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Sample GSM4699105 Query DataSets for GSM4699105
Status Public on Dec 01, 2020
Title MYC4-bHLH-PBM.GenomeDesign
Sample type protein
 
Source name Protein expressed in E.coli
Organism Arabidopsis thaliana
Characteristics protein expressed: Recombinant fusion protein MBP-MYC4
Growth protocol E.coli (BL21 strain) was induced with 1 mM IPTG at OD600=0.6, and incubated for 4 hours at 28 ºC. After induction, cultures were centrifuged and cell pellets frozen at -80 ºC
Extracted molecule protein
Extraction protocol Cell pellet from 25 ml cultures were resuspended in 1ml in 1 mL 1x binding buffer, sonicated (2x30 s) and centrifuged twice to obtain cleared extracts of soluble proteins.
Label Cy3
Label protocol DNA-protein complexes were incubated with 16 ug of rabbit polyclonal to MBP (Abcam, http://www.abcam.com/) in PBS–2% milk for 16 h at room temperature. Slides were washed 3x in PBS0.05% Tween 20, 3x in PBS-0.01% Triton X-100 (5 min each wash) and dried. Labeling of DNA-protein complexes was performed by incubating the microarrays with 0.4 ug of goat anti-rabbit IgG DyLight 549 conjugated (Pierce, http://www.piercenet.com/) in PBS–2% milk for 3 h at room temperature, followed by the same washes as before and the slides were then dried for scanning.
 
Hybridization protocol The binding mixture containing the protein extract in binding buffer was adjusted to 175 µl and contained 2% milk and 0.89 µg of denatured salmon sperm DNA (ssDNA). This mixture was added to an array and incubated for 2.5 hours at room temperature and later on was washed 3 times with PBS-1% Tween 20 (5 min), 3x in PBS-0.01% Triton X-100 (5 min) and spun dry by centrifugation (1000 g).
Scan protocol PBMs were scanned in a DNA Microarray Scanner at 5 µm resolution and quantified with Feature Extraction 9.0 software (Agilent Technologies)
Description bHLH-PBM GenomeDesign
Data processing Raw intensities were adjusted to account for spatial non-uniformities across the microarray using the script ‘normalize_agilent_array.pl’ included in the PBM Analysis Suite (http://thebrain.bwh.harvard.edu/PBMAnalysisSuite/indexSep2017.html)
 
Submission date Jul 28, 2020
Last update date Dec 04, 2020
Contact name Jose M. Franco-Zorrilla
Organization name Centro Nacinal de Biotecnologia-CSIC
Department Plant Molecular Genetics
Street address Darwin, 3
City Madrid
State/province Madrid
ZIP/Postal code 28049
Country Spain
 
Platform ID GPL28933
Series (2)
GSE155320 DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [GenomeData]
GSE155321 DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs

Data table header descriptions
ID_REF
VALUE Log2 Signal intensity (A.U.)

Data table
ID_REF VALUE
1 14.5294029
2 14.61874946
3 14.71405923
4 14.83230492
5 14.89143219
6 14.97235613
7 14.89253665
8 14.86649287
9 14.84743588
10 14.80568787
11 14.8763353
12 14.92224926
13 15.02104151
14 15.0672107
15 15.03454909
16 15.05222385
17 15.02081315
18 15.12721494
19 14.98870032
20 14.99200531

Total number of rows: 180880

Table truncated, full table size 3214 Kbytes.




Supplementary file Size Download File type/resource
GSM4699105_US10313828_256565410001_S01_PBM-proteina_1_2.txt.gz 22.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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