NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2090960 Query DataSets for GSM2090960
Status Public on May 25, 2016
Title HBL1 shOCT2_3410 DOX Treated - 1 day - mAdbID:117931
Sample type RNA
 
Channel 1
Source name HBL1 shOCT2_3410 DOX Treated - 1 day
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: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_3410. shRNA expression was induced with 50 ng/mL doxycycline for 1 day.
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 - 1 day
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: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with 50 ng/mL doxycycline for 1 day.
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: 117931
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 0.011 40187.61 39198.45 0.86013742
2 -0.028 4.623023 4.931808 1
3 -0.029 4.629014 4.952794 1
4 -0.031 4.633802 4.971662 1
5 -0.032 4.63754 4.988311 1
6 -0.033 4.639533 5.002612 1
7 -0.034 4.640246 5.013826 1
8 -0.034 4.639751 5.023136 1
9 -0.035 4.638466 5.031016 1
10 -0.036 4.635887 5.036558 1
11 -0.037 4.632701 5.040808 1
12 -0.037 4.627665 5.042248 1
13 0.190 7.843346 5.063179 0.68528357
14 -0.012 194.4179 199.7137 0.85359456
15 0.042 20.29101 18.42073 0.7990467
16 0.084 10151.94 8357.008 0.17224258
17 -0.039 4.593244 5.028669 1
18 -0.014 131.3597 135.5077 0.83618973
19 0.049 98552.02 87958.38 0.42257063
20 -0.040 4.564289 5.004224 1

Total number of rows: 45015

Table truncated, full table size 1720 Kbytes.




Supplementary file Size Download File type/resource
GSM2090960_117931.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