title: Input_P0_PSG_Nsd1_KO

extract_protocol:
Testes were isolated and incubated at 37℃ for 5-8 minutes in 0.25% trypsin/0.5 mM EDTA/DNaseⅠ/PBS with serial pipetting to obtain single cell suspensions. After quenching the reaction with fetal bovine serum (FBS), cells were washed once with FACS buffer (2% FBS/1 mM EDTA/PBS), stained with Propidium Iodide (PI) and passed through a 35 μm cell strainer (Falcon). FACS was carried out on a BD Influx. Following removal of doublet/triplet cells, OCT3/4-EGFP+ (PI-) cells were sorted.
ULI-N-ChIP-seq protocol (Brind'Amour et al., 2015) was used for generating ChIP-seq libraries with some modifications. Briefly, chromatin was fragmentated by MNase (NEB), diluted in native ChIP buffer (20 mM Tris-HCl pH 8.0; 2 mM EDTA; 150 mM NaCl; 0.1% Triton X-100) containing 1 mM PMSF and EDTA-free protease inhibitor cocktail (Roche) and sonicated 10 second sonication cycles for 3 times with low power (Bioruptor). Following pre-clearing of chromatin fragments with protein A and G beads (ThermoFisher Scientific) or Dynabeads M-280 Sheep anti-Mouse IgG beads (ThermoFisher Scientific), chromatin fragments were split and incubated with each of the histone methylation antibodies at 4 degree for overnight. Following purification of ChIPed DNA by AMPure XP beads, end repair and A-tailing were performed using NEBNext UltraII End Repair/dA-Tailing Module (NEB) and ligation was carried out using NEBNext Ultra II Ligation Module (NEB) with an in-house adaptor which is compatible with Illumina sequencers. After purification of adaptor-ligated products by AMPure XP beads, libraries were amplified with unique indexing primers for 12-14 cycles. Following purification of the amplified libraries by AMPure XP beads, libraries were pooled, run on 2% E-Gel EX Gel (ThermoFisher Scientific) and the fragments from 200-600 bp was excised and purified by Zymoclean Gel DNA Recovery Kit (Zymo Research).

value: postnatal day 0


title: Tconv_aCD3-CD28_Donor2

status: Public on Jul 10 2020

type: SRA

city: Leiden

first: Mark

last: Mensink

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Center

description: Sample 2: 5076_2_27_sort_33B_Tconv_aCD3-28_CGATGTA

library_source: transcriptomic

data_processing:
The 65 bp single end reads were mapped to the human reference genome (hg38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using a custom script that gives the same output as HTSeq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample.

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

growth_protocol: Naïve Tconv and Treg cells were sorted from human buffy coats from male healthy donors (Sanquin) by flow cytometry. Human sorted Tconv and Treg cells were plated in 96-well round bottom plates (Greiner; 1x10^4 cells per well) and cultured in IMDM (Gibco, Life Technologies), supplemented with 8% FCS (Sigma), penicillin/streptomycin (Roche) and 300 IU/mL IL-2 (DuPont Medical) (T cell medium) at 37 °C/5% CO2. Activating mAbs to CD3 (clone CLB-T3/4.E, Sanquin, 0.1 µg/ml) and CD28 (clone CLB-CD28/1, Sanquin, 0.2 µg/ml,) were used for T cell expansion. From day 7 to 14, T cells (5x10^5 cells/mL) were plated in 24-well plates (Greiner). After 1 or 2 weeks of culture, Tconv and Treg cells (1 x 10^6 cells/mL) were cultured in 6-well plates (Corning) for 4 days in fresh T cell medium supplemented with 300 IU/mL IL-2, but without anti-CD3/CD28 mAbs. Dead cells were removed by Ficoll density gradient centrifugation prior to restimulation experiments.

extract_protocol:
Restimulated T cells were washed in cold PBS and resuspended in RLT buffer (Qiagen). Total RNA isolation was performed according to manufacturer’s protocol using the RNeasy MinElute Cleanup Kit (Qiagen) including an on-column DNAse digestion (Qiagen). Quality and quantity of the total RNA were assessed on a 2100 Bioanalyzer using a Nano chip (Agilent).
Library preparation was performed on RNA samples with a measured RNA Integrity Number (RIN) between 8.0 and 10.0. Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc.) according to manufacturer’s instructions (Illumina, Part # 15031047 Rev. E). RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Following the expansion protocol, 1x10^5 T cells were treated with anti-CD3, anti-CD3/CD28 or anti-CD3/TNFR2 (clone MR2-1, Hycult Biotech) agonistic mAbs for 24 hours, in the presence of IL-2, and were subsequently harvested for whole transcriptome analysis.

tag: cell type

value: Conventional CD4+ T cell

tag: treatment

value: IL-2 and anti-CD3/CD28 agonistic mAbs

tag: individual


title: Tconv_aCD3_Donor2

description: Sample 1: 5076_1_26_sort_33B_Tconv_aCD3_ATCACGA

value: IL-2 and anti-CD3 agonistic mAb


title: H3K36me2_P0_PSG_Nsd1_KO

city: Vancouver

first: Kenjiro

last: Shirane

state: British Columbia

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

library_source: genomic

data_processing:
ChIP-seq: Reads were aligned to the mouse genome (mm10) using bwa (Li and Durbin 2009). PCR duplicates were removed by Picard-tools (http://broadinstitute.github.io/picard) and remaining reads with low mapping quality (MAPQ < 5) were excluded by Samtools (http://www.htslib.org/). Smoothed bigWig files were generated by deeptools (Ramírez et al., 2014) with BINSIZE=100 and SMOOTHLENGTH=1000 options.
WGBS: Reads with adaptor sequences at the 5’-end or low-quality bases at the 3’-end were trimmed by Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and the remaining reads were then aligned to the mouse genome (mm10) using Bismark (Krueger and Andrews 2011) with bowtie2 and pbat options (Langmead and Salzberg 2012). Reads that were not aligned with paired-end mode were then separately mapped to mm10 using single-end mode. bismark_methylation_extractor was used for extracting methylated and unmethylated counts of each CpG.
RNA-seq: Reads were aligned to the mouse genome (mm10) and transcripts using STAR (Dobin et al., 2013) with --sjdbGTFfile and --twopassMode Basic options.
Aligned reads were converted to bigWig format using bedtools (Quinlan et al., 2010) and bedGraphToBigWig (UCSC).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: p0 prospermatogonia

tag: strain background

tag: developmental stage

tag: genotype/variation

value: Nsd1 KO

tag: chip antibody

value: H3K36me2 (Cosmo Bio, MABI0332)


title: H3K27me3_P0_PSG_Nsd1_KO


title: Treg_unstimulated_Donor4

description: Sample 15: 4848_15_81_tTreg_rest_24h_metab_sort_19_CAGATCA

treatment_protocol: Following the expansion protocol, 1x10^5 T cells were either unstimulated or restimulated using anti-CD3/CD28 mAbs for 24 hours, in the presence of IL-2, and were subsequently harvested for whole transcriptome analysis.

value: Regulatory CD4+ T cell


title: H3K4me3_P0_PSG_Nsd1_KO


title: Tconv_CD3-CD28_Donor4

description: Sample 14: 4848_14_80_Tconv_stim_24h_metab_sort_19_GCCAATA


title: Tconv_unstimulated_Donor4

description: Sample 13: 4848_13_79_Tconv_rest_24h_metab_sort_19_ACAGTGA


title: Treg_CD3-CD28_Donor3

description: Sample 12: 4848_12_70_tTreg_stim_24h_metab_sort_18_TGACCAA


title: H3K36me2_P0_PSG_Nsd1_Control

value: Nsd1 HET


title: Treg_aCD3_Donor2

description: Sample 4: 5076_5_31_sort_33B_tTreg_aCD3_ACAGTGA


title: Input_P12_GO

source_name: p12 growing oocyte

extract_protocol:
Ovaries were incubated in 2 mg/mL collagenaseA/0.2% trypsin/PBS at 37℃ for 10-20 minutes with serial pipetting and the same volume of M2 medium was added. Oocytes were then passed into 0.1% BSA/PBS and collected into drops of M2 medium. Oocytes with surrounding somatic cells were passed through several times into pulled glass capillaries to exclude somatic cells from oocytes and oocytes were collected in drops of M2 medium. Oocytes were then passed through 3-5 times into 0.1%BSA/PBS drops and collected.
ULI-N-ChIP-seq protocol (Brind'Amour et al., 2015) was used for generating ChIP-seq libraries with some modifications. Briefly, chromatin was fragmentated by MNase (NEB), diluted in native ChIP buffer (20 mM Tris-HCl pH 8.0; 2 mM EDTA; 150 mM NaCl; 0.1% Triton X-100) containing 1 mM PMSF and EDTA-free protease inhibitor cocktail (Roche) and sonicated 10 second sonication cycles for 3 times with low power (Bioruptor). Following pre-clearing of chromatin fragments with protein A and G beads (ThermoFisher Scientific) or Dynabeads M-280 Sheep anti-Mouse IgG beads (ThermoFisher Scientific), chromatin fragments were split and incubated with each of the histone methylation antibodies at 4 degree for overnight. Following purification of ChIPed DNA by AMPure XP beads, end repair and A-tailing were performed using NEBNext UltraII End Repair/dA-Tailing Module (NEB) and ligation was carried out using NEBNext Ultra II Ligation Module (NEB) with an in-house adaptor which is compatible with Illumina sequencers. After purification of adaptor-ligated products by AMPure XP beads, libraries were amplified with unique indexing primers for 12-14 cycles. Following purification of the amplified libraries by AMPure XP beads, libraries were pooled, run on 2% E-Gel EX Gel (ThermoFisher Scientific) and the fragments from 200-600 bp was excised and purified by Zymoclean Gel DNA Recovery Kit (Zymo Research).

value: postnatal day 12

value: WT


title: Tconv_CD3-CD28_Donor3

description: Sample 10: 4848_10_68_Tconv_stim_24h_metab_sort_18_ATTCCTT


title: H3K27me3_E16.5_PSG_Dnmt3l_KO

source_name: e16.5 prospermatogonia

value: embryonic day 16.5

value: Dnmt3l KO


title: Input_E16.5_PSG_Dnmt3l_KO


title: Treg_unstimulated_Donor3

description: Sample 11: 4848_11_69_tTreg_rest_24h_metab_sort_18_CGATGTA


title: H3K27me3_P0_PSG_Nsd1_Control


title: H3K36me2_E16.5_PSG_Dnmt3l_KO


title: Tconv_unstimulated_Donor3

description: Sample 9: 4848_09_67_Tconv_rest_24h_metab_sort_18_ACTGATA


title: Treg_CD3-CD28_Donor2

description: Sample 8: 4848_08_58_tTreg_stim_24h_GPA33_D6_GAGTGGA


title: Treg_unstimulated_Donor2

description: Sample 7: 4848_07_57_tTreg_rest_24h_GPA33_D6_CGTACGT


title: Tconv_unstimulated_Donor2

description: Sample 5: 4848_05_55_Tconv_rest_24h_GPA33_D6_GTGGCCT


title: Treg_CD3-CD28_Donor4

description: Sample 16: 4848_16_82_tTreg_stim_24h_metab_sort_19_CTTGTAA


title: H3K36me2_E16.5_PSG_Dnmt3l_Control

value: Dnmt3l HET


title: Treg_CD3-CD28_Donor1

description: Sample 4: 4848_04_28_tTreg_stim_24h_GPA33_D1_GGCTACA


title: Tconv_CD3-CD28_Donor2

description: Sample 6: 4848_06_56_Tconv_stim_24h_GPA33_D6_GTTTCGG


title: Treg_unstimulated_Donor1

description: Sample 3: 4848_03_27_tTreg_rest_24h_GPA33_D1_TAGCTTA


title: H3K4me3_P0_PSG_Nsd1_Control


title: H3K27me3_E16.5_PSG_Dnmt3l_Control


title: Input_P0_PSG_Nsd1_Control


title: H3K36me2_E16.5_PSG_Nsd1_KO3


title: Tconv_CD3-CD28_Donor1

description: Sample 2: 4848_02_26_Tconv_stim_24h_GPA33_D1_GATCAGA


title: Input_E16.5_PSG_Dnmt3l_Control


title: Tconv_unstimulated_Donor1

description: Sample 1: 4848_01_25_Tconv_rest_24h_GPA33_D1_ACTTGAA


title: H3K9me3_E16.5_PSG_Nsd1_KO3

value: H3K9me3 (Active Motif, 39161)


title: bulk MM087 SOX10-KD 72h

city: Leuven

first: k

last: spanier

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
The 10x samples were processed (alignment, barcode assignment and UMI counting) with the CellRanger count pipeline; pools with samples from different cell lines were demultiplexed using demuxlet (Kang et al. 2018); cells expressing less than 1000 genes and cells with more than 20% mitochondrial reads were removed
The Drop-seq samples were cleaned with fastq-mcf from the ea-utils package (v1.04.807; Aronesty 2011) and processed (alignment, barcode assignment and UMI counting) with the Drop-seq tools pipeline (v1.12) developed by James Nemesh from the McCarroll lab (Macosko et al. 2015), using Picard tools (v1.140; Broad Institute) and the STAR aligner (v2.5.1b; Dobin 2013); cells expressing less than 1000 genes, more than 50000 and/or more than 10% mitochondrial reads were removed.
bulk RNA-Seq reads were cleaned with fastq-mcf from the ea-utils package (v1.04.807; Aronesty 2011), mapped using STAR (v2.5.1b; Dobin 2013) and counted with HTSeq (v0.6.1p1; Anders 2014); normalized count matrices were made with DESeq2 (v1.18.1; Love et al. 2014)
Omni-ATAC-Seq raw reads were mapped using Bowtie (v2.2.6; Langmead and Salzberg 2012); Duplicate reads were removed with Picard (v1.134; Broad Institute 2019) and low quality reads were removed with SAMtools (Q30) (v1.8; Li et al. 2009). bigWig files were created with deepTools (Ramírez et al. 2016).
Genome_build: hg19

molecule: polyA RNA

source_name: melanoma cell line

extract_protocol: Not Provided

treatment_protocol: The MM lines were cultured in Ham's F10 nutrient mix (ThermoFisher Scientific) supplemented with 10% fetal bovine serum (Invitrogen) and 100 µg ml-1 penicillin/streptomycin (ThermoFisher Scientific). The A375 cell line was maintained in Dulbecco’s Modified Eagle’s Medium with high glucose and glutamax (ThermoFisher Scientific), supplemented with 10% fetal bovine serum (Invitrogen) and penicillin-streptomycin (ThermoFisher Scientific). Cell cultures were kept at 37°C, with 5% CO2 and were regularly tested for mycoplasma contamination, and were found negative. Knockdown of SOX10 was performed using a SMARTpool of four siRNAs (SMARTpool: ON-TARGETplus SOX10 siRNA, number L017192-00, Dharmacon) at a final concentration of 20nM in Opti-MEM medium (Thermo Fisher Scientific) after which cells were sampled at the indicated time points. To control for transfection artefacts, we used a pool of non-targeting siRNAs (SMARTpool: ON-TARGETplus Non-targeting Pool, number D001810-10-05, Dharmacon). Inhibition of CDK7-dependent transcription was achieved by treatment with THZ2 (HY-12280, MedChemExpress). For each treated melanoma culture, IC50 concentrations were calculated for 48 hours of treatment. As a control, DMSO treatment was used. For bulk RNA-seq, RNA was extracted from attached cells using the innuPREP RNA mini kit (Analytik Jena), according to the manufacturer’s instructions. For scRNA-seq and Omni-ATAC-seq, cells were detached by trypsinization, counted and processed according to downstream protocols.

tag: tissue

value: melanoma cell line

tag: cell line

value: siSOX10 72h

tag: sequencing method

value: bulk RNA-Seq


title: H3K36me2_E16.5_PSG_Nsd1_Control3


title: H3K27me3_E16.5_PSG_Nsd1_Control3


title: bulk MM087 NTC 72h

value: siNTC 72h


title: H3K9me3_E16.5_PSG_Nsd1_Control3


title: Input_E16.5_PSG_Nsd1_KO2


title: DLD-1 cells transfected with RCC1-AID Replicate 3

city: Bethesda

first: Alexei

last: Arnaoutov

state: MD

address: 49 Convent Dr, Bldg 49 Room 5A10

department: PCRM

country: USA

institute: NICHD

data_processing:
CASAVA version 1.8.2 (Illumina, San Diego, CA) was used for the base calling
We used STAR aligner version 2.6.1 (Dobin et al., 2013, PMID: 23104886) with the default parameters for mapping of the short reads.
We measured Gene-level read counts using featureCounts version 1.6.3 (Liao et al., 2014, PMID: 24227677) with "-O" (allowMultiOverlap) and "-p" (isPairedEnd) parameters.
Genome_build: Human reference genome GRCh38 (Ensembl release 87)
Supplementary_files_format_and_content: Tab-limited text files with Ensembl gene IDs and read counts from featureCounts.

growth_protocol: DLD-1 cells (human colorectal adenocarcinoma cells) were cultured in DMEM media supplemented with 10% heat-inactivated fetal bovine serum, 2mM Glutamax, 50 ug/ml Penicillin, 50 ug/ml Streptomycin at 37°C in 5% CO2 incubator. Around 75,000 to 100,000 cells were seeded on 6-well plates. Cells were harvested at 85% of confluency, washed with PBS, and lysed with RLT buffer for RNA extraction.

extract_protocol:
RNAeasy Mini Kit (Qiagen) was used for RNA extraction as in manufacturer's protocol.
The Molecular Genomics Core at the Eunice Kennedy Shriver National Institutes of Child Health and Human Development (NICHD, Bethesda, MD) performed the library preparation using TruSeq total RNA library preparation kit (Illumina, San Diego, CA), and sequenced the outcome

treatment_protocol: RNA was extracted from cell lines after 0, 4, 6,  and 9hrs of 1mM Auxin treatment (I5184, Sigma Aldrich).

value: cell line

tag: transfection


title: DLD-1 cells transfected with RCC1-AID Replicate 2


title: DLD-1 cells transfected with RCC1-AID Replicate 1


title: DLD-1 cells transfected with RCC1-AID and treated with Auxin for 6hr Replicate 3

tag: treatments

value: Auxin

tag: incubation time


title: H3K36me2_E16.5_PSG_Nsd1_KO2


title: H3K36me3_E16.5_PSG_Nsd1_KO2

value: H3K36me3 (EpiCypher, SKU13-0031)


title: H3K4me3_E16.5_PSG_Nsd1_KO2

value: Nsd1 KO


title: Input_E16.5_PSG_Nsd1_Control2


title: DLD-1 cells transfected with RCC1-AID and treated with Auxin for 6hr Replicate 2


title: DLD-1 cells transfected with RCC1-AID and treated with Auxin for 6hr Replicate 1


title: H3K27me3_E16.5_PSG_Nsd1_KO3


title: H3K27me3_E16.5_PSG_Nsd1_KO2


title: DLD-1 cells transfected with AID-RanBP3 Replicate 2


title: DLD-1 cells transfected with AID-RanBP3 Replicate 1


title: DLD-1 cells transfected with AID-RanBP3 and treated with Auxin for 4hr Replicate 3


title: DLD-1 cells transfected with AID-RanBP3 and treated with Auxin for 4hr Replicate 2


title: H3K4me3_E16.5_PSG_Nsd1_Control2


title: H3K27me3_E16.5_PSG_Nsd1_Control2


title: Input_E16.5_PSG_Nsd1_KO1


title: DLD-1 cells transfected with AID-RanBP3 and treated with Auxin for 4hr Replicate 1


title: H3K36me3_E16.5_PSG_Nsd1_KO1

value: H3K36me3 (Abcam, ab9050)


title: DLD-1 cells transfected with NUP96-NeonGreen-AID Replicate 3

data_processing:
For base-calling,  CASAVA version 1.8.2 (Illumina, San Diego, CA) was used.
STAR aligner version 2.6.1 was used (Dobin et al., 2013, PMID: 23104886) with the default parameters for mapping of the short reads
Gene-level read counts were determined using featureCounts version 1.6.3 (Liao et al., 2014, PMID: 24227677) with "-O" (allowMultiOverlap) and "-p" (isPairedEnd) parameters.
Genome_build: Human reference genome GRCh38 (obtained from Ensembl release 87)
Supplementary_files_format_and_content: Tab-limited text files that contain Ensembl gene IDs and read counts from featureCounts.

growth_protocol: Human Colorectal adenocarcinoma cells (DLD-1) were maintained in DMEM media supplemented with 10% heat-inactivated fetal bovine serum, 2mM Glutamax, 50 ug/ml Penicillin, 50 ug/ml Streptomycin. Cells were maintained at 37°C under 5% CO2. incubator. 75,000 to 100,000 cells were seeded on 6-well plates. Cells at 85% of confluency were harvested, washed with PBS, and lysed with RLT buffer for RNA extraction.

extract_protocol:
We used RNAeasy Mini Kit (Qiagen) was used for RNA extraction as in the manufacturer's manual.
The library preparation (TruSeq total RNA library preparation kit, Illumina, San Diego, CA) and sequencing were performed at the Molecular Genomics Core at the Eunice Kennedy Shriver National Institutes of Child Health and Human Development (NICHD, Bethesda, MD).

treatment_protocol: RNA was harvested from cell lines after 0hr, 4hr and 10hrs of 1mM Auxin treatment (I5184, Sigma Aldrich).

value: Colorectal adenocarcinoma cell line DLD-1

tag: genotype


title: DLD-1 cells transfected with NUP96-NeonGreen-AID Replicate 2


title: H3K27me3_E16.5_PSG_Nsd1_KO1


title: DLD-1 cells transfected with NUP96-NeonGreen-AID Replicate 1


title: DLD-1 cells transfected with NUP96-NeonGreen-AID treated with Hydroxyurea & Auxin for 10hr Replicate 3

value: HU & Auxin


title: H3K9me3_E16.5_PSG_Nsd1_KO1


title: DLD-1 cells transfected with AID-RanBP3 Replicate 3


title: H3K4me3_E16.5_PSG_Nsd1_KO1


title: H3K36me3_E16.5_PSG_Nsd1_Control2

value: Nsd1 HET


title: H3K36me2_E16.5_PSG_Nsd1_Control2

value: H3K36me2 (Cosmo Bio, MABI0332)


title: H3K36me3_E16.5_PSG_Nsd1_Control1

value: embryonic day 16.5


title: Input_E16.5_PSG_Nsd1_Control1


title: H3K36me2_E16.5_PSG_Nsd1_Control1


title: H3K27me3_E16.5_PSG_Nsd1_Control1


title: DLD-1 cells transfected with NUP96-NeonGreen-AID treated with Hydroxyurea & Auxin for 10hr Replicate 2


title: DLD-1 cells transfected with NUP96-NeonGreen-AID treated with Hydroxyurea for 10hr Replicate 1

description: DLD-1 cells transfected with NUP96-NeonGreen-AID HU NA Replicate 1

value: HU


title: DLD-1 cells transfected with NUP96-NeonGreen-AID treated with Hydroxyurea for 10hr Replicate 2

description: DLD-1 cells transfected with NUP96-NeonGreen-AID HU NA Replicate 2


title: Input_E16.5_PSG_Setd2_KO

value: Setd2 KO


title: H3K9me3_E16.5_PSG_Nsd1_Control1

value: H3K9me3 (Active Motif, 39161)


title: DLD-1 cells transfected with NUP96-NeonGreen-AID treated with Auxin for 4hr Replicate 1


title: H3K36me2_E16.5_PSG_Nsd1_KO1


title: H3K36me3_E16.5_PSG_Setd2_KO

value: H3K36me3 (GeneTex, GTX50908)


title: DLD-1 cells transfected with NUP96-NeonGreen-AID treated with Auxin for 4hr Replicate 2


title: H3K36me2_E16.5_PSG_Setd2_KO


title: DLD-1 cells transfected with NUP96-NeonGreen-AID treated with Auxin for 10hr Replicate 2


title: H3K4me3_E16.5_PSG_Nsd1_Control1


title: DLD-1 cells transfected with NUP96-NeonGreen-AID treated with Auxin for 10hr Replicate 1


title: Input_E16.5_PSG_Setd2_Control

value: WT


title: DLD-1 cells transfected with NUP96-NeonGreen-AID treated with Auxin for 10hr Replicate 3


title: H3K36me2_E16.5_PSG_Setd2_Control


title: DLD-1 cells transfected with NUP96-NeonGreen-AID treated with Hydroxyurea & Auxin for 10hr Replicate 1


title: DLD-1 cells transfected with NUP96-NeonGreen-AID treated with Auxin for 4hr Replicate 3


title: H3K36me3_E16.5_PSG_Setd2_Control


title: DLD-1 cells transfected with NUP85-NeonGreen-AID Replicate 3


title: DLD-1 cells transfected with NUP85-NeonGreen-AID Replicate 2


title: DLD-1 cells transfected with NUP96-NeonGreen-AID treated with Hydroxyurea for 10hr Replicate 3

description: DLD-1 cells transfected with NUP96-NeonGreen-AID HU NA Replicate 3


title: DLD-1 cells transfected with NUP85-NeonGreen-AID Replicate 1


title: H3K36me3_E13.5_male_PGC

source_name: e13.5 male primordial germ cells

value: embryonic day 13.5


title: IPT_4

city: Seattle

first: John

last: Scott

state: Washington

address: 1959 NE Pacific Street, HSB K316

department: Pharmacology

institute: University of Washington

description: rRNA-depleted total RNA inputs into immunoprecipitation experiments

data_processing:
Sequencing reads were pseudoaligned to the mouse GRCm38 reference transcriptome and the gene transcript abundances were quantified using Kallisto (Bray. et al, Nat Biotech, 2016)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of gene counts were generated from Kallisto transcript abundance files for downstream analysis with DESeq2

source_name: MA10 cell  RNA

growth_protocol: MA10 cells were routinely passaged in Roswell Park Memorial Institute 1640 Medium (RPMI 1640; Gibco) supplemented with 10% horse serum (HS; Gibco) and 1% PenStrep (PS; Gibco).

extract_protocol:
Total RNA was extracted with Trizol. Following immunoprecipitation, RNA was isolated from beads with Trizol followed by two chloroform extractions.
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq Stranded Total RNA Kit with Ribo Zero Depletion (RS-122-9007)

value: untreated

value: Leydig cell line


title: IPT_3


title: DLD-1 cells transfected with NUP85-NeonGreen-AID treated with Auxin for 4hr Replicate 3

value: Auxin


title: DLD-1 cells transfected with NUP85-NeonGreen-AID treated with Auxin for 4hr Replicate 2


title: IPT_2


title: IPT_1


title: DLD-1 cells transfected with NUP85-NeonGreen-AID treated with Auxin for 4hr Replicate 1


title: DLD-1 cells transfected with NUP85-NeonGreen-AID treated with Auxin for 10hr Replicate 2


title: KHT_3

description: Data collected from negative control immunoprecipitation experiments. Total MA10 RNA was incubated with purified protein bait, followed by immunoprecipitation with antiMBP antibody.

source_name: MA10 cell RNA immunoprecipitation

value: KHT bait


title: KHT_2


title: DLD-1 cells transfected with NUP85-NeonGreen-AID treated with Auxin for 10hr Replicate 1


title: KHT_1


title: DLD-1 cells transfected with NUP160-NeonGreen-AID Replicate 3


title: DLD-1 cells transfected with NUP160-NeonGreen-AID Replicate 2


title: DLD-1 cells transfected with NUP85-NeonGreen-AID treated with Auxin for 10hr Replicate 3


title: KHT_4


title: NEG_4

value: negative controls (empty antiMBP beads, MBP, or KHT(GDDG)) bait


title: DLD-1 cells transfected with NUP160-NeonGreen-AID treated with Auxin for 4hr Replicate 3


title: DLD-1 cells transfected with NUP160-NeonGreen-AID treated with Auxin for 4hr Replicate 1


title: DLD-1 cells transfected with NUP160-NeonGreen-AID treated with Auxin for 10hr Replicate 3


title: NEG_1


title: E18brain (951 cells) [Illumina]

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
Cells from a combined cortex, hippocampus and sub ventricular zone of an E18 mouse.
PolyA RNA

data_processing:
10x Genomics cellranger v2.0 possorted_genome bam files. The Cell Ranger Single Cell Software Suite 2.0 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Processing of Nanopore reads is described at https://github.com/ucagenomix/Sicelore
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx: Cellranger v2.0 filtered gene barcodes matrices.
Supplementary_files_format_and_content: *.isoforms.matrix.txt: Gene/cell barcode matrices of UMIs count as the isoform level.

source_name: E18 brain

extract_protocol:
Samples were processed on the 10x Genomics Chromium system following the User Guide for v2 Chemistry (https://support.10xgenomics.com/single-cell/sample-prep/doc/user-guide-chromium-single-cell-3-reagent-kit-v2-chemistry).
Single cell RNA-Seq libraries were made following the User Guide for v2 Chemistry (https://support.10xgenomics.com/single-cell/sample-prep/doc/user-guide-chromium-single-cell-3-reagent-kit-v2-chemistry). Libraries were sequenced as follows: 26bp Read 1 (16bp Chromium barcode and 10bp UMI), 57bp Read 2 (transcript), and 8bp i7 library barcode. For Nanopore sequencing cDNA was re-amplified, sequencing libraries were prepared with the Oxford Nanopore LSK-109 library preparation kit.

value: Cortex, hippocampus and sub ventricular zone

tag: strain


title: DLD-1 cells transfected with NUP160-NeonGreen-AID treated with Auxin for 10hr Replicate 2

value: Colorectal adenocarcinoma cell line DLD-1


title: DLD-1 cells transfected with NUP160-NeonGreen-AID treated with Auxin for 10hr Replicate 1


title: DLD-1 cells transfected with AID-NeonGreen-NUP133 Replicate 2


title: DLD-1 cells transfected with AID-NeonGreen-NUP133 Replicate 1


title: Sample_cko_tac_sil5_200129

city: Bunkyo-ku

first: Takashi

last: Shimizu

country: Japan

institute: University of Tokyo

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
Reads were trimmed with Trimmomatic.
The trimmed reads were aligned to the mouse reference genome mm10 with HISAT2.
Sequencing tracks normalized by the mapped read counts were generated with deepTools.
Genome_build: Genome Reference Consortium Mouse Build 38 (mm10)
Supplementary_files_format_and_content: bigwig

source_name: heart

extract_protocol:
Total RNA was isolated from hears by using a miRNeasy micro Kit (Qiagen) with the DNase digestion step, according to the manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions.

value: heart

value: PERK mutant

value: sildenafil


title: Sample_cko_tac_sil12_200129


title: Sample_cko_tac_sil11_200129


title: NEG_5


title: NEG_3


title: NEG_2


title: DLD-1 cells transfected with NUP160-NeonGreen-AID Replicate 1


title: DLD-1 cells transfected with AID-NeonGreen-NUP133 treated with Auxin for 10hr Replicate 3


title: DLD-1 cells transfected with AID-NeonGreen-NUP133 treated with Auxin for 10hr Replicate 1


title: DLD-1 cells transfected with NUP160-NeonGreen-AID treated with Auxin for 4hr Replicate 2


title: DLD-1 cells transfected with AID-NeonGreen-NUP133 treated with Auxin for 4hr Replicate 2


title: Sample_cko_tac9

value: no sildenafil treatment


title: Sample_cko_tac8


title: DLD-1 cells transfected with AID-NeonGreen-NUP107 Replicate 1


title: DLD-1 cells transfected with AID-NeonGreen-NUP133 treated with Auxin for 4hr Replicate 3


title: Sample_cko_tac7


title: Sample_flx_tac_sil6_200129

value: wild-type


title: DLD-1 cells transfected with AID-NeonGreen-NUP107 Replicate 3


title: DLD-1 cells transfected with AID-NeonGreen-NUP107 Replicate 2


title: DLD-1 cells transfected with AID-NeonGreen-NUP133 treated with Auxin for 4hr Replicate 1


title: Sample_flx_tac_sil5_200129


title: Sample_flx_tac3_200129


title: Sample_flx_tac_200129


title: E18brain (190 cells) [Illumina]


title: DLD-1 cells transfected with AID-NeonGreen-NUP133 Replicate 3


title: Sample_flx_tac2_200129


title: DLD-1 cells transfected with AID-NeonGreen-NUP107 treated with Auxin for 4hr Replicate 3


title: P61 V-SVZ Emx1Cre

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay Street

institute: Hospital for Sick Children

data_processing:
FASTQ sequencing reads were processed, aligned to the mouse genome (mm10) and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite. Cell Ranger filtered_gene_bc_matrices files were subsequently run through our custom made computational pipeline described in the manuscript
The number of cell barcodes per sample was identified using the CellRanger Single Cell Software Suite.
In order to detect EYFP expression, EYFP ORF was concatenated to the mm10 reference genome
Genome_build: mm10
Supplementary_files_format_and_content: The data packages contain the filtered digital gene expression for each sample obtained from the Cell Ranger Pipeline (filtered_gene_bc_matrices files). The processed data files uploaded have not been run through our custom computational pipeline described in the manuscript.

source_name: Adult postnatal V-SVZ tissue

extract_protocol:
Relevant tissue (see above) was dissected, dissociated into single-cell suspensions, FACS sorted for viability and single cell transcriptomes were captured using the 10X Chromium version 2 chemistry
Libraries were prepared according to the manufacturer's instructions (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit.

tag: transgenic

value: Neural

tag: age

tag: brain region

value: V-SVZ

tag: enzymatic digestion

value: Papain (30 min 37°C)

tag: facs

value: Propidium iodide (cell viability) + Draq5


title: P20 V-SVZ Emx1Cre

source_name: Late postnatal V-SVZ tissue

value: Propidium iodide (cell viability)


title: DLD-1 cells transfected with AID-NeonGreen-NUP107 treated with Auxin for 4hr Replicate 2


title: P34 V-SVZ Emx1Cre


title: Sample_flx_tac_sil4_200129

tag: treatment


title: DLD-1 cells transfected with AID-NeonGreen-NUP133 treated with Auxin for 10hr Replicate 2


title: DLD-1 cells transfected with AID-NeonGreen-NUP107 treated with Auxin for 4hr Replicate 1


title: P7 V-SVZ Emx1Cre

description: cDNA library was sequenced twice due to low read depth in first sequencing run. Library was re-sequenced to obtain a read top up. FastQ files from first NGS sequencing run is labeled as "set1" and FastQ files from second sequencing run is labeled as "set2"

source_name: Early postnatal V-SVZ tissue

value: No


title: P6 V-SVZ Nkx2.1Cre (N=1)


title: P6 V-SVZ Emx1Cre


title: DLD-1 cells transfected with AID-NeonGreen-NUP107 treated with Auxin for 10hr Replicate 2


title: DLD-1 cells transfected with AID-NeonGreen-NUP107 treated with Auxin for 10hr Replicate 1


title: DLD-1 cells transfected with AID-NeonGreen-NUP107 treated with Auxin for 10hr Replicate 3


title: Diabetic.9_versus_pool of non-diabetic

type: RNA

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

description: microRNA expression levels  in the skin of a Type 1 mouse model of diabetes

hyb_protocol: 2-color hybridization was performed using Exiqon miRCURY LNA microRNA array, 7th generation [miRBase v18]. 1.25ug of each labeled RNA were co-hybridized at 53°C for 16 hours. Hybridization and washing steps were performed on the HS 400 PRO hybridization station (Tecan).

scan_protocol: MicroRNA arrays were scanned using the GenePix 4100A microarray scanner and the GenePix Pro GenePix Pro 6.1.0.4 software (Molecular Devices).

data_processing:
The obtained signal intensities were analyzed by using the limma package (Bioconductor 2.5 on R 2.10.1 ). Background correction (normexp; cut-off=10) and within-array normalization (global LOESS) was performed. Differential expression and statistical significance were assessed for each miRNA species across all arrays using linear model fit and empirical Bayes method (lmFit, eBayes), taking into account the dye-swap. Spots showing intensities < 3 SNR (for Hy3 and Hy5) OR displaying diameters >130 or <70µm were considered as bad quality spot. The calling of a miRNA failed if 2 or more of the 4 replicates present per miRNA species were bad quality spots and if this occurred on 4 or more arrays.
Processed data file includes normalized log2 ratios representing diabetic/non-diabetic. P value adjusted for False Discovery Rate (Benjamini and Hochberg's method).

source_name: non-diabetic skin

label_protocol: 1.25 ug total RNA was labeled with Hy3, Hy5 resepctively according to the manufacturer's protocol (miRCURY LNA microRNA Array Power labeling kit, EXIQON).

growth_protocol: Mice were purchased form Charles River Laboratories (Calco, Lecco, Italy), and maintained on a standard diet. Food and water were given ad libitum.

extract_protocol: Back skin biopsies were collected and snap-frozen. For RNA extraction, frozen biopsies were maintained in liquid nitrogen and crushed to powder with a mortar and pestle. The frozen powder was poured into Trizol (Invitrogen), and RNA extracted following manufacturer’s instructions.

treatment_protocol: To obtain type1 diabetic mice, six week-old C57Bl/6 male mice were intraperitoneally injected with 160 mg/kg streptozotocin (Sigma-Aldrich, St. Louis, MO) in 0.05M Na citrate pH 4.5. Seven days after streptozotocin administration, blood glucose levels were measured, and mice with glycaemia above 250 mg/dL were included in the study. Three weeks later, glycaemia was checked again on selected mice, and diabetic mice were sacrificed immediately before collecting their skin.

tag: Sex

value: male

value: skin

tag: disease state

value: non-diabetic

source_name: diabetic skin

value: diabetic


title: Diabetic.7_versus_pool of non-diabetic_dye swap


title: Diabetic.4_versus_pool of non-diabetic


title: Diabetic.7_versus_pool of non-diabetic


title: Diabetic.6_versus_pool of non-diabetic


title: E14 Cortex + GE Emx1Cre N = 2

description: cDNA library was generated from a cell suspension from the same set of embryonic brains as Sample 3 (E14 Cortex + GE Emx1Cre N = 3). cDNA library was generated using a separate 10X chromium.

source_name: Embryonic cortex and ganglionic eminence

value: Cortex and Ganglionic Eminence


title: Diabetic.2_versus_pool of non-diabetic_dye swap


title: E14 Cortex + GE Emx1Cre N = 3

description: cDNA library was generated from a cell suspension from the same set of embryonic brains as Sample 2 (E14 Cortex + GE Emx1Cre N = 2). cDNA library was generated using a separate 10X chromium.


title: Diabetic.2_versus_pool of non-diabetic


title: Diabetic.1_versus_pool of non-diabetic


title: E14 Cortex + GE Emx1Cre N = 1


title: E17 V-SVZ Emx1Cre

source_name: Embryonic V-SVZ tissue


title: ExoT-seq_Dmc1.null_16dpp_rep1_adaptor.swap.F

city: New York

first: Shintaro

last: Yamada

state: New York

address: 1275 York Avenue

department: MOLECULAR BIOLOGY PROGRAM

institute: MEMORIAL SLOAN-KETTERING CANCER CENTER

description: ExoT-seq

data_processing:
Library strategy: DNA-seq
Base calls were perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Reads were trimmed and filtered by Trim Galore version 0.4.5  with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>.
Sequence reads were mapped onto the mouse reference genome (mm10) by bowtie2 version 2.2.1 (1) with the arguments -N 1 -X 1000.     1. B. Langmead, C. Trapnell, M. Pop, S. L. Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).
Duplicated reads were removed by Picard <https://broadinstitute.github.io/picard/>. Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools with the arguments  -q 20 <http://www.htslib.org/>.
Reads for S1-seq and ExoT-seq were counted at which a nucleotide next to biotinylated adaptor DNA was mapped (this corresponds to a position of a resection endpoint). Adaptors were swapped for some samples (indicated by sample names). For those samples, reads were counted at which a nucleotide next to the other (unbiotinylated) adaptor DNA was mapped Reads for ATAC-seq were counted at which Tn5 insertion positions were mapped. Maps were analyzed using R versions 3.2.3 to 3.3.1 <http://www.r-project.org>
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files include read counts at positions of resection endpoints for S1-seq and End-seq, and at Tn5 insertion positions for ATAC-seq. Reads were not normalized to RPM (reads per million mapped).  Letter "top" or "bottom" in S1-seq and End-seq sample names indicates that reads were mapped on top or bottom strand, respectively.

source_name: Spermatocytes

extract_protocol:
Testis dissociation  Unless otherwise stated, testis cells from12-dpp juvenile mice were obtained as described previously (1). Briefly, testes were decapsulated, and incubated in Gey's balanced salt solution (GBSS, Sigma) with 0.5 mg/ml collagenase type 1 (Worthington) at 33 °C for 15 min. Seminiferous tubules were then rinsed three times and further treated with 0.5 mg/ml trypsin (Worthington) and 1 μg/ml DNase I (Sigma) at 33 °C for 15 min. Trypsin was inactivated with 5% FCS and tubules were further dissociated by repeated pipetting. Cells were passed through a 70-μm cell strainer (BD Falcon) and washed 3 times in GBSS.    1. F. Cole et al., Mouse tetrad analysis provides insights into recombination mechanisms and hotspot evolutionary dynamics. Nat Genet 46, 1072-1080 (2014).
S1-seq and ExoT-seq  DNA extraction in plugs  Cells were embedded in plugs of 0.5% low-melting point agarose (Lonza) in GBSS. One plug mold (Bio-Rad) was used per 2 testes (1~2 million cells per plug). Plugs were incubated with 50 µg/ml of proteinase K (Roche) in lysis buffer (0.5 M EDTA pH 8.0, 1 % N-lauroylsarcosine sodium salt) overnight. Plugs were washed 5 times with TE (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH8.0), and then incubated with 50 μg/ml RNase A (ThermoFisher) at 37 °C for 3 hours. They were washed 5 times with TE and stored in TE at 4 °C    Library preparation  In-plug overhang removal with S1 and adaptor ligation were performed as previously described (1, 2). For ExoT-seq, the S1 treatment step was replaced with the following: Plugs were washed in 1 ml of NEBuffer 4 for 15 min 3 times, treated with 75 units of exonuclease T in 100 µl of NEBuffer 4 at 24°C for 90 min and washed 3 times with 8 ml of TE for 15 min (3). After adaptor ligation, plugs were washed 3 times in TE and incubated in TE at 4 °C overnight to diffuse excessive unligated adaptors out of plugs. Agarose was then digested by the Epicentre GELase Enzyme Digestion protocol. DNA was fragmented by vortex and further sheared to DNA fragment sizes ranging between 200-500 bp with a Bioruptor® waterbath sonicator (Diagenode) at 4 °C for 40 cycles of 30 seconds ON/OFF at the middle power setting. DNA was purified by ethanol precipitation and dissolved in 100 μl TE. Fragments containing the biotinylated adaptor were purified with streptavidin, ligated to adaptors at sheared end and amplified by PCR as previously described (1, 2). PCR products were purified with 0.9× AMPure XP Beads (Beckman Coulter) to remove primer dimers. DNA was sequenced on the Illumina HiSeq platform in the Integrated Genomics Operation at Memorial Sloan Kettering Cancer Center.    ATAC-seq  ATAC-seq library preparation was performed as described (4) with slight modifications. Briefly, nuclei extracted from 50,000 testis cells were treated with Tn5 transposase at 42 °C for 45 min. Libraries were amplified by PCR, and sequenced.     1. E. P. Mimitou, S. Yamada, S. Keeney, A global view of meiotic double-strand break end resection. Science 355, 40-45 (2017).  2. E. P. Mimitou, S. Keeney, S1-seq Assay for Mapping Processed DNA Ends. Methods Enzymol 601, 309-330 (2018).  3. A. Canela et al., Topoisomerase II-induced chromosome breakage and translocation is determined by chromosome architecture and transcriptional activity. Mol Cell 75, 252-266 e258 (2019).  4. J. D. Buenrostro, P. G. Giresi, L. C. Zaba, H. Y. Chang, W. J. Greenleaf, Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10, 1213-1218 (2013).

value: C57BL/6J & 129S1/SvImJ (mixed)

value: testis

value: 16 days post partum


title: ExoT-seq_wt_16dpp_rep2_adaptor.swap.F

description: ExoT-seq


title: Second sample prepared using nEMOTE protocol from dmazEF+pF strain, without PNK

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

data_processing:
Library strategy: nEMOTE-seq
nEMOTE reads were processed with the R package EMOTE v0.2 (https://github.com/pradosj/EMOTE). The package check the reads and parse them to extract the mapping sequence as well as the UMI sequence; it then aligns the reads on the genome (with Rbowtie package) and quantify the number of read with unique UMI starting at each genomic position.
The genomic positions with less than 4 UMI in ΔmazEF pRAB11-mazF-1_+PNK or ΔmazEF pRAB11-mazF-2_+PNK were not further considered
A beta-binomial model is used to estimate the probability that +PNK condition is significantly enriched compared to the corresponding -PNK condition. The p-values obtained for the 2 replicates are combined with Fisher's method, and the FDR computed to correct for multiple testing.
To determine confident 5’-OH ends generated by MazF, each genomic position had to match the following criteria:  an FDR < 0.1 for ΔmazEF pRAB11-mazF condition, and an FDR > 0.1 in ΔmazEF condition
Genomic position falling into a rRNA feature are processed separately
Remaining mazF cleavages are further annotated with genomic informations (DNA sequence arround the position, nearest gene)
RNA-seq reads are aligned on the reference genome with "bwa mem" command and "samtools" to generate files in BAM format. The BAM files are further processed to quantify the number of read in genes with the method "summarizeOverlaps(mode='IntersectionStrict',inter.feature=FALSE)" from R package GenomicAlignments. Quantification arround the cleavage sites are obtained with the method "coverage()" of the R package "GenomicAlignments"
Genome_build: NC_007795.1

organism: Staphylococcus aureus

source_name: bacterial cell

growth_protocol: S. aureus HG003 and S. aureus HG003 ΔmazEF were electroporated with anhydrotetracycline (ATc) inducible pRAB11 and pRAB11-mazF constructed vector. Strains carrying the pRAB11 vector were always grown in presence of chloramphenicol (15 µg/mL). Overnight cultures were diluted 1/1000 in 10 mL of Mueller-Hinton broth (cation adjusted, Difco) and incubated at 37ºC with shaking. At OD600 0.3, ATc was added to a final concentration of 0.2 µM. At each time point (0, 15, 30, 60 minutes postinduction) the samples were subject to 10-fold serial dilutions in 96-well plates using saline solution (0.9% NaCl), 10 µL aliquots were spotted in Mueller-Hinton (Difco) agar plates and incubated at 37ºC overnight. Colonies were then counted.

extract_protocol:
Overnight cultures were diluted 1/50 in 20 mL of Mueller-Hinton broth and incubated at 37ºC without shaking until OD600 0.3. ATc was added to a final concentration of 0.2 µM and incubated at 37ºC during 10 min. 8 mL of bacterial culture were immediately transferred to 40 mL of ice-cold ethanol:acetone (1:1), and centrifugated at 5000 rpm and 4ºC during 10 min. The supernatant was discarded, and pellet was washed with 1X TE. The pelleted cells were treated with lysostaphin (200 µg/mL) and RNasin Plus (Promega) in a final volume of 100 µL then placed in a heat block at 37ºC during 10 min. RNA extractions were done on the same day using the ReliaPrep (Promega) following the manufacturer’s instructions. Total RNA was frozen and kept at -80ºC.
nEMOTE as in Kirkpatrick, 2016. Briefly, mono-phosphorylated RNA was digested from 8 µg of high-quality total RNA with XRN-1. XRN-1 was removed with a phenol - chloroform - isoamyl alcohol 25:24:1 (Sigma) extraction, and the aqueous phase was recovered using MaXtract High Density (Qiagen) tubes. The recovered RNA was split into two pools, one pool was treated with PNK (+PNK) and the other was subject to the same treatment without PNK (-PNK). Rp6 RNA oligonucleotide was ligated to the 5’-phosphorylated RNA followed by an ethanol precipitation. Reverse transcription was carried out using semi-random primer DROAA and the cDNA was purified using Wizard SV Gel and PCR clean-up system (Promega). Second-strand synthesis and barcode incorporation were performed using Q5 Hot Start High Fidelity DNA polymerase (New England Biolabs). The PCR products were purified, mixed and size-selected between 300 – 1000 bp. The sample was then quantified and sequenced in an Illumina HiSeq 2500 sequencer using 50 bp single-read cycle.

value: dmazEF


title: Wild type replicate 3

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

country: Spain

institute: IGTP

description:
wild type in vitro differentiated myoblasts derived from FACS sorted alpha 7-integrin/CD34 double positive microsatellite primary cultures
WT.C

data_processing:
Sequencing was performed at the Genomics Unit of the Center for Genomic Regulation (CRG) on an Illumina HiSeq2500 sequencer using TruSeq v4 chemistry to generate between 46 and 62 million 2x50 bp paired end reads per sample.
Bioinformatics and statistical analysis was performed at the High Content Genomics and Bioinformatics Unit of the IGTP. Raw sequencing data was assessed for quality with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc; Andrews 2010) and
Quality based trimming was performed using Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic; Bolger et al. 2014).
Trimmed reads were aligned to the mouse reference genome (Ensembl release 85, Mus_musculus.GRCm38.dna.primary_assembly) with Tophat v2.0.8 (http://ccb.jhu.edu/software/tophat/index.shtml, Trapnell et al. 2009), which uses Bowtie v2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). We provided Tophat with the corresponding Ensembl GFT annotation file (Mus_musculus.GRCm38.85.gtf) containing feature coordinates.
The resulting BAM files were further analyzed using the QualiMap software (http://qualimap.bioinfo.cipf.es/; García-Alcalde et al. 2012).
Aligned reads were counted using FeatureCounts (Liao et al. 2014) based on annotation at the gene, transcripts and exon level.
Differential gene expression analysis between WT and KO mice was performed with the DESeq2 R package (Love, Huber, & Anders, 2014) with p value correction adjusting for multiple testing by the false discovery rate (FDR) method of Benjamini and Hochberg.
Functional enrichment was assessed with several different tools. First, gene ontology enrichment analysis was performed using the GOrilla web server (http://cbl-gorilla.cs.technion.ac.il/; (Eden, Navon, Steinfeld, Lipson, & Yakhini, 2009)) on the top significant upregulated and downregulated genes after applying a cutoff of an absolute fold change larger than 1.2 and adjusted p-value under 0.05. We also used Enrichr (http://amp.pharm.mssm.edu/Enrichr/, Chen et al. 2013, Kuleshov et al. 2016) to search for further functional enrichment]. We then used the same gene lists as input for the compareCluster function in clusterProfiler (G. Yu, Wang, Han, & He, 2012) and the Pathview (Luo & Brouwer, 2013) packages in the R statistical programming environment to graphically depict individual gene expression in enriched KEGG pathways. Finally we performed gene set enrichment analysis (using the GSEA software, (Subramanian et al., 2005) on preranked log2ratio data using the weighted statistic option to explore the following MaSigDB geneset collections: C2 (‘cgp’, curated literature genesets from cellular and genetic perturbation, and ‘cp’ canonical gene pathways including KEGG, REACTOME, SA,PID,), C3 (miRNA, for miRNA targets, and ‘tft’, transcription factors), C5 (gene ontology) and C7 (immunological gene sets). For GSEA analysis we converted mouse symbols to the closest human orthologues using the MART tool in ENSEMBL and reducing the list such that a gene with several orthologues passed the log2ratio value to al hits and log2 ratio values of several genes with a common orthologue were averaged.
Genome_build: Ensembl release 85, Mus_musculus.GRCm38.dna.primary_assembly

source_name: hindlimb skeletal muscle

growth_protocol: WT and HDAC11-deficient mouse myoblasts were cultured in growth medium (Ham’s F-10, 20% v/v inactivated foetal bovine serum, 4 mM of L-glutamine, 2 mM of pyruvate, 100 U/ml of penicillin and 100 µg/ml streptomycin supplemented with 1/10,000 v/v of basic fibroblast growth factor (Ref. 100-18B, Prepotech) at low density.

extract_protocol:
RNA was extracted following the manufacturer protocol using PureLinkTM RNA Mini Kit (Ambion, Life Technologies), including On-Column PureLink® DNase treatment. RNA integrity was assessed by Bioanalyzer nano 6000 assay. All samples had RNA integrity number (RIN) values between 8 and 9.4.
Stranded mRNA sequencing libraries were generated with the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina starting from 100 ng of total RNA subjected to oligo-dT capture with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries obtained had an average size range between 344 and 424 bp as determined by Bioanalyzer DNA 1000 assay. Libraries were quantified by qPCR with the KAPA library quantification kit for Illumina GA.

treatment_protocol: To induce cell differentiation, subconfluent proliferating WT and HDAC11-deficient mouse myoblasts were plated at high density (26,000 cells/cm2) in matrigel basement membrane matrix (Ref. 354234, Corning, Becton and Dickinson) coated plates. Next day after plating, the proliferating media was changed to differentiation medium (DMEM, 2%  v/v inactivated horse serum, 4 mM of L-glutamine, 2 mM of pyruvate, 100 U/ml of penicillin and 100 µg/ml streptomycin) for 24 hours before collecting the cells an isolating total RNA.   HDAC11 total knockout mice (HDAC11-/-) were generated by crossing C57BL/6 mice carrying loxP sites flanking the exon 3 of Hdac11 gene (ENSMUSE00001222983, chr6: 91,109,155-91,109,255, mm9), with mice expressing CRE recombinase under the control of SOX2 promoter. The floxing of loxP sites causes a deletion of exon 3 leading to a premature stop codon in exon 4. That results in loss of function of HDAC11 by generating a truncated protein of 59 aa instead of 349 aa. HDAC11-/- animals were obtained from undercrossing heterozygote mice and WT littermates were used as controls.

tag: cell type

value: myoblasts

value: wild type


title: Second sample prepared using nEMOTE protocol from dmazEF+pF strain, with PNK


title: Wild type replicate 2

department: High Content Genomics and Bioinformatics

description:
wild type in vitro differentiated myoblasts derived from FACS sorted alpha 7-integrin/CD34 double positive microsatellite primary cultures
WT.B


title: First sample prepared using nEMOTE protocol from dmazEF+pF strain, with PNK


title: P6 V-SVZ Nkx2.1Cre (N=2)

description: During flow sorting, larger number of Nkx2.1-lineage cells were sorted using EYFP expression

tag: tissue

value: Neural


title: P2 V-SVZ Emx1Cre

value: V-SVZ


title: Hdac11 knock out replicate 3

description:
Hdac11 mutant in vitro differentiated myoblasts derived from FACS sorted alpha 7-integrin/CD34 double positive microsatellite primary culture
KO.C


title: First sample prepared using nEMOTE protocol from dmazEF+pF strain, without PNK


title: Second sample prepared using nEMOTE protocol from dmazEF strain, with PNK


title: Hdac11 knock out replicate 2

description:
Hdac11 mutant in vitro differentiated myoblasts derived from FACS sorted alpha 7-integrin/CD34 double positive microsatellite primary culture
KO.B


title: First sample prepared using nEMOTE protocol from dmazEF strain, with PNK


title: Hdac11 knock out replicate 1

description:
Hdac11 mutant in vitro differentiated myoblasts derived from FACS sorted alpha 7-integrin/CD34 double positive microsatellite primary culture
KO.A


title: Wild type replicate 1

description:
wild type in vitro differentiated myoblasts derived from FACS sorted alpha 7-integrin/CD34 double positive microsatellite primary cultures
WT.A


title: S1-seq_Exo1DA_12dpp_rep2_adaptor.swap.T

value: 12 days post partum


title: Second sample prepared using nEMOTE protocol from dmazEF strain, without PNK


title: First sample prepared using nEMOTE protocol from dmazEF strain, without PNK


title: S1-seq_B6.PWD.F1_12dpp_rep1_adaptor.swap.T

value: C57BL/6J & PWD/PhJ (F1 hybrid)


title: ExoT-seq_Dmc1.wt_16dpp_rep1_adaptor.swap.F

description: ExoT-seq


title: S1-seq_B6.PWD.F1_9dpp_rep2_adaptor.swap.T

value: 9 days post partum


title: S1-seq_B6.PWD.F1_12dpp_rep3_adaptor.swap.T


title: S1-seq_B6.PWD.F1_9dpp_rep1_adaptor.swap.T


title: S1-seq_B6.PWD.F1_12dpp_rep2_adaptor.swap.T


title: S1-seq_Spo11.het.Atm.null_12dpp_rep1_adaptor.swap.T


title: S1-seq_Dmc1.null_16dpp_rep3_adaptor.swap.T


title: ATAC-seq_wild.type_12dpp

description: ATAC-seq

data_processing:
Base calls were perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Reads were trimmed and filtered by Trim Galore version 0.4.5  with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>.
Sequence reads were mapped onto the mouse reference genome (mm10) by bowtie2 version 2.2.1 (1) with the arguments -N 1 -X 1000.     1. B. Langmead, C. Trapnell, M. Pop, S. L. Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).
Duplicated reads were removed by Picard <https://broadinstitute.github.io/picard/>. Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools with the arguments  -q 20 <http://www.htslib.org/>.
Reads for S1-seq and ExoT-seq were counted at which a nucleotide next to biotinylated adaptor DNA was mapped (this corresponds to a position of a resection endpoint). Adaptors were swapped for some samples (indicated by sample names). For those samples, reads were counted at which a nucleotide next to the other (unbiotinylated) adaptor DNA was mapped Reads for ATAC-seq were counted at which Tn5 insertion positions were mapped. Maps were analyzed using R versions 3.2.3 to 3.3.1 <http://www.r-project.org>
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files include read counts at positions of resection endpoints for S1-seq and End-seq, and at Tn5 insertion positions for ATAC-seq. Reads were not normalized to RPM (reads per million mapped).  Letter "top" or "bottom" in S1-seq and End-seq sample names indicates that reads were mapped on top or bottom strand, respectively.


title: S1-seq_Dmc1.null_16dpp_rep2_adaptor.swap.F


title: S1-seq_Dmc1.null_16dpp_rep1_adaptor.swap.F


title: S1-seq_Dmc1.wt_16dpp_rep2_adaptor.swap.F


title: S1-seq_Dmc1.wt_16dpp_rep1_adaptor.swap.F


title: S1-seq_Spo11.null_12dpp_rep3_adaptor.swap.F


title: S1-seq_Spo11.null_12dpp_rep2_adaptor.swap.F


title: S1-seq_Exo1DA_12dpp_rep1_adaptor.swap.F


title: non-carcinoma tissue,biological rep2 (lncRNA-mRNA)

city: haerbin

first: Ming

last: Liu

address: No. 246 xuefu road, nangang district

country: China

institute: The Second Affiliated Hospital, Harbin Medical University

description:
Raw file: US10313827_256740610490_S01_GE2_1105_Oct12_1_1.txt
2AB

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner(G2565CA)

data_processing: Separating two-color gene expression data to single channel data is analysed by red and green channels intensities respectively. The gProcessed Signal( green processed signal)and rProcessed Signal (red processed signal) are exported by Agilent Feature Extraction software with default protocol settings, which contain the multiplicatively detrended background Subtracted signal. Transformed all individual processed signals to log2 values, then normalize to the 75th percentile value.

source_name: larynx adjacent non-carcinoma epithelial tissue

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: The samples were acquired from patients diagnosed with laryngeal squamous cell carcinoma who underwent partial or total laryngectomy at the Department of Otorhinolaryngology, the Second Affiliated Hospital of Harbin Medical University.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The tissues were stored in liquid nitrogen within 10 minutes after surgical resection.

value: laryngeal carcinoma

tag: tnm


title: non-carcinoma tissue,biological rep3 (lncRNA-mRNA)

description:
Raw file: US10313827_256740610490_S01_GE2_1105_Oct12_1_2.txt
3AB

value: larynx adjacent non-carcinoma epithelial tissue


title: non-carcinoma tissue,biological rep4 (lncRNA-mRNA)

description:
Raw file: US10313827_256740610490_S01_GE2_1105_Oct12_1_3.txt
4AB


title: S1-seq_Dmc1.null_12dpp_rep3_adaptor.swap.F


title: S1-seq_Spo11.null_12dpp_rep1_adaptor.swap.F


title: S1-seq_Dmc1.null_12dpp_rep2_adaptor.swap.F


title: 125I-3

city: kunming

first: Zhenhuan

last: Ma

address: 176 Qingnian Road，650021，Kunming，China

institute: The Second People's Hospital of Yunnan Province

data_processing:
Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3).
Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs.
The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch.
The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach. Differentially expressed miRNAs between two samples were filtered through Fold change.
Ddifferentially expressed miRNA between two groups were filtered by Fold Change and P-value. miRNA targets were performed by popular miRNA target prediction softwares, miRNA-targets networks were plotted by cytoscape software (v2.8.0), and the GO and KEGG pathway analysis were performed based on the top 10 differentially expressed miRNA target genes.
Genome_build: hg19
Supplementary_files_format_and_content: excel format

source_name: Gastric cancer cell

extract_protocol:
Gastric cancer cells were used for RNA extraction and quality control. The NanoDrop ND-1000 instrument (Thermo Fisher Scientific, Waltham, MA, USA) was used to measure the RNA concentration of each sample. Take OD260/OD280 value as RNA purity index
High throughput sequencing service was provided by CloudSeq Biotech (Shanghai, China). Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3'-adaptor ligation;2) 5'-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) Size selection of ~150 bp PCR amplicons (corresponding to ~22nt miRNAs)The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina HiSeq sequencer following the manufacturer's instructions.

value: Gastric cancer cell


title: 125I-2


title: 125I-1


title: ctrl-3


title: ctrl-1


title: ctrl-2


title: carcinoma tissue,biological rep5 (lncRNA-mRNA)

description:
Raw file: US10313827_256740610490_S01_GE2_1105_Oct12_1_4.txt
7CA

source_name: larynx cancer tissue

value: larynx cancer tissue


title: S1-seq_Dmc1.null_12dpp_rep1_adaptor.swap.F


title: non-carcinoma tissue,biological rep5 (lncRNA-mRNA)

description:
Raw file: US10313827_256740610490_S01_GE2_1105_Oct12_1_4.txt
7AB


title: non-carcinoma tissue,biological rep1 (lncRNA-mRNA)

description:
Raw file: US10313827_256740610448_S01_GE2_1105_Oct12_1_4.txt
1AB


title: carcinoma tissue,biological rep1 (lncRNA-mRNA)

description:
Raw file: US10313827_256740610448_S01_GE2_1105_Oct12_1_4.txt
1CA


title: carcinoma tissue,biological rep4 (lncRNA-mRNA)

description:
Raw file: US10313827_256740610490_S01_GE2_1105_Oct12_1_3.txt
4CA


title: carcinoma tissue,biological rep2 (lncRNA-mRNA)

description:
Raw file: US10313827_256740610490_S01_GE2_1105_Oct12_1_1.txt
2CA


title: S1-seq_Dmc1.wt_12dpp_rep4_adaptor.swap.F


title: Control_3

city: Grand Forks

first: Derick

last: Thompson

state: ND

address: 504 Hamline Street

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Raw data was provided in Fastq format
Reads were trimmed for adaptor and poor quality using Trimmomatic and quality assessed by FASTQC before and after trimming.
Reads were aligned to the human (hg19) assembly using Hisat2 version 2.1.0 and indexed by Samtools version 1.9
Differential gene expression was performed using DESeq2 version 1.24.0. Differential genes were considered statistically significant if FDR < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files. A single file that includes counts, FDR values, fold change, and gene annotation for all samples. Individual files for each sample that contain counts and annotations.

source_name: Choroid Plexus Epithelia

growth_protocol: Primary human choroid plexus epithelial cells were obtained from ScienCell (Catalog #1310). Cells were maintained in tissue-treated T-75 flasks in epithelial cell medium (ScienCell, catalog #4101), supplemented with 2% FBS and EpiCGS (ScienCell, catalog #4125).

extract_protocol:
Cell cultures were thoroughly washed, and RNA was harvested by phenol-chloroform extraction via Trizol. The Rneasy Mini kit from Qiagen (catalog #74106) was used for isolation following manufacterer's instructions.
RNA libraries were prepared using the NEBNext Ultra II RNA-seq library kit (catalog #7775S) for Illumina sequencing following manufacterer's instructions.

treatment_protocol: Cell cultures were grown to approximately 80% confluency, washed, and medium replaced. B. burgdorferi was added to each flask at a 10:1 multiplicity of infection (10 bacteria: 1 cell) for 48 hours.

value: Primary choroid plexus epithelial cells

value: Non-infected Control


title: Treated48_2

value: B. burgdorferi infected - 48 hours


title: Treated48_1


title: Treated48_3


title: Control_2


title: Control_1


title: S1-seq_Dmc1.wt_12dpp_rep3_adaptor.swap.F

value: C57BL/6J & 129S1/SvImJ (mixed)

value: testis


title: S1-seq_Dmc1.wt_12dpp_rep1_adaptor.swap.F


title: S1-seq_Dmc1.wt_12dpp_rep2_adaptor.swap.F


title: PBMC from patient 4 sepsis only

city: Pittsburgh

first: Anuradha

last: Ray

state: PA

address: 3459 Fifth Ave, MUH 628 NW

department: Medicine/Pulmonary

institute: University of Pittsburgh

data_processing:
Samples were analyzed using Seurat (version 3.0, https://satijalab.org/seurat/) for batch correction and cell type identification. Alignment between samples was achieved by identifying gene–gene correlation patterns that are conserved across data sets through canonical correlation analysis (CCA). The cells were then embedded in a shared low-dimensional space and normalized using nonlinear 'warping' algorithms. We subsequently identified discrete cell populations by a shared-nearest neighbor (SNN) graph-based clustering method. Differential gene expression analysis was applied in each cell type with two methods as reciprocal validation: Wilcoxon rank number test and MAST, the former as the most commonly used and the latter customized for scRNA-seq data.
Genome_build: hg19
Supplementary_files_format_and_content: For all samples, the raw UMI count matrix is stored in a combined txt file with features as row names and cell barcodes as column names.

source_name: Blood

extract_protocol:
Sorted cells were loaded into the Single Cell Chip and processed through the 10X controller for droplet generation, resulting in droplets containing a single cell and bead per droplet
Chromium Single Cell 3' RNA-seq libraries were prepared for sequencing using standard 10X Genomics protocols
scRNA-seq was performed using 10X Genomics Single Cell 3’ solution, version 2, according to the manufacturer’s instructions with 7,000 cells loaded for each sample (n=4 sepsis only and n=3 sepsis+ARDS). Libraries were sequenced on the HiSeq Platform (Illumina) from Novogene and raw BCL/fastq files were analyzed using Cell Ranger version 3.0.2 (10X Genomics). Low-quality cells were removed if they expressed <3000 genes/cell and had more than 20% mitochondrial and 10% hemoglobin gene expression. Post-quality control, 24,806 cells with mean reads 50,419/cell remained for downstream bioinformatic analyses. Consistent analysis was performed and 3212 cells with 182,364 reads per cell were retained after quality control.

value: PBMC

tag: disease

value: sepsis


title: S1-seq_Atm.null_12dpp_rep1_adaptor.swap.F


title: PBMC from patient 2 sepsis only


title: PBMC from patient 2 sepsis+ARDS

value: sepsis+ARDS


title: PBMC from patient 3 sepsis only


title: PBMC from patient 3 sepsis+ARDS


title: S1-seq_Atm.null_12dpp_rep2_adaptor.swap.F


title: S1-seq_wild.type_12dpp_rep2_adaptor.swap.F


title: S1-seq_wild.type_12dpp_rep4_adaptor.swap.F


title: S1-seq_wild.type_12dpp_rep1_adaptor.swap.F


title: S1-seq_wild.type_12dpp_rep3_adaptor.swap.F


title: bulk MM057 no treatment (TGFb/TNFa negative control)

description:
MM057_Neg_S8
processed data file:
bulkRNASeq_TGFb_TNFa_72h_raw_counts.tsv
bulkRNASeq_TGFb_TNFa_72h_normalized_counts.tsv

data_processing:
The 10x samples were processed (alignment, barcode assignment and UMI counting) with the CellRanger count pipeline; pools with samples from different cell lines were demultiplexed using demuxlet (Kang et al. 2018); cells expressing less than 1000 genes and cells with more than 20% mitochondrial reads were removed
The Drop-seq samples were cleaned with fastq-mcf from the ea-utils package (v1.04.807; Aronesty 2011) and processed (alignment, barcode assignment and UMI counting) with the Drop-seq tools pipeline (v1.12) developed by James Nemesh from the McCarroll lab (Macosko et al. 2015), using Picard tools (v1.140; Broad Institute) and the STAR aligner (v2.5.1b; Dobin 2013); cells expressing less than 1000 genes, more than 50000 and/or more than 10% mitochondrial reads were removed.
bulk RNA-Seq reads were cleaned with fastq-mcf from the ea-utils package (v1.04.807; Aronesty 2011), mapped using STAR (v2.5.1b; Dobin 2013) and counted with HTSeq (v0.6.1p1; Anders 2014); normalized count matrices were made with DESeq2 (v1.18.1; Love et al. 2014)
Omni-ATAC-Seq raw reads were mapped using Bowtie (v2.2.6; Langmead and Salzberg 2012); Duplicate reads were removed with Picard (v1.134; Broad Institute 2019) and low quality reads were removed with SAMtools (Q30) (v1.8; Li et al. 2009). bigWig files were created with deepTools (Ramírez et al. 2016).
Genome_build: hg19
Supplementary_files_format_and_content: raw and normalized count matrices

source_name: MM_no treatment

extract_protocol: not provided; requested

treatment_protocol: The MM lines were cultured in Ham’s F10 nutrient mix (ThermoFisher Scientific) supplemented with 10% fetal bovine serum (Invitrogen) and 100 µg ml-1 penicillin/streptomycin (ThermoFisher Scientific). The A375 cell line was maintained in Dulbecco’s Modified Eagle’s Medium with high glucose and glutamax (ThermoFisher Scientific), supplemented with 10% fetal bovine serum (Invitrogen) and penicillin-streptomycin (ThermoFisher Scientific). Cell cultures were kept at 37°C, with 5% CO2, regular tests for mycoplasma contamination were negative. Knockdowns of SOX10, EGR3 and NFATC2 were performed using a SMARTpool (Dharmacon) of four siRNAs, respectively (ON-TARGETplus SOX10 siRNA (L017192-00); ON-TARGETplus EGR3 siRNA (L006528-00); ON-TARGETplus NFATC2 siRNA (L003606-00)). SMARTpool was applied at final concentrations of 20nM (SOX10) and 40 nM (EGR3 and NFATC2) in Opti-MEM medium (Thermo Fisher Scientific), after which cells were sampled at the indicated time points. To control for transfection artefacts, we used a pool of non-targeting siRNAs (SMARTpool: ON-TARGETplus Non-targeting Pool, number D001810-10-05, Dharmacon). Inhibition of CDK7-dependent transcription was achieved by treatment with THZ2 (HY-12280, MedChemExpress). For each treated melanoma culture, IC50 concentrations were calculated for 48 hours of treatment. As a control, DMSO treatment was used. Treatment with TGFbeta (10ng/ml; 100-21C, peprotech) and TNFalpha (1000 U/ml;  300-01A, peprotech) was performed in serum-free medium. As a control, also serum-free medium was used. For bulk RNA-seq, RNA was extracted from attached cells using the innuPREP RNA mini kit (Analytik Jena), according to the manufacturer’s instructions. For scRNA-seq and Omni-ATAC-seq, cells were detached by trypsinization, counted and processed according to downstream protocols.

tag: cell line

value: melanoma cell line

value: no treatment

tag: sequencing method

value: bulk RNA-Seq


title: bulk MM057 TGFb/TNFa  72h

description:
MM057_TGF_TNF_S7
processed data file:
bulkRNASeq_TGFb_TNFa_72h_raw_counts.tsv
bulkRNASeq_TGFb_TNFa_72h_normalized_counts.tsv

source_name: MM_treatment with TGFbeta and TNFalpha  72h

value: treatment with TGFbeta and TNFalpha  72h


title: bulk MM074 TGFb/TNFa  72h

description:
MM074_TGF_TNF_S9
processed data file:
bulkRNASeq_TGFb_TNFa_72h_raw_counts.tsv
bulkRNASeq_TGFb_TNFa_72h_normalized_counts.tsv


title: bulk MM087 TGFb/TNFa  72h

description:
MM087_TGF_TNF_S11
processed data file:
bulkRNASeq_TGFb_TNFa_72h_raw_counts.tsv
bulkRNASeq_TGFb_TNFa_72h_normalized_counts.tsv


title: control-3

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: BBS Program, Yale University

data_processing:
The resulting libraries were assessed, multiplexed, and sequenced as single-end 75 base pair reads (NextSeq 500, Illumina).
For RNA-seq analysis, demultiplexing was performed using bcl2fastq (version 2.17.1.14), trimming was performed using cutadapt, alignment was performed using STAR (version 2.5.3) and raw read counts were generated using HTSeq.
Normalized tables of counts were generated from raw counts using the DESeq2 R package and the rlog transformation function.
Gene expression data were analyzed for enrichment using GSEA software (Broad Institute-version 3.0) and MSigDB version 6.2.
Genome_build: mm10
Supplementary_files_format_and_content: "count.txt" contains gene expression count matrix

source_name: pulmonary primary endothelial cells

growth_protocol: pulmonary primary endothelial cells were cultured in EBM-2 (Lonza) basal medium supplement with EGMTM-2 MV SingleQuotsTM Supplement Pack (Lonza)

extract_protocol:
mRNA were isolated using RNeasy Plus Mini Kit (QIAGEN)
RNA-seq libraries for primary mouse pulmonary endothelial cells were prepared from 100 ng of total RNA using a mRNA-Seq Sample Prep Kit.

treatment_protocol: 300 uM H2O2 or H2O were added to cells that reach 80% confluence for 6 hours

value: primary cells

value: control


title: H2O2-2


title: bulk MM087 no treatment (TGFb/TNFa negative control)

description:
MM087_Neg_S12
processed data file:
bulkRNASeq_TGFb_TNFa_72h_raw_counts.tsv
bulkRNASeq_TGFb_TNFa_72h_normalized_counts.tsv


title: H2O2-3


title: H2O2-1


title: bulk MM074 no treatment (TGFb/TNFa negative control)

description:
MM074_Neg_S10
processed data file:
bulkRNASeq_TGFb_TNFa_72h_raw_counts.tsv
bulkRNASeq_TGFb_TNFa_72h_normalized_counts.tsv


title: control-2


title: bulk MM165 baseline

description:
bulkRNASeq_33MelanomaBaselines_raw_counts.tsv
bulkRNASeq_33MelanomaBaselines_normalized_counts.tsv

data_processing:
The 10x samples were processed (alignment, barcode assignment and UMI counting) with the CellRanger count pipeline; pools with samples from different cell lines were demultiplexed using demuxlet (Kang et al. 2018); cells expressing less than 1000 genes and cells with more than 20% mitochondrial reads were removed
The Drop-seq samples were cleaned with fastq-mcf from the ea-utils package (v1.04.807; Aronesty 2011) and processed (alignment, barcode assignment and UMI counting) with the Drop-seq tools pipeline (v1.12) developed by James Nemesh from the McCarroll lab (Macosko et al. 2015), using Picard tools (v1.140; Broad Institute) and the STAR aligner (v2.5.1b; Dobin 2013); cells expressing less than 1000 genes, more than 50000 and/or more than 10% mitochondrial reads were removed.
bulk RNA-Seq reads were cleaned with fastq-mcf from the ea-utils package (v1.04.807; Aronesty 2011), mapped using STAR (v2.5.1b; Dobin 2013) and counted with HTSeq (v0.6.1p1; Anders 2014); normalized count matrices were made with DESeq2 (v1.18.1; Love et al. 2014)
Omni-ATAC-Seq raw reads were mapped using Bowtie (v2.2.6; Langmead and Salzberg 2012); Duplicate reads were removed with Picard (v1.134; Broad Institute 2019) and low quality reads were removed with SAMtools (Q30) (v1.8; Li et al. 2009). bigWig files were created with deepTools (Ramírez et al. 2016).
Genome_build: hg19

source_name: melanoma cell line

extract_protocol: Not Provided

value: melanoma cells


title: control-1


title: S1-seq_wild.type_12dpp_rep5_adaptor.swap.F

value: 12 days post partum


title: bulk MM168 baseline


title: PBMC from patient 1 sepsis+ARDS


title: bulk MM164 baseline


title: PBMC from patient 1 sepsis only


title: bulk MM161 baseline


title: 1PP_K4me3_A

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

institute: University of Toronto

data_processing:
Reads were trimmed using bbduk with standard settings.
Reads were aligned to mm10 using STAR 2.7 standard setting
RNA-seq bedGraphs were generated using deeptools bamCoverage and normalized to library size (RPM).
ChIP-seq bedGraphs were generated using deeptools bamCompare and normalized to Input and library size (RPM).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: myometrial tissue

growth_protocol: All mice were grown, maintained, and euthanized as per standard protocol.

extract_protocol:
RNA was isolated using Trizol (Life Technologies) and DNase treated prior to library construction; genomic DNA was isolated using ChIP protocol prior to library construction
RNA and ChIP libraries were prepared for sequencing using standard Illumina HiSeq 2500 protocols

treatment_protocol: Following euthanization, mouse myometrial tissues were cut, isolated, and flash-frozen in liquid nitrogen.

value: wild type

tag: passage

value: 1 day postpartum

tag: antibody


title: bulk MM163 baseline


title: 1PP_K4me3_B

tag: strain

tag: genotype


title: bulk MM152 baseline


title: TNIL_K4me3_A

value: Term not in labour


title: carcinoma tissue,biological rep3 (lncRNA-mRNA)

description:
Raw file: US10313827_256740610490_S01_GE2_1105_Oct12_1_2.txt
3CA

value: laryngeal carcinoma

tag: age

value: larynx cancer tissue


title: LAB_K4me3_B

value: Term labour


title: D15_K4me3_B

value: Day 15


title: bulk MM150 baseline


title: bulk MM148 baseline


title: 1PP_K27ac_B


title: bulk MM147 baseline


title: D15_K4me3_A


title: bulk MM142 baseline


title: bulk MM146 baseline


title: 1PP_K27ac_A


title: bulk MM129 baseline


title: bulk MM131 baseline


title: LAB_K4me3_A


title: LAB_K27ac_B


title: 1PP_Input


title: bulk MM125 baseline


title: LAB_K27ac_A


title: LAB_Input


title: TNIL_K27ac_A


title: TNIL_Input


title: bulk MM099 baseline


title: TNIL_K4me3_B


title: D15_K27ac_A


title: D15_K27ac_B


title: TNIL_K27ac_B


title: bulk MM087 baseline


title: bulk MM098 baseline


title: bulk MM118 baseline


title: D15_Input


title: bulk MM074 baseline


title: bulk MM094 baseline


title: LAB_POL2_B


title: bulk MM057 baseline


title: bulk MM054 baseline


title: bulk MM070 baseline


title: D15_POL2_B


title: bulk MM116 baseline


title: D15_POL2_A


title: bulk MM050 baseline


title: LAB_POL2_A


title: bulk MM043 baseline


title: LAB_RNA_4


title: LAB_RNA_3


title: bulk MM032 baseline


title: LAB_RNA_2


title: LAB_RNA_5


title: bulk MM031 baseline


title: bulk MM034 baseline


title: LAB_RNA_1


title: D15_RNA_4


title: D15_RNA_5


title: bulk MM001 baseline


title: bulk MEL501 baseline


title: D15_RNA_3


title: bulk MM087 6h THZ2

value: THZ2 treatment 6h


title: D15_RNA_2


title: bulk SKMEL28 baseline


title: bulk MM087 6h DMSO

value: no treatment 6h


title: bulk MM087 48h THZ2

value: melanoma cell line

value: THZ2 treatment 48h


title: bulk MM087 48h DMSO

value: no treatment 48h

value: bulk RNA-Seq


title: bulk MM074 6h THZ2


title: bulk MM029 baseline

value: no treatment


title: bulk MM057 6h DMSO


title: bulk MM074 6h DMSO


title: bulk MM057 48h THZ2


title: bulk MM074 48h DMSO


title: bulk MM057 48h DMSO


title: 10x MM057 SOX10-KD Timeline

description: CellRanger v2.0.2

value: pool of siSOX10 sampled after 2h, 4h, 6h, 8h, 12h, 16h, 20h, 24h, 28h and 32h

value: single cell RNA-Seq 10x


title: bulk MM074 48h THZ2


title: 10x MM087 SOX10-KD Timeline

description: CellRanger v2.0.2


title: D15_RNA_1


title: 10x MM057 SOX10-KD 72h

description: CellRanger v1.3.1

value: siSOX10 72h


title: 10x MM074 SOX10-KD 72h

description: CellRanger v1.3.1


title: 10x MM074, MM057 and MM087 SOX10-KD 48h

description: CellRanger v2.0.2; Demultiplexed with demuxlet

source_name: melanoma cell lines

value: melanoma cell lines

value: siSOX10 48h


title: bulk MM057 6h THZ2


title: MSCDM_ LPS_b_M99

city: Zurich

first: Christian

middle: Andreas

last: Schaer

address: Raemistrasse 100

institute: University Hospital Zurich

description: Note: For the statistical analysis of our array experiments we imported the log10 ratios of the Feature Extraction result text files into JMP Genomis 5.1. As Feature Extraction Software does already a a linear-lowess normalization, we didn't perform any further normalization. That means that our normalized data are already included in the Agilent Feature Extraction Files, which have been uploaded with this Metadata Worksheet. Any further data processing, i.e. filtering for at least 2-fold over- or underexpression of significant features, we performed after the ANOVA analysis. As we understand the MIAME guidelines it is not necessary to provide a Matrix Table with data output from an ANOVA or Hierarchical Clustering analysis.

hyb_protocol: After purification of amplified cRNA according to the QIAgen RNeasy purification protocol (QIAGEN) 825 ng of Cy3 and Cy5 labeled cRNA were competitively hybridized for 17 hours at 65° C in a hybridization oven (Agilent G2545A) set to 10 rpm in GEx Hybridization buffer HI-RPM according to the manufacturer's protocol (Agilent’s Two-Color Microarray-Based Gene Expression Analysis). Washing was performed according to the recommended protocol including the Stabilization and Drying Solution step.

scan_protocol: Array slides were XDR scanned at 5 mcm resolution on a Agilent Microarray High-Resolution C Scanner (G2505C) with 100% PMT and 10% for lower intensity.

data_processing:
Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software Version 10.7.3.1. Spot values were normalized using the default linear-lowess normalization. To identify differentially expressed features, calculated log10 ratio values (Cy5/Cy3) were imported into JMP Genomics 5.1 without further normalization and the built-in Basic Expression Workflow (ANOVA, LSMeans Differences) was performed.
We imported the calculated and lowess-normalized log10 ratios of the Feature Extraction result text files directly into JMP Genomis 5.1 and performed the statistical analysis without further normalization.

label: Cy3 (green signal)

source_name: Murine stem cell derived macrophages, no treatment

label_protocol: Fluorescently labeled cRNA was generated from 500 ng total RNA with the Quick Amp Labeling Kit (Agilent) according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol Version 5.7, March 2008 (Agilent publication number G4140-90050). In short, total RNA was reverse transcripted to cDNA using T7 Promotor Primer and MMLV-RT. Then cDNA was converted to cRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.

extract_protocol: After washing and lysing the cells with Buffer RLT, total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Basel, Switzerland) according to the manufacturer’s instructions, including an on-column DNA digestion step (RNase-Free DNase Set; QIAGEN). To ensure that only high quality RNA (RIN >7.0) was used for gene expression analysis, each RNA sample was checked on a RNA Nanochip with a Bioanalyzer 2100 (Agilent Technologies, Basel, Switzerland). RNA was quantified spectrophotometrically with a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

value: Murine stem cell derived macrophages

tag: incubation time

label: Cy5 (red signal)

source_name: Murine stem cell derived macrophages, incubated with 10 ng/mL LPS

value: LPS 10ng/mL


title: 10x MM074, MM057 and MM087 SOX10-KD 24h

first: k

last: spanier

institute: KU Leuven

value: siSOX10 24h


title: MSCDM_ HemeAlb200_a_M98

source_name: Murine stem cell derived macrophages, incubated with 200 mcM heme-albumin

value: Heme-Albumin 200 mcM


title: MSCDM_ HemeAlb200_d_MR


title: MSCDM_ LPS_c_ML


title: C33_2_3

city: Oxford

first: Rebeca

middle: Casilda

last: Arroyo Hornero

state: Not applicable

address: John Radcliffe Hospital, Headington

department: NDS

country: United Kingdom

institute: University of Oxford

data_processing:
Illumina RTA3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, raw files of the same sample from different lanes were merged into a single file using Samtools (1.3). Processed files were then aligned using STAR (2.4.2a) against the human genome (UCSC hg38) and the quality was also checked by fastQC (0.10.1).
The non-adjusted read counts for each gene were assessed statistically for global differential expression between the specified populations using the edgeR package (3.22.2) on R (3.5.1). Genes that are significant at a 5% false discovery rate (calculated using a Benajmini-Hochberg adjusted p-value) were considered differentially expressed between populations as described 8. Gene ontology enrichment was assessed using the topGO package (2.32.0) and pathway enrichment was analysed on the ReactomePA package (1.24.0).
Genome_build: human genome build UCSC hg38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each Sample

growth_protocol: Human regulatory T cells (Tregs) were isolated from peripheral blood of healthy individuals by flow cytometry as CD4+CD25+CD127- cells. Tregs were then expanded in vitro using anti-CD3/CD28 coated beads and 1000U/ml recombinant human IL-2. After 2 weeks of expansion, Tregs were separeted into CD27+CD70- and CD27-CD70+ cells and expanded for 2 further weeks. 4 weeks expanded Treg subsets were re-sorted in CD27+CD70- and CD27-CD70+ and stored in liquid nitrogen. Tregs from 4 independent blood donors were analyzed.

extract_protocol:
Cells were thawed and RNA was isolated from 300,000 CD27+CD70- and CD27-CD70+ Treg cells. Each experiment was performed in triplicate.
mRNA capture and cDNA synthesis were performed using KAPA mRNA Hyper Kit for Illumina platform (Roche) according to the manufacturer’s protocol. After quality check using Qubit High-sensitivity kit (Life Technologies), 16 cycles of PCR were carried out for amplifying each library. Amplified cDNA libraries were sequenced on an Illumina HiSeq4000 machine using paired end reads (2 x 150 bp) at Novogene, China.

tag: individual


title: C33_2_2


title: C33_2_1


title: C33_1_3


title: MSCDM_ Control_c_ML

source_name: Murine stem cell derived macrophages, used as a control without treatment


title: MSCDM_ Control_b_M99


title: MSCDM_ HemeAlb50_c_ML

source_name: Murine stem cell derived macrophages, incubated with 50 mcM heme-albumin

value: Heme-Albumin 50 mcM


title: MSCDM_ HemeAlb200_c_ML


title: MSCDM_ HemeAlb200_b_M99


title: MSCDM_ HemeAlb50_a_M98


title: C33_1_2


title: RNA_seq_MRC5_rep1

city: Beijing

first: hebing

last: chen

address: taiping road 27

institute: Institute of Health Service  and Transfusion Medicine

data_processing:
Hi-C sequence alignment to the hg19 reference genome was performed using Bowtie2 with default parameters. The tag directory of each cell line was created using the MakeTagDirectory command of HOMER software v4.8. Normalized Hi-C contact maps were created using the analysisHiC command of HOMER software, where -coverageNorm parameter was used to remove bias in Hi-C data. The compartment score was calculated as previously described under 200 kb resolution. TADs were identified using TADsAndLoops.pl script of HOMER software, and the boundary of each TAD was defined as the first and last locus of each TAD.
RNA-seq data sequence alignment to the hg19 reference genome was performed using TopHat v2.1.0 with default parameters. Normalized gene expression was acquired using Cufflinks v2.2.0
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using TADsAndLoops.pl script of HOMER software

growth_protocol: The human lung carcinoma cell lines NCI-H209 and DMS153 and the noncancerous human lung fibroblast cell line MRC-5 were all provided by the China Infrastructure of Cell Line Resource. The cells were cultured in RPMI 1640 medium (Life Technologies, Inc.) with 20% FBS (HyClone) containing 0.1 mM nonessential amino acids (Invitrogen) and 0.1 mM GlutaMAX (Invitrogen). The cells were maintained at 37°C in a humidified atmosphere with 5% CO2 and passaged once a week. A split ratio of 1:3 was performed.

extract_protocol:
The crosslinked cell suspension was split and centrifuged at 800xg for 10 min. The supernatant was discarded by aspiration. The fixed cells were resuspended in 1 ml of lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630, 1/10 vol. of proteinase inhibitor cocktail (Sigma)) and then incubated on ice for 20 min. Nuclei were pelleted by centrifugation at 4°C and 600 g for 5 min and then washed with 1 ml of lysis buffer, followed by another centrifugation under similar conditions. After washing twice with restriction enzyme buffer, the nuclei were resuspended in 400 μl of restriction enzyme buffer and transferred to a safe-lock tube. Next, the chromatin was solubilized with dilute SDS and incubated at 65°C for 10 min. After quenching the SDS by Triton X-100 overnight, digestion was performed with 4 cutter restriction enzymes (400 units MboI) at 37°C on a rocking platform.
The proximal chromatin DNA was religated by the ligation enzyme. The nuclear complexes were reversed crosslinked by incubating with proteinase K at 65°C. DNA was purified by phenol-chloroform extraction. Biotin-C was removed from nonligated fragment ends using T4 DNA polymerase. Fragments were sheared to a size of 200-600 base pairs by sonication. The fragment ends were repaired by a mixture of T4 DNA polymerase, T4 polynucleotide kinase and Klenow DNA polymerase. Biotin-labelled HiC samples were specifically enriched using streptavidin C1 magnetic beads. The fragment ends were adding by A-tailing by Klenow(exo-) and then adding Illumina paired-end sequencing adaptor by ligation mix. Finally, the Hi-C libraries were amplified using 12-14 cycles of PCR and sequenced on the Illumina HiSeq platform. Sequencing interacting partners were obtained by an Illumina HiSeq instrument with 2×150-bp reads.

treatment_protocol: Approximately 2.5×107 cells were gently collected and thoroughly resuspended in fresh culture medium without serum. Cell clumps were broken up by pipetting up and down and crosslinking the cells by adding 2.5 ml of 37% formaldehyde in one shot (2% final concentration). The tube was mixed by inverting quickly several times, and the samples were incubated at room temperature (RT) for exactly 10 min. The tube was gently inverted every 1-2 min. To quench the formaldehyde in the reaction, 5 ml of 2.5 M glycine was added in one shot and mixed well. The sample was incubated for 5 min at RT and then incubated on ice for at least 15 min to stop crosslinking completely.

value: Normal lung fibroblast cell


title: RNA_seq_MRC5_rep3


title: RNA_seq_H209_rep2

value: Small lung carcinoma cell line


title: RNA_seq_DM153_rep2


title: RNA_seq_H209_rep1


title: RNA_seq_MRC5_rep2


title: C33_1_1


title: MSCDM_ LPS_d_MR


title: MSCDM_ Control_d_MR


title: RNA_seq_DM153_rep1


title: 10x MM074 and MM057 NTC

city: Leuven

address: Herestraat 49

description: CellRanger v1.3.1; Demultiplexed with demuxlet

value: siNTC 72h


title: MSCDM_ HemeAlb50_d_MR


title: HiC_MRC5


title: C29_2_2


title: C29_2_3


title: MSCDM_ HemeAlb50_b_M99


title: MSCDM_ Control_a_M98


title: C29_2_1


title: HiC_H209


title: C29_1_3


title: HiC_DMS153


title: C29_1_2


title: RNA_seq_DM153_rep3


title: C28_2_3


title: RNA-seq_normal_lung89

city: Shanghai

first: Linhu

last: Zhai

address: 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Pudong, Shanghai

institute: Shanghai Institute of Materia Medica

description: paired normal for sample LADC_89

data_processing:
RNASeq reads were adapter trimmed and data quality was assessed with the FastQC (version 0.11.7) software
Reads were mapped onto the human reference genome (GRCh38.p12 assembly) by using hisat2 software (v2.0.4).
The mapped reads were assembled into transcripts or genes by using StringTie software (v1.3.4d) and the genome annotation file (hg38_ucsc.annotated.gtf
For quantification purpose, the relative abundance of transcript/gene was measured by a normalized metrics, FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: GTF reports FPKMs, TPMs

source_name: Clinical normal lung tissue

extract_protocol:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Lung

value: normal tissue


title: C28_2_2


title: C29_1_1


title: RNA-seq_normal_lung72

description: paired normal for sample LADC_72


title: C28_2_1


title: C28_1_3


title: RNA-seq_normal_lung90

description: paired normal for sample LADC_90


title: RNA-seq_normal_lung71

description: paired normal for sample LADC_71


title: RNA-seq_normal_lung73

description: paired normal for sample LADC_73


title: C28_1_2


title: RNA-seq_normal_lung74

description: paired normal for sample LADC_74


title: C26_2_3


title: C28_1_1


title: RNA-seq_normal_lung67

description: paired normal for sample LADC_67


title: MSCDM_ LPS_a_M98


title: RNA-seq_normal_lung91

description: paired normal for sample LADC_91


title: C26_2_2


title: C_15M_19

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from lung tissue from mice exposed to filtered air for 15 months, biological replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data including background subtraction (GenomeStudioV2011.1 software, gene expression module version 1.9.0), removal of negative values by introducing an offset, quantile normalisation

label: Biotin

source_name: Lung tissue from mice exposed to filtered air for 15 months, biological replicate 1

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: Animals housed under spf conditions

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: Exposure to filtered air, cigarette smoke, and LTβR-Ig fusion protein as described in the paper. Briefly, Cigarette smoke (CS) was generated from 3R4F Research Cigarettes (Tobacco Research Institute, University of Kentucky, Lexington, KY), with the filters removed. Mice were whole body exposed to active 100% mainstream CS of 500 mg/m3 total particulate matter (TPM) for 50 min twice per day for 4 and 6 months (m) in a manner mimicking natural human smoking habits as previously described. The TPM level was monitored via gravimetric analysis of quartz fiber filters prior and after sampling air from the exposure chamber and measuring the total air volume. CO concentrations in the exposure chamber were constantly monitored by using a GCO 100 CO Meter (Greisinger Electronic, Regenstauf, Germany) and reached values of 288± 74 ppm. All mice tolerated CS-mediated CO concentrations without any sign of toxicity, with CO-Hb levels of 12.2 ± 2.4%.  In two parallel experiments, mice were treated with an LTβR-Ig fusion protein (80 µg i.p., weekly) (muLTβR-muIgG1, ref #14811-122; and CHO 14.3 Lot #7195-30) or control-Ig (MOPC21, clone #113) for 2m, starting from 2m and 4m of CS exposure. Control mice were kept in a filtered air (FA) environment, but exposed to the same stress as CS-exposed animals. 24 h after the last CS exposure, mice were sacrificed.

value: lung

tag: gender

value: female


title: C_15M_21

description: Gene expression data from lung tissue from mice exposed to filtered air for 15 months, biological replicate 3

source_name: Lung tissue from mice exposed to filtered air for 15 months, biological replicate 3


title: C_15M_20

description: Gene expression data from lung tissue from mice exposed to filtered air for 15 months, biological replicate 2

source_name: Lung tissue from mice exposed to filtered air for 15 months, biological replicate 2


title: C26_2_1


title: C26_1_3


title: S_15M_22

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 15 months, biological replicate 1

source_name: Lung tissue from mice exposed to cigarette smoke for 15 months, biological replicate 1


title: RNA-seq_normal_lung63

description: paired normal for sample LADC_63


title: C26_1_2


title: RNA-seq_normal_lung68

description: paired normal for sample LADC_68


title: RNA-seq_normal_lung61

description: paired normal for sample LADC_61


title: RNA-seq_normal_lung60

description: paired normal for sample LADC_60


title: RNA-seq_normal_lung66

description: paired normal for sample LADC_66


title: SL_15M_27

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 15 months plus the LTβR-Ig fusion protein, biological replicate 3

source_name: Lung tissue from mice exposed to cigarette smoke for 15 months plus the LTβR-Ig fusion protein, biological replicate 3


title: S_15M_23

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 15 months, biological replicate 2

source_name: Lung tissue from mice exposed to cigarette smoke for 15 months, biological replicate 2


title: RNA-seq_normal_lung57

description: paired normal for sample LADC_57


title: SL_15M_25

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 15 months plus the LTβR-Ig fusion protein, biological replicate 1

source_name: Lung tissue from mice exposed to cigarette smoke for 15 months plus the LTβR-Ig fusion protein, biological replicate 1


title: C26_1_1


title: S_15M_24

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 15 months, biological replicate 3

source_name: Lung tissue from mice exposed to cigarette smoke for 15 months, biological replicate 3


title: RNA-seq_normal_lung56

description: paired normal for sample LADC_56


title: RNA-seq_normal_lung55

description: paired normal for sample LADC_55


title: C_6M_12

description: Gene expression data from lung tissue from mice exposed to filtered air for 6 months, biological replicate 3

source_name: Lung tissue from mice exposed to filtered air for 6 months, biological replicate 3


title: C_6M_11

description: Gene expression data from lung tissue from mice exposed to filtered air for 6 months, biological replicate 2

source_name: Lung tissue from mice exposed to filtered air for 6 months, biological replicate 2