title: SS-T3-R22

city: New Delhi

first: Manoj

middle: K.

last: Sharma

state: Delhi

institute: Jawaharlal Nehru University

description:
Transcriptome
ICSV12012_NCBI_FPKM_processed_file   .xlsx

data_processing:
Low-quality reads with Phred score<30 were filtered
Adapter triming using cutadapt 1.8.1
ribosomal RNA sequences removal by aligning the reads with silva database using bowtie2 (2.2.9)
read alignment o the genome using Hisat2 program (version 2.0.5)
estimation of gene expression and transcript abundance using String_Tie program (version 1.3.3b)
pairwise differential expression analysis using cuffdiff
Genome_build: Sorghum bicolor BTx623 v3.1.1 downloaded from Phytozome database
Supplementary_files_format_and_content: FPKM values in excel format

organism: Sorghum bicolor

source_name: Stem Internode

growth_protocol: Seeds of Sorghum bicolor variety ICSV12012 were planted at ICAR - IARI, Pusa, New Delhi. For development stage samples, the seeds were directly sown into the prepared soil bed treated with nitrogen fertilizer. At three leaf stage, the plants were thinned. Weeding and watering was done at regular intervals.  For drought assay, 5-6 seeds were sown in a pot. At three leaf stage, plants were thinned so that only one healthy plant per pot was maintained.

extract_protocol:
Total RNA was isolated using a modified trizol method
Libraries were prepared using TruSeq® Stranded Total RNA kit using manufacturer’s instructions

treatment_protocol: Development samples were collected at four stages namely floral initiation, booting, milky stage and soft dough. For drought assay, at flag leaf stage, water was withheld and soil moisture was measured using Lutron PMS 175 soil moisture meter. Samples were harvested at Booting stage at three soil moisture readings which were ~13% (D1), ~7% (D2) and ~2% (D3).

value: Middle internode

tag: developmental stage/condition

value: Drought stage D3 ~2% soil moisture

tag: cultivar


title: TSM-3C+Y27632+ISRIB-3

status: Public on Dec 31 2023

type: SRA

city: Beijing

first: Yue

last: Wang

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

country: China

institute: Institute of zoology, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
OmicStudio
Sequence reads were trimmed for adaptor sequence/low-quality sequence using RSeQC 4.0.0.
Trimmed sequence reads were mapped to GRCh38.p7 using Hisat2 2.2.1.
Read count extraction and normalization were performed using Hisat2 2.2.1. and StringTie 2.1.6 with Fragments Per Kilobase Million value.
Assembly: GRCh38.p7
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: hTSC

growth_protocol: hTSCs are cultured in DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin,0.3% BSA, 1% ITS-X supplement, 1.5 mg/mL L-ascorbic acid, 50 ng/mL EGF, 2 mM CHIR99021, 1 mM SB431542, 0.5 mM A83-01, 0.0125% VPA, and 5 µM Y27632 in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using TRIzol (Invitrogen,15596018), and 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Invitrogen SuperScriptTM II Reverse Transcriptase following manufacturer's protocols.

treatment_protocol:
For the drug treatment, we cultured hTSCs in the medium contained 0.5 µM ISRIB and 10 µM Y27652, after removing CHIR99021, A83-01, SB431542 for 6 days.
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

tag: cell line

value: hTSC

tag: cell type

value: trophoblast stem cells

tag: treatment

value: drug treatment

tag: growth conditions

value: cultured in the medium without CHIR99021, A83-01, SB431542, and supplemented with 0.5 µm ISRIB  and 10 µM Y27632

tag: time

value: Day 6


title: CD11B-701_Well_D03

city: Ede

first: Alphonsus

middle: Chinedu

last: Ugwu

state: osun state

address: redeemers' university ede osun state

department: Biological Sciences

country: Nigeria

institute: Africa Centre of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s 6 University, Ede, Osun State, Nigeria

data_processing:
Sequence data were analysed using the Seven Bridges Genomics bioinformatics platform (BD: Precise Whole Transcriptome Assay Analysis Pipeline v2.0). This pipeline performs all required steps to demultiplex, align, and quantitate sequencing reads from BD™ Precise Whole Transcriptome Assay. After performing a quality control assessment using FastQC, the pipeline filters and demultiplexes sequencing reads based on the sequence of the 8 base sample barcode. It aligns reads from each sample to the transcriptome using STAR, with feature counting by the union rules of HTSeq-count. The initial quantification is performed by counting the unique molecular indices (MI) mapped to each feature. Lastly, the pipeline uses two error correction algorithms to remove MI errors. In brief, MI errors that are derived from sequencing base calls and PCR substitution errors are identified and adjusted to a single MI barcode using Recursive Substitution Error Correction™ (RSEC). Subsequently, MI errors that are derived from library preparation steps or sequencing base deletion errors are adjusted using Distribution-Based Error Correction™ (DBEC).
A cell was considered to be infected if there was at least one GFP sequence read count. This information was then used to define the groups to compare in EdgeR. Differential gene expression was measured between infected and uninfected cells in each subset (Adjusted p-value less than 0.05).
Precise WTA Sample Demultiplexing:Paired-end reads are demultiplexed per well based on the sequence of the sample index. This sample index is found in the first 8 bases of Read 01. The Molecular Index is found in Read 01, in positions 8 to 16. The demultiplexing process also includes a structure filtering step. After filtering, the final step in this process stores the Molecular Index in the demultiplexed FASTQ files by appending the index to the sequence headers of Read 02 FASTQ files. The Read 02s from each well are trimmed by Flexbar to remove any Illumina adapter contaminants and mapped to the reference genome using STAR.
Precise WTA Alignment Quantification: After Read 02s are aligned using STAR, the alignments are assigned to gene counts using a custom implementation of HTSeq-count. The number of reads mapping to each gene is generated in the DBEC Read Mapping Report. The unique counts for molecular indices are calculated in the DBEC Molecular Index Mapping Report
Genome_build: mm9
Supplementary_files_format_and_content: text document (after removal of Molecular indices error using Recursive Substitution Error Correction™ (RSEC) and Distribution-Based Error Correction™ (DBEC))

organism: Mus musculus

source_name: Bone marrow derived APC

growth_protocol: BM derived cells were generated by incubating bone marrow stem cells with growth factor (GM-CSF/ IL-4) for 6 days in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10 % foetal calf serum (FCS), 100 U penicillin/ml, 0.1 mg streptomycin/ml and 50 M 2-mercaptoethanol. Differentiated cells were harvested and sorted into the three BM geoups by flow cytometry before infection with LCMV or stimulation with poly (I:C).

extract_protocol:
The cells are collected in WTA single cell encoding plate, RNA secondary structure is done at 65C for 3 minutes (hold at 4C), mastermix containing BD customised RT enzymes is added (PN 650000041) and run at 42C for 30 minutes, heat inactivated at 80C for 5 minutes before holding at 4C. The samples is pooled and purify before library prep.
Libraries of the cellular RNA were made using the BD WTA single cell kit and sequenced using MiSeq V2 from Illumina (BM-DC, BM-M, DN).

treatment_protocol: Sorted CD11c+MHC class II+ bone marrow derived cell populations (dendritic cells [BMDC], macrophages [BM-M], double negative cells [DN]) were infected with LCMV clone 13 expressing GFP, as previously described for 12 and 48hr for single cell (from the 12 h culture) sorting into customised BD WTA single cell encoding plates for RNA extraction and reverse transcription (primary infection) according to manufacturer’s instructions (PN 910000014 Rev. 03). Furthermore, a subset of infected cells (from the 48 h culture) were stimulated with 100 µg poly (I:C)/ml and incubated for another 6hr before single cell sorting as above.

value: Bone marrow derived APC

tag: strain

value: 12hr infection with LCMV Cl 13


title: SS-T3-R11

country: India

tag: tissue


title: TSM-3C+Y27632+ISRIB-2


title: TSM-1

value: WT

value: none (original medium)


title: TSM-3C+Y27632+ISRIB-1


title: CD11B-701_Well_D02


title: SS-T2-R21

value: Drought stage D2 ~7% soil moisture


title: Nkx2 1/mKO2+ cells Control day10 rep1

city: Bruxelles

first: Sabine

last: Costagliola

address: 808 route de lennik

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

library_source: genomic

data_processing:
For main steps of pre-processing and mapping of ATACseq data, a local installation of Galaxy platform was used (use.galaxu.eu; Afgan et al 2018). Briefly, adapter sequences were removed with Trim Galore, using default parameters. ATACseq paired-end reads were  aligned to mouse genome Grcm38/mm10 with Bowtie2 (v.2.3.4.3), modifying default parameters to include fragments of up 1000bp, allowing dovetailing and using a “very sensitive option” preset. Subsequently, mitochondrial genes, bad quality mapped sequences and PCR  duplicates were removed. Peak calling was performed for each sample using MACS2(v.2.1.1.20160309.6), with parameters setting of -q 0.05 and -- shift 0. Peaks from all samples were merged for downstream analysis. Scaling of bam files generated by MACS2 were performed using BAMscale and used for visualization of data tracks with Integrative Genomics Viewer  (IGV).
Genome_build: Grcm38/mm10
Supplementary_files_format_and_content: Coverage ATAC-seq sample (bigwig format)

molecule: genomic DNA

source_name: mESC-derived differentiated cells

extract_protocol:
Trypsin based dissociation followed by FACS sorting of 50000 cells
Nextera DNA sample preparation kit, Illumina

value: Nkx2-1-T2a-mKO2 reporter mESC line

tag: time point

value: day 10


title: Muscle-invasive bladder cancer 66401

type: RNA

city: Bangor

first: Tim

last: Smith

address: Dean Street

department: School of Computer Science and Engineering

country: United Kingdom

institute: University of Bangor

description: Muscle-invasive bladder cancer

hyb_protocol: Sample hybridisation on Clariom S arrays was carried out by Yourgene Health (Manchester, UK). Batches of CEL files were GC SST (Signal Space Transformation with probe Guanine Cytosine Count Correction) RNA normalised using Affymetrix Array Power Tools. (https://www.thermofisher.com/uk/en/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-network.html)

scan_protocol: standard Affymetrix protocol

data_processing: The log2-summarised gene level expression values generated were batch-corrected using the ComBat function from the Bioconductor package sva.

label: biotin

source_name: Anonymised

label_protocol: RNA extracted from both sample cohorts were subject to Clariom S analysis. RNA (8 ng/µl in a 9 µl volume) was prepared for gene expression arrays with the Clariom S pico HT human assay (Thermo Fisher Scientific).

extract_protocol: Two 10µm sections from FFPE bladder cancer embodied blocks. RNA was extracted from the two 10 µm sections using the Roche High Pure FFPET RNA isolation kit. RNA yield was determined on Qubit fluorometer (Invitrogen, Paisley, UK).

tag: condition

value: Muscle-invasive bladder cancer


title: SS-T2-R11


title: Muscle-invasive bladder cancer 66501

description: Muscle-invasive bladder cancer


title: MCG076, shADAR1

city: LA JOLLA

first: QINGFEI

last: JIANG

state: CA

address: 2880 TORREY PINES SCENIC DR

country: USA

institute: UNIVERSITY OF CALIFORNIA SAN DIEGO

description: T-ALL leukemia initating cells transduced with ADAR1 knockdown lentivirus

data_processing:
Sequencing reads were trimmed with Trimmomatic and aligned to the human genome (GRCh38.p12) using the STAR aligner.
Read quantification was performed with RSEM and the Gencode release 29 annotation
The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis.
In brief, lowly expressed genes—those not having counts per million (cpm) ³ 5 in at least 80 of the samples—were filtered out and then trimmed mean of M-values (TMM) normalization was applied.
The experimental design was modeled upon risk and treatment. The voom method was employed to model the mean-variance relationship in the log-cpm values weighted for inter-subject correlations in repeated measures of patients, after which lmFit was used to fit per-gene linear models and empirical Bayes moderation was applied with the eBayes function. Significance was defined by using an adjusted p-value cut-off of 0.05 after multiple testing correction using a moderated t-statistic in limma and a minimum absolute log-fold-change threshold of 0.
Human Alu and non-Alu RNA editing sites were accurately identified by RNA editing analysis (https://github.com/ucsd-ccbb/MPN_atlas_methods/blob/master/RNAEditingAnalysis/scripts/RNA%20Editing%20Analysis.md)
Assembly: GRCh38.p12
Supplementary files format and content: Primary expression output from RSEM, including gene id, transcript id, expected count, TPM, and FPKM.
Supplementary files format and content: TMM Normalized log cpm values of gene expressions by edgeR
Supplementary files format and content: Human Alu and non-Alu RNA editing sites by RNA editing analysis

source_name: Blood

extract_protocol:
Rneasy Micro Kit protocol was used to extract RNA from all samples
Samples with RNA integrity numbers (RIN) ≥7 will be processed using SMART cDNA synthesis and NEBNext paired-end DNA Sample Prep Kit to prepare libraries.

value: Blood

value: patient sample

value: TALL Leukemia initating cells

tag: disease state

value: T-ALL


title: SS-T1-R21

value: Middle internode

value: Drought stage D1 ~13% soil moisture


title: Muscle-invasive bladder cancer 1201

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_C12


title: Muscle-invasive bladder cancer 66101

description: Muscle-invasive bladder cancer


title: SS-T1-R11


title: CD11B-701_Well_C11


title: MCG070, shADAR1


title: Muscle-invasive bladder cancer 6417

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 65506

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6425

description: Muscle-invasive bladder cancer


title: MCG076, shCTRL

description: T-ALL leukemia initating cells transduced with scramble control lentivirus

value: shCTRL


title: CD11B-701_Well_C10


title: SS-SD-R21

value: Soft dough


title: MCG070, shCTRL


title: CD11B-701_Well_D04


title: CD11B-701_Well_D01


title: SS-SD-R11


title: Muscle-invasive bladder cancer 65505

description: Muscle-invasive bladder cancer


title: SS-MS-R21

value: Milky stage


title: Muscle-invasive bladder cancer 13508

description: Muscle-invasive bladder cancer


title: DC10T20_3

city: Chengdu

first: Linhao

last: Zhang

state: Sichuan

address: No. 37 Guoxue Lane

department: Gastroenterology

institute: West China Hospital, Sichuan University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. 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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: HIBEpiC

growth_protocol: HIBEpiC cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Trizol (Thermo Scientific) following manufacturer's protocols. Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

treatment_protocol: HIBEpiC cells were cultured in vitro. Treatments were vehicle, 20 ng/mL of TGF-β (T20), combination of 10μM of celecoxib plus 20 ng/mL of TGF-β (C10+T20), or combination of 10μM of 2,5-dimethyl-celecoxib plus 20 ng/mL of TGF-β (DC10+T20). Vehicle: HIBEpiC cells were cultured in RPMI 1640 medium with 0.5% Bovine Serum Albumin (BSA) and 0.1% DMSO for 28 hours. T20: HIBEpiC cells were cultured in RPMI 1640 medium with 0.5% BSA and 0.1% DMSO for 4 hours, and then the TGF-β were added to the final concentration of 20 ng/mL for further 24 hours incubation. C10+T20: HIBEpiC cells were cultured in RPMI 1640 medium with 0.5% BSA and 10μM of celecoxib (final concentration of DMSO: 0.1%) for 4 hours, and then the TGF-β were added to the final concentration of 20 ng/mL for further 24 hours incubation. DC10+T20: HIBEpiC cells were cultured in RPMI 1640 medium with 0.5% BSA and 10μM of 2,5-dimethyl-celecoxib (final concentration of DMSO: 0.1%) for 4 hours, and then the TGF-β were added to the final concentration of 20 ng/mL for further 24 hours incubation. The cell experiments were performed in triplicate. Then, the cells were harvested for NGS.

value: HIBEpiC

value: human intrahepatic biliary epithelial cell line

tag: genotype

value: combination of 10uM of 2,5-dimethyl-celecoxib plus 20 ng/mL of TGF-beta (0.1% DMSO)


title: 18minGW8C

city: BeiJing

first: hao

last: dong

address: Datun Rd

institute: ibp

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: hg19
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Visium spatial

source_name: spinal cord

extract_protocol:
Freshly collected tissue processed as 10x protocal
Library was performed according to the single cell 3’ v2,v3 protocol, and Visium protocal of 10x Genomics.

value: spinal cord


title: CD11B-701_Well_C08

value: Bone marrow derived APC

value: 12hr infection with LCMV Cl 13


title: DC10T20_2

value: WT


title: SS-MS-R11


title: Muscle-invasive bladder cancer 65502

description: Muscle-invasive bladder cancer

value: Muscle-invasive bladder cancer


title: CD11B-701_Well_C06


title: SS-B-R22

value: Booting


title: C10T20_3

value: combination of 10uM of celecoxib plus 20 ng/mL of TGF-beta (0.1% DMSO)


title: DC10T20_1


title: CD11B-701_Well_C09


title: C10T20_2


title: SS-FI-R22

value: Floral Initiation


title: Muscle-invasive bladder cancer 65401

description: Muscle-invasive bladder cancer


title: C10T20_1


title: CD11B-701_Well_C04


title: CD11B-701_Well_C03


title: Muscle-invasive bladder cancer 64604

description: Muscle-invasive bladder cancer


title: SS-B-R12


title: T20_2

value: 20 ng/mL of TGF-beta (0.1% DMSO)


title: Muscle-invasive bladder cancer 64601

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 64602

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_C07


title: Muscle-invasive bladder cancer 65101

description: Muscle-invasive bladder cancer


title: SS-FI-R12

value: Middle internode


title: CD11B-701_Well_C01


title: Muscle-invasive bladder cancer 65501

description: Muscle-invasive bladder cancer


title: T20_3


title: CD11B-701_Well_C02


title: T20_1


title: CD11B-701_Well_C05


title: Muscle-invasive bladder cancer 64503

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_B12


title: Muscle-invasive bladder cancer 64502

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 65504

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_B11


title: Vehicle3

value: Vehicle (0.1% DMSO)


title: Vehicle2


title: CD11B-701_Well_B09


title: CD11B-701_Well_B10


title: Muscle-invasive bladder cancer 64501

description: Muscle-invasive bladder cancer


title: JQ1-treatment MDA-MB-231 input rep2

city: Xia Men

first: Xiao

last: Lu

address: Xiang'an south road

institute: Xiamen university

data_processing:
MeRIP and input sequencing data were sent to Cutadapt (v2.5) to remove low quality reads and adaptor sequence contaminants under default parameters.
Remaining reads were then aligned to human Ensemble genome GRCh38 using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”.
m6A peaks were identified using exomePeak R package (v2.13.2)　with PEAK_CUTOFF_PVALUE=0.05, PEAK_CUTOFF_FDR=NA, FRAGMENT_LENGTH=200 parameters.
Differential m6A peaks were identified using exomePeak R package (v2.13.2) with FDR<0.05.
The expression of gene transcripts was quantified using featurecount (v1.6.3), and differential gene expression analysis was conducted using DESeq2 R package (1.18.1).
Assembly: hg38
Supplementary files format and content: bw files include m6A peaks and genes expression

growth_protocol: MDA-MB-231 cells infected by the indicated lentiviruses were maintained in DMEM (Gibco) supplemented with 10% FBS. Cells were maintained at 37°C in a saturated humidity atmosphere containing 95% air and 5% CO2.

extract_protocol:
Total RNA was isolated from samples with TRIzol reagents following the manufacturer’s instructions.
Poly(A)+ RNAs were purified using Dynabeads mRNA purification kit, followed by fragmentation and immunoprecipitation with anti-m6A antibody in IP buffer (10 mM Tris-HCl, pH 7.4, 150 mM NaCl, 0.1% NP-40) for 2 h at 4°C. The m6A-IP mixture was then incubated with Dynabeads protein A for an additional 2 h at 4°C. The bound RNA was eluted by competition with N6-methyladenosine and purified using an RNA cleanup kit.

treatment_protocol: m6A methylome in i in MDA-MB-231 cells treated with 0.5 μM JQ1 for 24 hours.

value: breast cancer

value: 0.5 uM JQ1


title: CD11B-701_Well_B08


title: Vehicle1


title: Muscle-invasive bladder cancer 64408

description: Muscle-invasive bladder cancer


title: JQ1-treatment MDA-MB-231 input rep1


title: Muscle-invasive bladder cancer 64409

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_B05


title: JQ1-treatment MDA-MB-231 RIP rep1


title: CD11B-701_Well_B04


title: CD11B-701_Well_B06


title: CTRL MDA-MB-231 input rep2

value: DMSO


title: CTRL MDA-MB-231 input rep1


title: VICs, Calcific area-3

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

country: Japan

institute: Ehime University Graduate School of Medicine

hyb_protocol: 7.5 µg fragmented and labeled cRNA were hybridized for 16h at 45℃ on Human Genome U219 Array Strip. Array Strip was washed and stained in the GeneAtlas fluidics station.

scan_protocol: Array Strip was scanned in the GeneAtlas imaging station.

data_processing:
The robust multichip average (RMA) method was used background correction and normalization.
GeneSpring GX 14.9.1 software computed normalized signal intensity (log2).

label: Biotin

source_name: Calcific area

label_protocol: 10 ng of total RNA was labeled using a GeneAtlas 3'IVT Express Kit Assay (Affymetrix) according to the manufacturer's instructions.

growth_protocol: Cells were incubated under 10% CO2 and 2% oxygen concentrations at 37℃.

extract_protocol: Extraction of total RNA was performed with the use of ISOGEN II according to the manufacturer's instructions.

treatment_protocol: Cells were derived from non-calcific or calcific areas in calcific aortic valves.

tag: individual

value: donor 3

value: calcific aortic valve stenosis (CAVS) donor with calcification

value: Valve interstitial cells


title: Muscle-invasive bladder cancer 65402

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 64407

description: Muscle-invasive bladder cancer


title: VICs, Non calcific area-3

source_name: Non calcific area

value: non-calcific areas in calcific aortic valves


title: CTRL MDA-MB-231 RIP rep2


title: CD11B-701_Well_B07

value: Bone marrow derived APC


title: CD11B-701_Well_B02

value: 12hr infection with LCMV Cl 13


title: Muscle-invasive bladder cancer 64406

description: Muscle-invasive bladder cancer


title: VICs, Non calcific area-2

value: donor 2


title: CTRL MDA-MB-231 RIP rep1

value: WT


title: Muscle-invasive bladder cancer 64405

description: Muscle-invasive bladder cancer

value: Muscle-invasive bladder cancer


title: VICs, Calcific area-2

value: calcific areas in calcific aortic valves


title: VICs, Calcific area-1

value: donor 1


title: Muscle-invasive bladder cancer 64404

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 64402

description: Muscle-invasive bladder cancer


title: JQ1-treatment MDA-MB-231 RIP rep2


title: CD11B-701_Well_B03


title: Muscle-invasive bladder cancer 64401

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_B01


title: VICs, Non calcific area-1


title: CD11B-701_Well_A12

value: 12hr treatment with Phosphate buffer saline (PBS)


title: NC1

city: JiNan

first: Shu

address: 440 Jiyan Road

department: Department of Gastroenterology, Shandong Cancer Hospital and Institute

institute: Shandong First Medical University and Shandong Academy of Medical Sciences

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38
Supplementary files format and content: fpkm.txt

source_name: gastric cancer tissue

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: gastric cancer tissue

value: untreated


title: Muscle-invasive bladder cancer 64201

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_A11


title: FA4


title: CD11B-701_Well_A10


title: FA1


title: NC4


title: CD11B-701_Well_A08


title: CD11B-701_Well_A09


title: Muscle-invasive bladder cancer 64202

description: Muscle-invasive bladder cancer


title: sTL-CMs_Rep1

city: Shanghai

first: Bin

last: Li

address: Jinzun Road

institute: Shanghai jiaotong University

description: treated

data_processing:
Hi-C reads were mapped to the mm10 genome and filtered using the hiclib pipeline (https://bitbucket.org/mirnylab/hiclib) as described previously (Crane et al.).
The mapped Hi-C fragments of replicates were combined and converted into cooler format using the cooler package (https://github.com/mirnylab/cooler, Abdennur & Mirny, 2020).
Assembly: mm10
Supplementary files format and content: cool

source_name: cardiomyocytes

extract_protocol:
Cultured nTL-CMs and sTL-CMs at Day30 were collected and processed for Hi-C.
Hi-C libraries for normal and short telomere hiPSC-CM were constructed with previously described in situ Hi-C protocols with minor modifications4. Cells were fixed with 0.92 mL of 1% v/v formaldehyde at RT for 10 min. Next, 0.08mL of 2.5 M glycine was added. The samples were incubated at RT for 5 min and on ice for at least 15 min to quench crosslinking completely. The fixed samples were collected by centrifuging and then lysed with 1 mL of ice-cold lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630) with protease inhibitors subsequently. The samples were incubated on ice for 30 min and centrifuged for 5 min at 3,000 ×g at 4°C to collect the nuclei. The nuclear pellets were washed once with NEBuffer 3.1, then resuspended in 20 μL of 10× NEBuffer 3.1, 140 μL of ddH2O, and 40 μL of 0.5% SDS; and then incubated at 65°C for 5 min to open up chromatin. Next, 22 μL of 10% Triton X-100 (Sigma) was added before incubation at 37°C for 15 min to quench SDS. 5 μL of 10× NEBuffer 3.1, 15 μL of ddH2O, and 8 μL (400 U) of DpnII (NEB) were added to the samples to digest chromatin. Digestion was performed overnight at 37°C on a thermomixer with interval shaking. The samples were incubated at 65°C for 20 min to inactivate the restriction enzyme. To fill the restriction overhangs, 60 μL of fill-in mix (37.5 μL of 0.4 mM biotin-14-dATP (Life Technologies), 1.5 μL of 10 mM dCTP/dGTP/dTTP, 10 μL of 5 U/μL Klenow, 6 μL of 10× NEBuffer 3.1, and 2 μL of Milli-Q water) was added to the reaction, and the samples were incubated at 25°C for 4 h. Ligation mix (498 μL of water, 240 μL of 5× T4 DNA ligase buffer (Invitrogen), 100 μL of 10% Triton X-100, 12 μL of 10 mg/mL BSA., and 50 μL of 1 U/μL T4 DNA ligase (Invitrogen) were then added into the samples. The samples were incubated at 16°C for exactly 4 h. After ligation, the samples were centrifuged and then resuspended in 500 μL of 1× NEBuffer. To reverse crosslinking, 30 μL of 20 mg/mL proteinase K (NEB) and 50 μL of 10% SDS (Sigma) were added to the samples, and the samples were then incubated at 65°C overnight. Phenol-chloroform extraction and ethanol precipitation were performed. The purified DNA was sheared with a Covaris M220. End repair of DNA fragments and ligation with adapters were performed using the End Repair/dA-Tailing Module (NEB) and the Ligation Module (NEB) according to the product manuals after DNA shearing. To purify biotinylated DNA fragments, Dynabeads MyOne Streptavidin T1 beads (Life Technologies) were used to bind the biotinylated DNA. The beads were washed twice with 500 μL of 1× TWB on a Thermomixer at 55°C for 2 min with mixing and resuspended in 50 μL of Milli-Q water. The samples were amplified with Phusion High-Fidelity DNA Polymerase (Thermo Fisher) for 6-8 cycles. AMPure XP beads (Beckman Coulter) were agopted for size selection.

value: hiPSCs-derived cardiomyocytes

value: BIBR


title: sTL-CMs_Rep2

description: treated


title: nTL-CMs_Rep2

description: Control


title: Muscle-invasive bladder cancer 64106

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 64101

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 64102

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 62603

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 63401

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 64104

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_A06


title: nTL-CMs_Rep1

description: Control


title: Muscle-invasive bladder cancer 64103

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_A07


title: LNCaP abl

type: genomic

city: Alcala de Henares

first: Santiago

last: Ropero

state: Madrid

address: Medical School

department: Department of System Biology

country: Spain

institute: University of Alcala

description: Prostate Cancer Cell line

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software

label: Cy5 and Cy3

source_name: LNCaP

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine at 37o C under 5% CO2

extract_protocol: Genomic DNA isolation was performed according to a standard phenol/chloroform/isoamyl alcohol extraction protocol, after a proteinase K digestion.

tag: gender

value: Male


title: CD11B-701_Well_A05


title: Parthenolide-3 [P3]

city: HEFEI

first: wang

last: hiuru

state: State...

address: NO 17 Lujiang ROAD , HEFEI

department: The First Affiliated Hospital of USTC

institute: USTC

data_processing:
After quality filtering according to the FastQC, reads were trimmed using a Fastq Quality Trimmer, and mapped to the reference human genome GRCh38 using Top Hat and Bowtie
The abundance of Ref Seq genes was estimated using featureCounts. Differentially expressed genes between DMSO-treated and DMSO-treated  MGC-823 cells were identified using Deseq2.
Assembly: GRCh38
Supplementary files format and content: EXCEL files include FPKM values for Samples

growth_protocol: MGC 803 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37

extract_protocol:
RNA was harvested using Trizol.
Libraries were sequenced on an Illumina NovaSeq6000 system (Illumina, San Diego, CA)

treatment_protocol: MGC-803 cells treated with DMSO or Parthenolide (40 μM) for 24 h were collected.

value: Human gastric cancer

value: Parthenolide


title: Muscle-invasive bladder cancer 62602

description: Muscle-invasive bladder cancer


title: DU145

description: Prostate Cancer Cell line

source_name: ATCC


title: LNCaP

description: Prostate Cancer Cell line


title: Parthenolide-2 [P2]


title: Muscle-invasive bladder cancer 62601

description: Muscle-invasive bladder cancer


title: PC3

description: Prostate Cancer Cell line


title: CD11B-701_Well_A03


title: Primary GBM 6

city: Bangalore

first: Ruchi

last: Jain

state: Karnataka

address: C V Raman Road

department: Molecular Reproduction Development and Genetics

institute: Indian Institute of Science

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: NOT PROVIDED; REQUESTED

label: cy3, cy5

source_name: Unpaired, Primary GBM

label_protocol: standard Illumina protocol

extract_protocol: Samples extracted using Qiagen Genomic DNA Kit according to manufacturer's instructions.

tag: pair status

value: Unpaired

value: Primary GBM


title: Muscle-invasive bladder cancer 62502

description: Muscle-invasive bladder cancer


title: Control-2 [C2]

value: DMSO


title: Control-1 [C1]


title: MHC-P-701_Well_H12

value: Bone marrow derived APC

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: Primary GBM 5


title: Muscle-invasive bladder cancer 62501

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_H11


title: HepG2, SsA 4 h, rep3

city: Quzhou

first: Si-wei

address: No.100 Minjiang Road

institute: Quzhou people's hospital

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the homo sapiens genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: The cells were cultured in DMEM supplemented with 10% v/v fetal bovine serum and 100 U/mL penicillin/streptomycin at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

treatment_protocol: The cells were treated with DMSO or Saikosaponin A (20 μM) for 4 h.

value: Human hepatoellular carcinomas

value: Saikosaponin A


title: CD11B-701_Well_A04


title: Recurrent 8

source_name: Unpaired, Recurrent GBM

value: Recurrent GBM


title: MHC-P-701_Well_H10


title: Muscle-invasive bladder cancer 62102

description: Muscle-invasive bladder cancer

value: Muscle-invasive bladder cancer


title: Recurrent 7


title: HepG2, SsA 4 h, rep2


title: MHC-P-701_Well_H09


title: Muscle-invasive bladder cancer 61501

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 61201

description: Muscle-invasive bladder cancer


title: Primary GBM 1


title: Control-3 [C3]


title: Muscle-invasive bladder cancer 61101

description: Muscle-invasive bladder cancer


title: HepG2, DMSO 4 h, rep3


title: CD11B-701_Well_A02

value: 12hr treatment with Phosphate buffer saline (PBS)


title: Recurrent 6


title: Muscle-invasive bladder cancer 61102

description: Muscle-invasive bladder cancer


title: CD11B-701_Well_A01


title: Primary GBM 3


title: Muscle-invasive bladder cancer 59608

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 60402

description: Muscle-invasive bladder cancer


title: HepG2, DMSO 4 h, rep2


title: MHC-P-701_Well_H08


title: Parthenolide-1 [P1]


title: Muscle-invasive bladder cancer 59601

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_H07


title: HepG2, DMSO 4 h, rep1


title: 091-P18

city: Doha

first: nico

last: marr

email: nico_marr@outlook.com, tkhan@sidra.org

address: AL RAYYAN

department: Research

country: Qatar

institute: Sidra Medicine

data_processing:
Raw RNA-seq reads were aligned with UCSC human genome assembly version hg38, with STAR aligner (Dobin et al., 2013).
HTseq-count (Anders et al., 2015) was used to count the reads mapping to each gene feature. Downstream analysis and heatmap generation were performed with an in-house script in R [R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.], with DESEq2 (Love et al., 2014), and ComplexHeatmap (Gu et al., 2016)
Downstream analysis and heatmap generation were performed with an in-house script in R [R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.], with DESEq2 (Love et al., 2014), and ComplexHeatmap (Gu et al., 2016)
Assembly: hg38
Supplementary files format and content: Tab Separated File
Supplementary files format and content: quantile normalized count file

source_name: peripheral blood

extract_protocol: Peripheral whole blood samples were preserved with Tempus stabilization reagent. RNA was isolated using the Tempus™ Spin RNA Isolation Kit, Invitrogen, by folllowign the manufucterer's instructions.

value: Patient

value: female

value: peripheral blood

value: PBMCs

value: PIK3CD deficiency


title: Primary GBM 4


title: MHC-P-701_Well_H05


title: HepG2, SsA 4 h, rep1


title: MHC-P-701_Well_H06


title: Muscle-invasive bladder cancer 59507

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_H04


title: MHC-P-701_Well_H03


title: Pair V Recurrent GBM

source_name: Paired, Recurrent GBM

value: Paired


title: Pair V Primary GBM

source_name: Paired, Primary GBM


title: Muscle-invasive bladder cancer 59504

description: Muscle-invasive bladder cancer


title: 091-F09

value: Father of patient

value: male

value: control


title: MHC-P-701_Well_H02

source_name: Bone marrow derived APC


title: Muscle-invasive bladder cancer 59502

description: Muscle-invasive bladder cancer


title: Pair II Recurrent GBM


title: Primary GBM 2

value: Unpaired

value: Primary GBM


title: Muscle-invasive bladder cancer 59102

description: Muscle-invasive bladder cancer


title: Sarcoma cell line E15

city: Goyang

first: HYE JIN

last: YOU

email: hjyou@ncc.re.kr, hyejin.you@gmail.com

state: Gyeonggi

address: 323 Ilsan-ro, Ilsandong-gu

department: Cancer Biology

country: South Korea

institute: National Cancer Center

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCh38_NCBI_109.20200522
Supplementary files format and content: Excel file includes FPKM and count values for each Sample

source_name: UPS

extract_protocol:
RNA was harvested using Trizol reagent. The TruSeq Stranded mRNA Library Prep Kit was used with 1 ug of total RNA to construct the sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: UPS

value: Sarcoma cell

value: Control


title: Recurrent 5

value: Recurrent GBM


title: Pair IV Primary GBM


title: Sarcoma cell line E14


title: MHC-P-701_Well_H01

value: Bone marrow derived APC

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: Sarcoma cell line E13


title: Pair III Recurrent GBM


title: Muscle-invasive bladder cancer 59101

description: Muscle-invasive bladder cancer

source_name: Anonymised

value: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 55603

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_G11


title: Pair I Primary GBM


title: MHC-P-701_Well_G10


title: PA_in_BC_SN_FeHigh_2

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the P. aeruginosa PAO1 genome sequence (Stover et al. 2000) from the Pseudomonas Genome Database (Winsor et al. 2016) using the CLC Genomics Workbench v7.0 (QIAGEN CLC bio, Aarhus, DenmarkCLC bio) allowing up to 2 mismatches per read.
RNA-Seq count data were subsequently analyzed with the Bioconductor package DESeq2 version 1.6.3 (Love et al. 2014) in the R environment version 3.1.2 (R Development Core Team 2014).
Assembly: P. aeruginosa PAO1 genome sequence (Stover et al. 2000)
Supplementary files format and content: txt files include expression values, unique and total gene reads, RPKM and mean values for each sample

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 grown in 70% CAA medium and 30% Burkholderia cenocepacia H111 supernatant_high iron_replicate 2

growth_protocol: We first prepared two starter cultures of PA by inoculating 20 ml LB medium with 200 µl of a PA overnight culture in 100 ml Erlenmeyer. These starter cultures were then incubated at 37°C in an orbital shaker at 220 rpm. Once the cultures reached the late exponential growth phase, we adjusted their OD600 to 1, as described above, and used one starter culture each to either inoculate the iron limited or the iron rich replicates. The experimental cultures consisted of 200 ml media in one-liter Erlenmeyer flasks, inoculated to an initial density of OD600 = 1x10-2. The growth of the PAO1 cultures was monitored with a spectrophotometer. The cultures were harvested for total RNA isolation at mid to late exponential phase.

extract_protocol:
The cultures were transferred onto ice. We then distributed them to 50 ml tubes (Greiner) containing 5 ml ice cold stop solution (10% phenol buffered with Tris-HCl to pH8 (Sigma-Aldrich, Switzerland) and 90% ethanol). The suspension was mixed by manual inversion of tubes and centrifuged at 4°C, for 5 minutes at 9000 rpm. The supernatant was discarded, while the cell pellet was flash-frozen in liquid nitrogen and stored at -80°C. RNA was harvested using hot phenol protocol (Pessi et al 2007). Afterwards cDNA was produced. The supernatant treatments were each mixed with CAA and independently generated supernatants. So we used three biological repliactes of each supernatant to generate three independend biological replicates of our PAO1 culture for RNA isolation.
RNA libraries were prepared using Encore Complete Prokaryotic RNA-Seq DR Muliplex System

treatment_protocol: We generated 3 replicates per treatment. PAO1 was grown in either 100% fresh CAA medium only, in a mixture of 70% fresh CAA medium with 30% PAO1 supernatent or in 70% fresh CAA medium with 30% Burkholderia cenocepacia H111 supernatent. These treatments were each conducted under iron limited and iron rich conditions.

value: wt

tag: growth phase

value: planktonic cells, mid to late exponential phase

tag: medium

tag: iron availability

value: high, 20 uM FeCl3 (no Transferrin)


title: PA_in_BC_SN_FeHigh_1

source_name: PAO1 grown in 70% CAA medium and 30% Burkholderia cenocepacia H111 supernatant_high iron_replicate 1


title: Pair III Primary GBM


title: Sarcoma cell line E12

tag: cell line


title: Pair II Primary GBM


title: MHC-P-701_Well_G12

city: Ede

first: Alphonsus

address: redeemers' university ede osun state

institute: Africa Centre of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s 6 University, Ede, Osun State, Nigeria

data_processing:
Sequence data were analysed using the Seven Bridges Genomics bioinformatics platform (BD: Precise Whole Transcriptome Assay Analysis Pipeline v2.0). This pipeline performs all required steps to demultiplex, align, and quantitate sequencing reads from BD™ Precise Whole Transcriptome Assay. After performing a quality control assessment using FastQC, the pipeline filters and demultiplexes sequencing reads based on the sequence of the 8 base sample barcode. It aligns reads from each sample to the transcriptome using STAR, with feature counting by the union rules of HTSeq-count. The initial quantification is performed by counting the unique molecular indices (MI) mapped to each feature. Lastly, the pipeline uses two error correction algorithms to remove MI errors. In brief, MI errors that are derived from sequencing base calls and PCR substitution errors are identified and adjusted to a single MI barcode using Recursive Substitution Error Correction™ (RSEC). Subsequently, MI errors that are derived from library preparation steps or sequencing base deletion errors are adjusted using Distribution-Based Error Correction™ (DBEC).
A cell was considered to be infected if there was at least one GFP sequence read count. This information was then used to define the groups to compare in EdgeR. Differential gene expression was measured between infected and uninfected cells in each subset (Adjusted p-value less than 0.05).
Precise WTA Sample Demultiplexing:Paired-end reads are demultiplexed per well based on the sequence of the sample index. This sample index is found in the first 8 bases of Read 01. The Molecular Index is found in Read 01, in positions 8 to 16. The demultiplexing process also includes a structure filtering step. After filtering, the final step in this process stores the Molecular Index in the demultiplexed FASTQ files by appending the index to the sequence headers of Read 02 FASTQ files. The Read 02s from each well are trimmed by Flexbar to remove any Illumina adapter contaminants and mapped to the reference genome using STAR.
Precise WTA Alignment Quantification: After Read 02s are aligned using STAR, the alignments are assigned to gene counts using a custom implementation of HTSeq-count. The number of reads mapping to each gene is generated in the DBEC Read Mapping Report. The unique counts for molecular indices are calculated in the DBEC Molecular Index Mapping Report
Genome_build: mm9
Supplementary_files_format_and_content: text document (after removal of Molecular indices error using Recursive Substitution Error Correction™ (RSEC) and Distribution-Based Error Correction™ (DBEC))

extract_protocol:
The cells are collected in WTA single cell encoding plate, RNA secondary structure is done at 65C for 3 minutes (hold at 4C), mastermix containing BD customised RT enzymes is added (PN 650000041) and run at 42C for 30 minutes, heat inactivated at 80C for 5 minutes before holding at 4C. The samples is pooled and purify before library prep.
Libraries of the cellular RNA were made using the BD WTA single cell kit and sequenced using MiSeq V2 from Illumina (BM-DC, BM-M, DN).

tag: cell type


title: Sarcoma cell line E11

tag: treatment


title: 091-M09

value: Mother of patient

value: female

value: peripheral blood

value: PBMCs


title: PA_in_BC_SN_FeHigh_3

source_name: PAO1 grown in 70% CAA medium and 30% Burkholderia cenocepacia H111 supernatant_high iron_replicate 3


title: Sarcoma cell line E10


title: Recurrent GBM 4


title: Pair I Recurrent GBM

value: Paired


title: PA_in_PA_SN_FeHigh_3

source_name: PAO1 grown in 70% CAA medium and 30% PAO1 supernatant_high iron_replicate 3

value: 70% CAA medium and 30% PAO1 supernatant


title: MHC-P-701_Well_G09


title: MHC-P-701_Well_G08


title: Sarcoma cell line E9


title: MHC-P-701_Well_G07


title: Muscle-invasive bladder cancer 55403

description: Muscle-invasive bladder cancer


title: PA_in_PA_SN_FeHigh_1

source_name: PAO1 grown in 70% CAA medium and 30% PAO1 supernatant_high iron_replicate 1


title: MHC-P-701_Well_G06


title: PA_in_CAA_FeHigh_3

source_name: PAO1 grown in 100% CAA medium_high iron_replicate 3

value: 100% CAA medium


title: PA_in_CAA_FeHigh_2

source_name: PAO1 grown in 100% CAA medium_high iron_replicate 2


title: PA_in_PA_SN_FeHigh_2

source_name: PAO1 grown in 70% CAA medium and 30% PAO1 supernatant_high iron_replicate 2


title: Muscle-invasive bladder cancer 59602

description: Muscle-invasive bladder cancer


title: Sarcoma cell line E8

value: UPS


title: Sarcoma cell line E7

value: Sarcoma cell


title: Muscle-invasive bladder cancer 53608

description: Muscle-invasive bladder cancer


title: Recurrent GBM 3

value: Unpaired


title: Muscle-invasive bladder cancer 53607

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 55503

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 55406

description: Muscle-invasive bladder cancer


title: Sarcoma cell line E6

value: Control


title: Muscle-invasive bladder cancer 54501

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_G05

value: Bone marrow derived APC


title: Recurrent GBM 2

value: Recurrent GBM


title: MHC-P-701_Well_G04

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: PA_in_CAA_FeHigh_1

source_name: PAO1 grown in 100% CAA medium_high iron_replicate 1

value: wt


title: Sarcoma cell line E5


title: Recurrent GBM 1


title: Sarcoma cell line E4


title: PA_in_BC_SN_FeLow_2

source_name: PAO1 grown in 70% CAA medium and 30% Burkholderia cenocepacia H111 supernatant_low iron_replicate 2

value: planktonic cells, mid to late exponential phase

value: low, 100 ug/ml Transferrin


title: MHC-P-701_Well_G02


title: Sarcoma cell line E3


title: Sarcoma cell line E1


title: PA_in_PA_SN_FeLow_3

source_name: PAO1 grown in 70% CAA medium and 30% PAO1 supernatant_low iron_replicate 3


title: MHC-P-701_Well_G01


title: PA_in_BC_SN_FeLow_1

source_name: PAO1 grown in 70% CAA medium and 30% Burkholderia cenocepacia H111 supernatant_low iron_replicate 1


title: MHC-P-701_Well_F12


title: Muscle-invasive bladder cancer 53604

description: Muscle-invasive bladder cancer

value: Muscle-invasive bladder cancer


title: PA_in_PA_SN_FeLow_2

source_name: PAO1 grown in 70% CAA medium and 30% PAO1 supernatant_low iron_replicate 2


title: Pair IV Recurrent GBM

source_name: Paired, Recurrent GBM


title: Muscle-invasive bladder cancer 52601

description: Muscle-invasive bladder cancer


title: SH3

city: Nanjing

first: Yuanyuan

state: Jiangsu

address: 12 Jiang Wang Miao Street

institute: Hospital for Skin Diseases (Institute of Dermatology), Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: xls include FPKM values for each Sample

source_name: skin

growth_protocol: HaCaT cells were obtained from American Type Culture Collection (Manassas, VA, USA), and maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Clustering and sequencing (Novogene Experimental Department) The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Quality control: 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 1 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.   Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.   Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels

treatment_protocol: The HaCaT cells were infected with the lentivirus particles containing scrambled control shRNA (negative control group, NC group) and NCSTN targeting shRNA (interference group, SHRNA group). 72 h after transfection, shRNA-expressing cells were selected using 2 mg/L puromycin for 5 d, and total RNA  were extracted.

value: skin

value: HaCaT

value: keratinocytes

value: NCSTN knockdown


title: Muscle-invasive bladder cancer 52401

city: Bangor

first: Tim

address: Dean Street

institute: University of Bangor

description: Muscle-invasive bladder cancer

data_processing: The log2-summarised gene level expression values generated were batch-corrected using the ComBat function from the Bioconductor package sva.

extract_protocol: Two 10µm sections from FFPE bladder cancer embodied blocks. RNA was extracted from the two 10 µm sections using the Roche High Pure FFPET RNA isolation kit. RNA yield was determined on Qubit fluorometer (Invitrogen, Paisley, UK).


title: PA_in_BC_SN_FeLow_3

source_name: PAO1 grown in 70% CAA medium and 30% Burkholderia cenocepacia H111 supernatant_low iron_replicate 3


title: Sarcoma cell line E2

source_name: UPS


title: Muscle-invasive bladder cancer 15102

description: Muscle-invasive bladder cancer

source_name: Anonymised


title: MHC-P-701_Well_F11

source_name: Bone marrow derived APC


title: Muscle-invasive bladder cancer 15112

description: Muscle-invasive bladder cancer


title: SH2


title: MHC-P-701_Well_F10


title: Muscle-invasive bladder cancer 14402

description: Muscle-invasive bladder cancer


title: PA_in_CAA_FeLow_3

source_name: PAO1 grown in 100% CAA medium_low iron_replicate 3


title: MHC-P-701_Well_F09


title: MHC-P-701_Well_G03


title: Muscle-invasive bladder cancer 14404

description: Muscle-invasive bladder cancer


title: SH1


title: MHC-P-701_Well_F08


title: PA_in_CAA_FeLow_2

source_name: PAO1 grown in 100% CAA medium_low iron_replicate 2


title: MHC-P-701_Well_F07


title: PA_in_PA_SN_FeLow_1

source_name: PAO1 grown in 70% CAA medium and 30% PAO1 supernatant_low iron_replicate 1

value: 70% CAA medium and 30% PAO1 supernatant


title: PA_in_CAA_FeLow_1

source_name: PAO1 grown in 100% CAA medium_low iron_replicate 1

value: 100% CAA medium


title: WT_PS_STAPUT_ChIP_SETX

city: Bunkyo-ku

first: Yasuhiro

last: Fujiwara

address: 1-1-1 Yayoi

department: IQB

institute: The University of Tokyo

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic.
Trimmed sequence reads were mapped to GrCM38/mm10 using bowtie2

source_name: testis

extract_protocol:
WT pachytene spermatocytes used for ChIP-seq were isolated by a BSA dradient method. Setx-KO germ cells were purified by enzyme digestion method. Genomic DNA was fixed with formaldehyde and fragmented by sonication, followed by antibody immunoprecipitation.
The immunoprecipitated DNA fragments were subjected to sequencing library preparation using the Illumina TruPLEX DNA-seq kit. The prepared libraries were purified by AMPure XP magnetic beads.

value: testis

value: germ cells

value: WT


title: NC2


title: MHC-P-701_Well_F06


title: NC1


title: Setx_KO_ChIP_SETX_rep2

value: SetxKO


title: MHC-P-701_Well_F04

value: Bone marrow derived APC


title: K562 Micro-C, bio rep10

city: Shenzhen

first: Kun

last: Sun

state: Guangdong

address: Rm A1921, Guangming International Innovation Center,

institute: Shenzhen Bay Laboratory

data_processing:
library strategy: Micro-C
Raw sequencing reads from all replicates were analyzed together using Microcket (v1.0.0) with the following parameter: "-b"
Assembly: hg38
Supplementary files format and content: hic, containing interactions in various resolutions

growth_protocol: K562 cells (ATCC CCL-243) were maintained in RPMI 1640 medium with 10% FBS and 1x penicillin/streptomycin at 37 °C under 5% CO2.

extract_protocol:
K562 cells were first crosslinked with 1% formaldehyde (Sigma, 47608) for 10 min at room temperature and then quenched by 0.75 M Tris pH 7.5. After two rounds of PBS washes, cells were further crosslinked with 3mM DSG (Santa Cruz, sc-285455A) for 45 min at room temperature. After quenching with 0.75 M Tris pH 7.5 and the following two rounds of PBS washes, K562 cell pellets were snap frozen in liquid nitrogen and stored at -80 °C.
Micro-C libraries were prepared following the procedure as previously described (Hsieh et al., Mol Cell, 2020). In brief, 5 million of K562 cell pellets were treated in lysis buffer containing 0.2% NP-40. The extracted nuclei were then digested by 1,000 Gel Units of MNase (NEB, M0247S) at 37°C for 10 min with 80 to 90% of fragmented chromatin were mononucleosomes. The MNase-digested nucleosomes were then end repaired and incorporated with Biotin-14-dATP (Jena Bioscience, NU-835-BIO14-L) and Biotin-11-dCTP (Jena Bioscience, NU-809-BIOX-L). Then the nucleosomes were ligated by T4 DNA Ligase (NEB, M0202) and unligated products were removed by exonuclease III (NEB, M0206). The de-crosslinked DNA were purified by phenol/chloroform/isoamyl alcohol and separated on 6% PAGE gel. A band at the size of 250 to 400 bp were excised and DNA was extracted and then purified by MyOne™ Streptavidin C1 (Thermo Fisher Scientific, 65001). For the library preparation, end-repair/A-tailing, and adaptor ligation were performed on-bead using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607-01). Ligated DNA were then amplified using 12 cycles on the thermocycler and libraries were purified using the VAHTS DNA Clean Beads (Vazyme, N411-01). Micro-C libraries were sequenced paired-end 150 bp with Illumina Novaseq 6000 sequencer.

value: Chronic Myeloid Leukemia

value: wild type


title: MHC-P-701_Well_F05

last: Ugwu

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: K562 Micro-C, bio rep9


title: MHC-P-701_Well_F03


title: Setx_KO_ChIP_SETX_rep1


title: Muscle-invasive bladder cancer 12601

description: Muscle-invasive bladder cancer


title: NC3


title: K562 Micro-C, bio rep8


title: Muscle-invasive bladder cancer 12301

description: Muscle-invasive bladder cancer


title: Setx_KO_ChIP_input


title: MHC-P-701_Well_F02


title: Muscle-invasive bladder cancer 11502

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 14401

description: Muscle-invasive bladder cancer


title: K562 Micro-C, bio rep7


title: sp3PS-gH2AX-r2

data_processing:
CUT&Tag reads were aligned to the mm10 genome assembly using Bowtie2.
peaks were called using DROMPA2 with a pvalue threshold at 0.005.
Assembly: mm10
Supplementary files format and content: bigWig files
Supplementary files format and content: bed files of merged peaks from two biological replicates.
Library strategy: CUT&Tag

extract_protocol:
Cells bound to magnetic beads were treated with Digitonine, antibody, then pA-Tn5 fusion transposase. Genomic DNA was isolated and purifired using phenol-Chloroform.
Libraries were prepared according to previously reported method (PMID: 31036827). Briefly,  the adapter sequence-tagmented DNA fragments were amplified by PCR using Universal i5 and uniquely barcoded i7 primers and NEBNext High-Fidelity 2x PCR Master mix (New England BioLabs, M0541S) with 14 PCR cycles. The PCR products were purified by using Ampure XP beads, and cleaned with 80 % ethanol. The size distribution of libraries was confirmed by an Agilent 2100 Bioanalyzer Instrument (Agilent Technologies) and High Sensitivity DNA Chips (5067-4626) (Agilent Technologies). The barcoded libraries were quantified by KAPA Library Quantification Kit, Complete kit for ABI Prism, Illumina Platform (KK4835, 07960204001, Roche). The Paired-end sequencing of DNA libraries were sequenced on Illumina HiSeq X sequencer (Illumina) following the manufacturer's protocols.

treatment_protocol: Spermatocytes are purified by FACS cell-sorting using a VC dual-color reporter mouse (PMID: 25364737).


title: Muscle-invasive bladder cancer 11501

description: Muscle-invasive bladder cancer


title: K562 Micro-C, bio rep6


title: Muscle-invasive bladder cancer 11601

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 13102

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_F01


title: K562 Micro-C, bio rep5


title: MHC-P-701_Well_E12


title: WT_PS_STAPUT_ChIP_input


title: K562 Micro-C, bio rep4


title: sp3PS-IgG-r2


title: MHC-P-701_Well_E11


title: MHC-P-701_Well_E10


title: K562 Micro-C, bio rep3


title: sp3PS-gH2AX-r1


title: K562 Micro-C, bio rep1


title: SH1

first: Weixue

last: Jia

address: 12 Jiangwangmiao St., Nanjing, P.R. China.

institute: Hospital for Skin Diseases (Institute of Dermatology), Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Quality control: 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 1 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.   Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.   Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Enrichment analysis of differentially expressed genes Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
Gene Set Enrichment Analysis Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a predefined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO、KEGG、Reactome、DO and DisGeNET data sets were used for GSEA independently.
SNP analysis: GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10.
AS analysis: Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(3.2.5) software was used to analysis the AS event. PPI analysis of differentially expressed genes
PPI analysis: of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: MNT-1 cells were obtained from American Type Culture Collection (Manassas, VA, USA), and cultured according to standard procedures; Hecat cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Clustering and sequencing (Novogene Experimental Department) The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: MNT-1 cells were seeded at a density of 2×104 cells/ml and cultured for 24 h. Lentivirus-infected HaCaT cells were then seeded at a density of 4×104 cells/ml in high-glucose DMEM containing 20% fetal bovine serum for 72 h. The cells were digested with trypsin, and GFP-negative cells were isolated by flow cytometry, and total RNA was extracted.

value: skin derived melanoma cells

value: Cocultured with Hecat cells(trasfected with KRT5-KD lentivirus) for 72h


title: SH2


title: K562 Micro-C, bio rep2


title: SH3


title: NC3

value: Cocultured with Hecat cells(trasfected with non-targeted lentivirus) for 72h


title: S96_PS1


title: SETX_PS1


title: sp3PS-IgG-r1


title: PS-gH2AX-r2


title: S96_PS2


title: SETX_PS2


title: PS-gH2AX-r1


title: MYBL1_PS2


title: MHC-P-701_Well_E03


title: MHC-P-701_Well_E08


title: MHC-P-701_Well_E05


title: MHC-P-701_Well_E09


title: MHC-P-701_Well_E07


title: MHC-P-701_Well_E04


title: MHC-P-701_Well_E06


title: NC2

value: skin


title: Muscle-invasive bladder cancer 11402

last: Smith

description: Muscle-invasive bladder cancer

value: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6431

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 11203

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_E02


title: NC1


title: MYBL1_PS1


title: A3 input

city: Guangzhou

first: Yu

last: Kuang

address: 58 Zhongshan 2nd Road, Yuexiu District

department: Rheumatology and Immunology

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Cutadapt (v2.5 ) was used to trim adapters and filter for sequences, remaining reads were then aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”. m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”.  Differential m6A peak were identified using exomePeak R package under parameters:  “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200” . GO and KEGG analysis were performed using clusterprofile R package (v3.6.0). m6A-RNA-related genomic features were visualized using Guitar R package (v1.16.0).  Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
Assembly: Ensembl91_year_2017
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: synovial tissues

extract_protocol:
Briefly, the concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). Total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2. Subsequently, the purified RNA was incubated with anti-m6A polyclonal antibody (Sigma-Aldrich, ABE572) for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was eluted from the beads in RLT buffer supplied in RNeasy Mini Kit (QIAGEN, 74106).
The RNA-seq library was prepared by NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, E7775).
Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer

value: synovial tissues

value: rheumatoid fibroblast-like synoviocytes

value: ALKBH5 knockdown

value: ALKBH5 shRNA lentivirus


title: K4m3_PS2

value: testis


title: A2 input


title: K4m3_PS1

value: germ cells


title: IgG_PS2

value: WT


title: Muscle-invasive bladder cancer 6424

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 7504

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_E01


title: MHC-P-701_Well_D11


title: MHC-P-701_Well_D12


title: A1 input


title: Muscle-invasive bladder cancer 6423

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 11403

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6422

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6430

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 11104

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6427

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6429

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 11101

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1107

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 53606

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 59603

description: Muscle-invasive bladder cancer


title: IgG_PS1


title: postnatal day14

city: seoul

first: Jimin

last: Cha

address: 50-1, Yonsei-ro

institute: Yonsei university

description: 10x Genomics

data_processing:
Single cell gene expression data was analyzed using Cell Ranger v3.1.0
Briefly, raw BCL files from Illumina sequencing instrument were demultiplexed to generate FASTQ files using ‘cellranger mkfastq’.
Then, these raw FASTQ files were analyzed using ‘cellranger count’.
The ‘cellranger count’ step includes mapping to the reference genome (mm10-3.0.0), measuring gene expression with unique molecular identifier (UMI) and cell barcode, determining cell clusters, and conducting differential gene expression analysis.
Count can take input from multiple sequencing runs on the same library. Read count extraction and normalization were performed using Seurat v4.1.0.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Skin

extract_protocol:
skin tissues were digested with 1.7mg/ml Collagenase A (Roche, Switzerland) , ILC(CD45+, Lin-, Thy1.2+) were enriched using flow cytometry then were captured using Chromium GEM Single Cell 5' Kit v1 (10x Genomics, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin

value: ILC


title: MHC-P-701_Well_D10

value: Bone marrow derived APC


title: MHC-P-701_Well_D09


title: Muscle-invasive bladder cancer 59605

description: Muscle-invasive bladder cancer


title: C3 input

value: scramble lentivirus


title: C2 input


title: Muscle-invasive bladder cancer 1108

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_D08

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: C1 input


title: postnatal day1

description: 10x Genomics


title: RNA-seq-Mettl3KO rep2

city: Beijing

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

data_processing:
FastQC (Version 0.11.5) was used to identify features of the raw data that may indicate quality problems
Reads were mapped to the mouse reference genome (mm10) with STAR (Version 2.6.0a).Default parameter settings were used for alignment
The uniquely mapped reads were assigned to genes using HTseq (Version 0.6.1)
The fold change and p-value of all the detected genes were estimated by DESeq2 (Version 1.18.1)
Assembly: mm10
Supplementary files format and content: txt format. Read counts for each gene

source_name: thymocytes

extract_protocol:
iNKT cells (7AAD-CD1d-Tet+TCRβ+) were directly sorted into TRIzol reagent by a FACSAriaII sorter, and total RNA was extracted using standard Qiagen RNease columns.
libraries are constructed according to the standard protocol for Smart-seq2

value: thymocytes

value: iNKT (7AAD-CD1d-Tet+TCRbeta+) cells

tag: age

value: 6~8 weeks


title: A3 IP


title: MHC-P-701_Well_D07


title: Muscle-invasive bladder cancer 59501

description: Muscle-invasive bladder cancer


title: RNA-seq-Mettl3KO rep1


title: MHC-P-701_Well_D06


title: A2 IP


title: A1 IP


title: Muscle-invasive bladder cancer 59201

description: Muscle-invasive bladder cancer


title: RNA-seq-WT rep1


title: Muscle-invasive bladder cancer 59401

description: Muscle-invasive bladder cancer


title: RNA-seq-WT rep2


title: C3 IP


title: MHC-P-701_Well_D05


title: Muscle-invasive bladder cancer 58401

description: Muscle-invasive bladder cancer


title: C2 IP


title: MHC-P-701_Well_D03


title: MHC-P-701_Well_D02


title: C1 IP


title: DU145 tumor sample MBZ rep3

city: qingdao

first: qiaoling

last: song

address: Xiang Gang East Road NO.23

institute: Ocean University of China

description: MBZ rep3

data_processing:
The paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length)
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome (mapped against human (GRCh38) and mouse (GRCm38) genomes separately) with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml? t=example) in a reference-based approach.
The differential expression analysis was performed using the DESeq2/DEGseq/EdgeR.
Assembly: human (GRCh38) and mouse (GRCm38)
Supplementary files format and content: tab-delimited text file with raw gene counts for every gene and every sample

source_name: DU145 tumor sample

growth_protocol: Human prostate cancer cells DU145 (5x10e6/mouse) were injected into male nude  mice subcutaneously. Once tumors were touchable, mice were randomized into the individual groups.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.

treatment_protocol: In nude mice mice, Zelnorm were orally administrated daily at the indicated doses.

value: Nude mice

value: Zelnorm


title: DU145 tumor sample MBZ rep2

description: MBZ rep2


title: DU145 tumor sample MBZ rep1

description: MBZ rep1


title: MHC-P-701_Well_D01


title: MHC-P-701_Well_C12


title: A3

data_processing:
VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme Biotech, NR612-02) was used for library preparation according to the instructions. Reads were aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”. The reads mapped the genome were calculated using featureCounts (v1.6.3). Differential gene expression analysis was performed using the DESeq2 R-package.
Assembly: Ensembl91_year_2017
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Briefly, the concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). Total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2
Add DNase I to the RNA sample, digest at 37 °C for 30 min to remove the residual DNA in the sample, and purify the magnetic beads to recover the RNA. The 5XRT Buffer was added to sample RNA, ribosomal RNA probe was added, and the temperature gradient reaction fragments the RNA sample and remove rRNA. EpiScriptTM IV, RNase inhibitor, DTT, TSO, and random primers were added to the RNA samples in step2. Add 2XpfuMax HiFi PCR ProMix and sequencing primers to the first strand of cDNA sample, and then amplified in PCR apparatus after mixing. The PCR amplification product was purified in a 1X ratio using EpiTM DNA Clean Beads, and the purification product was recovered from 300-400 bp of DNA fragments in a 0.65X/0.2X ratio with magnetic beads. A second cycle of PCR amplification of the purified product was performed to enrich DNA fragments of 300-400 bp. Bioptic Qsep100 Analyzer was used to conduct quality inspection on the library to detect whether the size distribution of the library conforms to the theoretical size.

value: synovial tissues


title: A2

value: rheumatoid fibroblast-like synoviocytes


title: MHC-P-701_Well_C11


title: MHC-P-701_Well_D04


title: DU145 tumor sample NC rep2

description: NC rep2

value: control


title: A1

value: ALKBH5 knockdown

value: ALKBH5 shRNA lentivirus


title: DU145 tumor sample NC rep3

description: NC rep3


title: MHC-P-701_Well_C10


title: C3


title: Muscle-invasive bladder cancer 55607

description: Muscle-invasive bladder cancer

value: Muscle-invasive bladder cancer


title: MBZ rep4

data_processing:
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic [1] and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the human genome (GRCh38) using HISAT2. FPKM of each gene was calculated using Cufflinks.
The read counts of each gene were obtained by HTSeq- count
Differential expression analysis was performed using the DESeq (2012) R package
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file with raw gene counts for every gene and every sample

source_name: B16F10 tumor sample

growth_protocol: B16F10 (3´105/mouse) were into female C57BL/6J mice. Once tumors were touchable, mice were randomized into the individual groups.

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: In syngeneic tumor models, Zelnorm (1.25 mg/kg) were orally administrated once every two days.


title: DU145 tumor sample NC rep1

description: NC rep1


title: Muscle-invasive bladder cancer 55609

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 55602

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 59301

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 55604

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 55605

description: Muscle-invasive bladder cancer


title: C2

value: WT


title: Muscle-invasive bladder cancer 55402

description: Muscle-invasive bladder cancer


title: MBZ rep3


title: Muscle-invasive bladder cancer 55301

description: Muscle-invasive bladder cancer


title: C1


title: MBZ rep2


title: MHC-P-701_Well_C07


title: MBZ rep1


title: CD55+AMH-EGFP- hiGC, D11, biol rep2

first: Kehkooi

last: Kee

address: Shuangqing Road, Haidian District

department: Department of Basic Medical Sciences

institute: Tsinghua University

description:
CD55+AMH-EGFP-2
Fpkms_CD55+_CD55+AMH-_AMH+

data_processing:
Trim Galor (version 0.5.0)  was used to remove adaptors and index. FastQC (version 0.11.8) was used to check the quality of raw sequencing reads.
Hisat2  (version 2.1.0)  was used for mapping.
Read count extraction and normalization were performed using Cuffnorm (version 2.2.1).
Assembly: h19
Supplementary files format and content: csv files include FPKM values for each sample

source_name: in vtiro induced human granulosa cells

extract_protocol:
RNA was extracted from cells lysed in TRIZOL. 10ng of total RNA was used for the construction of sequencing libraries.
cDNA libraries were prepared according to smart-Seq2 protocol. Final DNA libraries used for RNA-Seq were prepared using TruePrepTM DNA Library Prep Kit V2 for Illumina following manufactures' protocol.

value: in vtiro induced human granulosa cells

value: FOXL2 & NR5A1 overexpression


title: MHC-P-701_Well_C06

value: Bone marrow derived APC


title: NC rep3


title: MHC-P-701_Well_C09


title: Muscle-invasive bladder cancer 53602

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 53601

description: Muscle-invasive bladder cancer


title: NC rep2


title: MHC-P-701_Well_C05


title: MHC-P-701_Well_C04


title: MHC-P-701_Well_C08


title: CD55+AMH-EGFP- hiGC, D11, biol rep1

description:
CD55+AMH-EGFP-1
Fpkms_CD55+_CD55+AMH-_AMH+


title: CD55+ hiGC, D11, biol rep1

description:
CD55-1
Fpkms_CD55+_CD55+AMH-_AMH+


title: CD55+ hiGC, D11, biol rep2

description:
CD55-2
Fpkms_CD55+_CD55+AMH-_AMH+


title: NC rep1


title: MHC-P-701_Well_C02


title: MHC-P-701_Well_C03


title: AMH-EGFP+ hiGC, D11, biol rep 1, sequenced at the same time with CD55+, CD55+AMH-EGFP- cells

description:
AMH-EGFP-1
Fpkms_CD55+_CD55+AMH-_AMH+


title: seed, Bolstar, Ina_TW2, rep6; Chrisbis48

city: Wageningen

first: Marie

last: Duhamel

address: Droevendaalsesteeg 1

department: Plant Science Group

country: Netherlands

institute: Wageningen University & Research

data_processing:
To analyse the raw sequences obtained and estimate methylation levels per chromosome and compare them across treatment between controls and seeds from plants primed by Ina, BaBa and MeJa, we used the pipeline MethPipe (Song et al.,2013)
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for adapter trimming as well as quality control, with some added functionality to remove biased methylation positions.
Abismal (de Sena Brandine et al., 2021) was used to construct the methylome and map bisulfite treated short reads on the tomato plant genome.
Supplementary files format and content: The file mw.bed is in a bed format and contains information of the hypomethylated regions from the genome of control Moneyberg tomato seeds (from untreated plants).
Supplementary files format and content: The file mb2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with Baba in time window 2.
Supplementary files format and content: The file mi2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with Ina in time window 2.
Supplementary files format and content: The file mm3.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with MeJA in time window 3.
Supplementary files format and content: The file mb3.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with MeJA in time window 3.
Supplementary files format and content: The file bb2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Bolstar tomato seeds from plants treated with Baba in time window 2.
Supplementary files format and content: The file bw.bed is in a bed format and contains information of the hypomethylated regions from the genome of the control Bolstar tomato seeds (from untreated plants).
Supplementary files format and content: The file bi2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Bolstar tomato seeds from plants treated with Ina in time window 2.

organism: Solanum lycopersicum

source_name: seed

extract_protocol:
The DNA extraction was performed following the manufacturer instructions using the Quick-DNA Plant/Seed Miniprep Kit from Zymoresearch. For each sample the DNA concentration and quality was measured using a Qubit fluorometer.
Ultralow Methyl-Seq System (Tecan/NuGEN, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions. DNA samples were quantified with Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay (Agilent technologies, Santa Clara, CA).
Libraries were then prepared for sequencing and sequenced on paired-end 150 bp mode on NovaSeq6000 (Illumina, San Diego, CA).

value: seed

value: Bolstar


title: Muscle-invasive bladder cancer 53501

description: Muscle-invasive bladder cancer


title: seed, Bolstar, Ina_TW2, rep5; Chrisbis47


title: mediastinal lymph node rep2

city: Shanghai

first: Liwen

last: Fan

address: No.241 West Huaihai Street

institute: Shanghai Chest Hospital

description: mediastinal lymph node sample from patient 1

data_processing:
Raw gene expression matrix was generated for each sample using the 10X genomics Cell Ranger toolkit (version 4.0.0) and mapped to the GRCh38 human reference genome.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

molecule: polyA RNA

extract_protocol:
Samples were collected, washed, miced, and digested into single-cell suspensions. Cells were then lysed, and the released RNA was barcoded via reverse transcription in individual GEMs.
RNA libraries were prepared with Chromium Single cell 3' v3.1 Kits according to the manufacturer's protocol.

tag: tumor stage

tag: patient number

value: patient 1


title: seed, Bolstar, Ina_TW2, rep4; Chrisbis46

tag: tissue