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Sample GSM5398239 Query DataSets for GSM5398239
Status Public on Apr 26, 2023
Title Fkh1_Fkh2_R0
Sample type SRA
 
Source name in vitro library
Organism synthetic construct
Characteristics round: 0
protein: none
Extracted molecule genomic DNA
Extraction protocol The protein of interest was incubated with the randomized library and run on a non-denaturing polyacrylamide gel at 4 ⁰C. Bound fragments were excised and purified using phenol:chloroform:isoamyl extraction. An aliquot was then used for an additional round of selection and extraction. Illumina adapters and barcodes and were then added to the selected libraries usng 4 cycle PCR, and samples were sent for sequencing.
A hand-mixed library containing a 16 bp randomized region was ordered from IDT with standard desalting. The library was made double stranded using the Klenow reaction.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing library strategy: SELEX-seq
Fixed adapters are trimmed using cutadapt v2.10, leaving only bases of the 16 bp variable region (Test Samples: cutadapt -g ^CGC -a CCTGGAATTCTCGGGTGCCAAGGAACTCCAG$ -O 10 -n 2 --discard-untrimmed --max-n 0 -m 16 -M 16; Production Samples: cutadapt -g ^CAG -a TCCGTATCGCTCCTCCAATG$ -O 10 -n 2 --discard-untrimmed --max-n 0 -m 16 -M 16)
Unexpected runs of cytidine were present in the Fhl1 samples, reads with runs of at least 7 cytidines were removed
The relative enrichment of various length k-mers are calculated using the same process as the SELEX package on bioconductor, the square root of the enrichment is provided for R2 samples
Supplementary files format and content:
tsv files that can be easily viewed in excel or a text editor of your choice
folders of tsv files are archived and compressed into tar.gz format
 
Submission date Jun 24, 2021
Last update date Apr 26, 2023
Contact name Remo Rohs
Organization name University of Southern California
Department Quantitative and Computational Biology
Lab Rohs Lab
Street address 1050 Childs Way
City Los Angeles
State/province CA
ZIP/Postal code 90089
Country USA
 
Platform ID GPL19424
Series (1)
GSE178811 DNA Binding Specificities of Fkh1, Fkh2, Hcm1, and Fhl1 Revealed by SELEX-seq
Relations
BioSample SAMN19855074
SRA SRX11218619

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record
Processed data provided as supplementary file

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