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Sample GSM658850 Query DataSets for GSM658850
Status Public on Apr 28, 2011
Title 18hrs_10μM_IPTG_2mM_3-AT_plates
Sample type SRA
 
Source name B1H selection
Organism synthetic construct
Characteristics iptg concentration (μm): 10
3-at concentration (mm): 2
duration of experiment (hours): 18
media: agarose gel
Extracted molecule other
Extraction protocol After each selection, all of the cells were scraped off the plate. The randomized portion of the prey vector containing the selected transcription factor binding sites were extracted and amplified using PCR. The PCR products from different experiments were digested with different restriction enzymes in the first step of uniquely encoding sequences from different experiments. The restriction enzyme fragments were then barcoded, pooled and sequenced using a Illumina Genome Analyzer IIx machine. See the supplemental material of Noyes et al. (2008). Cell. 133(7):1277-1289 for a more detailed description of the experimental protocol employed for each selection.
 
Library strategy OTHER
Library source synthetic
Library selection other
Instrument model Illumina Genome Analyzer IIx
 
Data processing The sequences from each B1H experiment were labeled using a 3bp barcode. The raw reads were parsed and assigned to the appropriate data set, based on the barcode sequence. Furthermore, only reads that matched the expected constant region, TGTACCGCNNNNNNATTTTTNNNNTGGCCAGCT, (N's indicate randomized positions) , except for up to two mismatches at non-randomized positions, were assigned to the appropriate data sets. All of the reads that did not meet these criteria were placed in the 'unassigned' set. Reads with randomized regions that included an 'N' character were also placed in the 'unassigned' set. The *.uniqSeq_2_counts.tsv files indicate the number of times each unique 6bp long randomized binding site was observed. The single liquid media experiment, 4hrs_50μM_IPTG_5mM_3-AT_liquid, was sequenced in a different lane together with other multiplexed experiments. It's barcode was GAT. The 6bp upstream of the constant region ATTTTT were parsed out and used to generate the corresponding *.uniqSeq_2_counts.tsv file.
 
Submission date Jan 20, 2011
Last update date May 15, 2019
Contact name Scot Wolfe
E-mail(s) scot.wolfe@umassmed.edu
Organization name UMass Medical School
Department MCCB
Street address 364 Plantation Street, LRB 619
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
 
Platform ID GPL11631
Series (1)
GSE26767 A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity
Relations
SRA SRX046025
BioSample SAMN00216951

Data table header descriptions
SEQUENCE
COUNT

Data table
SEQUENCE COUNT
GCGTAG 42606
GTGTAG 38937
ACGTAG 27087
GAGTAG 25385
CCGTAG 21163
GCGTTG 20080
CTGTAG 18401
GCGGAG 17977
GTGGAG 14487
ATGTAG 13752
CTGGAG 12802
GCGAGG 8754
CCGGAG 8382
GTGGGG 7841
GAGTGG 7810
GCGCGG 7304
CCGTGG 6933
GCGGGG 6660
GCGTCG 6344
ACGGGG 6254

Total number of rows: 2910

Table truncated, full table size 25 Kbytes.




Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data included within Sample table

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