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Sample GSM3272162 Query DataSets for GSM3272162
Status Public on Oct 01, 2018
Title HEK293T_139CWC27_alt-splice_rep3
Sample type RNA
 
Source name HEK293T, 139CWC27, rep3
Organism Homo sapiens
Characteristics cell line: HEK293T
Treatment protocol Cells were washed with 1X PBS before freezing in preparation for RNA extraction.
Growth protocol HEK293T cells were transduced with titered lentivirus containing either shRNA from the MISSION library or with scrambled shRNA. Puromycin was used to select for incorporation. Cells were grown to 80% confluency and harvested.
Extracted molecule total RNA
Extraction protocol total RNA was extracted and purified using the Bioline ISOLATE II kit according to manufacturer's instructions.
Label biotin
Label protocol Labeling was conducted by the Molecular Profiling Facility at the University of Pennsylvania. All protocols were conducted as described in the Affymetrix WT Plus Reagent Kit Manual and the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.
 
Hybridization protocol Hybridization was conducted by the Molecular Profiling Facility at the University of Pennsylvania. Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Transcriptome 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.
Scan protocol Scanning was conducted by the Molecular Profiling Facility at the University of Pennsylvania. A GeneChip 3000 7G scanner was used to collect fluorescence signal.
Data processing Probeset and gene normalized data was calculated from cel files in Affymetrix Expression Console software using RMA with default parameters.
 
Submission date Jul 16, 2018
Last update date Oct 01, 2018
Contact name Tara Davis
E-mail(s) Tara.Davis@DrexelMed.edu
Organization name Drexel University College of Medicine
Department Biochemistry and Molecular Biology
Lab Lab 10127
Street address 245 N. 15th St. MS 497
City Philadelphia
State/province PA
ZIP/Postal code 19102
Country USA
 
Platform ID GPL17585
Series (1)
GSE117144 Comparison of CWC27 knockdown in HEK293T cells compared to scrambled shRNA control
Relations
Alternative to GSM3272156

Data table header descriptions
ID_REF
VALUE Quantification
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
JUC01000001.hg.1 8.09418 0.0113729
JUC01000002.hg.1 6.20698 0.153161
JUC01000003.hg.1 9.18587 1.82534e-05
JUC01000004.hg.1 7.2802 0.0220505
JUC01000005.hg.1 9.35677 0.000380498
JUC01000006.hg.1 8.47583 0.00528207
JUC01000007.hg.1 6.53173 0.132988
JUC01000008.hg.1 6.82993 0.00558878
JUC01000009.hg.1 5.43372 0.00649996
JUC01000010.hg.1 4.5514 0.00448001
JUC01000011.hg.1 12.9761 4.90787e-09
JUC01000012.hg.1 9.30106 0.0119237
JUC01000013.hg.1 12.9745 4.63897e-09
JUC01000014.hg.1 11.537 4.49409e-09
JUC01000015.hg.1 9.04101 2.07612e-05
JUC01000016.hg.1 9.96407 3.05249e-06
JUC01000017.hg.1 7.56411 5.02819e-06
JUC01000018.hg.1 8.85878 0.0250305
JUC01000019.hg.1 9.95476 1.64358e-05
JUC01000020.hg.1 9.95476 1.64358e-05

Total number of rows: 914585

Table truncated, full table size 32313 Kbytes.




Supplementary file Size Download File type/resource
GSM3272162_5160_56578_3CWC27_HTA.CEL.gz 26.9 Mb (ftp)(http) CEL
GSM3272162_5160_56578_3CWC27_HTA.rma-alt-splice-dabg.chp.gz 9.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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