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Sample GSM5589257

Query DataSets for GSM5589257

Status

Public on May 23, 2022

Title

Selex-24mer-R0

Sample type

SRA

Source name

synthetic DNA

Organism

synthetic construct

Characteristics

genotype: N/A
chip antibody: N/A
genome build: N/A

Growth protocol

Drosophila larvae were grown on standard cornmeal or molasses food at 25°C.

Extracted molecule

genomic DNA

Extraction protocol

R0 DNA was from the Klenow product of the original synthetic random library, and R1 DNA was purified bound DNA fraction from the gel-free Selex experiments.
Selex-seq libraries were prepared by PCR amplification, followed by column purification

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

NextSeq 550

Data processing

Library strategy: Selex-seq
For ChIP-seq and ATAC-seq, mapping was done against dm3 with the “Map with Bowtie for Illumina” tool on usegalaxy.org, and only uniquely mapped reads were kept.
ChIP-seq peak calling was performed using the galaxy version of MACS2 (“MACS2 callpeak” on usegalaxy.org), with the following setting: --nomodel –extsize 200, and all other parameters were default
ATAC-seq peak calling was also performed with the galaxy version of MACS2, with the following setting: --nomodel –extsize 200 - -shift -100.
For RNA-seq, the cutadaptor tool on usegalaxy.eu was used to trim reads and remove reads shorter than 100bp. The filtered reads were then mapped to the genome build dm6 using the RNA STAR tool with the following parameters: --sjdbOverhang 149. The featurecount tool was used to obtain the transcript count tables.
Selex-seq data were processed using the NRLB algorithm
When analysing the Selex-seq raw data, the algorithm we used took the R0 and R1 data, and output the motifs enriched in the R1 data. This is somewhat similar to de novo motif search. The algorithm didn't output any intermediate quantitative data, and the motif logos were the only data it generated.
Genome_build: dm3 for ChIP-seq and ATAC-seq, dm6 for RNA-seq
Supplementary_files_format_and_content: bigwig (ChIP-seq and ATAC-seq) and count table (RNA-seq)

Submission date

Sep 20, 2021

Last update date

May 23, 2022

Contact name

Siqian Feng

E-mail(s)

sf2607@columbia.edu

Organization name

Columbia University

Street address

625 W. 130th Street