NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6938289 Query DataSets for GSM6938289
Status Public on Jan 20, 2023
Title CREB1_UV
Sample type protein
 
Source name Human CREB1
Organism Homo sapiens
Characteristics protein: CREB1
protein concentration: 540nM
array condition: UV
Growth protocol Cell growth protocol is detailed in the manuscript for all tested proteins and antibodies.
Extracted molecule protein
Extraction protocol Extract protocol is detailed in the manuscript for all tested proteins and antibodies.
Label Alexa 635
Label protocol Label protocol is detailed in the manuscript for all tested proteins and antibodies.
 
Hybridization protocol Commercially synthesized, high-density, single-stranded DNA microarrays from Agilent were first double-stranded via primer extension as done in previous assays (Berger et al, Nature Biotechnology 2006; Shen et al, Cell Systems 2018). The arrays were partially irradiated with UVC such that only some chambers were exposed to UVC while others were not. In order to irradiate only certain parts of the array, and protect the rest from UV irradiation, a cover/gasket slide was cut to the desired size are used to partially cover the DNA array. Next, the gasket slide was fully covered using Cryo-Babies® labels, and the array-gasket slide sandwich was placed in an open container with 1x PBS. To irradiate the DNA on the array, we used a Stratalinker® UV Crosslinker 1800 instrument and conducted a series of irradiations with UVC. Using the energy mode, the container was irradiated with 100 J/m2, randomly repositioned inside the crosslinker 15 times to achieve 1,500 J/m2. Midway through the series, the PBS was replaced in order to keep the solution at room temperature. This procedure resulted in a DNA array with some chambers of the array irradiated by UV and others not irradiated. Samples with the “UV” condition used irradiated chambers while those with a “Non-UV” condition used non-irradiated chambers. The arrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk for 1 hour as done in prior assays (Shen et al, Cell Systems 2018). Proteins were incubated at the indicated concentration using the buffers referred to in the manuscript for 1 hour. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min (Shen et al, Cell Systems 2018). Then the arrays were incubated with either Penta-His Alexa488-conjugated antibody and Penta-His Alexa647-conjugated antibody (1:20 and 1:40 ratio respectively) in a buffer with 2% (wt/vol) milk and 0.05% Tween for 1 hour (buffer details described in the manuscript). After incubation, the arrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min as done in prior work (Shen et al, Cell Systems 2018).
Scan protocol Protein bound microarrays were scanned at 488nm or 635nm using a GenePix 4400A at multiple laser power and gain settings to best capture the signal and avoid saturation of spots. The resulting TIF images were processed using GenePix Pro 7.3.
Data processing The raw data collected using the GenePix® 4400A microarray scanner was processed using the Seed and Wobble suite (Berger et al, Nature Biotechnology 2006), with modifications to adapt the k-mer data to our UV-Bind universal design, as described in the manuscript. For each unique sequence tested, median values over the spots containing that sequence were used unless otherwise noted (i.e. for the universal design sequences and for the competition tests). The number of replicate spots for each sequence varied between 3 and 20, depending on the DNA library. Processing of k-mers and PWMs using Seed-and-Wobble was done using the adjusted signal (i.e. Alexa488Adjusted or Alexa635Adjusted column) in the alldata.txt file as done by default (Berger et al, Nature Biotechnology 2006).
 
Submission date Jan 17, 2023
Last update date Jan 20, 2023
Contact name Raluca Gordan
E-mail(s) raluca.gordan@duke.edu
Organization name Duke University
Department Center for Genomic and Computational Biology
Street address 101 Science Dr, CIEMAS 2179
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platform ID GPL33028
Series (2)
GSE223017 UV irradiation remodels the specificity landscape of transcription factors [85438_Proteins]
GSE223023 UV irradiation remodels the specificity landscape of transcription factors

Data table header descriptions
ID_REF
VALUE Signal intensity

Data table
ID_REF VALUE
Ctrl_UVc_000001 1039
Ctrl_UVc_000002 823
Ctrl_UVc_000003 1626
Ctrl_UVc_000004 1935
Ctrl_UVc_000005 894
Ctrl_UVc_000006 678
Ctrl_UVc_000007 735
Ctrl_UVc_000008 1063
Ctrl_UVc_000009 1009
Ctrl_UVc_000010 1270
Ctrl_UVc_000011 775
Ctrl_UVc_000012 825
Ctrl_UVc_000013 1886
Ctrl_UVc_000014 831
Ctrl_UVc_000015 766
Ctrl_UVc_000016 1033
Ctrl_UVc_000017 641
Ctrl_UVc_000018 1838
Ctrl_UVc_000019 1677
Ctrl_UVc_000020 1127

Total number of rows: 61656

Table truncated, full table size 1228 Kbytes.




Supplementary file Size Download File type/resource
GSM6938289_CREB1_UV_85438_alldata.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap