics cell line: HBL1
cell type: ABC DLBCL cells
disease state: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)
Treatment protocol Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with 50 ng/mL doxycycline for 2 days.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).
Extracted molecule total RNA
Extraction protocol TRIzol Extraction Protocol
Other: Total RNA was prepared by the TRIzol method (Invitrogen) and purified using RNeasy Mini columns (Qiagen).
Label cy5
Label protocol Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
 
 
Hybridization protocol Agilent Hybridization
Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).
Scan protocol Scan_MicronsPerPixelX: 5
Scan_MicronsPerPixelY: 5
Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888
Agilent Scanning Protocol
Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.
Description mAdb experiment ID: 117932
Data processing Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)
 
Submission date Mar 16, 2016
Last update date May 25, 2016
Contact name Louis M. Staudt
E-mail(s) lstaudt@mail.nih.gov
Phone 301-402-1892
Organization name National Cancer Institute
Department Lymphoid Malignancies Branch
Lab Louis M Staudt
Street address 9000 Rockville Pike, Bldg 10, Rm 4N114
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL4133
Series (2)
GSE79292 Regulation of normal B cell differentiation and malignant B cell survival by OCT2 (expression)
GSE79482 Regulation of normal B cell differentiation and malignant B cell survival by OCT2

Data table header descriptions
ID_REF Agilent ID
VALUE normalized log10 ratio (Cy5/Cy3)
rProcessedSignal Red Channel Signal
gProcessedSignal Green Channel Signal
PValueLogRatio significance level of the log ratio

Data table
ID_REF VALUE rProcessedSignal gProcessedSignal PValueLogRatio
1 0.132 43176.66 31832.14 0.034443653
2 -0.080 11.3198 13.59467 0.77886869
3 0.132 9.620506 7.096079 0.7539135
4 -0.018 8.57653 8.934622 0.9648958
5 -0.307 5.383361 10.92023 0.49862521
6 -0.217 8.98797 14.8209 0.48583172
7 -0.102 8.974002 11.3387 0.77736985
8 -0.390 5.46611 13.40897 0.34429138
9 -0.156 10.48245 15.00424 0.59687348
10 -0.088 10.63821 13.01659 0.78105515
11 -0.116 12.55961 16.42011 0.65692735
12 -0.087 31.1966 38.15228 0.48062287
13 0.090 34.87616 28.35565 0.50024952
14 -0.080 194.6613 233.926 0.21471898
15 -0.204 38.07089 60.9183 0.042030962
16 0.115 11479.69 8817.702 0.065922707
17 -0.073 15.038 17.80965 0.75553722
18 0.022 194.9349 185.2163 0.73106037
19 0.019 107782.3 103214 0.7595129
20 -0.372 12.21341 28.75348 0.071331784

Total number of rows: 45015

Table truncated, full table size 1727 Kbytes.




Supplementary file Size Download File type/resource
GSM2090961_117932.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap