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Sample GSM2867582

Query DataSets for GSM2867582

Status

Public on Jun 13, 2018

Title

DGRP-913_0d_s9

Sample type

SRA

Source name

Adult Brain

Organism

Drosophila melanogaster

Characteristics

tissue: brain
age: 0 Days
genotype: DGRP-551

Treatment protocol

Flies were grown on molasses based flyfood at 25'C with a 12hour/12hour day night cycle

Extracted molecule

genomic DNA

Extraction protocol

Adult flies were anesthetised by placing them in ice cold glass dishes, heads were removed and brains were dissected removing any cuticle, retina and trachea. Dissected brains were placed in ice cold PBS. Two brains were used for each ATAC-seq reaction, one male and one female. ATAC-seq was performed as previously described in Davie and Jacobs et al 2015 (PLOS Genetics)
ATAC-seq

Library strategy

ATAC-seq

Library source

genomic

Library selection

other

Instrument model

Illumina HiSeq 4000

Data processing

The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger (version 2.0.0) count pipeline. All 10X samples were then merged with Cell Ranger (version 2.0.0) aggr pipeline.
The Drop-seq samples were each processed (alignment, barcode assignment and UMI counting) with the Drop-seq tools (version 1.12) developped by Jim Nemesh from McCarroll lab. Gene expression matrices where outer joined.
For the ATAC samples the raw reads were first filtered and scanned for adapters using fastq‐mcf from the ea‐utils r819 package. Read quality was then checked using FastQC 0.11.4. The reads were mapped to the Drosophila genome (dm6) using STAR 2.5.1. The outputted BAM file from STAR was then indexedand sorted using Samtools 1.2. Using genomeCoverageBed from Bedtools 2.23.0, the BAM file was converted to a BedGraph file. For fast, visualization in the IGV GenomeBrowser, the BedGraph file was further processed to a BigWig file using bedGraphtoBigWig.
Genome_build: dm6 (dmel_r6.16_FB2017_03)
Supplementary_files_format_and_content: 10X DGRP-551 + w1118 high quality dataset (57k) raw UMI count matrix stored in compressed Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively
10X DGRP-551 + w1118 large dataset (157k) raw UMI count matrix stored in compressed Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively
CEL-seq2 FAC-sorted R23E10 neurons raw count matrix
SMART-seq2 FAC-sorted R23E10 neurons raw count matrix
Adapted SMART-seq2 FAC-sorted R23E10 neurons raw count matrix
Drop-seq DGRP-551 dataset raw UMI matrix
ATAC-seq bigWig files

Submission date

Nov 28, 2017

Last update date

May 15, 2019

Contact name

Stein Aerts

E-mail(s)

[email protected]

Organization name

KULeuven/VIB

Department

Center for Brain & Disease Research