title: 103_036

first: Hideho

last: Okada

address: 1450 3rd Street

department: Department of Neurological Surgery

institute: University of California, San Francisco

data_processing:
The scRNA-seq reads were aligned to the GRCh38 reference genome and quantified using cellranger count (10x GENOMICS, version 4.0.0). Filtered gene-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the threshold for cell detection were used for further analysis. The scTCR-seq reads were aligned to the GRCh38 reference genome and consensus TCR annotation was performed using cellranger vdj (10x GENOMICS, version 4.0.0).
In bulk RNA-seq analyses, quality check (QC) and adapter-trimming were performed on the generated FASTQ sequencing data using fastq (v0.21.0) with default settings. An average of 180.8 million pass-QC sequencing read was obtained per tumor sample. Pass-QC read were then mapped to the human reference genome hg19 (GRCh37.p13) using STAR (v2.5.4b) with the guidance of transcriptome annotation Homo_sapiens.GRCh37.87.chr.gtf. The subsequent sorting and indexing were carried out using samtools (v1.10). Gene-level expression abundance was calculated using stringtie (v2.1.4) as count, fragments-per-kilobase-million (FPKM), and transcript-per-million reads (TPM) values.
Genome_build: GRCh38 (single cell analyses), hg19 (bulk RNA-seq)
Supplementary_files_format_and_content: Regarding the scRNA-seq analyses, barcodes.tsv, features.tsv, and atrix.mtx files were generated by cellranger count software (version 4.0.0). Regarding the scTCR-seq analyses, filtered_contig_annotations.csv files were generated by cellranger vdj (version 4.0.0). Regarding the bulk RNA-seq analyses, tab-delimited text files that include counts, FPKM, or TPM values were generated stringtie (version2.1.4) for each sample.

source_name: resected tumo

extract_protocol:
In bulk RNA-seq analyses, total RNA was extracted from frozed resected tumor specimens using AllPrep DNA RNA Mini Kit (Qiagen)
In scRNA-seq, Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10x GENOMICS) was used per the manufacturer's instructions. In brief, cryopreserved patient-derived PBMCs were washed with PBS containing 0.04% bovine serum albumin (BSA) and resuspended in PBS containing 0.04% BSA to a final concentration of 1,000 cells per mL. Cells were captured in droplets and nanoliter-scale Gel Beads-in-emulsion (GEMs) were generated. Following reverse transcription and cell barcoding, GEMs were broken, and cDNA was purified using Silane magnetic beads followed by amplified via PCR (98°C for 45 s; 13-18 cycles of 98°C for 20 s, 67°C for 30 s, 72°C for 1 min; 72°C for 1 min). Amplified cDNA was then used for both 5’ gene expression library construction and TCR enrichment. For gene expression library construction, 50 ng of amplified cDNA was fragmented and end-repaired, double-sided size-selected with SPRIselect beads, PCR-amplified with sample indexing primers (98°C for 45 s; 14-16 cycles of 98°C for 20 s, 54°C for 30 s, 72°C for 20 s; 72°C for 1 min), and double-sided size-selected with SPRIselect beads. For TCR library construction, TCR transcripts were enriched from 2 mL of amplified cDNA by PCR (primer sets 1 and 2: 98°C for 45 s; 10 cycles of 98°C for 20 s, 67°C for 30 s, 72°C for 1 min; 72°C for 1 min). Following TCR enrichment, 50 ng of enriched PCR product was fragmented and end-repaired, size-selected with SPRIselect beads, PCR-amplified with sample-indexing primers (98°C for 45 s; 9 cycles of 98°C for 20 s, 54°C for 30 s, 72°C for 20 s; 72°C for 1 min), and size-selected with SPRIselect beads. In bulk RNA-seq strand-specific and barcode indexed RNA-seq libraries were generated from 300 ng total RNA each after poly-A enrichment using the Kapa mRNA-seq Hyper kit (Kapa Biosystems) following the instructions of the manufacturer. The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis on a Bioanalyzer 2100. The libraries were quantified by fluorometry on a Qubit fluorometer (LifeTechnologies) and pooled in equimolar ratios.
The scRNA-seq and scTCR-seq libraries were sequenced on an Illumina NovaSeq 6000 to sequencing depth of 500 million reads and 60 million reads per sample, respectively. Bulk RNA-seq libraries were sequenced on an Illumina NovaSeq 6000 (Illumina) with paired-end 150 bp reads.

tag: modality

value: bulk RNA sequencing

tag: patient

value: resected tumo

value: Control


title: S019

status: Public on Feb 01 2022

type: RNA

city: Houston

first: Shervin

last: Assassi

state: TX

address: 6431 Fannin

department: Division of Rheumatology

country: USA

institute: The University of Texas Health Science Center at Houston

hyb_protocol: Fragmented Cy3-labeled cRNA was hybridized onto Agilent Human GE 44K V2 Microarray (Cat# G4845A, 4x44K) for 17 hrs at 65C with constant rotation (10 rpm).

scan_protocol: The slides were scanned using an Agilent microarray scanner.

data_processing: Data were examined for probes that were flagged by Agilent as non-uniform outliers.  Samples were excluded if >1% of probes for that sample were flagged.  Data were imported into BRB Array Tools (National Cancer Institute) as processed signal values, as recommended by Agilent.  Values were excluded if the mean signal was not significantly greater than background.  For genes with replicate probes, the average value of the replicates was used.  Values were then log2 transformed followed by quantile normalization.  Genes with >20% missing values across arrays were filtered out.

molecule: total RNA

organism: Homo sapiens

source_name: skin

label_protocol: Total RNA (100-200 ng) from each sample was reverse transcribed with Agilent spike RNA and amplification carried out using the one color Microarray-Based Gene Expression Analysis low RNA input quick amplification kit (Agilent).

growth_protocol: One 3-millimeter punch biopsy was obtained from the forearm skin.

extract_protocol: RNA was extracted using miRNeasy Mini kits (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Sample was immersed in RNAlater solution (Qiagen).

tag: condition

value: systemic sclerosis patient

tag: subject

tag: sample number within subject

tag: age

tag: gender

value: Male

tag: race

value: White

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Diffuse

tag: disease duration

tag: anti-topoisomerase i

value: Negative

tag: anti-rna polymerase iii

value: Positive

tag: anti-centromere


title: DHT_3

type: SRA

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description: DHT 1nM Rep3

library_source: transcriptomic

data_processing:
The quality of raw data was initially assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw FASTQ files were then filtered for short sequences using Cutadapt v1.16.6  with the following settings: minimum overlap length in Adaptor options: 3, Minimum length in filter options: 20, maximum error rate: 0.1, quality cut-off: 20.
To evaluate expression of protein-coding genes, reads were mapped against the human reference genome (hg19) using STAR version 2.6.0b-2 with default parameters. FeatureCounts was used to count and assign the mapped reads to genomic features . Count tables generated by featureCounts were used for differential expression analysis using R version 3.2.3 and edgeR version 3.3 as described previously.
Genome_build: GRCh37
Supplementary_files_format_and_content: CSV file containing counts per million (CPM) data for genes

source_name: LNCaP

extract_protocol:
Total RNA was extracted using Trizol and phenol-chloroform extraction method.
Libraries were generated using 300 ng of RNA and NEXTflex Rapid Illumina Directional RNA-Seq Library Prep Kits
RNA-Seq; Illumina NextSeq 500 (High Output v2) single-end 75 bp reads.

treatment_protocol: LNCaP cells were grown in baseline conditions (media supplemented with 10% FBS). Cells were treated with MeT and/or DHT for 6h and 24h.

tag: cell type

value: LNCaP

tag: treatment

value: DHT 1nM


title: LSC-CTCF rep2

city: Bengbu

first: Mingsen

last: Li

state: Anhui

address: No. 2600, Donghai Avenue, Bengbu City, Anhui Province

department: Interdisciplinary Eye Research Institute (EYE-X Institute)

country: China

institute: Bengbu Medical University

library_source: genomic

data_processing:
For ChIP-Seq data, reads were trimmed by trimmomatic tool and then aligned to human hg19 reference genome using BWA software (version 0.7.17). For Hi-C data, the clean Hi-C reads were iteratively mapped to the human genome by the ICE software package.
For ChIP-Seq data, duplicated reads were removed by Picard Markduplicates (version 2.18.16) and only uniquely mapping reads were retained for further analysis. For Hi-C data, we pooled the valid pairs of the two replicates together for further analysis.
For ChIP-Seq data, MACS2 (version 2.1.1) was used to call peak. For sharp peaks, we used the following parameters: -f BAMPE -B --SPMR -q 0.001 --call-summits --fix-bimodal --seed 11521 --extsize 200. For broad peaks (H3K27me3 and H3K9me2), the following parameters were used: -f BAMPE -B --SPMR --fix-bimodal --extsize 500 --broad --broad-cutoff 0.01 --seed 11521 -c input file.
For Hi-C data, principal component analysis of the normalized Hi-C matrices at 100-kb resolution was used for identification of chromatin A/B compartments. We determined the location and number of TADs and identified the locations of TAD borders using an insulation score algorithm based on normalized contact matrices at 40-kb resolution. The intra-chromosome interactions at 10-kb resolution were determined by Ay’s Fit-Hi-C software. The interactions with P value < 0.01, FDR < 0.01 and contact count > 2 were considered to be significant.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq peak files containing the enriched genomic site. A EXCEL file containing chromosome compartments, TADs and chromatin cis-interactions.

molecule: genomic DNA

source_name: limbal stem cells

growth_protocol: LSCs  were grown in DMEM/F-12 (1:1) medium containing  1% penicillin/streptomycin, 10% fetal bovine serum, 10 ng/ml EGF, 5 μg/ml insulin, 0.4 μg/ml hydrocortisone, 0.1 nM cholera toxin and 2 nM 3,3',5-triiodo-L-thyronine.

extract_protocol:
For ChIP-seq, chromatin was fixed with 1% formaldehyde for 10 min and sheared in a sonification buffer. Fragmented DNA was incubated with primary antibodies overnight at 4℃ and then with Protein A/G Dynabeads  for 1 h. The beads were collected and washed sequentially with the following solutions: high-salt buffer, low-salt wash buffer, and TE buffer.  Elution of the immunoprecipitated protein/DNA complexes was performed using elution buffer at 65℃ for 4 h. Next, the protein/DNA complexes were incubated with proteinase K (Invitrogen) and RNase A (Invitrogen) for 1 h. De-crosslinked DNA was purified using the PCR Purification Kit (Qiagen). For Hi-C, Following cellular cross-linking with 1% formaldehyde and nuclei extraction in hypotonic solution, the genomic DNA was digested with restriction enzyme MboI (NEB) at 37 °C overnight and labelled with biotinylated nucleotides when the cohesive ends were filled. Then, blunt-end proximity ligation was performed with T4 DNA ligase (NEB) at 16 °C for 4 h. After decrosslinking with proteinase K (Thermo) at 65°C overnight, ligated DNA was purified by QIAamp DNA Mini Kit (Qiagen) and sheared to ~400 bp. Next, Dynabeads™ MyOne™ Streptavidin C1 (Invitrogen) was used to pull down the biotin-marked ligation junctions.
Purified DNA was used to prepare ChIP-seq DNA libraries for Illumina sequencing by KAPA Hyper Prep Kit (KAPABIOSYSTEMS) according to the manufacturer’s instructions. The Hi-C library was generated using NEBNext Ultra™ II DNA library Prep Kit (NEB) according to the manufacturer’s instructions.
ChIP-seq, Hi-C

value: primary limbal stem cells

value: untreated


title: S206

value: Female

value: Asian

value: Limited


title: MeT_2

description: MeT 1nM Rep2

growth_protocol: LNCaP cells were grown in baseline conditions (media supplemented with 10% FBS).

value: MeT 1nM


title: S018


title: 103_035

city: San Francisco

state: CA

value: bulk RNA sequencing


title: FB_Day 3 post vaccination 1 (visit 8)

city: Seattle

first: Raphael

last: Gottardo

state: WA

address: 1100 Fairview Ave N

department: VIDD

institute: Fred Hutch

data_processing:
Raw count data was filtered to remove cells where 1) a mitochondrial RNA fraction greater than 7.5% of total RNA counts per cell, and 2) less than 200 or greater than 2500 genes were detected. The resultant count matrix was used to create a Seurat (v4.0.1) object.
Filtered read counts were normalized, scaled, and corrected for mitochondrial and rRNA read percentages with the SCTransform function. The FB matrix was normalized per feature using center log normalization.
Cell types in each sample were annotated by mapping to the annotated reference PBMC dataset provided in the Seurat v4 Azimuth workflow. Briefly, anchors between the query and reference datasets were identified using a precomputed supervised PCA on the reference dataset.
Next, cell type labels from the reference dataset, as well as imputations of all measured protein markers, were transferred to each cell of the query datasets through the previously identified anchors. The query datasets were then merged and projected onto the UMAP structure of the reference.
The genes expressed in each specific cell cluster were identified using the function FindAllMarkers() from the Seurat4 package, and filtered based on average logarithm of fold changes larger than 1 and FDR < 0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: Output from CellRanger (10X Genomics) which includes three files: barcodes.tsv, features.tsv, and matrix.mtx

source_name: PBMC

growth_protocol: PBMCs were isolated, cryopreserved, and thawed using standard protocols.

extract_protocol:
Live frozen PBMCs were obtained from a single vaccinated individual in cohort 1 of the IMRAS trial at day 0, and three- and 14-days post first vaccination. Cells were thawed and washed with RPMI supplemented with 10% FBS and benzonase nuclease (Millipore EMD 0.05 U/ml). PBMCs were resuspended in 100 µl of PBS supplemented with 2% w/v Fetal Bovine Serum (FBS) and incubated with Fixable Viability Stain 510  and Human BD Fc Block for 30 minutes at room temperature. Cells were washed with 2% FBS PBS before incubating with a panel of previously titrated 14 barcoded oligo-conjugated antibodies (BioLegend TotalSeq-C), including  FITC-anti-CD45. Stained PBMC samples were then sorted by fluorescence activated cell sorting (FACS) on a BD FACSMelody to enrich for live, hematopoietic cells. A standard viable CD45+ cell gating scheme was employed; FSC-A v SSCA (to exclude sub-cellular debris), two FSC-A doublet exclusion gates (FSC-W followed by FSC-H), dead cell exclusion gate (BV510 LIVE/DEAD negative) followed by CD45+ inclusion gate.
Sorted cells were resuspended in PBS supplemented with 1% BSA. Cells were loaded onto the 10X Chromium system, where we aimed for recovery of ~5000 cells per sample, and subject to partitioning with barcoded 5’ V1.1 chemistry gel-beads (10X Genomics) to generate the Gel-Bead in Emulsions (GEMs). The RT reaction was conducted in the GEMs, barcoded cDNA extracted by post-GEM RT-cleanup, and cDNA and antibody barcodes amplified for 14 cycles. Amplified cDNA was subjected to SPRI bead cleanup at 0.6X. Amplified antibody barcodes were recovered from the supernatant and were processed to generate TotalSeq-C libraries as instructed by the manufacturers (10X Genomics and BioLegend, TotalSeq-C with 10x Feature Barcoding Protocol). The remaining amplified cDNA was subjected to enzymatic fragmentation, end-repair, A-tailing, adapter ligation and 10X specific sample indexing as per manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) analysis. 10x Genomics scRNA-Seq and TotalSeq-C libraries were pooled and sequenced on an Illumina NovaSeq Sp100 flow cell using the recommended sequencing read lengths of 26 bp (Read 1), 8 bp (i7 Index Read), and 91 bp (Read 2), and depths of 50,000 and 5000 read pairs per cell for the 5’ Gene Expression and TotalSeq-C libraries respectively. Cell Ranger v3.1.0 (10x Genomics) was used to demultiplex raw sequencing data and quantitate transcript levels against the 10x Genomics GRCh38 reference.

treatment_protocol: PBMCs were stained with a panel of 14 barcoded, oligo-conjugated antibodies, and viable cells (CD45+) enriched by FACS.

tag: day

value: Day 3

tag: immune status

value: post vaccination 1

tag: visit

value: visit 8


title: MeT_1

description: MeT 1nM Rep1


title: HEK293T cells, PS_R2, CLIP-seq

city: beijing

first: Sun

last: Xianhui

state: 北京

address: No 15 Datun Road, Chaoyang District, Beijing

institute: institute of biophysics,chinese academy of sciences

data_processing:
Adapters and index sequences were removed with cutadapt2.7 using –u 4 and –a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCA.
Quality check were done by fastqc
Reads were mapped to h38 human genome using STAR-2.5.2a.
Read counts were done by a custom python script
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

molecule: cytoplasmic RNA

growth_protocol: HEK293T cells were grown in Dulbecco’s modified eagle medium (DMEM, Gibco) with 4.5 g/L D-glucose, 4 mM L-glutamine, 110 mg/L sodium pyruvate supplemented with 10% FBS.

extract_protocol:
Cell lysates were centrifugated at 36,000 r.p.m. for 2.5 hours in 10%-50% sucrose gradient and Ago2-RNA complexes were isolated with antibody
Ago2-RNA complexes were digested by micrococcal nuclease and treated with FastAP phosphatase. Preadenylylated 3'inker were ligated to Ago2-bound RNAs using truncated T4 RNA ligase 2. After purification by SDS-APGE, Ago2-bound RNAs were extracted, ligated by 5'inker, reverse transcription and PCR amplified with Illumina primers for 20 cycles.
CLIP-seq

treatment_protocol: Cells were treated with 100 ug/mL cycloheximide for 10 min at 37C and UV irradiated at 120 mJ/cm2

tag: cell line

value: Human embryonic kidney cells

tag: clip antibody

value: Ago2 (Abcam, ab186733)

tag: fraction

value: polysome


title: S214

tag: condition

value: systemic sclerosis patient

tag: subject

tag: sample number within subject

tag: age

value: Black

value: Diffuse

value: Negative


title: 103_029

tag: modality

tag: patient

value: resected tumo

value: Neoadjuvant vaccine


title: DHT_2

description: DHT 1nM Rep2

value: LNCaP

value: DHT 1nM


title: LSC-CTCF rep1

value: primary limbal stem cells

value: untreated


title: LSC-SMC1 rep1


title: siRNA SIAH-1 and SIAH2-N1

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed reads were aligned to the reference genome (hg38) with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differential gene expression was computed using DESeq2 (1.26.0), with standard parameters. Only genes with a minimum fold change of +- 1.5 (log2 = +-0.585), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
Genome_build: hg38
Supplementary_files_format_and_content: libaray size normalized counts

source_name: Hela cells

growth_protocol: HeLa cells were cultured in DMEM (Life Technologies) supplemented with 10% FCS, 100 U/mL penicillin and 100 µg/mL streptomycin. For knockdown experiments, HeLa cells were grown on 6-well plates. After reaching 60-70% confluence Lipofectamine transfection with siScramble (D-001810-10-05, Dharmacon) and siRNAs targeting SIAH1 (#4427037, Thermo Fisher) and/or SIAH2 (#L-006561-00-0010, Dharmacon) was carried out for 48 h. One day after transfection in DMEM containing 10% FCS without penicillin/streptomycin, medium was exchanged to full media.

extract_protocol:
RNA was extracted using RNeasy kit from Qiagen, 0.5 µg of RNA was used for cDNA synthesis using the PrimeScript RT Master Mix from Takara Bio Inc. Generated cDNA was diluted 1:5 using sterile RNase free water and equal volumes were used as a template for amplification by RT-qPCR using the SYBR Green ROX Mix (Thermo). For immunoblots lysates were cleared using
RNA-seq libraries were prepared from 1 µg total RNA using the VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme, #NR612) including poly(A) enrichment.

treatment_protocol: HeLa cells were treated with SIAH1/2-specific siRNAs or scrambled controls and two days later stimulated for 4 h with IL-1α (10ng/ml), followed by RNA-seq analysis

value: siRNA SIAH-1 and SIAH2


title: HEK293T cells, LRNP_rep2, CLIP-seq

value: light ribonucleoprotein


title: siRNA SIAH-1 and SIAH2+ Interleukin1a-N2

value: siRNA SIAH-1 and SIAH2+ Interleukin1a


title: 103_016

value: bulk RNA sequencing


title: 103_015


title: S192

tag: gender

value: Female

tag: race

tag: mrss at baseline sample

tag: diffuse at baseline sample

tag: disease duration

tag: anti-topoisomerase i


title: HEK293T cells, PS_R1, CLIP-seq

tag: cell type

value: Human embryonic kidney cells


title: 103_051

tag: treatment


title: Scrambled-N2

value: Scrambled


title: S194

value: systemic sclerosis patient

tag: anti-rna polymerase iii

tag: anti-centromere


title: Scrambled-N1


title: 103_004

value: Control


title: 103_051_screening

source_name: PBMCs

value: single cell RNA sequencing

value: PBMCs

value: Pre vaccine


title: 103_001

value: resected tumo


title: S316

value: White

value: Diffuse

value: Positive

value: Negative


title: siRNA SIAH-1 and SIAH2-N2

value: siRNA SIAH-1 and SIAH2


title: FB_Day 0 pre-immune (visit 4)

tag: day

value: Day 0

tag: immune status

value: pre-immune

tag: visit

value: visit 4


title: 103_026

value: bulk RNA sequencing

value: Neoadjuvant vaccine


title: S107

tag: condition

tag: subject

tag: sample number within subject

value: Female

value: Black


title: GBM6_AD

source_name: GBM6-AD cells

tag: modality

tag: patient

value: GBM6-AD cells


title: 103_018_surgery

value: single cell RNA sequencing

value: Post vaccine


title: A549_treated_rep3

city: New York

first: Seungyeul

last: Yoo

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
A549AMG0.1rep3
A549_Rawcount.txt

data_processing:
The RNA sequencing reads were processed through a standard protocol for STAR alignment and htseq-count to measure read counts for genes.
For reference genome and transcriptome, hg19 reference genome and UCSC refseq gtf files were downloaded (https://genome.ucsc.edu).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_Rawcount.txt: Tab-delimited text files include read counts for each sample.

source_name: A549 cell

growth_protocol: H1792 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% penicillin and 1% streptomycin. A549 cells were cultured in DMEM medium supplemented with 10% FBS, 1% penicillin and 1% streptomycin. Cells were maintained in 37°C and 5% CO2.

extract_protocol:
For RNA sequencing of A549 and NCIH-1792 cells treated with DMSO or 0.1uM AMG900 for 48hr, total RNA was purified from cells using RNeasy kit (Qiagen) for sequencing performed on NextSeq 500 (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: H1792 and A549 cells were seeded at a confluence of 70% in 6cm culture dish in 3 replicates for each treatment. Next day cells were treated with DMSO or 0.1uM AMG900. Cells were collected for RNA isolation 48hr after treatment.

tag: cell line

value: AMG900 treated


title: 103_025

value: resected tumo

value: Control


title: siRNA SIAH-1 and SIAH2+ Interleukin1a-N1

value: siRNA SIAH-1 and SIAH2+ Interleukin1a


title: 103_018


title: 103_028


title: S193

value: systemic sclerosis patient

tag: age

tag: gender

tag: race

tag: mrss at baseline sample

value: Diffuse


title: Scrambled + Interleukin1a- N2

value: Scrambled + Interleukin1a


title: MCF7-Input2

city: Beijing

first: Beibei

last: Liu

address: NO. 10 Xitoutiao Road

institute: Capital Medical University

data_processing:
Raw sequencing data was preprocessed using fastp v0.19.6
Alignment of the clean sequencing data was conducted using Bowtie2
Peak calling of ChIP-seq was conducted by using MACS2
Genome_build: hg38
Supplementary_files_format_and_content: bed: significant Peak from ChIP-seq

source_name: cell line

growth_protocol: MCF-7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
The chromatin DNA precipitated by antibodies against H3K27ac, and RNA polymerase II. Then the DNA was purified with the QIAquick PCR Purification Kit.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody

value: none (input)


title: Scrambled + Interleukin1a- N1

tag: treatment


title: S243

value: White

tag: diffuse at baseline sample

tag: disease duration

tag: anti-topoisomerase i

value: Negative

tag: anti-rna polymerase iii


title: S075

value: Positive

tag: anti-centromere


title: 103_026_screening

tag: cell type

value: PBMCs

value: Pre vaccine


title: 103_002

value: bulk RNA sequencing


title: S156

tag: condition

tag: subject

value: Female

value: Asian

value: Limited


title: A549_treated_rep4

description:
A549AMG0.1rep4
A549_Rawcount.txt

value: AMG900 treated


title: p_821

data_processing:
Globin related genes were removed prior to further analysis.
Transcripts which had counts per million (CPM) greater than 1 in at least two samples were used for the analysis
Transcript data were normalized with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: csv file format of DESeq2 normalized and log2 transformed counts.

source_name: whole blood sample, systemic sclerosis patient

extract_protocol:
PBC RNA was extracted according to the manufacturer’s protocol. RNA integrity was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies).   mRNA was enriched from total RNA using oligo(dt) beads (NEBNext Ultra II RNA Kit following the poly(A) enrichment workflow). The mRNA was subsequently fragmented randomly in fragmentation buffer, and reverse transcribed to cDNA.  The cDNAs were converted to double stranded cDNAs, then subjected to end-repair, A-tailing, and adapter ligation, size selection and PCR enrichment.
Libraries are pooled into Novaseq6000 machines according to molarity and expected data volume.

tag: visit

value: Month 12

tag: treatment arm

value: mycophenolate mofetil

tag: age at baseline visit

tag: fvc at baseline visit

tag: diffuse


title: S109

tag: sample number within subject

tag: age

tag: gender

tag: race

value: Black


title: 103_012

tag: modality

tag: patient

value: resected tumo

tag: treatment

value: Neoadjuvant vaccine


title: 103_026_surgery

value: single cell RNA sequencing

value: Post vaccine


title: 103_018_screening


title: 103_051_surgery


title: 103_029_screening


title: ChIP-MCF7-RNAPol2

tag: cell line

tag: chip antibody


title: A549_DMSO_rep2

description:
A549DMSOrep2
A549_Rawcount.txt

value: DMSO


title: 103_029_surgery

tag: cell type


title: p_810

tag: condition

value: systemic sclerosis patient

value: cyclophosphamide

value: African American


title: p_813

tag: subject


title: S074

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Diffuse

tag: disease duration

tag: anti-topoisomerase i

value: Positive

tag: anti-rna polymerase iii

value: Negative

tag: anti-centromere


title: ChIP-MCF7-H3K27ac


title: p_746

tag: visit

tag: treatment arm

tag: age at baseline visit

value: Male

tag: fvc at baseline visit

tag: diffuse


title: A549_DMSO_rep4

description:
A549DMSOrep4
A549_Rawcount.txt

tag: treatment


title: A549_treated_rep2

description:
A549AMG0.1rep2
A549_Rawcount.txt

tag: cell line


title: S108

tag: sample number within subject

tag: age

tag: gender

value: Female

tag: race


title: p_822

tag: condition

tag: subject

value: White


title: A549_treated_rep1

description:
A549AMG0.1rep1
A549_Rawcount.txt

value: AMG900 treated


title: S076

tag: mrss at baseline sample

tag: diffuse at baseline sample

tag: disease duration


title: H1792_treated_rep3

description:
HA3
H1792_Rawcount.txt

source_name: H1792 cell


title: p_742

value: Month 12

value: mycophenolate mofetil


title: p_823

value: Hispanic


title: A549_DMSO_rep3

description:
A549DMSOrep3
A549_Rawcount.txt


title: A549_DMSO_rep1

description:
A549DMSOrep1
A549_Rawcount.txt


title: p_741


title: S157

value: Asian

value: Limited

tag: anti-topoisomerase i

tag: anti-rna polymerase iii

tag: anti-centromere


title: p_819

tag: visit

tag: treatment arm

tag: age at baseline visit


title: H1792_DMSO_rep3

description:
HD3
H1792_Rawcount.txt

tag: treatment


title: S271


title: p_817

tag: fvc at baseline visit

tag: diffuse


title: S272

tag: sample number within subject

tag: age


title: p_735

tag: race

tag: gender


title: H1792_DMSO_rep2

description:
HD2
H1792_Rawcount.txt

tag: cell line


title: p_743

tag: condition

tag: subject


title: p_730


title: p_728


title: S223

tag: mrss at baseline sample

tag: diffuse at baseline sample

tag: disease duration


title: S305

tag: anti-topoisomerase i

tag: anti-rna polymerase iii

tag: anti-centromere


title: p_738

tag: visit

tag: treatment arm

tag: age at baseline visit


title: p_724

tag: fvc at baseline visit

tag: diffuse


title: Brain

city: Cambridge

first: Mariel

last: Young

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

data_processing:
alignment to hg19
Bowtie2 v2.3.2
default parameters for hg19 alignment
filter for duplicates
Picard v2.9.0
default parameters for marking and removing duplicates
remove mitochondrial reads
removeChrom.py
removeChrom - - chrM
peak calling
MACS2 v2.1.1.2
macs2 callpeak -f BAMPE -g hs --nolambda --keep-dup all --bdg
peak filtering
IDR https://github.com/nboley/idr
idr --samples rep1file rep2file --peak-list pooled_peaks --input-file-type narrowPeak --output-file IDR_output --rank p.value --soft-idr-threshold 0.05 –plot
Genome_build: hg19
Supplementary_files_format_and_content: bed format; contains the coordinates of the peaks called as described for the acetabulum ATAC-seq experiment

source_name: Human Brain E53-E54

growth_protocol: in vivo collected E53/E54 human pelvis chondrocytes

extract_protocol:
Upon arrival the sample was dissected under a light dissection microscope. Pelvis elements were complete but then manually separated from one another for the ATAC protocol. Element samples were then sent out for sequencing running a pooled library for 3 rounds of sequencing on the Illumina NextSeq 500 in order to obtain approximately 50 million reads per sample.
Samples were subjected to PCR amplification and barcoding following Buenrostro et al., 2015. 10 ul of transposed DNA was then placed in a reaction containing NEBNext High-Fidelity PCR Master Mix, ddH20, and primers. After amplification, samples were transferred to micro-centrifuge tubes and subjected to the OMEGA Bead Purification Protocol following manufacturers protocol. The samples were eluted in 30 ul of TE, run on a nanodrop, diluted to 5 ng/ul and run on a bioanalyzer. Prior to sequencing sample concentrations were determined using the KAPA Library Quantification Complete Kit (KK4824). Samples were then sent out to the Harvard University Bauer Core Facility for sequencing on one lane of the Illumina NextSeq 500, for three rounds, after which raw reads for each sample were pooled.

treatment_protocol: Human products of conception were collected from late first-trimester terminations through the Laboratory of Developmental Biology in full compliance with the ethical guidelines of the National Institutes of Health and with the approval of the University of Washington Institutional Review Boards for the collection and distribution of human tissues for research, and Harvard University for the receipt and use of such materials. The Laboratory of Developmental Biology obtained written consent from all tissue donors.

tag: cell type

value: chondrocytes

tag: tissue

value: Brain

tag: reagent

value: tn5 transposase


title: S304

value: systemic sclerosis patient

tag: sample number within subject

tag: age

tag: gender

tag: race


title: p_758

tag: condition

tag: subject

value: African American


title: p_733


title: p_744


title: H1792_treated_rep2

description:
HA2
H1792_Rawcount.txt

tag: cell line

tag: treatment


title: H1792_treated_rep1

description:
HA1
H1792_Rawcount.txt


title: S303

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Diffuse

tag: disease duration

tag: anti-topoisomerase i

tag: anti-rna polymerase iii

tag: anti-centromere


title: p_715

tag: visit

tag: treatment arm

value: cyclophosphamide

tag: age at baseline visit

tag: fvc at baseline visit

tag: diffuse


title: S220

tag: sample number within subject

tag: age

tag: gender

value: Negative

value: Positive


title: p_745

tag: condition

tag: subject

tag: race

value: Female


title: p_598

value: Baseline


title: p_595

value: White

value: Male


title: p_721

value: mycophenolate mofetil


title: p_725

value: Month 12

value: Hispanic


title: S270

tag: mrss at baseline sample


title: S155

value: Asian

tag: diffuse at baseline sample

value: Limited


title: H1792_DMSO_rep1

description:
HD1
H1792_Rawcount.txt

tag: cell line

tag: treatment

value: DMSO


title: p_740


title: p_593


title: S218

tag: disease duration

tag: anti-topoisomerase i

tag: anti-rna polymerase iii


title: S265

tag: anti-centromere


title: p_713

tag: visit

tag: treatment arm

tag: age at baseline visit


title: S264

tag: sample number within subject


title: p_711

tag: fvc at baseline visit

tag: diffuse


title: p_736

tag: condition

tag: gender


title: S222

tag: subject

tag: age

tag: race


title: p_718


title: p_588


title: Ischium

source_name: Human Ischium E53-54

tag: cell type

value: chondrocytes

tag: tissue

value: Ischium

tag: reagent

value: tn5 transposase


title: S134

value: systemic sclerosis patient

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Diffuse

tag: disease duration

tag: anti-topoisomerase i


title: p_594

tag: visit

tag: treatment arm

value: cyclophosphamide

value: African American


title: p_720

tag: age at baseline visit


title: p_585

value: Female

tag: fvc at baseline visit


title: S221

tag: sample number within subject

value: Negative

tag: anti-rna polymerase iii

tag: anti-centromere


title: Ilium

source_name: Human Ilium E53-54

value: Ilium


title: Pubis

source_name: Human Pubis E53-54

value: Pubis


title: Acetabulum

source_name: Human Acetabulum E53-54

value: Acetabulum


title: p_584

tag: condition

tag: subject

value: Baseline

value: White

tag: gender

value: Male

tag: diffuse


title: Gcnf_wt_1

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: E9.0 wt embryo

hyb_protocol: Following fragmentation, 12.5 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse MOE430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.

data_processing: Array intensities were processed using the RMA algorithm in R/bioconductor.

label: biotin

organism: Mus musculus

source_name: E9.0 Embryos wt

label_protocol: Biotinylated cRNA was prepared from 150 ng total RNA using the Ambion MessageAmpIII RNA Amplification kit, Catalog #1793.

extract_protocol: Total RNA was extracted from whole embryos using TRIzol reagent. Concentration and quality of RNA were determined by spectrophotometer and Agilent bioanalyzer analysis.

treatment_protocol: E9.0 wild type and Gcnf-/- embryos were isolated from pregnant mice.

tag: developmental stage

tag: tissue

value: embryo

tag: genotype

value: wt

tag: replicate


title: p_592

value: Month 12

value: mycophenolate mofetil

tag: race


title: p_591

value: Hispanic


title: Grain-feed rep2 [miRNA-Seq]

city: Yangling

first: Cunling

last: Jia

state: Shaanxi

address: Xinong road 22#

department: Animal science

institute: Northwest A&F University

data_processing:
Raw reads were processed by removing adapters and low quality reads, and using FastQC (Version 0.11.5) to perform qualify control.
These reads were compared with the known ncRNA by BLAST and thoes matched to rRNA, tRNA, miscRNA, snRNA and snoRNA were removed.
Reads after trimed to same length by Trimmomatic-0.36 were mapped Bos taurus reference genome.
The known miRNA were identified based on the miRBase 22.0 database by using mideep2 software
Genome_build: Bos taurus reference genome (ARS-UCD1.2)
Supplementary_files_format_and_content: tab-delimited text files include reads counts

organism: Bos taurus

source_name: Liver

extract_protocol:
Total RNA was extracted and purified from liver samples using the RNAeasy® Plus Mini Kit (Qiagen, Valencia, CA) according to the manual instruction.
Small RNA with 18-30 nt was obtained from the total RNA, and adapter ligation and RT-PCR was carried out to construct small RNA libraries for liver tissues of grass-fed and grain-fed cattle by TruseqTM Small RNA sample prep kit according to the protocols

treatment_protocol: After post-weaning, Wyu Angus cattle were raised by two method: grass-fed (mainly including alfalfa, hay or grass pasture) and grain-fed (mainly including corn silage, shelled corn, soybean and minerals, etc)

tag: breed

value: Wye Angus

value: Liver

tag: age

value: 14 months

tag: diet

value: grain


title: p_578

value: systemic sclerosis patient

tag: visit

tag: treatment arm

tag: age at baseline visit

value: African American


title: S005

source_name: skin

tag: sample number within subject

tag: diffuse at baseline sample

value: Limited

tag: disease duration

tag: anti-topoisomerase i

value: Negative

tag: anti-rna polymerase iii


title: p_586

tag: condition

tag: subject

value: cyclophosphamide

tag: gender

value: Female

tag: fvc at baseline visit

tag: diffuse


title: p_587

tag: race

value: White


title: p_571

value: Baseline


title: S219

tag: mrss at baseline sample

value: Diffuse

value: Positive

tag: anti-centromere


title: Gcnf_mutant_2

description: E9.0 GCNF mutant embryo

source_name: E9.0 Embryos GCNF mutant

tag: developmental stage

tag: tissue

value: embryo

tag: genotype

value: Gcnf-/-

tag: replicate


title: S135

tag: sample number within subject

tag: age

value: Hispanic


title: p_569

tag: visit

tag: treatment arm

value: mycophenolate mofetil

tag: age at baseline visit


title: S315

tag: condition

tag: diffuse at baseline sample

tag: disease duration

tag: anti-topoisomerase i

tag: anti-rna polymerase iii


title: p_577

tag: subject

tag: race

tag: gender

value: Male

tag: fvc at baseline visit

tag: diffuse


title: Gcnf_wt_2

description: E9.0 wt embryo

tag: developmental stage

tag: tissue

tag: genotype

value: wt


title: Grain-feed rep3 [miRNA-Seq]

tag: breed

value: Wye Angus

value: Liver

tag: age

value: 14 months

tag: diet

value: grain


title: S133

value: systemic sclerosis patient

tag: sample number within subject

tag: mrss at baseline sample

value: Negative

tag: anti-centromere


title: Gcnf_mutant_1

description: E9.0 GCNF mutant embryo

tag: replicate


title: p_568

tag: condition

tag: visit

tag: treatment arm

tag: age at baseline visit


title: p_583

tag: subject

value: Month 12

tag: race

tag: gender


title: Grain-feed rep1 [miRNA-Seq]


title: Grass-feed rep1 [miRNA-Seq]

value: 21 months

value: grass


title: Grass-feed rep3 [miRNA-Seq]


title: p_564

value: White

value: Female

tag: fvc at baseline visit

tag: diffuse


title: p_557

value: cyclophosphamide


title: p_566

value: Baseline


title: p_560


title: p_558

value: Hispanic


title: HCT116-SPARCLE_OE-DOX-a

city: Cuernavaca

first: Karla

middle: F

last: Meza-Sosa

state: Morelos

address: Av. Universidad

department: Institute for Biotechnology

country: Mexico

institute: UNAM

data_processing:
Reads were aligned with hisat 2.0.4 using the following parameters: --no-unal --rna-strandness R
sam files were sorted and converted to bam with samtools v1.7. Reads with QS < 10 were excluded
Read counts for the RNAseq inputs were calculated with featureCounts from the Rsubread package v1.22.3 in a R 3.3.3 environment
The read count table was analyzed with edgeR v3.12.1 in a R 3.3.3 environment and log2 TPM measurements were generated. After calculating normalization factors and estimating dispersion, DEG genes between KO, OE and Control cells were calculated using glm modeling with a FDR < 1e-5.
Genome_build: hg38, ensebml genes 85 annotation
Supplementary_files_format_and_content: tab-delimited txt with log2 TPM information from RNAseq inputs as calculated by edgeR

growth_protocol: Cells were grown in a CO2 incubator at 37ºC in DMEM supplemented with 10% FBS

extract_protocol:
Total RNA was extracted with Trizol following manufacturer's instructions. 1 ug was used for library construction.
Libraries were constructed using Illumina's TruSeq Stranded Total RNA kit

treatment_protocol: Cells were treated with either regular media or media containing 1uM doxorubicin for 48 hours prior RNA extraction

tag: cell line

tag: genotype

value: SPARCLE OVER-EXPRESSION

tag: treatment

value: Doxorubicin 1uM


title: HCT116-SPARCLE_OE-DOX-b


title: p_556


title: Grass-feed rep2 [miRNA-Seq]

tag: breed

tag: tissue

tag: age

tag: diet


title: p_555

value: mycophenolate mofetil

value: Asian


title: p_554

value: African American


title: p_547


title: p_562


title: p_552


title: S106

tag: sample number within subject

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Diffuse

tag: disease duration

tag: anti-topoisomerase i

tag: anti-rna polymerase iii

tag: anti-centromere


title: HCT116-SPARCLE_KO-DOX-b

value: SPARCLE KO


title: p_540

tag: condition

value: systemic sclerosis patient

tag: subject

tag: visit

tag: treatment arm

tag: age at baseline visit

tag: race

tag: gender

value: Male


title: S004

value: Limited

value: Negative


title: S314

value: Positive


title: S104


title: p_538

value: Month 12

tag: fvc at baseline visit

tag: diffuse


title: S048

tag: age

value: White


title: S049

tag: sample number within subject


title: S105

value: Female

tag: mrss at baseline sample


title: p_537


title: p_535

value: Baseline


title: S047

tag: diffuse at baseline sample


title: HCT116-WT-DOX-b

tag: cell line

tag: genotype

value: WT

tag: treatment


title: S123

value: Hispanic

tag: disease duration

tag: anti-topoisomerase i

tag: anti-rna polymerase iii

tag: anti-centromere


title: HCT116-WT-DOX-a

value: Doxorubicin 1uM


title: p_531

tag: condition

tag: subject

tag: visit

tag: treatment arm

value: cyclophosphamide


title: p_530

tag: age at baseline visit

tag: race

tag: gender

tag: fvc at baseline visit


title: p_534

tag: diffuse


title: HCT116-SPARCLE_OE-ctr-b

value: SPARCLE OVER-EXPRESSION


title: HCT116-SPARCLE_KO-DOX-a


title: p_524

value: mycophenolate mofetil

value: Asian


title: p_529

value: African American


title: p_523

value: systemic sclerosis patient


title: S121

tag: sample number within subject

tag: age

tag: mrss at baseline sample

tag: diffuse at baseline sample


title: HCT116-SPARCLE_KO-ctr-b

tag: cell line

tag: genotype

value: SPARCLE KO

tag: treatment


title: p_520


title: p_519


title: HCT116-WT-ctr-b


title: S239

value: Diffuse

tag: disease duration

tag: anti-topoisomerase i

tag: anti-rna polymerase iii

tag: anti-centromere


title: p_518

tag: condition

tag: subject

tag: visit

tag: treatment arm

value: Male


title: p_513

tag: age at baseline visit

tag: race

tag: gender

tag: fvc at baseline visit


title: S122

tag: sample number within subject

tag: age

tag: mrss at baseline sample

value: Limited

value: Negative

value: Positive


title: HCT116-SPARCLE_KO-ctr-a

tag: cell line

tag: genotype


title: S263

value: Female

value: White

tag: diffuse at baseline sample

tag: disease duration


title: HCT116-WT-ctr-a

value: WT

tag: treatment


title: S261

tag: anti-topoisomerase i

tag: anti-rna polymerase iii

tag: anti-centromere


title: HCT116-SPARCLE_OE-ctr-a


title: S262

tag: condition

tag: subject


title: p_507

tag: visit

value: Month 12

tag: treatment arm

tag: age at baseline visit

tag: diffuse


title: p_506

value: Baseline

tag: race

tag: gender

tag: fvc at baseline visit


title: p_504

value: cyclophosphamide


title: S238

tag: sample number within subject

tag: age

value: Hispanic

tag: mrss at baseline sample


title: p_502

value: mycophenolate mofetil


title: p_503


title: p_500


title: p_521


title: p_472


title: p_512


title: p_471


title: HCT116_1d

city: Xiamen

first: Chaoyong

last: Yang

state: Fujian

address: 422 Siming Road

institute: Xiamen University

description: with 4sU labeling and IAA treatment, treated by 5-AZA-CdR for 1 day

data_processing:
Well-paired-seq sequencing libraries produced paired-end reads: read 1 contains a cell barcode (12 bases) and a UMI (8 bases); read 2 contains the sequence of the transcript.
Data preprocessing and read alignment were implemented by using the Drop-seq core computational program (https://github.com/broadinstitute/Drop-seq/releases/tag/v2.3.0).
Pipeline of scNT-seq was adopted to further quantify labeled and unlabeled transcripts where uniquely mapped reads with a mapping score > 10 and T-to-C substitutions with a base Phred quality score > 27 were retained.
T-to-C substitutions in the control group without 4sU labeling and IAA treatment were used for background mutations correction. Then a UMI/transcript was identified as labeled (newly transcribed) if there was at least one T-to-C substitution in any one of the reads linked to the same UMI index.
For each gene, the total numbers of labeled and unlabeled mRNA were counted and assembled into matrices using the gene name as rows and cell barcode as columns.
Genome_build: GRCh38
Supplementary_files_format_and_content: digital gene expression

source_name: HCT116 cells

growth_protocol: Human K562 cells and human colorectal cancer HCT116 cells were cultured in high glucose Dulbecco's modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (Gibco, catalog no. 11965) and 1× penicillin–streptomycin (Gibco, catalog no. 15140122; 100 U/ml of penicillin, 100 µg/ml of streptomycin) and maintained at 37 °C with 5% CO2.

extract_protocol:
K562 cells were centrifuged and collected for scRNA-seq. HCT116 cells were centrifuged and fixed by methanol before scRNA-seq.
The 3’-end enriched sequencing library was prepared by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech, catalog no. TD503) according to the manufacturer’s instructions.
3’-end enriched sequencing library

treatment_protocol: For Sample 7, 8, and 9, the cells were treated by 300 nM 5-AZA-CdR for 1, 2, and 3 days, respectively.

tag: cell line

tag: related disease

value: human colorectal cancer


title: p_510


title: HCT116_2d

description: with 4sU labeling and IAA treatment, treated by 5-AZA-CdR for 2 day


title: p_470

value: Asian


title: K562_4sU_IAA

description: with 4sU labeling and IAA treatment

source_name: K562 cells

value: human chronic myeloid leukemia


title: HCT116_0d

description: with 4sU labeling and IAA treatment


title: HCT116_3d

description: with 4sU labeling and IAA treatment, treated by 5-AZA-CdR for 3 day


title: p_466

value: systemic sclerosis patient


title: S013

tag: diffuse at baseline sample

tag: disease duration

tag: anti-topoisomerase i


title: p_464

tag: condition


title: p_465

tag: subject


title: p_474

tag: visit


title: p_463

tag: treatment arm

value: African American


title: S139

value: Diffuse

tag: anti-rna polymerase iii

tag: anti-centromere


title: p_462

tag: age at baseline visit

tag: race

tag: diffuse


title: S140

tag: sample number within subject

tag: gender


title: K562_IAA

description: with IAA treatment


title: S138

tag: age

tag: mrss at baseline sample


title: p_459

tag: fvc at baseline visit


title: S164

tag: diffuse at baseline sample


title: p_457

value: Male


title: S163

tag: disease duration

value: Negative


title: K562_4sU

description: with 4sU labeling

tag: cell line

tag: related disease


title: HCT116_control

description: without 4sU labeling and IAA treatment


title: p_455

tag: condition

tag: subject


title: S165

tag: anti-topoisomerase i

value: Positive


title: S320

value: Female

tag: anti-rna polymerase iii


title: K562

description: without 4sU labeling and IAA treatment


title: p_453

tag: visit

tag: treatment arm

value: White


title: LSC-input

source_name: limbal stem cells

tag: cell type

value: primary limbal stem cells

tag: treatment

value: untreated


title: p_446

value: Baseline

tag: age at baseline visit

tag: race

tag: diffuse


title: p_445

tag: gender


title: p_451

value: Month 12

value: cyclophosphamide

tag: fvc at baseline visit


title: LSC Hi-C rep2


title: p_444

value: mycophenolate mofetil


title: S184

tag: sample number within subject

tag: age

tag: mrss at baseline sample

tag: diffuse at baseline sample

tag: anti-centromere


title: p_440

tag: condition

tag: subject


title: p_439


title: p_438


title: otic placode_3

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Data of RNA-seq (fastq file format) were quality-checked.
The remaining reads were mapped to the Human genome (hg19) using the STAR (ver.2.5.3a), and the output file (BAM file format) were summarized using the featureCounts (1.5.2).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: induced placodal cells

growth_protocol: See the citation

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: See the citation

value: otic placode cells


title: LSC Hi-C rep1


title: otic placode_2


title: p_436


title: otic placode_1


title: p_432

value: Hispanic


title: p_435


title: p_427


title: p_428


title: pre-placode_3

value: pre-placode cells


title: S321

value: systemic sclerosis patient

tag: disease duration

tag: anti-topoisomerase i

tag: anti-rna polymerase iii


title: S072

value: Black


title: p_424

tag: visit

tag: treatment arm


title: p_423

tag: age at baseline visit


title: S073

tag: race

value: Diffuse


title: pre-placode_2

tag: cell type


title: p_431

tag: gender

value: Male

tag: diffuse


title: S071

tag: sample number within subject

value: Negative


title: S041

tag: age


title: S183

tag: mrss at baseline sample


title: pre-placode_1


title: p_421

tag: fvc at baseline visit


title: p_420

value: African American


title: p_419


title: hESCs_3

source_name: embryonic stem cells

value: hESCs


title: S040

value: White

tag: diffuse at baseline sample

tag: anti-centromere


title: p_418

tag: condition

tag: subject

value: Female


title: p_417


title: S080

tag: disease duration

tag: anti-topoisomerase i

value: Positive


title: S079

tag: anti-rna polymerase iii


title: hESCs_2


title: p_416

tag: visit

value: Baseline

tag: treatment arm


title: p_425

value: Month 12

tag: age at baseline visit

tag: race


title: p_415

tag: gender


title: S035


title: S034


title: hESCs_1

tag: cell type


title: p_413

tag: diffuse


title: T3

city: Beltsville

first: Yahui

last: Gao

state: Maryland

address: 10300 Baltimore Ave Bldg 306

institute: ARS, USDA

description: one sample from cattle PBMC

data_processing:
We first processed 10X Genomics raw data by the Cell Ranger Single-Cell Software Suite (release 3.1.0), including using Cell Ranger “mkfastq” to demultiplex raw base call files into FASTQ files followed by use of Cell Ranger “count” to perform alignment, filtering, barcode counting, and UMI counting. The raw reads were aligned to the ARS-UCD1.2 cattle reference genome by Cell Ranger “pipeline” using default parameters
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz

molecule: polyA RNA

source_name: PBMC

extract_protocol:
four whole blood samples included either no LPS treatment - control sample CO, or three treated samples with LPS (2 μg/ml, Product Number: L2880, Sigma Aldrich, Saint Louis, MO, USA) for 2 hours - T1, 4hours - T2, and 8 hours - T3 at 37°C. PBMCs were isolated by centrifugation of whole blood on Hanks' Balanced Salt Solution (Solarbio; Beijing, China) at 500 g for 20 min at roomtemperature.
scRNA-seq Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3′ Reagent Kits v3 User Guide: CG000183 Rev C.

tag: breed

value: Holstein

tag: age

value: 2 years old

tag: treatment

value: LPS for 8 hours

value: PBMC


title: p_410

source_name: whole blood sample, systemic sclerosis patient

value: mycophenolate mofetil

tag: fvc at baseline visit


title: p_404

value: systemic sclerosis patient

value: cyclophosphamide


title: p_408


title: T1

description: one sample from cattle PBMC

value: LPS for 2 hours


title: T2

description: one sample from cattle PBMC

value: LPS for 4 hours


title: S132

tag: sample number within subject

value: Asian

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Limited

value: Negative

tag: anti-centromere


title: S131

tag: condition

tag: subject

tag: disease duration

tag: anti-topoisomerase i


title: S199

value: White

tag: anti-rna polymerase iii


title: p_406

tag: visit

tag: treatment arm

tag: age at baseline visit

tag: race

value: Male


title: p_401

tag: gender

tag: diffuse


title: CO

description: one sample from cattle PBMC

tag: breed

tag: age

tag: treatment

value: control

tag: cell type


title: p_403

value: Baseline

value: African American

tag: fvc at baseline visit


title: p_402

value: Month 12

value: Female


title: p_397


title: p_400


title: p_396


title: p_412


title: p_395


title: S039

tag: sample number within subject

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Diffuse

tag: anti-centromere


title: S290

tag: condition

tag: subject

tag: disease duration

tag: anti-topoisomerase i


title: S291

tag: anti-rna polymerase iii


title: S289

tag: race


title: Reflux Uropathy patient6 unmodified

city: Shanghai

first: qi

last: qi

address: 399 wanyuan road

department: Children’s Hospital

institute: Fudan university

description:
Raw data file:
V-6.txt
V-6(Sup)

hyb_protocol: The RNAs were combined and hybridized onto Arraystar Human mRNA Epitranscriptomic Microarray (8x60K, Arraystar) that contained 44,122 mRNA degenerate probes.

scan_protocol: the arrays were scanned in two-color channels by an Agilent Scanner G2505C.

data_processing:
mRNAs were analyzed for Gene Ontolog (GO) analysis using top GO package in R environment for statistical computing and graphics, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment calculated by fisher's exact test.
RNAs between two comparison groups were identified by filtering with the fold change and two-tailed Student’s t test. Fold-change (FC) ≥ 1.5 or ≤ 0.7, and p < 0.05 were used to identify the differentially m6A methylated RNAs.

source_name: ureter, VUR

label_protocol: the total RNAs were immunoprecipitated with Affinity purified anti-m6A rabbit polyclonal antibody (Synaptic Systems, 202003). The modifiedand unmodified RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

extract_protocol: Specimens were obtained from patients who underwent ureteral reimplantation surgeries at the urology department of our hospital. The length of the surgical cut in the ureter tissue was approximately 3 to 5 mm, and approximately 1 mm of tissue was taken from the distal ureter, and sent to the Department of Pathology. The remaining tissues were split into 1-mm blocks and placed in RNA preservation solution, stored at 4°C overnight, and then transferred to −80°C for long-term storage.

tag: sample type

value: unmodified RNA

tag: tissue

value: ureter

tag: disease

value: Reflux Uropathy


title: p_399

city: Houston

value: systemic sclerosis patient

tag: visit

tag: treatment arm

value: mycophenolate mofetil

tag: age at baseline visit

tag: gender

tag: diffuse


title: S284

data_processing: Data were examined for probes that were flagged by Agilent as non-uniform outliers.  Samples were excluded if >1% of probes for that sample were flagged.  Data were imported into BRB Array Tools (National Cancer Institute) as processed signal values, as recommended by Agilent.  Values were excluded if the mean signal was not significantly greater than background.  For genes with replicate probes, the average value of the replicates was used.  Values were then log2 transformed followed by quantile normalization.  Genes with >20% missing values across arrays were filtered out.

extract_protocol: RNA was extracted using miRNeasy Mini kits (Qiagen) according to manufacturer’s instructions.

tag: sample number within subject

tag: age

tag: mrss at baseline sample


title: Reflux Uropathy patient5 unmodified

description:
Raw data file:
V-5.txt
V-5(Sup)


title: p_392

tag: condition

tag: fvc at baseline visit


title: p_394

tag: subject

value: cyclophosphamide


title: p_390


title: p_388


title: p_384


title: p_387


title: p_386


title: p_385

value: Asian


title: p_393


title: p_391


title: Reflux Uropathy patient3 unmodified

description:
Raw data file:
V-3.txt
V-3(Sup)


title: p_383

value: Hispanic


title: p_389


title: p_381


title: p_382


title: p_380


title: S162

tag: diffuse at baseline sample

tag: disease duration

tag: anti-topoisomerase i

value: Negative

value: Positive

tag: anti-centromere


title: obstructive megaureter patient3 unmodified

description:
Raw data file:
M-3.txt
M-3(Sup)

source_name: ureter, obstructive megaureter

tag: sample type

tag: tissue

value: obstructive megaureter


title: Reflux Uropathy patient6 m6a

description:
Raw data file:
V-6.txt
V-6(IP)

value: m6a IP

tag: disease


title: obstructive megaureter patient4 unmodified

description:
Raw data file:
M-4.txt
M-4(Sup)


title: S281

tag: race

value: White

tag: anti-rna polymerase iii


title: S283

tag: gender


title: S280


title: p_379

tag: visit

tag: treatment arm

tag: age at baseline visit

value: African American

tag: diffuse


title: S160

tag: condition

tag: sample number within subject

tag: age

tag: mrss at baseline sample


title: obstructive megaureter patient1 unmodified

description:
Raw data file:
M-1.txt
M-1(Sup)


title: p_378

tag: subject

value: Baseline

tag: fvc at baseline visit


title: Reflux Uropathy patient5 m6a

description:
Raw data file:
V-5.txt
V-5(IP)


title: scyl/chrb - control1

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

data_processing:
Library strategy: Micro-C
Micro-C data was analyzed using the 4D Nucleome Hi-C analysis pipeline. Briefly, paired-end reads were mapped to the dm6 reference genome using BWA v0.7.17 [Li and Durbin, 2009], and alignments were filtered using pairtools v0.2.2 to retain only uniquely-mapping reads with alignment quality ≥3. Reads were assigned to 100bp genomic bins, and “inward”/”outward” reads assigned to adjacent bins (separated by less than 50bp) were removed. Matrix aggregation and normalization were performed using Cooler v0.8.3 [Abdennur and Mirny 2019], using the built-in ICE balancing method. Matrices were visualized using HiGlass [Kerpedjiev et al. 2018]. Visual inspection of contact matrices showed high concordance between biological duplicates, which were therefore pooled to generate final high-coverage contact matrices for each genotype.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: cool, validpairs

organism: Drosophila melanogaster

source_name: nc14 embryo

growth_protocol: Embryos were collected on yeasted apple juice plates at 25˚C. Following two 1-hour pre-lays, embryos were collected for 45 mins and subsequently incubated at 25˚C for 2 hours to enrich for nc14 embryos.

extract_protocol:
Chromatin was digested with a pre-determined amount of Micrococcal Nuclease (Worthington Biochem) to yield a 90% mononucleosome / 10% dinucleosome ratio given the appropriate number of embryos.
Micro-C libraries were constructed as previously described [Hsieh et al. 2020], with the following modifications.
Libraries were barcoded, pooled and subjected to paired-end sequencing on an Illumina Novaseq S1 100nt Flowcell (read length 50 bases per mate, 6-base index read).

treatment_protocol: Embryos were collected in nylon mesh sieves, dechorionated for 3 mins in 3% sodium hypochlorite, rinsed with deionized water, and transferred to glass scintillation vials containing 6 mL PBST (0.1% Triton-X in PBS), 7.5 mL N-heptane, and 1.5 mL fresh 16% formaldehyde. Crosslinking was carried out at room temperature for exactly 15 mins on an orbital shaker at 250rpm, followed by addition of 5.5 mL 2M Tris-HCl pH7.5 and shaking for 5 mins to quench the reaction. Embryos were washed twice with >15mL PBST and stored at 4˚C while an additional 2-3 collection rounds were carried out (45 mins each). Pooled embryos were subjected to a secondary crosslinking in 15 mL DSG+EGS (ThermoFisher, 3 mM each) at room temperature for 45 mins on a rotating mixer. Following quenching by addition of 5.5 mL 2M Tris-HCl pH7.5 and rotation for 5 mins, the embryos were washed twice with PBST and stored at 4˚C overnight. Samples were hand-sorted the following day under a dissection microscope to remove inappropriately staged embryos, snap-frozen in liquid nitrogen and stored at -80˚C.

tag: developmental stage

value: embryo

tag: genotype

value: yw


title: S001

first: Shervin

last: Assassi

institute: The University of Texas Health Science Center at Houston

value: Male

tag: diffuse at baseline sample

value: Diffuse

tag: disease duration

tag: anti-topoisomerase i

tag: anti-centromere


title: S282

tag: gender

value: Female

tag: race

tag: anti-rna polymerase iii


title: scyl tethers replacement1

tag: tissue

value: scyldelALL


title: p_377

value: systemic sclerosis patient

tag: visit

value: Month 12

tag: treatment arm

tag: age at baseline visit

tag: diffuse


title: S161

tag: condition

tag: sample number within subject

tag: age

tag: mrss at baseline sample


title: S002

tag: subject


title: obstructive megaureter patient3 m6a

description:
Raw data file:
M-3.txt
M-3(IP)

tag: sample type

value: ureter

tag: disease


title: obstructive megaureter patient1 m6a

description:
Raw data file:
M-1.txt
M-1(IP)


title: S295

tag: diffuse at baseline sample

value: Limited

tag: disease duration

tag: anti-topoisomerase i


title: Reflux Uropathy patient3 m6a

description:
Raw data file:
V-3.txt
V-3(IP)

value: Reflux Uropathy


title: knrl/kni - knrl tethers replacement1

tag: developmental stage

tag: genotype

value: AllGAF


title: knrl/kni - kni tether replacement2

tag: tissue


title: obstructive megaureter patient4 m6a

description:
Raw data file:
M-4.txt
M-4(IP)

value: obstructive megaureter


title: p_376

tag: visit

value: mycophenolate mofetil

tag: race

tag: gender

tag: fvc at baseline visit


title: p_321

tag: condition

tag: treatment arm

value: cyclophosphamide

tag: age at baseline visit

value: White

tag: diffuse


title: knrl/kni - knrl extended tethers replacement2


title: RNA-M231_b_16

data_processing:
Raw sequencing data was preprocessed using fastp v0.19.6
Alignment of the clean sequencing data was conducted using STAR v2.4.0 (RNA-seq) and Bowtie2 (ChIP-seq)
Abundance measurements of genes in RNA-seq was performed by using HTSeq-Count v0.12.4
Peak calling of ChIP-seq was conducted by using MACS2.
Differential gene expression analysis of RNA-seq was conducted using DESeq2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: xls: gene relative expression values from RNA-seq; bed: significant peaks from ChIP-seq

source_name: Cell line MDA-MB-231

growth_protocol: MCF-7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS); MDA-MB-231 cells were cultured in L-15 medium supplemented with 10% FBS and without CO2.

extract_protocol:
For ChIP-seq assay,the chromatin DNA precipitated by antibodies against BRD4, LSD1, MTA3, or H3K4me1. Then the DNA was purified with the QIAquick PCR Purification Kit. For RNA-seq assay, total RNAs were extracted from MCF-7 and MDA-MB-231 cells that were untreated or treated with JQ1 for 4 weeks using Trizol reagent.
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA-seq assay, MCF-7 and MDA-MB-231 cells that were untreated or treated with JQ1 for 4 weeks.

tag: cell line

tag: treatment


title: RNA-M231_b_DMSO

value: DMSO


title: knrl/kni - knrl extended tethers replacement1

value: embryo


title: S312

tag: subject

tag: sample number within subject

tag: age

tag: mrss at baseline sample

value: Negative

tag: anti-rna polymerase iii

tag: anti-centromere


title: S313

tag: diffuse at baseline sample

tag: disease duration

tag: anti-topoisomerase i


title: F1 generation ovarian granulosa cell-GD1~21-8mg/kg-rep2

type: genomic

city: Fuzhou

first: Lingfeng

last: Zeng

address: No. 1 Xuefu North Road, University Town

institute: Fujian Medical University

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: Microarrays were scanned using Agilent Scanner G2505C.

data_processing: Median-centering, quantile normalization and linear smoothing were performed in this analysis process by Bioconductor packages Ringo, limma, and MEDME

organism: Rattus norvegicus

source_name: ovarian granulosa cells_GD1~21_8mg/kg

label_protocol: For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours.

extract_protocol: Genomic DNA was extracted from the ovarian granulosa cells using the DNeasy Blood & Tissue Kit (Qiagen, Fremont, CA, USA),following the protocols given in the kit. The DNA samples from the ovarian granulosa cells in the control and 8.0mg/kg CdCl2 groups were sequenced (Illumina platform). Three biological replicates were sequenced for each group.

treatment_protocol: The female rats were mated with male rats (2:1) in proestrous, the gestation day was recorded as GD0. At GD0, pregnant rats(F0) were housed individually and randomly divided into four groups. Pregnant rats in the control group (0mg/kg) received water by gavage and in the experimental groups received cadmium chloride solution (8.0mg/kg body weight) by gavage during gestation periods (from GD1 to GD21). The day of parturition was counted as postnatal day 1(PND1). The F1 generation were breastfed, weaned on day 21 and with free access to lab diet and drinking water after weaned. At PND 56, vaginal smears were conducted to evaluate the stage of the estrous cycle, all female offspring were sacrificed after anesthesia and and ovarian granulosa cells were isolated from the SD rats. Ovaries were removed from the rats using a sterile technique, washed with saline and placed in phenol red Dulbecco’s modified Eagle medium containing the nutrient mixture F-12 (DMEM/F-12). Follicles were punctured using a 1-ml syringe needle and then the granulosa cells in follicular fluid were extruded into the medium under the stereoscopic microscope (×100 objective). The mix was then filtered through a cell strainer (200 meshes). After centrifugation at 1000 g at 4℃ for 10 min, the supernatant was discarded, purify the granulosa cells.

tag: strain

value: Sprague Dawley

tag: Sex

value: female

value: adult (56day)

tag: tissue

value: Ovary

tag: cell type

value: ovarian granulosa cells


title: total RNA from Lam Dm0 and Lam C KD testes, rep 3

city: Stockholm

first: Artem

last: Ilin

address: Svante Arrhenius väg 20C

department: MBW

country: Sweden

institute: Stockholm University

data_processing:
sequencing reads from three biological replicates of Lam-KD and control testes were adapter clipped, uniquely mapped to dm3/R5 genome assembly and low quality reads with the length of less than 20 nt were filtered out. Since replicates were highly correlated, they were merged, reads were counted for genes of BDGP5.78 annotation and converted to TPM values using Salmon (Patro et al. 2017).
Genome_build: dm3
Supplementary_files_format_and_content: sf.txt files for RNA-seq replicates represent read counts per gene (in TPM) obtained in Salmon.

source_name: 3rd instar larvae testes

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
total RNAs from ~200 testes per replicate (in three biological replicates), dissected from third instar larvae of UAS-LamDm0-RNAi/bam-Gal4-VP16; UAS-LamC-RNAi/+ (Lam-KD) males, were isolated using Trizol (Invitrogen). RNA was isolated using Trizol reagent (Invitrogen).
RNA samples were subjected to poly(A)+ selection, cDNA synthesis and deep sequencing on Illumina NovaSeq in the GENEWIZ (USA; www.GENEWIZ.com), resulting in 33-40 million 150-nt paired-end reads per sample.

value: Testes

tag: developmental stage

value: third instar larvae

tag: biological replicate


title: S294

address: 6431 Fannin

tag: condition

value: systemic sclerosis patient

tag: gender

value: Female

tag: race

value: Limited

value: Positive


title: S293

tag: subject

tag: sample number within subject


title: p_318

tag: visit

value: Baseline

tag: treatment arm

tag: age at baseline visit

tag: fvc at baseline visit

tag: diffuse


title: F1 generation ovarian granulosa cell-GD1~21-8mg/kg-rep3

tag: age

tag: treatment

value: cadmium chloride solution (8.0mg/kg body weight)


title: RNA-M231_S_DMSO

tag: cell line


title: p_320

value: Month 12

value: mycophenolate mofetil

value: White


title: p_319

value: Asian


title: RNA-M231_S_16


title: p_317

value: cyclophosphamide


title: p_316

value: Male


title: RNA-MCF7_DMSO

source_name: Cell line MCF-7

value: DMSO


title: S288

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Diffuse

tag: disease duration

tag: anti-topoisomerase i

value: Negative

tag: anti-rna polymerase iii

tag: anti-centromere


title: S286

tag: condition

tag: gender

tag: race


title: total RNA from Lam Dm0 and Lam C KD testes, rep 2

tag: tissue

value: Testes

tag: developmental stage

tag: strain

tag: biological replicate


title: F1 generation ovarian granulosa cell-GD1~21-0mg/kg-rep1

source_name: ovarian granulosa cells_GD1~21_0mg/kg

value: Sprague Dawley

tag: Sex

value: female

value: adult (56day)

value: control group (0mg/kg)

value: Ovary

tag: cell type

value: ovarian granulosa cells


title: F1 generation ovarian granulosa cell-GD1~21-8mg/kg-rep1

tag: age

tag: treatment

value: cadmium chloride solution (8.0mg/kg body weight)


title: F1 generation ovarian granulosa cell-GD1~21-0mg/kg-rep2


title: p_315

value: systemic sclerosis patient

tag: subject

tag: visit

value: Month 12

tag: treatment arm

tag: age at baseline visit

value: African American

value: Female

tag: fvc at baseline visit

tag: diffuse


title: S287

source_name: skin

tag: condition

tag: sample number within subject

value: White

tag: mrss at baseline sample

tag: diffuse at baseline sample

tag: disease duration

tag: anti-topoisomerase i

tag: anti-rna polymerase iii

value: Positive

tag: anti-centromere


title: RNA-MCF7_N_16

tag: cell line


title: total RNA from Lam Dm0 and Lam C KD testes, rep 1

tag: tissue

tag: developmental stage

value: third instar larvae

tag: strain

tag: biological replicate


title: RNA-MCF7_2_DMSO

tag: treatment

value: DMSO


title: RNA-MCF7_2_16


title: p_314

tag: subject

tag: visit

tag: treatment arm

value: cyclophosphamide

tag: age at baseline visit

tag: race

value: Native American

tag: gender


title: p_313

tag: condition

value: Baseline

value: Hispanic

tag: fvc at baseline visit

tag: diffuse


title: total RNA from control testes, rep 2

extract_protocol:
total RNAs from ~200 testes per replicate (in three biological replicates), dissected from third instar larvae of bam-Gal4-VP16 (control) males, were isolated using Trizol (Invitrogen). RNA was isolated using Trizol reagent (Invitrogen).
RNA samples were subjected to poly(A)+ selection, cDNA synthesis and deep sequencing on Illumina NovaSeq in the GENEWIZ (USA; www.GENEWIZ.com), resulting in 33-40 million 150-nt paired-end reads per sample.

value: Testes


title: p_312

value: mycophenolate mofetil


title: total RNA from control testes, rep 3


title: F1 generation ovarian granulosa cell-GD1~21-0mg/kg-rep3

value: Sprague Dawley

tag: Sex

value: female

tag: age

value: adult (56day)

value: control group (0mg/kg)

value: Ovary

tag: cell type


title: S175

value: systemic sclerosis patient

tag: sample number within subject

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Limited

tag: disease duration

tag: anti-topoisomerase i

value: Negative

tag: anti-rna polymerase iii

tag: anti-centromere


title: CD8-ctrl-3

first: Jianmin

last: Zhu

state: Shanghai

address: Dongfang road 1678

institute: Shanghai Children's Medical Center

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Genome_build: Mus_musculus(NCBI_GCF_000001635.26_GRCm38.p6)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: T cells

growth_protocol: mice were maintained in SPF animal facilities

extract_protocol:
Total RNA were extracted by Trizol
Libraries were prepared according to rNNA removal library construction (DNBseq)
The library was amplified with phi29 to make DNA nanoball (DNB) which have more than 300 copies of molecular. The DNBs were load into the patterned nanoarray and single end 50 (pair end 100) bases reads were generated in the way of combinatorial Probe-Anchor Synthesis (cPAS)

treatment_protocol: Splenic T cells were seperated by MACS after mice treated with AAV-IL-27/ctrl i.m. for a month

value: splenic T cells

tag: strain

tag: treatment

value: Control recombinant adeno-associated virus


title: p_311

tag: subject

tag: visit

tag: treatment arm

tag: age at baseline visit

tag: race

value: White

value: Female


title: total RNA from control testes, rep 1

extract_protocol:
total RNAs from ~200 testes per replicate (in three biological replicates), dissected from third instar larvae of bam-Gal4-VP16 (control) males, were isolated using Trizol (Invitrogen). RNA was isolated using Trizol reagent (Invitrogen).
RNA samples were subjected to poly(A)+ selection, cDNA synthesis and deep sequencing on Illumina NovaSeq in the GENEWIZ (USA; www.GENEWIZ.com), resulting in 33-40 million 150-nt paired-end reads per sample

tag: tissue

tag: developmental stage

value: third instar larvae

tag: biological replicate


title: S174

tag: condition

tag: sample number within subject

tag: age

tag: gender


title: p_309

extract_protocol:
PBC RNA was extracted according to the manufacturer’s protocol. RNA integrity was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies).   mRNA was enriched from total RNA using oligo(dt) beads (NEBNext Ultra II RNA Kit following the poly(A) enrichment workflow). The mRNA was subsequently fragmented randomly in fragmentation buffer, and reverse transcribed to cDNA.  The cDNAs were converted to double stranded cDNAs, then subjected to end-repair, A-tailing, and adapter ligation, size selection and PCR enrichment.
Libraries are pooled into Novaseq6000 machines according to molarity and expected data volume.

value: Month 12

value: cyclophosphamide

tag: fvc at baseline visit

tag: diffuse


title: CD8-IL-27-3

tag: cell type

value: IL-27-expressing recombinant adeno-associated virus


title: CD8-ctrl-1

tag: strain


title: SpC_Hi-C_rep2

city: Moscow

first: Anna

last: Kononkova

address: Nobel st., Building 1

department: Skoltech Center of Life Sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
Hi-C reads were mapped to the D. melanogaster reference genome using distiler-nf with default settings and an option no MAPQ filter. Cooler package was used for Hi-C maps generation, replicates downsampling, and iterative correction.
Genome build: dm3/R5
Supplementary files format and content: Processed data files are genome-wide Hi-C maps merged by replicates. The file corresponding to the SpC stage was downsampled so that the total number of contacts was nearly the same in merged files for both SpG and SpC stages. These are files with multiple resolutions in mcool format. For each replicate, processed files with resolution 10kb in cool format are also supplied. These are downsampled files with the same total number of contacts.

source_name: 3rd instar larvae testes mostly filled with spermatocytes

extract_protocol:
A total of 200-300 testes were fixed in PBS containing 2% formaldehyde for 10 min with occasional mixing. The reaction was quenched by an addition of 2 M glycine to a final concentration of 125 mM. Testes were pelleted by centrifugation at 1,000´g for 10 min at 4°C, resuspended in 50 ml PBS, snap-frozen in liquid nitrogen and stored at -80°C. Testes were lysed in 1.5 ml isotonic buffer [(50 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.5% (v/v) NP-40 substitute, 1% (v/v) Triton-X100, 1×Halt™ Protease Inhibitor Cocktail (Thermo Scientific)] on ice for 15 min after homogenization in glass tissue grinder. Cells were pelleted by centrifugation at 2,500×g for 5 min, resuspended in 100 ml DpnII buffer (New England Biolabs), and pelleted again. The pellet was resuspended in 200 ml 0.3% SDS in 1.1×DpnII buffer and incubated at 37°C for 1 h. Then, 330 ml 1.1×DpnII buffer and 53 ml 20% Triton X-100 were added, and the suspension was incubated at 37°C for 1 h. Next, 600 U of DpnII were added and the chromatin was digested overnight at 37°C with shaking at 1,400 rpm. Then, 200 U of DpnII was added and the cells were incubated for 2 h. DpnII was inactivated by incubation at 65°C for 20 min. The nuclei were harvested for 10 min at 5,000×g, washed with 100 ml NEBuffer 2 (New England Biolabs), and resuspended in 125 ml 1.2×NEBuffer 2. Cohesive DNA ends were biotinylated by adding 25 ml biotin fill-in mixture [0.025 mM dATP, 0.025 mM dGTP, 0.025 mM dTTP, 0.025 mM biotin-14-dCTP (Invitrogen), 0.8 U/μl Klenow enzyme (New England Biolabs)]. The samples were incubated at 37°C for 75 min with shaking at 1,400 rpm. Nuclei were pelleted by centrifugation at 3,000´g for 5 minutes, resuspended in 300 ml T4 DNA ligase buffer, and pelleted again. The pellet was resuspended in 300 ml T4 DNA ligase buffer and 75 U of T4 DNA ligase (Thermo Scientific) was added. Chromatin fragments were ligated at 20°C for 6 h. The cross-links were reversed by overnight incubation at 65°C in the presence of proteinase K (100 μg/ml). After cross-link reversal, the DNA was purified by single phenol-chloroform extraction, followed by ethanol precipitation (glycogen at a concentration of 20 μg/ml was used as co-precipitator). After precipitation, the pellets were dissolved in 100 μl 10 mM Tris-HCl, pH 8.0. To remove residual RNA, samples were treated with 50 mg of RNase A (Thermo Scientific) for 45 min at 37°C. To remove residual salts and DTT, DNA was purified using Agencourt AMPure XP beads (Beckman Coulter).
Biotinylated nucleotides from the non-ligated DNA ends were removed by incubating the Hi-C libraries (2 μg) in the presence of 6 U of T4 DNA polymerase in NEBuffer 2 supplemented with 0.025 mM dATP and 0.025 mM dGTP, at 20°C for 4 h. Next, DNA was purified using Agencourt AMPure XP beads. DNA was then dissolved in 500 μl sonication buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0.1% SDS) and was sheared to a size of approximately 100-1,000 bp using a VirSonic 100 (VerTis). The samples were concentrated and simultaneously purified using AMICON Ultra Centrifugal Filter Units (Merck), to a total volume of approximately 50 μl. The DNA ends were repaired by adding of 62.5 μl MQ water, 14 μl 10×T4 DNA ligase buffer, 3.5 μl 10 mM dNTP mix, 5 μl of T4 DNA polymerase (3 U/μl, New England Biolabs), 5 μl of T4 polynucleotide kinase (10 U/μl, New England Biolabs), and 1 μl of Klenow DNA polymerase (5 U/μl, New England Biolabs) and incubating at 20°C for 30 min. DNA was purified with Agencourt AMPure XP beads and eluted with 50 μl 10 mM Tris-HCl (pH 8.0). To perform an A-tailing reaction, DNA samples were supplemented with 6 μl 10×NEBuffer 2, 1.2 μl 10 mM dATP, 1 μl MQ water and 3.6 μl Klenow (exo-) fragment (5 U/μl, New England Biolabs). The reactions were performed for 30 min at 37°C in a PCR machine, and the enzyme was then heat-inactivated by incubation at 65°C for 20 min. DNA was purified using Agencourt AMPure XP beads and eluted with 200 μl 10 mM Tris-HCl (pH 8.0). Biotin pulldown of the ligation junctions was performed as described previously, with minor modifications. Briefly, 10 μl MyOne Dynabeads Streptavidin C1 (Invitrogen) beads were used to capture the biotinylated DNA, and the volumes of all buffers were decreased by 4-fold. The washed beads attached to captured ligation junctions were resuspended in 50 μl adapter ligation mixture, composed of 41.5 μl MQ water, 5 μl 10×T4 DNA ligase buffer, 2.5 μl Illumina TruSeq adapters and 1 μl T4 DNA ligase (5 U/μl, Thermo Scientific). Adapter ligation was performed at 22°C for 2.5 h, and the beads were washed twice with 100 μl buffer (5 mM Tris-HCl, pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), once with 100 μl buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 2 M NaCl), and once with 100 μl buffer (10 mM Tris-HCl, pH 8.0 and 50 mM NaCl), and then resuspended in 20 μl MQ water. Test PCR reactions containing 4 μl streptavidin-bound Hi-C library were performed to determine the optimal number of PCR cycles necessary to generate sufficient PCR products for sequencing. The PCR reactions were performed using KAPA High Fidelity DNA Polymerase (KAPA) and Illumina PE1.0 and PE2.0 PCR primers (10 pmol each). The temperature profile was 5 min at 98°C, followed by 6, 9, 12, 15, and 18 cycles of 20 s at 98°C, 15 s at 65°C, and 20 s at 72°C. The PCR reactions were separated on a 2% agarose gel supplemented with ethidium bromide, and the number of PCR cycles necessary to obtain a sufficient amount of DNA was determined based on the visual inspection of gels (typically 9-12 cycles). Four preparative PCR reactions were performed for each sample. The PCR mixtures were combined and the products were purified using Agencourt AMPure XP beads.

value: testes

value: 3rd instar larvae

tag: genotype

value: vas-GFP

value: mainly germline


title: SpC_Hi-C_rep1

data_processing:
Hi-C reads were mapped to the D. melanogaster reference genome using distiler-nf with default settings and an option no MAPQ filter. Cooler package was used for Hi-C maps generation, replicates downsampling, and iterative correction.
Genome build: dm3/R5.
Supplementary files format and content: Processed data files are genome-wide Hi-C maps merged by replicates. The file corresponding to the SpC stage was downsampled so that the total number of contacts was nearly the same in merged files for both SpG and SpC stages. These are files with multiple resolutions in mcool format. For each replicate, processed files with resolution 10kb in cool format are also supplied. These are downsampled files with the same total number of contacts.


title: S252

tag: subject

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Diffuse

tag: disease duration

tag: anti-topoisomerase i

value: Positive

tag: anti-rna polymerase iii

tag: anti-centromere


title: p_308

data_processing:
Globin related genes were removed prior to further analysis.
Transcripts which had counts per million (CPM) greater than 1 in at least two samples were used for the analysis
Transcript data were normalized with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: csv file format of DESeq2 normalized and log2 transformed counts.

value: systemic sclerosis patient

tag: visit

tag: treatment arm

value: mycophenolate mofetil

tag: age at baseline visit

tag: race


title: S251

tag: condition

tag: sample number within subject

tag: age

tag: gender

value: Negative


title: p_306

tag: fvc at baseline visit

tag: diffuse


title: p_305

tag: subject

value: Baseline

value: Hispanic

value: Male


title: CD8-IL-27-1

tag: cell type

value: splenic T cells

tag: strain

tag: treatment


title: S010

value: Black

tag: mrss at baseline sample

tag: diffuse at baseline sample

tag: disease duration

tag: anti-topoisomerase i


title: LATS1,2-1 [L1-2-i-PB-3]

city: Daejeon

first: Seunghyeok

last: Choi

address: Daehakro 291

country: South Korea

institute: KAIST

description:
RiboTag
PDGFRβ

data_processing:
Illumina NextSeq500 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Read count

growth_protocol: RiboTag mice were purchased from Jackson Laboratory (Jackson Lab, Bar Harbor, ME). Pdgfrb-Cre-ERT2 mice were bred into a background of RiboTag mice.

extract_protocol:
Total RNAs were extracted using Trizol RNA extraction kit (Invitrogen). The quality and quantity of the RNA samples were analyzed using Agilent 2100 Bioanalyzer with RNA 6000 pico kit (Agilent).
Quant-Seq library Prep kit

treatment_protocol: In order to induce Cre activity in the Cre-ERT2 mice, 2 mg of tamoxifen (Sigma), dissolved in corn oil (Sigma), was injected intraperitoneally (i.p.)

tag: tissue

value: Kidney

value: Mesangial cells (MCs)

tag: genotype

value: Lats1/2 Knock Out


title: LATS1,2-2 [L1-2-i-PB-4]

description:
RiboTag
PDGFRβ


title: S011

growth_protocol: One 3-millimeter punch biopsy was obtained from the forearm skin.

treatment_protocol: Sample was immersed in RNAlater solution (Qiagen).

tag: race

tag: anti-rna polymerase iii

tag: anti-centromere


title: p_303

tag: condition

tag: visit

tag: treatment arm

tag: age at baseline visit


title: LATS1,2-3 [L1-2-i-PB-6]

description:
RiboTag
PDGFRβ


title: 32

city: San Diego

first: Lara

last: Ibrahim

state: California

address: 10550 N Torrey Pines Rd

institute: Scripps Research

description:
replicate 1
CJL-DARK-LUNG-1

data_processing:
Kallisto (https://pachterlab.github.io/kallisto/) was used to align to the reference transcriptome (ftp://ftp.ensembl.org/pub/current_fasta/mus_musculus/cdna/) and estimate transcript abundance.
Supplementary_files_format_and_content: TPM

source_name: KrasG12D/+  murine lung

growth_protocol: KrasLSL-G12D/+ (K) mice in pure C57BL/6J background were infected intratracheally with lentivirus containing Cre recombinase, lenti-Cre (PGK-Cre, gift from Tyler Jacks), at a viral titer of 5 x 10^5 plaque forming units (PFU) per mouse.

extract_protocol:
Total RNA from lung tumors and remaining lung tissues was isolated using Qiazol reagent using standard protocols (Qiagen cat # 799306). RNA purity was assessed by Agilent 2100 Bioanalyzer.
Total RNA samples were sent to BGI Group, Beijing, China, for library preparation and sequencing. Reads (single-end 50bp at a sequencing depth of 20 million reads per sample) were generated by BGISEQ-500

treatment_protocol: Mice were housed into standard light conditions (12:12LD) or chronic jetlag (CJL) 5 weeks post infection with lenti-Cre, for 20 weeks. Sacrifices during the light (ZT9) or dark phase (ZT21) were carried out under normal or red light, respectively, at 25 weeks post lentivirus infection. Mice were euthanized by carbon dioxide asphyxiation. Lung tumors and remaining lung tissues were snap-frozen into liquid nitrogen ad stored at -80∘C until RNA extraction.

tag: background strain

tag: tissue (lung tumor vs rest of lung)

value: lung

tag: chronic jetlag conditions (standard light conditions 12

value: 12ld vs chronic jetlag cjl):CJL

tag: time of sample collection (zt9 light phase vs zt21 dark phase)


title: 59

description:
replicate 2
CJL-DARK-LUNG-2


title: S250

state: TX

tag: subject

tag: sample number within subject

tag: age

tag: gender

value: Female

value: White

tag: mrss at baseline sample


title: 60

description:
replicate 2
12:12-DARK-LUNG-2

value: 12ld vs chronic jetlag cjl):12:12LD


title: Control5 [PB-CON-5]

description:
RiboTag
PDGFRβ

source_name: Control

tag: tissue

tag: cell type

tag: genotype

value: Control


title: p_302

value: systemic sclerosis patient

tag: race

tag: fvc at baseline visit

tag: diffuse


title: 27

description:
replicate 1
12:12-DARK-LUNG-1


title: 63

description:
replicate 2
CJL-LIGHT-LUNG-2


title: Control3 [PB-CON-3]

description:
RiboTag
PDGFRβ


title: p_300

tag: condition

tag: visit

value: Month 12

tag: treatment arm

value: cyclophosphamide


title: S173

tag: diffuse at baseline sample

value: Limited

tag: disease duration

tag: anti-topoisomerase i

value: Negative

tag: anti-rna polymerase iii

tag: anti-centromere


title: S277

tag: subject

tag: sample number within subject

tag: age


title: S279

tag: gender

tag: mrss at baseline sample


title: knrl/kni - kni tether replacement1

tag: developmental stage

tag: tissue

value: embryo

tag: genotype


title: S278

tag: race


title: p_298

tag: condition

tag: age at baseline visit

value: Hispanic

tag: fvc at baseline visit

tag: diffuse


title: 26

description:
replicate 1
CJL-LIGHT-LUNG-1

tag: background strain

tag: tissue (lung tumor vs rest of lung)

tag: chronic jetlag conditions (standard light conditions 12

tag: time of sample collection (zt9 light phase vs zt21 dark phase)


title: 58

description:
replicate 2
12:12-LIGHT-LUNG-2


title: S009

tag: subject

value: Male

value: Black

tag: diffuse at baseline sample

value: Diffuse

tag: disease duration

tag: anti-topoisomerase i

tag: anti-rna polymerase iii

tag: anti-centromere


title: Control1 [PB-CON-1]

description:
RiboTag
PDGFRβ

tag: tissue

value: Kidney

tag: cell type

value: Mesangial cells (MCs)


title: A20+/- treated with bleomycin rep2

city: Ann Arbor

first: Swati

last: Bhattacharyya

state: MI

address: 1150 W. Medical Center Drive

institute: University of Michigan

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 version2.1.0 with parameters -p --dta -x
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using stringtie-2.0.6 following the protocol from Pertea et al., Nature Protocols, 2016.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Sample.

extract_protocol:
Skin were harvested, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library  Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

treatment_protocol: 6-8 weeks female mice were randomized to start treatment with s.c. bleomycin, a fibrosis inducing agent (5 mg/kg/day), or PBS given for 10 days (5 days/week). Mice were then sacrificed at day 22

tag: strain

value: skin

tag: age

value: 9-11 week

tag: genotype

value: A20fl/fl mice with EIIa-Cre mice

tag: treatment

value: subcutaneous injection with 5mg/kg/day bleomycin for 10 days


title: p_295

tag: condition

tag: visit

tag: treatment arm

tag: age at baseline visit

tag: race

value: White

tag: gender

value: Female

tag: fvc at baseline visit

tag: diffuse


title: Control4 [PB-CON-4]

description:
RiboTag
PDGFRβ

value: Control


title: 31

description:
replicate 1
12:12-LIGHT-LUNG-1

tag: background strain

tag: tissue (lung tumor vs rest of lung)

value: lung

tag: chronic jetlag conditions (standard light conditions 12

value: 12ld vs chronic jetlag cjl):12:12LD

tag: time of sample collection (zt9 light phase vs zt21 dark phase)


title: Control1 [PB-CON-2]

description:
RiboTag
PDGFRβ

tag: tissue

tag: cell type


title: p_301

value: systemic sclerosis patient

tag: subject

value: Baseline

value: mycophenolate mofetil


title: 57

description:
replicate 6
CJL-DARK-6

source_name: KrasG12D/+  murine lung tumor

value: lung tumor

value: 12ld vs chronic jetlag cjl):CJL


title: A20+/- treated with bleomycin rep1

tag: strain

tag: age

tag: genotype


title: S045

tag: condition

tag: sample number within subject

value: Male

value: Black

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Diffuse

tag: disease duration

tag: anti-topoisomerase i

value: Negative

tag: anti-rna polymerase iii

tag: anti-centromere


title: p_294

tag: visit

tag: treatment arm

tag: age at baseline visit

tag: race

value: African American

tag: gender

tag: fvc at baseline visit

tag: diffuse


title: S046

tag: subject

tag: age


title: 24

description:
replicate 5
CJL-DARK-5

tag: background strain

tag: tissue (lung tumor vs rest of lung)

tag: chronic jetlag conditions (standard light conditions 12

tag: time of sample collection (zt9 light phase vs zt21 dark phase)


title: S026

tag: condition

tag: sample number within subject

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Limited

tag: disease duration


title: A20+/- treated with PBS rep2

tag: strain

tag: tissue

value: skin

value: 9-11 week

tag: genotype

value: A20fl/fl mice with EIIa-Cre mice

tag: treatment

value: subcutaneous injection with PBS for 10 days


title: S027

tag: gender

tag: race

value: White

tag: anti-topoisomerase i

tag: anti-rna polymerase iii

tag: anti-centromere


title: p_293

tag: subject

tag: visit

tag: treatment arm

value: cyclophosphamide

tag: age at baseline visit

value: Female

tag: fvc at baseline visit

tag: diffuse


title: S211

tag: condition

value: systemic sclerosis patient

tag: sample number within subject

tag: age

tag: mrss at baseline sample

tag: diffuse at baseline sample


title: p_297

value: Month 12


title: p_292

value: Baseline


title: A20+/- treated with PBS rep1

tag: strain

tag: tissue

tag: genotype

tag: treatment


title: 20

description:
replicate 4
CJL-DARK-4

tag: background strain

tag: tissue (lung tumor vs rest of lung)

value: lung tumor

tag: chronic jetlag conditions (standard light conditions 12

value: 12ld vs chronic jetlag cjl):CJL

tag: time of sample collection (zt9 light phase vs zt21 dark phase)


title: S210

tag: subject

tag: gender

tag: race

value: Black

tag: disease duration

tag: anti-topoisomerase i

tag: anti-rna polymerase iii

tag: anti-centromere


title: 12

description:
replicate 3
CJL-DARK-3


title: WT treated with bleomycin rep2

tag: age

value: wild type

value: subcutaneous injection with 5mg/kg/day bleomycin for 10 days


title: p_291

tag: condition

tag: visit

tag: treatment arm

value: mycophenolate mofetil

tag: age at baseline visit

tag: fvc at baseline visit

tag: diffuse


title: 8

description:
replicate 2
CJL-DARK-2

tag: background strain

tag: tissue (lung tumor vs rest of lung)


title: 4

description:
replicate 1
CJL-DARK-1

tag: chronic jetlag conditions (standard light conditions 12

tag: time of sample collection (zt9 light phase vs zt21 dark phase)


title: p_290

tag: subject

value: African American

tag: gender


title: WT treated with PBS rep2

tag: strain

tag: tissue

value: skin

tag: genotype

tag: treatment


title: WT treated with bleomycin rep1

tag: age

value: 9-11 week


title: p_289

tag: condition

tag: race

value: Hispanic


title: 46

description:
replicate 6
12:12-DARK-6

value: 12ld vs chronic jetlag cjl):12:12LD