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Sample GSM2090962 Query DataSets for GSM2090962
Status Public on May 25, 2016
Title HBL1 shOCT2_3410 DOX Treated - 2 days - mAdbID:117933
Sample type RNA
 
Channel 1
Source name HBL1 shOCT2_3410 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_3410. 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: 117933
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 0.254 95208.14 53098.65 0.00011211499
2 -0.351 7.881772 17.68186 0.48630931
3 -0.559 7.72427 27.99037 0.15537066
4 -0.156 7.913257 11.3371 1
5 -0.157 7.874034 11.29546 1
6 -0.157 7.831685 11.24724 1
7 -0.158 7.789668 11.19764 1
8 -0.158 7.749949 11.15002 1
9 -0.158 7.708032 11.0977 1
10 -0.159 7.667537 11.04642 1
11 -0.159 7.627875 10.9947 1
12 0.247 32.46465 18.39224 0.31896226
13 0.375 27.00392 11.38434 0.25408769
14 -0.039 202.9574 222.0366 0.56407568
15 0.230 23.45083 13.82153 0.47831143
16 0.172 14703.2 9887.228 0.0065681408
17 -0.089 8.743463 10.73961 1
18 0.162 289.0232 198.8575 0.016454696
19 -0.020 107289 112232.7 0.75018066
20 0.133 14.63303 10.77964 0.76595575

Total number of rows: 45015

Table truncated, full table size 1717 Kbytes.




Supplementary file Size Download File type/resource
GSM2090962_117933.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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