title: HeLa_JNK1/2_8h

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

description: Gene expression in JNK1/2 DKO cells at 8 hours after IKE treatment.

hyb_protocol: 0.6µg of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/µg cRNA) was fragmented at 60˚C for 30 minutes in a reaction volume of 25µl containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 25µl of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE microarray 8x60K Ver. 3.0 (G4858A #72363, Agilent Technologies) for 17 hours at 65˚C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37˚C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 1 x 60K array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentG3_GX_1Color and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: HeLa, JNK1/2 DKO cell, 8h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 10% FBS, DMEM + 1%penicillin/streptomycin

extract_protocol: Total RNA was extracted with NucleoSpin RNA (Takara Bio, Kusatsu, Japan) according to the manufacturer's instructions.

value: HeLa cell line


title: 22Rv1_mir-9_1_2

status: Public on Jun 19 2023

type: RNA

city: Los Angeles

first: Minhyung

last: Kim

state: CA

address: 8700 Beverly Blvd

department: Urology

country: USA

institute: Cedars-Sinai Medical Center

description: Gene expression after stable transfection of miR-9 producing vector

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to the Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray (catalog number G4851C) for 17 hours at 65 C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with pre-warmed at 37 °C overnight Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using one color scan setting for G3 Microarray formats :Scan region  61x21.6 mm, Scan resolution 3um,Tiff file dynamic range 20 bit, Green PMT gain 100%.

data_processing: The scanned images were analyzed with Feature Extraction Software v11.5.1.1 (Agilent).

molecule: total RNA

organism: Homo sapiens

source_name: 22Rv1 Prostate Cancer cell line

label_protocol: 0.2 ug RNA was labeled with cyanine 3-dUTP by using One-Color Microarray -Based Gene Expression Analysis Low Input Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: RPMI 1640 10% FBS

extract_protocol: Qiagen Rneasy mini extraction with DNAse treatment

treatment_protocol: Cells were transfected stably and FAC sorted to ensure positivity

tag: cell type

value: Prostate cancer

tag: cell line

tag: treated

value: Treated

tag: treatment


title: HeLa_JNK1/2_12h

country: Japan

description: Gene expression in JNK1/2 DKO cells at 12 hours after IKE treatment.

source_name: HeLa, JNK1/2 DKO cell, 12h


title: embryo, day-5, global, rep9

type: SRA

city: DIJON

first: Bastien

last: Ducreux

address: Batiment B3, 15 boulevard Maréchal de Lattre de Tassigny

country: France

institute: Inserm U1231

library_source: transcriptomic

data_processing:
We computed sequencing quality checks with FastQC v0.11.9 and trimming of adapters and low-quality sequences using TrimGalore! v0.6.6. Paired-end reads alignment was performed onto Human reference genome (hg38) with STAR v2.7.9a 86 reporting randomly one position, allowing 6% of mismatches. As recommended in Teissandier et al. 87 repeat annotation was downloaded from RepeatMasker and joined with basic gene annotation from Gencode v19. The merged file was used as input for quantification with featureCounts v2.0.1. Genes with a minimum of count per million (cpm) > 1 in at least 4 samples were retained for further analysis. Principal component analyses were implemented with PCAtools v2.8.0 on log2(cpm+1) of all genes for single datasets and common genes for multiple datasets, excepting the lowest 10% genes based on variance. Differential expression analysis was performed using edgeR’s normalization (v3.38.1) combined with voom transformation from limma package v3.52.1.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: embryo

extract_protocol:
Free-zona pellucida embryo (after using acidic Tyrode’s solution) was individually placed in a lysis buffer containing MgCl2 (4379878, Applied Biosystems), DTT, Nonidet P-40 (11332473001, Roche), SUPERase-In (AM2694, Ambion) and RNase-inhibitor (AM2682, Ambion). Then, we performed a reverse transcription reaction (SuperScript III reverse transcriptase - 18080-044, Invitrogen) and a poly(A) tailing to the 3’ end of the first-strand cDNA (by using terminal deoxynucleotidyl transferase - 10533-073, Invitrogen). After the second-strand cDNA synthesis, 20 and 18 cycles (at day-2 and day-5, respectively) of PCR were performed to amplify the embryo cDNA using the TaKaRa ExTaq HS (TAKRR006B, Takara) and IS PCR primer (IDT). Following purification with Zymoclean Gel DNA Recovery Kit (ZD4008, Takara), product size distribution and quantity were assessed on a Bioanalyzer using an Agilent 2100 high-sensitivity DNA assay kit (5067-4626, Agilent Technologies).
The library preparation (KAPA Hyper Plus Library prep kit) and the sequencing of the scRNA-seq was performed by the ICGex - NGS platform (Curie Institute) on HiSeq 2500 Illumina sequencer for day-2 embryos and NovaSeq 6000 for day-5 embryos, for 100-bp paired-end sequencing

treatment_protocol:
All embryos used in the current study were cryopreserved individually 2 days post fertilization and had been in vitro cultured in different culture media (Global medium, LifeGlobal with or without 200µM methionine; FertiCult IVF medium, FertiPro; SSM, Irvine Scientific).
Embryos were thawed according to the strict protocol routinely used in human IVF-clinic to maintain as much as possible their integrity (Bechoua et al. 2009)
Immediately after thawing, embryos were transferred into preequilibrated Embryoslides (Unisense Fertilitech, Vitrolife) with 25 μl of culture medium and covered with 1.2 mL of oil (Nidoil, Nidacon). They were cultured up to the blastocyst stage at 37°C and a tri-gaz atmosphere (6%CO2, 5%O2, 89% N2)
Only blastocysts with at least B2 blastocoel cavity without lysis were analyzed.

tag: tissue

value: embryo

tag: day

tag: culture media_day-2

value: Global

tag: culture media_day-5

tag: couple


title: Sup. Fig. 6, HeLa-R634Q ICS screen, upper, lib 5

city: Heidelberg

first: Julia

last: Kornienko

state: Baden-Württemberg

address: Meyerhofstraße 1

country: Germany

institute: EMBL

description:
ICS R634Q screen upper 5
R634Q_screen_gene_stats.txt

library_source: other

data_processing:
library strategy: HeLa ICS screen Amplicon seq
RNAseq: Reads were aligned to GRCh38.101 using STAR (v2.7.5c), and bam files were sorted by coordinate using samtools (v.1.9). Read count files were generated with featureCounts52 v1.6.4 for each exon. For differential gene expression analysis, DeSeq253 (v. 1.36.0) was used, and pairwise comparisons between genotypes were performed (expression ~ genotype).
ICS screen: Abundance of gRNA was quantified from the sequencing reads using MAGeCK (v 0.5.9) tool with default parameters. To account for differences in sequencing depth, raw gRNA counts were normalized to the median count of the targeting control gRNAs in the corresponding sample. Scaling of the normalized counts was done by multiplication with the median count of targeting controls across all samples. The MAUDE package for R was used for hit calling, using targeting controls as a reference for MAUDE analysis.
Assembly: GRCh38.101
Supplementary files format and content: For RNAseq: tab-delimited text files containing read counts for all samples for all genes;  For ICS screen: csv file containing gene stats from MAUDE.

molecule: other

source_name: HeLa (Feldman at al., 2019)

growth_protocol: HeLa were maintained in DMEM, high glucose supplemented with 10% FBS, 1% Sodium Pyruvate, and 1% Penicillin-Streptomycin; in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA from HeLa: Direct-Zol (Zymo) kit was used according to manufacturer's instructions. DNA from HeLa: cells were palleted and genomic DNA was extracted using NEB Monarch genomic DNA purification kit, including the RNase treatment and elution in 50 µl elution buffer; 100-500 ng of DNA was used for library preparation.
HeLa RNAseq: Library preparation for HeLa cells was done based on RNA extracts from live cells. Barcoded stranded mRNA-seq libraries were prepared from 150ng of high quality total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA) implemented on the liquid handling robot Beckman i7. Obtained libraries that passed the QC step were pooled in equimolar amounts; 2.1 pM solution of this pool was loaded on the Illumina NextSeq 500and sequenced bi-directionally, generating ~500 million paired-end reads, each 75 bases long.HeLa ICS screen: see detailed methods in Schraivogel et al., 2022.

value: HeLa (Feldman at al., 2019)

value: human adenocarcinoma

tag: genotype

value: TetO:Cas9; RBM20-R634Q

value: upper


title: mES, METTL14KO+METTL14R298A, H3K27me3, rep1

city: Shanghai

first: Hongjie

last: Shen

state: Shanghai

address: No.130, Dong'an Road, Xuhui District

department: Institutes of Biomedical Sciences

country: China

institute: Fudan University

library_source: genomic

data_processing:
Raw reads were aligned to the mm10 genome using Bowtie2 (v 2.2.5).
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Assembly: Genome_build: mm10
Supplementary files format and content: Genome coverage bigwig files

molecule: genomic DNA

organism: Mus musculus

growth_protocol: E14Tg2a murine embryonic stem cells (mES) were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% fetal bovine serum (FBSGibco #16000-044), 1% MEM non-essential amino acid (Gibco #11140), 55 mM β-Mercaptoethanol (Gibco#21985-023), 100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1000 units/mL LIF (Millipore #ESG1107,) and MEK inhibitor PD0325901 (1μM) and GSK3β inhibitor CH99021 (3μM) at 37℃ with 5% CO2.

extract_protocol:
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

value: Embryonic stem cells

value: METTL14 R298A

tag: chip antibody


title: embryo, day-5, global_methionine, rep9


title: mES, METTL14KO+METTL14WT, H3K27me3, rep2

value: METTL14 WT


title: HeLa_JNK1/2_4h

description: Gene expression in JNK1/2 DKO cells at 4 hours after IKE treatment.

source_name: HeLa, JNK1/2 DKO cell, 4h


title: HeLa_JNK1/2_0h

description: Gene expression in JNK1/2 DKO cells at 0 hours after IKE treatment.

source_name: HeLa, JNK1/2 DKO cell, 0h


title: mES, METTL14KO+METTL14D312A, H3K27me3, rep2

value: METTL14 D312A


title: embryo, day-5, global, rep7


title: HeLa_CTL_12h

description: Gene expression in control cells at 12 hours after IKE treatment.

source_name: HeLa, control cell, 12h


title: Sup. Fig. 6, HeLa-R634Q ICS screen, upper, lib 3

description:
ICS R634Q screen upper 3
R634Q_screen_gene_stats.txt


title: mES, METTL14KO+METTL14WT, H3K27me3, rep1


title: mES, METTL14KO, H3K27me3, rep2

value: METTL14 KO


title: HeLa_CTL_8h

description: Gene expression in control cells at 8 hours after IKE treatment.

source_name: HeLa, control cell, 8h


title: HeLa_CTL_4h

description: Gene expression in control cells at 4 hours after IKE treatment.

source_name: HeLa, control cell, 4h


title: embryo, day-5, global, rep6


title: Sup. Fig. 6, HeLa-R634Q ICS screen, upper, lib 2

description:
ICS R634Q screen upper 2
R634Q_screen_gene_stats.txt


title: Sup. Fig. 6, HeLa-R634Q ICS screen, lower, lib 1

description:
ICS R634Q screen lower 1
R634Q_screen_gene_stats.txt

value: lower


title: embryo, day-5, global, rep5


title: Sup. Fig. 6, HeLa-R634Q ICS screen, upper, lib 1

description:
ICS R634Q screen upper 1
R634Q_screen_gene_stats.txt


title: Sup. Fig. 6, HeLa-R634Q ICS screen, upper, lib 4

description:
ICS R634Q screen upper 4
R634Q_screen_gene_stats.txt


title: mES, H3K27me3, rep2

value: WT


title: embryo, day-5, global_methionine, rep8


title: embryo, day-5, global, rep4


title: Sup. Fig. 6, HeLa-R634Q ICS screen, input, lib 5

description:
ICS R634Q screen input 5
R634Q_screen_gene_stats.txt

value: input


title: embryo, day-5, global, rep3


title: Sup. Fig. 6, HeLa-R634Q ICS screen, input, lib 4

description:
ICS R634Q screen input 4
R634Q_screen_gene_stats.txt


title: METTL14KO mES, METTL14

value: METTL14 (Sigma, #HPA038002)


title: mES, H3K27me3, rep1


title: Sup. Fig. 6, HeLa-R634Q ICS screen, input, lib 3

description:
ICS R634Q screen input 3
R634Q_screen_gene_stats.txt


title: HeLa_CTL_0h

description: Gene expression in control cells at 0 hours after IKE treatment.

source_name: HeLa, control cell, 0h

value: HeLa cell line


title: embryo, day-5, global, rep2


title: embryo, day-5, global, rep1


title: Sup. Fig. 6, HeLa-R634Q ICS screen, input, lib 2

description:
ICS R634Q screen input 2
R634Q_screen_gene_stats.txt


title: mES, METTL14KO, H3K27me3, rep1


title: embryo, day-5, ferticult, rep6

value: Ferticult


title: Sup. Fig. 6, HeLa-R634Q ICS screen, input, lib 1

description:
ICS R634Q screen input 1
R634Q_screen_gene_stats.txt


title: mES, METTL14, rep1


title: mES, input


title: mES, METTL14, rep2


title: HeLa R634Q rep 3

description:
HeLa RNAseq sample 6
HeLa_read_counts.txt

data_processing:
RNAseq: Reads were aligned to GRCh38.101 using STAR (v2.7.5c), and bam files were sorted by coordinate using samtools (v.1.9). Read count files were generated with featureCounts52 v1.6.4 for each exon. For differential gene expression analysis, DeSeq253 (v. 1.36.0) was used, and pairwise comparisons between genotypes were performed (expression ~ genotype).
ICS screen: Abundance of gRNA was quantified from the sequencing reads using MAGeCK (v 0.5.9) tool with default parameters. To account for differences in sequencing depth, raw gRNA counts were normalized to the median count of the targeting control gRNAs in the corresponding sample. Scaling of the normalized counts was done by multiplication with the median count of targeting controls across all samples. The MAUDE package for R was used for hit calling, using targeting controls as a reference for MAUDE analysis.
Assembly: GRCh38.101
Supplementary files format and content: For RNAseq: tab-delimited text files containing read counts for all samples for all genes;  For ICS screen: csv file containing gene stats from MAUDE.


title: Healthy Control 12

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado - Anschutz Medical Campus

hyb_protocol: per Manufacturer Instructions

scan_protocol: per Manufacturer Instructions

data_processing: normal-exponential background correction followed by quantile normalization implemented in the limma R package

source_name: Bronchoalveolar lavage cells from: Healthy Control 12

label_protocol: per Manufacturer Instructions

growth_protocol: Cells were stored in RLT buffer at –80°C

extract_protocol: genomic DNA and RNA were extracted using Qiagen AllPrep DNA/RNA extraction mini kit

tag: diagnosis

value: Control

tag: Sex

value: F

tag: age

tag: race

value: White

tag: hispanic

value: No

tag: smoker

value: Never

tag: tlc

tag: fvc

tag: dlco

tag: white_blood_cell_count (x 10^6)

tag: slide


title: embryo, day-5, ferticult, rep4

tag: tissue

value: embryo

tag: day

value: Global


title: embryo, day-5, ferticult, rep5

tag: culture media_day-2

tag: culture media_day-5


title: HeLa R634Q rep 2

description:
HeLa RNAseq sample 5
HeLa_read_counts.txt

tag: cell line

value: HeLa (Feldman at al., 2019)

tag: cell type

value: human adenocarcinoma

tag: genotype

value: TetO:Cas9; RBM20-R634Q


title: embryo, day-5, ferticult, rep3

tag: couple


title: Healthy Control 11

source_name: Bronchoalveolar lavage cells from: Healthy Control 11

tag: diagnosis

tag: Sex

value: M

tag: age

value: Yes


title: Healthy Control 10

source_name: Bronchoalveolar lavage cells from: Healthy Control 10

tag: race

tag: hispanic

tag: smoker


title: Healthy Control 9

source_name: Bronchoalveolar lavage cells from: Healthy Control 9

value: Former

tag: tlc

tag: fvc

tag: dlco


title: Col12 KO

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

institute: University of Cologne

library_source: transcriptomic single cell

data_processing:
none provided
Assembly: mm10-2020-A

source_name: joints

extract_protocol:
Hindlimb knee joints of P7 mice of both sexes were isolated WT and Col12a1 KO mice, skin and paws were removed. Then they were digested in 4 mg/mL collagenase II (Worthington, USA) in DMEM/F-12 (supplied with 10% FBS) for 6 hours. After digestion, isolated cells were passed through 100 µm and 40 µm cell strainers (BD Bioscience, USA) to obtain single cell suspensions. Cells were washed three times with 0.04 % bovine serum albumin (Serva Electrophoresis GmbH, Germany) (v/v in PBS, pH = 7.4) by centrifugation at 400 g for 5 minutes and brought to a density of 1,000 cells / µL. Cell viability (> 90 %) was confirmed by 0.4 % trypan blue staining
cDNA generation and library was prepared and 10µl of the cDNA solution was used ( 10× Genomics protocol) to create an Illumina library (P5 and P7 adapters for 3′mRNA) for sequencing (Illumina NovaSeq6000 systems). Reads were aligned, feature-barcode matrices were generated and data set from two independent experiments (1st experiment 1xWT vs 1x Col12a1 KO samples; 2nd experiment 2x WT vs 2x Col12a1 KO samples) were merged (Cell Ranger software, V7.0.0, 10X Genomics).
Chemistry Single Cell 3' v3

tag: tissue

value: joints

value: Col12a1 KO gene+


title: Col12 WT

value: Col12a1 wt gene+


title: Healthy Control 7

source_name: Bronchoalveolar lavage cells from: Healthy Control 7

tag: white_blood_cell_count (x 10^6)

tag: slide


title: Healthy Control 6

source_name: Bronchoalveolar lavage cells from: Healthy Control 6


title: Healthy Control 5

source_name: Bronchoalveolar lavage cells from: Healthy Control 5


title: HeLa R634Q rep 1

description:
HeLa RNAseq sample 4
HeLa_read_counts.txt


title: Healthy Control 8

source_name: Bronchoalveolar lavage cells from: Healthy Control 8


title: embryo, day-5, ferticult, rep2

source_name: embryo

tag: day

tag: culture media_day-2

value: Ferticult

tag: culture media_day-5


title: M149 KD

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
The reads were trimmed for adapters and filtered by sequencing Phred quality (>= Q15) using fastp.
Trimmed reads were aligned to the mouse transcriptome (Ensembl version 99) using kallisto.
Transcript counts were converted to gene counts using tximport.
Assembly: GRCm38
Supplementary files format and content: CSV file included gene counts for each sample

source_name: Islets

extract_protocol:
Islets were resuspended in RNA extraction buffer and the RNeasy Micro Kit (No. 74004) was used to purify RNA.
RNA libraries for RNA-seq were prepared using Truseq Stranded mRNA Prep Kit following manufacturer's protocols.

value: Islets

tag: treatment

value: KD


title: HeLa WT rep 3

description:
HeLa RNAseq sample 3
HeLa_read_counts.txt

source_name: HeLa (Feldman at al., 2019)

tag: cell line

tag: cell type

tag: genotype

value: TetO:Cas9; RBM20-WT


title: embryo, day-5, ferticult, rep1

tag: couple


title: Umbilical Cord MSC rep3

city: TianJin

first: Yuchen

last: Gao

address: 288 Nanjin Road, Tianjin

institute: Institute of Hematology &Blood Disease Hospital,Chinese Academy of Medical Sciences

description: single cell rna

data_processing:
Basecalls performed using bcl2fastq version 2.1.9
The quality of raw sequencing data was evaluated by FastQC. The Cellranger toolkit (version 2.2.0, 10X Genomics) was used to perform sample demultiplexing and mapping reads to the human genome reference data with default settings
Each sample was generated with a gene expression matrix which records the UMI counts per gene associated with each cell barcode. Further analysis (data filtering and normalizing, identification of highly variable genes, dimensionality reduction and clustering, discovery of differentially expressed genes) was performed using R (version 3.6.1) and the Seurat R package (version 3.1.0). Cells with low-quality and very high mitochondrial genome transcripts were removed according to a sample specific cutoff.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every single cell

source_name: Umbilical cord mesenchymal stroma cells

growth_protocol: The collected MSCs from different tissue origins were separately seeded into 75cm2 cell culture flask at the density of 1×106/cm2 with DMEM/F12 medium plus 10% FBS, 2mM L-glutamine and 1% penicillin/streptomycin solution. Cells were cultivated at 37°C in a saturated humidified atmosphere containing 5% CO2 in the incubator . After 72 h, the non-adherent cells were removed by washing with PBS solution, after then the medium was changed every three days. The collection of MSCs from each sample was performed at P3 when the cells reached 80% confluence. Samples were treated with 0.05% trypsin for 3 min at 37˚C, the digestion was then stopped by washing twice and re-suspending in PBS containing 0.04% BSA. Cell viability and counting were assessed with trypan blue by microscopy, and single cell suspensions with viabilities >85% were used for library preparation.

extract_protocol:
Each sample was calculated to an appropriate volume for a target capture of 5000 cells. Single cells were then encapsulated into emulsion droplets using Chromium Controller (10x Genomics).
scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Reagent Kits V2 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s protocol.

value: Wharton's Jelly of umbilical cord

tag: age

tag: gender

value: female


title: Healthy Control 2

source_name: Bronchoalveolar lavage cells from: Healthy Control 2

tag: diagnosis

value: Control

tag: Sex

value: F

tag: race

value: White

tag: hispanic

value: No

tag: smoker

value: Never


title: HeLa WT rep 1

description:
HeLa RNAseq sample 1
HeLa_read_counts.txt

value: HeLa (Feldman at al., 2019)

value: human adenocarcinoma


title: M145 KD

tag: tissue


title: Healthy Control 3

source_name: Bronchoalveolar lavage cells from: Healthy Control 3

value: M

tag: tlc

tag: fvc

tag: dlco

tag: white_blood_cell_count (x 10^6)

tag: slide


title: M150 KD

tag: treatment


title: male ME/CFS patient, recovery, replicate 13

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

data_processing:
Raw reads were mapped to the reference human genome (GRCh38, release 86) using GSNAP, HISAT2, and STAR software.
For the analysis of differentially expressed known genes, reads for each gene aligned by GSNAP and HISAT2 were counted using HTSeq software. Alignment by STAR was run with the option “quantMode TranscriptomeSAM” that allowed for the counting of reads aligned to each gene.
Raw counts from HTSeq and STAR were imported into Bioconductor/R package DESeq2, normalized, and tested for differential gene expression. We used the Bioconductor/R package DEXSeq to count individual exons and compare expression of exons. This analysis was done separately for the files produced by each aligner.
Only genes with raw counts equal or more than 50 in all samples in at least one group were used for the differential gene expression analysis
For further analysis, we selected genes and exons that were differentially expressed based on one of the following two criteria: (a) either a fold change (FC) > |1.5| and false discovery rate (FDR) < 0.10 in one out of the three aligners and FC > |1.4| and FDR < 0.15 in the remaining two aligners, OR (b) a FC > |1.5| and FDR < 0.10 in two out of three aligners.
Assembly: GRCh38, release 86
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample, where only genes that had raw counts equal or more than 50 in all samples in at least one group

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted using RNAzol (Molecular Research Center) according to the manufacturer’s instructions. RNA quality was assessed using Agilent TapeStation 4200 (Agilent Technologies). All RNA samples had an RNA Integrity number (RIN) above seven.
The libraries were generated using Illumina TruSeq Stranded Total RNA Library Prep Kit

tag: cell type

value: peripheral blood mononuclear cells

tag: disease state

value: ME/CFS patients

tag: time point in exercise

value: T2 (recovery)

value: male


title: Umbilical Cord MSC rep2

description: single cell rna

tag: age


title: M153 CTRL

value: Islets

value: CTRL


title: M152 CTRL


title: Healthy Control 1

source_name: Bronchoalveolar lavage cells from: Healthy Control 1


title: male ME/CFS patient, recovery, replicate 12


title: M151 CTRL


title: Placenta Chorionic Membrane MSC rep2

description: single cell rna

source_name: Placenta chorionic membrane mesenchymal stroma cells

value: Chorion of placenta

tag: gender


title: Umbilical Cord MSC rep1

description: single cell rna

value: Wharton's Jelly of umbilical cord


title: Placenta Chorionic Membrane MSC rep3

description: single cell rna

value: female


title: male ME/CFS patient, recovery, replicate 10


title: Placenta Chorionic Membrane MSC rep1

description: single cell rna


title: M148 CTRL


title: M146 KD

value: KD


title: HeLa WT rep 2

description:
HeLa RNAseq sample 2
HeLa_read_counts.txt

tag: cell line

tag: genotype

value: TetO:Cas9; RBM20-WT


title: male ME/CFS patient, recovery, replicate 11

tag: Sex


title: male ME/CFS patient, recovery, replicate 9


title: Beryllium Sensitized 30

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 30

tag: diagnosis

value: BeS

tag: race

value: White

tag: hispanic


title: Healthy Control 4

source_name: Bronchoalveolar lavage cells from: Healthy Control 4

value: Control

value: Yes

tag: smoker

value: Never

tag: tlc


title: Beryllium Sensitized 29

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 29

value: F

value: No

value: Former

tag: fvc

tag: dlco


title: Beryllium Sensitized 27

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 27

value: M

tag: white_blood_cell_count (x 10^6)

tag: slide


title: Beryllium Sensitized 28

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 28


title: Beryllium Sensitized 24

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 24


title: Bone Marrow MSC rep3

description: single cell rna

source_name: Bone marrow mesenchyaml stroma cells

tag: tissue

value: Bone marrow

value: male


title: male ME/CFS patient, recovery, replicate 8

tag: cell type

value: peripheral blood mononuclear cells

tag: disease state

value: ME/CFS patients

value: T2 (recovery)


title: male ME/CFS patient, recovery, replicate 7

tag: time point in exercise


title: Mus musculus_male_tibialis anterior_6 months_rep6

city: Tarrytown

first: Kun

last: Xiong

state: NY

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

data_processing:
Sequencing reads were processed with ArrayStudio RNA-seq pipeline to quantify gene expression levels
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: tibialis anterior

growth_protocol: Male and female C57BL/6J mice were purchased from Jackson Laboratory (USA) at various ages and maintained at Regeneron animal holding facilities for ~12 weeks prior to tissue collection under specific pathogen free (SPF) conditions. Mice were housed in groups of 5 per cage with controlled temperature and light (22℃, 12-h light/12-h dark cycle: lights on at 0600h/lights off at 1800h) and with ad libitum access to food (PicoLab Rodent Diet 20, Lab Supply) and water. Male Sprague Dawley (SD) rats were purchased at 3-4 weeks of age from Envigo (Indianapolis, USA) and aged at Envigo under specific pathogen free (SPF) conditions. Rats were imported to New York Medical College animal holding facilities 8-12 weeks prior to tissue collection. Once imported, rats were housed two per cage at the SPF facility with controlled temperature and light (22℃, 12-h light/12-h dark cycle: lights on at 0600h/lights off at 1800h) and with ad libitum access to food (2014 Teklad Global 14% Protein diet, Envigo) and water.

extract_protocol:
Tissue collection occurred over several months and tissues from the same age group (n = 8-12 per group) were collected on the same day between 9am and 1pm. Prior to tissue collection, mice were killed by CO2 asphyxiation. Diaphragm, gastrocnemius, soleus, and tibialis anterior muscles were preserved in RNA later and stored at -80℃. RNA was extracted from tissues preserved in RNA later using MagMax-96 Total RNA isolation kit (Thermo Fisher). The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies) and the integrity assessed using Fragment Analyzer (Agilent).
The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies) and the integrity assessed using Fragment Analyzer (Agilent). Strand specific total RNA-seq libraries were prepared using Kapa RNA HyperPrep kit (Roche) with Fastselect rRNA HMR ribosome RNA removal kit (Qiagen).

value: tibialis anterior

tag: strain

tag: time

value: 6 months


title: Mus musculus_male_tibialis anterior_6 months_rep7


title: Mus musculus_male_tibialis anterior_6 months_rep5


title: Adipose Tissue MSC rep3

description: single cell rna

source_name: Adipose tissue mesenchyaml stroma cells

value: Adipose tissue

tag: age

tag: gender

value: female


title: male ME/CFS patient, recovery, replicate 4

tag: Sex


title: male ME/CFS patient, recovery, replicate 6


title: Mus musculus_male_tibialis anterior_6 months_rep4


title: Mus musculus_male_tibialis anterior_6 months_rep3


title: Beryllium Sensitized 25

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 25

tag: diagnosis

value: BeS

tag: race

value: White


title: Adipose Tissue MSC rep1

description: single cell rna


title: Beryllium Sensitized 26

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 26

tag: hispanic

tag: smoker


title: Adipose Tissue MSC rep2

description: single cell rna


title: Beryllium Sensitized 22

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 22

value: African American

tag: tlc

tag: fvc


title: male ME/CFS patient, recovery, replicate 3


title: Bone Marrow MSC rep1

description: single cell rna


title: Beryllium Sensitized 23

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 23

tag: dlco

tag: white_blood_cell_count (x 10^6)


title: male ME/CFS patient, recovery, replicate 5


title: male ME/CFS patient, recovery, replicate 2


title: Mus musculus_male_tibialis anterior_6 months_rep1

tag: tissue


title: A03

city: SHANGHAI

first: Grayson

last: Gong

state: SHANGHAI

address: xinjunhuan road

institute: OEBIO

data_processing:
The Cell Ranger software pipeline (version 2.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: mesenchymal stem cells (MSCs)

growth_protocol: The culture medium for MSCs was added 1% antibiotics and 10%FBS with 1ug/100 bFGF. All of the cells were cultured in  the humidified incubator with standard cultivation conitions(37C,5%CO2)

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v2 Kits according to the manufacturer’s protocol.

treatment_protocol: At the first or second passage, the MSCs for individual donors were trypsinized with TrypLE Express and washed twice with 1xPBS at the same day. All of the cells were sorted by flow cytometry for specific surface markers(Positive for CD90,CD73,CD105, and negative for CD11b,CD19,CD34,CD45, and HLA-DR)

value: Adipose

tag: cell type

value: Adipose-derived MSCs

tag: growth protocol

value: In vitro expansion


title: Bone Marrow MSC rep2

description: single cell rna


title: A02


title: Mus musculus_male_tibialis anterior_6 months_rep2


title: A01


title: Beryllium Sensitized 21

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 21

value: F

value: No

value: Never

tag: slide


title: Mus musculus_male_tibialis anterior_27 months_rep9

tag: strain

value: male

value: 27 months


title: male ME/CFS patient, recovery, replicate 1

source_name: peripheral blood mononuclear cells

value: peripheral blood mononuclear cells

tag: disease state

value: ME/CFS patients

tag: time point in exercise


title: male ME/CFS patient, maximal exertion, replicate 13

value: T1 (maximal exertion)


title: Beryllium Sensitized 20

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 20

value: M

tag: age


title: Mus musculus_male_tibialis anterior_6 months_rep0

value: tibialis anterior

tag: Sex

tag: time

value: 6 months


title: U02

value: Umbilical cord

value: Umbilical-cord-derived MSCs


title: Beryllium Sensitized 18

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 18

tag: diagnosis

value: BeS

tag: race

value: White

value: Former


title: Beryllium Sensitized 19

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 19

tag: hispanic

tag: smoker


title: Beryllium Sensitized 16

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 16

tag: tlc

tag: fvc


title: Mus musculus_male_tibialis anterior_27 months_rep7


title: male ME/CFS patient, maximal exertion, replicate 11


title: Beryllium Sensitized 17

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 17

tag: dlco

tag: white_blood_cell_count (x 10^6)


title: male ME/CFS patient, maximal exertion, replicate 12

tag: cell type


title: Mus musculus_male_tibialis anterior_27 months_rep6

tag: tissue


title: U01

tag: growth protocol

value: In vitro expansion


title: male ME/CFS patient, maximal exertion, replicate 10


title: B03

value: Bone marrow

value: Bone-marrow-derived MSCs


title: Mus musculus_male_tibialis anterior_27 months_rep5

tag: strain


title: male ME/CFS patient, maximal exertion, replicate 9

tag: disease state


title: Mus musculus_male_tibialis anterior_27 months_rep4


title: B02


title: Mus musculus_male_tibialis anterior_27 months_rep8


title: male ME/CFS patient, maximal exertion, replicate 8

tag: time point in exercise


title: Beryllium Sensitized 13

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 13

tag: age

value: No

tag: slide


title: D03

value: Dermis

value: Dermis-derived MSCs


title: male ME/CFS patient, maximal exertion, replicate 7

value: peripheral blood mononuclear cells

tag: Sex

value: male


title: Beryllium Sensitized 14

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 14

tag: diagnosis

value: F


title: Beryllium Sensitized 11

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 11

value: M

tag: race


title: Beryllium Sensitized 12

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 12

tag: hispanic


title: Beryllium Sensitized 10

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 10

tag: smoker


title: Beryllium Sensitized 15

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 15

value: Yes

value: Never

tag: tlc


title: Mus musculus_male_tibialis anterior_27 months_rep2

source_name: tibialis anterior

value: tibialis anterior

tag: time

value: 27 months


title: male ME/CFS patient, maximal exertion, replicate 6

value: ME/CFS patients

value: T1 (maximal exertion)


title: male ME/CFS patient, maximal exertion, replicate 5


title: Mus musculus_male_tibialis anterior_27 months_rep1


title: Mus musculus_male_tibialis anterior_27 months_rep0


title: male ME/CFS patient, maximal exertion, replicate 4


title: D01


title: D02


title: Beryllium Sensitized 9

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 9

value: BeS

value: White

tag: fvc

tag: dlco


title: Mus musculus_male_tibialis anterior_24 months_rep9

value: 24 months


title: Mus musculus_male_tibialis anterior_27 months_rep3


title: male ME/CFS patient, maximal exertion, replicate 3

tag: cell type


title: Mus musculus_male_tibialis anterior_24 months_rep8

tag: tissue


title: B01

value: Bone marrow

value: Bone-marrow-derived MSCs

tag: growth protocol

value: In vitro expansion


title: male ME/CFS patient, maximal exertion, replicate 2


title: male ME/CFS patient, maximal exertion, replicate 1


title: male ME/CFS patient, baseline, replicate 9

value: T0 (baseline)


title: Mus musculus_male_tibialis anterior_24 months_rep7

tag: strain


title: male ME/CFS patient, baseline, replicate 8

value: peripheral blood mononuclear cells

tag: disease state


title: Mus musculus_male_tibialis anterior_24 months_rep6

value: male


title: male ME/CFS patient, baseline, replicate 7

tag: time point in exercise


title: Mus musculus_male_tibialis anterior_24 months_rep5


title: Mus musculus_male_tibialis anterior_24 months_rep4


title: Mus musculus_male_tibialis anterior_24 months_rep3


title: Beryllium Sensitized 7

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 7

tag: age

value: No

tag: white_blood_cell_count (x 10^6)


title: Beryllium Sensitized 5

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 5

tag: Sex

value: M

tag: slide


title: Mus musculus_male_tibialis anterior_24 months_rep2


title: Beryllium Sensitized 8

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 8

tag: diagnosis

value: F

tag: race

value: Former


title: Beryllium Sensitized 4

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 4

tag: hispanic

tag: smoker


title: Beryllium Sensitized 3

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 3

value: Never

tag: tlc


title: Beryllium Sensitized 1

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 1

tag: fvc


title: Chronic Beryllium Disease 30

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 30

value: CBD

tag: dlco


title: Beryllium Sensitized 6

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 6


title: male ME/CFS patient, baseline, replicate 5

source_name: peripheral blood mononuclear cells

tag: cell type

value: ME/CFS patients


title: Beryllium Sensitized 2

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 2


title: Mus musculus_male_tibialis anterior_24 months_rep1

tag: tissue

value: tibialis anterior

tag: time


title: male ME/CFS patient, baseline, replicate 4


title: Chronic Beryllium Disease 28

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 28


title: Chronic Beryllium Disease 29

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 29


title: male ME/CFS patient, baseline, replicate 6


title: Mus musculus_male_tibialis anterior_21 months_rep7

tag: strain

value: 21 months


title: male ME/CFS patient, baseline, replicate 2

tag: disease state


title: Mus musculus_male_tibialis anterior_21 months_rep6


title: male ME/CFS patient, baseline, replicate 1

tag: time point in exercise


title: Mus musculus_male_tibialis anterior_24 months_rep0


title: Mus musculus_male_tibialis anterior_21 months_rep5


title: male healthy control, recovery, replicate 5

value: healthy control

value: T2 (recovery)


title: Mus musculus_male_tibialis anterior_21 months_rep4


title: Chronic Beryllium Disease 26

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 26

tag: age

value: White


title: Mus musculus_male_tibialis anterior_21 months_rep3


title: male healthy control, recovery, replicate 3


title: male healthy control, recovery, replicate 4


title: Mus musculus_male_tibialis anterior_21 months_rep2


title: Chronic Beryllium Disease 25

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 25

tag: white_blood_cell_count (x 10^6)


title: male healthy control, recovery, replicate 2

tag: Sex


title: Chronic Beryllium Disease 24

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 24

tag: slide


title: Chronic Beryllium Disease 22

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 22

tag: diagnosis


title: Mus musculus_male_tibialis anterior_21 months_rep0

source_name: tibialis anterior


title: male healthy control, recovery, replicate 1


title: male healthy control, maximal exertion, replicate 5

value: T1 (maximal exertion)


title: Chronic Beryllium Disease 23

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 23

tag: race


title: Chronic Beryllium Disease 21

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 21

tag: hispanic


title: Healthy Control 8

type: genomic

data_processing: .idat files were processed using default parameters in the sesame R package.

label: Cy5 and Cy3

source_name: Bronchoalveolar lavage cells from: Healthy Control 8

value: Control

tag: smoker

tag: array


title: Chronic Beryllium Disease 19

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 19

value: Yes

value: prednisone & methotrexate

tag: tlc

tag: fvc


title: male ME/CFS patient, baseline, replicate 3

tag: cell type

value: peripheral blood mononuclear cells

value: T0 (baseline)

value: male


title: Chronic Beryllium Disease 20

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 20

value: F

value: No

tag: dlco


title: Healthy Control 10

source_name: Bronchoalveolar lavage cells from: Healthy Control 10

value: M

value: Never


title: Chronic Beryllium Disease 18

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 18

value: CBD


title: Mus musculus_male_tibialis anterior_18 months_rep6

tag: tissue

value: tibialis anterior

tag: time

value: 18 months


title: male healthy control, maximal exertion, replicate 4

tag: disease state

value: healthy control


title: Chronic Beryllium Disease 27

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 27


title: Mus musculus_male_tibialis anterior_21 months_rep1

tag: strain

value: 21 months


title: Mus musculus_male_tibialis anterior_18 months_rep5


title: Healthy Control 12

source_name: Bronchoalveolar lavage cells from: Healthy Control 12

tag: age

value: White


title: male healthy control, maximal exertion, replicate 2

source_name: peripheral blood mononuclear cells

tag: time point in exercise

value: T1 (maximal exertion)


title: Mus musculus_male_tibialis anterior_18 months_rep4

tag: Sex


title: Chronic Beryllium Disease 17

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 17

tag: white_blood_cell_count (x 10^6)

tag: slide


title: male healthy control, maximal exertion, replicate 3


title: Mus musculus_male_tibialis anterior_18 months_rep3


title: Healthy Control 7

source_name: Bronchoalveolar lavage cells from: Healthy Control 7

tag: diagnosis

value: Control

tag: race

value: Former


title: Chronic Beryllium Disease 16

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 16

tag: hispanic

tag: smoker


title: male healthy control, baseline, replicate 1


title: Mus musculus_male_tibialis anterior_18 months_rep1


title: Chronic Beryllium Disease 15

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 15

value: prednisone & methotrexate

tag: tlc


title: Chronic Beryllium Disease 14

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 14

tag: fvc


title: Healthy Control 5

source_name: Bronchoalveolar lavage cells from: Healthy Control 5

tag: array


title: Mus musculus_male_tibialis anterior_18 months_rep0

source_name: tibialis anterior


title: Chronic Beryllium Disease 12

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 12

value: Yes

tag: dlco


title: Healthy Control 2

source_name: Bronchoalveolar lavage cells from: Healthy Control 2


title: Mus musculus_male_tibialis anterior_12 months_rep7

tag: tissue

value: 12 months


title: male healthy control, maximal exertion, replicate 1

tag: cell type

value: peripheral blood mononuclear cells

value: male


title: Mus musculus_male_tibialis anterior_18 months_rep2

tag: time


title: Healthy Control 11

source_name: Bronchoalveolar lavage cells from: Healthy Control 11


title: Chronic Beryllium Disease 13

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 13


title: Chronic Beryllium Disease 11

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 11

value: No

value: prednisone


title: Mus musculus_male_tibialis anterior_12 months_rep6

tag: strain


title: Chronic Beryllium Disease 10

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 10

value: M

tag: age


title: Mus musculus_male_tibialis anterior_12 months_rep4


title: Healthy Control 6

source_name: Bronchoalveolar lavage cells from: Healthy Control 6

value: Never


title: Chronic Beryllium Disease 9

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 9

value: CBD

value: F


title: Healthy Control 1

source_name: Bronchoalveolar lavage cells from: Healthy Control 1


title: Healthy Control 3

source_name: Bronchoalveolar lavage cells from: Healthy Control 3


title: Mus musculus_male_tibialis anterior_12 months_rep3

value: tibialis anterior


title: Healthy Control 4

source_name: Bronchoalveolar lavage cells from: Healthy Control 4


title: Healthy Control 9

source_name: Bronchoalveolar lavage cells from: Healthy Control 9


title: Chronic Beryllium Disease 7

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 7


title: CHP134-ChIPseq-DMSO_WDR5-rep3

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Peaks were called by MACS2 with a q-value of 0.05.
Differential binding peaks were identified using DiffBind.
Assembly: hg19
Supplementary files format and content: peaks for each sample

growth_protocol: CHP-134 and IMR-32 cell lines were maintained in RPMI 1640 with l-glutamine (Corning) with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin

extract_protocol:
For ChIP-seq, chromatin from 10 million IMR-32 cells or CHP-134 cells treated with 0.005% dimethyl sulfoxide were crosslinked in 1% formaldehyde for 10 min, followed by quenching in 0.125 M glycine. Nuclei were extracted and chromatin was generated from nuclei through lysis in FALB buffer (50 mM HEPES, pH 7.5, 1% Triton, 1 mM EDTA, 140 mM NaCl) containing 1% SDS, PMSF, and protease inhibitor cocktail (Roche) using a Diagenode Bioruptor Plus instrument.
Three ChIPs from identical samples were pooled together and purified using a Qiagen PCR purification kit. Eluted DNA was used to generate libraries  using the Ultra II DNA library Prep protocol (New England Biolabs).
Ultra II DNA library Prep protocol (New England Biolabs) with dual index primers.

treatment_protocol: IMR-32 cells were untreated prior to chromatin collection. CHP-134 cells were treated with either 0.0005% DMSO or C91 (419) for 4 hrs prior to chromatin collection.

tag: cell line

tag: agent

value: DMSO

tag: chip antibody

value: 5 microliter of anti-WDR5 (Cell Signaling, 13105)


title: Beryllium Sensitized 29

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 29

value: BeS

tag: Sex

value: White

tag: white_blood_cell_count (x 10^6)

tag: slide


title: Chronic Beryllium Disease 6

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 6

tag: diagnosis

tag: race

tag: hispanic

value: Former


title: Mus musculus_male_tibialis anterior_12 months_rep2


title: CHP134-ChIPseq-DMSO_WDR5-rep2


title: Mus musculus_male_tibialis anterior_12 months_rep1


title: Beryllium Sensitized 25

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 25

tag: smoker

tag: tlc

tag: fvc


title: Mus musculus_male_tibialis anterior_12 months_rep5

source_name: tibialis anterior

tag: tissue


title: Chronic Beryllium Disease 5

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 5

tag: dlco


title: Beryllium Sensitized 26

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 26

tag: array


title: CHP134-ChIPseq-DMSO_WDR5-rep1


title: Mus musculus_male_tibialis anterior_12 months_rep0

tag: strain

tag: time


title: CHP134-ChIPseq-DMSO_MYC-rep3

tag: cell line

value: 5 microliter of custom serum to target N-MYC


title: Mus musculus_male_soleus_6 months_rep7

source_name: soleus

value: soleus

value: 6 months


title: Beryllium Sensitized 28

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 28

tag: age


title: Chronic Beryllium Disease 4

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 4


title: Beryllium Sensitized 23

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 23


title: CHP134-ChIPseq-DMSO_MYC-rep2

tag: agent

tag: chip antibody


title: Mus musculus_male_soleus_6 months_rep6

tag: Sex


title: Beryllium Sensitized 22

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 22

value: African American

tag: white_blood_cell_count (x 10^6)

tag: slide


title: Chronic Beryllium Disease 3

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 3

tag: diagnosis

tag: race


title: Chronic Beryllium Disease 2

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 2

tag: hispanic

tag: smoker


title: CHP134-ChIPseq-DMSO_MYC-rep1


title: Beryllium Sensitized 24

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 24

tag: tlc

tag: fvc


title: Beryllium Sensitized 20

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 20

tag: dlco


title: CHP134-ChIPseq-IgG-rep3

value: 800 ng IgG (Cell Signaling, 2729S)


title: Mus musculus_male_soleus_6 months_rep4

tag: tissue

value: male


title: Mus musculus_male_soleus_6 months_rep5

tag: strain


title: CHP134-ChIPseq-IgG-rep2


title: Mus musculus_male_soleus_6 months_rep3

tag: time


title: Beryllium Sensitized 30

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 30

value: No

tag: array


title: Chronic Beryllium Disease 8

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 8

value: M

tag: age

value: Yes


title: Beryllium Sensitized 21

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 21

value: Never


title: Chronic Beryllium Disease 1

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 1

value: CBD


title: CHP134-ChIPseq-IgG-rep1

tag: cell line


title: Mus musculus_male_soleus_6 months_rep2


title: Embryonic hippocampal neurons, RO48-treated, Day 2, Sample 2

city: Port Washington

first: Jeffrey

middle: Adam

last: Lowell

state: New York

address: 74A Firwood Road

institute: Northwell Health

data_processing:
Alignment was performed using the splice-aware map- ping tool STAR with default parameters.
Mapped reads aligned to genes were tabulated by gene ID and counted using the STAR package implementation of htseq-count with default parameters.
A read is counted if it overlaps with only one gene (uniquely mapped read), and paired-end reads are checked for overlap on both ends for greater fidelity.
Assembly: Rattus norvegicus (Rnor_6.0.97)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Embryonic hippocampal neurons

growth_protocol: Embryonic hippocampal neurons were grown in NbActiv4 media at 1 × 10^6 cells per well in a 12-well PDL-coated plate

extract_protocol:
RNA was collected from neurons according to the manu- facturer’s instructions using the PureLink RNA Mini Kit
Library preparation and RNA-seq were performed by Novogene (Sacramento, CA) using the Illumina TruSeq library preparation protocol. The libraries were sequenced using the next-generation Illumina NovaSeq 6000 platform

treatment_protocol: Neurons were treated with either DMSO (0.025%) or RO48 (10 μM) added to wells as 1 mL of CO2- equilibrated, 37 °C NbActiv4, 3 h after neurons were added to the culture dish.

tag: cell type

value: Embryonic hippocampal neurons

tag: genotype

value: WT

tag: treatment


title: Embryonic hippocampal neurons, RO48-treated, Day 2, Sample 3


title: Embryonic hippocampal neurons, RO48-treated, Day 2, Sample 1


title: Embryonic hippocampal neurons, DMSO-treated, Day 2, Sample 3

value: DMSO


title: Fig.3, HeLa ICS screen, lower, lib 6

description:
ICSscreen_maude_gene_stats.csv
ICS screen lower 6

data_processing:
RNAseq: Reads were aligned to GRCh38.101 using STAR (v2.7.5c), and bam files were sorted by coordinate using samtools (v.1.9). Read count files were generated with featureCounts52 v1.6.4 for each exon.   For differential gene expression analysis, DeSeq253 (v. 1.36.0) was used, and pairwise comparisons between genotypes were performed (expression ~ genotype). To calculate the percentage of spliced-in values (PSI-values), inclusive and exclusive reads were counted directly from the BAM files as described in Schafer et al., 2015. The PSI-values are then calculated as the ratio of inclusive reads to the sum of inclusive and exclusive reads per each exon.
ICS screen: Abundance of gRNA was quantified from the sequencing reads using MAGeCK (v 0.5.9) tool with default parameters. To account for differences in sequencing depth, raw gRNA counts were normalized to the median count of the targeting control gRNAs in the corresponding sample. Scaling of the normalized counts was done by multiplication with the median count of targeting controls across all samples. The MAUDE package for R was used for hit calling, using targeting controls as a reference for MAUDE analysis.
Assembly: GRCh38.101
Supplementary files format and content: For RNAseq: tab-delimited text files containing read counts for all samples for all genes;  tab-delimited text files containing PSI values for all samples for all exons;  For ICS screen: csv file containing gene stats from MAUDE.

source_name: HeLa (Feldman at al., 2019)

growth_protocol: iPSC-CMs: RPMI 1640 supplemented with addition of B27 supplement, culture plates were coated with Vitronectin (VTN-N) Recombinant Human Protein, Truncated; HeLa: were maintained in DMEM, high glucose supplemented with 10% FBS, 1% Sodium Pyruvate, and 1% Penicillin-Streptomycin; in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA from iPSC-CMs: fixed cells were pelleted after ICS sorting, reverse crosslinked at 56C for 1h in the presence of proteinase K, and RNA was extracted using the TRIzol-chloroform-isopropanol protocol; 1-10ng of RNA were used for library preparation. DNA from HeLa: cells were pelleted and genomic DNA was extracted using NEB Monarch genomic DNA purification kit, including the RNase treatment and elution in 50 µl elution buffer; 100-500 ng of DNA was used for library preparation.
iPSC-CMs: RNA libraries were generated using SMARTer RNA-Seq Kit v3 - pico (Takara Bio) according to manufacturer's instructions; HeLa ICS screen: see detailed methods in Schraivogel et al., 2022.
iPSC-CMs: RNAseq; HeLa ICS screen: Amplicon seq.

value: HeLa (Feldman at al., 2019)

value: human adenocarcinoma

value: TetO-Cas9; eGFP-RBM20-WT

value: lower


title: Beryllium Sensitized 27

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 27

value: BeS

tag: Sex

value: White

tag: white_blood_cell_count (x 10^6)

tag: slide


title: Mus musculus_male_soleus_6 months_rep1

value: soleus

value: 6 months


title: Embryonic hippocampal neurons, DMSO-treated, Day 2, Sample 2


title: Mus musculus_male_soleus_6 months_rep0

value: male


title: Beryllium Sensitized 17

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 17

tag: diagnosis

value: F

tag: race

tag: hispanic

value: No

value: Former


title: Fig.3, HeLa ICS screen, lower, lib 5

description:
ICSscreen_maude_gene_stats.csv
ICS screen lower 5


title: Embryonic hippocampal neurons, DMSO-treated, Day 2, Sample 1


title: Beryllium Sensitized 19

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 19

value: M

tag: smoker

value: Never

tag: tlc

tag: fvc


title: Fig.3, HeLa ICS screen, lower, lib 4

description:
ICSscreen_maude_gene_stats.csv
ICS screen lower 4


title: Mus musculus_male_soleus_27 months_rep9

source_name: soleus

tag: tissue

tag: strain

value: 27 months


title: Rattus norvegicus_male_tibialis anterior_9 months_rep9

data_processing:
Sequencing reads were processed with ArrayStudio RNA-seq pipeline to quantify gene expression levels
Assembly: B6.0
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: tibialis anterior

value: tibialis anterior

value: Sprague Dawley

tag: time

value: 9 months


title: Beryllium Sensitized 16

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 16

tag: age

tag: dlco

tag: array


title: Mus musculus_male_soleus_27 months_rep8


title: Rattus norvegicus_male_tibialis anterior_9 months_rep8


title: Fig.3, HeLa ICS screen, lower, lib 2

description:
ICSscreen_maude_gene_stats.csv
ICS screen lower 2

tag: cell line

value: HeLa (Feldman at al., 2019)

tag: cell type

value: human adenocarcinoma

tag: genotype


title: Mus musculus_male_soleus_27 months_rep7

tag: Sex


title: Rattus norvegicus_male_tibialis anterior_9 months_rep7


title: Fig.3, HeLa ICS screen, lower, lib 1

description:
ICSscreen_maude_gene_stats.csv
ICS screen lower 1

value: TetO-Cas9; eGFP-RBM20-WT

tag: treatment

value: lower


title: Mus musculus_male_soleus_27 months_rep6


title: Fig.3, HeLa ICS screen, lower, lib 3

description:
ICSscreen_maude_gene_stats.csv
ICS screen lower 3


title: Beryllium Sensitized 13

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 13

tag: diagnosis

value: BeS

value: White

tag: white_blood_cell_count (x 10^6)

tag: slide


title: Rattus norvegicus_male_tibialis anterior_9 months_rep6


title: Beryllium Sensitized 18

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 18

tag: race

tag: hispanic

tag: smoker


title: Beryllium Sensitized 12

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 12

tag: tlc

tag: fvc


title: Rattus norvegicus_male_tibialis anterior_9 months_rep5

tag: tissue

tag: strain

tag: time


title: Mus musculus_male_soleus_27 months_rep5

value: soleus


title: Beryllium Sensitized 14

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 14

tag: age

tag: dlco

tag: array


title: Mus musculus_male_soleus_27 months_rep4

value: male


title: Beryllium Sensitized 15

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 15

value: Yes


title: Fig.3, HeLa ICS screen, upper, lib 5

description:
ICSscreen_maude_gene_stats.csv
ICS screen upper 5

tag: cell line

tag: cell type

tag: genotype

value: upper


title: Beryllium Sensitized 11

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 11

tag: diagnosis

tag: Sex

value: No

value: Former


title: Rattus norvegicus_male_tibialis anterior_9 months_rep3


title: Rattus norvegicus_male_tibialis anterior_9 months_rep4


title: Fig.3, HeLa ICS screen, upper, lib 3

description:
ICSscreen_maude_gene_stats.csv
ICS screen upper 3

tag: treatment


title: Mus musculus_male_soleus_27 months_rep3


title: Rattus norvegicus_male_tibialis anterior_9 months_rep2


title: Fig.3, HeLa ICS screen, upper, lib 2

description:
ICSscreen_maude_gene_stats.csv
ICS screen upper 2


title: Mus musculus_male_soleus_27 months_rep2


title: Mus musculus_male_soleus_27 months_rep1


title: Fig.3, HeLa ICS screen, upper, lib 1

description:
ICSscreen_maude_gene_stats.csv
ICS screen upper 1


title: Mus musculus_male_soleus_27 months_rep0


title: Fig.3, HeLa ICS screen, upper, lib 6

description:
ICSscreen_maude_gene_stats.csv
ICS screen upper 6


title: Beryllium Sensitized 10

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 10

value: M

tag: race

tag: white_blood_cell_count (x 10^6)

tag: slide


title: Rattus norvegicus_male_tibialis anterior_9 months_rep10


title: Rattus norvegicus_male_tibialis anterior_9 months_rep11


title: Rattus norvegicus_male_tibialis anterior_9 months_rep1


title: Mus musculus_male_soleus_24 months_rep9

value: 24 months


title: Fig.3, HeLa ICS screen, input, lib 6

description:
ICSscreen_maude_gene_stats.csv
ICS screen input 6

value: input


title: Mus musculus_male_soleus_24 months_rep8


title: Rattus norvegicus_male_tibialis anterior_9 months_rep0

value: tibialis anterior

value: Sprague Dawley


title: Fig.3, HeLa ICS screen, input, lib 5

description:
ICSscreen_maude_gene_stats.csv
ICS screen input 5

value: HeLa (Feldman at al., 2019)


title: Fig.3, HeLa ICS screen, input, lib 4

description:
ICSscreen_maude_gene_stats.csv
ICS screen input 4

value: human adenocarcinoma


title: Mus musculus_male_soleus_24 months_rep7


title: Fig.3, HeLa ICS screen, input, lib 3

description:
ICSscreen_maude_gene_stats.csv
ICS screen input 3

value: TetO-Cas9; eGFP-RBM20-WT


title: Fig.3, HeLa ICS screen, input, lib 2

description:
ICSscreen_maude_gene_stats.csv
ICS screen input 2


title: Mus musculus_male_soleus_24 months_rep6


title: Mus musculus_male_soleus_24 months_rep5


title: Beryllium Sensitized 6

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 6

tag: hispanic

tag: smoker

value: Never

tag: tlc


title: Beryllium Sensitized 9

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 9

value: BeS

tag: fvc


title: Beryllium Sensitized 5

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 5

value: White


title: Fig.3, HeLa ICS screen, upper, lib 4

description:
ICSscreen_maude_gene_stats.csv
ICS screen upper 4

source_name: HeLa (Feldman at al., 2019)


title: Beryllium Sensitized 8

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 8

value: F


title: Rattus norvegicus_male_tibialis anterior_6 months_rep8

tag: tissue

tag: strain

value: male

tag: time

value: 6 months


title: Beryllium Sensitized 7

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 7

tag: age

tag: dlco

tag: array


title: Beryllium Sensitized 3

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 3


title: Beryllium Sensitized 4

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 4


title: Fig.3, HeLa ICS screen, input, lib 1

description:
ICSscreen_maude_gene_stats.csv
ICS screen input 1

tag: cell line

tag: cell type

tag: genotype


title: Mus musculus_male_soleus_24 months_rep4

source_name: soleus

value: soleus

tag: Sex


title: Rattus norvegicus_male_tibialis anterior_6 months_rep9

source_name: tibialis anterior


title: Rattus norvegicus_male_tibialis anterior_6 months_rep6


title: Chronic Beryllium Disease 28

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 28

tag: diagnosis

value: CBD

tag: race

value: No


title: Mus musculus_male_soleus_24 months_rep3


title: Rattus norvegicus_male_tibialis anterior_6 months_rep5


title: Beryllium Sensitized 1

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 1

value: M

tag: white_blood_cell_count (x 10^6)

tag: slide


title: Rattus norvegicus_male_tibialis anterior_6 months_rep4


title: Fig.2, iPSC-CMs, FS+NLS-R634Q, rep 2

description:
NLSseq_read_counts_all.txt
NLSseq_all.psi.txt
NLSseq_NLS-R634Q_2
NLS-R634Q sample 8

source_name: hiPSC-CMs (Briganti et al., 2020)

value: hiPSC-CMs (Briganti et al., 2020)

value: human cardiomyocites derived from iPSCs

value: FrameShift

tag: treatment

value: eGFP-NLS-RBM20-R634Q OE


title: Fig.2, iPSC-CMs, FS+NLS-R634Q, rep 1

description:
NLSseq_read_counts_all.txt
NLSseq_all.psi.txt
NLSseq_NLS-R634Q_1
NLS-R634Q sample 7


title: Mus musculus_male_soleus_24 months_rep2

value: 24 months


title: Mus musculus_male_soleus_24 months_rep1


title: Chronic Beryllium Disease 30

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 30

tag: hispanic

tag: smoker

tag: tlc


title: Rattus norvegicus_male_tibialis anterior_6 months_rep7

tag: tissue

value: tibialis anterior

tag: strain

value: Sprague Dawley


title: Chronic Beryllium Disease 26

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 26

tag: age

value: Never

tag: fvc


title: Fig.2, iPSC-CMs, FS+R634Q, rep 3

description:
NLSseq_read_counts_all.txt
NLSseq_all.psi.txt
NLSseq_R634Q_3
NLS-R634Q sample 6

value: eGFP-RBM20-R634Q OE


title: Mus musculus_male_soleus_24 months_rep0

tag: time


title: Rattus norvegicus_male_tibialis anterior_6 months_rep2


title: Rattus norvegicus_male_tibialis anterior_6 months_rep3


title: Fig.2, iPSC-CMs, FS+R634Q, rep 2

description:
NLSseq_read_counts_all.txt
NLSseq_all.psi.txt
NLSseq_R634Q_2
NLS-R634Q sample 5

tag: cell line


title: Mus musculus_male_soleus_21 months_rep7

value: 21 months


title: Rattus norvegicus_male_tibialis anterior_6 months_rep11


title: Chronic Beryllium Disease 24

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 24

value: White

tag: dlco

tag: array


title: Fig.2, iPSC-CMs, FS+R634Q, rep 1

description:
NLSseq_read_counts_all.txt
NLSseq_all.psi.txt
NLSseq_R634Q_1
NLS-R634Q sample 4

tag: cell type

tag: genotype


title: Chronic Beryllium Disease 25

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 25

tag: diagnosis

tag: Sex

tag: race


title: Mus musculus_male_soleus_21 months_rep6

value: male


title: Fig.2, iPSC-CMs, FS+NLS-R634Q, rep 3

description:
NLSseq_read_counts_all.txt
NLSseq_all.psi.txt
NLSseq_NLS-R634Q_3
NLS-R634Q sample 9

tag: treatment


title: Rattus norvegicus_male_tibialis anterior_6 months_rep10

value: 6 months


title: Rattus norvegicus_male_tibialis anterior_6 months_rep1


title: Fig.2, iPSC-CMs, FS+WT, rep 3

description:
NLSseq_read_counts_all.txt
NLSseq_all.psi.txt
NLSseq_WT_3
NLS-R634Q sample 3

value: eGFP-RBM20-WT OE


title: Mus musculus_male_soleus_21 months_rep5

value: soleus


title: Chronic Beryllium Disease 22

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 22

value: CBD

tag: hispanic

value: No

value: Former

tag: white_blood_cell_count (x 10^6)

tag: slide


title: Fig.2, iPSC-CMs, FS+WT, rep 2

description:
NLSseq_read_counts_all.txt
NLSseq_all.psi.txt
NLSseq_WT_2
NLS-R634Q sample 2

value: hiPSC-CMs (Briganti et al., 2020)

value: human cardiomyocites derived from iPSCs


title: Rattus norvegicus_male_tibialis anterior_6 months_rep0

tag: tissue


title: Mus musculus_male_soleus_21 months_rep3

tag: strain


title: Chronic Beryllium Disease 29

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 29

value: F

tag: age

tag: smoker

tag: tlc


title: Fig.1, iPSC-CMs, R634Q, rep 3

description:
P633Lsort_read_counts_all.txt
P633Lsort_all.psi.txt
P633Lsort_R634Q_3
P633L sort sample 12

tag: cell line


title: Fig.1, iPSC-CMs, R634Q, rep 2

description:
P633Lsort_read_counts_all.txt
P633Lsort_all.psi.txt
P633Lsort_R634Q_2
P633L sort sample 11


title: Fig.2, iPSC-CMs, FS+WT, rep 1

description:
NLSseq_read_counts_all.txt
NLSseq_all.psi.txt
NLSseq_WT_1
NLS-R634Q sample 1

value: FrameShift


title: Chronic Beryllium Disease 20

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 20

tag: fvc

tag: dlco


title: Chronic Beryllium Disease 23

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 23

value: M

tag: array


title: Mus musculus_male_soleus_21 months_rep2

tag: time


title: Mus musculus_male_soleus_21 months_rep1


title: Rattus norvegicus_male_tibialis anterior_27 months_rep7

value: tibialis anterior

value: Sprague Dawley

value: 27 months


title: Rattus norvegicus_male_tibialis anterior_27 months_rep8


title: Rattus norvegicus_male_tibialis anterior_27 months_rep9


title: Fig.1, iPSC-CMs, R634Q, rep 1

description:
P633Lsort_read_counts_all.txt
P633Lsort_all.psi.txt
P633Lsort_R634Q_1
P633L sort sample 10

tag: cell type

tag: genotype


title: Chronic Beryllium Disease 27

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 27

tag: diagnosis

tag: Sex

tag: race

value: Never


title: Mus musculus_male_soleus_21 months_rep0

value: 21 months


title: Chronic Beryllium Disease 19

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 19

value: White

tag: hispanic

value: Yes

value: prednisone & methotrexate

tag: white_blood_cell_count (x 10^6)


title: Chronic Beryllium Disease 21

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 21

tag: slide


title: Chronic Beryllium Disease 18

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 18


title: Beryllium Sensitized 2

source_name: Bronchoalveolar lavage cells from: Beryllium Sensitized 2

value: BeS


title: Rattus norvegicus_male_tibialis anterior_27 months_rep5

source_name: tibialis anterior

tag: tissue

tag: strain

value: male


title: Rattus norvegicus_male_tibialis anterior_27 months_rep6


title: Chronic Beryllium Disease 17

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 17

value: CBD

tag: age

value: No

tag: smoker


title: Mus musculus_male_soleus_18 months_rep7

source_name: soleus

value: soleus

value: 18 months


title: Mus musculus_male_soleus_18 months_rep6


title: Rattus norvegicus_male_tibialis anterior_27 months_rep4


title: Fig.1, iPSC-CMs, P633L-cyt, rep 2

description:
P633Lsort_read_counts_all.txt
P633Lsort_all.psi.txt
P633Lsort_P633Lcyt_2
P633L sort sample 8

source_name: hiPSC-CMs (Briganti et al., 2020)

tag: cell line

value: hiPSC-CMs (Briganti et al., 2020)

value: human cardiomyocites derived from iPSCs

tag: localization

value: RBM20 cytoplasmic


title: Fig.1, iPSC-CMs, P633L-cyt, rep 1

description:
P633Lsort_read_counts_all.txt
P633Lsort_all.psi.txt
P633Lsort_P633Lcyt_1
P633L sort sample 7


title: Fig.1, iPSC-CMs, P633L-nuc, rep 3

description:
P633Lsort_read_counts_all.txt
P633Lsort_all.psi.txt
P633Lsort_P633Lnuc_3
P633L sort sample 6

value: RBM20 nuclear


title: Rattus norvegicus_male_tibialis anterior_27 months_rep3

value: tibialis anterior

value: Sprague Dawley


title: dTAG-ZC3H18 - dTAGv1 treated - rep3

city: Aarhus

first: Jerome

middle: O

last: Rouviere

address: Universitetsbyen 81

country: Denmark

institute: Aarhus University

data_processing:
Raw sequence reads from RNA-seq experiments quality checked using FastQC (Babraham Bioinformatics group).
Reads were then trimmed for adaptors and filtered using Trim Galore (Babraham Bioinformatics group).
Trimmed reads were mapped to Hg38, using Hisat2 (Kim et al., 2019) in paired-end mode.
Mapped files were sorted and checked for pairing using Samtools (Danecek et al., 2021).
Reads were then deduplicated using MarkDuplicates (Picard – Broad Institute) and further filtered to keep only unique mappers by using Samtools (Danecek et al., 2021).
A size factor was calculated with DEseq2 (Love et al., 2014) based on counts measured on mapped data using HTSeq-counts (Putri et al., 2022)
Finally, reads were converted to bigwig (bw) files normalized to size factor using bamCoverage (Deeptools – Ramirez et al., 2016).
Assembly: Hg38
Supplementary files format and content: stranded bigwig (bw) files

source_name: cervix

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
RNA was extracted using TRIzol (Ambion) and then further treated with TURBO DNAse (Ambion), according to manufacturer’s recommendations
Library construction and sequencing was a paid service from the Beijing Genome Institute (BGI) which performed rRNA depletion followed by strand-specific library preparation and PE100 sequencing on DNBSEQ equipment

treatment_protocol: dTAGv1 100 nM for 4h

value: cervix

value: HeLa Kyoto

value: epithelial

tag: treatment

value: dTAGv1 100 nM for 4h


title: Rattus norvegicus_male_tibialis anterior_27 months_rep2

value: 27 months


title: dTAG-ZC3H18 - dTAGv1 treated - rep2


title: Fig.1, iPSC-CMs, P633L-nuc, rep 2

description:
P633Lsort_read_counts_all.txt
P633Lsort_all.psi.txt
P633Lsort_P633Lnuc_2
P633L sort sample 5


title: Mus musculus_male_soleus_18 months_rep3


title: Rattus norvegicus_male_tibialis anterior_27 months_rep11


title: Mus musculus_male_soleus_18 months_rep4


title: dTAG-ZC3H18 - dTAGv1 treated - rep1


title: Chronic Beryllium Disease 16

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 16

value: M

value: White

value: Never

tag: tlc

tag: fvc

tag: dlco

tag: array


title: Chronic Beryllium Disease 13

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 13

tag: diagnosis

value: CBD

value: Yes


title: Chronic Beryllium Disease 14

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 14

tag: Sex

value: No


title: Fig.1, iPSC-CMs, P633L-nuc, rep 1

description:
P633Lsort_read_counts_all.txt
P633Lsort_all.psi.txt
P633Lsort_P633Lnuc_1
P633L sort sample 4

value: hiPSC-CMs (Briganti et al., 2020)

tag: cell type

tag: genotype


title: Mus musculus_male_soleus_21 months_rep4

value: soleus

value: male

tag: time

value: 21 months


title: Fig.1, iPSC-CMs, P633L-cyt, rep 3

description:
P633Lsort_read_counts_all.txt
P633Lsort_all.psi.txt
P633Lsort_P633Lcyt_3
P633L sort sample 9

value: human cardiomyocites derived from iPSCs

value: RBM20 cytoplasmic


title: Mus musculus_male_soleus_18 months_rep2

value: 18 months


title: Mus musculus_male_soleus_18 months_rep1


title: Rattus norvegicus_male_tibialis anterior_27 months_rep1

value: tibialis anterior

value: Sprague Dawley


title: Rattus norvegicus_male_tibialis anterior_27 months_rep10


title: dTAG-ZC3H18 - non treated - rep2

value: cervix

value: HeLa Kyoto

value: epithelial


title: dTAG-ZC3H18 - non treated - rep3


title: Fig.1, iPSC-CMs, WT, rep 2

description:
P633Lsort_read_counts_all.txt
P633Lsort_all.psi.txt
P633Lsort_WT_2
P633L sort sample 2

value: WT


title: Rattus norvegicus_male_tibialis anterior_27 months_rep0

value: 27 months


title: Fig.1, iPSC-CMs, WT, rep 3

description:
P633Lsort_read_counts_all.txt
P633Lsort_all.psi.txt
P633Lsort_WT_3
P633L sort sample 3


title: Chronic Beryllium Disease 15

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 15

value: CBD

value: F

tag: race

value: White

tag: hispanic

value: Never

value: prednisone & methotrexate

tag: white_blood_cell_count (x 10^6)

tag: slide


title: Mus musculus_male_soleus_12 months_rep7

tag: tissue

value: soleus

tag: strain

value: male

value: 12 months


title: Mus musculus_male_soleus_18 months_rep0


title: dTAG-ZC3H18 - non treated - rep1

tag: cell line


title: Human brain vascular pericytes, SicPlod2, Rep3

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

institute: University Würzburg

data_processing:
The sequencing reads were trimmed with flexbar (3.5.0) with default settings and –min-read-length 20
RNA-seq reads were mapped against the reference genome (GENCODE release 38, GRCh38.p13) using STAR (version 2.7.6a) with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 2   --alignSJDBoverhangMin 15 --alignSJoverhangMin 15 --chimSegmentMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --chimJunctionOverhangMin 15
circRNAs were detected and quantified with the workflow Calcifer  which can detect and analyze circRNAs from single or multiple datasets
Aligned reads were counted into the exons of all annotated genes (GENCODE release 38, GRCh38.p13) using htseq-count (version 0.11.3)
Differential gene expression was analyzed using DESeq2 (version 1.34.0) without independent filtering. Only genes and circRNAs with a mean normalized read count > 1 were considered.
Assembly: hg38
Supplementary files format and content: Csv-file with DESeq2 normalized read counts for each sample
Supplementary files format and content: Csv-file with raw counts for each sample

source_name: Human brain vascular pericytes

growth_protocol: Human brain vascular pericytes (passages 2-6; from ScienCell, Carlsbad, CA, USA) were cultured as recommended by the manufacturer. Cells were kept at 5% CO2, 20% O2, 37°C and humidified atmosphere. Pericytes medium consisted of DMEM Glutamax (Thermo Fischer Scientific) supplemented with Penicillin/Streptomycin (Roche Diagnostics) and 10% fetal bovine serum (Lonza).

extract_protocol:
Cells were lysed with Qiazol (#79306; Qiagen) for 5min. The RNA was isolated using the RNeasy Mini Kit (#217004; Qiagen) according to the manufacturer’s instructions, with an additional DNase-I (#79254; Qiagen) digestion.
RNA deep sequencing was performed by analyzing ribosomal-depleted total RNA. NextSeqTM 500 High Output Kit from Illumina was used for sequencing.

treatment_protocol: Cells were transfected with control siRNA (siScr CGUACGCGGAAUACUUCGATT; final concentration of 60nm) or siRNA targeting cPLOD2 (siPLOD2 UACUGAAUGAUAAAUUAUUTT, final concentration of 60nM by using Lipofectamin RNaiMax (#L13778075; Thermo Fischer Scientific) in Opti-MEM-I GlutaMAX (#51985-026; Life technologies), according to the manufacturer’s instructions. The siRNAs were purchased from Sigma Aldrich.

value: Human brain vascular pericytes

tag: treatment


title: ZC3H4 siRNA - rep4

data_processing:
Raw sequence reads from RNA-seq experiments quality checked using FastQC (Babraham Bioinformatics group).
Reads were then trimmed for adaptors and filtered using Trim Galore (Babraham Bioinformatics group).
Trimmed reads were mapped to Hg38, using Hisat2 (Kim et al., 2019) in paired-end mode.
Mapped files were sorted and checked for pairing using Samtools (Danecek et al., 2021).
Reads were then deduplicated using MarkDuplicates (Picard – Broad Institute) and further filtered to keep only unique mappers by using Samtools (Danecek et al., 2021).
Finally, reads were converted to bigwig (bw) files normalized to library sizes (Reads per Millions) using bamCoverage (Deeptools – Ramirez et al., 2016). A binning of 5 was used.
An additional set of bw tracks, normalized to size factors is also provided. These data were processed identically, but the normalization factor used for bw files generation with bamCoverage is a size factor calculated with DEseq2 (Love et al., 2014) based on counts measured on mapped data using HTSeq-counts (Putri et al., 2022)
Assembly: Hg38
Supplementary files format and content: stranded bigwig (bw) files

treatment_protocol: Two rounds of transfections were performed. The first transfections were performed using SilentFect (final dilution 1:1000) in RPMI 1640 medium. Two days after the first transfection, the media was changed, and the transfection was repeated using Lipofectamine 3000 (final dilution 1:1000) in RPMI 1640 medium. siRNAs were used at a final concentration of 15 nM of each siRNA. 24 hours after the second round of transfections, cells were harvested.

value: ZC3H4 siRNA


title: Fig.1, iPSC-CMs, WT, rep 1

description:
P633Lsort_read_counts_all.txt
P633Lsort_all.psi.txt
P633Lsort_WT_1
P633L sort sample 1

value: hiPSC-CMs (Briganti et al., 2020)

value: human cardiomyocites derived from iPSCs


title: Mus musculus_male_soleus_12 months_rep6


title: Human brain vascular pericytes, SiScr, Rep3

value: SiScr


title: ZC3H4 siRNA - rep3

value: cervix

value: HeLa Kyoto


title: Mus musculus_male_soleus_12 months_rep5


title: Rattus norvegicus_male_tibialis anterior_24 months_rep9

value: tibialis anterior

value: Sprague Dawley

value: 24 months


title: Rattus norvegicus_male_tibialis anterior_24 months_rep7


title: ARS2 siRNA - rep4

value: epithelial

value: ARS2 siRNA


title: Chronic Beryllium Disease 12

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 12

value: CBD

value: M

tag: age

value: White

value: Yes

tag: smoker

value: Never

tag: tlc


title: Mus musculus_male_soleus_12 months_rep4

value: soleus

value: male

value: 12 months


title: Human brain vascular pericytes, SicPlod2, Rep2

value: Human brain vascular pericytes


title: Chronic Beryllium Disease 11

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 11

value: No

value: Former

value: prednisone

tag: fvc

tag: dlco

tag: array


title: Human brain vascular pericytes, SiScr, Rep2

tag: cell type

value: SiScr


title: Mus musculus_male_soleus_18 months_rep5

tag: Sex

value: 18 months


title: ARS2 siRNA - rep3

value: cervix

value: HeLa Kyoto


title: Rattus norvegicus_male_tibialis anterior_24 months_rep5

value: tibialis anterior

value: Sprague Dawley

tag: time

value: 24 months


title: Human brain vascular pericytes, SicPlod2, Rep1


title: Control siRNA - rep4

value: epithelial

value: EGFP siRNA


title: Rattus norvegicus_male_tibialis anterior_24 months_rep6


title: Rattus norvegicus_male_tibialis anterior_24 months_rep4


title: Mus musculus_male_soleus_12 months_rep3


title: Mus musculus_male_soleus_12 months_rep2


title: Control siRNA - rep3


title: Mus musculus_male_soleus_12 months_rep1


title: Rattus norvegicus_male_tibialis anterior_24 months_rep3


title: Chronic Beryllium Disease 10

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 10

tag: diagnosis

value: CBD

value: M

tag: race

value: White


title: Chronic Beryllium Disease 9

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 9

value: F

tag: hispanic

value: Never

tag: white_blood_cell_count (x 10^6)


title: ARS2 3'UTR siRNA - ARS2-ZnF-mut transfected - TET treated - rep2

treatment_protocol: Two rounds of transfections were performed. The first transfections were performed using SilentFect (final dilution 1:1000) in RPMI 1640 medium. One day after transfection, cells were mock treated or transfected using Lipofectamine 3000 with a plasmid expressing ARS2 WT or ZnF-mut under TET promoter. Two days after the first transfection, the media was changed, and the siRNA transfection was repeated using Lipofectamine 3000 (final dilution 1:1000) in RPMI 1640 medium. siRNAs were used at a final concentration of 15 nM of each siRNA. 4h after the second round of siRNA transfection, cells were treated with Tetracycline (sigma) at a final concentration of 250ng/ml. 24 hours after the second round of transfections, cells were harvested.

tag: tissue

value: ARS2 3'UTR siRNA - Transient transfection with a TET-inducable ARS2-ZnF-mut expressing plasmid - TET 250 ng/ml for 18-20h


title: Arabidopsis cold 6mA IP rep2

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

data_processing:
The reads of raw data were trimmed according to adapt sequence using cutadapt (v1.1) . then the clean data were mapped to Arabidopsis genome (TAIR10) using bowtie, the parameter of maximum insert size was reset to 1000. Only unique reads were used to detect 6mA enrichment region by SCIER (v1.1) (using parameters redundancy threshold = 1 window size (bp) = 200 fragment size = 100 effective genome fraction = 0.74 gap size (bp) = 200 FDR = 0.01). Overlapping peaks (at least 1 bp overlap) between 2 biological replicates of a sample were retained for next analyses. DESeq2 (1.24.0) [41] was used to compare all 6mA region from normal and cold stress with the consideration of sample variation. Differential regions with p value < 0.05 (false discovery rate<0.05) were considered significant (DMRs)
The sequencing data were mapped to the Arabidopsis genome with matching annotation by tophat (v2.1.1)]using default parameters. The expression value (FPKM) of each gene were calculated with cufflinks (v2.1.1). And cuffdiff (v2.1.1) was used to calculate the fold change of gene expression and FDR. Differential expression genes (DEGs) with false discovery rate < 0.05 were considered significant.
Assembly: Arabidopsis genome (TAIR10)  Rice (Tigr7)
Supplementary files format and content: Processed data were stored in bigWig files and xlsx files.

organism: Arabidopsis

source_name: leaves

growth_protocol: Arabidopsis thaliana Col-0 was grown in a growth chamber at 22℃ under long day conditions (16 h light/8 h dark) with a light intensity of 100 µmol m-2 sec-1.Rice was grown in a growth chamber at 28°C under long-day conditions (16 h light/8 h dark) with a light intensity of 200 µmol m-2 sec-1 for 2 weeks.

extract_protocol:
gDNA of Arabidopsis and rice were extracted by using a DNAsecure Plant Kit (TIANGEN, Cat. DP320-03) according to its procedures. Isolated gDNA was sonicated into 200-400 bp with Biorupter UCD-600, followed by end repair, 3′-adenylation, and adaptor ligation according to NEB Next Ultra Ⅱ DNA Library Prep Kit for Illumina (E764S, NEB). The ligated DNA was denatured at 95°C for 10 min and chilled on ice for 10 min. 10 µl of denatured DNA was saved as input. 1µg DNA was incubated with 3 µg of anti-m6A antibody (202-003, Synaptic Systems) at 4°C for 6 h in 1×IP buffer (10 mM Tris-HCl PH 7.4, 150 mM NaCl, 0.1% IGEPAL CA-630). Dynabeads Protein A (10001D, Invitrogen) was washed twice with 1×IP buffer and pre-blocked in 0.5 ml 1×IP buffer with 20 µg/µl BSA for 2 h at 4°C. After pre-blocked beads were washed twice with 1×IP buffer, the DNA-antibody mixture was added to beads, rotating overnight at 4°C. The beads were washed 4 times with 1×IP buffer. Methylated DNA was eluted twice by 100 ml elution buffer containing N6-methyladenosine 5’-monophosphatesodium salt (M2780, Sigma) at 4°C for 1 h. Eluted DNA was combined, then added to 20ml of 3 M NaOAc (PH 5.3), 500 ml ethanol, and 0.5 ml glycogen. The mixture was frozen at -80°C overnight, and centrifuged. The precipitated DNA was dissolved in 20 ml ddH2O, followed by 8-10 cycles PCR amplification. The PCR product was purified by VAHTS DNA clean beads (N411-01, Vazyme). Sequencing was conducted by the Illumina NovaSeq6000 platform with 150-bp paired-end reads at Jiangbei New Area Biopharmaceutical Public Service Platform Co., Ltd. (Nanjing, China).
RNA-seq and 6mA-IP-seq

treatment_protocol: In arabidopsis, 3-week-old plants were transfer to 4℃ for 24 h. In rice, 2-week-old seedlings were transferred to 4°C for 6 days.

value: leaves


title: Human brain vascular pericytes, SiScr, Rep1

value: Human brain vascular pericytes


title: Rattus norvegicus_male_tibialis anterior_24 months_rep2

tag: strain

value: male


title: Chronic Beryllium Disease 5

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 5

value: No

value: Former

tag: slide


title: ARS2 3'UTR siRNA - ARS2-ZnF-mut transfected - TET treated - rep1

value: cervix

tag: cell line

value: HeLa Kyoto

tag: treatment


title: Mus musculus_male_soleus_12 months_rep0

value: soleus

value: 12 months


title: Rattus norvegicus_male_tibialis anterior_24 months_rep8

value: tibialis anterior

value: Sprague Dawley

value: 24 months


title: Arabidopsis cold 6mA IP rep1


title: Chronic Beryllium Disease 7

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 7

value: CBD

tag: age

tag: smoker


title: Rattus norvegicus_male_tibialis anterior_24 months_rep11

source_name: tibialis anterior


title: Rattus norvegicus_male_tibialis anterior_24 months_rep10


title: ARS2 3'UTR siRNA - ARS2-WT transfected - TET treated - rep2

value: epithelial

value: ARS2 3'UTR siRNA - Transient transfection with a TET-inducable ARS2-WT expressing plasmid - TET 250 ng/ml for 18-20h


title: Mus musculus_male_gastrocnemius_6 months_rep6

source_name: gastrocnemius

value: gastrocnemius

value: 6 months


title: ARS2 3'UTR siRNA - ARS2-WT transfected - TET treated - rep1


title: Rattus norvegicus_male_tibialis anterior_24 months_rep1


title: Arabidopsis normal 6mA IP rep2

value: leaves

value: CK


title: Mus musculus_male_gastrocnemius_6 months_rep5

value: male


title: Arabidopsis normal Input


title: ARS2 3'UTR siRNA - TET treated - rep2

value: ARS2 3'UTR siRNA - TET 250 ng/ml for 18-20h


title: Mus musculus_male_gastrocnemius_6 months_rep4


title: Rattus norvegicus_male_tibialis anterior_24 months_rep0


title: Mus musculus_male_gastrocnemius_6 months_rep7


title: Chronic Beryllium Disease 4

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 4

value: M

value: White

value: No

value: Never

tag: tlc

tag: fvc


title: Mus musculus_male_gastrocnemius_6 months_rep3


title: Chronic Beryllium Disease 6

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 6

value: Former

tag: dlco

tag: array


title: Control - TET treated - rep2

source_name: cervix

value: cervix

value: HeLa Kyoto

tag: cell type

value: TET 250 ng/ml for 18-20h


title: Mus musculus_male_gastrocnemius_6 months_rep2

tag: Sex

tag: time


title: RNAseq Mutant IL-3 Treated Day5 replicate-2

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

description: Immortalized fetal liver cells from βc-/-βIL-3 mice

data_processing:
Reads were mapped against the mouse reference genome (mm10) using the STAR spliced alignment algorithm version 2.6.1d with default parameters and --chimSegmentMin 20, --quantMode GeneCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file of gene expression

source_name: RNAseq Mutant IL-3 Treated Day5

growth_protocol: FDH cell lines expressing wild-type IL3Ra or IL3Ra P248L and bc were grown in IMDM + 10% heat-inactivated fetal bovine serum + penicillin-streptomycin + doxycycline + mouse SCF (100 ng/ml)

extract_protocol:
RNA was extracted from 10^6 cells/condition using the Ambion mirVana miRNA isolation kit with phenol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: FDH cell lines expressing wild-type IL3Ra or IL3Ra P248L and bc were washed twice with PBS prior to plating in IMDM + 10% heat-inactivated fetal bovine serum + penicillin-streptomycin + IL-3 (100 ng/ml) and incubated for 2 or 5 days.

value: BALB/c

tag: strain background

tag: genotype/variation

value: bc-/- mice transduced with IL3Ra P248L and bc

value: Immortalized fetal liver cells

tag: passages

value: mouse fetal liver cells from E14.5; Experiment performed for cell lines at passages 10-12


title: Chronic Beryllium Disease 3

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 3

tag: diagnosis

value: CBD

tag: race

tag: hispanic

tag: white_blood_cell_count (x 10^6)


title: Control - TET treated - rep1

tag: tissue

tag: cell line

value: epithelial

tag: treatment


title: RNAseq Mutant IL-3 Treated Day5 replicate-1

tag: strain


title: Rattus norvegicus_male_tibialis anterior_21 months_rep9

value: tibialis anterior

value: Sprague Dawley

value: 21 months


title: Rattus norvegicus_male_tibialis anterior_21 months_rep8

value: male


title: RNAseq Mutant IL-3 Treated Day5 replicate-3


title: Rattus norvegicus_male_tibialis anterior_21 months_rep7


title: RNAseq Mutant IL-3 Treated Day2 replicate-3

source_name: RNAseq Mutant IL-3 Treated Day2


title: Mus musculus_male_gastrocnemius_6 months_rep0

value: gastrocnemius

value: 6 months


title: Chronic Beryllium Disease 8

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 8

value: M

tag: age

value: White

value: Yes

tag: smoker

tag: tlc

tag: fvc

tag: slide


title: RNAseq Mutant IL-3 Treated Day2 replicate-2

tag: cell type


title: RNAseq Mutant IL-3 Treated Day2 replicate-1

tag: strain background


title: WT_Electrode_rep2

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description:
WTvsGSU1771_Electrode.txt
WT_4

data_processing:
Illumina bcl2fastq software were used for basecalling
Reads were aligned to the GCF_000007985.2/ASM798v2 genome assembly using smalt
The number of reads falling in the genes  were counted using coveragebed software and normalized with DESeq2 software
Assembly: GCF_000007985.2
Supplementary files format and content: tab-delimited text file includes the differential expression results of DESeq2 and raw and normalized counts  for each sample.

organism: Geobacter sulfurreducens

source_name: DL1 wild-type strain

growth_protocol: G. sulfurreducens biofilms grown on glass supports were grown in NBAF medium at 25 oC for 48 hours. The planktonic cells were separated from the biofilm that grew at the bottom of the culture tube. On the other hand, biofilms of G. sulfurreducens grown on graphite electrodes were separated from microbial fuel cells poised at 60 mV versus Ag/AgCl as the electron acceptor operated for 2 weeks. In the MFC, to grow G. sulfurreducens, FWAF medium was used.

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer's instructions, and residual DNA was removed by DNaseI treatment (Thermo Scientific). RNA samples were quantified using the NanoDrop 200c (Thermo Scientific) and examined with an Agilent 2100 Bioanalyzer.
cDNA libraries were constructed using the TruSeq Stranded mRNA kit (Illumina) following the manufacturer´s protocol. The cDNA libraries were purified with the Zymoclean Gel DNA Recovery Kit (Zymo Research).

treatment_protocol: The cells present in the biofilms were resuspended in 1 mL of NBAF and incubated with 100 uL of RNAlater. Cells were pelleted by centrifugation and frozen at -70 oC until use.

value: bacterial cell

tag: genotype

value: Wild type

value: biofilm grown on graphite electrode in microbial fuel cell operated for 2 weeks


title: Mus musculus_male_gastrocnemius_27 months_rep9

tag: Sex

tag: time

value: 27 months


title: Chronic Beryllium Disease 1

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 1

tag: diagnosis

tag: race

value: No

value: Never

tag: dlco

tag: array


title: Mus musculus_male_gastrocnemius_27 months_rep8

tag: tissue


title: GSU1771_Electrode_rep1

description:
WTvsGSU1771_Electrode.txt
GSU1771_1

source_name: DL1 with gsu1771-deletion

tag: treatment


title: WT_Electrode_rep1

description:
WTvsGSU1771_Electrode.txt
WT_3

tag: strain


title: Rattus norvegicus_male_tibialis anterior_21 months_rep4


title: Rattus norvegicus_male_tibialis anterior_21 months_rep5


title: RNAseq Mutant Untreated replicate-3

source_name: RNAseq Mutant Untreated

value: BALB/c

tag: genotype/variation

value: bc-/- mice transduced with IL3Ra P248L and bc

value: Immortalized fetal liver cells

tag: passages

value: mouse fetal liver cells from E14.5; Experiment performed for cell lines at passages 10-12


title: GSU1771_Electrode_rep2

description:
WTvsGSU1771_Electrode.txt
GSU1771_2


title: Rattus norvegicus_male_tibialis anterior_21 months_rep6

value: tibialis anterior

value: Sprague Dawley

value: 21 months


title: Rattus norvegicus_male_tibialis anterior_21 months_rep3

value: male