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Sample GSM2090955 Query DataSets for GSM2090955
Status Public on May 25, 2016
Title BJAB shOCT2_1196 DOX Treated - 1 day - mAdbID:117926
Sample type RNA
 
Channel 1
Source name BJAB shOCT2_1196 DOX Treated - 1 day
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: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_1196. 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 BJAB shControl DOX Treated - 1 day
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: 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: 117926
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 0.101 66662.5 52840.54 0.10418972
2 -0.884 35.60021 272.6927 7.5784494e-29
3 -0.978 15.79999 150.2097 8.2110093e-20
4 -0.257 6.116634 11.05667 1
5 -0.256 5.884206 10.60335 1
6 -0.255 5.683202 10.2129 1
7 -0.253 5.488742 9.83397 1
8 -0.252 5.314585 9.496069 1
9 -0.251 5.156996 9.19073 1
10 -0.250 5.016319 8.918079 1
11 -0.249 4.882998 8.66087 1
12 0.278 1047.144 551.4997 2.9723328e-05
13 0.096 10.17361 8.162222 0.83097433
14 -0.144 436.9388 608.4975 0.022917543
15 0.273 32.19207 17.16376 0.11746965
16 0.012 11993.69 11658.22 0.8410379
17 -0.244 4.294078 7.527386 1
18 -0.010 299.4103 306.3158 0.87412194
19 0.041 99386.9 90452.1 0.50613628
20 -0.280 8.625992 16.42327 0.35234794

Total number of rows: 45015

Table truncated, full table size 1733 Kbytes.




Supplementary file Size Download File type/resource
GSM2090955_117926.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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