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| Status |
Public on Nov 05, 2023 |
| Title |
L4-Bsh-Dam, rep3 |
| Sample type |
SRA |
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| Source name |
Lamina neuron 4
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Lamina neuron 4
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| 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)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
GSM-L4-6
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| 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
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| Submission date |
Nov 01, 2023 |
| Last update date |
Nov 05, 2023 |
| Contact name |
Chris Doe |
| E-mail(s) |
cdoe@uoregon.edu
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| Organization name |
University of Oregon
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| Street address |
1440 Franklin Blvd
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| City |
Eugene |
| ZIP/Postal code |
97403 |
| Country |
USA |
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| Platform ID |
GPL25244 |
| Series (1) |
| GSE246726 |
Homeodomain proteins hierarchically specify neuronal diversity and synaptic connectivity |
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| Relations |
| BioSample |
SAMN38044089 |
| SRA |
SRX22290883 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7876068_Bsh_Dam_L4_r3-vs-Dam.kde-norm.gatc-FDR0.01.peaks.genes.in.peak.csv.gz |
19.4 Kb |
(ftp)(http) |
CSV |
| GSM7876068_Bsh_Dam_L4_r3-vs-Dam.kde-norm.gatc-FDR0.01.peaks.gff.gz |
42.6 Kb |
(ftp)(http) |
GFF |
| GSM7876068_Bsh_Dam_L4_r3-vs-Dam.kde-norm.gatc.bedgraph.gz |
4.8 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
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