title: 3_PTC_L25

city: ROCHESTER

first: Douglas

middle: Glenn

last: Brownfield

state: Minnesota

address: 200 1ST ST SW

department: PCCM

institute: Mayo Clinic

description: Sample used for quality control. No quantitative processed data produced for this sample.

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.Â
adapter sequences were removed using cutadapt-1.2.1
trimming by base quality was performed and low complexity reads were removed using prinseq-lite-0.20.3
paired reads were aligned against mm10 using bowtie2-2.1.0 and tophat-2.0.8
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Column headers are: tracking_id, gene_ID, gene short name, tss_id, locus, q0_FPKM, q0_FPKM_low, q0_FPKM_hi

source_name: E18.5 mouse lung

extract_protocol:
To obtain cells from the embryonic  lung, the pulmonary vasculature was cleared and lungs were gently incubated with digestion buffer prior to trituration. All tissue was digested at 37C for 15 min using dispase and DNase I, triturated and subsequently filtered using 100µm and 40µm strainers to obtain a single cell suspension. Mesenchymal and endothelial cells were enriched by magnetic-assisted cell sorting using CD45, Pecam, and EpCAM depletion. Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions. As a bulk control, cDNA was prepared from approximately 200 cells in a PCR tube using the same protocol and reagents as used for the single cells.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

value: bulk CD45- negative cells

tag: strain


title: Primary astrocyte, control_01

status: Public on Aug 17 2022

type: SRA

city: Kingston

first: Willam

middle: Van

last: Nostrand

state: Rhode Island

address: 7 Greenhouse Rd

department: College of Pharmacy

country: USA

institute: University of Rhode Island

library_source: transcriptomic

data_processing:
Basespace RNA-Seq Alignment APP     - Read mapping using the STAR aligner; Quantification of reference genes and transcripts using salmon; Rattus norvegicus UCSC rn5 (RefSeq gene annotation)  - SNVs and INDELs called by Strelka Variant caller  - Gene fusions detected by Manta     https://support.illumina.com/help/BS_App_RNASeq_Alignment_v2_OLH_1000000006112/Content/Source/Informatics/Apps/WkflDescr_swBS_appRNASeq.htm
Read mapping using the STAR aligner; Quantification of reference genes and transcripts using salmon; Rattus norvegicus UCSC rn5 (RefSeq gene annotation)
SNVs and INDELs called by Strelka Variant caller
Gene fusions detected by Manta
Basespace DESeq2 APP -  produces gene counts, gene FPKMs
Assembly: Rattus norvegicus UCSC rn5 (RefSeq gene annotation)
Supplementary files format and content: tab-delimited text files include  gene FPKMs  values for each Sample

molecule: total RNA

organism: Rattus norvegicus

source_name: brain

extract_protocol:
E.Z.N.A.® Total RNA Kit II - https://www.omegabiotek.com/product/e-z-n-a-total-rna-kit-ii/
RNA sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc., San Diego, CA, USA) according to the manufacturer`s protocol by Omega Bioservice Company.

tag: tissue

value: brain

tag: cell type

value: Primary astrocyte cells

tag: genotype

value: WT

tag: treatment

value: control

tag: time


title: 2_PTC_L25

molecule: polyA RNA

organism: Mus musculus


title: fNFA_C4

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

country: Germany

institute: University Hospital Halle (Saale)

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads
HTSeq was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was isolated using Sigma Genelute total RNA isolation Kit
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (New England Biolabs, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Kidney

tag: gender

value: female

value: renal cortex


title: 1_PTC_L25


title: 1lpp_L26_C82

value: E18.5 Mouse lung endothelial cell


title: MPNST-28

city: NEW YORK

first: Ping

last: Chi

state: NY

address: 1275 YORK AVENUE

institute: MEMORIAL SLOAN KETTERING CANCER CTR

data_processing:
The sequence data were processed and mapped to the human reference genome (hg20) using STAR v2.3 (Dobin et al., 2013)
Gene expression was quantified to transcripts-per-million (TPM) using the STAR (Trapnell et al., 2010) and Log 2 transformed.
Assembly: hg20
Supplementary files format and content: tab-delimited text file includes raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: MPNST tumor

extract_protocol:
Total RNA were isolated from tumor tissues using Trizol (Thermo Fisher #15596026).
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq by poly (A) capture

value: MPNST tumor

value: PRC2 loss of function


title: fICRE_M5

value: renal medulla


title: MPNST-27


title: RP-116, BOM, rep1 (cultured SCLC cells)

city: Seattle

first: Joseph

middle: Brian

last: Hiatt

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis software v1.18.66.3 for HiSeq 2500 data and v3.9.25 for NextSeq 2000 data, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v2.20. Fastq files were filtered to exclude reads that did not pass Illumina’s base call quality threshold.
STAR v2.7 with 2-pass mapping was used to align reads to mouse genome build mm10 and GENCODE gene annotation M23 (https://www.gencodegenes.org/mouse/).
FastQC 0.11.9 and RSeQC 3.0.0 were used for QC including insert fragment size, read quality, read duplication rates, gene body coverage and read distribution in different genomic regions.
FeatureCounts in Subread 2.0 was used to quantify gene-level expression by unstranded read counting.
Assembly: mm10
Supplementary files format and content: Each processed data file is in plain text format containing gene-level raw counts of each sample. Gene information is based on GENCODE gene annotation M23. The overall exonic length of each gene is included and used for computing normalized expression.

extract_protocol:
RNA was extracted from cell pellets or tumor samples using TRIzol reagent following manufacturers protocol.
RNAseq libraries were generated from 500ng of RNA using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs E7530L).

tag: cell line

value: cultured SCLC cells

tag: histology

value: mSCLC

value: BOM


title: fICRE_M3


title: MPNST-32


title: fICRE_M4


title: MPNST-26


title: fNFA_C5


title: fICRE_M2


title: MPNST-25


title: 1lp_L26_C64


title: 1lp_L26_C79


title: 1lp_L26_C57


title: 1lp_L26_C84


title: MPNST-30


title: 1lp_L26_C78


title: MPNST-24


title: 1lp_L26_C81


title: 1lp_L26_C01


title: fICRE_C5


title: MPNST-23


title: MPNST-29


title: 1lpp_L26_C51


title: 1llpp_L26_C60


title: 1llpp_L26_C68


title: MPNST-22


title: fICRE_C4


title: fICRE_C3


title: 1llpp_L26_C16


title: 1llpp_L26_C27


title: 1llpp_L26_C07


title: MPNST-21


title: 1lpp_L26_C80


title: 1llpp_L26_C04


title: 1llp_L26_C89


title: fICRE_C2


title: MPNST-20


title: 1llp_L26_C74


title: 1llp_L26_C45


title: MPNST-19


title: 1llp_L26_C12


title: KO_600_1-Rep1

value: Kidney primary IMCD cells Nfat5-KO

value: 600 mosmol/kg


title: 1ll_L26_C69


title: KO_600_2-Rep2


title: 1ll_L26_C62


title: MPNST-18


title: KO_300_2-Rep2

value: 300 mosmol/kg


title: MPNST-17


title: 1ll_L26_C59


title: KO_300_1-Rep1


title: 1ll_L26_C58


title: fICRE_C7


title: 1ll_L26_C52


title: WT-600-Rep2

value: Kidney primary IMCD cells WT


title: MPNST-16


title: MPNST-14

value: PRC2 intact


title: WT-600-Rep1


title: 1ll_L26_C41


title: 1ll_L26_C46


title: 1ll_L26_C40


title: 1ll_L26_C47


title: 1ll_L26_C39


title: WT-300-Rep2


title: 1ll_L26_C37


title: WT-300-Rep1


title: MPNST-13


title: 1ll_L26_C32


title: 1ll_L26_C31


title: MPNST-12


title: 1ll_L26_C28


title: SiCD4_8

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description: library of 96 CD45+ TCRb+ CD4+ SI T cells - biological replica 2

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2(Hiseq2500) or Control Software HD 3.4.0.38 / RTA2.7.7 / Recipe Fragment HD 3.5.0.4(Hiseq3000) was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters (Li and Durbin, 2010). The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapped by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the unique molecular identifier (UMI) followed by six bases representing the cell specific barcode. The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts, representing processed data files (Grun et al., 2014)
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: small intestine lamina propria - uninfected

growth_protocol: C57BL/6J mice (RRID: IMSR_JAX:000664) were purchased from the Jackson Laboratory. All mice were maintained in specific-pathogen-free conditions in the animal facility of the Max Planck Institute for Immunobiology and Epigenetics (Freiburg, Germany)

extract_protocol:
Isolation of cells from mFAT and SI LP: For isolation of cells from mFAT mice were euthanised and transcardially perfused with 10ml of ice-cold PBS. mFAT was separated from mLN, intestine and omentum, minced and digested in 3ml of low glucose DMEM containing 25mM HEPES, 1% low fatty acid BSA, 2mM L-glutamine (L-glut), 100U/ml Penicillin/Streptomycin (P/S), with the addition of Liberase TL (0.2mg/ml, Roche) and DNase I (0.25mg/ml, Roche) for 30-40min in 37°C rotating. After digestion 2ml DMEM containing 2mM EDTA was added and the suspension filtered through 70um strainer. Cells in SVF were then separated from the adipocyte layer by centrifugation. For isolation of cells from SI LP small intestines were open longitudinally, cleaned, cut into 2cm pieces and placed in RPMI medium containing 3% FBS, 25mM HEPES, 2mM L-glut, 100U/ml P/S, 1mM DTT and agitated for 25min, after which samples were washed 3-4 times with RPMI containing 2mM EDTA. Intestines were digested in RPMI medium containing 25mM HEPES, 2mM L-glut, 100U/ml P/S, Liberase TL
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: To induce H. polygyrus infection mice were gavage with 200 L3 infectious stage larvae in PBS. For primary infection mice were left for 11-13 days before being sacrificed. For recovery mice were orally treated with anti-helminth pyrantel pamoate (1mg/mouse) and left for 4-5 weeks. For secondary infection mice were gavaged with 200 L3 H. polygyrus at the end of recovery stage and sacrificed at 11-13 days post-secondary infection

value: C57BL/6 - female

value: small intestine lamina propria

tag: age

value: 6-8 weeks


title: MPNST-11


title: 1ll_L26_C23


title: 1ll_L26_C25


title: MPNST-10


title: SiCD4_7


title: 1ll_L26_C20


title: MPNST-9


title: SiCD4_6


title: MPNST-15


title: 1ll_L26_C14


title: 1ll_L26_C09


title: SiCD4_5


title: 1ll_L26_C08


title: MPNST-8


title: MPNST-7


title: 1ll_L26_C05


title: 1ll_L26_C03


title: 1ll_L26_C06


title: SiCD4_4

description: library of 96 CD45+ TCRb+ CD4+ SI T cells - biological replica 1


title: SiCD4_3


title: 1l_L26_C96


title: MPNST-6


title: 1l_L26_C95


title: MPNST-5


title: SiCD4_2


title: 1l_L26_C91


title: SiCD4_1


title: MPNST-4


title: 1l_L26_C87


title: 1ll_L26_C13


title: MPNST-3


title: 1l_L26_C86


title: CD4mLN_8

description: library of 96 CD45+ TCRb+ CD4+ mLN T cells - biological replica 2

source_name: mesenteric lymph node - uninfected

value: mesenteric lymph node


title: CD4mLN_7


title: 1l_L26_C77


title: MPNST-2


title: 1l_L26_C76


title: CD4mLN_6


title: MPNST-1


title: 1l_L26_C72


title: 1l_L26_C66


title: 1l_L26_C71


title: H3K36me3_M3sgSUZ12_1

library_source: genomic

data_processing:
Reads were trimmed by the software Trim Galore and then aligned to the human genome (hg19) using the Bowtie2 alignment software (v2.3.5)
Assembly: hg19
Supplementary files format and content: bigWig, aligned and quantified peaks
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: human malignant peripheral nerve sheath tumor cells

growth_protocol: All cells were tested to be mycoplasma free by the MycoAlertPlus MycoPlasma Detection Kit (Lonza). All these cells were cultured in DMEM supplemented with L-glutamine (2 mM), penicillin (100 U/ml), and streptomycin (100 μg/ml), and 10% heat-inactivated fetal bovine serum (FBS) in 5% CO2 incubator at 37°C.

extract_protocol:
CUT&RUN assay was performed using the commercial kit and protocol (CST, #86652). Primary antibodies (1μg per assay) for CUT&RUN are as below: anti-H3K27me3 (CST, #9733), anti-H3K27ac (Abcam #ab4729), anti-H3K37me2 (Thermo Fisher Scientific, #MA5-14867), and anti-H3K36me3 (Active motif, # 61021)
After purification of DNA from CUT&RUN, the library was amplified by PCR and subjected to paired-end 50 base-pair high-throughput sequencing on an Illumina HiSeq2500 platform as previously described (Buenrostro et al., 2013) (Buenrostro et al., 2015).

tag: suz12 status

value: Knockout

tag: prc2 status

value: loss

tag: chip antibody


title: H3K36me3_M3sgSUZ12_2


title: CD4mLN_4

description: library of 96 CD45+ TCRb+ CD4+ mLN T cells - biological replica 1


title: 1l_L26_C90

value: E18.5 Mouse lung endothelial cell


title: 1l_L26_C65


title: CD4mLN_5


title: H3K36me3_M3sgCon_2

value: wild type

value: intact


title: 1l_L26_C56


title: Total1_SmallRNA

city: Pasadena

first: Riley

last: Galton

state: CA

address: 1200 E California Blvd

department: BBE

institute: Caltech

data_processing:
Reads were trimmed and mapped to the chicken genome (galGal6) using Bowtie4 with no mismatches end to end and multimapping reads included (-V 0 -k 1 --best).
Sequences mapping to genes and repetitive elements were counted using featurecounts, as were sequences mapping in antisense orientation to genes and repetitive elements.
Reads were analyzed for sequence length, gene type they mapped to and whether they mapped sense or antisense to a feature. Reads mapping to TEs were extracted and analyzed for 5’ to 5’ complementarity and sequence length.
TE mapping reads were then deduplicated and sequence logos were generated for the first 18nt of each sequence.
Genome_build: galGal6
Supplementary_files_format_and_content: raw count files for genes and repetitive elements

organism: Gallus gallus

source_name: HH9- cranial midbrain region

growth_protocol: Chick embryos were grown at 37C for ~30 hours to reach HH9-

extract_protocol:
Total RNA was extracted from the midbrain region of HH9- chick embryo heads. After RNA extraction, small RNA was size selected by acrylamide gel purification and half of each sample was oxidized with sodium periodate to select for 2'O-methylated species (piRNAs).
RNA libraries were prepared for sequencing using standard Illumina protocols for small RNA cloning

treatment_protocol: Wildtype embryos

tag: Stage

value: Cranial midbrain region

tag: rna treatment

value: Size selected, Not oxidized


title: CD4mLN_2


title: Total2_SmallRNA


title: 1l_L26_C85


title: CD4mLN_3


title: 1l_L26_C55


title: CD4mLN_1


title: H3K36me2_M3sgSUZ12_2


title: Oxidized1_SmallRNA

value: Size selected, Oxidized


title: 1l_L26_C75


title: Cd4Fat_4

description: library of 96 CD45+ TCRb+ CD4+ mFAT T cells

source_name: mesenteric fat - uninfected

value: mesenteric fat


title: 1l_L26_C35


title: H3K36me2_M3sgSUZ12_1


title: 1l_L26_C36


title: 1l_L26_C70


title: Cd4Fat_3


title: 0.05 mGy/h batch2, replicate 5

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

country: France

institute: IRSN

description: treated batch2

data_processing:
Quality (selection of Q>30) and adapter trimming with Trimgalor v0.4.2
Mapping with  STAR v020201
Quantification and normalization with Deseq2 v1.22.2
Assembly: GRCz11
Supplementary files format and content: Read count files from RNAstar

organism: Danio rerio

source_name: brain telencephalon

growth_protocol: Maintenance of adult zebrafish in Zebtech (Techniplast) system

extract_protocol:
Total RNA was harvested using Trizol extraction method and precipitated with isopropanol. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Stranded mRNA-Seq Library Prep Kit from ILLUMINA using single index, following manufacturer's protocols.

treatment_protocol: Exposure to external gamma exposure (CS137 source) for 36 days at 0.05 mGy/h, 0.5 mGy/h or 5 mGy/h. Or untreated

value: brain telencephalon

value: AB

value: continuous gamma radiation at 0.05 mGy/h

value: Day 36


title: 0.05 mGy/h batch2, replicate 6

description: treated batch2


title: Cd4Fat_2

value: C57BL/6 - female


title: H3K36me2_M3sgCon_2


title: 0.05 mGy/h batch2, replicate 4

description: treated batch2


title: H3K36me3_M3sgCon_1


title: 1l_L26_C26


title: Cd4Fat_1


title: H3K27ac_M3sgSUZ12_2


title: 1l_L26_C29


title: 0.05 mGy/h batch2, replicate 2

description: treated batch2


title: H3K27ac_M3sgSUZ12_1


title: High fiber diet sample 1

city: New York

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to mm10 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: ILC2s sorted from colon

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols

value: ILC2s sorted from colon

tag: diet

value: High-fiber


title: 1l_L26_C24


title: H3K27ac_M3sgCon_2


title: Oxidized2_SmallRNA


title: 0.05 mGy/h batch2, replicate 1

description: treated batch2


title: 1l_L26_C15


title: Control batch 2, replicate 6

description: non treated control batch2


title: 1l_L26_C11


title: Control diet sample 2

value: Control


title: 1l_L26_C30


title: H3K27ac_M3sgCon_1


title: AT3 sgEed-2 tumor 4

data_processing:
The sequence data were processed and mapped to the mouse reference genome (mm9) using STAR v2.3 (Dobin et al., 2013)
Gene expression was quantified to transcripts-per-million (TPM) using the STAR (Trapnell et al., 2010) and Log 2 transformed.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and every sample

source_name: mammary tumor

growth_protocol: PRC2-isogenic AT3 cells were grafted into mammary fat pads of C57BL/6J mice. Tumors were collected on day 17 post grafting.

extract_protocol:
Total RNA were isolated from fresh  tumor tissues using Trizol (Thermo Fisher #15596026).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mammary fat pad transplant tumor

tag: eed

value: Knockout


title: Control batch 2, replicate 5

description: non treated control batch2


title: H3K36me2_M3sgCon_1


title: Control diet sample 1

tag: strain


title: 0.05 mGy/h batch2, replicate 3

description: treated batch2

tag: tissue


title: Control batch 2, replicate 4

description: non treated control batch2


title: H3K27me3_M3sgSUZ12_1

value: loss


title: High fiber diet sample 2


title: H3K27me3_M3sgSUZ12_2


title: H3K27me3_M3sgCon_2

value: wild type


title: AT3 sgEed-2 tumor 2


title: 1_L25_C95

tag: cell type

value: E18.5 Mouse lung mesenchymal cell


title: Control batch 2, replicate 3

description: non treated control batch2

tag: genotype


title: 1_L25_C94


title: Control batch 2, replicate 2

description: non treated control batch2

tag: treatment


title: H3K27me3_M3sgCon_1

value: intact


title: 1_L25_C93


title: AT3 sgEed-2 tumor 1


title: Control batch 2, replicate 1

description: non treated control batch2

tag: time


title: 1_L25_C89


title: 1_L25_C96


title: EU286_YP2

city: Chicago

first: Tauras

last: Vilgalys

state: Illinois

address: 5801 S Ellis Ave

institute: University of Chicago

data_processing:
Adaptor sequences and low quality score bases (Phred score < 20) were first trimmed using Trim Galore (version 0.2.7).
Reads were mapped to the human genome reference sequence (Ensembl GRCh37 release 75) using STAR (2.4.1d) with a hg19 transcript annotation GTF file downloaded from Ensembl.
Gene-level expression estimates were calculated using RSEM (version 1.2.21) with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing gene name, gene symbol, and expression (counts)

growth_protocol: Blood mononuclear cells were isolated by Ficoll-Paque centrifugation. Monocytes were purified from peripheral blood mononuclear cells by positive selection with magnetic CD14 Mi-croBeads (Miltenyi Biotech). Monocytes were then cultured for 7 days in RPMI-1640 (Fisher) supplemented with 10% heat-inactivated FBS (FBS premium, US origin, Wisent), L-glutamine(Fisher) and M-CSF (20ng/mL; R&D systems). Cell cultures were fed every 2 days with com-plete medium supplemented with the cytokines previously mentioned. Before infection, we checked the differentiation/activation status of the monocyte-derived macrophages by flow cytometry, using antibodies against CD1a, CD14, CD83, and HLA-DR (BD Biosciences). Only samples presenting the expected phenotype for non-activated macrophages (CD1a+, CD14+,CD83, and HLA-DRlow) were used in downstream experiments

extract_protocol:
Total RNA was extracted from the non-infected and infected macrophages using the miRNeasy kit (QIAGEN). RNA quantity was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies). Only samples with no evidence for RNA degradation (RNA integrity number > 8) were kept for further experiments.
RNA- sequencing libraries were prepared using the Illumina TruSeq protocol.

treatment_protocol: Macrophages were stimulated for 4 hours with lysate of heat-killed Y. pestis (strain CO92) at a value of 10 colony forming units (CFUs) per cell, or with endotoxin-free water (negative control).

tag: subject id

value: TRUE

tag: population

value: EUR

value: monocyte-derived macrophages


title: AT3 sgEed-1 tumor 4


title: 5 mGy/h batch1, replicate 3

description: treated batch1

value: brain telencephalon

value: continuous gamma radiation at 5 mGy/h


title: 1_L25_C88


title: 5 mGy/h batch1, replicate 2

description: treated batch1

value: AB


title: EU286_NI2

value: FALSE


title: AT3 sgEed-1 tumor 3


title: EU284_YP2


title: AT3 sgEed-2 tumor 3


title: 5 mGy/h batch1, replicate 1

description: treated batch1

value: Day 36


title: AT3 sgEed-1 tumor 1


title: 0.5 mGy/h batch1, replicate 3

description: treated batch1

value: continuous gamma radiation at 0.5 mGy/h


title: 1_L25_C83


title: AT3 sgEed-1 tumor 2


title: AT3 sgCon tumor 4


title: 1_L25_C82


title: 0.5 mGy/h batch1, replicate 1

description: treated batch1


title: 1_L25_C80


title: EU268_YP2


title: EU264_YP2


title: EU268_NI2


title: 0.5 mGy/h batch1, replicate 2

description: treated batch1


title: 1_L25_C79


title: Control batch 1, replicate 3

description: non treated control batch1


title: AT3 sgCon tumor 2


title: EU284_NI2


title: 1_L25_C78


title: EU264_NI2


title: Control batch 1, replicate 2

description: non treated control batch1


title: AT3 sgCon tumor 1


title: 1_L25_C76


title: Control batch 1, replicate 1

description: non treated control batch1


title: EU262_YP2


title: AT3 sgCon tumor 3


title: EU258_YP2


title: EU262_NI2


title: Sample_18207

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Demultiplexing was perfomed using bcl2fastq2 v2.20
Alignment with STAR (2.5.2a) usign standard parameters
Reads were counted with STAR (--quantMode GeneCounts; implementation of htseq-count with default parameters)
reads mapped to each transcript against the RefSeq hs38
Normalization using DeSeq2
Assembly: hs38
Supplementary files format and content: comma separated files include raw count table

source_name: Jurkat

growth_protocol: BxPC-3 and Jurkat were cultured and treatred in RPMI medium (10% FCS + PS)

extract_protocol:
Cells were lysed in Trizol. Total RNA was extracted using the miRNeasy kit (Qiagen) and checked the RNA integrity and quantity using the tapestation RNA assay on a tapestation4200 instrument (Agilent).
750ng total RNA were used to generate NGS libraries using the TruSeq stranded total RNA kit (Illumina) following manufacturer's instructions

treatment_protocol: Cells were treated with cisplatin 3 uM for 6 h.

value: T cell leukemia

value: treated

tag: time point

tag: replicate


title: Infected, treated with 10 ppm for 15 mins, week 6, fish 58

type: RNA

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent G2565BA DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Gill

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon post smolts were kept in tanks with sea water

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

treatment_protocol: Amoebic gill disease was induced in the fish. Twenty days after infection, fish were treated with peracetic acid (5 ppm for 30 mins or 10 ppm for 15 mins). Untreated control and untreated-infected fish were also included.

value: Gill

tag: treatment group


title: Sample_18206


title: Infected, treated with 10 ppm for 15 mins, week 6, fish 57


title: Sample_18208


title: Sample_18205


title: 1_L25_C72


title: Infected, treated with 10 ppm for 15 mins, week 6, fish 53


title: Infected, treated with 10 ppm for 15 mins, week 6, fish 56


title: EU258_NI2


title: 1_L25_C70


title: 1_L25_C69


title: 1_L25_C68


title: Infected, treated with 10 ppm for 15 mins, week 6, fish 52


title: 1_L25_C73


title: 1_L25_C67


title: EU256_NI2


title: Sample_18202

value: control

value: ctrl


title: AF155_YP2

value: AFR


title: Infected, treated with 5 ppm for 30 mins, week 6, fish 48


title: Sample_18201

value: Pancreatic cancer


title: AF155_NI2


title: Infected, treated with 5 ppm for 30 mins, week 6, fish 47


title: Sample_18204


title: Sample_18200


title: AF133_YP2


title: Sample_18199


title: Infected, treated with 5 ppm for 30 mins, week 6, fish 46


title: 1_L25_C62

value: E18.5 Mouse lung mesenchymal cell


title: AF133_NI2


title: AF131_YP2

value: TRUE


title: 1_L25_C56


title: 1_L25_C64


title: Sample_18203


title: Infected, treated with 5 ppm for 30 mins, week 6, fish 43


title: AF131_NI2


title: 1_L25_C51


title: Sample_18198


title: Infected, treated with 10 ppm for 15 mins, week 6, fish 51


title: Sample_18197


title: Infected, treated with 5 ppm for 30 mins, week 6, fish 42


title: AF129_YP2


title: Sample_18196


title: Infected, treated with 5 ppm for 30 mins, week 6, fish 41


title: AF129_NI2


title: 1_L25_C50


title: 1_L25_C47


title: Infected untreated, week 6, fish 38

value: Infected untreated, week 6


title: Sample_18195


title: AF127_YP2

value: monocyte-derived macrophages


title: Infected untreated, week 6, fish 37


title: Sample_18194


title: 1_L25_C42


title: 1_L25_C54


title: Sample_18193


title: Infected untreated, week 6, fish 36


title: 1_L25_C45


title: AF121_YP2


title: AF127_NI2


title: Infected untreated, week 6, fish 33


title: TUL_010_09

city: Tsukuba

first: Satoshi

last: Nitta

address: 1-1-1 Tennodai

department: Urology

country: Japan

institute: Tsukuba University

data_processing:
Sequencing reads were mapped on the mm10 human reference genome, quantified, and then normalized with the quantile method using CLC Genomics Workbench version 10.1.1 (Qiagen)
Differentially expressed gene (DEG) analyses were performed using the Empirical Analysis of DGE tool in CLC Genomics Workbench
The statistical threshold for DGEs was defined as a false discovery rate (FDR) < 0.05 and absolute fold-change >2.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized total gene counts for every gene and every sample (from TUL_010_01 to 09)

extract_protocol:
Total RNA isolation was performed using the RNeasy Mini Kit (Qiagen) according to the manufacturers’ instructions
Library preparation was performed using an NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). Libraries were validated via Bioanalyzer (Agilent Technologies) to determine size distribution and concentration. Validated libraries were then sequenced at Tsukuba i-Laboratory LLP (Tsukuba, Japan) on a NextSeq500 (Illumina) with the paired-end 36-base read option.

tag: cell line

value: ACHN

value: renal cell carcinoma

tag: condition


title: AF121_NI2


title: 1_L25_C36


title: Infected untreated, week 6, fish 32


title: AF119_YP2


title: TUL_010_07


title: Infected untreated, week 6, fish 31


title: TUL_010_06


title: AF119_NI2


title: Uninfected untreated, week 6, fish 8

value: Uninfected untreated, week 6


title: 1_L25_C34


title: TUL_010_05


title: Uninfected untreated, week 6, fish 7


title: 1_L25_C26


title: EU282_YP2

value: EUR


title: 1_L25_C31


title: TUL_010_04


title: 1_L25_C39


title: 1_L25_C23


title: EU282_NI2

value: FALSE


title: Uninfected untreated, week 6, fish 6


title: 1_L25_C20


title: EU278_NI2


title: TUL_010_08


title: 1_L25_C19


title: TUL_010_02

source_name: sgControl

value: sgControl


title: EU276_YP2


title: TUL_010_01


title: 1_L25_C17


title: Uninfected untreated, week 6, fish 1


title: EU276_NI2


title: Infected, treated with 10 ppm for 15 mins, week 4, fish 58


title: AF165_NI2


title: 1_L25_C10


title: TUL_010_03


title: LiCl Donor 2

city: Pathumwan

first: Thanaphum

last: Osathanon

state: Bangkok

address: 34 Henri-dunant Rd. Wongmai

country: Thailand

institute: Chulalongkorn University

data_processing:
Illumina software used for basecalling.
Reads quality was checked, trimmed and filtered by FastQC and Trimmomatic.
Raw data fastq files were generated on NextSeq using bcl2fastq2 V2.19 software
Reads mapping with Homo sapiens UCSC hg38 using HISAT2
Transcripts quantification using HTSeq
Gene differential expression using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Human dental pulp stem cells

extract_protocol:
After treatment, total RNA was isolated using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LiCl


title: EU278_YP2


title: LiCl Donor 3


title: Uninfected untreated, week 6, fish 3


title: LiCl Donor 1


title: 1_L25_C06


title: 1_L25_C04


title: AF153_YP2


title: BIO Donor 3

value: BIO


title: Infected, treated with 10 ppm for 15 mins, week 4, fish 56

value: Gill


title: Infected, treated with 10 ppm for 15 mins, week 4, fish 53


title: AF153_NI2


title: Infected, treated with 10 ppm for 15 mins, week 4, fish 52


title: BIO Donor 2


title: 1_L25_C01


title: AF145_YP2


title: Uninfected untreated, week 6, fish 2


title: FGSCs_Stella_ChIP_rep2

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

data_processing:
For m6A RIP-Seq, the m6A-enriched peaks in each m6A IP sample were identified by MACS2 peak-calling software (version 2.0.10)with the corresponding input sample acting as control. For ChIP-Seq, The software ChIPseeqer-2.0 was applied to the ChIP-Seq data with sequencing data from input DNA as control to identify genomic enrichment (peak) of specific histone modifications and transcription factor. For DNA MeDIP-Seq, we first divided the UCSC known gene promoter regions into 500bp windows and calculated the methylation level in each window and then calculated the Pearson correlation coefficient between them.
Mapping sequencing RNA reads to align genome assembly using sofeware Hisat2
Genome_build: mm9
Supplementary_files_format_and_content: bw files

source_name: Female germ line stem cells

extract_protocol:
For RIP-Seq,total RNA was extracted from FGSCs and STO using Trizol reagent (Life Technologies, CA). Next, 20ug of the digested RNA was used to puritying mRNA and the mRNA was used for the VAHTSTM mRNA-seqv2 Library Prep kit for Illumina1, and sequencing libraries were created according to the manufacturer's protocol. For ChIP-Seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For MeDIP-Seq, genomic DNA were extrated and sonicated,and the incubated the antibody.
For RIP-Seq, Isolation of mRNA was performed using the Oligotex mRNA Mini Kit (Qiagen GmbH, Hilden, Germany) and the mRNA was then used for RIP-Seq library preparation with the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). The library was then subjected to Illumina sequencing with paired-end 2x150 as the sequencing mode.For ChIP-Seq and MeDIP-Seq,Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Female germ line stem cells

tag: passages

tag: ip antibody

value: anti-Stella (Abcam, ab19878)


title: AF145_NI2

value: AFR


title: BIO Donor 1


title: FGSCs_Stella_input

description: input used for both Stella ChIP replicates

value: none (input)


title: 1_L25_C08

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.Â
adapter sequences were removed using cutadapt-1.2.1
trimming by base quality was performed and low complexity reads were removed using prinseq-lite-0.20.3
paired reads were aligned against mm10 using bowtie2-2.1.0 and tophat-2.0.8
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Column headers are: tracking_id, gene_ID, gene short name, tss_id, locus, q0_FPKM, q0_FPKM_low, q0_FPKM_hi

extract_protocol:
To obtain cells from the embryonic  lung, the pulmonary vasculature was cleared and lungs were gently incubated with digestion buffer prior to trituration. All tissue was digested at 37C for 15 min using dispase and DNase I, triturated and subsequently filtered using 100µm and 40µm strainers to obtain a single cell suspension. Mesenchymal and endothelial cells were enriched by magnetic-assisted cell sorting using CD45, Pecam, and EpCAM depletion. Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions. As a bulk control, cDNA was prepared from approximately 200 cells in a PCR tube using the same protocol and reagents as used for the single cells.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

value: E18.5 Mouse lung mesenchymal cell


title: AF143_YP2

value: TRUE


title: Infected, treated with 10 ppm for 15 mins, week 4, fish 57


title: Control Donor 3 (BIO and lithium chloride control)

value: control


title: Infected, treated with 5 ppm for 30 mins, week 4, fish 48


title: Infected, treated with 5 ppm for 30 mins, week 4, fish 46


title: AF143_NI2

value: monocyte-derived macrophages


title: Control Donor 1 (BIO and lithium chloride control)


title: AF139_YP2


title: Control Donor 2 (BIO and lithium chloride control)


title: STO_DNAme_input_rep2

source_name: SIM embryonic fibroblasts cells

value: SIM embryonic fibroblasts cells


title: Infected, treated with 5 ppm for 30 mins, week 4, fish 43


title: Infected, treated with 10 ppm for 15 mins, week 4, fish 51


title: FGSCs_Stella_ChIP_rep1


title: STO_DNAme_input_rep1


title: EU300_YP2


title: siRNA_CTRL_rep_02

first: Ryan

last: Moy

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Alignment with STAR aligner (v2.7; default settings apart from --outFilterMultimapNmax 1)
Read counting with featureCounts (v1.6.3)
Clustering analysis with the R package umap of rlog-normalized counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: SW480 cancer cells

growth_protocol: 400,000 SW480 cells were grown in 6-well plates and transfected with siRNAs as specified above. Cells were collected 72 hours later for RNA extraction.

extract_protocol:
RNA extraction with the Total RNA Purification kit (Norgen Biotek) according to manufacturer's instructions.
Lexogen 3' FWD kit

treatment_protocol: Cells were transfected using Lipofectamine with siRNAs targeting genes as indicated above.

value: colorectal cancer

value: siRNA CTRL


title: siRNA_CTRL_rep_01


title: Infected, treated with 5 ppm for 30 mins, week 4, fish 42


title: STO_DNAme_IP_rep2


title: STO_DNAme_IP_rep1


title: Infected, treated with 5 ppm for 30 mins, week 4, fish 41


title: siRNA_PRSS37_rep_02

value: siRNA PRSS37


title: AF139_NI2

value: FALSE


title: EU296_YP2

value: EUR


title: siRNA_PRSS37_rep_01


title: Infected untreated, week 4, fish 38

value: Infected untreated, week 4


title: EU300_NI2


title: STO_mRNA m6A _input_rep2


title: STO_mRNA m6A _IP_rep2

value: anti-m6A (Abcam, ab151230)


title: EU296_NI2


title: Infected, treated with 5 ppm for 30 mins, week 4, fish 47

value: Gill


title: siRNA_MTMR9_rep_02

value: siRNA MTMR9


title: STO_mRNA m6A _input_rep1


title: Infected untreated, week 4, fish 33


title: Infected untreated, week 4, fish 36


title: EU294_NI2


title: siRNA_SPACA1_rep_02

value: siRNA SPACA1


title: STO_mRNA m6A _IP_rep1


title: siRNA_SPACA1_rep_01


title: EU270_YP2


title: FGSCs_mRNA m6A _input_rep2

value: Female germ line stem cells


title: FGSCs_mRNA m6A _IP_rep2


title: siRNA_MTMR9_rep_01


title: Infected untreated, week 4, fish 32


title: EU270_NI2


title: EU294_YP2


title: Infected untreated, week 4, fish 31


title: siRNA_FGF8_rep_01

value: siRNA FGF8


title: AF151_YP2

value: AFR


title: AF165_YP2

value: TRUE


title: EU256_YP2


title: FGSCs_mRNA m6A _input_rep1

value: none (input)


title: FGSCs_mRNA m6A _IP_rep1


title: Uninfected untreated, week 4, fish 7

value: Uninfected untreated, week 4


title: siRNA_CMTM6_rep_02

value: siRNA CMTM6


title: siRNA_FGF8_rep_02

value: colorectal cancer


title: Uninfected untreated, week 4, fish 8


title: Infected untreated, week 4, fish 37


title: ST2 6h PBS

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 h at 45 °C on mouse Clariom D Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0.1.36) using  default analysis settings (version 2) and Gene + Exon - SST-RMA as summarization and normalization method.

label: proprietary DNA Labeling Reagent, covalently linked to biotin

source_name: ST2, 6h PBS

label_protocol: Proprietary labeled 2nd-cycle ss-cDNA was prepared from 100 ng total RNA using the mouse Clariom D kit according to the GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays user guide (version 23 January 2017) from ThermoFisher Scientific

growth_protocol: ST2 cells were plated at a density of 10000 cells/cm² in 12-well format cell culture dishes. Cells were cultured in alpha-MEM with 10% FCS at 37 °C, 5 % CO2, 95 % rH for 1 day.

extract_protocol: RNA was extraced 6 h after treatment using the Nucleospin RNA kit (Macherey-Nagel) according to the manufacturer's instructions.

treatment_protocol: ST2 cells were serum starved over night and treated with 100 ng recombinant murine Wnt1/Sfrp1 complex or 50 ng recombinant murine Sfrp1 or the equivalent volume PBS for 6 h

value: PBS


title: AF151_NI2

value: monocyte-derived macrophages


title: siRNA_CMTM6_rep_01


title: ST2 6h Sfrp1

source_name: ST2, 6h 50 ng rSfrp1


title: EU298_YP2


title: EU298_NI2

value: FALSE


title: Uninfected untreated, week 4, fish 3


title: ST2 6h rWnt1

source_name: ST2,6h 100 ng rWnt1/Sfrp1


title: Uninfected untreated, week 4, fish 1


title: EU288_NI2

value: EUR


title: Uninfected untreated, week 4, fish 2


title: EU288_YP2


title: siRNA_ODAM_rep_02

value: siRNA ODAM


title: siRNA_IGF1R_rep_01

value: siRNA IGF1R


title: Uninfected (2)

city: Oxford

first: Peter

last: Wing

address: Old Road Campus, Roosevelt Drive,

country: United Kingdom

institute: University of Oxford

data_processing:
Illumina adapters were removed and data transformed to sequencing reads by CASAVA base recognition
Reads were mapped against the reference mesocricetus auratus (MesAur1.0) genome using STAR aligner.
Non-hamster reads were aligned to the SARS-CoV-2 genome (Wuhan strain) reference; NC_045512.2
Read counts were transformed to FPKM to account for sequencing depth and gene length (Mortazavi et al. 2008)
Genome_build: MesAur1.0
Supplementary_files_format_and_content: FPKM and readcount values for every gene in n=12 samples

organism: Mesocricetus auratus

source_name: Bulk lung tissue

growth_protocol: Animals were housed in a flexible film isolator within a containment level 3 facility. Clincal evaluation of hamsters was performed twice daily including daily monitoring of body wieht and temperature.

extract_protocol:
Tissue was lysed in RLT buffer and RNA extracted using Qiagen RNAeasy kit. RNAs were treated with on-column DNAse (Qiagen), and 2uG of material was used for the construction of sequencing libraries.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hamsters aged 6-8 weeks were infected intranasally with SARS-CoV-2 (Australia/VIC01/2020) and harvested 4 days post-infection. Treatment with FG-4592 commenced either 24h before of after infection

value: Lung

tag: culture condition

value: No treatment

tag: agent


title: AF169_YP2


title: Infected, treated with 10 ppm for 15 mins, week 2, fish 58

value: Gill


title: Infected, treated with 10 ppm for 15 mins, week 2, fish 57


title: siRNA_MRPL24_rep_02

value: siRNA MRPL24


title: Post-infection (6)

value: Post-infection treatment 30mg/kg FG-4592

value: + SARS-CoV-2


title: siRNA_MRPL24_rep_01


title: Post-infection (5)


title: Uninfected (1)


title: Infected, treated with 10 ppm for 15 mins, week 2, fish 56


title: siRNA_ODAM_rep_01


title: siRNA_NOB1_rep_02

value: siRNA NOB1


title: Uninfected untreated, week 4, fish 6


title: AF167_YP2

value: TRUE

value: AFR


title: siRNA_IGF1R_rep_02


title: Post-infection (4)


title: Infected, treated with 10 ppm for 15 mins, week 2, fish 53


title: AF167_NI2


title: Infected, treated with 10 ppm for 15 mins, week 2, fish 52


title: Infected, treated with 10 ppm for 15 mins, week 2, fish 51


title: siRNA_GPR173_rep_02

value: siRNA GPR173


title: AF169_NI2


title: AF163_NI2


title: Infected, treated with 5 ppm for 30 mins, week 2, fish 48


title: Post-infection (1)


title: Infected, treated with 5 ppm for 30 mins, week 2, fish 47


title: NK_EV_5

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adaptor contaminations were removed using cutadapt, discarding those that were shorter than 15 nt or longer than 35 nt after trimming.
Resulting reads were aligned against a collection of 2588 human, mature miRNA sequences extracted from miRBase (release 21), to obtain expression estimates with RSEM.
Expected expression counts were then processed with an analysis pipeline that used Bioconductor package Limma for normalization (using TMM method), taking into account that samples had been obtained from five donors and considering only 708 miRNA species for which expression was at least 1 count per million (CPM) in at least 3 samples.
Genome_build: miRBase21
Supplementary_files_format_and_content: Raw estimated counts as calculated by RSEM

source_name: NK cell-derived small EVs

growth_protocol: Resting human NK cells were usolated from healthy donor´s buffy coats using the NK cell isolation Miltenyi kit. Activated NK cells  were obtained after peripheral blood mononuclear cells (PBMCs) stimulation for 5-6 days in RPMI medium supplemented with 10% human serum, 10% foetal bovine serum, a mixture of irradiated feeder cells (721.221 and RPMI8866) and a combination of NK-polarising cytokines; 10 U/ml IL-12 (Peprotech) and 25ng/ml IL-18 (MBL). Activated PBMCs were further incubated with 50U/ml of IL-2 prior to activated NK cell isolation. Activated NK cells were cultured for 72 hours in RPMI supplemented with 10% EV-depleted FBS (by ultracentrifugation at 100,000 g for 16 h) for EV accumulation and small EVs were isolated by culture supernatant differential ultracentrifugation for NGS analysis.

extract_protocol:
Samples were lysed in QIAzol Lysis Reagent and RNA was extracted using the miRNeasy Mini Kit. RNA integrity was evaluated using an Agilent 2100 Bioanalyzer.
300 ng of total RNA were used to generate barcoded miRNA-seq libraries using the NEBNext Multiplex SmallRNA Library Prep Set from Illumina.
The quantity and quality of the miRNA libraries were determined using the Agilent 2100 Bioanalyzer High Sensitivity DNA chip.

treatment_protocol: Resting NK cells were isolated from healthy donor buffy coats, wile activated NK cells were cultured as described and isolated using the Miltenyi isolation kit. Activated NK cells were cultured in EV-depleted medium for 72h for EV accumulation and small EVs obtained by differential ultracentrifugation of cell culture supernatants (100,000g). Detailed information of small EVs isolation can be found in EV‐TRACK (ID: EV210234).

tag: donor

value: From activated NK cells


title: AF159_NI2


title: siRNA_TMEM164_rep_02

tag: tissue

value: colorectal cancer

value: siRNA TMEM164


title: Pre-treatment (5)

value: Pre-infection treatment 30mg/kg FG-4592


title: AF159_YP2

tag: cell type

value: monocyte-derived macrophages


title: siRNA_TMEM164_rep_01


title: siRNA_MYH7_rep_02

value: siRNA MYH7


title: Infected, treated with 5 ppm for 30 mins, week 2, fish 42


title: Pre-treatment (3)


title: Infected, treated with 5 ppm for 30 mins, week 2, fish 43


title: Pre-treatment (2)


title: NK_REST_5

source_name: Resting human NK cells


title: Infected, treated with 5 ppm for 30 mins, week 2, fish 41


title: siRNA_GPR173_rep_01


title: siRNA_OR10A5_rep_02

value: siRNA OR10A5


title: Infected, treated with 5 ppm for 30 mins, week 2, fish 46


title: siRNA_MYH7_rep_01


title: Pre-treatment (4)

value: Lung


title: NK_ACT_4

source_name: Activated human NK cells

value: IL-12/IL-18 and IL-2


title: Infected untreated, week 2, fish 38

value: Gill

value: Infected untreated, week 2


title: NK_EV_4

source_name: NK cell-derived small Evs


title: NK_REST_4


title: Vehicle, Control (5)

value: Vehicle (Control)


title: Infected untreated, week 2, fish 37


title: Vehicle, Control (4)

value: + SARS-CoV-2


title: siRNA_NOB1_rep_01

value: siRNA NOB1


title: NK_ACT_5


title: siRNA_COL6A1_rep_02

value: siRNA COL6A1


title: Post-infection (3)

value: Post-infection treatment 30mg/kg FG-4592


title: AF163_YP2

value: TRUE

value: AFR


title: Post-infection (2)


title: siRNA_COL6A1_rep_01

value: colorectal cancer


title: Vehicle, Control (3)


title: siRNA_MST1R_rep_02

value: siRNA MST1R


title: Infected untreated, week 2, fish 33


title: 1_L25_C85

city: ROCHESTER

first: Douglas

last: Brownfield

address: 200 1ST ST SW

institute: Mayo Clinic

source_name: E18.5 mouse lung

value: E18.5 Mouse lung mesenchymal cell

tag: strain


title: Pre-treatment (6)

value: Pre-infection treatment 30mg/kg FG-4592


title: NK_ACT_3

tag: treatment


title: siRNA_OR10A5_rep_01


title: Pre-treatment (1)


title: siRNA_MST1R_rep_01


title: Vehicle, Control (2)


title: Infected untreated, week 2, fish 31


title: siRNA_UBR4_rep_02

value: siRNA UBR4


title: Vehicle, Control (1)


title: NK_REST_3


title: Infected untreated, week 2, fish 36


title: NK_EV_2

value: From activated NK cells


title: Uninfected untreated, week 2. fish 8

value: Uninfected untreated, week 2


title: Uninfected untreated, week 2. fish 7


title: NK_ACT_2

value: IL-12/IL-18 and IL-2


title: NK_EV_3


title: siRNA_UBR4_rep_01


title: NK_REST_2


title: NK_EV_1


title: Uninfected untreated, week 2. fish 6

value: Gill


title: siRNA_INSR_rep_01

value: siRNA INSR


title: siRNA_PLG_rep_02

value: siRNA PLG


title: NK_ACT_1


title: Uninfected untreated, week 2. fish 3


title: Uninfected untreated, week 2. fish 2


title: NK_REST_1


title: Infected untreated, week 2, fish 32

value: Infected untreated, week 2


title: siRNA_ITPR3_rep_02

value: siRNA ITPR3


title: TBS_RB_CHLA_33

city: Los Angeles

first: Gangning

last: Liang

address: 1441 Biggy street

institute: USC Keck school of medicine

data_processing:
Data was processed using EPIC TABSAT v1.7
Assembly: hg19
Supplementary files format and content: tab-delimited text file including methylated and unmethylated reads numbers of each region.
Library strategy: Targeted Bisulfite-seq

source_name: CHLA RB patient tumor DNA

extract_protocol:
DNAs were extracted using the QIAgen QIAamp FFPE DNA Extraction Mini kit as recommended by the manufacturer.
DNA library was prepared by Genewiz.

value: Retinoblastoma


title: TBS_Retina

source_name: CHLA normal retina DNA

value: Retina


title: siRNA_PLG_rep_01


title: TBS_RB_CHLA_49


title: TBS_RB_CHLA_41


title: TBS_RB_CHLA_31


title: G4_M3_sgSUZ12_IFNγ_rep2

city: NEW YORK

first: Ping

last: Chi

address: 1275 YORK AVENUE

institute: MEMORIAL SLOAN KETTERING CANCER CTR

data_processing:
ATAC-seq reads were quality and adapter trimmed using Trim Galore before aligning to human genome assembly hg19 with Bowtie2 using the default parameters.
Aligned reads with the same start position and orientation were collapsed to a single read before subsequent analysis.
Density profiles were created using the BEDTools suite, with subsequent normalization to a sequencing depth of ten million reads for each library.
To ascertain regions of open chromatin, MACS2 (https://github.com/taoliu/MACS) was used with a p-value setting of 0.001 against a cell line-matched input sample.
A global peak atlas was created by first removing blacklisted regions then merging all peaks within 500 bp and counting reads with version 1.6.1 of featureCounts (http://subread.sourceforge.net).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, aligned and quantified peaks

source_name: human malignant peripheral nerve sheath tumor cells

extract_protocol:
Cells were washed with PBS, trypsinized from 6-well plates and harvested as a single-cell suspension in precool PBS. For each sample, cell nuclei were prepared from 50,000 cells, and incubated with 2.5 μl of transposase (Illumina) in a 50-μl reaction for 30 min at 37 °C.
After purification of transposase-fragmented DNA, the library was amplified by PCR and subjected to paired-end 50 base-pair high-throughput sequencing on an Illumina HiSeq2500 platform as previously described (Buenrostro et al., 2013) (Buenrostro et al., 2015).

treatment_protocol: M3 sgCon and sgSUZ12 cells were treated with PBS or 10 ng/ml IFNγ for 24 hours.

value: human MPNST tumor-derived cell line

value: 10 ng/ml IFNγ stimulation for 24 hr

value: Knockout

tag: prc2 status

value: loss


title: siRNA_ITPR3_rep_01

value: colorectal cancer


title: siRNA_INSR_rep_02


title: G4_M3_sgSUZ12_IFNγ_rep1


title: TBS_RB_CHLA_29


title: normal control, N5

city: Beijing

first: Min

last: Liu

state: Beijing

address: No.2 Yinghua Dong Street, Hepingli, Chao Yang District

institute: China-Japan Friendship Hospital

data_processing:
sequenced reads were trimmed for adptor sequence and masked for low-complexily sequence
mapped to human reference genome
Obtain mapped data (reads, etc.), for subsequent transcription assembly and expression count
The distribution of reads compared to the genome in different regions of the reference genome was statistically analyzed, and the target regions were divided into CDS (coding region) Intron (Intron) Intergenic region and UTR (5' and 3 untranslated region).
The FPKM value of each gene/transcript in the sample was calculated, and the value was taken as the expression amount of gene/transcript in the sample
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Gene/transcript COUNT expression matrix

source_name: human

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard illumina protacal

value: blood

tag: disease state

value: control

tag: age


title: TBS_RB_CHLA_46


title: TBS_RB_CHLA_28


title: TBS_RB_CHLA_24


title: normal control, N4


title: siRNA_CORO1B_rep_02

value: siRNA CORO1B


title: G3_M3_sgCon_IFNγ_rep2

value: wild type

value: intact


title: siRNA_CORO1B_rep_01


title: normal control, N3


title: siRNA_CCL5_rep_02

value: siRNA CCL5


title: G3_M3_sgCon_IFNγ_rep1


title: TBS_RB_CHLA_20


title: normal control, N2


title: normal control, N1


title: G2_M3_sgSUZ12_rep2

value: PBS


title: Uninfected untreated, week 2. fish 1

source_name: Gill

value: Gill

value: Uninfected untreated, week 2


title: siRNA_CCL5_rep_01


title: G2_M3_sgSUZ12_rep1


title: siRNA_MEF2D_rep_02

value: siRNA MEF2D


title: G1_M3_sgCon_rep2


title: Sample_18353

data_processing:
Demultiplexing was perfomed using bcl2fastq2 v2.20
Adapter trimming was performed using Trimmomatic v0.36 with following parameters ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:36 CROP:48
Alignment was performed using bowtie2 v2.3.5 against the human reference genome hg38.
Duplicated reads were removed using picard "dedup" function and the transposase-induced offset was removed using the deeptools v3.1.3 "alignmentSieve" function.
Sorting and indexing of bam files was done using samtools v1.9
Peak calling was performed using MACS2 v2.1.2.
Unification of peak regions from sample-specific peak calling results was performed in R 3.6.2 using the "reduce" function implemented in the GenomicRanges package v1.38.0.
Quantification of sequencing reads in unified peak regions was performed in R 3.6.2 using the "summarizeOverlaps" function implemented in the GenomicAlignments package v1.22.1.
Assembly: hg38
Supplementary files format and content: comma separated files include raw count table

source_name: Jurkat

extract_protocol:
Cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and tagmented with an in-house Tn5 in TAPS-DMF buffer
Barcoded Nextera i7 and i5 primers were used to amplify the tagmented gDNA and preapare it for Illumina sequencing

value: T cell leukemia

value: treated

tag: time point


title: TBS_RB_CHLA_14

value: Retinoblastoma


title: Sample_18352

tag: replicate


title: siRNA_MEF2D_rep_01


title: CTEPH patients, C6

value: CTEPH


title: Sample_18351


title: G1_M3_sgCon_rep1

value: human MPNST tumor-derived cell line


title: Sample_18350


title: CTEPH patients, C5


title: CTEPH patients, C4


title: CTEPH patients, C7


title: siRNA_RELB_rep_01

value: siRNA RELB


title: M3_sgSUZ12_rep1

value: Knockout

value: loss


title: Sample_18348

value: control

value: ctrl


title: Sample_18349


title: siRNA_GPR56_rep_02

value: colorectal cancer

value: siRNA GPR56


title: CTEPH patients, C3

value: blood


title: M3_sgSUZ12_rep2

value: PBS


title: M3_sgCon_rep2

value: wild type

value: intact


title: siRNA_GPR56_rep_01


title: CTEPH patients, C2


title: CTEPH patients, C1


title: siRNA_DDR2_rep_02

value: siRNA DDR2


title: M3_sgCon_rep1


title: Sample_18347

value: T cell leukemia


title: KO_DAC_Input

address: 417 East 68th Street

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Adaptor sequences were removed from resulting data with TrimGalore
ChIP-seq reads were aligned to the aligned to the human genome assembly hg19 with bowtie2 using the following settings (--very-sensitive-local, --no-mixed, --no-discordant)
Coverage bigwig files were created via bamCoverage command from deepTools to normalize to total reads and human genome size use the follwing settings (--normalizeUsing RPGC, ---binSize 10, --ignoreDuplicates)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files containing all ChIP-seq peaks for the sample

source_name: M3 MPNST cells

growth_protocol: All cells are cultured in DMEM:F-12 (1:1) High Glucose media supplemented with 10% FBS, 1% Penicillin/Streptomycin, 2 mM L-glutamine, 15 mM HEPES. They are grown as adherent cells on standard tissue culture treated plates at 37oC at 5% CO2.

extract_protocol:
Cells were fixed with formaldehyde followed by neutralization. Cells were then harvested followed, cell lysis. Lysates were sonicated, and clarified by centrifugation. Sonicated nuclei and histone-DNA complexes were isolated with antibody of interest.  Antibody bound DNA with magnetic beads were washed, and DNA was eluted followed by reverse cross-linking, and DNA purification.
DNA fragments range from 200-600 bp were size-selected for subsequent ChIP-seq  library preparation with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.  Sequencing libraries were multiplexed and ran on a Hiseq2500 platform

treatment_protocol: Cells are plated in plates. Next day, cells are switched to fresh new media containing Vehicle (DMSO), or 4000 nM GSK862, or 50 nM DAC. Cells are further cultured for 5 days.

tag: sgrna

value: 50 nM Decitabine (DAC)

tag: chip antibody


title: Sample_18346

value: Pancreatic cancer


title: siRNA_DDR2_rep_01

source_name: SW480 cancer cells

tag: condition


title: siRNA_RELB_rep_02


title: siRNA_PLK4_rep_02

value: siRNA PLK4


title: Sample_18345

value: treated


title: Sample_18344


title: 42hpf-NI

city: xinxiang

first: chune

last: zhou

address: jian she east road 46

institute: henan normal university

data_processing:
to get high quality clean reads, reads were further filtered by fastp
Short reads alignment tool Bowtie2  (version 2.2.8) was used for mapping reads to ribosome  RNA (rRNA) database. The rRNA mapped reads then will be removed.
An index of the reference genome was built, and paired-end clean reads were mapped to the  reference genome using HISAT2. 2.4 [3] and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 [4][5]  in a  reference-based approach. For each transcription region, a FPKM (fragment per kilobase of  transcript per million mapped reads) value was calculated to quantify its expression  abundance and variations, using RSEM [6]  software.
Assembly: GRCz11
Supplementary files format and content: processed data.xlxs

source_name: embryos

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according  to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryos

tag: genotype

value: WT


title: siRNA_PLK4_rep_01


title: KO_Vehicle_Input

value: Vehicle (DMSO)


title: 24hpf-NI=1


title: Sample_18343


title: WT_DAC_Input

value: sgCon


title: 24hpf=NI


title: WT_GSK862_Input


title: SW480_sgITPR3_3

data_processing:
Adapter and polyA trimming with BBDuk (v38.31; options k=13, ktrim=r, forcetrimleft=11, useshortkmers=t, mink=5, qtrim=t, trimq=10, minlength=20)
Alignment with STAR aligner (v2.6.0a; ENCODE settings apart from --outFilterMismatchNoverLmax 0.1)
Read counting with featureCounts (v1.6.3)
Differential gene expression analysis with DESeq2 (gene ranking with apeglm)
Pathway analysis (R package ReactomePA v1.28)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: colorectal cancer

growth_protocol: sgCtrl versus sgITPR3 SW480 cells were injected into the portal circulation of NSG mice to form liver metastases.

extract_protocol:
Livers were chopped, digested with collagenase IV, and red blood cells lysed in ACK buffer. Tumor cells were then isolated by density gradient followed by a mouse cell depletion kit (Miltenyi Biotec). RNA was extracted using the Total RNA purification kit (Norgen Biotek).
Lexogen 3' FWD kit

treatment_protocol: sgCtrl versus sgITPR3 cells (knockout confirmed by Western Blot).

tag: cell line

value: SW480 cancer cells

tag: tumor stage

value: liver metastasis


title: Sample_18342


title: 18hpf-NI-1


title: SW480_sgITPR3_2

value: colorectal cancer


title: SW480_sgITPR3_1


title: Sample_18341

value: control

value: ctrl


title: 18hpf-NI


title: KO_DAC_H3K27ac

value: H3K27ac (Abcam, ab4729 )


title: WT_Vehicle_Input


title: KO_GSK862_Input


title: SW480_sgCTRL_3

value: sgCtrl


title: 42hpf-NI-1


title: Sample_18340


title: KO_GSK862_H3K27ac


title: Tcf12-cKO-4-cell-Rep 2

city: Hangzhou

first: Lan-Rui

last: Cao

state: Zhejiang

address: 866 Yu Hang Tang Rd

department: Life Sciences Institute

institute: Zhejiang University

data_processing:
RNA-Seq was performed with biological replicates for all samples.
Paired-end RNA-seq reads were trimmed and mapped to the mm9 genome by HISAT2 (version 2.1.0) .
Cufflinks v2.2.1 was used to calculate the FPKM per gene based on mm9 refFlat from UCSC genome annotation database.
Differential expression analysis was performed with R package edgeR. Genes with FDR of <0.01 and log2(fold change) >=2 were considered as differentially expressed.
Expression level  was further normalized with the ERCC spike-in.
Assembly: mm9
Supplementary files format and content: Tab-delimited text files include FPKM values of all RNA-seq samples

extract_protocol:
Oocytes and embryos were collected from indicated genotypes (10 oocytes per sample). Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina NovaSeq 6000 platform.

tag: developmental stage

value: Mouse 4-cell embryos

value: TCF12 conditional knockout

tag: time


title: Tcf12-cKO-4-cell-Rep 3

tag: tissue


title: SW480_sgCTRL_2


title: SW480_sgCTRL_1


title: Sample_18338


title: UPNR_532

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

data_processing:
Low quality reads or reads with adapters were filtered out by using fastp software
Cleaned reads were aligned to the human genome (GRCh37/hg19) using STAR and processed with Samtools.
Read counts per gene were generated using HTseq package
Bioconductor/R DESeq2 package was used for normalization and differential expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts generated for each Sample

source_name: Unsorted Bone Marrow Cells

extract_protocol:
RNA were extracted from bone marrow cells of patients using a QIAamp RNA Blood Mini Kit (Qiagen). Libraries were prepared at Novogene, (Cambridge, UK), following the NEBNext® Ultra™ RNA Library Prep Kit on polyA-enriched mRNA.
RNA libraries were prepared using manufacturer’s recommended protocol andsequenced on Illumina NovaSeq 6000 with 150bp paired-end read run (Illumina San Diego, CA).

value: T-ALL

tag: cell type

value: Unsorted Bone Marrow Cells

tag: chromothripsis status

value: negative

tag: subtype

value: Not Available


title: KO_Vehicle_H3K27ac

city: New York

tag: treatment


title: WT_GSK862_H3K27ac


title: Tcf12-cKO-4-cell-Rep 1

tag: strain

value: embryos


title: WT_DAC_H3K27ac

value: 50 nM Decitabine (DAC)


title: Tcf12-WT-4-cell-Rep 3

value: WT


title: WT_Vehicle_H3K27ac

value: sgCon

value: Vehicle (DMSO)


title: UPNR_531

tag: disease state

tag: age


title: Tcf12-WT-4-cell-Rep 2


title: Tcf12-WT-4-cell-Rep 1


title: Tcf12-cKO-2-cell-Rep 2

value: Mouse 2-cell embryos


title: KO_DAC_H3K4me3

value: H3K4me3 (Cell Signaling Technology, 9751)


title: UPNR_528

value: near-ETP


title: KO_GSK862_H3K4me3


title: UPNR_526

value: ETP


title: KO_Vehicle_H3K4me3


title: WT_DAC_H3K4me3


title: Tcf12-cKO-2-cell-Rep 3


title: Tcf12-WT-2-cell-Rep 3


title: WT_GSK862_H3K4me3


title: UPNR_525


title: UPNR_529


title: Sample_18339

address: Carl-Troll-Strasse 31

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

value: Pancreatic cancer

value: control

tag: time point

value: ctrl

tag: replicate


title: UPNR_524


title: Tcf12-WT-2-cell-Rep 1


title: UPNR_522


title: UPNR_530

value: early


title: Tcf12-cKO-fGV-Rep 3

source_name: oocytes

value: oocytes

value: Mouse fully-grown GV

value: TCF12 conditional knockout


title: WT_DAC_H3K27me3

tag: sgrna

tag: chip antibody

value: H3K27me3 (Cell Signaling Technology, 9733)


title: Tcf12-cKO-fGV-Rep 2

tag: genotype


title: KO_Vehicle_H3K27me3


title: UPNR_523

value: T-ALL

value: Unsorted Bone Marrow Cells

value: negative


title: Tcf12-cKO-fGV-Rep 1


title: Tcf12-cKO-2-cell-Rep 1

value: embryos


title: Tcf12-WT-fGV-Rep 3

value: WT


title: Tcf12-WT-fGV-Rep 2


title: Tcf12-WT-fGV-Rep 1


title: UPNR_519

value: cortical


title: SW480 cells, D1KO_3

city: Seoul

first: Jeong

middle: Hoon

last: Kim

address: Irwon-dong Gangnam-gu

country: South Korea

institute: Sungkyunkwan University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat.
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of gene expression measurements in FPKM

growth_protocol: SW480 cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNAs were purified using RNeasy Plus Mini Kit (Qiagen).
RNA-seq libraries were prepared using SMARTer Stranded RNA-Seq Kit (Clontech) according to the manufacturer’s instructions.

treatment_protocol: The DBC1/CCAR2 gene was knocked out using transcription activator-like effector nucleases (TALENs) in SW480 cells.

tag: cell line

value: colorectal cancer cells

value: DBC1 KO


title: WT_Vehicle_H3K4me3

value: sgCon

value: Vehicle (DMSO)

value: H3K4me3 (Cell Signaling Technology, 9751)


title: SW480 cells, D1KO_1


title: Tcf12-cKO-gGV-Rep 3

value: Mouse growing GV


title: UPNR_517

value: early


title: SW480 cells, WT_3


title: UPNR_516

value: ETP


title: SW480 cells, WT_2


title: UPNR_515


title: SW480 cells, WT_1


title: UPNR_514

value: near-ETP


title: SW480 cells, D1KO_Input DNA_2

data_processing:
Basecalls performed using bcl2fastq2 Conversion Software (v2.20). ChIP-seq reads were trimmed using trimmomatic (v0.38) to filter out low-quality reads (QC<30) and remove adapter sequences.
ChIP-seq reads were aligned to the hg19 human reference genome using Bowtie (v1.1.2), and duplicate reads were removed using Picard (v0.118).
ChIP-seq peaks for histone H3 modifications were called using MACS2 (v2.1.1) with the following parameters : Fold enrichment > 4 and FDR < 0.01.
ChIPseeker (v1.16.1) were used to annotate ChIP-seq peaks with nearest genes.
Differential Binding analysis was peformed using MAnorm, and overlapped peaks were analyzed using ChIPpeakAnno R package. Deeptools was used to generate heatmaps. Enrichment of DBC1-regulated motifs were analyzed using MEME-ChIP. Super-enhancers were identified using ROSE (Ranking Of Super Enhancer) with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files (.bw) contained ChIP-seq tag densities and were used for visualize ChIP-seq data.

source_name: SW480 DBC1 KO

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were immunoprecipitated with histone H3 modification antibodies. ChIP DNAs were purified using PCR purification kit (QIAGEN).
ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (Part# 15023092 Rev. B).


title: UPNR_513

value: positive


title: WT_GSK862_H3K27me3

value: H3K27me3 (Cell Signaling Technology, 9733)


title: UPNR_521

value: T-ALL


title: UPNR_520

value: Unsorted Bone Marrow Cells


title: WT_Vehicle_H3K27me3


title: Tcf12-WT-gGV-Rep 3

value: oocytes


title: Tcf12-WT-gGV-Rep 2


title: SW480 cells, D1KO_H3K27ac_ChIP-seq

value: H3K27ac (abcam, ab4729)


title: UPNR_512


title: SW480 cells, D1KO_2


title: Tcf12-WT-gGV-Rep 1

value: WT


title: UPNR_518

value: negative

value: mature


title: Tcf12-cKO-gGV-Rep 2

value: TCF12 conditional knockout


title: SW480 cells, D1KO_H3K4me1_ChIP-seq

value: colorectal cancer cells

value: DBC1 KO

value: H3K4me1 (abcam, ab8895)


title: Tcf12-cKO-gGV-Rep 1

value: Mouse growing GV


title: UPNR_509


title: SW480 cells, D1KO_Input DNA_1


title: SW480 cells, D1KO_H3K4ac_ChIP-seq

value: H3K4ac (ActiveMotif, 39381)


title: UPNR_508

value: ETP


title: SW480 cells, D1KO_H3K9/K14ac_ChIP-seq

value: H3K9/K14ac (SantaCruz Biotechnologies, SC-8655R)


title: D1KO_Input DNA

data_processing:
Basecalls performed using bcl2fastq2 Conversion Software (v2.20). ChIP-seq reads were trimmed using trimmomatic (v0.38) to filter out low-quality reads (QC<30) and remove adapter sequences.
ChIP-seq reads were aligned to the hg19 human reference genome using Bowtie (v1.1.2), and duplicate reads were removed using Picard (v0.118).
ChIP-seq peaks for epigenomic modifiers were called using MACS2 (v2.1.1) with the following parameters : FDR < 0.05.
ChIPseeker (v1.16.1) were used to annotate ChIP-seq peaks with nearest genes.
Differential Binding analysis was peformed using MAnorm. Deeptools was used to generate heatmaps.
Assembly: hg19
Supplementary files format and content: Bigwig files (.bw) contained ChIP-seq tag densities and were used for visualize ChIP-seq data.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were immunoprecipitated with DBC1, KMT2D, or p300 antibodies. ChIP DNAs were purified using PCR purification kit (QIAGEN).
ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (Part# 15023092 Rev. B).

value: DBC1 knock-out


title: MXSGD3

city: Changsha

first: Fangguo

last: Lu

state: Hunan

address: Xueshi Road No. 300

institute: Hunan University of Chinese Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as  differentially expressed.

source_name: Lung tissue

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Lung tissue

value: Balb/c mice

value: MXSGD + Influenza A virus pneumonia


title: MOD6

value: Influenza A virus pneumonia


title: MXSGD1


title: MOD5


title: SW480 cells, WT_Input DNA_2

source_name: SW480 WT


title: UPNR_527

value: T-ALL

value: Unsorted Bone Marrow Cells

value: early


title: MXSGD2


title: SW480 cells, D1KO_H3K4me3_ChIP-seq

value: H3K4me3 (ActiveMotif, 39159)


title: SW480 cells, WT_H3K27ac_ChIP-seq

value: WT

value: H3K27ac (abcam, ab4729)


title: MOD4


title: D1KO_p300_ChIP-seq

value: colorectal cancer cells


title: D1KO_KMT2D_ChIP-seq


title: SW480 cells, WT_H3K4me1_ChIP-seq

value: H3K4me1 (abcam, ab8895)


title: D1KO_DBC1_ChIP-seq


title: UPNR_511

value: positive

value: near-ETP


title: LPS_high_16h_rep1

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
cellranger-atac version 1.1.0 pipeline
Assembly: refdata-cellranger-atac-mm10-1.1.0

source_name: kidney

extract_protocol:
Mouse kidneys were minced and homogenized using Dounce homogenizer (5x loose, 10x tight, Kimble Chase KT885300-0002) in 2 mL of Nuclei EZ lysis buffer (Sigma N-3408) supplemented with SuperaseIn and cOmplete ULTRA Tablets Mini (Roche, 05892791001). Samples were rediluted in the lysis buffer, filtered through a 40-µm cell strainer, and centrifuged for 5 min at 500 g. The pellet was resuspended in 3.5 mL of lysis buffer. After another centrifugation, the pellet was resuspended in Nuclei Buffer provided by 10X Genomics, and nuclei counts were adjusted with additional filtering and centrifugation. Final nuclei concentration of 3000/µL or higher was applied to targeting nuclei recovery of 10,000.
Tagmentation, GEM generation, barcoding, and library preparation were done using Chromium Single Cell ATAC Reagent Kits User Guide, CG000168 Rev A (10X Genomics).

value: kidney

value: LPS 5 mg/kg 16 hrs


title: UPNR_510

value: ETP


title: WT_Input DNA


title: SW480 cells, WT_Input DNA_1


title: LPS_low_24h_high_24h_rep2

description: 10X Genomics

value: LPS 0.25 mg/kg 24 hrs followed by LPS 5 mg/kg 24 hrs


title: SW480 cells, WT_H3K9/K14ac_ChIP-seq

value: H3K9/K14ac (SantaCruz Biotechnologies, SC-8655R)


title: SW480 cells, WT_H3K4ac_ChIP-seq

value: H3K4ac (ActiveMotif, 39381)


title: WT_KMT2D_ChIP-seq


title: LPS_low_24h_rep2

description: 10X Genomics

value: LPS 0.25 mg/kg 24 hrs


title: control_rep2

description: 10X Genomics


title: LPS_low_24h_high_24h_rep1

description: 10X Genomics


title: WT_DBC1_ChIP-seq


title: LPS_low_24h_rep1

description: 10X Genomics


title: LPS_low_04h_rep1

description: 10X Genomics

value: LPS 0.25 mg/kg 4 hrs


title: HCT116_D1KO_3

data_processing:
bcl2fastq2-2.20.0 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (using Trimmomatic 0.38), then mapped to hg19 whole genome using HISAT2.
Read count extraction and nomalization were performed using StringTie.
Assembly: hg19
Supplementary files format and content: gene expression measurements in FPKM

growth_protocol: HCT116 cells were grown in RPMI supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNAs were purified using RNeasy Plus Mini Kit (Qiagen).
RNA-seq libraries were prepared using TruSeq Standed mRNA LT Sample Prep Kit (illumina) according to the manufacturer’s instructions.

treatment_protocol: The DBC1/CCAR2 gene was knocked out using CRISPR/Cas9 in HCT116 cells.

value: DBC1 knock-out


title: WT_p300_ChIP-seq


title: control_rep1

description: 10X Genomics


title: SW480 cells, WT_H3K4me3_ChIP-seq


title: Frontal-Cortex_Saline_3-hours-post-injection_8

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
Fastq files were generated using bcl2fastq2 v. 2.20.0
Reads were aligned to the GRCm38 primary assembly using STAR v. 2.7.2b against a reference built using the GENCODE vM25 gene model
Aligned reads were counted against the same gene model using featureCounts v. 1.6.2 counting only reads where both ends mapped to the same strand
Counts from the two sequencing runs were added together
Assembly: mm10
Supplementary files format and content: csv file with read counts

source_name: Frontal Cortex

extract_protocol:
Total RNA was isolated using an RNeasy mini kit (Qiagen, #74106) according to the manufacturer’s protocol
Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA protocol (Illumina). Poly-A containing mRNAs were purified by poly-T attached magnetic beads, fragmented, and cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was adenylated to prime for adapter ligation and after a clean-up using AMPure beads (Beckman coulter), DNA fragments were amplified using PCR followed by a final clean-up. Libraries were quality-controlled using a Fragment Analyzer instrument (Agilent Technologies) and subjected to 52-bp paired-end sequencing on a NovaSeq 6000 (Illumina). A total of 2.7 billion reads were generated.

treatment_protocol:
Ten-week-old chow-fed male C57BL/6J mice (group-housed) were randomized into one of four treatment groups (n=8 per group) as follows: Group 1: A single intraperitoneal injection of 3 mg/kg psilocybin, followed by tissue harvest 3 hours after treatment. Group 2: A single intraperitoneal injection of isotonic saline followed by tissue harvest 3 hours after treatment. Group 3: A single intraperitoneal injection of 3 mg/kg psilocybin followed by tissue harvest four weeks after treatment. Group 4: A single intraperitoneal injection of isotonic saline followed by tissue harvest 4 weeks after treatment.
Mice received a single intraperitoneal injection according to their grouping, and were sacrificed (decapitation) according to the above schedule. Prefrontal cortex and whole hypothalamus were immediately dissected out and flash frozen on dry ice. Mice were euthanized in the morning, four hours after the onset of the light phase, to ensure minimal diurnal variation in gene expression. Dissected brain regions were stored at -80⁰C until isolation of RNA was performed.

value: Frontal Cortex

value: Saline

tag: timepoint

value: 3 hours post-injection

tag: cage

tag: extraction pool

value: D


title: HCT116_WT_3

value: colorectal cancer cells

value: WT


title: HCT116_D1KO_1


title: Frontal-Cortex_Psilocybin_4-weeks-post-injection_8

tag: tissue

value: Psilocybin

value: 4 weeks post-injection


title: S375E_08

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

institute: University of Trieste

description: Replicate TDP-43 S375E-08

data_processing:
1 Raw Data    The original raw data from Illumina are transformed to Sequenced Reads by base calling. Raw data are recorded in a FASTQ file, which contains sequence information (reads) and corresponding sequencing quality information.    Every read in FASTQ format is stored in four lines as follows:    @HWI-ST1276:71:C1162ACXX:1:1101:1208:2458 1:N:0:CGATGT     ANTTGTTAACAGGTCAAAATGCAGATCTTCGTGAAGACCCTGACCGGCAAGACCATCACCCTAGAGGTGGAGCCCAGTGACACCATCGAGAACGTGAAG  +  F#,FFFFFFFFFFFFF:FFFF::FFFFF:FFFFFFFFFFFFFFFFFF:F,FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FF:FFFFFF:FFFFFFF    Line 1 begins with a '@' character and is followed by the Illumina Sequence Identifiers and an optional description.  Line 2 is the raw sequence read.  Line 3 begins with a '+' character and is optionally followed by the same sequence identifier and description.  Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of characters as there are bases in the sequence.
2 Data Filtering    Raw reads are filtered to remove reads with adapter contamination or reads with low quality. Only clean reads were used in the downstream analyses.    The filtering process is as follows:  (1) Discard reads with adaptor contamination.  (2) Discard reads when uncertain nucleotides constitute more than 10% of either read (N > 10%).  (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50% of the read.
3 Mapping To Reference Genome    Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. Novogene use STAR to accomplish the mapping. For the Human species, if only need the differential expression significant genes, can map reads to the transcriptome directly. In order to avoid losing a lot of effective junction reads, Novogene use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely, as shown below.
4 Quantification  Gene expression level is measured by transcript abundance. The greater the abundance, the higher is the gene expression level. In our RNA-seq analysis, the gene expression level is estimated by counting the reads that map to genes or exons. Read count is not only proportional to the actual gene expression level, but is also proportional to the gene length and the sequencing depth. In order for the gene expression levels estimated from different genes and experiments to be comparable, the FPKM is used.    HTSeq software was used to analyze the gene expression levels in this experiment, using the union mode.    The result files present the number of genes with different expression levels and the expression level of single genes.  In general, an FPKM value of 0.1 or 1 is set as the threshold for determining whether the gene is expressed or not.    Comparison between Gene Expression Levels: To compare gene expression levels under different conditions, an FPKM distribution diagram and violin Plot are used. For biological replicates, the final FPKM would be the mean value.

Genome_build: Homo Sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: fpkm_genename.xlsx: FPMK + Gene annotations (Excel format)
Supplementary_files_format_and_content: readcount_genenames.xlsx: Readcounts + Gene annotations (Excel format)

source_name: Hek293 Flp-In T-REx  monoclone expressing S375E TDP-43

growth_protocol: Hek293 Flp-In T-REx cells (ThermoFisher Scientific, Waltham, MA, USA)  were maintained in Dulbecco’s Modified Eagle Medium (DMEM)+Glutamax, supplemented with 10% tetracycline-free fetal bovine serum (FBS) and Blasticidin S HCL 15µg/ml (ThermoFisher Scientific, Waltham, MA, USA). For stable transfections, cells were co-transfected with a mixture of pOG44 plasmid and recombinant pcDNA5 FRT/TO vector carrying either the wild-type (WT) or mutant (S375G and S375E) version of the human flag-tagged TDP-43 (TARDBP, NM_007375) Open Reading Frame. Monoclonal colonies were selected and expanded under double selection (Blasticidine 15µg/ml and hygromicine 100µg/ml).

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA sequencing  (150PE, 60M read pair per sample) was performed by Novogene (https://en.novogene.com/).  RNA libraries were prepared for sequencing using standard Illumina protocols.  Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies).  Insert size was checked on an Agilent 2100 and quantified using quantitative PCR (Q-PCR).

treatment_protocol: All experiments using the stable clones were performed after 48 hours from the induction of TDP-43 expression with Tetracycline 1µg/ml (Sigma-Aldrich, St. Louis, MO, USA).

tag: cell type

value: Hek293 Flp-In T-REx

value: 48hrs - Tetracycline induction


title: S375G_06

description: Replicate TDP-43 S375G-06

source_name: Hek293 Flp-In T-REx  monoclone expressing S375G TDP-43


title: S375E_07

description: Replicate TDP-43 S375E-07


title: Frontal-Cortex_Saline_4-weeks-post-injection_8


title: HCT116_WT_1


title: HCT116_WT_2


title: Frontal-Cortex_Psilocybin_3-hours-post-injection_8


title: WT_03

description: Replicate TDP-43 wild-type-03

source_name: Hek293 Flp-In T-REx  monoclone expressing Wild-Type TDP-43

value: Wild-Type


title: S375G_04

description: Replicate TDP-43 S375G-04


title: Frontal-Cortex_Saline_4-weeks-post-injection_7


title: HCT116_D1KO_H3K4me3_ChIP-seq

data_processing:
Basecalls performed using bcl2fastq2 Conversion Software (v2.20). ChIP-seq reads were trimmed using trimmomatic (v0.38) to filter out low-quality reads (QC<30) and remove adapter sequences.
ChIP-seq reads were aligned to the hg19 human reference genome using Bowtie (v1.1.2), and duplicate reads were removed using Picard (v0.118).
ChIP-seq peaks for histone H3 modifications were called using MACS2 (v2.1.1) with the following parameters : FDR < 0.05.
ChIPseeker (v1.16.1) were used to annotate ChIP-seq peaks with nearest genes.
Differential Binding analysis was peformed using MAnorm. Deeptools was used to generate heatmaps.
Assembly: hg19
Supplementary files format and content: Bigwig files (.bw) contained ChIP-seq tag densities and were used for visualize ChIP-seq data.


title: HCT116_D1KO_2


title: Frontal-Cortex_Psilocybin_3-hours-post-injection_7


title: WT_01

description: Replicate TDP-43 wild-type-01


title: S375G_05

description: Replicate TDP-43 S375G-05


title: HCT116_D1KO_H3K27ac_ChIP-seq


title: HCT116_WT_Input DNA


title: Frontal-Cortex_Saline_3-hours-post-injection_7


title: Frontal-Cortex_Psilocybin_4-weeks-post-injection_7


title: HCT116_WT_H3K4me3_ChIP-seq


title: HCT116_D1KO_Input DNA


title: HCT116_WT_H3K27ac_ChIP-seq


title: Frontal-Cortex_Saline_3-hours-post-injection_6


title: RA-FLS, VGLL3 overexpression

city: Shanghai

first: Yu

last: Du

address: 600 Yishan Road

department: Department of Rheumatology and Immunology

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

data_processing:
Illumina Casavasoftware used for basecalling.
Remove adapter polluted reads (reads contain adapter more than 5bp), low-quality reads (reads in which more than 15% bases with base calling quality Q≤19), and reads which contain N higher than 5%.
The reference genomes and the annotation file were downloaded from ENSEMBL database. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT v2.0.5.
Reads Count for each gene in each sample was counted by HISAT v2.0.5, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with nonbiological replicates.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.

source_name: rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS)

growth_protocol: RA-FLS were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
After four days of transfection, total RNA was harvested using Trizol reagent.
NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used with 2 ug of total RNA for the construction of sequencing libraries using standard Illumina protocols.

treatment_protocol: RA-FLS were transfected with negative control lentivirus or VGLL3-overexpressing lentivirus.

value: rheumatoid arthritis (RA)

value: VGLL3 overexpression


title: WT_02

description: Replicate TDP-43 wild-type-02


title: Frontal-Cortex_Saline_4-weeks-post-injection_6