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Sample GSM7876066 Query DataSets for GSM7876066
Status Public on Nov 05, 2023
Title L4-Bsh-Dam, rep1
Sample type SRA
 
Source name Lamina neuron 4
Organism Drosophila melanogaster
Characteristics cell type: Lamina neuron 4
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using a QIAamp DNA Micro Kit (Qiagen), digested with DpnI (NEB) overnight, and cleaned up using Qiagen PCR purification columns. DamID adaptors were ligated using T4 DNA ligase (NEB) followed by DpnII (NEB) digestion for 2 h and PCR amplification using MyTaq HS DNA polymerase (Bioline).
DamID-adaptors removed by AlwI-digestion, end-repaired, A-tailed, followed by ligation of Sequencing-adaptors and PCR-amplification (Marshall, O et al., 2016, Nat Protoc)
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description GSM-L4-4
Data processing each fastq file was assessed for quality using FastQC (v0.11.9)
The damidseq pipeline was run to generate Log2 ratio bedgraph files
The Log2 ratio bedgraph files were used for calling Bsh peaks in L4 neurons using find_peaks (FDR<0.01; 1126 min_quant=0.9)
Supplementary files format and content: bedgraph: it contains Log2 ratio (Bsh-Dam/Dam-only)
Supplementary files format and content: peak.gff: a gff file containing the mean binding intensity of the peak and FDR score
Supplementary files format and content: peaks.genes.in.peak.csv: a tab-delimited text file where 1st column is gene name and the 2nd column is score
 
Submission date Nov 01, 2023
Last update date Nov 05, 2023
Contact name Chris Doe
E-mail(s) cdoe@uoregon.edu
Organization name University of Oregon
Street address 1440 Franklin Blvd
City Eugene
ZIP/Postal code 97403
Country USA
 
Platform ID GPL25244
Series (1)
GSE246726 Homeodomain proteins hierarchically specify neuronal diversity and synaptic connectivity
Relations
BioSample SAMN38044087
SRA SRX22290881

Supplementary file Size Download File type/resource
GSM7876066_Bsh_Dam_L4_r1-vs-Dam.kde-norm.gatc-FDR0.01.peaks.genes.in.peak.csv.gz 19.0 Kb (ftp)(http) CSV
GSM7876066_Bsh_Dam_L4_r1-vs-Dam.kde-norm.gatc-FDR0.01.peaks.gff.gz 39.6 Kb (ftp)(http) GFF
GSM7876066_Bsh_Dam_L4_r1-vs-Dam.kde-norm.gatc.bedgraph.gz 4.8 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA

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