title: scATAC-seq_MM087_Sox10KD_24hr_Cell_27


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_20

status: Public on Feb 18 2019

type: SRA

city: Leuven

first: Stein

last: Aerts

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

description:
MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts
MM087_Sox10KD_24hr_Aggregate_GoodCells_SizeFactorsNorm.sorted.bw

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Melanoma cell line

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).

extract_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).

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.

tag: cell line

tag: time point after sox10 kd

value: 24 hours


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_19


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_21


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_18


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_15


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_17


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_14


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_16


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_11


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_13


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_09


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_10


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_06


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_07


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_02


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_08


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_05


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_01


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_04


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_93

description:
MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts
MM087_Sox10KD_0hr_Aggregate_GoodCells_SizeFactorsNorm.sorted.bw

value: 0 hours


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_03


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_91


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_92


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_95


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_94


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_22


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_96


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_90


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_88


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_12


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_86


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_85


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_84


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_83


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_80


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_82


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_79


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_78


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_81


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_19

description:
MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts
MM087_Sox10KD_48hr_Aggregate_GoodCells_SizeFactorsNorm.sorted.bw

value: 48 hours


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_75


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_73


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_76


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_74


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_72


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_77


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_68


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_70


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_69


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_66


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_71


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_63


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_65


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_62


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_64


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_87


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_89


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_61


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_60


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_57


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_67


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_56


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_55


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_59


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_54


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_51


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_46


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_43


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_45


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_47


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_44


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_41


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_39


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_52


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_48


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_49


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_37


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_36


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_50


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_38


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_40


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_35


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_34


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_58


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_33


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_31


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_32


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_53


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_42


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_27


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_29


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_25


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_28


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_24


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_23


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_21


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_20


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_22


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_16


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_15


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_13


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_14


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_17


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_11


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_12


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_18


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_05


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_08


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_04


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_06


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_30


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_02


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_07


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_03


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_26


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_01


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_93

description:
MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts
MM057_Sox10KD_72hr_Aggregate_GoodCells_SizeFactorsNorm.sorted.bw

value: 72 hours


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_96


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_95


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_92


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_19


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_10


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_90


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_91


title: scATAC-seq_MM087_Sox10KD_0hr_Cell_09


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_89


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_83


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_82


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_85


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_81


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_78


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_80


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_84


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_77


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_86


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_76


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_75


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_79


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_73


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_74


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_71


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_94


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_87


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_70


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_69


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_68


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_67


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_66


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_65


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_88


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_64


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_61


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_60


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_59


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_72


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_52


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_54


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_55


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_51


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_53


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_50


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_49


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_58


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_46


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_44


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_48


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_42


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_47


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_45


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_40


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_43


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_63


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_38


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_37


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_36


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_62


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_35


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_39


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_33


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_56


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_57


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_32


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_31


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_29


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_34


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_25


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_28


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_27


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_41


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_24


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_26


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_23


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_21


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_30


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_19


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_20


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_17


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_16


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_14


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_13


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_11


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_18


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_12


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_22


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_09


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_08


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_15


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_10


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_05


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_06


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_04


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_07


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_03


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_01


title: scATAC-seq_MM057_Sox10KD_72hr_Cell_02


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_92

description:
MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts
MM057_Sox10KD_48hr_Aggregate_GoodCells_SizeFactorsNorm.sorted.bw


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_96


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_95


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_94


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_91


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_86


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_93


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_89


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_85


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_88


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_90


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_87


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_83


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_81


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_82


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_80


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_79


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_77


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_74


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_76


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_72


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_78


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_73


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_70


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_68


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_65


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_67


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_66


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_64


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_63


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_84


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_69


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_60


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_61


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_59


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_75


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_55


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_56


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_51


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_53


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_57


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_58


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_71


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_54


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_50


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_48


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_47


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_44


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_46


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_45


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_62


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_42


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_41


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_39


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_38


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_40


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_36


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_35


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_34


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_52


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_33


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_32


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_30


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_29


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_28


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_31


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_27


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_26


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_23


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_25


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_24


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_22


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_20


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_21


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_43


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_19


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_17


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_16


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_18


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_37


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_15


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_14


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_12


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_13


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_09


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_10


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_07


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_08


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_06


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_05


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_03


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_04


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_02


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_01


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_92

description:
MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts
MM057_Sox10KD_24hr_Aggregate_GoodCells_SizeFactorsNorm.sorted.bw


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_87


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_84


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_83


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_82


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_88


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_80


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_81


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_79


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_75


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_76


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_73


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_78


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_77


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_11


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_74


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_68


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_72


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_69


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_70


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_67


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_64


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_65


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_62


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_66


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_61


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_58


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_60


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_57


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_56


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_71


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_55


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_52


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_59


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_49


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_53


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_48


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_51


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_50


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_45


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_43


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_47


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_44


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_42


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_63


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_46


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_40


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_39


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_41


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_36


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_38


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_35


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_54


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_33


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_32


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_30


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_29


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_28


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_26


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_31


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_25


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_24


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_22


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_23


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_19


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_21


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_20


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_15


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_18


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_37


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_14


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_17


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_12


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_13


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_34


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_11


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_27


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_09


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_01


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_07


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_96

description:
MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts
MM057_Sox10KD_0hr_Aggregate_GoodCells_SizeFactorsNorm.sorted.bw


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_02


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_04


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_08


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_03


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_06


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_05


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_94


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_16


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_93


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_92


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_91


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_90


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_89


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_95


title: scATAC-seq_MM057_Sox10KD_24hr_Cell_10


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_86


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_88


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_87


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_84


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_83


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_81


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_80


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_79


title: OmniATAC__MM087_Sox10_KD_0h

description:
OmniATAC_mergedPeaks_correctformat.counts
OmniATAC__MM087_Sox10_KD_0h_NormSF_sorted.bw

extract_protocol:
OmniATAC-seq was performed as described previously [Corces et al., 2017]. Cells were washed, trypsinised, spun down at 1000 RPM for 5 min to remove the medium and resuspended in 1 mL. Cells were counted and experiments were only continued when a viability of above 90% was observed. 50,000 cells were pelleted at 500 RCF at 4°C for 5 min, medium was carefully aspirated and the cells were washed and lysed using 50 uL of cold ATAC-Resupension Buffer (RSB) (see Corces et al., 2017 for composition) containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin by pipetting up and down three times and incubating the cells for 3 min on ice. The lysis was washed out by adding 1 mL of cold ATAC-RSB containing 0.1% Tween-20 and inverting the tube three times. Nuclei were pelleted at 500 RCF for 10 min at 4°C, the supernatant was carrefully removed and nuclei were resuspended in 50 uL of transposition mixture (25 uL 2x TD buffer (see Corces et al., 2017 for composittion), 2.5 uL transposase (100 nM), 16.5 uL DPBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O) by pipetting six times up and down, followed by 30 minutes incubation at 37°C at 1000 RPM mixing rate. Samples were cleaned-up by MinElute.
After MinElute clean-up and elution in 21 uL elution buffer, the transposed fragments were pre-amplified with Nextera primers by mixing 20 uL of transposed sample, 2.5 uL of both forward and reverse primers (25 uM) and 25 uL of 2x NEBNext Master Mix (program: 72°C for 5 min, 98°C for 30 sec and 5 cycles of [98°C for 10 sec, 63 °C for 30 sec, 72°C for 1 min] and hold at 4°C). To determine the required number of additional PCR cycles, a qPCR was performed [see Bruenrostro et al., 2015 for the determination of the number of cycles to be added]. The final amplification was done with the additional number of cycles, samples were cleaned-up by MinElute and libraries were further prepped using the KAPA Library Qunatificaton Kit as previously described [Corces et al., 2017].


title: OmniATAC__MM087_Sox10_KD_48h

description:
OmniATAC_mergedPeaks_correctformat.counts
OmniATAC__MM087_Sox10_KD_48h_NormSF_sorted.bw


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_75


title: OmniATAC__MM057_Sox10_KD_72h

description:
OmniATAC_mergedPeaks_correctformat.counts
OmniATAC__MM057_Sox10_KD_72h_NormSF_sorted.bw


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_78


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_82


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_74


title: OmniATAC__MM087_Sox10_KD_72h

description:
OmniATAC_mergedPeaks_correctformat.counts
OmniATAC__MM087_Sox10_KD_72h_NormSF_sorted.bw


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_71


title: OmniATAC__MM057_Sox10_KD_24h

description:
OmniATAC_mergedPeaks_correctformat.counts
OmniATAC__MM057_Sox10_KD_24h_NormSF_sorted.bw


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_73


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_76


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_85


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_69


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_66


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_67


title: ChIP_H3K27ac_MM032

description: ChIP_H3K27ac_MM032.nofirst5bp.minMQ4.sorted.bw

data_processing:
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. We used as control the merged control profiles of five cell lines, namely A375, MM011, MM032, MM047 and MM057. We used MACS2 (v2.0.10) with the command 'callpeak -t ChIPseq_file -c  Control_file -g hs --qvalue 0.001 -n name'.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bam files using BEDTools (v2.23.0) and the scores represent the coverage. Bedfiles supplied with FDR0.001

extract_protocol:
Chromatin was extracted using the MagnaChIP-seq kit (millipore). 4 µg of antibody was used on 2 million cells. Sonication was performed for 12 cycles, 30 sec pulses using the biorupter.
Illumina TruSeq

tag: time point

value: Base line


title: OmniATAC__MM057_Sox10_KD_0h

description:
OmniATAC_mergedPeaks_correctformat.counts
OmniATAC__MM057_Sox10_KD_0h_NormSF_sorted.bw

data_processing:
Library strategy: Tn-Seq
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.
Genome_build: hg19
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


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_70


title: ChIP_H3K27ac_A375

description: ChIP_H3K27ac_A375.nofirst5bp.minMQ4.sorted.bw

data_processing:
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. We used as control the merged control profiles of five cell lines, namely A375, MM011, MM032, MM047 and MM057. We used MACS2 (v2.0.10) with the command 'callpeak -t ChIPseq_file -c  Control_file -g hs --qvalue 0.001 -n name'.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bam files using BEDTools (v2.23.0) and the scores represent the coverage. Bedfiles supplied with FDR0.001.


title: OmniATAC__MM057_Sox10_KD_48h

description:
OmniATAC_mergedPeaks_correctformat.counts
OmniATAC__MM057_Sox10_KD_48h_NormSF_sorted.bw


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_68


title: scATAC-seq_MM057_Sox10KD_48hr_Cell_49


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_64


title: DNase_noTreatment_SE

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

country: Germany

institute: University of Regensburg

data_processing:
Reads were aligned to hg19 assembly using bowtie2 version 2.2.2 with the following configurations: --very-sensitive-local  ( additionally for paired-end sequencing: --no-discordant -X 2000 )
Aligned reads exhibiting a mapping quality MAPQ < 30 were discarded using samtools version 1.1
Genome_build: hg19
Supplementary_files_format_and_content: biwig files were generated using the bamCoverage script from the deepTools package (paired-end: --extendReads -binSize 1; single-end: --extendReads 150 -binSize 1) and show the normalized (--normalizeTo1x 2451960000) genome coverage

source_name: HeLa cells

growth_protocol: HeLa cells were grown on DMEM-Dubelco´s modified Eagle Medium containing Glutamax (TM from Gibco) supplemented with 10% Fetal Bovine serum, and maintained at 37°C with 5% CO2.

extract_protocol:
Samples were treated with RNase A and Proteinase K prior to DNA extraction with phenol-chloroform-isoamylalcohol.
Libraries were prepared according to NEBNext ChIP-Seq Kit for Illumina sequencing. Adapter were removed by size selection using AMPure XP magnetic beads.

treatment_protocol: Two million cells were used to purify chromatin according the REAP protocol (Sizuki et al. 2010) and digested with 5 to 30 units of Dnase I for 5 minutes at 25°C.

tag: chromation digestion

value: Dnase I

tag: treatment

value: HeLa


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_65


title: Input_SE

value: Sonication


title: OmniATAC__MM087_Sox10_KD_24h

description:
OmniATAC_mergedPeaks_correctformat.counts
OmniATAC__MM087_Sox10_KD_24h_NormSF_sorted.bw


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_77


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_72


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_62


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_60


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_59


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_58


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_55


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_57


title: DNase_CL_RNase_SE

value: RNase digestion (100 µg, 5 minutes), TO treated (50 µM, 10 minutes), and cross-linking (formaldehyde 1%, 8 minutes)


title: INPUT_ChIPSeq_dKO_rep1

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

country: USA

institute: St Jude Children's Research Hospital

data_processing:
ChIP-Seq reads were aligned to mm9 (MGSCv37) using the BWA software (version 0.7.12-r1039, default parameter).
Duplicated reads were marked using the Picard software (version 2.6.0-SNAPSHOT) and only non-duplicated reads used for analysis using SAMtools (parameter “-q 1 -F 1024” version 1.2).
Data quality control (QC) follows ENCODE criteria. Relative strand correlation (RSC) values were calculated and the fragment size estimated under the support of R (version 2.14.0) by SPP (version 1.1) with packages caTools (version 1.17) and bitops (version 1.0-6). At least 10 million unique reads with RSC > 1 was required to pass QC. 2 control and 2 Lats1/2 dKO samples passed QC. Bigwig files were generated by extending each read to the best fragment size (the smallest fragment size estimated by SPP) and manually inspected using IGV genome browser for clear peaks and low background noise.
MACS2 (version 2.1.1.20160309) was used to call peaks using the best fragment size with a cutoff of FDR < 0.05
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using bedtools genomeCoverageBed and bedGraphToBigWig sequentially, bed files were generateted with MACS2 and contain narrow peak calls

organism: Mus musculus

extract_protocol:
Each E12.5 mouse brain was dissociated in 1 ml of cold PBS by pipetting. Protein−DNA complexes were crosslinked by incubating in 1% formaldehyde/PBS (Sigma F1635) for 10 min at RT with gentle rotation. Crosslinking was stopped with 125 mM glycine/PBS for 5 min and washed 3 times with cold PBS. Cells were lysed in 1 ml lysis buffer (50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100) supplemented with protease and RNAse inhibitors for 10 min at 4ºC with gentle rotation. Nuclei were pelleted at 1800 rcf for 2 min, washed with 1 ml wash buffer (10 mM Tris-HCl [pH 8.0], 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) supplemented with protease and RNAse inhibitors for 10 min, and lysed in 900 µl nuclear lysis buffer (10 mM Tris-HCl [pH 8.0], 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine) for 10 min. Lysed nuclei (300 µl/1.5 ml sonication tube) were sonicated for 5 cycles of 15-sec on and 45-sec off in a Qsonica Q800R2 sonicator. Chromatin was quantitated and diluted with nuclear lysis buffer to ~500 ng/µl and further sonicated for 10 cycles of 15-sec on and 45-sec off to obtain an average DNA fragment size of ~300 bp. Sonicated chromatin was centrifuged at 14,000 rpm for 10 min and the supernatant chromatin was either used for ChIP or flash frozen and stored at −80ºC.
Sequencing libraries were prepared from 10 ng of DNA using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext Q5 Hot Start HiFi PCR Master Mix according to the manufacturer’s instructions (New England Biolabs) with the following modifications: a second 1:1 Ampure cleanup was added after adaptor ligation and the Ampure size selection step prior to PCR eliminated.

tag: strain background

value: mixed

tag: genotype/variation

value: Lats1/2;Nestin-Cre dKO

tag: Stage

tag: tissue

value: brain


title: DNase_CL_SE

value: TO treated (50 µM, 10 minutes), and cross-linking (formaldehyde 1%, 8 minutes)


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_54


title: INPUT_ChIPSeq_dKO_rep2


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_53


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_56


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_52


title: INPUT_ChIPSeq_WT_rep2

value: wild type


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_50


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_63


title: H3K4me3_ChIPSeq_dKO_rep1

tag: chip antibody

value: H3K4me3 antibody (Millipore 07-473)


title: H3K4me3_ChIPSeq_WT_rep2


title: H3K4me3_ChIPSeq_dKO_rep2


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_51


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_49


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_61


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_48


title: Hi-C_RS_bio1_tech2

city: Cincinnati

first: Satoshi

middle: H

last: Namekawa

state: Ohio

address: Cincinnati Children's Hospital Medical Center

department: Division of Reproductive Sciences

description:
RS_pooled_validpairs.txt.gz
RS_pooled.mcool

data_processing:
Libraries were sequenced on Illumina HiSeq2500 or HiSeq4000 machines following the manufacturer's instructions. Bases were called using Illumina's HiSeq Control Software.
Paired-end .fastq files of Hi-C libraries were mapped and processed using the cMapping package (https://github.com/dekkerlab/cMapping).
Hi-C reads were iteratively mapped to the Mus musculus mm10 genome via Bowtie2 (version 2.3.3.1), which was called with the following arguments: --very-sensitive --no-head --no-sq --qc-filter --reorder.
Uniquely aligned, paired reads were kept and assigned to the 5’ position of HindIII restriction fragments.
Mapped reads were filtered for fragment ends and uniqueness; PCR duplicates, defined as sequence matches with the exact same start and end, were excluded.
Using the cooler package (version 0.7.10; https://github.com/mirnylab/cooler), valid pairs pooled from biological replicates (in validpairs.txt.gz files) were binned at multiple resolutions (resulting in .mcool files).
To correct for noisy and/or low-signal bins prior to matrix balancing with cooler, bins whose log marginal sum is less than ≤20 genome-wide median absolute deviations below the median log marginal sum of all the bins in the same chromosome were excluded.
Matrices were balanced using Sinkhorn balancing such that the sum of every row and column is equal.
Genome_build: mm10
Supplementary_files_format_and_content: validpairs: Tab-delimited text files listing valid interacting pairs of Hi-C reads; mcool: A file containing chromosome interractions, made from the validPairs files, binned at multiple resolutions (kb) as follows: 1, 2, 5, 8, 10, 15, 20, 30, 40, 64, 100, 128, 250, 256, 512, 1024, 2048, 4096, and 8192.

source_name: Round spermatids

extract_protocol:
Pachytene spermatocytes and round spermatids were isolated from adult testes through sedimentation velocity at unit gravity as described (PMID 8231890). At least 12 independent mice, 90-120 days in age, were used for each isolation of germ cells. Wet lab procedures for Hi-C were performed as described (PMID 28435001), and samples were treated with HindIII restriction enzyme.
Hi-C library construction was performed as described (PMID 28435001) with the following detail: For DNA sequencing, NEBNext Oligos for Illumina, Index Primer Set 1, were used.

tag: strain

tag: source tissue

value: Testis

tag: cell type

value: Round spermatids

tag: number of mice

tag: age

tag: genotype


title: H3K4me3_ChIPSeq_WT_rep1


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_46


title: Hi-C_RS_bio1_tech1

institute: Cincinnati Children's Hospital Medical Center


title: Lats1/Lats2 DKO replicate 3

type: RNA

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Mouse Gene 2.0 ST GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expresson Console software v1.1.

label: biotin

molecule: total RNA

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).

growth_protocol: Cortices of E12.5 mouse embryos were dissected in cold PBS prior to isolation of RNA. Each sample was derived from an independent embryo.

extract_protocol: RNA was extracted using Trizol (Thermo Fisher Scientific)

treatment_protocol: Samples were untreated

tag: developmental stage

value: Cortex


title: INPUT_ChIPSeq_WT_rep1


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_44

tag: cell line

value: 0 hours


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_42

tag: time point after sox10 kd


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_41


title: Control replicate 2

source_name: control

value: control


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_40


title: wild-type 6mA-IP

city: Heidelberg

first: Jan

last: Mauer

state: BW

address: Im Neuenheimer Feld, 583

institute: BioMed X Innovation Center

description:
processed data file:
deseq.6mA.IP.txt

library_source: transcriptomic

data_processing:
library strategy: iCLIP
To analyze 6mA coverage at the transcription start nucleotide (TSN) the following steps were carried out: Input and 6mA-IP reads were aligned to mm10 with STAR to generate RPM-normalized bedgraphs and sorted bam files (version 2.5.2a;). Bedgraphs were visualized using the Integrative Genomics Viewer (IGV, version 2.4.4). Sorted bam files were converted to bed format and read coverage was determined in 20 nucleotide windows flanking annotated TSSs (UCSC) using bedtools (version 2.25.0). 6mA-IP TSS coverage reads were then counted and normalized to input coverage reads using the Deseq2 pipeline adjusted for CLIP-Seq (version 1.18.1; commands: design= ~ assay + condition + assay:condition; test="LRT", reduced= ~ assay + condition). Analysis and visualization was carried out with custom in-house generated R-scripts using RStudio (Version 1.0.136). Only transcripts with normalized read counts > 10 were included in the analyses.
Genome_build: mm10
Supplementary_files_format_and_content: the tab-delimited text files are deseq2 output files; the bedgraphs are derived from STAR

source_name: wild type mouse liver

extract_protocol:
Total RNA was extracted using the TRIzol reagent, and was DNase-treated prior to library construction according to the miCLIP protocol.
Libraries were constructed using the iCLIP cloning process, as previously described (see GSE63753).

value: wild-type

value: liver biopsy

tag: number of replicates


title: Fto knockout input

description:
processed data file:
deseq.input.txt

source_name: Fto knockout mouse liver

value: Fto knockout


title: Control replicate 3


title: Control replicate 1


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_38


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_43


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_39


title: Mycobacterium smegmatis infected with mycobacteriophage Crossroads DEM phgg419 for 2 hrs and 30 minutes (Late)

city: Pittsburgh

first: Rebekah

middle: M

last: Dedrick

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Basecalls performed with MiSeq Reporter
Reads were trimmed at both ends using cutadapt version 1.8.3 using a quality score cutoff of 30
Reads were aligned simultaneously to host and phage genomes using bowtie2 version 2.2.6
Reads that did not uniquely map to the reference genomes were removed with the sed command line utility using the "XS:i" flag in the bowtie alignment output
SAM format was converted to BAM format using samtools version 1.2
BAM format was converted to BED format using bedtools version 2.25.0
Expression levels were computed as reads mapped per base pair per strand ("top" and "bottom") using the genomecov tool of bedtools version 2.25.0
Genome_build: NC_008596.1 (Mycobacterium smegmatis mc2155)
Genome_build: KP027201 (Sbash)
Genome_build: KF024731 (Crossroads)
Supplementary_files_format_and_content: bedgraph formatted files containing strand-specific ("top" and "bottom" strands) expression coverage levels per base pair across the genome, computed by the genomecov tool in bedtools

organism: Mycobacterium phage Crossroads

source_name: Cells grown in liquid media

growth_protocol: Cells were grown in 7H9 media to OD(600) of 0.7-1.0 (mid-log phase)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen), rRNA was depleted using Ribo-Zero (Illumina)
Libraries were generated using TruSeq Stranded mRNA Sample Prep Kit (Illumina)

tag: host strain

value: Mycobacterium smegmatis mc2155

tag: phage

value: Mycobacteriophage Crossroads DEM phgg419

tag: infection timepoint

value: 2 hours 30 minutes


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_37


title: Candida albicans, WGBS

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Reads generated from MethylC-seq were aligned to each species respective genome assembly using the latest version of methylpy (Schultz et al. 2015; doi: 10.1038/nature14465; https://bitbucket.org/schultzmattd/methylpy/wiki/Home). MethylC-seq analysis was performed as described in Schmitz et al. (2013; doi: 10.1101/gr.152538.112).
Genome_build: Agaricus bisporus. http://genome.jgi.doe.gov/Agabi_varbisH97_2/Agabi_varbisH97_2.home.html. Aspergillus flavus. http://genome.jgi.doe.gov/Aspfl1/Aspfl1.home.html. Aureobasidium pullulans. http://genome.jgi.doe.gov/Aurpu_var_pul1/Aurpu_var_pul1.home.html. Botrytis cinerea. http://genome.jgi.doe.gov/Botci1/Botci1.home.html. Candida albicans. http://genome.jgi.doe.gov/Canalb1/Canalb1.home.html. Candida auris. https://www.ncbi.nlm.nih.gov/genome/?term=Candida+auris%5Borgn%5D. Clavispora lusitianiae. https://www.ncbi.nlm.nih.gov/genome/286. Coemansia reversa. http://genome.jgi.doe.gov/Coere1/Coere1.home.html. Coemansia spiralis. http://genome.jgi.doe.gov/Coespi1/Coespi1.home.html. Coprinopsis cinerea. http://genome.jgi.doe.gov/Copci1/Copci1.home.html. Cordyceps militaris. http://genome.jgi.doe.gov/Cormi1/Cormi1.home.html. Cryptococcus neoformans. http://genome.jgi.doe.gov/Cryne_H99_1/Cryne_H99_1.home.html. Fusarium fujikuroi. http://genome.jgi.doe.gov/Fusfu1/Fusfu1.home.html. Hesseltinella vesiculosa. http://genome.jgi.doe.gov/Hesve2finisherSC/Hesve2finisherSC.home.html. Heterobasidion irregulare. http://genome.jgi.doe.gov/Hetan2/Hetan2.home.html. Kirkomyces cordense. http://genome.jgi.doe.gov/Kircor1/Kircor1.home.html. Laccaria bicolor. http://genome.jgi.doe.gov/Lacbi2/Lacbi2.home.html. Leptosphaeria maculans. http://genome.jgi.doe.gov/Lepmu1/Lepmu1.home.html. Lobosporangium transversale. http://genome.jgi.doe.gov/Lobtra1/Lobtra1.home.html. Magnaporthe oryzae. http://genome.jgi.doe.gov/Maggr1/Maggr1.home.html. Metarhizium robertsii. http://genome.jgi.doe.gov/Metro1/Metro1.home.html. Microbotryum lychnidis. http://genome.jgi.doe.gov/Micld1/Micld1.home.html. Mixia osmundae. http://genome.jgi.doe.gov/Mixos1/Mixos1.home.html. Neurospora crassa. http://genome.jgi.doe.gov/Neucr2/Neucr2.home.html. Parasitella parasitica. http://genome.jgi.doe.gov/Parpar1/Parpar1.home.html. Phanerochaete chrysosporium. http://genome.jgi.doe.gov/Phchr2/Phchr2.home.html. Pholiota alnicola. http://genome.jgi.doe.gov/Phoaln1/Phoaln1.home.html. Phycomyces blakesleeanus. http://genome.jgi.doe.gov/Phybl2/Phybl2.home.html. Pleurotus ostreatus. http://genome.jgi.doe.gov/PleosPC15_2/PleosPC15_2.home.html. Podospora anserina. http://genome.jgi.doe.gov/Podan2/Podan2.home.html. Postia placenta. http://genome.jgi.doe.gov/Pospl1/Pospl1.home.html. Pseudogymnoascus destructans. http://fungi.ensembl.org/Pseudogymnoascus_destructans_20631_21/Info/Index. Radiomyces spectabilis. http://genome.jgi.doe.gov/Radspe1/Radspe1.home.html. Saccharomyces cerevisiae. http://genome.jgi.doe.gov/Sacce1/Sacce1.home.html. Spinellus fusiger. http://genome.jgi.doe.gov/Spifus1/Spifus1.home.html. Sporobolomyces roseus. http://genome.jgi.doe.gov/Sporo1/Sporo1.home.html. Syncephalis fuscata. http://genome.jgi.doe.gov/Synfus1/Synfus1.home.html. Tilletiopsis washingtonensis. http://genome.jgi.doe.gov/Tilwa1/Tilwa1.home.html. Uncinocarpus reesii. http://genome.jgi.doe.gov/Uncre1/Uncre1.home.html. Wolfiporia cocos. http://genome.jgi.doe.gov/Wolco1/Wolco1.home.html.
Supplementary_files_format_and_content: Tab delimited; please see metadata.txt file (on series record) for column headers.

organism: Candida albicans

source_name: Whole organism

extract_protocol:
Candida albicans, Candida auris, and Clavispora lusitianiae. MasturePure yeast DNA purification kit (Epicentre) following the manufacturer's instructions. Microbotryum lychnidis. Qiagen Kit 10243 (Courtaboeuf, France) following the manufacturer's instructions and using a Carver hydraulic press (reference 3968, Wabash, IN) for breaking cell walls. Lobosporangium transversale, Syncephalis fuscata, Spinellus fusiger, Parasitella parasitica, Kirkomyces cordense, Radiomyces spectabilis, and Sporobolomyces roseus. CTAB/Chloroform protocol (http://1000.fungalgenomes.org/home/protocols/high-quality-genomic-dna-extraction/). Aureobasidium pullulans, Coemansia reversa, Coemansia spiralis, Coprinopsis cinerea, Heterobasidion irregulare, Mixia osumundae, Phanerochaete chrysosporium, Pleurotus ostreatus, Pseudogymnoascus destructans, Tilletiopsis washingtonensis, and Wolfiporia cocos. A modified CTAB/Chloroform protocol (James et al. 2008; doi: 10.1111/j.1558-5646.2008.00462.x). Pholiota alnicola. EZNA Fungal DNA Mini Kit (Omega Bio-tek, Norcross, GA) following the manufacturer's instructions.
MethylC-seq libraries were prepared using the protocol described in Urich et al. (2015; doi:10.1038/nprot.2014.114). Lambda phage DNA was used as a control for the sodium bisulfite non-conversion rate.

value: Whole organism

value: Lab colony


title: Mycobacterium smegmatis infected with mycobacteriophage Crossroads DEM phgg419 for 30 minutes (Early)

value: 30 minutes


title: Lats1/Lats2 DKO replicate 2

tag: genotype/variation


title: Fto knockout 6mA-IP

description:
processed data file:
deseq.6mA.IP.txt

tag: strain background


title: Lats1/Lats2 DKO replicate 1

tag: tissue


title: Mycobacterium smegmatis: pGG05 infected with mycobacteriophage Crossroads for 2 hrs and 30 minutes (Late)

value: Mycobacterium smegmatis mc2155:pGG05

value: Mycobacteriophage Crossroads


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_47


title: Mycobacterium smegmatis: pGG05 infected with mycobacteriophage Crossroads for 30 minutes (Early)


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_34


title: wild-type input

description:
processed data file:
deseq.input.txt


title: Mycobacterium smegmatis infected with mycobacteriophage Crossroads DEM phgg417 for 30 minutes (Early)

value: Mycobacteriophage Crossroads DEM phgg417


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_35


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_36


title: Mycobacterium smegmatis infected with mycobacteriophage Crossroads DEM phgg413 for 2 hrs and 30 minutes (Late)

value: Mycobacteriophage Crossroads DEM phgg413


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_33


title: Mycobacterium smegmatis infected with mycobacteriophage Crossroads DEM phgg413 for 30 minutes (Early)


title: Mycobacterium smegmatis infected with mycobacteriophage Crossroads DEM phgg417 for 2 hrs and 30 minutes (Late)


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_32


title: sgC11-INPUT rep2

city: Shanghai

first: Yun

last: Liu

address: Dongan Road 130

country: China

institute: Fudan University

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa aln version 0.7.15 with default parameters
data were filter with the following specification: 1. keep only unique mapped reads(except C13); 2. remove PCR duplicates with samtools version 1.5
peaks were called using MACS version 2.1 with parameters “-t chip -c input -g hs -f BAMPE -B”
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file were generated using UCSC utility bedGraphToBigWig

growth_protocol: HEK293T cells were cultured at 37°C under 5% CO2 in high-glucose Dulbecco’s Modified Eagle’s Medium (DMEM; Life Technologies, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (Sigma, St. Louis, MO, USA), 1% penicillin/streptomycin (Life Technologies), and passaged at 1:5 every 2 days.

extract_protocol:
The cells were lysed and sonicated, biotinylated protein-DNA complexes were affinity purified with M-280 Streptavidin Dynabeads. DNA was purified with QIAquick PCR Purification Kit (Qiagen, Hilden, Germany).
DNA libraries were prepared using the Ultra II DNA Library Prep Kit for Illumina (NEB)
CAPLOCUS-seq

tag: passages


title: sgC11-IP rep2

tag: target

value: Cells transfected with sgRNAs targeting C11, then pull down with M-280 Streptavidin Dynabeads


title: Mycobacterium smegmatis infected with mycobacteriophage Crossroads DEM phgg348 for 2 hrs and 30 minutes (Late)

value: Mycobacteriophage Crossroads DEM phgg348


title: Mycobacterium smegmatis infected with mycobacteriophage Crossroads DEM phgg348 for 30 minutes (Early)


title: Mycobacterium smegmatis infected with mycobacteriophage Crossroads for 2 hrs and 30 minutes (Late)


title: Mycobacterium smegmatis infected with mycobacteriophage Crossroads for 30 minutes (Early)


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_29

value: 0 hours


title: sgC13-INPUT rep2


title: sgC13-IP rep2

value: Cells transfected with sgRNAs targeting C13, then pull down with M-280 Streptavidin Dynabeads


title: sgC11-IP rep1


title: sgC13-INPUT rep1


title: sgC13-IP rep1


title: Mycobacteriophage Sbash lysogen

organism: Mycobacterium phage Sbash

value: Mycobacteriophage Sbash

value: no exogenous phage added


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_27


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_26


title: HIC_library_CBL0137-treated_replicate2

city: Moscow

first: Artem

last: Luzhin

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
Reads for each biological replicate were pooled and mapped to the human genome (version hg19) using hiclib(Imakaev Et al. 2012(PMID: 22941365 )) (https://bitbucket.org/mirnylab/hiclib/).
Reads mapped in close proximity to DpnII restriction sites (5 bp), reads mapped on the same fragment, and possible PCR duplicates were eliminated. Resulting pairs were binned into 20 Kb genomic windows, and contact maps were generated.
Contact maps were iteratively corrected(Imakaev, 2012) using cooler (https://github.com/mirnylab/cooler)
Genome_build: hg19
Supplementary_files_format_and_content: cool files were generated using cooler version 0.7.9

source_name: connective tissue

extract_protocol: Hi-C was performed in two biological replicates using the DpnII restriction endonuclease according to a previously published protocol(Lieberman-Aiden Et al. 2009 (PMID: 19815776);Belton Et al. 2012(PMID: 22652625 )).Each Hi-C library was sequenced using paired end sequencing on an Illumina HiSeq 3000 in two technical replicates;

treatment_protocol: Exposure of cells to CBL0137 (3 μm final concentration in the culture medium) was for 6 h.

value: HT1080 cells

tag: disease

value: fibrosarcoma

tag: oncogene

value: ras +


title: sgGAL4-IP rep2

tag: cell type

value: Cells transfected with sgRNAs targeting GAL4, then pull down with M-280 Streptavidin Dynabeads


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_31


title: Gordonia terrae infected with Gordonia phage Kita for 2 hours and 30 minutes (Late)

data_processing:
Basecalls performed with MiSeq Reporter
Reads were trimmed at both ends using cutadapt version 1.8.3 using a quality score cutoff of 30
Reads were aligned simultaneously to host and phage genomes using bowtie2 version 2.2.6
Reads that did not uniquely map to the reference genomes were removed with the sed command line utility using the "XS:i" flag in the bowtie alignment output
SAM format was converted to BAM format using samtools version 1.2
BAM format was converted to BED format using bedtools version 2.25.0
Expression levels were computed as reads mapped per base pair per strand ("top" and "bottom") using the genomecov tool of bedtools version 2.25.0
Genome_build: NZ_CP016594 (Gordonia terrae strain 3612)
Genome_build: KU963257 (Kita)
Genome_build: KX557275 (CarolAnn)
Genome_build: KU998248 (Utz)
Supplementary_files_format_and_content: bedgraph formatted files containing strand-specific ("top" and "bottom" strands) expression coverage levels per base pair across the genome, computed by the genomecov tool in bedtools

organism: Gordonia phage Kita

growth_protocol: Cells were grown in PYCa media to OD(600) of 0.7-1.0 (mid-log phase)

value: Gordonia terrae

value: Gordonia phage Kita

value: 2 hours, 30 minutes


title: HIC_library_Conrtol_replicate2


title: Gordonia terrae infected with Gordonia phage Kita for 30 minutes (Early)

value: 30 minutes


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_25


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_30


title: sgC11-INPUT rep1


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_24


title: HIC_library_CBL0137-treated_replicate1


title: Kita lysogen infected with Gordonia phage CarolAnn for 2 hours and 30 minutes (Late)

organism: Gordonia phage CarolAnn

value: Gordonia phage CarolAnn


title: sgGAL4-IP rep1


title: Gordonia phage Utz lysogen

organism: Gordonia phage Utz

value: Gordonia phage Utz lysogen


title: HiC_library_Control_replicate1


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_21


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_22


title: sgGAL4-INPUT rep2


title: Gordonia phage Blueberry lysogen

organism: Gordonia phage Blueberry

value: Gordonia phage Blueberry lysogen


title: Gordonia phage CarolAnn lysogen

value: Gordonia phage CarolAnn lysogen


title: Mycobacterium smegmatis infected with mycobacteriophage ZoeJ for 210 minutes

description: Cells grown in liquid media

data_processing:
Basecalls performed with MiSeq Reporter
Reads were trimmed at both ends using cutadapt version 1.8.3 using a quality score cutoff of 30
Reads were aligned simultaneously to host and phage genomes using bowtie2 version 2.2.6
Reads that did not uniquely map to the reference genomes were removed with the sed command line utility using the "XS:i" flag in the bowtie alignment output
SAM format was converted to BAM format using samtools version 1.2
BAM format was converted to BED format using bedtools version 2.25.0
Expression levels were computed as reads mapped per base pair per strand ("top" and "bottom") using the genomecov tool of bedtools version 2.25.0
Genome_build: NC_008596.1 (Mycobacterium smegmatis mc2155)
Genome_build: KJ510412 (ZoeJ)
Supplementary_files_format_and_content: bedgraph formatted files containing strand-specific ("top" and "bottom" strands) expression coverage levels per base pair across the genome, computed by the genomecov tool in bedtools

organism: Mycobacterium phage ZoeJ

source_name: M. smegmatis infected with mycobacteriophage ZoeJ

value: Mycobacterium smegmatis mc2155

value: Mycobacteriophage ZoeJ

value: 210 minutes


title: Mycobacterium smegmatis infected with mycobacteriophage ZoeJ for 150 minutes

description: Cells grown in liquid media

value: 150 minutes


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_20

value: 0 hours


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_19


title: Phanerochaete chrysosporium, WGBS

organism: Phanerodontia chrysosporium

value: Whole organism

tag: strain

value: Lab colony


title: Mycobacteriophage ZoeJ lysogen G8

description: Cells grown in liquid media

source_name: Mycobacteriophage ZoeJ lysogen

value: no exogenous phage added


title: Mycobacterium smegmatis infected with mycobacteriophage ZoeJ for 30 minutes

description: Cells grown in liquid media


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_18


title: Mycobacteriophage ZoeJ lysogen 3D

description: Cells grown in liquid media


title: Mycobacterium smegmatis infected with mycobacteriophage ZoeJ for 90 minutes

description: Cells grown in liquid media

value: 90 minutes


title: Parasitella parasitica, WGBS, run 2

description:
Run 1 (GSM3074707) and Run 2 (GSM3074708) samples were produced with separate libraries made from DNA extracted from the same biological sample.
processed data file can be found on GSM3074707

organism: Parasitella parasitica

tag: genotype


title: Kita lysogen infected with Gordonia phage CarolAnn for 30 minutes (Early)

value: Gordonia terrae


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_17


title: Parasitella parasitica, WGBS, run 1

description: Run 1 (GSM3074707) and Run 2 (GSM3074708) samples were produced with separate libraries made from DNA extracted from the same biological sample.


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_23


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_16


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_28


title: s24-9 survivor

first: Lei

middle: Frank

last: Huang

address: 2600 Clifton Ave

institute: Uiversity of Cincinnati

data_processing:
Basecalls performed using Alta-Cyclic version 0.2.2
RNA-seq reads were aligned to the galGal5.0 genome assembly using Hisat2 version 2.1.0 with the default configurations; We re-assembly transcriptome using StringTie version 1.3.3b with default parameter.
Data filtration: transcripts shorter than 200nt and without strand information were removed; Second,  transcripts with class code “=”, “e”, “p” and “c” were discarded; Third, transcripts with  low expression level (FPKM<1)
lncRNA identification was implemented by CPC, PLEK, CNCI and CSF algorithm.
Genome_build: Gallus_gallus-5.0 (GCA_000002315.3)
Supplementary_files_format_and_content: Reads counts file (.csv) was generated using StringTie python script: prepDE.py. Every transcript in every sample was listed.

organism: Gallus gallus

source_name: infected spleen tissue

growth_protocol: All the tissues were preserved in RNAfixer (BioTeke Co. Ltd., Beijing, China) at 4°C overnight and transferred to −80°C until RNA isolation.

extract_protocol:
Total RNA was isolated using TRIZOL Reagent according to manufacturer’s instruction (Life Technologies, Carlsbad, CA).
A total amount of 3μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: treatments were infected intraperitoneally with 2,000 plaque-forming units (PFU) of the MDV-GA, and noninfected birds were injected with the same volume of diluent (0.2 mL) at 1 d of age.

value: spleen

tag: tumor stage

value: normal tissue


title: s24-8 survivor


title: s24-7 survivor


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_14

tag: cell line


title: s24-6 survivor


title: Agaricus bisporus, WGBS

organism: Agaricus bisporus


title: Clavispora lusitianiae, WGBS

organism: Clavispora lusitaniae


title: s24-11 survivor


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_12

tag: time point after sox10 kd


title: Pholiota alnicola, WGBS

organism: Flammula alnicola

value: Dried fruiting body

value: Voucher MICH-232899


title: Input_library_CBL0137treated_replicate2

description:
processed data file:
CBL__PePr_peaks.bed
Diff_intra___PePr_CBL_peaks.bed

data_processing:
Reads for each biological replicate were mapped to the human genome (version hg19) using Bowtie2 (version 2.2.3) with very sensitive preset.
Non-uniquely mapped reads were filtered using 'XS:i' flag. Resulted sam files were sorted,possible PCR and optical duplicates were filtered using Samtools (version 1.5) .
Peaks were called using PePr (https://github.com/shawnzhangyx/PePr, PMID: 24894502) with p-value cutoff 0.05 and sliding window size 100bp.
Differential peak calling was performed using PePr  (https://github.com/shawnzhangyx/PePr, PMID: 24894502) with --diff option and intra-group normalization
Bigwig files were generated using deepTools version 2.0, for each biological replicate bigwig file was generated as ratio of ChIP signal to Input, with RPKM normalization and bin size 50bp. Smoothed bigwig files were generated as normal bigwig's but with smoothLength parameter = 3bins.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig and bed files (as specified at https://genome.ucsc.edu/FAQ/FAQformat.html#format13)

extract_protocol:
ChIP was performed in two biological replicates according to Abcam X-ChIP protocol (https://www.abcam.com/protocols/cross-linking-chromatin-immunoprecipitation-x-chip-protocol) with minor changes (see Materials and Methods section).
Each library was sequenced using paired end sequencing on an Illumina NextSeq 550;

tag: tissue source

value: connective tissue

value: fibrosarcoma

value: ras +

tag: treatment

value: CBL0137 for 6hrs


title: sgGAL4-INPUT rep1


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_10

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


title: Input_library_Conrtol_replicate2

description:
processed data file:
Control__PePr_peaks.bed
Diff_intra___PePr_Control_peaks.bed


title: s6-3 tumorous

value: tumorous tissue


title: s7-2 tumorous


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_11


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_09


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_15


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_08


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_13


title: ChIP_library_CBL0137treated_replicate2

tag: chip antibody

value: anti-CTCF pAb (ActiveMotif ; Cat. No. 61311, Lot 34614003)


title: s9-2 tumorous


title: Mixia osmundae, WGBS

organism: Mixia osmundae


title: s16-2 tumorous


title: Input_library_CBL0137treated_replicate1

organism: Homo sapiens


title: s13-2 tumorous


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_06


title: ChIP_library_Conrtol_replicate2


title: Aureobasidium pullulans, WGBS

organism: Aureobasidium pullulans


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_05


title: s12-1 noninfected

source_name: noninfected spleen tissue


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_04


title: ChIP_library_CBL0137treated_replicate1


title: Chip_library_Control_replicate1


title: Input_library_Control_replicate1


title: ChIP-seq control library human

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

institute: Rutgers, the State University of New Jersey

description:
H_Day4-Input_NK09
Human embryonic stem cells (line H9, WiCell Research Institute, NIH registration number 0062) were maintained and differentiated into endoderm, hindgut and intestinal organoids as published previously
human Wnt+Fgf-specified intestinal culture cells

data_processing:
Alignment: ChIP-seq:bowtie2 version 2.2.6. RNA-seq: Tophat, version 2.1.0
peak calling: macs 1.4.1
RNA-seq cxb files: cuffquant v2.2.1
Bigwig: bamCoverage 2.4.2
Genome_build: mm9, hg19
Supplementary_files_format_and_content: ChIP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: cxb file for expression profile and cuffnorm table with normalized gene expression values

extract_protocol:
Intestinal Specified Endoderm culture cells were fixed and frozen for subsequent chromatin pulldown
Whole cell lysates were sonicated and incubated without any antibody overnight for determining background chromatin pulldown.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries

value: Wild-Type

value: NO


title: s21-5 noninfected


title: s14-5 noninfected


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_03

description:
MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts
MM057_Sox10KD_0hr_Aggregate_GoodCells_SizeFactorsNorm.sorted.bw

value: 0 hours


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_02


title: Adult Duodenal cells human patient 2

description:
Hbiopsy_Cdx2_rep2_NK77
human Adult Duodenal cells

source_name: human Adult Duodenal cells

extract_protocol:
Patient Duodenal biopsy tissue was dissected, epithelial cells were scrapped and fixed for subsequent chromatin pull down
Whole cell lysates were sonicated and incubated with 6 uL CDX2  antibody overnight for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries

value: human Adult Duodenal cells


title: s17-2 noninfected


title: Adult Duodenal cells human patient 1

description:
Hbiopsy_Cdx2_rep1_NK69
human Adult Duodenal cells


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_01


title: s14-8 tumorous


title: Fusarium fujikuroi, WGBS

organism: Fusarium fujikuroi

value: Whole organism

value: Lab colony


title: s17-1 noninfected


title: Microbotryum lychnidis, WGBS

organism: Microbotryum lychnidis-dioicae


title: s10-4 tumorous


title: Coemansia spiralis, WGBS

organism: Coemansia spiralis


title: Naïve endoderm + induced CDX2 human culture rep2

description:
TetON_Cdx2_rep2_NK76
Human embryonic stem cells (line H9, WiCell Research Institute, NIH registration number 0062) were maintained and differentiated into endoderm, hindgut and intestinal organoids as published previously
human Naïve endoderm + induced CDX2 culture cells

extract_protocol:
Naïve endoderm + induced CDX2 culture cells were fixed and frozen for subsequent chromatin pulldown
Whole cell lysates were sonicated and incubated with 6 uL CDX2  antibody overnight for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries

value: human Naive endoderm + induced CDX2 culture cells

value: Doxycycline


title: Naïve endoderm + induced CDX2 human culture rep1

description:
TetON_Cdx2_rep1_NK68
Human embryonic stem cells (line H9, WiCell Research Institute, NIH registration number 0062) were maintained and differentiated into endoderm, hindgut and intestinal organoids as published previously
human Naïve endoderm + induced CDX2 culture cells


title: Wnt+Fgf-specified gut human culture rep2

description:
D4CF_Cdx2_rep2_NK75
Human embryonic stem cells (line H9, WiCell Research Institute, NIH registration number 0062) were maintained and differentiated into endoderm, hindgut and intestinal organoids as published previously
human Wnt+Fgf-specified intestinal culture cells

extract_protocol:
Intestinal Specified Endoderm culture cells were fixed and frozen for subsequent chromatin pulldown
Whole cell lysates were sonicated and incubated with 6 uL CDX2  antibody overnight for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries


title: Tilletiopsis washingtonensis, WGBS

organism: Tilletiopsis washingtonensis


title: Radiomyces spectabilis, WGBS

organism: Radiomyces spectabilis


title: Wolfiporia cocos, WGBS

organism: Wolfiporia cocos


title: Wnt+Fgf-specified gut human culture rep1

description:
D4CF_Cdx2_rep1_NK03
Human embryonic stem cells (line H9, WiCell Research Institute, NIH registration number 0062) were maintained and differentiated into endoderm, hindgut and intestinal organoids as published previously
human Wnt+Fgf-specified intestinal culture cells


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_45

extract_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).


title: Pleurotus ostreatus, WGBS

organism: Pleurotus ostreatus


title: Podospora anserina, WGBS

organism: Podospora anserina


title: Coprinopsis cinerea, WGBS

organism: Coprinopsis cinerea

value: Okayama 7


title: Leptosphaeria maculans, WGBS

organism: Plenodomus lingam

value: brassicae


title: Candida auris, WGBS

organism: Candidozyma auris


title: Sporobolomyces roseus, WGBS

organism: Sporobolomyces roseus


title: Kirkomyces cordense, WGBS

description: processed data file can be found on GSM…

organism: Kirkomyces cordensis


title: Spinellus fusiger, WGBS

organism: Spinellus fusiger


title: Hesseltinella vesiculosa WGBS run2

description:
Run 1 (GSM3074699) and Run 2 (GSM3074700) samples were produced with separate libraries made from DNA extracted from the same biological sample.
processed data file can be found on GSM3074699.

organism: Hesseltinella vesiculosa


title: DNase_CL

data_processing:
Library strategy: DNase-seq
Paired-end reads were aligned to hg19 assembly using bowtie2 version 2.2.2 with the following configurations: --very-sensitive-local  --no-discordant -X 2000
Aligned reads exhibiting a mapping quality MAPQ < 30 were discarded using samtools version 1.1
Genome_build: hg19
Supplementary_files_format_and_content: biwig files were generated using the bamCoverage script from the deepTools package (--extendReads -binSize 1 ) and show the normalized (--normalizeTo1x 2451960000) genome coverage

organism: Homo sapiens

value: HeLa

tag: chromation digestion

value: Dnase I

value: TO treated (50 microM, 10 minutes), and cross-linking (formaldehyde 1%, 8 minutes)


title: DNase_noTreatment


title: Lobosporangium transversale, WGBS

organism: Lobosporangium transversale


title: Hesseltinella vesiculosa WGBS run1

description: Run 1 (GSM3074699) and Run 2 (GSM3074700) samples were produced with separate libraries made from DNA extracted from the same biological sample.


title: Heterobasidion irregulare, WGBS

organism: Heterobasidion irregulare


title: Pseudogymnoascus destructans, WGBS

organism: Pseudogymnoascus destructans


title: Botrytis cinerea, WGBS

organism: Botrytis cinerea


title: DNase_CL_RNase

value: RNase digestion (100 microgram, 5 minutes), TO treated (50 microM, 10 minutes), and cross-linking (formaldehyde 1%, 8 minutes)


title: TAZ_genomic DNA

status: Public on Feb 17 2019

city: Beijing

first: yuqiong

last: hu

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

description:
genomic DNA
TAZ

data_processing:
Library strategy: DNA-seq
ESC_EC_MSC_counts.txt and FOXD1_NTC_counts.txt were generated from RNA-seq data. RNA-seq reads were aligned to hg19 reference genome with the Tophat software (http://tophat.cbcb.umd.edu/). Reads were counted with HT-Seq.
hESC_depth.txt was used for CNV identification. We used the published R package HMMcopy. In brief, the genome was binned into consecutive 1 Mb windows with readCounter and then we calculated the absolute number of reads detected in each window. We estimated the copy number with GC and mappability corrections with HMMcopy.
Genome_build: hg19
Supplementary_files_format_and_content: ESC_EC_MSC_counts.txt and FOXD1_NTC_counts.txt include the counts of RefSeq genes. hESC_depth.txt was used for CNV identification.

source_name: Human ESCs

extract_protocol:
Total RNA was extracted from cultured cells using RNeasy Mini Kit（Qiagen）following the manufacturer's protocol.
1-2 μg of total RNA was used to build sequencing libraries using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: CRISPR-Cas9 mediated YAP and TAZ knockout: CRISPR-Cas9 mediated gene targeting was performed as previously described with some modifications (Wang et al., 2018). YAP-gRNA sequence is CATCAGATCGTGCACGTCCGCGG; TAZ-gRNA sequence is TGTCTAGGTCCTGCGTGACGTGG. The YAP or TAZ gRNA was cloned into gRNA vector (Addgene #41824). The donor plasmid for homologous recombination including homology arms and neo cassette was described previously (Pan et al., 2016). In brief, 5x 106 H9 ESCs were mixed with plasmid cocktail and electroporated. After electroporation, cells were plated on G418-resistant MEF feeders. Two days later, cells were treated with 50 ug/ml G418 (Gibco) for screening. After 2 weeks of selection, G418-resistant clones were manually picked to 96-well plates and expanded for genotyping. Gene-targeted clones were determined by genomic PCR. Lentiviral CRISPR-Cas9 mediated FOXD1 knockdown:Lentiviral CRISPR-Cas9 mediated gene editing was performed as previously described (Sanjana et al., 2014; Shalem et al., 2014). Briefly, the single guide RNA targeting FOXD1 was cloned into lentiCRISPRv2 (Addgene#52961) which contained two expression cassettes, hSpCas9 and the chimeric guide RNA. Then the plasmid was packaged into lentivirus and transduced to hMSCs. 72hs later, infected cells were treated with 1 ug/ml puro (Gibco) for screening.

value: ESC

tag: genotype/variation

value: TAZ KO


title: Coemansia reversa, WGBS

organism: Coemansia reversa


title: YAP_genomic DNA

description:
genomic DNA
YAP

value: YAP KO


title: Syncephalis fuscata, WGBS

organism: Syncephalis fuscata


title: FOXD1_3

description:
polyA RNA
FOXD1_3

data_processing:
ESC_EC_MSC_counts.txt and FOXD1_NTC_counts.txt were generated from RNA-seq data. RNA-seq reads were aligned to hg19 reference genome with the Tophat software (http://tophat.cbcb.umd.edu/). Reads were counted with HT-Seq.
hESC_depth.txt was used for CNV identification. We used the published R package HMMcopy. In brief, the genome was binned into consecutive 1 Mb windows with readCounter and then we calculated the absolute number of reads detected in each window. We estimated the copy number with GC and mappability corrections with HMMcopy.
Genome_build: hg19
Supplementary_files_format_and_content: ESC_EC_MSC_counts.txt and FOXD1_NTC_counts.txt include the counts of RefSeq genes. hESC_depth.txt was used for CNV identification.

source_name: Human MSCs

value: MSC

value: FOXD1 Knockdown


title: NTC_2

description:
polyA RNA
NTC_2

value: non-targeting control


title: NTC_1

description:
polyA RNA
NTC_1


title: Input

extract_protocol:
Samples were treated with RNase A and Proteinase K prior to DNA extraction with phenol-chloroform-isoamylalcohol.
Libraries were prepared according to NEBNext ChIP-Seq Kit for Illumina sequencing. Adapter were removed by size selection using AMPure XP magnetic beads.

value: Sonication


title: WT_genomic DNA

description:
genomic DNA
WT

value: WT


title: FOXD1_2

description:
polyA RNA
FOXD1_2


title: FOXD1_1

description:
polyA RNA
FOXD1_1


title: hMSC_TAZ_3

description:
polyA RNA
hMSC_TAZ_3


title: NTC_3

description:
polyA RNA
NTC_3


title: hMSC_TAZ_2

description:
polyA RNA
hMSC_TAZ_2


title: hMSC_TAZ_1

description:
polyA RNA
hMSC_TAZ_1


title: hMSC_YAP_2

description:
polyA RNA
hMSC_YAP_2


title: hMSC_YAP_1

description:
polyA RNA
hMSC_YAP_1


title: hMSC_YAP_3

description:
polyA RNA
hMSC_YAP_3


title: hESC_TAZ_2

description:
polyA RNA
hESC_TAZ_2


title: hESC_TAZ_1

description:
polyA RNA
hESC_TAZ_1


title: hESC_TAZ_3

description:
polyA RNA
hESC_TAZ_3


title: hESC_YAP_3

description:
polyA RNA
hESC_YAP_3


title: hESC_YAP_2

description:
polyA RNA
hESC_YAP_2


title: hESC_WT_3

description:
polyA RNA
hESC_WT_3


title: hESC_YAP_1

description:
polyA RNA
hESC_YAP_1


title: mouse_joint_mYAP_3

description:
polyA RNA
sample name in processed data files:
Y3
mouse.counts.txt; mouse.merge.FPKM.gene.txt

data_processing:
mouse.counts.txt and mouse.merge.FPKM.gene.txt were generated from RNA-seq data. RNA-seq reads were aligned to mm10 reference genome with the Tophat software (http://tophat.cbcb.umd.edu/).
Genome_build: mm10
Supplementary_files_format_and_content: mouse.counts.xls includes the counts of RefSeq genes. mouse.merge.FPKM.gene.xls includes the FPKM of RefSeq genes

organism: Mus musculus

source_name: mouse joints

extract_protocol:
Total RNA was extracted from cultured cells using RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.
1-2 μg of total RNA was used to build sequencing libraries using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: We subjected mice to anterior cruciate ligament transection (ACLT), which is widely used to induce osteoarthritis. After ACLT, we injected lentiviruses expressing YAP, FOXD1, or luciferase intra-articularly. We extracted mRNA from mouse joints and did RNA-seq.

value: joints

value: ACLT and YAP

tag: Sex

value: male


title: mouse_joint_mYAP_2

description:
polyA RNA
sample name in processed data files:
Y2
mouse.counts.txt; mouse.merge.FPKM.gene.txt

tag: tissue


title: hMSC_WT_3

description:
polyA RNA
hMSC_WT_3


title: hESC_WT_2

description:
polyA RNA
hESC_WT_2


title: mouse_joint_mYAP_1

description:
polyA RNA
sample name in processed data files:
Y1
mouse.counts.txt; mouse.merge.FPKM.gene.txt


title: mouse_joint_mLUC_3

description:
polyA RNA
sample name in processed data files:
L3
mouse.counts.txt; mouse.merge.FPKM.gene.txt

value: ACLT and Luciferase


title: mouse_joint_mFOXD1_3

description:
polyA RNA
sample name in processed data files:
F3
mouse.counts.txt; mouse.merge.FPKM.gene.txt

value: ACLT and FOXD1


title: mouse_joint_mLUC_2

description:
polyA RNA
sample name in processed data files:
L2
mouse.counts.txt; mouse.merge.FPKM.gene.txt


title: mouse_joint_mFOXD1_1

description:
polyA RNA
sample name in processed data files:
F1
mouse.counts.txt; mouse.merge.FPKM.gene.txt


title: mouse_joint_mControl_3

description:
polyA RNA
sample name in processed data files:
C3
mouse.counts.txt; mouse.merge.FPKM.gene.txt

value: no treatment


title: mouse_joint_mFOXD1_2

description:
polyA RNA
sample name in processed data files:
F2
mouse.counts.txt; mouse.merge.FPKM.gene.txt


title: mouse_joint_mControl_1

description:
polyA RNA
sample name in processed data files:
C1
mouse.counts.txt; mouse.merge.FPKM.gene.txt


title: mouse_joint_mControl_2

description:
polyA RNA
sample name in processed data files:
C2
mouse.counts.txt; mouse.merge.FPKM.gene.txt


title: hMSC_WT_2

description:
polyA RNA
hMSC_WT_2


title: hMSC_WT_1

description:
polyA RNA
hMSC_WT_1


title: hESC_WT_1

description:
polyA RNA
hESC_WT_1


title: mouse_joint_mLUC_1

description:
polyA RNA
sample name in processed data files:
L1
mouse.counts.txt; mouse.merge.FPKM.gene.txt


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV094]

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

hyb_protocol: The samples were hybridized to Human Gene 2.1 ST microarrays according to standard Affymetrix protocols. This was performed by at the Ramaciotti Centre for Genomics, The University of New South Wales.

scan_protocol: The samples were scanned on an Affymetrix scanner at the Ramaciotti Centre for Genomics, The University of New South Wales.

data_processing: The raw microarray data was processed in R employing the RMA algorithm. A custom chip description file was used (hugene21sthsentrezg, version 20).

label: Biotin

source_name: Nasal swab specimen

label_protocol: Standardized kits from Affymetrix were used to label the samples at the Ramaciotti Centre for Genomics, The University of New South Wales.

growth_protocol: Samples were collected from children during a naturally occuring asthma or wheezing exacerbation.

extract_protocol: Total RNA was extracted with TRIzol followed by RNeasy.

treatment_protocol: Nasal swab specimens were collected using flocked swabs.

tag: phenotype

value: Acute asthma/wheeze

tag: rv status

value: Rhinovirus negative


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV096]

value: Rhinovirus positive


title: Nasal swab specimen from child with Convalescent [MAV092]

value: Convalescent


title: Nasal swab specimen from child with Control [MAV095]

value: Control


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV083]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV085]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV081]


title: Nasal swab specimen from child with Control [MAV082]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV093]


title: Nasal swab specimen from child with Convalescent [MAV084]


title: Nasal swab specimen from child with Control [MAV079]


title: Nasal swab specimen from child with Control [MAV087]


title: Nasal swab specimen from child with Control [MAV074]


title: Nasal swab specimen from child with Convalescent [MAV075]


title: Nasal swab specimen from child with Convalescent [MAV076]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV091]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV073]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV072]


title: Nasal swab specimen from child with Control [MAV071]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV069]


title: Nasal swab specimen from child with Control [MAV066]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV077]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV088]


title: Nasal swab specimen from child with Control [MAV090]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV078]


title: Nasal swab specimen from child with Convalescent [MAV068]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV065]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV070]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV064]


title: scATAC-seq_MM057_Sox10KD_0hr_Cell_07

description:
MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts
MM057_Sox10KD_0hr_Aggregate_GoodCells_SizeFactorsNorm.sorted.bw

source_name: Melanoma cell line

value: 0 hours


title: Nasal swab specimen from child with Convalescent [MAV060]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV048]


title: Nasal swab specimen from child with Control [MAV037]


title: Nasal swab specimen from child with Control [MAV039]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV045]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV059]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV057]


title: Nasal swab specimen from child with Convalescent [MAV052]


title: Nasal swab specimen from child with Control [MAV031]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV054]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV035]


title: Nasal swab specimen from child with Control [MAV058]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV051]


title: Nasal swab specimen from child with Convalescent [MAV036]


title: Nasal swab specimen from child with Control [MAV055]


title: Nasal swab specimen from child with Control [MAV050]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV062]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV041]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV033]


title: Nasal swab specimen from child with Convalescent [MAV028]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV030]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV040]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV049]


title: Nasal swab specimen from child with Control [MAV042]


title: Nasal swab specimen from child with Convalescent [MAV044]


title: Nasal swab specimen from child with Control [MAV034]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV056]


title: Nasal swab specimen from child with Control [MAV026]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV025]


title: Nasal swab specimen from child with Control [MAV063]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV024]


title: Nasal swab specimen from child with Control [MAV023]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV022]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV021]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV017]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV019]


title: Nasal swab specimen from child with Control [MAV018]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV014]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV003]


title: Nasal swab specimen from child with Control [MAV010]


title: Nasal swab specimen from child with Convalescent [MAV004]


title: Nasal swab specimen from child with Convalescent [MAV012]


title: Nasal swab specimen from child with Convalescent [MAV112]


title: Nasal swab specimen from child with Control [MAV015]


title: Nasal swab specimen from child with Convalescent [MAV020]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV005]


title: Nasal swab specimen from child with Control [MAV007]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV016]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV001]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV011]


title: Nasal swab specimen from child with Control [MAV120]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV006]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV111]


title: Nasal swab specimen from child with Control [MAV002]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV008]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV013]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV104]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV009]


title: Nasal swab specimen from child with Control [MAV103]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV102]


title: Nasal swab specimen from child with Control [MAV110]


title: Nasal swab specimen from child with Convalescent [MAV116]


title: Nasal swab specimen from child with Convalescent [MAV100]


title: Nasal swab specimen from child with Acute asthma/wheeze [MAV109]


title: Nasal swab specimen from child with Convalescent [MAV108]


title: Nasal swab specimen from child with Control [MAV118]


title: HFD RWAT 3

status: Public on Feb 16 2019

city: Oxford

first: Haifei

last: Shi

state: OH

address: 501 E. High Street

department: Biology

institute: Miami University

data_processing:
Remove Truseq3-SE adapter sequence using Trimmomatic (version 0.36)
Single-end sequencing reads were aligned to the mouse genome (ENSEMBL 84 release, GRCm38.p4) using RSEM (version 1.3.0)
Differential gene expression analysis was performed by DESeq2 (version 1.10.1) using the estimated gene-level counts from RSEM
Genome_build: RNA-Seq clean reads  were mapped to mouse genome (ENSEMBL 84 release, GRCm38.p4)

source_name: retroperitoneal white adipose tissue

growth_protocol: High-fat diet

extract_protocol:
RNA extraction using E.Z.N.A® Total RNA kit II (Omega Bio-tek)
Libraries were sequenced as single-end 75 bp on Illumina NextSeq500 sequencing system at Cofactor Genomics Inc (St. Louis, MO). Approximately 30 millions of reads were retrieved from each sample
Ribosomal RNA was removed by using TruSeq Standard Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina)

treatment_protocol: Surgical denervation

tag: tissue type

value: white adipose tissue

value: wild type

tag: procedure

value: denervation

tag: diet

value: high-fat rodent diet


title: HFD RWAT 2

tag: strain


title: HFD IWAT 3

source_name: inguinal white adipose tissue

tag: genotype


title: HFD RWAT 1


title: HFD IWAT 1


title: HFD IWAT 2