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Sample GSM3143986 Query DataSets for GSM3143986
Status Public on Feb 18, 2019
Title scATAC-seq_MM057_Sox10KD_0hr_Cell_06
Sample type SRA
 
Source name Melanoma cell line
Organism Homo sapiens
Characteristics cell line: MM057
time point after sox10 kd: 0 hours
Treatment protocol SOX10-KD was performed using a SMARTpool of four siRNAs against SOX10 (SMARTpool: ON-TARGETplus SOX10 siRNA, number L017192-00-0005, Dharmacon) at a concentration of 20nM using as medium Opti-MEM (Thermo Fished Scientific) and omitting antibiotics. The cells were incubated for 24, 48 or 72 hours before processing.  
Growth protocol Cells were kept at 37°C, with 5% CO2 and were maintained in Ham's F10 nutrient mix (Thermo Fished Scientific) supplemented with 10% fetal bovine serum (FBS; Invitrogen) and 100 µg ml-1 penicillin/streptomycin (Thermo Fished Scientific).
Extracted molecule genomic DNA
Extraction protocol Cells were trysinised, spun down (1000 RPM, 5 min), medium was removed and cells were resuspended in fresh medium and passed through a 40 um filter, counted and diluted till 200,000 cells per mL. Cells were loaded (using a 40:60 ratio of RGT:cells) on a primed Open App IFC (10-17 um) and scATAC-seq was performed using the Fluidigm C1 system as described before [Buenrostro et al., 2015] (the protocol for ATAC-seq from the C1 Script Hub was used). After cell loading, the plate was visually checked under a microscope and the number of cells in each of the capture chambers was noted. Next, the “Sample prep” was performed on the Fluidigm C1 during which the cells underwent lysis and ATAC-seq fragments were prepared.
Library prep was performed as described before [Buenrostro et al., 2015]. After the first steps of the library construction by the “Sample prep” on the Fluidigm C1, the libraries were harvested into a 96-well plate and were amplified in a 25 uL PCR reaction. The PCR products were pooled and purified on a single MinElute PCR purification column for a final library volume of 15 uL. Quality checks were performed using the Bioanalyzed high sensitivity chips. Fragments under 150 bp were removed by bead-cleanup using AMPure XP beads (1.2x bead ratio) (Beckman Coulter).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts
MM057_Sox10KD_0hr_Aggregate_GoodCells_SizeFactorsNorm.sorted.bw
Data processing Library strategy: Tn-Seq
The reads from scATAC-seq samples were first cleaned for adapters using fastq-mcf (as part of ea utils; v1.1.2-686). Read quality was then checked using FastQC (v0.11.5). Paired-end reads were mapped to the human genome (hg19-Gencode v18) using STAR (v2.5.1) applying the parameters --alignIntronMax 1, --aslignIntronMin 2 and --alignMatesGapMax 2000. Mapped reads were filtered for quality using SAMtools (v1.2) view with parameter –q4, sorted with SAMtools sort and indexed using SAMtools index. Duplicates were removed using Picard (v1.134) MarkDuplicates using OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500. To filter out cell of bad quality, transcription start site aggregation plots were made using a custom script and cell having a noisy profile were removed from further analyses. This lead to a final of 598 good quality cells over 8 Fluidigm C1 runs. Bam files of good quality single cells were aggregated per condition and peaks were called on these aggregated samples using MACS2 (v2.1.1) callpeak using the parameters --nomodel and --call-summits. The peak files per condition were merged (78,661 peaks in total before blacklisting) and a count matrix was generated by using featureCounts (as part of Subread; v1.4.6) of all separate single cell bam files on the merged peak file (after conversion of the merged peak bed file to a gff format using a custom script). To visualise the aggregated cells per sample, normalised bedGraphs were produced by genomeCoverageBed (as part of bedtools; v2.23.0) using as scaling parameter (-scale) size factors obtained from DEseq2 (v1.18.1). BedGraphs were converted to bigWigs by the bedtools suit functions bedSort to sort the bedGraphs, followed by bedGraphToBigWig to create the bigWigs.
The reads from OmniATAC-seq samples were first cleaned for adapters using fastq-mcf (as part of ea utils; v1.1.2-686). Read quality was then checked using FastQC (v0.11.5). The reads were mapped to the human genome (hg19-Gencode v18) using STAR (v2.5.1) applying the parameters --alignIntronMax 1 and --aslignIntronMin 2. Mapped reads were filtered for quality using SAMtools (v1.2) view with parameter –q4, sorted with SAMtools sort and indexed using SAMtools index. Peaks were called using MACS2 (v2.1.1) callpeak using the parameters --nomodel and --call-summits on the 8 conditions separately. A count matrix was generated by using featureCounts (as part of Subread; v1.4.6) of all separate bam files on the merged peak file (after conversion of the merged peak bed file to a gff format using a custom script). Normalised bedGraphs were produced by genomeCoverageBed (as part of bedtools; v2.23.0) using as scaling parameter (-scale) size factors obtained from DEseq2 (v1.18.1). BedGraphs were converted to bigWigs by the bedtools suit functions bedSort to sort the bedGraphs, followed by bedGraphToBigWig to create the bigWigs, which were used in IGV for visualisation.
Reads obtained from H3K27Ac ChIP-seq were mapped to the genome using Bowtie2 (v2.1.0). The sensitive-local setting for Bowtie2 was used to correct for a high percentage of mismatches at the start of a read. bigWig files were generated from bam files using BEDTools (v2.17.0) and the scores represent the coverage.
Genome_build: hg19
Supplementary_files_format_and_content: scATAC-seq abundance measurement is a raw count matrix containing peaks (called from the aggregates per condition) as row and the single cells as columns.
Supplementary_files_format_and_content: OmniATAC-seq abundance measurement is a raw count matrix containing peaks as row and the single cells as columns.
Supplementary_files_format_and_content: bigWig files were generated from bam files using BEDTools (v2.23.0) and the scores represent the coverage
 
Submission date May 16, 2018
Last update date Feb 18, 2019
Contact name Stein Aerts
E-mail(s) stein.aerts@kuleuven.vib.be
Organization name KU Leuven
Street address O&N4 Herestraat 49 PO Box 602
City Leuven
ZIP/Postal code 3000
Country Belgium
 
Platform ID GPL20301
Series (1)
GSE114557 cisTopic: cis-regulatory topic modelling on single-cell ATAC-seq data
Relations
BioSample SAMN09216051
SRA SRX4090921

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

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