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Sample GSM2090957 Query DataSets for GSM2090957
Status Public on May 25, 2016
Title BJAB shOCT2_1196 DOX Treated - 2 days - mAdbID:117928
Sample type RNA
 
Channel 1
Source name BJAB shOCT2_1196 DOX Treated - 2 days
Organism Homo sapiens
Characteristics cell line: BJAB
cell type: GCB DLBCL cells
disease state: germinal center B cell-restricted (GCB) 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 BJAB shControl DOX Treated - 2 days
Organism Homo sapiens
Characteristics cell line: BJAB
cell type: GCB DLBCL cells
disease state: germinal center B cell-restricted (GCB) 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: 117928
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 0.041 57969.72 52753.43 0.50572274
2 -0.074 6.237963 7.388822 1
3 -0.073 6.195528 7.325431 1
4 -0.825 5.801796 38.79689 0.0030659529
5 -0.071 6.109069 7.196412 1
6 -0.070 6.071173 7.139461 1
7 -0.070 6.032895 7.081993 1
8 -0.069 5.999725 7.031581 1
9 -0.068 5.966474 6.981059 1
10 -0.067 5.934219 6.931845 1
11 -0.067 5.903473 6.884967 1
12 0.334 1198.541 554.867 1.1673689e-06
13 -0.064 19.98786 23.18352 0.73970643
14 -0.078 414.9278 496.7289 0.21101892
15 0.255 39.1185 21.75637 0.086541444
16 -0.001 10335.26 10368.35 0.98196689
17 -0.063 5.750581 6.647368 1
18 -0.057 300.2166 342.6232 0.36156557
19 0.062 98117.32 85021 0.31310128
20 0.413 17.66639 6.831802 0.22263348

Total number of rows: 45015

Table truncated, full table size 1745 Kbytes.




Supplementary file Size Download File type/resource
GSM2090957_117928.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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