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Sample GSM2867574 Query DataSets for GSM2867574
Status Public on Jun 13, 2018
Title w1118_9d_r2
Sample type SRA
 
Source name Adult Brain
Organism Drosophila melanogaster
Characteristics tissue: brain
age: 9 Days
genotype: W[1118]
Treatment protocol Flies were grown on molasses based flyfood at 25'C with a 12hour/12hour day night cycle
Extracted molecule polyA RNA
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. When 40 brains were collected, brains were dissociated at 25'C for 2 hours in a mix of Collagenase (75µl @ 100mg/ml) and Dispase (50µl @ 3mg/ml), the sample was pipette mixed every 15 minutes. Cells washed in PBS twice centrifuging at 800 xg) and resuspended in 400µl PBS. A single cell suspension was obtained by filtering with an 11µm cell strainer.
Drop-seq and 10x Genomics CHROMIUM Single Cell 3’ Solution V2 Chemistry
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
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) stein.aerts@kuleuven.vib.be
Organization name KULeuven/VIB
Department Center for Brain & Disease Research
Lab S. Aerts Lab of Computational Biology
Street address Herestraat 49, bus 602
City LEUVEN
ZIP/Postal code 3000
Country Belgium
 
Platform ID GPL21306
Series (1)
GSE107451 A single-cell transcriptome atlas of the ageing Drosophila brain
Relations
BioSample SAMN08105393
SRA SRX3426782

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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