title: HK-GFP-hMR_mRNA_Aldosterone-and-Spironolactone

city: Le Kremlin-Bicêtre

first: Florian

last: Le Billan

address: 63, Gabriel Péri street

country: France

institute: INSERM

data_processing:
Data analyses were performed using the Galaxy web-based platform, including read filtering and mapping, alignment filtering and formatting.
For each experimental condition, before mapping, poly N read tails were trimmed, reads ≤ 20 bases were removed, and reads with quality mean ≤ 20 were discarded using the Trim Galore pipeline (version 0.4.3.1).
Reads were then aligned against the hg19 (GRCh37) annotation of the human genome using TopHat2 (version 2.1.0) with a max edit distance of 2, a final read mismatches of 2, an anchor length of 8, a 70 minimum intron length, max insertion and deletion length of 3 and with a Bowtie 2 sensitive option.
Transcripts were then assembled, and their abundances estimated using cufflinks (version 2.2.1.0) with standard parameters and the assembled transcripts were then merged using the cuffmerge subfunction.
Differential expression levels between the six experimental conditions were estimated using the cuffdiff function (version 2.2.1.5) and expressed as FPKM.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: .tabular
Supplementary_files_format_and_content: transcript quantification using Cufflinks

growth_protocol: Human renal GFP-hMR cells (HK-GFP-MR) (Le Billan et al., FASEB J 2019) were routinely cultured at 37°C in a humidified incubator with 5% CO2 and seeded on 6-well plates with 2 mL DMEM (high glucose DMEM with L-glutamine) that contained 2.5% fetal bovine serum (FBS), 100 U/mL penicillin, 100 mg/mL streptomycin and geneticin G418 (200 mg/mL).

extract_protocol:
At the end of the treatment time, cells were washed twice with ice-cold 1X PBS and frozen at -80°C. For each experimental condition, RNA from four 12-well plates were extracted with the NucleoSpin miRNA extraction kit (Macherey-Nagel) following the manifacturer instructions.
Each sample consisted on a pool of an equal volume of the four biological replicates.
Directional transcriptomic libraries were prepared and sequenced on an Illumina NextSeq 500 sequencer (single read, 75 bases).

treatment_protocol: Geneticin was omitted from cell medium 5 d before experiments. Forty-eight hours before experiments, HK-GFP-MR cells were washed twice with 1X PBS and incubated in DMEM that contained 2.5% DCC FBS. Cells were then incubated for 3 h at 37°C with either 1:1000 ethanol, 10 nM aldosterone, 1 μM finerenone, 1 μM spironolactone or a combination of ligands as indicated on the files name and description, all in DMEM that was supplemented by 2.5% DCC FBS.

value: HK-GFP-hMR

value: Aldosterone and Spironolactone


title: HK-GFP-hMR_mRNA_Aldosterone-and-Finerenone

status: Public on May 09 2022

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: treatment

value: Aldosterone and Finerenone


title: input-G1

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

library_source: genomic

data_processing:
For RNA-seq, the raw sequence reads (fastq file) were mapped to the GRCm38 reference genome using HISAT2 (D. Kim et al., 2015, M. Pertea et al., 2016, D. Kim et al., 2019) (version 2.1.0), and BAM files were created using SAMtools (H. Li, 2009, H. Li, 2011)  (version 1.6).
Mapped reads were counted using featureCounts (Liao Y et al., 2014) (version 1.5.0) and a count matrix was created.
The downstream analysis was carried out with R (version 4.0.1).
For ChIP-seq analysis, Bowtie2 (B. Langmead et al., 2012) (version 2.3.0) was used to map the raw sequence reads (fastq) to the mouse mm10 reference genome, and BAM files were created using SAMtools.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: ChIP-seq signal tracks (bigWig) were created using deepTools (Ramírez et al., 2016) (version 3.5.0). The bin size was 200 bp and window size was 10 kbp, except for H3K27me3 where the bin size was 200 bp and window size was 10 kbp.
Supplementary_files_format_and_content: *.csv file include comma-delimited RNA-seq read count matrix.

molecule: genomic DNA

organism: Mus musculus

source_name: C2C12 cell line

growth_protocol: The mouse myoblast C2C12 cell line was maintained in Dulbecco’s modified Eagle’s medium (DMEM) with 1 g/L glucose (Gibco™, Thermo Fisher Scientific) containing 20% fetal bovine serum (FBS), 2 mM L-glutamine, and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was obtained from the C2C12 cells using Sepasol-RNA I Super G (Nacalai Tesque Inc.) and ethanol precipitation.
Sequencing was performed in an Illumina Illumina HiSeq1500 system with 101 cycles for both read 1 and read 2 using HiSeq PE Rapid Cluster Kit v2 and  HiSeq Rapid SBS Kit v2 (200 Cycles) for RNA-seq, and with 51 cycles for read 1 using TruSeq SBS Kit v3-HS (50 Cycles) and TruSeq SR Cluster Kit v3-cBot-HS for ChIP-seq.
C2C12 cells were sorted into three groups on the basis of the cell cycle (G1, S, and G2-M phases) and used for RNA-seq analysis. The C2C12 cells in the three groups (G1, S, and G2-M phases) were used for the ChIP-seq analysis.

treatment_protocol: C2C12 cells in the growing state were treated with trypsin and centrifuged for 5 min. The pelleted cells were resuspended and stained with 1× PBS containing Hoechst 33342 (Nacalai Tesque Inc.) for 15 min. The suspension was analyzed using a cell sorter (SONY, SH800).

tag: cell line

value: growing state, G1 phase

tag: chil antibody

value: Input


title: HK-GFP-hMR_mRNA_Aldosterone

source_name: HK-GFP-hMR mRNA Aldosterone

value: Aldosterone


title: H3K4me3-G1

value: mouse anti-H3K4me3 CMA304  [PMID 18227620]


title: HK-GFP-hMR_mRNA_Vehicle

source_name: HK-GFP-hMR mRNA Vehicle

value: Vehicle


title: B6

city: Taian

first: Victoria

middle: Anthony

last: Uyanga

state: Please select

address: 61 Daizong Street, China

department: Animal Nutrition and Feed Science

country: China

institute: Shandong Agricultural University

data_processing:
The raw data provided by the sequencing platform (Fastq files) were filtered for quality check.
The filtered reads were aligned to the chicken reference genome (assembly Gallus gallus_4.0) and annotated transcripts of the Ensembl gene annotation using an upgraded version of hisat2 with tophat
The htseq statistics (https://htseq.readthedocs.io/en/release_0.9.1/) was applied to compare the read count value of each gene as the original expression of the gene
RSeQC was used to analyze the expression saturation of the sequencing results and calculated the expression levels of all genes
The DE-Seq R package (http://www.bioconductor.org/packages/release/bioc/html/DESeq.html) was used to analyze and screen the differential expression of genes among groups
Assembly: Gallus_gallus.GRCg6a.dna.toplevel.fa
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
Supplementary files format and content: excel table with raw gene counts for every gene and every sample

organism: Gallus gallus

source_name: Brain

growth_protocol: The chicks were reared at 32oC for the first 3 days and the temperature was reduced by 2oC at 3 days interval until 24oC. Each chamber had three battery cages with double-tiers and a total of 8 cages per battery cage. The cage dimension was 38 × 47 × 35 cm and three birds were housed per cage.

extract_protocol:
The hypothalamic samples (n =6/group) were lysed using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) for RNA extraction in accordance to the manufacturer's protocol. The concentration and purity were detected and the quality of the library was tested by Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Birds were fed two dietary treatments; basal diets or 1% L-Citrulline supplemented diets. At 28 days old. Birds were allocated to thermoneutral (TNZ- 24oC, 60% RH) or high temperature (HS-35oC, 60% RH) environments. The study had four (4) treatments comprising of CON (TNZ + basal diet); A (TNZ + L-Cit diet); B (HS + basal diet); C (HS+ L-Cit diet). Each treatment had 6 replicates of 12 chickens each.

tag: strain

value: Ros 308

tag: tissue

value: Hypothalamus

tag: age

value: Posthatch day 42

value: Basal diet +  35oC


title: H3K4me3-G2M

value: growing state, G2-M phase


title: HK-GFP-hMR_mRNA_Spironolactone

source_name: HK-GFP-hMR mRNA Spironolactone

value: Spironolactone


title: HK-GFP-hMR_mRNA_Finerenone

source_name: HK-GFP-hMR mRNA Finerenone

value: Finerenone


title: H3K27me3-G2M


title: NK cells from liver counterpart in HCC patients, rep8

type: RNA

city: Parma

first: ALESSANDRA

last: ZECCA

state: Parma

address: Via gramsci, 14

country: Italy

institute: University of Parma

hyb_protocol: cDNA was hybridized to 60-mer oligonucleotide whole-human-genome microarrays (Human GE 8x60K v2 sureprint g3, Agilent Technologies), following the manufacturer's protocol.

scan_protocol: Microarray slides were scanned with an Agilent dual-laser DNA microarray scanner. The Agilent Feature Extraction software (user manual version 7.5) was used with default settings to obtain normalized expression values from the raw scans.

data_processing: The Agilent Feature Extraction software with default settings (user manual version 7.5) was used to obtain normalized expression values from the raw scans. The software package GeneSpring GX v13.1.1 (Agilent Technologies) was used for quality control checks, data normalization by the 75th percentile method.

source_name: Liver counterpart infiltrating NK cells from HCC patients, rep8

label_protocol: Total RNA was amplified with the Transplex Whole Transcriptome Amplification (WTA2) kit (Sigma) and purified with GenElute PCR Clean-Up silica spin-columns (Sigma) following manufacturer’s instructions. cDNA was labeled with the SureTag DNA Labeling kit (Agilent Technologies)

extract_protocol: RNA was purified from sorted NK-cells with the RNase-Free DNase I Kit (Norgen Biotek), according to the manufacturer's instructions. Total RNA concentration was determined using a Nanodrop spectrophotometer, and RNA integrity was evaluated with a Bioanalyzer 2100 traces system (Agilent Technologies).

treatment_protocol: Liver and Tumor Infiltrating Lymphocytes were isolated from surgical speciments by enzimatyc and mechanic digestion. After digestion, the samples were filtered with a Cell Strainer. The filtrated was selected separately by centrifugation on Ficoll-Hypaque density gradient centrifugation. The ring of lymphomononuclear infiltrating cells at the interface between Ficoll and supernatant was collected and washed. Cells were cryopreserved in liquid nitrogen until analysis. After thawing, infiltrating lymphocytes were stained with CD3, CD16, CD56 and then 7AAD (7-amino-actinomycin D) vitality dye, in order to distinguish NK-cells in the various samples. Infiltrating NK-cells identified as CD3-, CD56+, CD16+ or CD16- were sorted by FACSAria III Cell Sorter (BD, Biosciences).

value: NK Cells

value: Non tumorous Liver surgical sample


title: H3K4me3-S

value: growing state, S phase


title: NK cells from liver counterpart in HCC patients, rep10

source_name: Liver counterpart infiltrating NK cells from HCC patients, rep10


title: NK cells from liver counterpart in HCC patients, rep11

source_name: Liver counterpart infiltrating NK cells from HCC patients, rep11


title: H3K27me3-S


title: NK cells from liver counterpart in HCC patients, rep9

source_name: Liver counterpart infiltrating NK cells from HCC patients, rep9


title: NK cells from liver counterpart in HCC patients, rep6

source_name: Liver counterpart infiltrating NK cells from HCC patients, rep6


title: NK cells from liver counterpart in HCC patients, rep7

source_name: Liver counterpart infiltrating NK cells from HCC patients, rep7


title: C2C12-G-S-lot1-replicate2

description:
kudou_mRNAseq_genes_featurecounts.txt
C2C12-S-L2.bam


title: H3K27me3-G1


title: NK cells from liver counterpart in HCC patients, rep5

source_name: Liver counterpart infiltrating NK cells from HCC patients, rep5


title: Prx1Cre;Rosa26-tdTomato bone marrow single cell RNA-sequencing

city: Durham

first: Matthew

middle: J.

last: Hilton

state: NC

address: 450 Research Drive, LSRC B321C

country: USA

institute: DUKE UNIVERSITY SCHOOL OF MEDICINE

data_processing:
Raw base call demultiplex into Fastq Files
Matrix generation 10X cell ranger software 3.0.1
PCA analysis, clustering, and gene expression analysis Seurat version 4
RNA Velocity
Assembly: mm10
Supplementary files format and content: RDS file provided after PCA and clustering, from which gene expression was taken and RNA velocity was performed

source_name: Muscle

growth_protocol: Animals were bred in accordance to Duke University IACUC protocols and aged to 21 days

extract_protocol:
Animals were euthanized according to IACUC protocol and hind limb muscles were isolated. Muscles were mechanically and enzymatically digested with Collagenase B/Dispase mixture for 30 minutes. Following a red blood cell lysis, cells were stained with DAPI and FACS sorted on tomato expression and submitted for 10X Genomics single cell isolation and barcoding.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: C57/BL6 background;Prx1Cre

value: muscle interstitial


title: chip_GR_dual_rep1

city: Rehovot

first: Ido

last: Goldstein

address: POB 12

department: Institute of Biochemistry, Food Science and Nutrition

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Binary Base Call (BCL) output files from a Nextseq 500 machine were converted to FASTQ format, using BCL to FASTQ (bcl2fastq v2.20.0.422 Copyright (c) 2007-2017 Illumina, Inc.).
Fastq files were mapped to the mm10 mouse genome assembly using Bowtie2
Genome_build: mm10

source_name: hepatocytes

growth_protocol: as described in PMID: 33111119

extract_protocol:
RNA: Total RNA was isolated from primary mouse hepatocytes using NucleoSpin kit (Macherey-Nagel cat# 740955.25) according to the manufacturer’s protocol. ChIP: cells were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with 0.125M glycine. Crosslinked samples were washed in PBS, resuspended in ChIP lysis buffer (0.5% SDS, 10mM EDTA, 50mM Tris-HCl pH8) and sonicated (Bioruptor, Diagenode) to release 100-1000 bp fragments. Antibodies (4 μg per 300 μg chromatin) against H3K27ac (Active motif #39133) or GR (CST #3660) were conjugated to magnetic beads (Sera-Mag, Merck #GE17152104010150) for 2 h at 4°C. Chromatin was immunoprecipitated with antibody-bead conjugates over night at 4°C. Immunocomplexes were washed sequentially with the following buffers: low-salt buffer (0.01% SDS, 1% Triton x-100, 2 mM EDTA, 20mM Tris-HCl pH8, 150mM NaCl), high salt buffer (0.01% SDS, 1% Triton x-100, 2mM EDTA, 20mM Tris-HCl pH8, 500mM NaCl), low salt buffer and TE buffer (10mMTris-HCl, 1mM EDTA pH8). Chromatin was de-proteinized with proteinase K (Hy Labs EPR9016) for 2 h at 55°C and de-crosslinked over night at 65°C. DNA was subsequently phenol-chloroform purified and ethanol precipitated
For quality control of RNA yield and library synthesis products, the RNA ScreenTape and D1000 ScreenTape kits (both from Agilent Technologies), Qubit® RNA HS Assay kit, and Qubit® DNA HS Assay kit (both from Invitrogen) were used for each specific step. mRNA libraries were prepared from 1 µg RNA using the KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads (KAPA biosystems, cat# KK8421). ChIP DNA libraries were prepared using the KAPA HyperPrep Kit (KAPA biosystems, cat# KR0961).

treatment_protocol: Cells were treated with glucagon (100nM) and corticosterone (1 µM) for 3h (RNA-seq) or 1h (ChIP-seq)

value: liver

tag: antibody

value: GR (Cell Signaling Technologies cat# 3660)

value: hepatocytes


title: C2C12-G-G2M-replicate2

description:
kudou_mRNAseq_genes_featurecounts.txt
C2C12-G2M-L2.bam


title: chip_GR_cort_rep2


title: chip_GR_cort_rep1


title: C2C12-G-S-lot1-replicate1

description:
kudou_mRNAseq_genes_featurecounts.txt
C2C12-S-L1.bam


title: chip_GR_gluc_rep2


title: NK cells from liver counterpart in HCC patients, rep3

source_name: Liver counterpart infiltrating NK cells from HCC patients, rep3


title: C2C12-G-G2M-replicate1

description:
kudou_mRNAseq_genes_featurecounts.txt
C2C12-G2M-L1.bam


title: NK cells from liver counterpart in HCC patients, rep1

source_name: Liver counterpart infiltrating NK cells from HCC patients, rep1


title: chip_GR_dual_rep2


title: NK cells from liver counterpart in HCC patients, rep4

source_name: Liver counterpart infiltrating NK cells from HCC patients, rep4


title: NK cells from liver counterpart in HCC patients, rep2

source_name: Liver counterpart infiltrating NK cells from HCC patients, rep2


title: C2C12-G-G1-replicate2

description:
kudou_mRNAseq_genes_featurecounts.txt
C2C12-G1-L2.bam

source_name: C2C12 cell line

value: growing state, G1 phase


title: NK cells from HCC tumor samples, rep10

source_name: Tumor infiltrating NK cells from HCC patients, rep10

value: Tumor (HCC) surgical sample


title: chip_GR_gluc_rep1


title: C2C12-G-G1-replicate1

description:
kudou_mRNAseq_genes_featurecounts.txt
C2C12-G1-L1.bam


title: NK cells from HCC tumor samples, rep11

source_name: Tumor infiltrating NK cells from HCC patients, rep11


title: S16_DKO.CAF

city: Marburg

first: Magdalena

last: Huber

address: Hans-Meerweinstr. 02

department: Mikrobiology

country: Germany

institute: University of Marburg

data_processing:
Paired-end reads were mapped to the mouse transcriptome (Ensembl 102) using salmon (v1.3.0)
Differential gene expression analysis was performed using DESeq2 (v1.28.1)
Assembly: GRCm38
Supplementary files format and content: Textfiles including TPM and Number of Reads

source_name: pancreatic stellate cells

growth_protocol: 6 x10^5 PSC were seeded in a 70µl matrigel drop, mixed at a 1:1 ratio with DMEM (10 % FCS) on a 3.5 cm suspension dish.The matrigel-embedded PSC were covered with 0.5 % FCS-containing DMEM and incubated for 48 h. Thereafter, the qPSC were treated with  conditioned media (CM)  at a 1:1 ratio with DMEM (0.5 % FCS), followed by an incubation for 48 h .

extract_protocol:
RNA was isolated fibroblasts with the NucleoSpin RNA Macherey-Nagel kit according to manufacturer’s protocol.
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Nano chip on Agilent's bioanalyzer. Barcoded mRNA seq libraries were prepared from 400 ng total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual. All quality controls were done using Invitrogen’s Qubit HS assay and fragment size was determined on Agilent’s 2100 Bioanalyzer HS DNA assay.

treatment_protocol: For CM production, in vitro differentiated CTLs, Tc17 and Tc17-DKO cells were harvested, washed with PBS and reseeded for 24 h in fresh DMEM (5% FCS) with plate-bound anti-CD3 mAb (5µg ml-1). Supernatants were harvested cell-free by centrifugation at 400x g, 10 min, 4°C and stored at -80°C for further use.

value: Tc17 conditioned media  from IL17A/F KO mice treated

value: pancreatic stellate cells


title: S14_DKO.CAF


title: S15_DKO.CAF


title: chip_GR_nt_rep2


title: chip_H3K27ac_dual_rep3

value: H3K27ac (Active Motif cat# 39133)


title: chip_GR_nt_rep1


title: NK cells from HCC tumor samples, rep9

source_name: Tumor infiltrating NK cells from HCC patients, rep9


title: chip_H3K27ac_dual_rep2


title: S13_DKO.CAF


title: S12_Tc17.iCAF

value: Tc17 conditioned media treated


title: NK cells from HCC tumor samples, rep7

source_name: Tumor infiltrating NK cells from HCC patients, rep7


title: NK cells from HCC tumor samples, rep8

source_name: Tumor infiltrating NK cells from HCC patients, rep8


title: S11_Tc17.iCAF


title: chip_H3K27ac_dual_rep1


title: NK cells from HCC tumor samples, rep6

source_name: Tumor infiltrating NK cells from HCC patients, rep6


title: NK cells from HCC tumor samples, rep4

source_name: Tumor infiltrating NK cells from HCC patients, rep4


title: S10_Tc17.iCAF


title: chip_H3K27ac_cort_rep3


title: chip_H3K27ac_cort_rep2


title: NK cells from HCC tumor samples, rep3

source_name: Tumor infiltrating NK cells from HCC patients, rep3


title: S9_Tc17.iCAF


title: S4_qPSC

value: untreated


title: chip_H3K27ac_gluc_rep3


title: S2_qPSC


title: chip_H3K27ac_nt_rep3


title: S1_qPSC


title: ASP14_day7_R3

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

institute: Institut Curie

data_processing:
Reads were trimmed with Atropos
Mapping againt human genome (hg19) was performed with TopHat for run B69 and STAR for run D066. Cufflinks was used to quantify gene expression (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited files with FPKM for each genes (Cufflinks output).

molecule: polyA RNA

source_name: Ewing sarcoma cell line

growth_protocol: Cells were cultured in DMEM (ASP14) or RPMI (SKNMC, TC71 and MHH-ES1) media supplemented with 10% fetal bovine serum.

extract_protocol:
RNA was extracted using RNeasy plus mini kit and further processed for RNA-seq
The library construction was performed using TruSeq Stranded mRNA (Illumina, ref #20020594) according to manufacturer recommendations

treatment_protocol: SKNMC, TC71 and MHH-ES1 Ewing sarcoma cell lines were transfected (RNAiMAX) with siCT or siEWSR1-FLI1 according to manufacturer recommendations. RNA of these cells were extracted 96 hours post-transfection. For ASP14, the invalidation of EWSR1-FLI1 was induced by treatment with 1µg/ml of doxycycline for 7 days

value: A673/TR/shEF inducible

tag: condition

value: dox

tag: time


title: chip_H3K27ac_gluc_rep1


title: MiaPaCa2_ATAC_rep2

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Scientific Institute

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38) (PMID:24695404),  then single-end with min 36-bp reads length were aligned to human genome build GRCh38/hg38 using Bowtie2 v2.2.6 (PMID: 22388286) with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools. Then read positions were corrected for transposon insertion offset as described in (PMID:24097267).
Peak calling was performed using MACS2 with the “--nomodel”, “--extsize 146”,  “--qvalue 0.05”, "--nolambda" and "--keep-dup all" flags and arguments
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.narrowPeak, list of the peaks called by MACS2

source_name: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

growth_protocol: See additional columns of the SAMPLES section

extract_protocol: 50000 cells were pelleted by centrifugation and re-suspended in 50 µl of cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin). After incubation on ice for three minutes, lysis was washed out by adding 1 mL of lysis buffer without NP40 and digitonin. Nuclei were pelleted by centrifugation for 10 min at 500g, 4 ºC.  The supernatant was discarded and nuclei were re-suspended in 50 µl of reaction buffer containing 1 µl of Tn5 transposase (made in house),  10 ul of 5x transposase buffer (50mM Tris-HCl, pH 8.4 and 25mM MgCl2), 16.5 µl PBS, 0.5 µl of 1% digitonin, 0.5 µl of 10% Tween-20. The reaction was incubated at 37ºC for 30 minutes with 600 RPM mixing. Then 5 µl of clean up buffer (900mM NaCl, 300mM EDTA), 2ul of 5% SDS and 2 µl of Proteinase K (20 µg/µl) (New England Biolabs) were added and incubated for 30 min at 40 ºC. Tagmented DNA was isolated using SPRI beads (2x) and amplified by PCR. Fragments smaller than 600 bp were isolated using SPRI cleanup and libraries where sequenced on an Illumina NextSeq500 platform.

value: MiaPaCa2 wild-type cell line

tag: growth protocol

value: DMEM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

value: Bulk cell line, untreated


title: chip_H3K27ac_cort_rep1

source_name: hepatocytes


title: ASP14_day7_R1


title: chip_H3K27ac_nt_rep2


title: ASP14_day7_R2


title: chip_H3K27ac_nt_rep1


title: NK cells from healthy liver, rep6

source_name: Infiltrating NK cells from healthy liver, rep6

value: NK Cells

value: Normal Liver surgical sample


title: MiaPaCa2_ATAC_rep1

treatment_protocol: See additional columns of the SAMPLES section


title: chip_H3K27ac_gluc_rep2

value: liver


title: NK cells from HCC tumor samples, rep5

source_name: Tumor infiltrating NK cells from HCC patients, rep5


title: ASP14_day0_R3


title: NK cells from healthy liver, rep3

source_name: Infiltrating NK cells from healthy liver, rep3


title: S3_qPSC


title: NK cells from healthy liver, rep5

source_name: Infiltrating NK cells from healthy liver, rep5


title: NK cells from HCC tumor samples, rep2

source_name: Tumor infiltrating NK cells from HCC patients, rep2


title: NK cells from healthy liver, rep1

source_name: Infiltrating NK cells from healthy liver, rep1


title: NK cells from healthy liver, rep4

source_name: Infiltrating NK cells from healthy liver, rep4


title: NK cells from HCC tumor samples, rep1

source_name: Tumor infiltrating NK cells from HCC patients, rep1


title: 6-AGM_B6_A5

city: Wako

first: Chiawen

last: Lin

state: Saitama

address: 2-1, Hirosawa

department: CBS

institute: RIKEN

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Cellranger mkfastq (10x genomics) modeule raw BCL files into FASTQ files
Cellranger count (10x genomics) takes FASTQ from cellranger mkfastq and performs alignment, filtering,   barcode counting, and UMI counting.
1) Aligns short reads to the reference genome and transcriptome using STAR.  2) Populates the cellular and molecular barcode and generic header tags in the aligned BAM file  using barcode reads and read alignments.  3) Removes barcodes not associated with cellular GEM partitions.  4) Generates gene-barcode matrices by counting unique molecules.  5) Runs principal component analysis to reduce gene expression to its most highly variable  components.  6) Runs graph-based clustering and modularity optimization to partition the data into  subpopulations based on PCA results.  7) Runs k-means clustering to partition the data into subpopulations based on PCA results.  05  8) Runs t-Distributed Stochastic Neighbor Embedding to visualize PCA results in two dimensions.  9) Runs Uniform Manifold Approximation and Projection to visualize PCA results in two dimensions.  10) Merge graph-based clusters which have insufficient differential expression between them.  11) Combines the different clustering results into a single file.  12) Identifies the most differentially expressed genes in each cluster relative to other clusters.  13) Creates CSV and HTML files summarizing sequencing run performance.
Genome_build: mm10
Supplementary_files_format_and_content: 10x genomics, filtered feature barcode matrix

source_name: AGM

extract_protocol:
YS/ AGM regions were digested with 0.25%/ 0.1% collagenase I. Cell concentration was adjusted for single-cell library preparation using Chromium Single Cell 3’ Library & Gel Bead Kit v.3.1 (10x Genomics) according to the manufacturer’s protocol. In brief, 1.65 × 104 cells were added into Chromium Next, GEM Chip and loaded on Chromium Controller to generate 10,000 single-cell gel bead emulsions per sample.
Library was prepared by Chromium Single Cell 3’ Library & Gel Bead Kit v.3.1 (10x Genomics) according to the manufacturer’s protocol.

tag: Stage


title: MHH-ES1_siEF1_96h_R2


title: 5-AGM_BRC_H4

value: RIKEN BRC BTBR


title: ASP14_day0_R2


title: MHH-ES1_siEF1_96h_R1


title: rna_dual_rep3

value: hepatocytes


title: 2-Ys_BRC_E4

source_name: yolk sac


title: ASP14_day0_R1


title: rna_dual_rep2


title: POE_input

data_processing:
Reads were mapped with bowtie2 against human genome (hg19)
Peaks were called with MACS2 2.1.1 with the option narrow for FLI1 and HA-EGR2 and broad for histone marks. For each cell line, ChIP-seq were normalized according to their respective input DNA sample.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

growth_protocol: POE shEGR2_4#22 clone and POE were cultured in RPMI media supplemented with 10% fetal bovine serum.

extract_protocol:
ChIP were done following manufacturer protocol using iDeal ChIP-seq kit for transcription factors and histones (Diagenode) with anti-HA , rabbit polyclonal anti-Fli, rabbit polyclonal anti-H3K4me3 and rabbit polyclonal anti-H3K27ac
TruSeq Chip library preparation kit (Illumina)

treatment_protocol: The inhibition of endogenous EGR2 in  POE shEGR2_4#22 clone was induced by treatment with 1µg/mldoxycycline for 5 days

value: POE

value: WT

value: input


title: rna_dual_rep1


title: MHH-ES1_siCT_96h_R1

value: siCT


title: rna_cort_rep3


title: Intestinal_tumoroids_rep_3

first: Silvia

last: Fre

address: 26 rue d’Ulm

department: Genetics and Developmental Biology

data_processing:
Sequencing reads were aligned on the Mouse reference genome (mm10) using the STAR mapper (v2.5.3a)
Protein-coding genes from the Gencode annotation (vM13) have been used to generate the raw count table.
Transcripts Per Kilobase Million (TPM) was calculated.
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes TPM values for each sample.
csv file includes reads count for each sample.

source_name: Intestinal tumor cells

growth_protocol: Organoids were cultured in 50%DMEM-F12 / 50% Matrigel drops, polymerized for 15' at 37°C prior to add organoid medium (mEGF 50ng/ml, mNOG 100ng/ml, mRPSO1 500ng/ml and B27 1X in DMEM-F12 with 2% Penicilin-Streptomycin) and maintained at 37°C 5%CO2. Medium was replaced every 3-4 days.

extract_protocol:
Total mRNA was extracted using Qiagen RNEasy mini kit
RNA sequencing libraries were prepared from 1µg of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit which allows to prepare libraries for strand specific mRNA sequencing. A first step of polyA selection using magnetic beads was done to address sequencing specifically on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed followed by dA-tailing before ligation of the TruSeq indexed adapters (Unique Dual Indexing strategy). PCR amplification was finally achieved to create the final cDNA library. After qPCR quantification, sequencing was carried out using 2x100 cycles (paired-end reads, 100 nucleotides) on a Illumina NovaSeq 6000 system (S1 flow cells) to get around 45M paired-end reads per sample.

treatment_protocol: After fresh passage, organoids were incubated in 50% organoid medium 2X / 50% conditioned medium (cM) for treated or organoid medium 1X for untreated conditions.

value: Epithelial intestinal tumor cells

tag: genotype

value: MIX


title: POE_Fli1


title: POE22_nodox_input

value: POE shEGR2_4#22


title: Intestinal_tumoroids_rep_1

value: untreated


title: POE22_nodox_H3K4me3


title: TC71_siEF1_96h_R2


title: rna_cort_rep1


title: rna_gluc_rep3


title: TC71_siEF1_96h_R1


title: Intestinal_organoids_24h_Organoids_conditioned_medium_treated_rep_3

source_name: Small Intestine

value: Epithelial intestinal cells

value: 24h T-cM


title: TC71_siCT_96h_R1


title: MHH-ES1_siCT_96h_R2


title: Intestinal_organoids_24h_Tumoroids_conditioned_medium_treated_rep_3

value: 24h WT-cM


title: Intestinal_tumoroids_rep_2


title: rna_gluc_rep2


title: POEHAEGR_PLUSDOX_HA

value: HA


title: rna_gluc_rep1


title: SKNMC_siEF1_96h_R2

value: SKNMC


title: 1-Ys_B6_D4


title: POE22_nodox_H3K27ac


title: NK cells from healthy liver, rep2

source_name: Infiltrating NK cells from healthy liver, rep2

value: NK Cells

value: Normal Liver surgical sample


title: Intestinal_organoids_24h_Organoids_conditioned_medium_treated_rep_2


title: POEHAEGR_MINDOX_HA


title: SKNMC_siEF1_96h_R1


title: Intestinal_organoids_24h_Tumoroids_conditioned_medium_treated_rep_2


title: rna_nt_rep3

value: liver


title: rna_cort_rep2

value: hepatocytes


title: TC71_siCT_96h_R2


title: POEHAEGR_MINDOX_INPUT


title: rna_nt_rep2


title: Intestinal_organoids_24h_Organoids_conditioned_medium_treated_rep_1


title: SKNMC_siCT_96h_R1


title: Intestinal_organoids_24h_Tumoroids_conditioned_medium_treated_rep_1


title: rna_nt_rep1


title: POEHAEGR_PLUSDOX_INPUT


title: Os18SrRNA Root_DMS(-)

status: Public on May 08 2022

city: Nanjing

first: Xiaorong

last: Fan

address: Nanjing city Wei Tong Road 6

department: 1State Key Laboratory of Crop Genetics and Germplasm Enhancement

institute: Nanjing Agricultural University

data_processing:
Adapters were trimmed by TrimGalore, clean reads over 70bp were retained.
Reads were aligned using Tophat allowing 10% mismatches. Next, uniquely mapped reads were extracted using the Linux command grep with NH:I:1 tag.
Mismatch count and coverage in each nuclotide were called, and mismatches located within 3nt of an insertions or deletion were masked for future analysis.
Assembly: MSU Rice Genome Annotation Project Release 7
Supplementary files format and content: text files include mismatch count and coverage in each nucleotide for each Sample.

organism: Oryza sativa Japonica Group

source_name: rice roots

extract_protocol:
DMS-treated or DMS-Untreated samples were pelleted and resuspended in 1 mL Trizol, RNA was extracted by phenol-chloroform extraction and isopropanol precipitation.rRNA was subtracted with Ribo-zero rRNA removal kit for plant (illumina).
For target-specific DMS-MaPseq, 6 µg of DMS-treated sample was mixed with gene-specific RT primers. The reverse transcription was proceeded with TGIRT-III (Ingex). Then specific gene cDNA were amplified using KOD hot start DNA polymerase with gene-specific primers. For genome-wide DMS, DMS-MaPseq library was constructed using Illumina TruSeq® Stranded Total RNA Sample Prep Plant kit (Illumina) and TGIRT enzyme (InGex).

treatment_protocol: Three-week-old rice seedlings were collected and immersed in 20ml of 1X DMS reaction buffer (40mM HEPES pH7.5, 100mM KCl and 0.5mM MgCl2).  200,  400, 500µl of DMS was added to the reaction buffer to give a final concentration of 1%, 2% and 2.5% , respectively.The same volume of DEPC-treated water was added into the reaction buffer for the mock treatment. DMS treatment was performed for 15 min at 30°C with shaking at 250rpm or under vacuum (approximately 12 psi) at room temperature without shaking. To quench the reaction, 6 ml β-Mercaptoethanol was added to a final concentration of 23%, and the mixture was incubated for 5 min under vacuum.

value: roots

value: Three-week-old


title: Os18SrRNA Root_DMS(+)Shaking1%


title: c-FOS-KOSUMO-def-FOS + STm infection - rep3

city: PUNE

first: Girish

middle: S

last: Ratnaparkhi

state: MH

address: Dr. Homi Bhabha Road Pashan Pune 411008

department: Biology

country: India

institute: Indian Institute of Science Education & Research

description:
c-FOS-Knock out MEFs expressing SUMO-def-c-FOS under SRE + STm infection
Fos-SUMODef_I-3

data_processing:
Bcl2fastq for base calling and adapter trimming
On an average 9 million reads per sample were mapped to Human genome using Bluebee Genomics Platform
Gene expression counts were generated and DE analysis was performed using Bluebee Genomics Platform
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include count values for each Sample ...

source_name: f10 MEFs cells

growth_protocol: All MEFs were cultured in Serum starved DMEM medium for 16 hrs [DMEM D5648 supplemented with 1% penicillin-streptomycin] at 37 oC and 5% (v/v) CO2. Salmonella infected cells were cultured in 20% FBS containing antibiotic free DMEM medium for 4hrs.

extract_protocol: Post infection cells were washed with 1XPBS, trypsinized and RNA was extracted according to standard protocol using Rneasy Mini kit .

treatment_protocol: Post serum starvation, cells were infected with Salmonella in 20% FBS containing antibiotic free DMEM medium for 4hrs.

value: f10 MEFs

value: STm infection


title: c-FOS-KOSUMO-def-FOS + STm infection - rep1

description:
c-FOS-Knock out MEFs expressing SUMO-def-c-FOS under SRE + STm infection
Fos-SUMODef_I-1


title: c-FOS-KOWT-FOS - rep2

description:
c-FOS-Knock out MEFs expressing WT-c-FOS under SRE
Fos-WT_C-2

value: no infection


title: c-FOS-KOWT-FOS - rep3

description:
c-FOS-Knock out MEFs expressing WT-c-FOS under SRE
Fos-WT_C-3


title: c-FOS-KOSUMO-def-FOS - rep1

description:
c-FOS-Knock out MEFs expressing SUMO-def-c-FOS under SRE
Fos-SUMODef_C-1


title: c-FOS-KOSUMO-def-FOS + STm infection - rep2

description:
c-FOS-Knock out MEFs expressing SUMO-def-c-FOS under SRE + STm infection
Fos-SUMODef_I-2


title: c-FOS-KOSUMO-def-FOS - rep3

description:
c-FOS-Knock out MEFs expressing SUMO-def-c-FOS under SRE
Fos-SUMODef_C-3


title: c-FOS-KOWT-FOS + STm infection - rep3

description:
c-FOS-Knock out MEFs expressing WT-c-FOS under SRE + STm infection
Fos-WT_I-3


title: SKNMC_siCT_96h_R2

source_name: Ewing sarcoma cell line

value: siCT


title: c-FOS-KOSUMO-def-FOS - rep2

description:
c-FOS-Knock out MEFs expressing SUMO-def-c-FOS under SRE
Fos-SUMODef_C-2


title: c-FOS-KOWT-FOS - rep1

description:
c-FOS-Knock out MEFs expressing WT-c-FOS under SRE
Fos-WT_C-1


title: c-FOS-KOWT-FOS + STm infection - rep1

description:
c-FOS-Knock out MEFs expressing WT-c-FOS under SRE + STm infection
Fos-WT_I-1


title: Previously published AMP Rheumatoid Arthritis Phase 1 data from PMID: 31061532 [amp]

city: Boston

first: Anna Helena

last: Jonsson

state: MA

address: 60 Fenwood Road

department: Dept of Medicine/Division of Rheumatology, Inflammation, and Immunity

institute: Brigham and Women's Hospital/Harvard Medical School

library_source: transcriptomic single cell

data_processing:
To characterize heterogeneity of T cells within RA synovial tissue, we aggregated synovial single cell profiles from 4 newly collected and 15 publicly available synovial tissue samples from RA patients. We performed quality control by removing cells from the raw count matrices with fewer than 500 genes detected or more than 25% mitochondrial reads. We scaled the aggregated data by mean 0 variance 1 and performed Log2 normalization.
Assembly: GRCh38
Supplementary files format and content: The processed data files shows log2 normalization

source_name: Synovial tissue

extract_protocol:
As described in PMID: 31061532
CEL-Seq2

value: Synovial tissue

value: T cells

tag: cell isolation_method

value: Plate-based (384-well plates)


title: c-FOS-KOWT-FOS + STm infection - rep2

description:
c-FOS-Knock out MEFs expressing WT-c-FOS under SRE + STm infection
Fos-WT_I-2


title: Patient 30 primary (frozen)

city: Helsinki

first: Katja

last: Eloranta

address: Tukholmankatu 8

department: Children's Hospital

country: Finland

institute: University of Helsinki

data_processing:
QuantSeq 3’ mRNA-Seq Integrated Data Analysis Pipeline on Bluebee® (Lexogen) was used for preliminary quality evaluation and alignment of the RNA sequencing data.
To filter out lowly expressed genes, sample read counts were transformed into count-per-million (CPM) values using edgeR (doi: 10.1093/bioinformatics/btp616) package (cut-off CPM > 0.4 in at least 8 samples)
Filtered data were normalized and transformed using the voomfunction from the limma package (doi: 10.1093/nar/gkv007).
Differential gene expression analyses were performed using the lmfit function (limma package) (doi: 10.1093/nar/gkv007)
Assembly: GRCh38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: Granulosa cell tumor tissue

extract_protocol:
FFPE samples: Ten AGCT FFPE tissue sections of 5 µm thickness were mounted on objective slides, and areas with >80% AGCT cellularity based on hematoxylin and eosin slide review were scraped off into a microcentrifuge tube.Total RNA was extracted from the FFPE tissue using Maxwell RSC RNA FFPE kit. Fres frozen samples (F1-F6): Fresh tumor samples were snap frozen and stored in -80°C until RNA extraction. RNA was extracted using The Maxwell RSC simplyRNA Tissue Kit.
Single-indexed mRNA libraries were prepared from 100 ng of RNA with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD

value: Granulosa cell tumor tissue

tag: tissue sample type

value: Fresh frozen tumor tissue

tag: sample type

value: Primary tumor (frozen)


title: Patient 31 relapse (frozen)

value: Relapsed tumor (frozen)


title: Patient 32 relapse (frozen)


title: Patient 28 primary (frozen)


title: Patient 33 relapse (frozen)


title: Patient 29 primary (frozen)


title: DS5_C1 10uM_F3

city: Houston

first: Cintia

middle: S.

last: de Paiva

state: TX

address: 6565 Fannin Street NC505G

department: Ophthalmology

institute: Baylor College of Medicine

hyb_protocol: One hundred nanograms of total RNA were hybridized with the NanoString Technologies nCounter Gene Expression GE- Mouse -Inflammation v2 Panel Codeset. Overnight hybridization occurred for 20 hours at 65°C. Removal of excess probes with magnetic bead purification was performed on the nCounter Prep Station (software v4.0.11.2) on the High Sensitivity assay. Briefly, the probe-mRNA structure was affinity purified by its 3’ end to remove excess reporter probes, then by its 5’ end to remove excess capture probes. Once unbound probes were washed away, the tripartite structure was bound to the streptavidin-coated cartridge by the biotin capture probe, aligned by an electric current (negative to positive), and immobilized. Photobleaching and fluorophore degradation was prevented with the addition of SlowFade.

scan_protocol: The cartridge containing immobilized samples was transferred to the nCounter Digital Analyzer (software v3.0.1.4) and scanned at 555 field of view (FOV). An epi-fluorescent microscope and CCD camera identified sets of fluorescent spots, which were tabulated for data output. Quality control metrics were recorded using the nSolver Analysis Software v4.0.6.2.

data_processing: Data processing was analyzed with nCounter and ROSALIND software. Data in Matrix is after normalization by ROSALIND.

label: not provided

label_protocol: not provided

extract_protocol: RNA was extracted using the Qiagen mini plus columns according to the manufacturer's protocol. RNA quantity and quality was measured with NanoDrop and Bioanalyzer.

treatment_protocol: Mice were exposed to desiccating stress (DS) conditions which included a drafty low humidity (<30% relative humidity) environment and received scopolamine in the drinking water (to inhibit tear secretion) . During DS, mice received twice a day eye drops of either vehicle, C1 or pan.

tag: Sex

value: female

value: 3 months

tag: cells

value: Cornea epithelia

value: Cornea

tag: group

tag: age (months)


title: DS5_C1 10uM_F4


title: DS5_C1 10uM_F2


title: DS5_pan 10uM-F4

value: DS5_pan 10uM-F4


title: DS5_pan 10uM-F2

value: DS5_pan 10uM-F2


title: DS5_pan 10uM-F1

value: DS5_pan 10uM-F1


title: DS5_Vehicle-F3


title: Q808 for 28 day-2

city: Changchun

first: Wei

last: Li

state: Jilin

address: No 155 Chuangju Street

institute: Jilin Provincial Academy of Traditional Chinese Medicine

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then theclean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene  were obtained by htseq-count. DEGs were identified using the DESeq(2012) R package  functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or  foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical  cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment  and KEGG pathway enrichment analysis of DEGs were respectively performed using R  based on the hypergeometric distribution
If it was transcript-level quantification, FPKM and read counts value of each transcript  (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using  the DESeq(2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and  foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential  expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts  expression pattern. GO enrichment and KEGGpathway enrichment analysis of DEGs were  respectively performed using R based on the hypergeometric distribution
The reads were reassembled using StringTie. Then gene structure extension and novel  transcripts identification were performed by comparing the reference genome and the known  annotated genes using cuffcompare software.
The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was  performed using ASprofile.  SNP and INDEL were called using samtools and bcftools, and the details were shown on  samtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then snpeff annotates  and predicts the effects of variants on genes.
Assembly: ronr 6.0
Supplementary files format and content: FPKM

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
Total RNA was extracted from hippocampal tissue sample (about 100 mg)  using TRIzol kit (Invitrogen, USA)  according to the manufacturer’s instructions. RNA purity was checked and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA). Samples with an absorbance (260/280) ratio between 1.8 and 2.2 were considered acceptable. Agilent 2100 Bioanalyzer (Agilent Technologies,  USA) was used to assess the RNA integrity.
The sequencing library was generated by using MGIEasy Universal Library Convert Kit (MGI, China), VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, China), and VAHTS® mRNA Capture Beads (Vazyme, China) according to the manufacturer’s protocols.

value: hippocampus

value: wild type

tag: treatment

value: gavage of Q808 for 28 day


title: DS5_Vehicle-F2

tag: strain


title: shTFRC_2nd (KD-2)

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description:
expressed_gene_reads.txt
expressed_gene_FPKM.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 20 -p 16 --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  and Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: hela cell

growth_protocol: The human HeLa cell line was purchased from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. Cells were seeded into a petridish (100 mm) at a density of 1 × 105 cells/mL per well, and cultured at 37 ℃with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (Hyclone), penicillin (100 U/ml) and streptomycin (100 g/ml). TFRC silencing plasmid transfection of HeLa cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Transfected cells were harvested after 48 h.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

value: TFRC silencing in hela cell

tag: cell line

value: HeLa


title: shCtrl_1st(NC-1)

value: hela cell- control plasmid


title: New RA synovial tissue T cell data from sample bwh075

extract_protocol:
Single Cell 3′ kit, 10X Genomics
Single Cell 3′ kit, 10X Genomics

tag: tissue

value: Synovial tissue

tag: cell type

value: T cells

value: 10x Chromium chip


title: shCtrl_2nd(NC-2)


title: control macrophage, M66C, Hour 6

city: Bethesda

first: Adam

middle: Christian

last: Knapp

state: Maryland

address: 7005 Clarendon Rd Apt 2

institute: University of Florida

data_processing:
Samples were sequenced in 2 runs, and R1s and R2s for each samples were pooled together separately. The sequenced raw RNA-seq reads were checked for quality control using FASTQC v0.11.8, and trimmed using Trimmomatic v0.39. The cleaned reads were then aligned to the Ensembl GRCh38v96 reference genome using STAR v2.7.2b, and Qualimap v2.2.1 was used to check the quality of alignment. Read-count matrix was created by using the column with reads for reverse strandedness (i.e. column 4) from readspergene.tab STAR output files.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: Human monocyte-derived macrophage

growth_protocol: Mononuclear cells were isolated from Buffy coats using Ficoll gradients. CD14+ CD16- monocytes were isolated using EasySep Human Monocyte Isolation Kit and differentiated into macrophages by culture. Flow cytometry was used to assess the purity of macrophages after 7 days of culture.

extract_protocol:
RNeasy Plus mini kit, Qiagen
KAPA-Stranded mRNA-seq kit

treatment_protocol: Macrophages were co-cultured with Aspergillus conidia at a 1:1 ratio.

value: Human monocyte-derived macrophage

value: control

value: Hour 6


title: macrophage co-cultured with A. fumigatus, M64F, Hour 4

value: co-culture

value: Hour 4


title: control macrophage, M68C, Hour 8

value: Hour 8


title: control macrophage, M64C, Hour 4


title: New RA synovial tissue T cell data from sample bwh064


title: control macrophage, M58C, Hour 8


title: macrophage co-cultured with A. fumigatus, M56F, Hour 6


title: New RA synovial tissue T cell data from sample bwh002, also known as BRI002


title: control macrophage, M60, Hour 0

value: Hour 0


title: control macrophage, M62C, Hour 2

value: Hour 2


title: Q808 for 28 day-1

value: hippocampus


title: shTFRC_1st(KD-1)


title: macrophage co-cultured with A. fumigatus, M62F, Hour 2


title: DS5_Vehicle-F1

value: female

tag: age

value: 3 months

value: Cornea epithelia

value: Cornea


title: DS5_C1 10uM_F1


title: macrophage co-cultured with A. fumigatus, M68F, Hour 8

tag: time


title: New RA synovial tissue T cell data from sample bwh076


title: macrophage co-cultured with A. fumigatus, M66F, Hour 6


title: Q808 for 28 day-3

value: wild type

value: gavage of Q808 for 28 day


title: control macrophage, M54C, Hour 4


title: DS5_pan 10uM-F3

value: DS5_pan 10uM-F3


title: P028_SF_CD8_Gzm_neg_AHJ6578

data_processing:
Single-end reads were mapped to transcripts from the Ensembl GRCh38 reference using Kallisto version 0.42.3 to generate transcripts per million (TPM) matrices. We included protein-coding genes, pseudogenes, and lncRNA genes in our reference.
We analyzed TapeStation results generated from an Agilent D1000 ScreenTape System in order to approximate mean fragment length and standard deviation for accurate single-end mapping.
We noticed a sample effect in the gene expression space, so we removed the sample effect using R package removeBatchEffect.
Assembly: Ensembl GRCh38
Supplementary files format and content: log2tpm_batch_corrected.txt

source_name: Sorted CD8 T cell subset

extract_protocol:
RNA was isolated using a QIAGEN RNeasy FFPE kit following the manufacturer’s protocol starting with resuspend of the cell pellet in PKD buffer.
Clontech SMARTer cDNA synthesis kit

tag: participant id

value: Sorted CD8 T cell subset

tag: sorting and_rna_isolation_batch

tag: cell subset

value: Gzm neg


title: P033_SF_CD8_GzmKplus_AHJ6578_S9

value: GzmK+


title: P033_SF_CD8_Gzm_neg_AHJ6578


title: macrophage co-cultured with A. fumigatus, M58F, Hour 8

value: Human monocyte-derived macrophage


title: Synovial fluid CD8 T cells from participant P012

description: 10X Genomics scRNA-seq

data_processing:
scRNA-seq reads were processed with Cell Ranger v3.1.02.10.0, and quantification was performed using STAR aligner against the GRCh38 transcriptome.
Assembly: GRCh38
Supplementary files format and content: Both processed data files (csv and rds formats) contain normalized counts.

source_name: Synovial fluid

extract_protocol: Single Cell 3′ kit, 10X Genomics

value: Synovial fluid

value: CD8 T cells


title: macrophage co-cultured with A. fumigatus, M48F, Hour 8

value: co-culture

value: Hour 8


title: P033_SF_CD8_GzmBplus_AHJ6578_S10

value: GzmB+


title: control macrophage, M50, Hour 0

value: control

value: Hour 0


title: control macrophage, M52C, Hour 2

value: Hour 2


title: P033_SF_CD8_GzmKplusBplus_AHJ6578_S11

value: GzmB+ GzmK+


title: SFCD8_DiSF84_Unstim_biolrep2

data_processing:
We mapped the reads to the GRCh38 using kallisto (version 0.43.0)
Assembly: GRCh38 using kallisto (version 0.43.0)
Supplementary files format and content: The processed data file presents normalized counts as log2tpm

extract_protocol: Human RA synovial fibroblasts were stimulated with supernatants from the indicated T cell population (synovial fluid CD8 T cells, synovial fluid CD4 T cells, or peripheral blood memory CD8 T cells; either unstimulated or stimulated with anti-CD3/CD28 antibody-coated beads (Dynabeads)) or with recombinant human IFNγ (100 ng/mL) or TNF (0.1ng/mL or 1 ng/mL). In some wells, anti-TNF antibodies (TNFAb)were added to the T cell supernatants prior to transfer to the fibroblasts.

tag: t cell_donor

value: Synovial fibroblast

tag: alternative sample_id

tag: barcode sequence

value: TCCTGAGC-TATGCAGT


title: P028_SF_CD8_GzmKplusBplus_AHJ6578_S7


title: control macrophage, M48C, Hour 8


title: macrophage co-cultured with A. fumigatus, M54F, Hour 4

value: Hour 4


title: SFCD8_DiSF84_Dyna_biolrep2

value: TCCTGAGC-TACTCCTT


title: PBmemCD8_ZZ_Unstim_biolrep2

value: ZZ

value: TCCTGAGC-ATAGAGAG


title: P012_SF_CD8_Gzm_neg_AHJ6578

value: Sorted CD8 T cell subset

value: Gzm neg


title: macrophage co-cultured with A. fumigatus, M46F, Hour 6

value: Human monocyte-derived macrophage

value: Hour 6


title: P028_SF_CD8_GzmBplus_AHJ6578_S6


title: control macrophage, M46C, Hour 6


title: control macrophage, M56C, Hour 6


title: macrophage co-cultured with A. fumigatus, M52F, Hour 2

value: co-culture


title: PBmemCD8_ZZ_Dyna_biolrep2

value: TCCTGAGC-AGAGGATA


title: P028_SF_CD8_GzmKplus_AHJ6578_S5

value: GzmK+


title: SFCD8_DiSF48_Dyna_TNFAb_biolrep1

value: TAGGCATG-AGGCTTAG


title: macrophage co-cultured with A. fumigatus, M44F, Hour 4


title: PBmemCD8_AHJ3_Unstim_biolrep2

value: TAGGCATG-ATAGAGAG


title: P012_SF_CD8_GzmKplus_AHJ6578_S1


title: P012_SF_CD8_GzmKplusBplus_AHJ6578_S3


title: macrophage co-cultured with A. fumigatus, M42F, Hour 2

value: Hour 2


title: PBmemCD8_AHJ3_Dyna_biolrep2

value: TAGGCATG-AGAGGATA


title: SFCD8_DiSF48_Unstim_biolrep1

value: Synovial fibroblast

value: TAAGGCGA-TATGCAGT


title: TNF_0_1ng_mL_biolrep2

value: GTAGAGGA-TACTCCTT


title: PBmemCD8_TT_Dyna_biolrep1

value: TT

value: TAAGGCGA-AGAGGATA


title: control macrophage, M42C, Hour 2

value: control


title: P012_SF_CD8_GzmBplus_AHJ6578_S2

value: Sorted CD8 T cell subset

value: GzmB+


title: DMEM_alone_biolrep1

value: GTAGAGGA-AGGCTTAG


title: PBmemCD8_TT_Unstim_biolrep1

value: TAAGGCGA-ATAGAGAG


title: control macrophage, M44C, Hour 4

value: Human monocyte-derived macrophage

value: Hour 4


title: SFCD4_DiSF84_Unstim_biolrep2

value: GTAGAGGA-ATAGAGAG


title: SFCD8_DiSF86_Dyna

value: GGACTCCT-TACTCCTT


title: SFCD4_DiSF84_Dyna_biolrep2

value: GTAGAGGA-AGAGGATA


title: PBmemCD8_AHJ3_Unstim_biolrep1

value: GGACTCCT-ATAGAGAG


title: macrophage co-cultured with A. fumigatus, M38F, Hour 8

value: co-culture

value: Hour 8


title: IFNg_100ng_mL_biolrep1

value: Synovial fibroblast

value: GCTCATGA-TATGCAGT


title: control macrophage, M40, Hour 0

value: Hour 0


title: SFCD8_DiSF48_Dyna_biolrep1

value: TAAGGCGA-TACTCCTT


title: control macrophage, M38C, Hour 8

value: control


title: Cell ID-86

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: Single cell isolated from OVCA429 shGRHL2 Tet-inducible single cells suspension by dielectrophoresis

data_processing:
Reads were quality-checked and filtered by Novogene company.
The single cell Hi-C libraries were mapped, processed, and filtered according to NucProcess.
The usable Hi-C contacts results generated from the NucProcess, were then analysed by Nuctools for subsequent 3D genome structure model analysis
Assembly: hg38
Supplementary files format and content: Nucprocess hic read output file, ncc.gz

extract_protocol:
Single cells stained for EpCAM and GRHL2 prior to isolation on DEPArray™ NxT system.
Single cell HiC libraries were constructed using MboI enzyme and Ampli1TM WGA Kit (Menarini Silicon Biosystems), with minor modifications to the kit protocol.
single-cell HiC

value: OVCA429 shGRHL2 Tet-inducible

value: ovarian cancer cell


title: control macrophage, M36C, Hour 6

value: Hour 6


title: SFCD4_DiSF86_Unstim

value: GCTCATGA-ATAGAGAG


title: Cell ID-93

source_name: OVCA429 shGRHL2 Tet-inducible single cell


title: Cell ID-90


title: macrophage co-cultured with A. fumigatus, M36F, Hour 6

value: Human monocyte-derived macrophage


title: Cell ID-56


title: TNF_1ng_mL_biolrep1

value: GCTCATGA-TACTCCTT


title: SFCD4_DiSF86_Dyna

value: GCTCATGA-AGAGGATA


title: Cell ID-89


title: SFCD4_DiSF48_Unstim_biolrep1

value: CTCTCTAC-ATAGAGAG


title: Cell ID-49


title: SFCD8_DiSF84_Dyna_TNFAb_biolrep2

value: CTCTCTAC-AGGCTTAG


title: Cell ID-44


title: control macrophage, M34C, Hour 4

value: Hour 4


title: Cell ID-43


title: SFCD8_DiSF48_Unstim_biolrep2

value: CGTACTAG-TATGCAGT


title: control macrophage, M32C, Hour 2

value: Hour 2


title: PBmemCD8_TT_Unstim_biolrep2

value: TT

value: Synovial fibroblast

value: CGTACTAG-ATAGAGAG


title: SFCD8_DiSF48_Dyna_biolrep2

value: CGTACTAG-TACTCCTT


title: macrophage co-cultured with A. fumigatus, M32F, Hour 2

value: co-culture


title: DMEM_alone_biolrep2

value: GCTCATGA-AGGCTTAG


title: PBmemCD8_AHJ3_Dyna_biolrep1

value: GGACTCCT-AGAGGATA


title: Cell ID-23

description: Single cell isolated from PEO1/HEYA8 cells suspension by dielectrophoresis

data_processing:
Reads were quality-checked and filtered by Novogene company.
The single cell Hi-C libraries were mapped, processed, and filtered according to NucProcess.
The usable Hi-C contacts results generated from the NucProcess, were then analysed by Nuctools for subsequent 3D genome structure model analysis
Assembly: hg38
Supplementary files format and content: NucProcess exported hic reads file, ncc format.

extract_protocol:
Single cells stained for EpCAM and Vimentin prior to isolation on DEPArray™ NxT system.
Single cell HiC libraries were constructed using MboI enzyme and Ampli1TM WGA Kit (Menarini Silicon Biosystems), with minor modifications to the kit protocol.
single-cell HiC

value: ovarian cancer cell


title: macrophage co-cultured with A. fumigatus, M34F, Hour 4


title: TNF_1ng_mL_biolrep2

value: ATCTCAGG-TACTCCTT


title: SFCD4_DiSF48_Dyna_biolrep2

value: CGAGGCTG-AGAGGATA


title: control macrophage, M30, Hour 0

value: Human monocyte-derived macrophage

value: control

value: Hour 0


title: IFNg_100ng_mL_biolrep2

value: ATCTCAGG-TATGCAGT


title: SFCD4_DiSF48_Unstim_biolrep2

value: CGAGGCTG-ATAGAGAG


title: Cell ID-21


title: macrophage co-cultured with A. fumigatus, M26F, Hour 6

value: Hour 6


title: Cell ID-84

value: OVCA429 shGRHL2 Tet-inducible


title: Cell ID-22


title: control macrophage, M28C, Hour 8

value: Hour 8


title: SFCD4_DiSF48_Dyna_TNFAb_biolrep1

value: Synovial fibroblast

value: CGAGGCTG-AGGCTTAG


title: PBmemCD8_TT_Dyna_TNFAb

value: TT

value: ATCTCAGG-ATAGAGAG


title: SFCD4_DiSF48_Dyna_biolrep1

value: CTCTCTAC-AGAGGATA


title: PBmemCD8_TT_Dyna_biolrep2

value: CGTACTAG-AGAGGATA


title: Cell ID-20

value: ovarian cancer cell


title: macrophage co-cultured with A. fumigatus, M28F, Hour 8

value: co-culture


title: PBmemCD8_ZZ_Dyna_TNFAb

value: ZZ

value: ATCTCAGG-AGAGGATA


title: control macrophage, M24C, Hour 4

value: Human monocyte-derived macrophage

value: control

value: Hour 4


title: PTC_6

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

description:
Papillary thyroid carcinoma
tumor tissue

data_processing:
CASAVA version 1.4 software used for basecalling.
The "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads were  removed, then mapped to Human whole genome using bowtie2 with parameters for PE reads: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RPKM) method was used in calculated expression level.
Supplementary files format and content: tab-delimited text files include reads count values for each sample ...

source_name: Papillary thyroid carcinoma

extract_protocol:
The study was approved by the clinical research ethics committee in Shenzhen Hospital (Guangming), University of Chinese Academy of Sciences and followed the Declaration of Helsinki.
All the participants had signed the informed consents. A total of 6 patients diagnosed with papillary thyroid carcinoma were recruited. The tissues were collected during surgery.
The tumor tissues and the paired normal tissues adjacent to tumors were then dissected by a pathologist for RNA sequencing.

value: Papillary thyroid carcinoma


title: Cell ID-24


title: Cell ID-19


title: Cell ID-18


title: PTC_4


title: PBmemCD8_ZZ_Unstim_biolrep1

value: AGGCAGAA-ATAGAGAG


title: control macrophage, M26C, Hour 6

value: Hour 6


title: SFCD8_DiSF84_Dyna_biolrep1

value: AGGCAGAA-TACTCCTT


title: control macrophage, M22C, Hour 2

value: Hour 2


title: PBmemCD8_AHJ3_Dyna_TNFAb

value: Synovial fibroblast

value: ATCTCAGG-CTCCTTAC


title: SFCD8_DiSF84_Unstim_biolrep1

value: AGGCAGAA-TATGCAGT


title: macrophage co-cultured with A. fumigatus, M24F, Hour 4


title: control macrophage, M20, Hour 0

value: Hour 0


title: PTC_3


title: PTC_5


title: macrophage co-cultured with A. fumigatus, M18F, Hour 8

value: Hour 8


title: Cell ID-17

value: ovarian cancer cell


title: Cell ID-16


title: PBmemCD8_ZZ_Dyna_biolrep1

value: AGGCAGAA-AGAGGATA


title: Cell ID-15


title: TNF_0_1ng_mL_biolrep1

value: AAGAGGCA-TACTCCTT


title: SFCD4_DiSF84_Dyna_biolrep1

value: AAGAGGCA-AGAGGATA


title: normal_6

description:
paired normal tissues
normal tissue

source_name: paired normal tissue

value: paired normal tissue


title: PTC_1


title: Cell ID-12


title: SFCD4_DiSF84_Unstim_biolrep1

value: AAGAGGCA-ATAGAGAG


title: normal_4

description:
paired normal tissues
normal tissue


title: normal_3

description:
paired normal tissues
normal tissue


title: control macrophage, M18C, Hour 8

value: Human monocyte-derived macrophage

value: control


title: macrophage co-cultured with A. fumigatus, M22F, Hour 2

value: co-culture


title: control macrophage, M16C, Hour 6

value: Hour 6


title: Cell ID-13


title: normal_5

description:
paired normal tissues
normal tissue


title: H23_sox7_2

first: SIQIN

last: ZHOU

address: 14 Medical Drive

institute: Cancer Science Institute of Singapore

hyb_protocol: RNAs were prepared for labeling and hybridization using standard Illumina Human HT-12 v4 Expression BeadChip protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized followed by log2 transformed using beadarray Bioconductor package.

label: biotin

source_name: SOX7 overexpressing cells

growth_protocol: cells were growth until 90% confluent, and then RNA was extracted.

extract_protocol: RNA was harvested using RNeasy Mini Kit.

value: lung cancer

tag: genotype

value: SOX7 overexpressing cells


title: Cell ID-11


title: PTC_2

value: Papillary thyroid carcinoma


title: Cell ID-14


title: SFCD4_DiSF84_Dyna_TNFAb_biolrep2

value: Synovial fibroblast

value: AAGAGGCA-AGGCTTAG


title: Cell ID-8


title: macrophage co-cultured with A. fumigatus, M16F, Hour 6


title: normal_1

description:
paired normal tissues
normal tissue


title: Cell ID-10


title: macrophage co-cultured with A. fumigatus, M14F, Hour 4

value: Hour 4


title: Cell ID-9


title: H23_control_1

source_name: GFP overexpression control cells

label_protocol: RNAs were prepared for labeling and hybridization using standard Illumina Human HT-12 v4 Expression BeadChip protocol

value: GFP overexpression control cells


title: MKO rep_1

first: Yu-Yao

last: Guo

address: Donghu Road 115

institute: Wuhan University

data_processing:
Cutadapt Data filtering At least 10 bp overlap (agatcggaag), allowing a base error rate of 20%
Library quality inspection (2100 detection of library size, fluorescence quantitative detection of total library concentration < quantifluor st fluorometer, Promega, e6090; quant it PicoGreen dsDNA assay kit, Invitrogen, p7589) >, qPCR quantitative detection of effective library concentration < Thermo Scientific steponeplus real time PCR systems >)
All RNA-seq data wrer aligned to Mus musculus GRCm38 genome with Ensembl byTophat2 microexon-search and library-type=fr-firststrand
Illumina NovaSeq 6000
Quantitative gene expression using union scheme in HTSeq
Assembly: Mus_musculus.GRCm39.dna.toplevel.fa
Supplementary files format and content: excel with FPKM for every gene and every sample

source_name: Bone Marrow

growth_protocol: Femurs and tibias were dissected from Trpv2fl/fl and Lyz2-Cre;Trpv2fl/fl mice. Bone marrow was flushed from the bones, and the red blood cells were lysed with ACK lysis buffer. Debris was removed by passing cells through a 70 μM strainer and cells were counted via Countess II FL Automated Cell Counter. Approximately 5 × 106 bone marrow cells were cultured in 100 mm dishes in DMEM (Thermo Fisher Scientific, MA, USA) containing 10% heat-inactivated fetal bovine serum (FBS, Gibco, Thermo Fisher Scientific) and 1% streptomycin-penicillin at 37 °C in a humidified incubator gassed with 5% CO2. GM-CSF (20 ng/mL, Peprotech) and M-CSF (10 ng/mL, Peprotech) were added to the bone marrow cultures for differentiation of BMDCs and BMDMs, respectively. The medium was changed every 3 days. On day 7, cells were collected.

extract_protocol:
The cells were homogenized in 2 ml of TRIzol (Invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis.
TruSeq Stranded mRNA LT Sample Prep Kit was used to synthesized the first strand cDNA through the action of random primers and reverse transcriptase, the second strand cDNA is synthesized with the first strand cDNA as the template, cDNA library construction followed by sequencing on an Illumina NovaSeq 6000 platform.  RNA-sequencing reads were first trimmed to remove poly(A) and unqualified reads with cutadapt, then aligned to Mus musculus GRCm38 genome with Ensembl. The numbers of counts were summarized at the gene level using HTseq.

value: bone marrow-derived macrophages (BMDMs)


title: control macrophage, M14C, Hour 4


title: NF11 cells, siDEIK 2

city: Guangzhou

first: Chengcheng

last: Deng

state: Guangdong

address: No.2 lujing Road

institute: Dermatology Hospital, Southern Medical University

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 N base 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. Differential expression analysis was carried out using Ballgown with a cut-off of P <0.05 and abs (log2FC) >1.0. The R programming language and ggplot2 package was used to generate heatmaps.
Assembly: hg38
Supplementary files format and content: comma-delimited text files include FPKM values for each Sample

growth_protocol: Keloid tissues were harvested during plastic surgery from patients confirmed to have clinical evidence of keloid (Supplementary Table 1). Normal skin tissues were obtained from volunteers as control subjects (Supplementary Table S1). Fibroblast cultures were established as described previously (). The cell strains were maintained and stored in a liquid nitrogen container, and cells from passages 3 through 7 were used in this study.

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq was performed at Beijing Novogene Co., Ltd. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: fibroblast

value: DEIK knockdown


title: control macrophage, M12C, Hour 2

value: Hour 2


title: MKO rep_2


title: MWT rep_1


title: Cell ID-5

value: ovarian cancer cell


title: control macrophage, M10, Hour 0

value: Hour 0


title: Cell ID-6


title: MWT rep_2


title: NF11 cells, siDEIK 1


title: macrophage co-cultured with A. fumigatus, M12F, Hour 2

value: Human monocyte-derived macrophage


title: Cell ID-7


title: normal_2

description:
paired normal tissues
normal tissue

value: paired normal tissue


title: Cell ID-2


title: DCKO rep_1

value: bone marrow-derived dendritic cells (BMDCs)


title: DCKO rep_2


title: Cell ID-3


title: H23_sox7_1


title: NF5 cells, siScramble

value: WT


title: HEYA8 Hi-C, replicate 2

description:
Ovarian cancer cell line HEYA8, replicate 2
HiSeq 3000/4000
HEYA8.hic.gz

data_processing:
Reads were quality-checked and filtered by Novogene company.
The Hi-C sequencing reads were aligned separately using Hicup v0.61 and subsequently filtered out using default settings of HiCUP.
The usable Hi-C contacts results generated from the HiCUP was then analyzed using HOMER v4.10 and HiCExplorer
Assembly: hg38
Supplementary files format and content: hic-matrix in juicer hic format

extract_protocol: In-situ Hi-C experiments were performed in duplicate, using HindIII enzyme, following the original protocol by Rao et. al., 2014 (doi: 10.1038/s41467-018-03748-1).


title: HEYA8 Hi-C, replicate 1

description:
Ovarian cancer cell line HEYA8, replicate 1
HiSeq 3000/4000
HEYA8.hic.gz


title: PEO1 Hi-C, replicate 2

description:
Ovarian cancer cell line PEO1, replicate 2
HiSeq 3000/4000
PEO1.hic.gz


title: Cell ID-1


title: H23_control_2

value: lung cancer


title: NF11 cells, siScramble


title: NF5 cells, siDEIK 2


title: Cell ID-4


title: NF5 cells, siDEIK 1


title: RNAseq in Trim71(R595H) mESCs 1

status: Public on May 07 2022

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

description: poly(A)+ RNA

data_processing:
Basecalls performed using CASAVA version 1.4
For CLIPseq, sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using hisat2 with parameters--mp 6,2. The resulting sam file is converted into bam file using samtools. The uniquely mapped reads were isolated using samtools.
The CLIPseq peak calling were performed by the Piranha, iCount, and CLIPper. The common peaks from these 3 programs were retained as Trim71(R595H)-binding regions
For the Cut&Run, raw reads were mapped to the mouse mm10 genome assembly using Bowtie2 (v2.4.5) with options: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. Then reads that mapped to the mitochondrial DNA were removed. PCR duplicates were removed by Picard (v.2.26.11) and peak calling was performed using SEACR (v1.3) in “stringent” mode. Differential binding peaks were identified with DiffBind (v3.2.7) with FDR cut-off of 0.05 and peaks were annotated using ChIPSeeker (v1.28.3). Motif discovery was performed using HOMER (v4.10).
Assembly: mm10
Supplementary files format and content: The csv file contains Trim71(595)-binding regions from the CLIPseq; Ctnnb1-binding regions from the Cut&Run, and counts per million reads from the RNA-seq

source_name: mouse embryonic stem cells (mESCs)

growth_protocol: All the mESCs used in this study were cultured on 0.5% gelatin-coated tissue culture plates in the 2i + Lif medium (DMEM/F12, 2% FBS, 2mM L-Glutamine, 0.1mM MEM NEAA, 1% Penicillin-Streptomycin, 0.1 mM β-mercaptoethanol and 1000 U/mL mLIF, 1 x N2N27, 3 uM CHIR99021 and 1 uM PD0325901).

extract_protocol:
Total RNA were isolated from mESCs via Trizol reagent
The Trim71(R783H) CLIP-seq was performed using the previously established HITS-CLIP protocol (Moore et al., 2014). The cut&run was performed using the CUT&RUN Assay Kit (Cell Signaling Technology, Cat#86652) according to its instruction manual.
CLIP-seq, RNA-seq, and Cut&Run

value: FLAG-Trim71 (R595H) mESCs

tag: genetic background


title: Cut&Run on Ctnnb1 in Trim71 wild-type mESCs

value: wild type ESC

tag: antibody

value: beta-Catenin(D10A) (Cell Signaling Technologies #8480); Rabbit IgG


title: tomato_drought2

city: Bunkyoku-Yayoi

first: Hiroko

last: Asakura

state: TOKYO

address: １－１－１

institute: The University of Tokyo

hyb_protocol: cRNA 15µg were flagmentated, and hybridized for 16hr at 45C on GeneChip Tomato Genome Array. GeneChips were washed and stained with Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalized using the statistical software R, and the dfw method.

organism: Solanum lycopersicum

source_name: Tomatoes grown under drought conditions

label_protocol: Biotin-labeled cRNA was synthesized from 100ng total RNA according to the manufacture's protocol.

growth_protocol: Grows in a greenhouse controlled at 25 ° C in the daytime and 20 ° C in the evening, and harvests fruits for 30-40 days after flowering

extract_protocol: Total RNA was extracted from the tomato sample using TRIzol Reagent(Thermo Fisher Scientific) , according to the manufacture's protocol. The extracted total RNA was cleaned up with RNeasy Mini Kit (QIAGEN).

treatment_protocol: The control group gave liquid fertilizer (manufactured by Sumitomo Chemical) diluted 500 times until it was planted. In the stress area, liquid fertilizer diluted 500 times was given once a week.

tag: cultivar

value: MicroTom

value: mature green fruit


title: DCWT rep_1


title: DCWT rep_2


title: Cut&Run on Ctnnb1 in Trim71(R595H)

description: beta-catenin associated DNA

value: FLAG-Trim71 (R595H)


title: RNAseq in Trim71(R595H) mESCs 2

description: poly(A)+ RNA


title: Trim71(R595H) CLIPseq in mESCs

description: Trim71(R595H) bound mRNA

value: FLAG-M2 (Sigma)


title: Cut&Run on Ctnnb1 in Trim71 wild-type mESCs IgG

value: IgG


title: tomato_drought3


title: PEO1 Hi-C, replicate 1

description:
Ovarian cancer cell line PEO1, replicate 1
HiSeq 3000/4000
PEO1.hic.gz


title: Trim71(R595H) CLIPseq in mESCs input

value: input


title: RNAseq in Trim71(R595H) mESCs 3

description: poly(A)+ RNA


title: JHv_unstim_6h_N3_R1

city: Amsterdam

first: Brendon

middle: P.

last: Scicluna

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC Locatie AMC

data_processing:
Sequence read quality was assessed by means of the FastQC methods and Trimmomatic was used to trim the Illumina adapters containing, poor-quality bases and ambiguous nucleotide-containing sequences.
High-quality reads were used to align against the Genome Reference Consortium human genome build 38 (GRCh38). Mapping was performed by HISAT2 version 2.1.0[34] with parameters as default.
Count data were generated by means of the featureCounts.
DESEq2 was used for differential expression analysis
Assembly: Genome Reference Consortium Human Genome Build 38 (GRCh38)
Supplementary files format and content: tab-delimited text files including raw counts

source_name: THP1-MD2 cell line

growth_protocol: Blood samples were obtained from 6 patients with sepsis caused by community-acquired pneumonia within 24 hours after admission to the intensive care unit of Amsterdam UMC, location Academic Medical Center (AMC), University of Amsterdam, the Netherlands and from 4 healthy subjects. Monocytes were isolated using fluorescence-activated cell sorting (FACS) and stored in RNA protect cell reagent (Qiagen, Hilden, Germany). Monocytes were sorted on FACS Canto II flow cytometer (BD Biosciences) with anti-CD14 antibody (Miltenyi Biotech). The Medical Ethics Committee of the Academic Medical Center approved the study (IRB no. 10-056C) and written informed consent was obtained from all patients (or legal representative) and healthy controls.

extract_protocol:
RNeasy mini kits (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA quality was assessed by bioanalysis (Agilent), with all samples having RNA integrity numbers > 7. Total RNA concentrations were determined by Qubit® 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA).  and sequenced using the Illumina HiSeq4000 instrument (Illumina) to generate single reads (50bp).
RNA-sequencing libraries were prepared from 300ng total RNA using KAPA RNA Hyperprep with RiboErase (Roche) library kits

tag: group

value: overexpression ectopic JHDM1D-AS1

tag: treatment

value: medium

tag: treatment hours


title: JHv_unstim_6h_N4_R1

tag: cell line


title: JHv_unstim_6h_N1_R1


title: JHv_unstim_6h_N2_R1


title: tomato_control1

source_name: Tomatoes grown under normal conditions

tag: tissue


title: tomato_control3


title: tomato_control2


title: tomato_drought1


title: JHv_Unstim_2h_N4_R1


title: JHv_Unstim_2h_N3_R1


title: JHv_LPS_6h_N2_R1

value: LPS


title: JHv_LPS_6h_N1_R1


title: JHv_Unstim_2h_N1_R1


title: crlv_unstim_6h_N3_R1

value: control


title: JHv_Unstim_2h_N2_R1


title: JHv_LPS_2h_N4_R1


title: JHv_LPS_2h_N3_R1


title: crlv_unstim_6h_N1_R1


title: Crlv_Unstim_2h_N3_R1


title: JHv_LPS_6h_N4_R1


title: Crlv_Unstim_2h_N2_R1


title: crlv_LPS_6h_N4_R1


title: Crlv_LPS_2h_N4_R1


title: crlv_unstim_6h_N4_R1


title: JHv_LPS_2h_N2_R1


title: crlv_LPS_6h_N2_R1


title: crlv_LPS_6h_N3_R1


title: Crlv_Unstim_2h_N4_R1


title: JHv_LPS_6h_N3_R1


title: crlv_LPS_6h_N1_R1


title: Crlv_LPS_2h_N2_R1


title: Crlv_LPS_2h_N3_R1


title: Hematopoietic progenitors, blf;drl, 20hpf, rep2

first: Yuxi

last: Yang

state: Jiangsu

address: Room 402, 12 Xuefu Road, Nanjing University

department: Medical School

institute: Nanjing University

data_processing:
Illumina bcl2fastq2-v 2.20.0.422 software was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Read quality was checked for each sample by using FastQC v 0.11.9.
High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.2.1 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10.
Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0.
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text files include raw counts for each sample.

organism: Danio rerio

source_name: embryos

extract_protocol:
At 20 hpf,  zebrafish embryos were dissociated into single cells with Librase treatment, RFP+ hematopoietic progenitors were purified with FACS, and RNA was extracted by using the Direct-zol RNA prep Kit (ZYMO Research, Cat. No. 2052).
NEBNext Single Cell_Low Input RNA Library Prep Kit for Illumina (NEB, Cat No.6420) was used with 30,000 RFP+hematopoietic progenitors for the construction of sequencing libraries.

value: embryos

tag: developmental stage

value: 20 hpf

tag: cell type

value: RFP+ hematopoietic progenitors

value: blf-/-; drl 4KO

value: Digested with Liberase and enriched by FACS


title: Hematopoietic progenitors, blf, 20hpf, rep2

value: blf-/-


title: Crlv_Unstim_2h_N1_R1


title: Spleen, DKO/hA-I, 2

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

institute: University of Milan

description:
spleen.raw.counts.csv
73-57-1 S

data_processing:
Bowtie+Tophat+Cuffdiff
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to GrCM38/mm10 Bowtie
Read count extraction and normalization were performed using Tophat
Differential expression analysis was performed by CuffDiff
Assembly: mm10
Supplementary files format and content: csv files include raw counts for each sample, average FRPKM values across conditions and FDR for differential expression

source_name: Spleen

growth_protocol: 30 weeks old mice fed with normal laboratory diet

extract_protocol:
RNA was isolated using the NucleoSpin RNA extraction kit (Macherey-Nagel, Duren, Germany) according to the manufacturer's instructions
RNA libraries for RNA-seq were prepared using the Illumina RNA-Seq sample Prep Kit following manufacturer's protocols.

value: Spleen

value: DKO/hA-I

value: normal laboratory diet

tag: age

value: 30 weeks


title: Spleen, DKO, 3

description:
spleen.raw.counts.csv
73-55-12 S

value: DKO


title: JHv_LPS_2h_N1_R1


title: Hematopoietic progenitors, blf;drl, 20hpf, rep3


title: Crlv_LPS_2h_N1_R1


title: Spleen, DKO, 1

description:
spleen.raw.counts.csv
73-56-2 S


title: D6M, Input, rep2

city: Erlangen

first: Michaela

last: Petter

address: Wassertrumstr. 3-5

department: Mirkobiologisches Institut

institute: Univeritätsklinikum Erlangen

data_processing:
Quality control of samples using FastQC version 0.11.8
Read trimming using TrimGalore 0.6.4, and if necessary Cutadapt 2.8 and again FastQC
Read alignment using Bowtie2 version 2.3.4.3 default settings
generation of bam files and merging of files by samtools 1.9
generation of bigwig files and correlation plots by Deeptools 3.1.2
visualisation by IGV 2.6.3 and pyGenometracks 3.6
peak calling using MACS2 2.1.2.1
further data analysis by bedtools 2.28.0, mixtools 1.2.0, ggplot2 3.3.2, scanpy 1.8.1
Assembly: PlasmoDB-28_Pfalciparum3D7_Genome.fasta / PlasmoDB-28_Pfalciparum3D7.gff (available on PlasmoDB)
Supplementary files format and content: bigwigfiles filtered by quality > 28, normalized using RPKM

organism: Plasmodium falciparum

source_name: cell culture

growth_protocol: 3D7::ABCG2-GFP P. falciparum parasites were cultivated at 5 % haematocrit in complete culture medium (RPMI-1640 complete medium (Gibco, Thermo Fisher Scientific) complemented with 25 mM HEPES pH 7.3 and 20 µg/ml gentamycin (Thermo Fisher Scientific) and supplemented with 0.25 %  AlbuMAX II Lipid-Rich BSA (Thermo Fisher Scientific) and 5 % human AB Rh+ serum purchased from the Bavarian Red Cross Service (BRK). The parasites were propagated in erythrocytes of blood group 0+ (purchased from BRK) in a gas environment of 1 % O2, 5 % CO2, and 94 % N2 at 37 °C.  Developing gametocytes were magnetically purified using MACS columns and separated by sex using flow cytometry. Male gametocytes were GFP low and female gametocytes GFP high. Mitotracker was used to sort for viable cells.

extract_protocol:
Parasites were crosslinked at a final concentration of 1% PFA for 10 min at 37°C and subsequently quenched with 125 mM glycine for 5 min on ice. The cells were then spun down and lysed using 0.075% saponin in PBS. After lysis the cells were washed twice with PBS and then resuspended in cold lysisbuffer (10 mM Hepes pH 7.9, 10 mM KCl, 0.1 mM EDTA pH 8.0, 0.1 mM EGTA pH 8.0, 1 mM DTT, 1x Protease Inhibitor (Roche); 1ml per 5*10^7 cells). The mix was then transferred to a tissue grinder and incubated on ice for 30 min. Then Igepal was added to a final concentration of 0.25% and cells were lysed with 100 strokes. The resulting free nuclei were again pelleted and lysed by SDS lysis buffer (1 % SDS, 10 mM EDTA, 50 mM Tris pH 8.1, 1x Protease Inhibitor). The DNA was then sheared by sonication (2 times 8 min with 30s ON 30s OFF cycles). The sheared material was spun and the supernatant was transferred and diluted 1:10 with ChIP dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 150 mM NaCl). The diluted chromatin was then precleared by BSA-blocked agarose G beads (GE Healthcare) for 1h. Subsequently 50µl material were set aside as input. For the IP 15µl agarose G beads were used per antibody per sample. The IP was incubated under agitation at 4°C over night and thereafter washed sequentially with different buffers: Low Salt Wash Buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), then High Salt Wash Buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), then LiCl Wash Buffer (0.25 M LiCl, 1 % Igepal, 1 % Sodium-Desoxycholat, 1 mM EDTA, 10 mM Tris-HCl pH 8.1), then twice at RT with TE (10 mM Tris-HCl pH 8, 1 mM EDTA pH 8). The immunoprecipitated chromatin was eluted from the beads with 100 µl Elution Buffer (2 % SDS, 200 mM NaHCO3) for 15 min at RT, twice. The Input sample was also diluted to the same volume with Elution Buffer. 500 mM NaCl were added for decrosslinking (45 °C over night). Finally, the proteins were digested by addition of 2 µl Proteinase K (Thermo Fisher Scientific) for 1 h at 37 °C, and DNA was purified using the MinElute Kit (QIAGEN 28006).
Libraries were generated using the Accel-NGS (TM) 2S Plus DNA Library Kit for Illumina platforms (SWI Swift Bioscience) and Accel-NGS (TM) 2S Indexing Kit (SWI Swift Bioscience) according to the manufacturer's guidelines. AmpureXP beads (Beckman Coulter) were used for the purification steps and the amplification step was performed with 15 cycles using the KAPA Hifi PCR kit (KK2101; Roche) according to published procedures (PMID: 26067602).
directional paired-end ChIP-Seq

treatment_protocol: Gametocytogenesis was induced by stressing the parasites through lowering the hematocrit and cultivation in partially spent medium. Asexual parasites were selectively inhibited by addition of N-acetyl-D-glucosamine, from day 0 to day 6 of gametocytogenesis. Gametocytes were enriched magnetically on a MACS CS column on day 3 and FACS sorted using GFP only or GFP and Mitrotracker Deep Red (as defined below) directly before nuclei were harvested. Asexual parasites were not sorted.

tag: parasite line

tag: sort strategy

value: GFP low, mitotracker

tag: Sex

value: male

tag: chip antibody


title: Hematopoietic progenitors, blf, 20hpf, rep3


title: Hematopoietic progenitors, blf;drl, 20hpf, rep1


title: D6F, H2B.Z, rep6

value: GFP high, mitotracker

value: female

value: anti-H2B.Z, Azizan et al. in preparation


title: Spleen, DKO, 2

city: Milan

description:
spleen.raw.counts.csv
73-57-3 S


title: Hematopoietic progenitors, blf, 20hpf, rep1


title: D6M, H3K9me3, rep2

value: anti-H3K9me3, Active Motif 39161


title: Aln, DKO/hA-I, 2

description:
axillary-lymph-nodes.raw.counts.csv
73-77-4 AL

source_name: Axillary lymph node

value: Axillary lymph node


title: Vav2Onc TSC rep4

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description:
Gene expression data from tumor stem cells
T.TSC ONCO-VAV2 887_(MoGene-1_0-st-v1)

hyb_protocol: Mouse Gene 1.0 ST arrays (Affymetrix) under standard conditions

scan_protocol: Standard Affymetrix protocol

data_processing: Upon microarray hybridization, the raw data was normalized with RMA using R (v.3.6.3).

source_name: Tumor stem cells from Vav2Onc mice

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 mg/sample) to generated labeled cRNA probes according to the manufacturer's instructions (Affymetrix).

growth_protocol: This experiment has been done with animals.

extract_protocol: RNeasy Micro Kit (QIAGEN, Catalog No. 74004) was used according to the manufacturer's instructions.

treatment_protocol: No treatment was applied to the animals except for DMBA-based carcinogenesis for the generation and isolation of tumor stem cells. Please refer to accompanying manuscript for protocol details.

tag: strain background

value: 6 months

tag: tissue/cell type

value: Stem cells from skin papillomas


title: WT TSC rep3

description:
Gene expression data from tumor stem cells
O.TSC WT 924_(MoGene-1_0-st-v1)

source_name: Tumor stem cells from WT mice

tag: genotype

value: WT


title: Spleen, DKO/hA-I, 3

description:
spleen.raw.counts.csv
73-57-2 S


title: D6M, H2A.Z, rep2

value: anti-H2A.Z, Petter et al. 2011


title: DKO SSC rep3

description:
Gene expression data from epidermal stem cells
L.DKO_J+K_(MoGene-1_0-st-v1)

source_name: Epidermal stem cells from DKO mice

value: 2.5 months

value: Stem cells from the epidermis


title: Aln, DKO/hA-I, 1

description:
axillary-lymph-nodes.raw.counts.csv
73-76-4 AL

value: DKO/hA-I


title: Aln, DKO/hA-I, 3

description:
axillary-lymph-nodes.raw.counts.csv
73-78-5 AL

value: normal laboratory diet


title: Spleen, DKO/hA-I, 1

description:
spleen.raw.counts.csv
73-55-13 S

value: Spleen

value: 30 weeks


title: D6F, H3K9me3, rep6


title: D6F, Input, rep6


title: Vav2Onc TSC rep3

description:
Gene expression data from tumor stem cells
S.TSC ONCO-VAV2 SC1_(MoGene-1_0-st-v1)


title: crlv_unstim_6h_N2_R1

value: control

value: medium


title: Vav2Onc TSC rep2

description:
Gene expression data from tumor stem cells
R.TSC ONCO-VAV2 889+1_(MoGene-1_0-st-v1)


title: D6M, H3K9me3, rep1

value: GFP low, mitotracker

value: male


title: D6F, H2A.Zac, rep6

value: GFP high, mitotracker

value: female

value: anti-H2A.Zac, Azizan et al. in preparation


title: WT TSC rep1

description:
Gene expression data from tumor stem cells
M.TSC WT SC1_(MoGene-1_0-st-v1)

value: 6 months


title: WT (DKO) SSC rep1

description:
Gene expression data from epidermal stem cells
G.WT_F+H_(MoGene-1_0-st-v1)

source_name: Epidermal stem cells from WT mice


title: D6M, H2A.Zac, rep1


title: WT TSC rep2

description:
Gene expression data from tumor stem cells
N.TSC WT SC2_(MoGene-1_0-st-v1)

value: Stem cells from skin papillomas


title: Vav2Onc SSC rep3

description:
Gene expression data from epidermal stem cells
F.ONCO-VAV2_F_(MoGene-1_0-st-v1)

source_name: Epidermal stem cells from Vav2Onc mice


title: Vav2Onc SSC rep2

description:
Gene expression data from epidermal stem cells
E.ONCO-VAV2_D+E_(MoGene-1_0-st-v1)


title: D6F, H2A.Z, rep6


title: DKO SSC rep2

description:
Gene expression data from epidermal stem cells
K.DKO_G+H_(MoGene-1_0-st-v1)

value: DKO


title: DKO SSC rep1

description:
Gene expression data from epidermal stem cells
J.DKO_D+I_(MoGene-1_0-st-v1)


title: WT TSC rep4

description:
Gene expression data from tumor stem cells
P.TSC WT 925_(MoGene-1_0-st-v1)

value: WT


title: Vav2Onc TSC rep1

description:
Gene expression data from tumor stem cells
Q.TSC ONCO-VAV2 888+1_(MoGene-1_0-st-v1)


title: PSC-KO-3

city: Tokyo

first: Masayuki

last: Tsukasaki

address: 7-3-1 Hongo Bukyo-ku

department: Department of Immunology  Graduate School of Medicine and Faculty of Medicine

data_processing:
cDNA and sequencing libraries were processed with FastQC (v0.1.1.8), TrimGalore (v0.6.4) and Kallisto (v0.46.0) using the mouse transcriptome index (mus musculus GRCm38.96).
Supplementary_files_format_and_content: Excel files include RPKM values for each sample

source_name: periosteal stem cells

extract_protocol:
Primary periosteal stem cells were collected by FACS sorting as described previously (Debnath et al., Nature 2018). In vitro osteoclastogenesis was performed as previously reported (Tsukasaki et al., JBMR 2017). Total RNA was extracted from periosteal steal stem cells and osteoclasts using the Maxwell 16 LEV simply RNA Tissue Kit (Promega) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Ion Torrent Proton protocols

tag: strain

value: FACS-sorted primary periosteal stem cells

value: 3-6 weeks old


title: PSC-KO-2


title: D6M, H2A.Z, rep1

value: anti-H2A.Z, Petter et al. 2011


title: Aln, DKO, 2

description:
axillary-lymph-nodes.raw.counts.csv
73-75-7 AL

value: Axillary lymph node

value: normal laboratory diet


title: PSC-KO-1


title: PSC-Control-2


title: D6F, H3K9me3, rep5

value: anti-H3K9me3, Active Motif 39161


title: Aln, DKO, 1

description:
axillary-lymph-nodes.raw.counts.csv
73-75-6 AL

value: 30 weeks


title: D6F, H2A.Zac, rep5


title: Aln, DKO, 3

description:
axillary-lymph-nodes.raw.counts.csv
73-75-8 AL


title: Osteoclast-KO-3

source_name: osteoclasts

value: In vitro cultured osteoclasts (72h after RANKL stimulation)

value: 11 weeks old


title: Osteoclast-KO-2


title: PSC-Control-3

extract_protocol:
Primary periosteal stem cells were collected by FACS sorting as described previously (Debnath et al., Nature 2018). In vitro osteoclastogenesis was performed as previously reported (Tsukasaki et al., Nat Metab 2020). Total RNA was extracted from periosteal steal stem cells and osteoclasts using the Maxwell 16 LEV simply RNA Tissue Kit (Promega) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Ion Torrent Proton protocols


title: D6M, Input, rep1

value: GFP low, mitotracker

value: male


title: Root, P415, low P, rep3 [LP_P415_3]

city: Montpellier

first: Christophe

last: Maurel

address: 2 place Pierre Viala

department: Water, signaling and hydraulic architecture

institute: Institute for Plant Sciences of Montpellier (IPSiM)

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp tool  (parameter: --qualified_quality_phred 20 --unqualified_percent_limit 50 –n_base_limit 10)
Trimmed sequence reads were mapped to B73_RefGen_v4, release 44 using hisat2
Read count extraction were performed using htseq-count (parameter: --mode union)
Assembly: Zea_mays.B73_RefGen_v4, release 44
Supplementary files format and content: Tab-separated text files include read count values for each sample
Supplementary files format and content: Tab-separated text files include FPKM values for each sample

organism: Zea mays

source_name: Root

extract_protocol:
RNA was harvested using innuPREP Plant RNA Kit (Analytik Jena AG, Jena, Germany).
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

value: Root

value: low P


title: Root, P415, low P, rep2 [LP_P415_2]


title: Root, P415, low P, rep1 [LP_P415_1]


title: Root, F7, low P, rep2 [LP_F7_2]


title: WT (DKO) SSC rep2

description:
Gene expression data from epidermal stem cells
H.WT_E+G_(MoGene-1_0-st-v1)

value: 2.5 months

value: Stem cells from the epidermis


title: Osteoclast-KO-1


title: WT (DKO) SSC rep3

description:
Gene expression data from epidermal stem cells
I.WT_D+I_(MoGene-1_0-st-v1)


title: Osteoclast-Control-3


title: D6F, Input, rep5

value: GFP high, mitotracker

value: female


title: PSC-Control-1

value: FACS-sorted primary periosteal stem cells


title: Vav2Onc SSC rep1

description:
Gene expression data from epidermal stem cells
D.ONCO-VAV2_C+G_(MoGene-1_0-st-v1)


title: WT (Vav2Onc) SSC rep3

description:
Gene expression data from epidermal stem cells
C.WT_C+E_(MoGene-1_0-st-v1)

value: WT


title: WT (Vav2Onc) SSC rep1

description:
Gene expression data from epidermal stem cells
A.WT_A+F_(MoGene-1_0-st-v1)


title: WT (Vav2Onc) SSC rep2

description:
Gene expression data from epidermal stem cells
B.WT_B+D_(MoGene-1_0-st-v1)


title: Root, F7, low P, rep3 [LP_F7_3]


title: Osteoclast-Control-1


title: Root, P024, low P, rep3 [LP_P024_3]


title: D6F, H2A.Z, rep5

value: anti-H2A.Z, Petter et al. 2011


title: Root, F7, low P, rep1 [LP_F7_1]