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Sample GSM1148694 Query DataSets for GSM1148694
Status Public on May 21, 2014
Title RPE1-BAZ1B-D5-1
Sample type RNA
 
Source name hTERT-RPE1 (retinal pigment epithelial cells), BAZ1B knockout
Organism Homo sapiens
Characteristics cell line: hTERT-RPE1
genotype/variation: BAZ1B knockout
gender: female
clone: D5
Treatment protocol The BAZ1B gene was knocked out by targeting both copies of exon-7 using zinc finger nucleases (D5, F3 and M1 - all independent clones). Clone A6 is targeted at one allele only and is a heterozygous mutant clone.
Growth protocol Cells were grown in DMEM/F12, supplemented with 10% FBS, Pen/Strep, 2mM L-Glutamine, 0.348% NaBicarbonate. Cells were maintained at 37C in 5% CO2, humidified.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Qiagen RNeasy Spin Kit. RNA was treated with DNaseI, before cleaning on an RNeasy spin column. Confirmation of DNA absence was performed by PCR to the repeat element DXZ4, and RNA quality was determined by agarose gel electrophoresis.
Label Cy3
Label protocol Labeling was performed at a NimbleGen Systems certified core facility at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed at a NimbleGen Systems certified core facility at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed at a NimbleGen Systems certified core facilty at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.
Description RPE1 BAZ1B homozygous mutant.
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date May 26, 2013
Last update date May 21, 2014
Contact name Brian P Chadwick
E-mail(s) chadwick@bio.fsu.edu
Phone 850-645-9279
Organization name Florida State University
Department Biological Science
Street address 319 Stadium Drive, King 3076
City Tallahassee
State/province FL
ZIP/Postal code 32306
Country USA
 
Platform ID GPL16025
Series (1)
GSE47390 Changes in gene expression in BAZ1B knockout and heterozygous targeted clones

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AB000409 1210.067
AB000463 784.275
AB000781 16.271
AB001328 5.903
AB002294 1174.233
AB002308 7214.633
AB002311 952.25
AB002313 11487.978
AB002360 4.695
AB002377 4702.116
AB002381 3504.226
AB002382 11120.229
AB002384 3.704
AB003177 4970.116
AB003333 5339.988
AB006589 12.361
AB006590 19.321
AB006621 17.636
AB006625 3.937
AB007457 3976.101

Total number of rows: 45033

Table truncated, full table size 773 Kbytes.




Supplementary file Size Download File type/resource
GSM1148694_549702A04_2012-11-01_1syhyb_2012-11-01T142751_532.pair.gz 2.4 Mb (ftp)(http) PAIR
GSM1148694_549702A04_2012-11-01_1syhyb_532_norm_RMA.pair.gz 2.4 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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