title: no RNA_polysome-associated mRNA_rep1

description:
mSeq of poly-A enriched RNA
mRNA


title: AT3 PD-1 int CD8

status: Public on Dec 08 2021

type: RNA

city: Heidelberg

first: Martina

last: Seiffert

address: Im Neuenheimer Feld 280

department: Department of Molecular Genetics

country: Germany

institute: German Cancer Research Center

description: PD-1int replicate 3

hyb_protocol: 20 μg of cRNA was then converted to sensestrand DNA (ss-cDNA). After fragmentation and terminal labeling, 5,5 ug of biotinylated ss-cDNA were hybridized for 17 hr at 45°C on Affymetrix Mouse Gene 2.0 ST Arrays

scan_protocol: Microarray scanning was done using an Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: Samples were processed with Affymetrix Power Tools using 'Robust Microarray Analysis' approach for the normalization. Log2-transformed transcript-level gene expression was calculated for ‘meta’ probe sets. Quality control of the samples was carried out by examining average raw intensity signal (pm_mean) or mean absolute deviation of the residuals (all_probeset_mad_residual_mean). 'Detected above background' measure was used to filter ‘meta’ probe sets if less than 50% of probe sets were called as ‘detected’ (P value <0.05) within less than 50% of the samples in each experimental group.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse spleen CD8 T-cells_PD-1int

label_protocol: Biotin-labeled ss-cDNA samples for hybridization on GeneChip™ Mouse Gene 2.0 ST Arrays (Affymetrix) were prepared according to Affymetrix's recommended sample labeling procedure as described in the Gene Chip WT Pico Reagent Kit guide

growth_protocol: C57BL/6 mice transplanted with murine CLL cells and after 6 weeks total RNA was isolated from splenic CD8+ T-cell (Lin- TCRb+ CD8+) subsets that were sorted by flow cytometry from leukemic mice (Naïve: CD127hi CD44low, Memory: CD127hi CD44hi, PD-1int effector: CD127low CD44int-hi PD-1int, and PD-1hi effector: CD127low CD44int-hi PD-1hi).

extract_protocol: RNA was extracted from sorted cells using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol

tag: strain

tag: gender

value: female

tag: transplanted with

value: murine CLL cells from Eµ-TCL1 mice

tag: timepoint

value: 6 weeks of transplantation

tag: cell type

value: spleen CD8 T-cells

tag: cell subtype


title: AT4 PD-1 int CD8

description: PD-1int replicate 4


title: 10/27 twi:CD2+ DNA

type: SRA

city: Boston

first: Stephen

last: Gisselbrecht

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

country: USA

institute: Brigham and Women's Hospital

description: UMI-tagged amplicon containing degenerate sequence tag

library_source: genomic

data_processing:
Reads were processed to remove and retain UMI tags using a custom python script, available upon request.
Common 5' and 3' regions of the remaining sequence were removed using cutadapt 1.14.
The remaining sequence was mapped to a lookup table of degenerate sequence tags using bowtie.
The resulting file of tag-UMI pairs was processed to extract an UMI count using a custom python script, available upon request.
In R 3.5.1, DNA or RNA UMI counts per tag were normalized to total DNA or RNA UMI counts within each replicate and a normalized expression measure (RNA UMI count / DNA UMI count) calculated, then all replicates for one experiment were collected to give a table of individual normalized expression measurements.
In R 3.5.1, tables of all expression measurements within an experiment were filtered to remove individual measurements resulting from <65 DNA UMIs, then to remove enhancers measured in fewer than 4 replicates. Summary statistics (mean and s.e.m.) were calculated for enhancers passing these filters.
Genome_build: n/a
Supplementary_files_format_and_content: tagCounts files contain 4 columns: Enhancer, Tag, UMI count, and Read count
Supplementary_files_format_and_content: fullFiltered files contain 11 columns: Tag, Enhancer_RNA, UMI_count_RNA, Read_count_RNA, Enhancer_DNA, UMI_count_DNA, Read_count_DNA, normUMI_DNA, normUMI_RNA, normUMI, and replicate
Supplementary_files_format_and_content: fullSummaryFiltered files contain 6 columns: Enhancers, numTags, avgUMIcount, sdUMIcount, totalUMIcount, and standardError

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: sorted embryonic mesoderm

growth_protocol: Transformant male flies containing random picks from a pool of sequence-tagged reporter constructs were crossed to twi:CD2 or mef2[IE-D5]:CD2 virgin females in population cages. Embryos were collected for 2.25 hours from pre-layed cages and aged 11 hours at 18°.

extract_protocol:
RNA and DNA were simultaneously purified from sorted cells, using the back extraction method for DNA. RNA samples were treated with TURBO DNase and reverse-transcribed with a custom primer specific to the reporter gene amplicon.
A single round of primer extension with a custom primer specific to the reporter gene amplicon added an 8-base degenerate UMI sequence, along with the standard Illumina read 1 sequencing primer and Illumina P5 cluster generation primer. After SPRI purification, the target amplicon (including UMI) was amplified with an additional custom primer specific to the reporter gene and the Illumina P5 + read 1 sequencing primer.

treatment_protocol: Single-cell suspensions were prepared from dechorionated embryos and stained with Alexa647-anti-rat CD2 (Biorad MCA154A647), then CD2-positive and -negative populations were sorted.

value: reporter insertion pool crossed to twi:CD2


title: no RNA_total mRNA_rep3

city: Bern

first: Norbert

last: Polacek

address: Freiestrasse 3

department: Chemistry and Biochemistry

country: Switzerland

institute: University of Bern

description:
mSeq of poly-A enriched RNA
mRNA

library_source: transcriptomic

data_processing:
Quality control using fastqc tool.
Mapping performed using HISAT2; more than 95% mapping rate, -p 8.
Counting was performed using featureCounts.
Genome_build: Strain BY4742 (PRJNA260311, Oct-12-2014)
Supplementary_files_format_and_content: *.txt: Tab-delimited text file; counts table.

organism: Saccharomyces cerevisiae

source_name: yeast strain trm10∆

extract_protocol:
Yeast spheroplasts were electroporated with or without RNA, recovered and harvested by centrifugation. Pellets were opened using a FastPrep. Lysates were cleared by centrifugation and total RNA was extracted by hot acid phenol extraction.
Poly-A-Enrichment via oligo-dT-beads.
PolyA enriched mRNAs were transformed into a cDNA library using the Illumina TruSeq stranded mRNA Kit. Library size was determined using Qbit.

tag: electroporation

value: no RNA

tag: mrna fraction

value: total


title: no RNA_total mRNA_rep2

description:
mSeq of poly-A enriched RNA
mRNA


title: 10/27 twi:CD2+ RNA


title: in vitro zymosan treatment - rep1 [HO_Z_1]

city: Szeged

first: Attila

last: Szűcs

address: Somogyi utca 4

department: Faculty of Medical Research

country: Hungary

institute: University of Szeged

description:
HO_Z_1
HO_ZvsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf

data_processing:
Illumina Casava1.7 software used for basecalling.
Remove reads with adaptor contamination, uncertain nucleotides constitute more than 10 percent of either read or low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Mapping reads by hisat2 v2.0.5 with parameters --dta --phred33
Quantification by FeatureCounts v1.5.0-p3.
Differential expression Analysis by edgeR with parameters padj =< 0.05 and |log2(FoldChange)|>=1
Enrichment Analysis by ClusterProfiler v3.8.1 with parameter padj < 0.05.
GSEA Analysis by gseq c3.0.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: *.tdf: Tab-delimited text files include FPKM values, raw gene counts for each Sample and pvalue, padj value and log2 fold change values and gene descriptions (name, localisation, description, biotype and Transcription Factor family).

molecule: polyA RNA

organism: Homo sapiens

source_name: oral squamous cell carcinoma

growth_protocol: HSC-2 (JCRB0622) cells were cultured in EMEM, while HO-1-N-1 (JCRB0831) cells in DMEM/F-12 medium, both containing 10% heat-inactivated (56°C, 30 min) fetal bovine serum (FBS) (EuroClone) supplemented with 4mM glutamine, 100U/mL penicillin and 100mg/mL streptomycin. Cells were maintained at 37°C in the presence of 5% CO2.

extract_protocol:
In vitro: mRNA was purified using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's protocol. RNA quality and quantity were analyzed by Bioanalyzer Instrument (Agilent). In vivo: Mice were sacrificed and tongues were removed. Mouse tongue tissues were removed from the tumor with the help of scalpel. 30mg tumor tissue was homogenized (Bioneer) in RLT buffer and RNA was extracted with RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions. RNA quality and quantity were analyzed by Bioanalyzer Instrument (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol:
In vitro: 1x10^5 cancer cells were seeded into 24-well plates with three technical replicates. After 12h, the tumor cells were treated with zymosan (10µg/ml), heat-killed C. albicans (MOI 1:10), heat-killed C. parapsilosis (MOI 1:10), live C. albicans (MOI 1:25) or live C. parapsilosis (MOI 1:4) for 12h.
In vivo: Oral candidiasis was induced: calcium alginate swabs were placed in C. albicans suspension (1x10^9/ml) approximately 5 min prior to use, then saturated calcium alginate swabs were placed under the tongues of each mouse for 75 minutes.

tag: cell line

value: oral squamous cell carcinoma cell line

tag: treatment

value: 10 mg/ml zymosan


title: no RNA_total mRNA_rep1

description:
mSeq of poly-A enriched RNA
mRNA


title: in vitro heat-killed C. parapsilosis treatment -rep2 [HO_hCp_2]

description:
HO_hCp_2
HO_hCpvsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf

value: heat-killed C. parapsilosis (CLIB214)


title: in vitro heat-killed C. parapsilosis treatment -rep3 [HO_hCp_3]

description:
HO_hCp_3
HO_hCpvsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: 10/26 twi:CD2+ DNA


title: in vitro heat-killed C. parapsilosis treatment -rep1 [HO_hCp_1]

description:
HO_hCp_1
HO_hCpvsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: 11/1 mef2:CD2- DNA

source_name: sorted embryonic cells depleted of fusion-competent myoblasts

value: reporter insertion pool crossed to mef2[IE-D5]:CD2


title: AT1 PD-1 int CD8

description: PD-1int replicate 1


title: 10/26 twi:CD2+ RNA


title: in vitro heat-killed C. albicans treatment - rep3 [HO_hCa_3]

description:
HO_hCa_3
HO_hCavsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf

value: heat-killed C. albicans (SC5314)


title: 10/25 twi:CD2+ RNA


title: AT3 memory CD8

description: Memory CD8 replicate 3

source_name: Mouse spleen CD8 T-cells_Memory CD8

value: Memory CD8


title: AT4 naive CD8

description: Navie CD8 replicate 4

source_name: Mouse spleen CD8 T-cells_Navie CD8

value: Navie CD8


title: 10/25 twi:CD2+ DNA


title: in vitro heat-killed C. albicans treatment - rep1 [HO_hCa_1]

description:
HO_hCa_1
HO_hCavsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: in vitro heat-killed C. albicans treatment - rep2 [HO_hCa_2]

description:
HO_hCa_2
HO_hCavsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: AT2 PD-1 int CD8

description: PD-1int replicate 2


title: AT2 memory CD8

description: Memory CD8 replicate 2


title: AQUOLIVE®_head kidney_3

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

hyb_protocol: The hybridization protocol was carried out according to Agilent's instructions. Briefly, 1.65 μg of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/mg cRNA) was fragmented at 60°C for 30 min in a total reaction volume of 55 µl containing 25X Agilent fragmentation buffer and 10X Agilent blocking agent. On completion of the fragmentation reaction, 55 µl of 2X GEx hybridization buffer was added to the fragmentation mixture and hybridized to the custom-commercial Salmo salar oligonucleotide microarray platform (AMADID 084881; Agilent Technologies; USA) at 65°C and 10 rpm for 17 hours in a rotating hybridization oven.

scan_protocol: After hybridization, microarrays were washed 1 min at room temperature (RT) with GEWash Buffer 1 (Agilent), 1 min with GE Wash buffer 2 (Agilent) pre-incubated at 37°C, 45 s at RT with Acetonitrile (Sigma, St Louis, MO, USA), and 30 s at RT with stabilization and drying solution (Agilent). Slides were scanned immediately afterwashing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area: 61 x21.6 mm; Scan resolution: 5 µm; Dye channel set to green; Green PMT: 100%). Spot intensities and other quality control features were extracted with Feature Extraction software version 10.4.0.0 (Agilent).

data_processing: Nofima's bioinformatic package STARS was used for data processing and mining. After filtration of low quality spots, Lowess normalization of log2-expression ratios (ER) was performed. The differentially expressed genes were selected by difference between the control and Aquolive-supplemented diet based on an unpaired t-test statistical analysis and following the criteria: p < 0.05 and log2-ER >|0.8|.

organism: Salmo salar

source_name: fed 0.15% AQUOLIVE® diet pool 3

label_protocol: One-color microarray was carried out according to manufacturer’s protocols. Briefly, 200 ng of total RNA was reversed transcribed along with spike-in (Agilent One-Color RNA Spike-In kit, Agilent Technologies, USA). Then, the solution was used as template for Cyanine-3 (Cy3) labeled cRNA synthesis and amplification with the Low Input Quick Amp Labelling kit (Agilent).  Samples of cRNA were purified using the RNeasy micro kit (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol:
A total of 1.500 unvaccinated Atlantic salmon parrs (body weight, BW = 55.0 ± 0.1 g; mean ± standard deviation) were obtained from a commercial fish farm (SARL SALMO, Gonneville-Le Thiel, France) and transported by road to IRTA-Sant Carles de la Ràpita research facilities (Sant Carles de la Ràpita, Spain).
At the end of the nutritional assay, total RNA from HK of individual fish (n = 18 fish per dietary treatment) was extracted using TRI reagent (Sigma-Aldrich, Sant Louis, MO, USA), according to manufacturer’s instructions. Total RNA concentration and purity were quantified using a Nanodrop-2000® spectrophotometer (Thermo Scientific, USA) and stored at -80 °C for further analysis. Samples were diluted to 133.33 ng/µL concentration and checked for integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Spain). All the samples used in this study were selected by the criteria of a RNA Integrity Number (RIN) value > 8.5.

treatment_protocol: All animal experimental procedures were complied with the Guiding Principles for Biomedical Research Involving Animals (EU2010/63), the guidelines of the Spanish laws (law 32/2007 and RD 1201/2015), and authorized by the Ethical Committee of the Institute for Research and Technology in Food and Agriculture (IRTA, Spain) for the use of laboratory animals (FUE-2020-01314717). After transport, fish received three treatments with hydrogen peroxide and two treatments with formaldehyde (150 ppm, during one hour each) to treat injuries and avoid the presence of any parasite. After the on-growing period of 133 days, 696 fish (BW = 55.0 ± 0.1 g) were randomly distributed in eight aerated 450 L square-shaped tanks with smoothed corners, using an IRTAmar® recirculation system (5-10 % water replacement per day) under natural photoperiod. Water temperature (12.2 ± 1.0 °C), oxygen (9.4 ± 0.8 mg/L) and pH (7.4 ± 0.3) were daily controlled, whereas salinity (35‰) as well as ammonia (0.13 ± 0.1 mg NH4+ L−1) and nitrite (0.18 ± 0.1 mg NO2- L−1) levels were weekly monitored. The nutritional assay was carried out in six replicate tanks with an initial density of 2 kg/m3 (58 fish per tank). Fish were fed both diets two times per day at the daily rate of 3.0% of the stocked biomass, which approached apparent satiation.  At day 133 of feeding, three fish were randomly selected from each tank (n total= 18 fish per dietary treatment), euthanized with anaesthetic (MS-222, Sigma-Aldrich) and a section from the head kidney was sampled and stored in RNAlater™, incubated overnight at 4 °C, and stored at -80 °C until analysed.

tag: tissue

value: Head kidney

tag: age

value: juveniles, 252 g

tag: diet

value: 0.15% inclusion of AQUOLIVE


title: AT4 memory CD8

description: Memory CD8 replicate 4

value: female


title: 93-6: UMUC3 100 DEC 7 days_2

city: Duesseldorf

first: Michèle

middle: J

last: Hoffmann

state: NRW

address: Moorenstr. 5

department: Urology

institute: Heinrich Heine University, Medical Faculty

data_processing:
Illumina bcl2fastq v2.17.1.4 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Illumina TrueSeq)and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2), then mapped to hg38 whole genome using CLC Genomics Workbench v20.0.3 with standard parameters.
Reads Per Kilobase and per Megabase (RPKM) were calculated using CLC Genomics Workbench v20.0.3 with standard parameters. Multi-group comparisons were calculated using the Empirical Analysis of DGE (version 1.1, cutoff = 5) after grouping of samples (three biological replicates each) according to their respective experimental condition. The resulting p values were corrected for multiple testing by FDR and Bonferroni-correction. A p value of ≤ 0.05 was considered significant. Cut-off for differential gene expression was set to 1.5 fold.
Genome_build: hg38
Supplementary_files_format_and_content: The Excel file includes RPKM values for each sample.

source_name: urothelial carcinoma cell line

growth_protocol: UC cells were cultured in DMEM GlutaMAX-I (Gibco, Darmstadt, Germany) supplemented with 4.5 g/l d-glucose, pyruvate, and 10 % FBS (Biochrom, Berlin, Germany).

extract_protocol:
Rneasy Mini Kit, Qiagen according to manufacturer with optional DNAse treatment
Libraries were prepared according to Vazyme instructions accompanying the VAHTS™ Universal V6 RNA-Seq Library Prep Kit for Illumina. Briefly, 300 ng total RNA were used for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification. Bead purified libraries were normalized and finally sequenced on the HiSeq 3000/4000 system (Illumina Inc. San Diego, CA, USA), following the manufacturer's protocols, with a read setup of 1 × 150 bp.

treatment_protocol: 5-Aza-2'-Desoxycytidin (DEC) was purchased from Sigma-Aldrich (Steinheim, Germany) and dissolved in DMSO. 100 nM DEC was added 24 h after cell seeding. The compound was freshly added every 24 hours for three days during medium change. Hereafter, cells were cultured for four additional days (i.e. seven days of treatment in total). DMSO control samples were treated and harvested accordingly.

value: urothelial carcinoma

value: 100 nM DEC 7 days


title: Gut_Bb_ADKO_rep2

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

country: China

institute: Zhejiang University

data_processing:
Tick transcript data was downloaded from the VectorBase (https://vectorbase.org/vectorbase/app/) and indexed using the kallisto-index.
The reads from the sequencer were pseudo-aligned with the index reference transcriptome using kallisto.
The counts generated were processed by DESeq2 in RStudio (https://rstudio.com).
Genome_build: IscaW1
Supplementary_files_format_and_content: tab-delimited text files include baseMean, log2Foldchange etc. for each gene

organism: Ixodes scapularis

source_name: Gut

extract_protocol:
Tick gut was dissected, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gut

value: Borrelia burgdorferi

value: AdipoR dsRNA


title: AT1 naive CD8

description: Navie CD8 replicate 1

value: murine CLL cells from Eµ-TCL1 mice

value: 6 weeks of transplantation

value: spleen CD8 T-cells


title: AT3 naive CD8

description: Navie CD8 replicate 3


title: AT1 memory CD8

description: Memory CD8 replicate 1


title: AQUOLIVE®_head kidney_1

source_name: fed 0.15% AQUOLIVE® diet pool 1


title: 93-7: UMUC3 100 DEC 7 days_3


title: Gut_Bb_ADKO_rep3


title: in vitro control - rep2 [HO_C_2]

description:
HO_C_2
HO_CavsHO_C_DEG_all.tdf
HO_CpvsHO_C_DEG_all.tdf
HO_hCavsHO_C_DEG_all.tdf
HO_hCpvsHO_C_DEG_all.tdf
HO_ZvsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf

value: oral squamous cell carcinoma cell line

value: no treatment


title: Control_head kidney_3

source_name: control group pool 3

value: control


title: 93-4: UMUC3 DMSO 7 days_3

value: DMSO


title: in vitro control - rep3 [HO_C_3]

description:
HO_C_3
HO_CavsHO_C_DEG_all.tdf
HO_CpvsHO_C_DEG_all.tdf
HO_hCavsHO_C_DEG_all.tdf
HO_hCpvsHO_C_DEG_all.tdf
HO_ZvsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: 93-5: UMUC3 100 DEC 7 days_1


title: 93-3: UMUC3 DMSO 7 days_2


title: in vitro Candida parapsilosis treatment -rep2 [HO_Cp_2]

description:
HO_Cp_2
HO_CpvsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf

value: live C. parapsilosis (CLIB214)


title: in vitro Candida parapsilosis treatment -rep3 [HO_Cp_3]

description:
HO_Cp_3
HO_CpvsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: AT2 naive CD8

description: Navie CD8 replicate 2

value: Navie CD8


title: HCT116_ALYREF_siRNA_02

city: Graz

first: Christiane

last: Klec

state: Styria

address: Stiftingtalstraße 24

department: Oncology

country: Austria

institute: Medical University of Graz

description: Gene expression after 48 h of transfection with ALYREF siRNA

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v5.0 (8 x 60K, Arraystar).

scan_protocol: After washing the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images.
Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies). ). After quantile normalization of the raw data, mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed mRNAs with statistical significance were identified through Fold Change filtering between two samples. Differentially expressed mRNAs with statistical significance were identified through Volcano filtering between two groups.

source_name: colorectal cancer cell line

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

growth_protocol: HCT116 colorectal cancer cells were grown in full growth medium McCoy’s 5A modified Medium (w/o L-glutamine, 2.2 g/L sodium bicarbonate) with 10% foetal bovine serum (FBS) in the presence of antibiotics (50 units per ml of penicillin, 50 μg/ml of streptomycin). Cells were incubated in a 5% CO2 humidified atmosphere at 37°C.

extract_protocol: Total RNA was isolated with a standard Trizol protocol according to manufacturer's instructions, RNA concentration and purity were measured on a NanoDrop and RNA integrity was assessed with denaturing gel electrophoresis. Samples were shipped to the company on dry ice.

treatment_protocol: HCT116 cells were seeded and transfected on 6-cm dishes with 20 nM of siRNA (either negative control siRNA C1-C3 or ALYREF siRNA A1-A3) with Hiperfect transfection reagent (Qiagen, Hilden, Germany) with the fast-forward protocol according to manufacturer's instructions for 48 h.

value: colorectal cancer

value: ALYREF siRNA


title: Control_head kidney_1

source_name: control group pool 1

value: Head kidney

value: juveniles, 252 g


title: Control_head kidney_2

source_name: control group pool 2


title: in vitro control - rep1 [HO_C_1]

description:
HO_C_1
HO_CavsHO_C_DEG_all.tdf
HO_CpvsHO_C_DEG_all.tdf
HO_hCavsHO_C_DEG_all.tdf
HO_hCpvsHO_C_DEG_all.tdf
HO_ZvsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: Gut_Bb_ADKO_rep1


title: HCT116_ALYREF_siRNA_03

label: Arraystar Flash RNA Labeling Kit, Arraystar


title: AQUOLIVE®_head kidney_2

source_name: fed 0.15% AQUOLIVE® diet pool 2

value: 0.15% inclusion of AQUOLIVE


title: 93-2: UMUC3 DMSO 7 days_1

value: urothelial carcinoma


title: Gut_Bb_GFP_rep2

value: gut

value: Borrelia burgdorferi

value: GFP dsRNA


title: in vitro Candida parapsilosis treatment -rep1 [HO_Cp_1]

description:
HO_Cp_1
HO_CpvsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: Gut_Bb_GFP_rep3


title: 92-16: UMUC3 100 DEC 3 days_1

value: 100 nM DEC 3 days


title: Gut_Clean_ADKO_rep2

value: clean

value: AdipoR dsRNA


title: 92-14: UMUC3 DMSO 3 days_2


title: wt_rep2

city: Nagatsuta-cho,Midori-ku, Yokohama-shi

first: Yuhei

last: Chadani

state: Kanagawa

department: Institute of Innovative Research

country: Japan

institute: Tokyo Institute of Technology

description: Ribosome Profiling

data_processing:
library strategy: Ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with STAR v2.7.0a
Alignment with STAR v2.7.0a
Read quantitation using custom scripts
Genome_build: NC_000913.2
Supplementary_files_format_and_content: text files contain three columns: 1. gene ID; 2. Position (nt) for sorting; 3. Position (nt) from start codon; 4. Position (aa) from start codon;  5. read counts

organism: Escherichia coli

source_name: wt_ribosome profiling

extract_protocol: MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification

tag: strain background

tag: genotype/variation

value: WT


title: 93-1: UMUC3 100 DEC 3 days_3


title: in vivo OSCC xenograft - rep3 [Contr_3]

description:
Contr_3
OCvsControl_DEG_alltdf
fpkm_genename_invivo.tdf

source_name: OSCC in mouse tongue

tag: host

value: Mus musculus

tag: host strain

value: BALB/C

tag: injected cell line

value: Control - no treatment

value: OSCC in mouse tongue


title: in vivo OSCC xenograft - rep4 [Contr_4]

description:
Contr_4
OCvsControl_DEG_alltdf
fpkm_genename_invivo.tdf


title: 92-17: UMUC3 100 DEC 3 days_2


title: in vitro Candida albicans treatment - rep3 [HO_Ca_3]

description:
HO_Ca_3
HO_CavsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf

value: oral squamous cell carcinoma cell line

value: live C. albicans (SC5314)


title: dL31_rep1

description: Ribosome Profiling

source_name: dL31_ribosome profiling

value: delta rpmE


title: Gut_Bb_GFP_rep1


title: in vitro Candida albicans treatment - rep2 [HO_Ca_2]

description:
HO_Ca_2
HO_CavsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: dL31_rep2

description: Ribosome Profiling


title: in vitro Candida albicans treatment - rep1 [HO_Ca_1]

description:
HO_Ca_1
HO_CavsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: HCT116_Control_siRNA_02

description: Gene expression after 48 h of transfection with negative control siRNA

value: colorectal cancer

value: negative control siRNA


title: HCT116_Control_siRNA_03


title: HCT116_Control_siRNA_01


title: 92-15: UMUC3 DMSO 3 days_3

value: urothelial carcinoma

value: DMSO


title: Gut_Clean_ADKO_rep3

value: gut


title: HCT116_ALYREF_siRNA_01

value: ALYREF siRNA


title: Gut_Clean_GFP_rep2

value: GFP dsRNA


title: in vivo OSCC xenograft - rep1 [Contr_1]

description:
Contr_1
OCvsControl_DEG_alltdf
fpkm_genename_invivo.tdf


title: 92-13: UMUC3 DMSO 3 days_1


title: Gut_Clean_GFP_rep3

value: clean


title: 92-11: BFTC905 100 DEC 7 days_2

value: 100 nM DEC 7 days


title: wt_rep1

description: Ribosome Profiling

value: WT


title: HeLa_25mM_RNaseR24h

city: Los Angeles

first: Minjie

last: Zhang

state: CA

address: 1985 Zonal Avenue

department: Department of Pharmacology and Pharmaceutical Sciences

institute: University of Southern California

data_processing:
Library strategy: SHARC-seq
Sequencing data were preprocessed to remove adapters form the 5'end and 3’end using Trimmomatic software; PCR duplicates are removed using splitFastqLibrary (in the icSHAPE pipeline)
Reads were mapped to hg38 genome using STAR program.
The primary mapping alignments were filtered to remove low-confidence segments, rearranged and classified into six different types using gaptypes.py (https://github.com/zhipenglu/CRSSANT).
Filtering alignments were assembled to DGs and NGs using the crssant.py script (https://github.com/zhipenglu/CRSSANT).
Bedtools v2.25.0 was used to annotate gapped and chimeric alignments.
Genome_build: hg38
Supplementary_files_format_and_content: BEDPE file contains disjoint RNA structures and interaction.

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) + 10% fetal bovine serum (FBS, Gibco) + Pen/Strep antibiotic, in 37°C incubator with 5% CO2.

extract_protocol:
TNA method was used to extract crosslinked RNA.
Library was prepared using optimized PARIS protocol (Lu. et al. Cell, 2016).

treatment_protocol: 5mM, 12.5mM and 25mM SHARC in vivo crosslinking; RNaseR (E049, ABM) were used to trim 3'end of RNA fragments.

value: epithelial cells

tag: crosslinker

value: 25mM SHARC

tag: passages/age

tag: molecule subtype

value: crosslinked total RNA


title: 92-12: BFTC905 100 DEC 7 days_3

tag: cell type


title: Gut_Clean_ADKO_rep1

value: AdipoR dsRNA


title: in vivo OSCC xenograft - rep2 [Contr_2]

description:
Contr_2
OCvsControl_DEG_alltdf
fpkm_genename_invivo.tdf

value: Mus musculus

value: BALB/C

value: Control - no treatment

value: OSCC in mouse tongue


title: Gut_Clean_GFP_rep1


title: demultiplexed_tTreg_assay_2

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

data_processing:
Fast5 files were basecalled with Megalodon (using the Rerio ONT model “res_dna_r941_min_modbases_5mC_5hmC_v001.cfg”) and aligned with minimap2 to the mm10 mouse genome. The methylation status of each CpG site was determined by Megalodon after demultiplexing with Deepbinner (v.0.2.0) (Liu et al., 2021; Wick et al., 2018).
Genome_build: mm10
Supplementary_files_format_and_content: bed files (bedmethyl files, as described in megalodon documentation: https://nanoporetech.github.io/megalodon/)

source_name: Tregs

growth_protocol: Murine CD4+ T cells were purified using the MACS CD4+ T cell negative selection kit (Miltenyi Biotec) and naive CD4+ T cells from female and male adult C57BL6/J, FoxP3-GFP, or ERBB2-CAR transgenic mice were sorted on the basis of a CD4+CD8-CD62L+CD44−GFP−CD25- expression profile on a FACSAria flow cytometer (BD Biosciences). Thymic Tregs (tTregs) were sorted from FoxP3-GFP reporter mice based on a CD4+CD8-CD62L+CD44−GFP+ profile. T cell activation (0.5-1e6 cells/well/ml) was performed on non-tissue-treated 24-well plates (ThermoFisher) using plate-bound α-CD3 (clone 145-2C11, 1 μg/ml) and α-CD28 (clone PV-1, 1 μg/ml) monoclonal antibodies in RPMI 1640 medium (Life Technologies) supplemented with 10% FCS (PAN-Biotech, Eurobio), 1% penicillin/streptomycin (GIBCO-Life technologies) and β-mercaptoethanol (50 μM). For Treg-polarizing conditions, hTGF-β (3 ng/ml) and rhIL-2 (100 U/ml), were added to the cultures.

extract_protocol:
T cells (from male mice) were polarized in the indicated conditions and DNA (3 μg) from each sample (2 biological replicates) was enriched in immune identity genes using cas9 guided RNPs, as previously published (Gilpatrick et al., 2020) and characterized (Goldsmith et al., 2021a; Goldsmith et al., 2021b).
TracrRNA and crRNA were purchased from Integrated DNA Technologies (IDT). Targeted genes included: Itgb8, Foxp3, Il17a, Rorc, Ifng, Il10, Maf, Il4 and Gata3. Samples were barcoded and multiplexed using the Nanopore Ligation Sequencing kit (SQK-LSK109) and Native barcode expansion kit according to manufacturer’s instructions (Oxford Nanopore Technology, Oxford UK) without PCR amplification.
Sequencing of native DNA was conducted on a MinION sequencer on ONT flow cells with protein pore R9.4 1D chemistry for 48h.  MinION Mk 1B (ONT).

treatment_protocol: When indicated, cell permeable αKG (dimethyl ketoglutarate, 3.5 mM; Sigma), malonate (dimethyl malonate, 10mM; Sigma) was added. Cells were split 2-3 days later with medium supplemented with rhIL-2 (100U/mL) and drugs were added at their original or half-dose concentrations. Cells were maintained in a standard tissue culture incubator containing atmospheric O2 and 5% CO2.

tag: assay

tag: ligation kit

tag: barcoding kit

tag: barcodes

value: tTreg


title: demultiplexed_Treg_assay_1

value: Treg


title: demultiplexed_Treg_assay_2


title: 92-9: BFTC905 DMSO 7 days_3

tag: cell line

value: urothelial carcinoma

tag: treatment

value: DMSO


title: demultiplexed_tTreg_assay_1


title: 92-10: BFTC905 100 DEC 7 days_1


title: hiPSC-CM treated with T3 [C3]

city: Rome

first: Alessandra

last: Ulivieri

address: Via Don Carlo Gnocchi 3

department: Laboratory of Biomedical Research

country: Italy

institute: Niccolò Cusano University Foundation

description:
Sample C3
Data_Matrix_Avsc.xlsx
Filtered_Normalized_Data_AvsC.xlsx
Differential_Expression_AvsC.xlsx

data_processing:
The reads were mapped and analyzed with the Torrent Suite (version 5.12.1).  AmpliseqRNA plugin (version 5.12.0.1) was used to map the sequencing reads on Target Regions.
Reference Library: hg19_ampliseq_transcriptome_ercc_v1(hg19 AmpliSeq Transcriptome ERCC v1)
Target Regions: hg19_AmpliSeq_Transcriptome_21K_v1.bed
Genome_build: hg19 AmpliSeq Transcriptome ERCC v1
Normalization method CPM (counts per million): counts scaled by total number of reads
The differential analysis was carried out with the R  package edgeR
Supplementary_files_format_and_content: Data matrix
Supplementary_files_format_and_content: Filtered Normalized Data
Supplementary_files_format_and_content: Differential Expression

source_name: Induced Pluripotent Stem Cell derived cardiomyocytes

growth_protocol: The cardiomyocytes were thawed in iCell Cardiomyocytes Plating Medium and directly plated onto fibronectin-coated CytoView MEA 48 wells white plates (Axion Biosystem, Atlanta, GA, USA) at 3x104 plated viable cells per well, based on lot specific plating efficiency. The hiPSC-CMs were incubated at 37 °C with 5% CO2 and allowed to attach for 2 h in moisturized conditions, prior filling each well with 0.3 mL of Plating medium. On day 2 post-plating, the spent medium was replaced with iCell Maintenance (iCM) medium and thereafter 50% of the medium was replaced every 2-3 days, up to cells treatment. Before the experiments, hiPSC-CMs were cultured for four weeks after plating to improve their functional maturation.

extract_protocol:
RNA was isolated using total RNA mini kit (Norgen Biotech Corp.) following manufacturer’s instructions.
RNA libraries were prepared Ion AmpliSeq™  Transcriptome Human Gene Expression Kit (following Ion Torrent user guide, Publication Number  MAN0010742 ); for sequencing was usde  Ion 540™ Kit – Chef  (following Ion Torrent user guide, Publication Number MAN0010851)

treatment_protocol: The day before treatment, the cells were fed with serum-free (BMCC) medium. The culture media were completely replaced with fresh media prior to compound addition and, after four hours of stabilization at 5% CO2 and at 37 °C, cells were treated for 24h with a 1:10 dilution of each 10x compound working solutions. The final compound concentrations used were 0.01% EtOH, 1 nM T3 and 100nM T3. Total RNA was extracted 24h after treatments.

value: iCell cardiomyocytes (Cellular Dynamics)

value: T3 100nM for 24 hours


title: HeLa_12.5mM_RNaseR24h

value: 12.5mM SHARC


title: 92-7: BFTC905 DMSO 7 days_1


title: demultiplexed_DMK_assay_2

value: DMK


title: hiPSC-CM treated with T3 [C1]

description:
Sample C1
Data_Matrix_Avsc.xlsx
Filtered_Normalized_Data_AvsC.xlsx
Differential_Expression_AvsC.xlsx


title: HeLa_25mM_RNaseR2h


title: hiPSC-CM treated with T3 [C2]

description:
Sample C2
Data_Matrix_Avsc.xlsx
Filtered_Normalized_Data_AvsC.xlsx
Differential_Expression_AvsC.xlsx


title: HeLa_25mM_RNaseR0h


title: HeLa_12.5mM_RNaseR12h


title: 92-5: BFTC905 100 DEC 3 days_2

value: 100 nM DEC 3 days


title: 92-6: BFTC905 100 DEC 3 days_3


title: hiPSC-CM treated with T3 B2

description:
Sample B2
Data_Matrix_AvsB.xlsx
Filtered_Normalized_Data_AvsB.xlsx
Differential_Expression_AvsB.xlsx
GO_BP_Functional_Analysis_AvsB.xlsx

data_processing:
The reads were mapped and analyzed with the Torrent Suite (version 5.12.1).  AmpliseqRNA plugin (version 5.12.0.1) was used to map the sequencing reads on Target Regions.
Reference Library: hg19_ampliseq_transcriptome_ercc_v1(hg19 AmpliSeq Transcriptome ERCC v1)
Target Regions: hg19_AmpliSeq_Transcriptome_21K_v1.bed
Genome_build: hg19 AmpliSeq Transcriptome ERCC v1
Normalization method CPM (counts per million): counts scaled by total number of reads
The differential analysis was carried out with the R  package edgeR
Supplementary_files_format_and_content: Data matrix
Supplementary_files_format_and_content: Filtered Normalized Data
Supplementary_files_format_and_content: Differential Expression
Supplementary_files_format_and_content: GO.BP functional analysis

treatment_protocol: The day before treatment, the cells were fed with serum-free (BMCC) medium. The specific culture media were completely replaced with fresh media prior to compound addition and after four hours of stabilization at 5% CO2 and at 37 °C, cells were treated by adding a 1:10 dilution of each 10x compound working solutions. The final compound concentrations used were 0.01% EtOH and 1 nM T3. Total RNA was extracted 24h after treatments.

value: T3 1nM for 24 hours


title: hiPSC-CM treated with T3 B3

description:
Sample B3
Data_Matrix_AvsB.xlsx
Filtered_Normalized_Data_AvsB.xlsx
Differential_Expression_AvsB.xlsx
GO_BP_Functional_Analysis_AvsB.xlsx


title: HeLa_12.5mM_RNaseR2h

value: epithelial cells


title: Sample_si_control3

city: Tianjin

first: Miaomiao

last: Wang

address: No. 23 Pingjiang Road, Hexi District, Tianjin

department: Urology Institute of Tianjin

institute: Second Hospital Affiliated to Tianjin Medical University

data_processing:
libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or Illumina HiSeq X Ten)
Raw data (raw reads) were processed using Trimmomatic[1]. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2[
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count .
Supplementary_files_format_and_content: FPKM

source_name: Bladder Cancer cells

growth_protocol: 5637 cells were rountinely  cultured in 1640 medium supplemented with 10% fetal bovine serum (Sera Pro) and penicillin (1:100) and maintained in an incubator at 37 C with 5% CO2.

extract_protocol:
5637 cells' total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

tag: strain

value: 5637 cells

tag: tissue

value: urinary bladder

tag: genetype

value: wild type


title: Sample_si_control2


title: hiPSC-CM treated with T3 B1

description:
Sample B1
Data_Matrix_AvsB.xlsx
Filtered_Normalized_Data_AvsB.xlsx
Differential_Expression_AvsB.xlsx
GO_BP_Functional_Analysis_AvsB.xlsx


title: HeLa_12.5mM_RNaseR0h

value: crosslinked total RNA


title: Sample_si_control1


title: 92-4: BFTC905 100 DEC 3 days_1


title: 92-3: BFTC905 DMSO 3 days_3


title: 92-8: BFTC905 DMSO 7 days_2


title: hiPSC-CM control A2

description:
Sample A2
Data_Matrix_AvsB.xlsx
Filtered_Normalized_Data_AvsB.xlsx
Differential_Expression_AvsB.xlsx
GO_BP_Functional_Analysis_AvsB.xlsx

value: EtOH 0.01% for 24 hours


title: 92-2: BFTC905 DMSO 3 days_2


title: Sample_si_BUB2

value: sic


title: Sample_si_BUB3


title: HeLa_5mM_RNaseR12h

value: 5mM SHARC


title: hiPSC-CM control A1

description:
Sample A1
Data_Matrix_AvsB.xlsx
Filtered_Normalized_Data_AvsB.xlsx
Differential_Expression_AvsB.xlsx
GO_BP_Functional_Analysis_AvsB.xlsx


title: HeLa_5mM_RNaseR0h


title: demultiplexed_DMK_assay_1


title: 92-1: BFTC905 DMSO 3 days_1


title: HeLa_5mM_RNaseR2h


title: Tc0 cells untreated - mouse 728

status: Public on Dec 07 2021

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
FASTQ files were mapped using STAR v2.5.2 aligner with transcript coordinates from GENCODE release M19 using mouse genome GRCm38 (mm10) (see also St-Paul et al. 2020, PMID: 31964625).
Reads were summarized per transcript using RSEM v1.3.0 (35) using the Gencode transcript coordinates (see also St-Paul et al. 2020, PMID: 31964625).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files containing per-gene raw counts for each sample, and for all samples combined, with one Ensembl gene id per row.

source_name: CD8+ T-cells

extract_protocol:
RNA was extracted from CD8+ T cells activated for three days in the presence of CoA or Vehicle using Qiagen RNEasy kit. Libraries were prepared using TruSeq Stranded Total RNA kit.
Two hundred nanograms from RNA samples were ribosomal RNA depleted using Ribo-zero Gold rRNA beads, following purification the RNA was fragmented. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using RNase H and DNA Polymerase I. A single “A” based were added and adapter ligated followed by purification and enrichment with PCR to create cDNA libraries. Final cDNA libraries were size validated using Agilent Bioanalyzer and concentration validated by qPCR. All libraries were normalized to 10nM and pooled together.
10pM of pooled libraries were loaded onto Illumina cBot for cluster generation. Clustered flow cell was then sequenced Pair-end 100 cycles V3 using Illumina HighSeq 2000 to achieve ~30 million reads per sample.

tag: agent


title: Tc22 cells untreated - mouse 725


title: Tc0 cells untreated - mouse 725


title: Tc0 cells untreated - mouse 715


title: Tc22 cells untreated - mouse 715


title: Tc0 cells + CoA - mouse 728

value: CoA


title: Tc22 cells untreated - mouse 728


title: Tc0 cells + CoA - mouse 725


title: Tc0 cells + CoA - mouse 715


title: hiPSC-CM control A3

description:
Sample A3
Data_Matrix_AvsB.xlsx
Filtered_Normalized_Data_AvsB.xlsx
Differential_Expression_AvsB.xlsx
GO_BP_Functional_Analysis_AvsB.xlsx


title: tAT3

city: Singapore

first: Lei

last: Sun

address: 8 College Road

country: Singapore

institute: Duke-NUS

data_processing:
Reads were aligned to mm10, using Tophat (version tophat-2.0.9) and genes were quantified using Cufflinks (Version 2.1.1)
Genome_build: mm10

source_name: Thigh adipose

extract_protocol:
Adipose tissues were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Thigh adipose


title: BAT3

source_name: Brown Adipose

value: Brown Adipose


title: tAT2


title: BAT1


title: tAT1


title: tAT4


title: iWAT4

source_name: Inguinal

value: Inguinal


title: iWAT2


title: iWAT1


title: eWAT2

source_name: Epididymal

value: Epididymal


title: eWAT4


title: Sample_si_BUB1


title: iWAT3


title: H3K27ac_mdx_Rep1

city: Montral

first: Jun

last: Ding

state: Quebec

address: 1001 Decarie Blvd.

department: Medicine

institute: McGill University

description:
H3K27ac mdx rep1
H3K27ac_mdx_W200-G600-FDR0.01-island.bed
H3K27ac_mdx.bw

data_processing:
Basecalls performed using CASAVA version 1.8
The adapters were removed using cutadapt (v1.15).
ChIP sequencing reads that passed quality score were aligned to the mouse reference genome (mm10) using bowtie2 (v2.3.4). Reads from replicates were pooled together.
Bigwig files were generated using the bam_to_bigwig function from pybedtools (v0.8.1) based on the bam files.
Broad Peaks were called using sicer (v2.0) with FDR<0.01 based on the treatment vs. input ChIP-seq data for each of 3 conditions (WT, mdx, mdxTLR4).
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files (.bw) present the normalized ChIP-seq signal; The peak file (.bed) provides all the identified broadPeaks for the ChIP-seq data

source_name: Bone marrow derived macrophages

growth_protocol: For BMDM culture, Bone marrow cells were plated in RPMI media supplemented with 2 mM L-glutamine, 10 % FBS, 1 % non-essential amino acids, 1 % essential amino acids, 0.14 % 5 N NaOH, 2 % HEPES,1 mM sodium pyruvate, 100 U/ml penicillin, 100 mg/ml streptomycin (all from Wisent) and 30 % L929 supernatant for 7 days in order to obtain differentiated BMDM.

extract_protocol:
Cultured BMDM were washed twice with cold PBS and cells were non-enzymatically detached from the plate using Corning™ CellStripper Dissociation Reagent. Cells were washed three times with cold PBS and cells were then resuspended in douncing buffer (10 mM Tris-HCl, pH 7.5, 4 mM MgCl2, 1 mM CaCl2 and 1 x protease inhibitor cocktail (PIC)) and homogenized through a syringe. Chromatin was digested in Micrococcal nuclease (New England Biolabs, Canada) at 37 °C for 7 min, and the reaction was inactivated by 0.5 M EDTA. Chromatin was resuspended in hypotonic buffer (0.2 mM EDTA, pH 8.0, 0.1 mM benzamidine, 0.1 mM phenylmethylsulfonyl fluoride, 1.5 mM dithiothreitol and 1x PIC) and incubated for 1 h on ice. After spinning down the cell debris the supernatant was recovered. Chromatin was pre-cleared with 100 μl of protein A Dynabeads (Invitrogen, USA) and immunoprecipitation was carried out by incubating with a complex of beads and H3K27me3 and H3K27Ac  overnight at 4 °C. The complexes were washed twice with ChIP wash buffer I (20 mM Tris-HCl, pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA and 150 mM NaCl) and once with 400 μl of ChIP wash buffer II (20 mM Tris-HCl (pH 8.0), 0.1% SDS, 1% Triton X-100, 2 mM EDTA and 500 mM NaCl). Finally, protein–DNA crosslinks were reversed in 200 μl of elution buffer (100 mM NaHCO3 and 1% SDS) for 2 h at 68 °C and the isolated DNA was purified using phenol chloroform.
For library preparation, ChIP DNA ends were first repaired at 20°C for 30 min with repair buffer (2.9 μl of H2O, 0.5 μl 1% Tween-20, 1 μl dNTP mix (10 mM, Affymetrix 77119), 5 μl 10x T4 ligase buffer (Enzymatics L6030-HC-L), 0.3 μl T4 DNA pol, 0.3 μl T4 PNK and 0.06 μl Klenow. Next, a mixture of 1 μl of Seradyn 3 EDAC SpeedBeads and 93 μl of 20% PEG8000/2.5 M NaCl (13% final) was added and incubated for 10 min. Magnetic beads were washed twice with 80% ethanol and air-dried for 10 min before elution in 15 μl ddH2O. dA-Tailing was performed by incubating DNA at 37°C for 30 min in the mixture of solution with 10.8 μl ddH2O, 0.3 μl 1% Tween-20, 3 μl Blue Buffer, 0.6 μl dATP (10 mM), 0.3 μl Klenow 3-5 Exo. Furthermore, 20% PEG8000/2.5 M NaCl (13% final) was added and incubated for 10 min. Beads were eluted in 14 μl of elution buffer. For adapter ligation, sample was mixed with 0.5 μl of a BIOO barcode adapter  with 15 μl Rapid Ligation Buffer, 0.33 μl 1% Tween-20 and 0.5 μl T4 DNA ligase HC and incubated for 15 min at RT. Beads were further cleaned with 7 μl of 20% PEG8000/2.5 M NaCl. Lastly, beads were eluted in 21 μl of elution buffer. From the eluted volume, 10 μl was further used for PCR amplification (16 cycles) with IGA primers (AATGATACGGCGACCACCGA) and IGB primers (CAAGCAGAAGACGGCATACGA) in 1:1 ratio.

tag: cell types

value: Primary cells

tag: age

value: 21 weeks

value: Untreated_basal level

tag: antibodies

value: H3K27Ac (39133, Active Motif)


title: H3K27ac_mdx_Rep2

description:
H3K27ac mdx rep2
H3K27ac_mdx_W200-G600-FDR0.01-island.bed
H3K27ac_mdx.bw

value: 22 weeks


title: H3K27ac_mdxTLR4_Rep1

description:
H3K27ac mTLR4 rep1
H3K27ac_mTLR4_W200-G600-FDR0.01-island.bed
H3K27ac_mTLR4.bw

value: 23 weeks


title: eWAT1


title: BAT2


title: H3K27ac_WT_Rep2

description:
H3K27ac WT rep2
H3K27ac_WT_W200-G600-FDR0.01-island.bed
H3K27ac_WT.bw

value: 20 weeks


title: H3K27ac_WT_Rep1

description:
H3K27ac WT rep1
H3K27ac_WT_W200-G600-FDR0.01-island.bed
H3K27ac_WT.bw

value: 19 weeks


title: tr004

city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

data_processing:
Basecalls performed using Ion Torrent Suite 4.0
XmaI-RRBS reads were aligned to the hg19 genome assembly using Bismark v0.12.2 with bowtie2 v2.2.3 with settings --non_directional -L 24 --rdg 0,3 --rfg 0,3; cutadapt 3.4 was used to clean sequencing adapters.
Data were filtered to remove artificial methylation using custom script
Methylation state called using bismark_methylation_extractor
Genome_build: hg19
Supplementary_files_format_and_content: .cov files were generated using bismark_methylation_extractor

source_name: Breast

extract_protocol:
Phenol:chloroform protocol after proteinase K treatment
XmaI-RRBS protocol as in: Tanas AS, Borisova ME, Kuznetsova EB et al. Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-reduced representation bisulfite sequencing. Epigenomics. 9 (6), 833-847 (2017).

value: Breast Cancer

value: Tissue

tag: t (tumor)

tag: n (node)

tag: m (metastasis)

tag: molecular subtype

value: LumB


title: tob004

tag: cell type


title: tob013


title: tg157


title: H3K27ac_Input

description:
ChIP-Input for H3K27ac
H3K27ac_ChIP_Input.bw

value: 18 weeks


title: H3K27me3_mTLR4__Rep2

description:
H3K27me3 mTLR4 rep2
H3K27me3_mTLR4_merged_sorted-W200-G600-FDR0.01-island.bed
H3K27me3_mTLR4_merged_sorted.bw

value: 17 weeks

value: H3K27me3 antibody (#9733, Cell Signaling)


title: H3K27me3_mTLR4_Rep1

description:
H3K27me3 mTLR4 rep1
H3K27me3_mTLR4_merged_sorted-W200-G600-FDR0.01-island.bed
H3K27me3_mTLR4_merged_sorted.bw

value: 16 weeks


title: eWAT3


title: taUNKN1


title: tb112


title: tg131


title: H3K27me3_mdx_Rep1

description:
H3K27me3 mdx rep1
H3K27me3_mdx_merged_sorted-W200-G600-FDR0.01-island.bed
H3K27me3_mdx_merged_sorted.bw

value: 14 weeks


title: H3K27me3_WT_Rep2

description:
H3K27me3 WT rep2
H3K27me3_WT_merged_sorted-W200-G600-FDR0.01-island.bed
H3K27me3_WT_merged_sorted.bw

value: 13 weeks


title: H3K27me3_Input_mTLR4__Rep2

description:
ChIP-Input for H3K27me3 mTLR4 rep2
H3K27me3_ChIP_Input_mTLR4_merged_sorted.bw

value: Primary cells

value: 11 weeks


title: tk069


title: H3K27me3_Input_mTLR4_Rep1

description:
ChIP-Input for H3K27me3 mTLR4 rep1
H3K27me3_ChIP_Input_mTLR4_merged_sorted.bw

value: 10 weeks

value: Untreated_basal level


title: ts059


title: tv077


title: tg086


title: H3K27me3_mdx_Rep2

description:
H3K27me3 mdx rep2
H3K27me3_mdx_merged_sorted-W200-G600-FDR0.01-island.bed
H3K27me3_mdx_merged_sorted.bw

value: 15 weeks


title: H3K27me3_WT_Rep1

description:
H3K27me3 WT rep1
H3K27me3_WT_merged_sorted-W200-G600-FDR0.01-island.bed
H3K27me3_WT_merged_sorted.bw

value: 12 weeks


title: H3K27me3_Input_mdx_Rep1

description:
ChIP-Input for H3K27me3 mdx rep1
H3K27me3_ChIP_Input_mdx_merged_sorted.bw

value: 8 weeks


title: H3K27me3_Input_WT_Rep2

description:
ChIP-Input for H3K27me3 WT rep2
H3K27me3_ChIP_Input_WT_merged_sorted.bw

value: 7 weeks


title: ts088

value: Breast Cancer


title: tg014

value: Tissue


title: td071

value: LumB


title: H3K27me3_Input_WT_Rep1

description:
ChIP-Input for H3K27me3 WT rep1
H3K27me3_ChIP_Input_WT_merged_sorted.bw

value: 6 weeks


title: tk104


title: H3K27me3_Input_mdx_Rep2

description:
ChIP-Input for H3K27me3 mdx rep2
H3K27me3_ChIP_Input_mdx_merged_sorted.bw

value: 9 weeks


title: tk078


title: HI_Hep_I_III_4

city: Aurora

first: Christophe

last: Langouët-Astrié

state: CO

department: Pulmonary Sciences and Critical Care

institute: University of Colorado Denver, Anschutz

description: Gene expression data from total lungs treated with IT Heat-Inactivated Heparanase I/III for 24 hrs

data_processing:
Illumina reads were trimmed for adaptor sequence and for quality in CLC Genomics Workbench (v.21.0.5)
Trimmed sequences were mapped to to the reference genome sequence of Mus musculus assembly GRCm39, with the parameters: mismatch cost, 2; insertion and deletion cost, 3; length and similarity fraction, 0.8.
Uniquely mapped transcripts from each sample were exported from CLC Genomics Workbench and used for normalization and differential gene expression analysis with an R package, DESeq2 version 1.32.0
Genome_build: mm10
Supplementary_files_format_and_content: Hep_gene_exp_diff contains differential gene expression between Hep I/III vs HI-Hep I/III treatment. Includes gene names, ENSEMBL, baseMean, log2FoldChange, IfcSE, stat, pvalue, padj. Raw_gene_counts_matrix contains uniquely mapped transcripts for each sample with gene name and ENSEMBL ID.

source_name: Lung

extract_protocol:
Lungs were removed, homogenized, and RNA isolated using Qiagen RNeasy Midi Kit (Cat#75144).
RNA libraries were prepared using Nugen Universal mRNA Library Prep Kit (Cat# 0520) with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Lungs were administered intracheally with Hep I/III or HI-Hep I/III and were let to recover for 24 hours

value: Lung

value: Male

value: IT Heat-Inactivated Heparanase I/III


title: tb070


title: HI_Hep_I_III_3


title: HI_Hep_I_III_1


title: tc063


title: tzh043


title: Hep_I_III_4

description: Gene expression data from total lungs treated with IT Heparanase I/III for 24 hrs

value: IT Heparanase I/III


title: t077


title: Hep_I_III_3


title: t018


title: Hep_I_III_1


title: t050


title: t053


title: IGG1_PC_R3: IgG1 PC biological replicate 3

city: London

first: Pavel

last: Tolar

state: London

address: 1 Midland Rd

country: United Kingdom

institute: Francis Crick Institute

description: RNA-seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”.
The RSEM package (version 1.3.0) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to all M. musculus genes downloaded from the Ensembl genome browser (assembly GRCm38, release 89; Kersey et al., 2016). The parameters used were “--star-output-genome-bam --star-gzipped-read-file --forward-prob 0”, and all other parameters were kept as default.
Differential expression analysis was performed with the DESeq2 package (version 1.12.3) (Love et al., 2014) within the R programming environment (version 3.3.1) (REF). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

source_name: In vitro differentiated IgG1 PC

growth_protocol: B cells were cultured on 40LB feeder cells for 6 days in the presence of 100ng/ml IL-4. Bulk day 6 sample was taken at this point. For all other subsets, cells were isolated from the feeders and cutured in RPMI without stimulation for a further 2 days prior to sorting.

extract_protocol:
Total RNA was extracted from cells using a QIAGEN RNeasy kit in RLT buffer, following the manufacturer’s instructions. Extracts were digested with DNase I to eliminate genomic DNA.
The total RNA samples were quality controlled to determine RNA integrity and concentration using Agilent Bioanalyzer prior to library preparation. Libraries were prepared using the KAPA mRNA HyperPrep kit (Roche) and sequenced as 76bp single-end, stand-specific reads on the Illumina HiSeq 4000 platform (Francis Crick Institute).

value: In vitro differentiated IgG1 PC

tag: genotype

value: wild-type

tag: timepoint

value: day 8 of in vitro culture


title: t013


title: t080


title: IGG1_NON_R1: IgG1 iGC biological replicate 1

description: RNA-seq

source_name: In vitro differentiated IgG1 iGC cells

value: In vitro differentiated IgG1 iGC cells


title: IGG1_NON_R2: IgG1 iGC biological replicate 2

description: RNA-seq


title: IGG1_NON_R3: IgG1 iGC biological replicate 3

description: RNA-seq


title: IGG1_PC_R2: IgG1 PC biological replicate 2

description: RNA-seq


title: IGE_PC_R2: IgE PC biological replicate 2

description: RNA-seq

source_name: In vitro differentiated IgE PC

value: In vitro differentiated IgE PC


title: IGE_PC_R3: IgE PC biological replicate 3

description: RNA-seq


title: IGE_PC_R1: IgE PC biological replicate 1

description: RNA-seq


title: IGE_NON_R3: IgE iGC biological replicate 3

description: RNA-seq

source_name: In vitro differentiated IgE iGC cells

value: In vitro differentiated IgE iGC cells


title: IGG1_PC_R1: IgG1 PC biological replicate 1

description: RNA-seq


title: t010


title: t047


title: t044


title: t042


title: t046


title: t035


title: IGE_NON_R1: IgE iGC biological replicate 1

description: RNA-seq


title: IGE_NON_R2: IgE iGC biological replicate 2

description: RNA-seq


title: t078


title: t033


title: t032


title: D6_R3: D6 biological replicate 3

description: RNA-seq

source_name: Bulk day 6 unsorted cells from in vitro B cell culture

value: day 6 of in vitro culture


title: t031


title: t017


title: hfq replicate 1

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

institute: Würzburg University

data_processing:
Library strategy: RIL-seq
adaptor sequences removed together with low quality ends and low-complexity reads
First 25 nucleotides of each read were mapped to SL1344 genome (NC_016810.1)
sorting of fragments into single or chimeric fragments
RILseq, deposited at pypi (https://pypi.python.org/pypi/RILseq)
Genome_build: NC_016810.1
Supplementary_files_format_and_content: spread sheet table, counts of statistically significant chimeras

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: UV crosslinked bacterial culture, anti-FLAG coIP, ligation

growth_protocol: wt and hfq-FLAG-tagged SL1344 strain was grown in LB to OD2.0

extract_protocol:
TRIzol RNA extraction
sRNA NEBNext kit for Illumina

treatment_protocol: anti-FLAG coIP of Hfq-3xFLAG, proximinity RNA ligation

value: Hfq-3xFLAG SL1344

value: hfq


title: hfq replicate 2


title: t030

value: Breast Cancer

value: Tissue


title: t090

value: LumB


title: wt reference replicate 1

value: wt


title: D6_R2: D6 biological replicate 2

description: RNA-seq

value: Bulk day 6 unsorted cells from in vitro B cell culture


title: t096


title: t014


title: t025


title: t023


title: RNA seq WT CME 1

city: Beijing

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

institute: Peking University Third Hospital

description: RNA-seq

data_processing:
RNA-seq data were aligned to the hg19 reference genome. RNA seq alignment, differential gene expression analysis and GSEA were performed as described (Anelli et al., 2017). Differentially expressed genes were defined by log2 fold change greater than 2 or less than −2 and an adjusted p value < 0.01.
Genome_build: hg19

source_name: human stem cell differentiated CME

growth_protocol: For cardiac differentiation, a chemically defined monolayer differentiation protocol was used as previously described (Lian et al., 2012). Briefly, hESCs at 40% confluence were incubated with differentiation basal medium comprising RPMI 1640 medium (Invitrogen) and B27 supplement minus insulin (Invitrogen). 6uM CHIR99021 was added to the differentiation basal medium. On day 2, medium was removed and replaced with differentiation basal medium minus CHIR99021. On day 3, 5uM IWP2, the Wnt antagonist, was added to the medium.On day 5, medium was removed and replaced with differentiation basal medium without any inhibitors. On day 7, the cells were incubated with complete CM medium consisting of RPMI 1640 medium and B27 supplement plus insulin (Invitrogen). The medium was changed every 2 days. At day 9 cells were incubated with cardiac enrichment medium (RPMI 1640 without glucose (Life technologies) + 4 mM sodium L-lactate (Sigma-Aldrich). Cells were kept in enrichment medium for 3 days. After enrichment phase medium was switched back to complete CM medium (RPMI + B27).

extract_protocol:
For RNA seq, total RNA was isolated with the RNeasy Mini Kit.
Illumina TruSeq RNA Library Prep Kit v2

treatment_protocol: No treatments were applied prior to RNA extraction

value: WT


title: RNA seq WT CME 2

description: RNA-seq


title: RNA seq TKO CME 2

description: RNA-seq

value: TET1/2/3 KO


title: RNA seq TKO CME 1

description: RNA-seq


title: t089


title: t022


title: t006


title: t021


title: Input sample from D7 CP cell

description: ChIP-seq

data_processing:
After PicoGreen quantification and quality control by Agilent BioAnalyzer, pooled libraries were run over one lane of a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina). The loading concentration was 2nM and a 5% spike-in of PhiX was added to the run to increase diversity and for quality control purposes.
Sequencing data was aligned to the hg19 reference genome using mem module from bwa-0.7.17
Peak calling was performed by macs14 1.4.2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: peak files in .txt format

source_name: D7 CP cell

growth_protocol: For cardiac differentiation, a chemically defined monolayer differentiation protocol was used as previously described (Lian et al., 2012). Briefly, hESCs at 40% confluence were incubated with differentiation basal medium comprising RPMI 1640 medium (Invitrogen) and B27 supplement minus insulin (Invitrogen). 6uM CHIR99021 was added to the differentiation basal medium. On day 2, medium was removed and replaced with differentiation basal medium minus CHIR99021. On day 3, 5uM IWP2, the Wnt antagonist, was added to the medium. On day 5, medium was removed and replaced with differentiation basal medium without any inhibitors. On day 7, the cells were incubated with complete CM medium consisting of RPMI 1640 medium and B27 supplement plus insulin (Invitrogen). The medium was changed every 2 days.

extract_protocol:
Genomic DNA was isolated from WT cardiac progenitors (CP) at D7 using DNeasy Blood & Tissue Kits (Qiagen).
Libraries were prepared using the NEBNext® Ultra II DNA Library Prep Kit (NEB, E7103S) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1; NEB, E7335S).
Samples were pooled and submitted to MSKCC Integrated Genomics Operation core for quality control and performed CHIP-seq.

treatment_protocol: No treatments were applied prior to chromatin isolation and fixation.

value: Wild type


title: TET1-V5 ChIP-Seq on D7 CP cell

description: ChIP-seq

tag: input

value: Input sample from D7 CP cell


title: GW20-P

first: Xin

last: Zhou

address: 15 Datun Road

department: State key laboratory of Brain and Cognitive Science

institute: Institute of Biophysics, Chinese Academy of Sciences

description: Sample 19

data_processing:
Cell ranger 2.0.1 was used to perform quality control and read counting of Ensemble genes with default parameter (v2.0.1) by mapping to the hg19 human genome.
We excluded poor quality cells after the gene expression matrix was generated by Cell Ranger with Scanpy (V1.4.4) package.
Scanpy1(V1.4.4) package was used to perform preprocessing of the scRNA-Seq data. The filtered gene expression matrix was normalized to 104 molecules per cell for sequencing depth with normalize_total function and log transformed with log1p function.
Genome_build: hg19
Supplementary_files_format_and_content: TSV,MTX

source_name: hypothalamus cells

extract_protocol:
Hypothalamic tissues were micro-dissected from serial coronal sections using a vibratome and dissociated into single-cell suspension using a papain-based dissociation protocol. Single cells were partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) by 10x™ GemCode™ Technology. The cDNA libraries were generated with Single Cell 3’ Reagent Kits, according to the manufacturer’s protocol. The library was processed on the Illumina HiSeq4000 platform for sequencing with 150 bp paired-end reads.
Illumina HiSeq4000 platform

value: hypothalamus

tag: embryonic stage


title: GW20-M

description: Sample 18


title: D6_R1: D6 biological replicate 1

description: RNA-seq

value: wild-type

tag: treatment


title: wt reference replicate 2

tag: strain


title: t094

tag: tissue


title: GW18-02-lane3

description: Sample 16


title: GW18-02-lane2

description: Sample 15


title: malignant_hypertension_192

city: Bern

first: Philipp

last: Kirchner

address: Murtenstrasse 31

department: Pathology

institute: University of Bern

data_processing:
Illumina RTA v1.18.66.3 was used for base calling
Reads were converted to FASTQ format while masking adapter sequences (bcl2fastq v2.17.1.4, Illumina, San Diego, U.S.A). Sequences mapping to rRNA, tRNA, mtRNA and transposons were removed by alignment against a custom reference list (bwa v0.7.14, samtools v1.8). Remaining reads were mapped to the Rattus norvegicus reference genome Rnor 6.0, Ensembl gene annotation 93, using a splice-aware aligner (STAR v2.5.4a) and quantified as reads per gene while excluding exons shared between more than one gene (subread v1.5.3)
Differentially expressed genes were determined using the negative binomial model as implemented in DESeq2 (DESeq2 v1.20.0, R v3.5.0). Analysis was performed in following groups: MH vs. NMH, MH vs. [NMH+sham], [MH+NMH] vs. sham. Results from significance tests were corrected for multiple testing (Benjamini-Hochberg)
Genome_build: Rnor 6.0
Supplementary_files_format_and_content: tab-delimited text file with counts per gene per sample obtained from Subread featureCounts

organism: Rattus norvegicus

source_name: kidney

growth_protocol: Rats were housed in a room maintained at 22±2°C, exposed to a 12h dark/light cycle. The animals were allowed unlimited access to chow (Altromin, Lage, Germany) and tap water

extract_protocol:
After organ weighing, kidneys were decapsulated. Both poles of each kidney were immediately snap frozen on liquid nitrogen for RNA extraction. RNA was isolated from tissue samples after homogenization with a disperser (T10 basic Ultra-Turrax; IKA, Staufen, Germany) using the RNeasy Fibrous Tissue Midi Kit (Qiagen, Hilden, Germany)
Sequencing libraries were generated from 0.5 ug high quality RNA using the TruSeq Stranded mRNA Kit (Illumina, San Diego, U.S.A.) according to manufacturer’s instructions. Libraries were sequenced on a HiSeq 2500 platform (Illumina, San Diego, U.S.A.) as 101 bp single-end reads to a depth of at least 25 million reads.

treatment_protocol: Two-kidney, one-clip renovascular hypertension (2K1C) was induced in male MH and NMH Sprague-Dawley rats (Charles River, Sulzfeld, Germany) weighing 150–170g by placing a silver clip of 0.2 mm internal diameter around the left renal artery through a flank incision. Control animals (sham) underwent sham operation without placement of the clip. Five weeks after clipping of the left renal artery, the experiment was terminated, animals were weighted and renal tissue was studied. Besides significant weight loss, MH animals were characterized by the presence of onion skin lesions and fibrinoid necroses in the contralateral kidney exposed to high blood pressure. NMH only showed elevated blood arterial pressure without the combination of significant postinterventional weight loss and specific renal lesions.

value: Sprague-Dawley

tag: Sex

value: male

value: two-kidney, one-clip

tag: time point

value: five weeks post surgery

tag: disease state

value: malignant hypertension

value: kidney


title: GW18-02-lane1

description: Sample 14


title: malignant_hypertension_233


title: malignant_hypertension_131


title: GW18-01-P

description: Sample 13


title: malignant_hypertension_59


title: malignant_hypertension_181


title: malignant_hypertension_41


title: non_malignant_hypertension_154

value: non-malignant hypertension


title: GW18-01-A

description: Sample 11


title: non_malignant_hypertension_157


title: CLCS_3

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

institute: Cardiff University

data_processing:
FastQ files that contained high quality RNA sequencing reads were aligned to the ‘oryCun2.0’ using TopHat and Bowtie
‘eXpress’ software package was used  to guide downstream specific analysis and the identification of differentially expressed genes
DEseq2 was used to calculate differential gene expression between sample types, normalised using an internal negative binomial model, in order to account for variation in sequencing depth between individual samples
Genome_build: oryCun2.0
Supplementary_files_format_and_content: Tab-delimited text file including per sample: gene ID, gene symbol, total counts

organism: Oryctolagus cuniculus

source_name: Injured cartilage tissue

growth_protocol: Animals were properly mantained in the core veterinary facilities until treatment was delivered in the surgery.

extract_protocol:
At desired timepoints, animals were sacrificed and cartilage tissue from the damaged untreated, CLCS treated or healthy areas was harvested and snapfrozen on dry ice. Homogenization of the tissue and total RNA extraction was performed using Trizol following Qiagen RNAeasy protocols.
cDNA libraries were prepared at the Epigenomics Core of Weill Cornell Medical College after mRNA selection (polyA tail mediated), fragmentation (TruSeq kit protocol) using TruSeq adaptor sequences.

treatment_protocol: Under IRB approved protocol IS00004559 at Houston Methodist Research Institute, New zealand rabbits underwent surgical procedure to generate a critical size defect in the trochlear groove of the knee joint. Defects were left untreated or treated with CLCS scaffolds prior to the closure of the wound.

value: cartilage

value: Collagen-chondroitin sulphate (CLCS) scaffold


title: MYC_light_1

city: Bethesda

first: Daniel

middle: R

last: Larson

address: 41 Medlar Dr.

institute: NIH

data_processing:
Whole transcriptome sequencing was performed instead of 3’ end sequencing.
Reads are pre-processed with fastp (https://github.com/OpenGene/fastp) and then mapped by SlamDunk map, filter and snp (http://t-neumann.github.io/slamdunk/).
T>C converted reads were separated by Alleyoop. The reads with T>C conversion were normalized by total mapped reads in each group.
Due to the multimapper reconciliation strategy used in SlamDunk (multimappers are assigned towards 3’ end), there is a distort of the signal to the 3’ end of the gene.
Metagene coverage matrix and profile were generated through deepTools (https://deeptools.readthedocs.io/en/develop/).

growth_protocol: Samples were cultured in Keratinocyte Serum-Free Media supplemented with bovine pituitary extract, EGF, and 1% Pen-Strep.

extract_protocol: Whole cell lysates (~1M cells per sample) were clarified with Trizol/chloroform to extract RNA in the aqueous phase.

treatment_protocol: Addition of 4sU followed by 180min incubation in the dark or under 455nm blue light.

tag: expressed gene

value: Pi-MYC

tag: growth condition

value: light

tag: biological replicate


title: MYC_light_2


title: GW20-A

description: Sample 17


title: MYC_null_1

value: dark


title: non_malignant_hypertension_101


title: GW15-P

description: Sample 10


title: CLCS_2


title: MYC_null_2


title: C_light_2

value: Pi-mCherry


title: t029

value: Breast Cancer

value: Tissue

tag: t (tumor)

tag: n (node)

tag: age

value: LumB


title: non_malignant_hypertension_77


title: GW15-A

description: Sample 8

value: hypothalamus


title: C_null_2


title: CLCS_1


title: GW15-M

description: Sample 9


title: non_malignant_hypertension_68

value: Sprague-Dawley


title: GW18-01-M

description: Sample 12


title: C_light_1


title: kidney_control_141

value: male

value: sham operation


title: C_null_1


title: kidney_control_139

value: five weeks post surgery


title: kidney_control_134


title: GW10

description: Sample 5


title: t088

tag: cell type

tag: m (metastasis)

tag: molecular subtype


title: GW8-2

description: Sample 4


title: Control_2

description: Processed_untreated.txt,Processed_CLCS.txt

source_name: Healthy cartilage tissue

value: Control


title: GW8-1

description: Sample 3


title: control, rep3

city: Xi'an

first: jiwen

last: cheng

state: Shaanxi

address: Xiwu Road

institute: Xi'an Jiaotong University

description:
gene_all_counts.csv
gene_all_fpkm.csv
WYY_ZC

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38, version 23(Ensembl 81) using TopHat v2.0.9
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: normal lung tissue

extract_protocol:
lesion and normal lung control tissue were removed, flash frozen on dry ice, and RNA was harvested using miRNeasy Mico Kit(QIAGEN 217084).
The strand-specific RNA-seq libraries were prepared using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Vazyme #NR601) following the manufacturer’s instructions.

tag: developmental stage

value: infant

tag: condition

value: control

value: normal lung tissue


title: Control_1

value: cartilage

tag: treatment


title: Control_3


title: control, rep2

description:
gene_all_counts.csv
gene_all_fpkm.csv
HLX_ZC


title: MUT MSC

first: Ming

last: Kuang

address: Xueyuan Road 38 #, Haidian District

institute: Peking University

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to human hg38 genome using subread, which produced the BAM type file directly.
The featureCounts command line tool was used to calculate the gene count matrix.
Then the count matrix was normalized with FPKM formula.
The GFOLD software was used to identify the differantially expressed genes.
Genome_build: UCSC hg38 genome was used as reference genome.
Supplementary_files_format_and_content: Excel spreadsheet includes the FPKM value for each sample.

source_name: MSC

growth_protocol: Healthy donor- and LMNA R527C mutant patient-derived MSCs were seeded 5000 cells/ml in hMSC medium (Nuwacell, RP02010, China) at 37 °C in 5% CO2.

extract_protocol:
MSCs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer’s recommendations.

value: MSC

tag: cell source

value: PBMC derived

tag: genotype

value: LMNA R527C mutant

value: progeria


title: GW7-lane2

description: Sample 2

tag: tissue

tag: embryonic stage


title: Untreated_3

value: Untreated


title: kidney_control_128

tag: strain

tag: Sex

tag: time point

tag: disease state

value: kidney


title: MUT D7, rep2

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to human hg38 genome using subread, which produced the BAM type file directly.
The featureCounts command line tool was used to calculate the gene count matrix.
Then the count matrix was normalized with FPKM formula.
The GFOLD software was used to identify the differantially expressed genes.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: spleen

extract_protocol:
Mice were sacrificed at day 0 or day 7 post 4Gy irradiation. Spleen were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer’s recommendations.

treatment_protocol: 6 weeks old wild type and  Lmna R527C mutant mice were treated with 4Gy irradiation or not.

value: spleen

value: Lmna R527C mutant

value: 6 weeks old

value: 4Gy irradiation

tag: time


title: kidney_control_127

value: Sprague-Dawley

value: male

value: sham operation


title: Untreated_2


title: control, rep1

description:
gene_all_counts.csv
gene_all_fpkm.csv
WXR_ZC

value: infant


title: GW7-lane1

description: Sample 1

value: hypothalamus


title: GW12_02

description: Sample 7


title: MUT D7, rep1


title: GW12_01

description: Sample 6


title: WT MSC

value: WT

value: healthy


title: ILS-CPAM, rep3

description:
gene_all_counts.csv
gene_all_fpkm.csv
HLX_BB

source_name: lesion tissue

value: ILS-CPAM

value: lesion tissue


title: WT D7, rep2

value: wild type


title: Untreated_1

value: cartilage


title: ILS-CPAM, rep2

description:
gene_all_counts.csv
gene_all_fpkm.csv
YYN_BB


title: S2KO_Rep3

city: Baltimore

first: Michael

last: Matunis

state: MD

address: 615 N. Wolfe Street

department: Biochemistry and Molecular Biology

institute: Johns Hopkins University

description: U2OS SUMO2 KO cells

data_processing:
Illumina PE150 reads were trimmed and clipped for quality control using NGqc software, which is built into Novogene Inc.'s bioinformatics anlaysis pipeline.
Read quality was checked for each sample using an in-house script developed by Novogene, Inc.
High quality reads were aligned into BAM files and mapped using STAR version 2.5.
Read counts were quantified using HTSeq v0.6.1 by Novogene. The results from this file were used to follow the F100 Law et al. 2019 paper on using Limma, Glimma and EdgeR to do RNA-seq analysis.
FPKM and log10 counts per million values were quantified, lowly expressed genes were removed, data were TMM normalized and voom transformed. lmFit and eBayes were used to to make contrasts between conditions (SUMO KO conditions vs WT) and differentially expressed genes at an FDR <0.05 were captured using decideTests function.
Genome_build: hg19
Supplementary_files_format_and_content: csv file with TMM normalized log10 counts per million and gene identifiers. Also, excel sheets with differentially expressed genes in SUMO KO conditions as compared to WT, with gene identifiers, chromosomal locations, logFC values (KO vs WT), average expression values, and statistical values (t, p, adj. p and B values)

source_name: U2OS osteosarcoma cells

growth_protocol: All cells were incubated at 37C in 5% CO2 and grown to 80-90% confluence in DMEM with 10% FBS cell culture medium.

extract_protocol:
total RNA
mRNA was purified from total RNA using poly-T oligo attached magnetic beads and 0.8ug RNA was reverse transcribed using random hexamer primers to generate first strand cDNA. Second second cDNA was generated, purified and overhangs were converted into blunt ends. Ends were then adenylated and NEBNext adaptor was ligated for hybridization and PCR amplified for 12 cycles. Sequencing was performed using an Illumina Hiseq 4000 Platform with 2x150 paired-end (PE150) sequence reads.

value: Human bone osteosarcoma epithelial cells

tag: cell line

value: SUMO2 KO


title: WT D7, rep1

value: spleen

tag: age


title: ILS-CPAM, rep1

description:
gene_all_counts.csv
gene_all_fpkm.csv
YYL_BB


title: MUT D0, rep2

value: Lmna R527C mutant

value: control


title: ILS, rep3

description:
gene_all_counts.csv
gene_all_fpkm.csv
YMD_BB

value: ILS


title: S1KO_Rep3

description: U2OS SUMO1 KO cells

tag: cell type

value: SUMO1 KO


title: MUT D0, rep1

value: 6 weeks old


title: ILS, rep2

description:
gene_all_counts.csv
gene_all_fpkm.csv
WLFZZ_BB


title: ILS, rep1

description:
gene_all_counts.csv
gene_all_fpkm.csv
ZSQ_BB


title: WT D0, rep2


title: S1KO_Rep1

description: U2OS SUMO1 KO cells


title: WT D0, rep1


title: S2KO_Rep1

description: U2OS SUMO2 KO cells


title: CPAM-II, rep3

description:
gene_all_counts.csv
gene_all_fpkm.csv
WYY_BB

value: CPAM-II


title: S2KO_Rep2

description: U2OS SUMO2 KO cells


title: CPAM-II, rep2

description:
gene_all_counts.csv
gene_all_fpkm.csv
WPW_BB

value: infant


title: WT_Rep1

description: Parental/Wildtype U2OS cells


title: t048

source_name: Breast

value: Breast Cancer

value: Tissue

tag: t (tumor)

tag: n (node)

tag: m (metastasis)

value: LumB


title: CPAM-I, rep3

description:
gene_all_counts.csv
gene_all_fpkm.csv
MHY

tag: developmental stage

tag: condition

value: CPAM-I


title: S1KO_Rep2

description: U2OS SUMO1 KO cells


title: Dam-R527C LMNA

description: NC

data_processing:
Library strategy: DamID-Seq
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to human hg38 genome using Bowtie2, which produced the SAM type files.
The SAM files were transformed, sorted and indexed by samtools software, producing the BAM files.
Mitochondrial reads, PCR duplicates and Non-unique alignments were removed from the mentioned above BAM files using samtools and picard prior to peak calling.
The peak-calling were conducted by  MACS2, which would produce the BED, bedgraph type file and so on.
The bedgraph(.bedgraph) files could be transformed to bigwig(.bw) type file accomplished by UCSC bedgraphtobigwig script, which can be visualized with IGV
The bedtools were used to merge each peak files from different sample to one matrix.
The peaks annotation were completed by R/Bioconductor package ChIPSeeker.
Genome_build: UCSC hg38 genome was used as reference genome.
Supplementary_files_format_and_content: Spreadsheet peak files for of each sample

source_name: Dam-R527C LMNA stabilized LMNA KO Hela cells

growth_protocol: Hela cells were cultured in DMEM medium (Gibco) supplemented with 10% FBS (PAN), 100 U/mL Penicillin-Streptomycin at 37 °C in 5% CO2.

extract_protocol:
The gDNA was ethanol-precipitated overnight at −20°C and dissolved in tris-EDTA (pH 7.5) to a concentration of 1 mg/ml.  gDNA (2.5 ml) was digested with 0.5 ml of Dpn I overnight and inactivated by heating to 80°C for 20 min. Dpn I–digested gDNA was ligated to the adaptor AdR [top (5′- CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA- 3′)  bottom(5′-TCCTCGGCCG-3′)] by T4 Ligase and inactivated by heating to 65°C for 10 min. Next we use Dpn II digestion at 37°C for 1 hour. PCR amplify the regions flanked by adaptors. The PCR products were cleaned with the Qiagen MinElute PCR Purification Kit and eluted in 20-ml ddH2O.
Each sample (3 mg) was sonicated and pulled down using Dynabeads MyOne Streptavidin T1 (Invitrogen).DNA was released off the beads by Dpn II digestion at 37°C for 1 hour after wash. The supernatant was saved and cleaned using the Qiagen MinElute Reaction Cleanup Kit. DNA was eluted in 20-ml H2O and quantified with Qubit.

value: Hela

value: LMNA KO

tag: dam construct

value: Dam-R527C LMNA


title: CPAM-I, rep2

description:
gene_all_counts.csv
gene_all_fpkm.csv
ZYS_BB

value: lesion tissue


title: Dam-WT LMNA

description: NW

source_name: Dam-WT LMNA stabilized LMNA KO Hela cells

tag: genotype

value: Dam-WT LMNA


title: RNA neuron_m_35_36

city: Houston

first: Harry

last: MacKay

state: TX

address: 1100 Bates Ave

institute: Baylor College of Medicine

data_processing:
Fastq reads were quality trimmed using TrimGalore (v0.4.4) with a minimum quality score of 20 and a minimum read length of 50. Read quality was analyzed using fastqc (v0.11.5). WGBS: After trimming the reads were aligned to the mouse genome (mm10) using Bismark (v0.18.1) set to paired-end mode and using all other default settings. Read groups corresponding to each individual sample were added to these BAM alignments using Picard (v2.10.10) ‘AddOrReplaceReadGroups’ BAM files were query-name sorted using Picard ‘SortSam’, and then deduplicated using Picard ‘MarkDuplicates’. RNA-Seq: Quality-trimmed reads were aligned to the mouse genome (mm10) using Hisat2 (v2.1.0). Mapped reads were annotated and counted using featureCounts (v1.5.3) along with the gencode comprehensive gene annotation (gencode vM15 gff3 file). Differential expression testing was performed using DESeq2 (v1.16.1).
WGBS reads were also analyzed using PReLIM  and CluBCpG according to directions in (Scott, Duryea, et al., 2020)
Genome_build: mm10
Supplementary_files_format_and_content: Merged CpG coverage files, RNA-seq counts (.csv), CluBCpG clusters (.csv)

molecule: nuclear RNA

source_name: Microdissected ARH

extract_protocol:
Arcuate nuclei (ARH) were microdissected from coronal sections.  Nuclei were isolated by ultralcentrifugation, stained with Anti-NeuN (Millipore ABN78, 1:2000) and purified by FACS. DNA extracted by QIAGEN AllPrep Micro kit, RNA by RNA-STAT60
Tagmentation-based whole-genome bisulfite library preparation was performed on genomic DNA extracted from ARH NeuN+ and NeuN- nuclei as previously described (Wang et al., 2013).  Briefly, adaptors were pre-annealed and transposomes were assembled according to the protocol described in (Wang et al., 2013).  Next, 10-30 ng of mouse genomic DNA was tagmented by adding the assembled transposome and incubating at 55C for 8 min. Following purification using SPRI beads, ligonucelotide replacement and gap repair were performed using Ampligase and T4 DNA Polymerase. The product was purified using SRPI beads and followed by bisulfite treatment using the EZ DNA Methylation Gold kit (Zymo Research). Subsequently libraries were generated by PCR amplification using KAPA 2G robust hotstart ready mix. After purification using SPRI beads, libraries were diluted and loaded onto Illumina Hiseq2500 Sequencer for 100 bp paired-end sequencing. Libraries for RNA sequencing were prepared using the SMART-Seq v4 Ultra Low Input kit (Takara Clontech) according to the manufacturer’s instructions.  Briefly, purified RNA was incubated with lysis buffer for 5 minutes.  First strand cDNA synthesis was performed using the included 3-SMART-seq CDS primer II and V4 oligonucleotide.  cDNA was amplified using PCR Primer II A, and subsequently purified using Ampure XP beads (Beckman). Illumina libraries were prepared using Nextera XT DNA library preparation kit (Illumina), and sequenced on the Illumina Hiseq 2500 platform generating 100 bp paired-end reads.

value: neuron

value: m


title: RNA neuron_m_35_37


title: RNA neuron_m_35_35


title: WT_Rep3

description: Parental/Wildtype U2OS cells

value: Human bone osteosarcoma epithelial cells

value: WT


title: RNA neuron_m_35_39


title: WT_Rep2

description: Parental/Wildtype U2OS cells


title: CPAM-I, rep1

description:
gene_all_counts.csv
gene_all_fpkm.csv
GXQZN_BB

tag: tissue


title: Dam-Vector

description: NDAM

source_name: Dam-Vector stabilized LMNA KO Hela cells

value: Dam-Vector


title: RNA neuron_m_12_29


title: RNA neuron_m_12_28


title: MUT LMNA IP

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to human hg38 genome using Bowtie2, which produced the SAM type files.
The SAM files were transformed, sorted and indexed by samtools software, producing the BAM files.
Mitochondrial reads, PCR duplicates and Non-unique alignments were removed from the mentioned above BAM files using samtools and picard prior to peak calling.
The peak-calling were conducted by  MACS2, which would produce the BED, bedgraph type file and so on.
The bedgraph(.bdg) files could be transformed to bigwig(.bw) type file accomplished by UCSC bedgraphtobigwig script, which can be visualized with IGV
The bedtools were used to merge each peak files from different sample to one matrix.
The peaks annotation were completed by R/Bioconductor package ChIPSeeker.
Genome_build: UCSC hg38 genome was used as reference genome.
Supplementary_files_format_and_content: Bigwig files for genomic coverage of each sample

extract_protocol:
MSCs were crosslinked with 1% formaldehyde and was quenched with 0.125M glycine for 5 min. The cells were washed  and pelleted at 2500 rpm for 5 min. After lysis and sonicate on, the sonicated chromatin was spun down at 12,000 rpm.
The soluble chromatin was incubated with 2-5 mg of antibodies overnight. After incubation, pre-washed Protein G Dynabeads (10004d, Invitrogen) were added and incubated for 4 h at in a rotator. Then the magnetic Dynabeads were washed and reverse crosslink. The next day, purify DNA with QIAquick PCR purification kit (Magen, D211102) and elute with 50 mL elution buffer.

value: MSC

tag: cell source

value: PBMC derived

value: Lmna R527C mutant

value: progeria

tag: chip antibody

value: Mouse anti-Lamin A Antibody (Abcam;Cat# ab8980)


title: MUT INPUT


title: BAT4

data_processing:
Reads were aligned to mm10, using Tophat (version tophat-2.0.9) and genes were quantified using Cufflinks (Version 2.1.1)
Genome_build: mm10

source_name: Brown Adipose

extract_protocol:
Adipose tissues were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brown Adipose


title: WT LMNA IP

value: healthy


title: RNA neuron_m_12_27

tag: Sex


title: CPAM-II, rep1

description:
gene_all_counts.csv
gene_all_fpkm.csv
SRX_BB

value: infant

value: CPAM-II


title: RNA neuron_m_12_26


title: WT_AGG_M_DS_1

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

country: Israel

institute: Technion

data_processing:
RNA-Seq analysis: RNA-Seq reads were filtered for rRNAs, tRNAs, microRNAs, and snoRNAs using STAR. The remaining reads were mapped to hg19 version of the human genome using STAR. Expression levels were quantified using RSEM to produce transcript and gene level quantification TPM (Transcript Per Million) values
Genome_build: hg19
Supplementary_files_format_and_content: Samples' read counts and TPM values

source_name: HEK293T cells

growth_protocol: HEK293T cells were grown in standard DMEM supplemented with 10% FBS, 1% Penicillin-Streptomycin in 37°C, 5% CO2 incubator.

extract_protocol: RNA was extracted from cells using RNeasy Mini kit (Qiagen, #74104).

treatment_protocol: Cells were transfected with either FUS-R521H-YFP or FUS-WT-YFP, together with either DNAJB14-FL, DNAJB14-short, or DsRed in 6 well plates. At 48 hours after transfection, cells were lifted from plates into standard DMEM supplemented with 10% FBS. FACS and sorting were performed on a BD FACSAria III sorter. Sorting cells into aggregate and diffused expressing populations was performed by the PulsA method. Tubes containing sorted cells were centrifuged for 7 minutes at 4 °C at 300 RCF, and the pelleted cell were flash-frozen in liquid nitrogen.

value: Human embryonic kidney 293 cells

tag: transfection

value: FUS-WT-YFP+DsRed

tag: fus aggregation state

value: diffused

tag: replicate


title: WT_AGG_M_B14SH_2


title: WT_AGG_M_B14SH_1


title: WT_AGG_M_DS_2


title: RNA neuron_f_35_19

value: neuron

value: f


title: RNA neuron_m_12_25

value: m


title: WT_AGG_M_B14FL_2


title: WT INPUT

value: WT

tag: disease state


title: MUT MSC, ATAC-seq

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to human hg38 genome using Bowtie2, which produced the SAM type files.
The SAM files were transformed, sorted and indexed by samtools software, producing the BAM files.
Mitochondrial reads, PCR duplicates and Non-unique alignments were removed from the mentioned above BAM files using samtools and picard prior to peak calling.
The peak-calling were conducted by  MACS2, which would produce the BED, bedgraph type file and so on.
The bedgraph(.bdg) files could be transformed to bigwig(.bw) type file accomplished by UCSC bedgraphtobigwig script, which can be visualized with IGV
The bedtools were used to merge each peak files from different sample to one matrix.
The peaks annotation were completed by R/Bioconductor package ChIPSeeker.
Genome_build: UCSC hg38 genome was used as reference genome.
Supplementary_files_format_and_content: bw, peak text files

extract_protocol:
Pellet 50,000 viable MSCs at 500 RCF at 4°C for 5 min. Aspirate all supernatant. Add 50 μL cold ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin into the cell pellet and pipette up and down 3 times. Incubate on ice for 3 minutes. Wash out lysis with 1 mL cold ATAC-RSB containing 0.1% Tween-20 but no NP40 or digitonin and invert tube 3 times to mix. Pellet nuclei at 500 RCF for 10 min at 4°C.
Aspirate all supernatant. Resuspend cell pellet in 50 μL of transposition mixture (25 μL 2x TD buffer, 2.5 μL transposase (100 nM final), 16.5 μL PBS, 0.5 μL 1% digitonin, 0.5 μL 10% Tween-20, 5 μL H2O) by pipetting up and down 6 times. Incubate reaction at 37°C for 30 minutes. Afterward, the DNA was purified with Magen DNA purify kit and amplified with primers containing barcodes by using the TruePrep DNA Library Prep Kit (TD501-01).

value: LMNA R527C mutant


title: RNA neuron_f_35_18

tag: age


title: WT_AGG_M_B14FL_1

tag: cell type


title: WT MSC, ATAC-seq

value: MSC


title: 970-75-L

type: genomic

city: Lebanon

first: Meghan

last: Muse

state: NH

address: One Medical Center Drive, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

description: Subject 970 Naevus Tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Normalized using functional normalization (Fortin et. al. Genome Biology 2014)

label: Cy5 and Cy3

source_name: skin tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA extraction was performed either using the QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany) or the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN, Hilden, Germany) according to manufacturer’s protocol

tag: subject

tag: age (years)

value: F

value: Naevus

tag: classification

value: Dysplastic


title: 822-RLA-P

description: Subject 822 Skin Tissue

value: Skin


title: 822-10-P

description: Subject 822 Skin Tissue


title: 970-75-P

description: Subject 970 Skin Tissue


title: 521_AGG_P_DS_2

value: aggregate


title: RNA neuron_f_35_16


title: 822-10-L

description: Subject 822 Naevus Tissue


title: 822-RLA-L

description: Subject 822 Naevus Tissue


title: 673-1-P

description: Subject 673 Skin Tissue

value: M


title: 521_AGG_P_DS_1


title: 61-115-P

description: Subject 61 Skin Tissue


title: 673-1-L

description: Subject 673 Naevus Tissue


title: RNA neuron_f_35_17


title: 61-115-L

description: Subject 61 Naevus Tissue

value: Benign


title: 510-2-P

description: Subject 510 Skin Tissue


title: 521_AGG_P_B14FL_2


title: 52-40-P

description: Subject 52 Skin Tissue


title: RNA neuron_f_35_15


title: 510-23-P

description: Subject 510 Skin Tissue


title: 510-2-L

description: Subject 510 Naevus Tissue


title: 61-133-P

description: Subject 61 Skin Tissue


title: 39-6-L

description: Subject 39 Naevus Tissue


title: 510-23-L

description: Subject 510 Naevus Tissue


title: 39-6-P

description: Subject 39 Skin Tissue


title: 521_AGG_P_B14FL_1


title: RNA neuron_f_12_5


title: 61-133-L

description: Subject 61 Naevus Tissue