title: S4_Oligo

city: Montreal

first: Olivier

last: Tastet

address: 900 Saint-Denis

institute: crCHUM

data_processing:
cell ranger analysis pipeline for alignment and count matrices
Seurat package for normalization: SCTransform (log UMI)
Seurat integration worflow using gene anchors (batch correction)
Genome_build: hg38
Supplementary_files_format_and_content: meta_data.single_cell_annotation.csv:  cell identity annotation
Supplementary_files_format_and_content: H805_1_filtered_feature_bc_matrix.tar:  cellranger output files
Supplementary_files_format_and_content: H805_4_filtered_feature_bc_matrix.tar:  cellranger output files
Supplementary_files_format_and_content: S2_OligoGlut_filtered_feature_bc_matrix.tar:  cellranger output files
Supplementary_files_format_and_content: S4_Oligo_filtered_feature_bc_matrix.tar:  cellranger output files
Supplementary_files_format_and_content: batch1.counts_matrix.csv:  raw counts from merged samples of the first batch
Supplementary_files_format_and_content: batch2.counts_matrix.csv:  raw counts from merged samples of the second batch
Supplementary_files_format_and_content: all_batch.sctransform_matrix.csv:  normalized assay from the integrated batches

source_name: Human oligodendrocytes in primary culture

growth_protocol: See Cui et al. Ann Neurol 2017. Brain tissue was obtained from adults undergoing surgical resections as a treatment for non–tumor-related intractable epilepsy in accordance with the guidelines set by the Biomedical Ethics Unit of McGill University. Tissue specimens were enzymatically digested and placed on a linear 30% Percoll density gradient. Microglia were separated and removed by an initial adhesion step in which the total cell fraction was cultured for 24 hours in non-coated flasks. The floating cell fraction was subjected to immunomagnetic bead selection with the A2B5 antibody (IgM), which recognizes gangliosides to remove a progenitor cell pool that comprises 3 to 5% of white matter cells. OLs (A2B5-depleted pool) were initially plated at a density of 2.5 X 105cells per milliliter on poly-lysine–coated chamber slides, and cultured in defined medium (DFM) consisting of Dulbecco modified essential medium DMEM-F12 supplemented with N1, 0.01% bovine serum albumin, 1% penicillin-streptomycin and B27 supplement, platelet-derived growth factor (PDGF)-AA (10ng/ml), basic fibroblast factor (bFGF, 10ng/ml), and triiodo-thyronine (T3, 2nM) for 4 days. Media was changed every 48 hours.

extract_protocol:
cells were harvested, filtered and processed for single cell capture (1 sample per chip)
cDNA libraries were created using the Chromium Single Cell 3' technology

treatment_protocol: vehicle (PBS) vs. glutamate 1mM for 12h

value: brain-resection path (normal tissue) from neurosurgery for epilepsy

value: Day 10 in vitro human oligodendrocytes in primary culture

tag: treatment

value: vehicle (PBS) for 12h

tag: batch

value: sequenced as a second batch


title: YH04_5C11

status: Public on Jul 25 2021

type: SRA

city: Northridge

first: Yoshie

last: Hanzawa

state: California

address: 18111 Nordhoff Street, CR 5217

department: Biology

country: USA

institute: California State University, Northridge

library_source: transcriptomic

data_processing:
Trimmomatic v0.36 was used to trim the low-quality base calls and the adapter content in single end mode with the adapter in TruSeq3-SE.fa, a leading and trailing base call threshold of 28 and a minimum read length of 30.
STAR v2.5.2b was used to align the reads with the --quantMode GeneCounts option to the reference genome file and the gene annotation file obtained from Phytozome.
the (relative) abundance of the mRNAs in transcripts per million (TPM) was quantitated using the relative mapping efficiency model.
Genome_build: Glycine max Wm82.a2.v1 (Soybean), release date: 6/10/2015, BioProject: PRJNA19861, Accession ID: ACUP02000000.
Supplementary_files_format_and_content: csv files include raw counts and normalized expression levels.

molecule: total RNA

organism: Glycine soja

source_name: The whole shoot above cotelydon

growth_protocol: soybeans were grown in either long day (14-hour) or short day (10-hour) conditions at 25C for 3 weeks.

extract_protocol:
RNA samples were prepared using the GeneJET Plant RNA Purification Kit following the manufacturer's protocol (ThermoFisher GeneJET #K0802)
RNA libraries were prepared for sequencing following standard Illumina protocols (TruSeq® Stranded mRNA Sample Preparation Guide)

treatment_protocol: 3 weeks after germination, soybeans were moved to long day (14-hour) or short day (10-hour) conditions at 16C, 25C or 32C.

tag: tissue

value: The whole shoot above cotelydon

tag: temperature (celsius)

tag: photoperiod

value: SD

tag: genotype

tag: sample time


title: Adult hCF day10_rep3

city: San Francisco

first: Todd

last: McDevitt

state: CA

address: 1650 Owens St

department: GICD

institute: Gladstone Institutes

data_processing:
Demultiplex with bcl2fastq v2.20.0
Align with HiSat2 v2.1.0
Count with featureCounts v1.6.2
Genome_build: GRCh37
Supplementary_files_format_and_content: Comma separated value

organism: Homo sapiens

source_name: Adult cardiac fibroblasts

growth_protocol: Fibroblasts were passaged in Human Cardiac Fibroblast Culture Media (Cell Applications #316K-500) and cultured to ~95% confluency. Cells collected at day zero were aliquoted from the cells trypsinized for seeding for the production of cell-derived matrices.

extract_protocol:
Cells were rinsed in PBS and harvested using the Trizol reagent. RNA was then separated via the introduction of chloroform, and purified on Qiagen RNeasy Mini Kit columns (Qiagen #74106).
RNA-seq libraries were created using the SMARTer Stranded Total RNA Sample Prep Kit (Takara Bio #634875) from 500ng initial RNA.
Samples were sequenced on the NextSeq 500 (Illumina) to a minimum depth of 25 million reads per sample.

treatment_protocol: ml 400kDa Ficoll and pen-strep.

tag: age

value: Adult

tag: cell type

value: cardiac fibroblast

tag: day


title: pLKO_MOLM_13_rep2

city: Rockville

first: Tongwu

last: Zhang

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standstard illumina base calling pipeline and stored in illumina cloud service BaseSpace. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned with the STASR aligner
FeatureCounts implemented in Subread will be used to count the sequencing reads from mapped BAM files. Analyses of differentially expressed genes (DEGs) were subsequently performed using a negative binomial test method (edgeR)10 implemented using SARTools R Package
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read count for each annoted gene.

source_name: AML cell line MOLM_13

extract_protocol:
RNA was prepared 7 days following RNF5 knockdown, and triplicates were used for RNAseq analysis. Libraries were prepared from isolated total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen, (Vienna, Austria). Barcoded libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: AML cell line

tag: knockdown

value: vector only control


title: HA805_1

country: Canada

value: sequenced as a first batch


title: YH06_1F5

value: LD


title: pLKO_MOLM_13_rep1


title: YH04_5A10


title: pLKO_U937_rep3

source_name: AML cell line U937


title: YH04_3E8


title: Adult hCF day10_rep2


title: Adult hCF day10_rep1


title: YH04_3G3


title: S2_OligoGlut

value: glutamate 1mM for 12h


title: shRNF5_MOLM_13_rep2


title: Adult hCF day5_rep3


title: YH04_2D10


title: HA805_4


title: YH05_4F6


title: Adult hCF day5_rep2


title: Adult hCF day5_rep1


title: Resistant endothelial cell, biological rep4

type: RNA

city: Daejeon

first: Kyunghee

last: Noh

address: 125 gahakro

country: South Korea

institute: KRIBB

description: Gene expression data from mouse endothelial cell

hyb_protocol: ollowing fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Mus musculus

source_name: mouse endothelial cell sorting with CD31 antibody

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 700ng total RNA

extract_protocol: We extracted total RNA from B20-sensitive and B20-resistant tumor endothelial cells with use of an RNeasy mini kit (Qiagen). A NanoDrop spectrophotometer (Thermo Fisher Scientific) was used for assessment of both RNA quality and quantity

treatment_protocol:
Tumor tissues harvested from B20-sensitive or B20-resistant groups were minced and digested with elastase, collagenase A, and DNase 1 at 37C for 90 min to obtain a single-cell suspension
Platelets and RBCs were removed by performing Percoll separation, and tumor cells were sorted by FACS by CD31 antibody

value: Resistant endothelial cell


title: YH03_9H2

value: Sh


title: Adult hCF day0_rep3


title: Resistant endothelial cell, biological rep3


title: YH04_2E7


title: Kdm5b sg-3

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

department: Pathology

institute: Yale University

description: Skin Melanoma Cell line

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using STAR with parameters default parameters
Reads per repeat element were counted using FeatureCount of subread package and repeat masker annotation
DESeq2 was used to determine differential signal using counts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene expression values normalized with DESeq2 variance stabilizing transformation (VST) for each Sample

source_name: Melanoma cancer cell line

growth_protocol: Cells were grown in monolay in DMEM/F12+5%FBS+1% Penicillin-streptomycin at 37°C, 5% CO2

extract_protocol:
RNA was extracted by Qiagen RNeasy Plus Mini Kit
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA Library Preparation protocol

value: YUMMER1.7(Braf V600E, Pten -/- and Cdkn2 -/- with high frequency of stable UV-induced somatic mutations

value: Skin Melanoma Cell line

value: Kdm5b deletion 3


title: YH03_9E7


title: Adult hCF day0_rep2


title: YH03_8A9


title: Adult hCF day0_rep1


title: Resistant endothelial cell, biological rep1


title: Kdm5b sg-1

description: Skin Melanoma Cell line

value: Kdm5b deletion 1


title: YH03_6C11


title: Control-3 [sz3]

description: Skin Melanoma Cell line

value: Control knockout


title: Fetal hCF day10_rep3

source_name: Fetal cardiac fibroblasts

value: Fetal


title: Resistant endothelial cell, biological rep2


title: YH02_9C11

value: The whole shoot above cotelydon


title: Sensitive endothelial cell, biological rep3

value: Sensitive endothelial cell


title: Fetal hCF day10_rep2


title: Control-2 [sz2]

description: Skin Melanoma Cell line


title: Sensitive endothelial cell, biological rep2


title: YH02_5B9

value: SD


title: Sensitive endothelial cell, biological rep4


title: Kdm5b sg-2

description: Skin Melanoma Cell line

value: Kdm5b deletion 2


title: YH02_4G4


title: Kdm5b sg2-1

description: Skin Melanoma Cell line

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were mapped to repeat element fasta using Salmon with default parameters
DESeq2 was used to determine differential signal using counts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene expression values normalized with DESeq2 variance stabilizing transformation (VST) for each Sample

value: 1445 (Cdkn2a and Pten inactivated with beta-catenin stabilization)


title: YH02_4E8


title: Fetal hCF day5_rep2

value: cardiac fibroblast


title: Fetal hCF day5_rep3


title: Kdm5b sg2-2

description: Skin Melanoma Cell line


title: YH01_4H1


title: Control endothelial cell, biological rep5

value: Control endothelial cell


title: Control endothelial cell, biological rep4


title: Sensitive endothelial cell, biological rep1


title: Control endothelial cell, biological rep2


title: SBC5_control

city: Bunkyo-ku

first: NAOYA

last: MIYASHITA

state: Tokyo

department: Respiratory Medicine

country: Japan

institute: The University of Tokyo

data_processing:
CLC Genomics workbench software (Qiagen) was used to generate RPKM data.
Adapter sequences were removed, and read mapping was carried out using the default settings of RNA-Seq analysis package (mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8, and maximum number of hits for a read set to: 30).
Genome_build: GRch38
Supplementary_files_format_and_content: Excel

growth_protocol: Lu134A cells were cultured inRPMI-1640 Medium with 10% fetal bovine serum and 1% penicillin-streptomycin. SBC5 cells were cultured in Dulbecco's Modified Eagle Medium with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted 48 h after siRNA or miRNA mimic transfection using the RNeasy Mini Kit (Qiagen).
The mRNA from eukaryotic organisms was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: Lu134A and SBC5 cells were transfected with 20 nM siRNA or miRNA mimic using Lipofectamine RNAiMAX.

value: transfected with control mimics


title: Kdm5b sg1-2

description: Skin Melanoma Cell line


title: YH01_1F6

value: LD


title: Fetal hCF day10_rep1


title: YH01_0E4


title: SBC5_miR455mimic

value: transfected with miR455 mimics


title: Lu134A_siASCL1

value: transfected with ASCL1 siRNAs


title: Fetal hCF day0_rep2


title: Control endothelial cell, biological rep1


title: Fetal hCF day0_rep3


title: Control-1

description: Skin Melanoma Cell line


title: Control-1 [sz1]

description: Skin Melanoma Cell line

value: YUMMER1.7(Braf V600E, Pten -/- and Cdkn2 -/- with high frequency of stable UV-induced somatic mutations


title: Control-2

description: Skin Melanoma Cell line

value: Skin Melanoma Cell line


title: Lu134_siNC

value: transfected with control siRNAs


title: Fetal hCF day0_rep1


title: Fetal hCF day5_rep1


title: Control endothelial cell, biological rep3


title: Live CD44hiTetramer+ CD8+ TILs

city: Cambridge

first: Tyler

last: Jacks

state: MA

address: 500 Main Street

institute: MIT

data_processing:
Raw sequencing data was processed using Cell Ranger, version 3.0.2, and sequencing reads were aligned to the mm10 reference mouse transcriptome (version 3.0.0). After processing, Cell Ranger reported 789 cell-associated barcodes and detected 31,053 genes. These data were loaded into R, version 4.0.3, and further processed with Seurat, version 3.2.2 (Butler et al., 2018). Genes not expressed in any cells were filtered out. After this, low-quality cells containing more than 10% of reads matching the mitochondrial genome were excluded. Cells with less than 100 detected genes were then filtered. Finally, cells lacking expression of either Cd8a or Cd3e were removed, and cells exceeding the 97th percentile (4,065) for number of detected genes were excluded to remove probable doublets. The resulting matrix used for downstream analyses was defined by 447 cells and 15,065 genes. Data normalization and scaling, variable feature selection, cell clustering, and differential gene expression analysis was performed using Seurat. Data were normalized by total expression per cell and scaled using a factor of 10,000 and log transformed (natural scale). The top 2,000 variable genes were selected using Seurat’s default “vst” method. The expression of these genes was then scaled and centered, and these genes were then used for all downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: processed_data_count_matrix.csv is the raw count matrix of the 447 cells remaining after the filtering described above. Processed_data_normalized_matrix.csv contains the same cohort of cells from the data slot of the Seurat object (after applying the described normalizaiton strategy).

molecule: polyA RNA

source_name: Immune-evasive murine tumors

growth_protocol: Orthotopically transplanted pancreatic organoids gave rise to immune-evasive neoantigen-expressing pancreatic tumors as described in the methods

extract_protocol:
Murine TILs were isolated from pancreatic tumors by collagenase digestion of tumor tissue and then FACS sorted
scRNA-seq libraries were prepared for sequencing with the 10X Genomics 3' Single Cell RNA v3 library preparation system per manufacturer's instructions.

treatment_protocol: No treatment

tag: strain

value: CD44hiTetramer+ CD8+ TILs

value: pancreatic tumor


title: Kdm5b sg1-1

description: Skin Melanoma Cell line

value: Kdm5b deletion 1


title: Pycnia_replicate_2

status: Public on Jul 24 2021

city: Champenoux

first: Sebastien

last: Duplessis

address: INRA Centre Grand Est - Nancy

department: UMR 1136 IAM

country: France

institute: INRA

description: Same sample as in GSM2856141, only RNAseq analysis differs as reads were mapped onto M. lrici-populina genome version 2

data_processing:
Data acquisition was performed in Beckman Coulter Genomics facilities according to standard Illumina’s procedures.
All reads per sample were mapped onto the 19,550 M. larici-populina transcripts (JGI Mycocosm M. larici-populina genome version 2) using the RNAseq analysis tool of the CLC Genomics Workbench 12.0 (QIAgen). Reads were QCed and trimmed (5 nucleotides removed on 5' and 3' sides) with the CLC Genomics Workbench program before to proceed with RNAseq analysis using default parameters except for the similarity fraction, which was set at 90% across 90% of the read length.
The count of unique reads mapped per transcript was recorded for each sample with CLC Genomics Workbench and the R package DESeq2 (v1.32.0) was used to determine normalized read counts of M. larici-populina transcripts.
Genome_build: Melampsora larici-populina 98AG31 transcripts (Mellp2_3_GeneCatalog_transcripts_20151130.nt.fasta.gz) available from https://genome.jgi.doe.gov/Mellp2_3/Mellp2_3.home.html (M. larici-populina v2.0: Project: 403230)
Supplementary_files_format_and_content: tab-delimited text files include for each sample the number of unique mapped reads recorded with CLC and the normalized count from DESeq2.

organism: Melampsora laricis-populina

growth_protocol: Basidia (BSD) were collected from rust-infected dead poplar leaves. Living poplar leaves were inoculated on previous autumn by M. larici-populina isolate 98AG31 urediniospores and let standoutside in grid bags for proper telia and basidia differentiation in natural conditions. Samples consisted of a mix of dead poplar leaf tissue, remains of overwintered telia, basidia and basidiospores. Pycnia (PYC) were collected from rust-infected larch needles one week after inoculation with M. larici-populina isolate 98AG31 basidiospores. Aecia (AEC) were collected from rust-infected larch needles two weeks after inoculation with M. larici-populina isolate 98AG31 basidiospores. PYC and AEC samples consisted of larch needle tissues and various in planta infection fungal cell types.

extract_protocol:
Total RNA from BSD samples were isolated with the QIAgen RNeasy Plant Minikit from several rounds of RNA isolation using low inputs of material (10 to 20mg). Total RNA from PYC and AEC samples were isolated from 100mg infected larch needles using a protocol adapted to RNA isolation from conifers (Chang et al 1993 Plant Mol Biol doi: 10.1007/BF02670468).
cDNA synthesis and RNA-Seq library construction were performed by Beckman Coulter Genomics using the Illumina TruSEQ RNA seq kit.

tag: host organism

value: Larix decidua

tag: host tissue

value: rust-infected larch needles

tag: sexual stage

value: pycnia


title: Aecia_replicate_1

description: Same sample as in GSM2856143, only RNAseq analysis differs as reads were mapped onto M. lrici-populina genome version 2

value: aecia


title: Aecia_replicate_2

description: Same sample as in GSM2856144, only RNAseq analysis differs as reads were mapped onto M. lrici-populina genome version 2


title: Pycnia_replicate_1

description: Same sample as in GSM2856140, only RNAseq analysis differs as reads were mapped onto M. lrici-populina genome version 2


title: Basidia_replicate_2

description: Same sample as in GSM2856138, only RNAseq analysis differs as reads were mapped onto M. lrici-populina genome version 2

value: Populus trichocarpa

value: rust-infected dead poplar leaves

value: basidia


title: Basidia_replicate_3

description: Same sample as in GSM2856139, only RNAseq analysis differs as reads were mapped onto M. lrici-populina genome version 2


title: RHCD_AR010_TAGCTT_L006_R1_goodreads_st15UCd

city: Berkeley

first: Richard

last: Harland

address: 571 Life Sciences Addition #3200

department: Department of Molecular and Cell Biology

institute: UC Berkeley

description: St10 Unijected control embryo d

data_processing:
100 bp paired-end sequencing reads (Illumina HiSeq2000) were aligned to the X. tropicalis genome version 7.1
RNA-seq data analysis for differential gene expression was performed using both the Tuxedo Suite (Tophat, Bowtie, Cufflinks, Cuffdiff; Illumina) (Trapnell et al., 2012) and the Bioconductor package DESeq (Love et al., 2014). RNA-seq data analysis for differential intron-exon usagewas performed using the Bioconductor package, DEXseq (Reyes et al., 2014) (www.bioconductor.org). In brief, read counts were normalized to library size per feature. The P-values are the result of the statistical modeling performed by DESeq2/DEXSeq and indicate the degree to which the difference in expression of a given gene or exon was significant (in morphants compared with controls). The P-values were then adjusted for false discovery rates (also performed by DESeq2/DEXSeq) for the number of features, because false positive calls are problematic when sampling a large number of features (genes or exons), as is performed in gene expression studies.
Genome_build: Xentro v7.1
Supplementary_files_format_and_content: Table S1. Differential Exon Usage, stage 10. DEXseq analysis of sequenced RNA from M+Z Taf15-depleted X. tropicalis embryos, stage 10; two-fold increase in expression cutoff; sorted by padj value.
Supplementary_files_format_and_content: Table S2. Differential Exon Usage, stage 15. DEXseq analysis of sequenced RNA from M+Z Taf15-depleted X. tropicalis embryos, stage 15; two-fold increase in expression cutoff; sorted by padj value.
Supplementary_files_format_and_content: Table S3. Stage-persistent Differential Exon Usage, Stage 10 and 15. Genes with conserved differential exon usage from stage 10 to 15. DEXseq analysis of sequenced RNA from M+Z Taf15-depleted X. tropicalis embryos; two-fold increase in expression cutoff; sorted by gene name.
Supplementary_files_format_and_content: Table S4. Increased Gene Expression, stage 15. DESeq analysis of sequenced RNA from M+Z Taf15-depleted X. tropicalis embryos, stage 15; two-fold increase in expression cutoff; sorted by padj value.
Supplementary_files_format_and_content: Table S5. All changes in Gene Expression, stage 10. DESeq analysis of sequenced RNA from M+Z Taf15-depleted X. tropicalis embryos, stage 10; sorted by padj value.
Supplementary_files_format_and_content: Table S6. Increased and Decreased Gene Expression, stage 15. DESeq analysis of sequenced RNA from M+Z Taf15-depleted X. tropicalis embryos, stage 15; two-fold increase or decrease in expression cutoff; sorted by fold change.
Supplementary_files_format_and_content: Table S7. Differential Exon Usage Characteristics, stages 10 and 15. Number and location of retained introns within the top 10 genes with differential exon usage (DEU) following DEXseq analysis, as sorted by adjusted P value.

organism: Xenopus tropicalis

source_name: St10 Unijected control embryo d

growth_protocol: Embryos were cultured in 1/9MR

extract_protocol:
RNA from individual X. tropicalis embryos was isolated using the Trizol Reagent (Ambion, 15596026), optimized for extracting small amounts of RNA from single embryos.
RNA-seq libraries were made following the Low Sample (LS) Protocol from the TruSeq RNA Sample Preparation v2 Guide. The important modification made to this protocol was that all reagents, except for the Bead Washing Buffer, were used at half volume. Final RNA-seq libraries were quantified using the KAPA Library Quantification Kits for Illumina sequencing platforms (Roche, KK4824).

treatment_protocol: Embryos were uninjected, or MO injected and collected at indicated stage

value: whole embryo

tag: dev stage

value: Unijected control


title: Aecia_replicate_3

description: Same sample as in GSM2856145, only RNAseq analysis differs as reads were mapped onto M. lrici-populina genome version 2


title: Basidia_replicate_1

description: Same sample as in GSM2856137, only RNAseq analysis differs as reads were mapped onto M. lrici-populina genome version 2


title: Pycnia_replicate_3

description: Same sample as in GSM2856142, only RNAseq analysis differs as reads were mapped onto M. lrici-populina genome version 2


title: RHCD_AR011_GGCTAC_L006_R1_goodreads_st15trns1MOd

description: St15 MO injected embryo d

source_name: St15 MO injected embryo d

tag: treatment

value: MO injected


title: tafTrns1s12p3_UCc1028_index3_TTAGGC_good_reads_R1

description: St15 uninjected embryo 3

source_name: St15 uninjected embryo 3

value: uninjected


title: RHCD_AR006_GCCAAT_L006_R1_goodreads_st10trns1MOa

description: St10 MO injected embryo a

source_name: St10 MO injected embryo a

value: stage 10


title: RHCD_AR019_GTGAAA_L006_R1_goodreads_st10trns1MOb

description: St10 MO injected embryo b

source_name: St10 MO injected embryo b


title: RHCD_AR001_ATCACG_L006_R1_goodreads_st10UCc

description: St10 Unijected control embryo c

source_name: St10 Unijected control embryo c


title: tafTrns1s12p3_taf15Trns1MOc1028_index4_TGACCA_good_reads_R1

description: St15 MO injected embryo 4

source_name: St15 MO injected embryo 4


title: RHCD_AR012_CTTGTA_L006_R1_goodreads_st10UCb

description: St10 Unijected control embryo b

source_name: St10 Unijected control embryo b


title: tafTrns1s12p3_UC_index1_ATCACG_good_reads_R1

description: St15 uninjected embryo 1

source_name: St15 uninjected embryo 1


title: tafTrns1s12p3_UCc636_index5_ACAGTG_good_reads_R1

description: St15 uninjected embryo 5

source_name: St15 uninjected embryo 5


title: Unpaired_CC_Healthy Control HC29

type: protein

city: Stanford

first: Allan

last: Feng

address: 269 Campus Dr

department: Imm/Rheum

institute: Stanford School of Medicine

description: Antibodies in patient serum samples bind to conjugated beads in protein array. The fluorescence measured as MFI from the secondary antibody was used to determine serum antibody reactivity.

hyb_protocol: A secondary antibody conjugated to a fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from serum samples.

scan_protocol: A Luminex FlexMAP 3D instrument was used to measure fluorescence (in MFI) from each  barcoded bead.

data_processing: Sample replicate MFI values were averaged for each antigen. The average barebead MFI was then subtracted from the average MFI of each sample and antigen.

label: R-PE conjugated goat anti-human IgG secondary antibody

molecule: protein

source_name: Healthy Control

extract_protocol: Blood was collected from patients and healthy controls from 3 different centers. The blood was then processed into serum which was then run on our arrays.

value: serum

tag: condition

value: Healthy Control


title: Unpaired_CC_Healthy Control HC26

label_protocol: A secondary antibody conjugated to a fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from serum samples.

tag: tissue


title: RHCD_AR008_ACTTGA_L006_R1_goodreads_st10trns1MOc

description: St10 MO injected embryo c

source_name: St10 MO injected embryo c


title: Unpaired_CC_Healthy Control HC25


title: Unpaired_CC_Healthy Control HC22


title: Unpaired_CC_Healthy Control HC28


title: RHCD_AR005_ACAGTG_L006_R1_goodreads_st10UCa

description: St10 Unijected control embryo a

source_name: St10 Unijected control embryo a


title: Unpaired_CC_Healthy Control HC27


title: tafTrns1s12p3_taf15Trns1MOc636_index6_GCCAAT_good_reads_R1

description: St15 MO injected embryo 6

source_name: St15 MO injected embryo 6


title: Unpaired_CC_Healthy Control HC24


title: Unpaired_CC_Healthy Control HC23


title: Unpaired_CC_Healthy Control HC19


title: Unpaired_CC_Healthy Control HC17


title: Unpaired_CC_Healthy Control HC07


title: Unpaired_CC_Healthy Control HC09


title: Unpaired_CC_Healthy Control HC08


title: Unpaired_CC_Healthy Control HC12


title: Unpaired_CC_Healthy Control HC21


title: Unpaired_CC_Healthy Control HC20


title: Unpaired_CC_Healthy Control HC04


title: Unpaired_CC_Healthy Control HC02


title: Unpaired_CC_Healthy Control HC15


title: Unpaired_CC_Healthy Control HC16


title: Unpaired_CC_Healthy Control HC14


title: Unpaired_CC_Healthy Control HC13


title: Unpaired_CC_Healthy Control HC11


title: Unpaired_CC_Healthy Control HC10


title: Unpaired_CC_Healthy Control HC06


title: Unpaired_CC_Patient UP46 D7

source_name: Hospitalized COVID-19

value: Hospitalized COVID-19


title: Unpaired_CC_Patient UP48 D7


title: Unpaired_CC_Healthy Control HC05


title: Unpaired_CC_Patient UP45 D7


title: Unpaired_CC_Patient UP43 D7


title: Unpaired_CC_Patient UP41 D7


title: Unpaired_CC_Patient UP39 D0


title: Unpaired_CC_Healthy Control HC03


title: Unpaired_CC_Patient UMR19 D6


title: Unpaired_CC_Healthy Control HC18


title: Unpaired_CC_Patient UP37 D0


title: Unpaired_CC_Patient UP35 D0


title: Unpaired_CC_Patient UP62 D7


title: Unpaired_CC_Healthy Control HC01


title: Unpaired_CC_Patient UP49 D7


title: Unpaired_CC_Patient UP44 D7


title: Unpaired_CC_Patient UP47 D7


title: Unpaired_CC_Patient UP42 D7


title: Unpaired_CC_Patient UP31 D0


title: Unpaired_CC_Patient UP32 D0


title: Unpaired_CC_Patient UP29 D0


title: Unpaired_CC_Patient UP28 D0


title: Unpaired_CC_Patient UP40 D0


title: Unpaired_CC_Patient UP38 D0


title: Unpaired_CC_Patient UP34 D0


title: Unpaired_CC_Patient UP36 D0


title: Unpaired_CC_Patient UP30 D0


title: Unpaired_CC_Patient UP33 D0


title: Unpaired_CC_Patient UP26 D0


title: Unpaired_CC_Patient UP27 D0


title: Unpaired_CC_Patient UP25 D0


title: Unpaired_CC_Patient UP23 D0


title: Unpaired_CC_Patient UP24 D0


title: Unpaired_CC_Patient UP20 D0


title: Unpaired_CC_Patient UP17 D0


title: Unpaired_CC_Patient UP18 D0


title: Unpaired_CC_Patient UP19 D0


title: Unpaired_CC_Patient UP22 D0


title: Unpaired_CC_Patient UP21 D0


title: PairedCC_Prototype_Patient Positive Control Serum AMI_1

source_name: Positive Control Serum

value: Autoimmune Prototype


title: PairedCC_Prototype_Patient Positive Control Serum APS-1_2


title: Unpaired_CC_Patient UP13 D0


title: Unpaired_CC_Patient UP03 D0


title: PairedCC_Prototype_Patient Positive Control Serum AMI_2


title: Unpaired_CC_Patient UP16 D0


title: Unpaired_CC_Patient UP15 D0


title: Unpaired_CC_Patient UP04 D0


title: Unpaired_CC_Patient UP07 D0


title: Unpaired_CC_Patient UP05 D0


title: Unpaired_CC_Patient UP08 D0


title: Unpaired_CC_Patient UP14 D0


title: Unpaired_CC_Patient UP09 D0


title: Unpaired_CC_Patient UP12 D0


title: PairedCC_Prototype_Patient Positive Control Serum AMI_3


title: Unpaired_CC_Patient UP11 D0


title: PairedCC_Prototype_Patient Positive Control Serum PAP


title: Unpaired_CC_Patient UP06 D0


title: Unpaired_CC_Patient UP02 D0


title: Unpaired_CC_Patient UP10 D0


title: Unpaired_CC_Patient UP01 D0


title: PairedCC_Prototype_Patient Positive Control Serum APS-1_3


title: PairedCC_Prototype_Patient Positive Control Serum APS-1_1


title: PairedCC_Healthy Control HC31


title: PairedCC_Healthy Control HC29


title: PairedCC_Healthy Control HC26


title: PairedCC_Healthy Control HC25


title: PairedCC_Healthy Control HC27


title: PairedCC_Healthy Control HC28


title: PairedCC_Healthy Control HC24


title: PairedCC_Healthy Control HC20


title: PairedCC_Patient UMR12 D15


title: PairedCC_Healthy Control HC18


title: PairedCC_Healthy Control HC23


title: PairedCC_Patient UMR20 D14


title: PairedCC_Patient UMR20 D6


title: PairedCC_Patient UMR11 D19


title: PairedCC_Healthy Control HC19


title: PairedCC_Patient UMR07 D2


title: PairedCC_Patient UMR07 D39


title: PairedCC_Healthy Control HC17


title: PairedCC_Healthy Control HC16


title: PairedCC_Healthy Control HC21


title: PairedCC_Healthy Control HC22


title: PairedCC_Patient UMR10 D29


title: PairedCC_Patient UMR11 D47


title: PairedCC_Patient UMR10 D20


title: PairedCC_Patient UMR15 D3


title: PairedCC_Patient UMR14 D18


title: PairedCC_Patient UMR12 D6


title: PairedCC_Patient UMR13 D3


title: PairedCC_Patient UMR13 D1


title: PairedCC_Healthy Control HC30


title: PairedCC_Patient UMR08 D13


title: PairedCC_Patient UMR14 D40


title: PairedCC_Patient UMR15 D40


title: PairedCC_Patient UMR16 D8


title: PairedCC_Patient UMR16 D6


title: PairedCC_Patient UMR08 D20


title: PairedCC_Patient UMR09 D21


title: PairedCC_Patient UMR06 D16


title: PairedCC_Patient UMR05 D10


title: PairedCC_Patient UMR03 D26


title: PairedCC_Patient UMR04 D16


title: PairedCC_Patient UMR05 D47


title: PairedCC_Patient UMR06 D52


title: PairedCC_Patient UMR04 D11


title: PairedCC_Patient UP70 D0


title: PairedCC_Patient UP70 D21


title: PairedCC_Patient UP69 D0


title: PairedCC_Patient UP71 D14


title: PairedCC_Patient UMR02 D16


title: PairedCC_Patient UMR01 D60


title: PairedCC_Patient UMR02 D29


title: PairedCC_Patient UMR01 D14


title: PairedCC_Patient UP71 D7


title: PairedCC_Patient UMR09 D3


title: PairedCC_Patient UP69 D7


title: PairedCC_Patient UP71 D0


title: PairedCC_Patient UP70 D7


title: PairedCC_Patient UP67 D0


title: PairedCC_Patient UP68 D0


title: PairedCC_Patient UP65 D0


title: PairedCC_Patient UP68 D14


title: PairedCC_Patient UP64 D0


title: PairedCC_Patient UP67 D7


title: PairedCC_Patient UP66 D7


title: PairedCC_Patient UP60 D7


title: PairedCC_Patient UMR03 D9


title: PairedCC_Patient UP64 D7


title: PairedCC_Patient UP63 D7


title: PairedCC_Patient UP63 D0


title: PairedCC_Patient UP59 D7


title: PairedCC_Patient UP61 D7


title: PairedCC_Patient UP60 D0


title: PairedCC_Patient UP58 D7


title: PairedCC_Patient UP61 D0


title: PairedCC_Patient UP57 D0


title: PairedCC_Patient UP65 D7


title: PairedCC_Patient UP59 D0


title: PairedCC_Patient UP66 D0


title: PairedCC_Patient UP56 D7


title: PairedCC_Patient UP57 D7


title: PairedCC_Patient UP58 D0


title: PairedCC_Patient UP55 D7


title: PairedCC_Patient UP56 D0


title: PairedCC_Patient UP55 D0


title: PairedCC_Patient UP54 D7


title: PairedCC_Patient UP52 D7


title: PairedCC_Patient UP53 D0


title: PairedCC_Patient UP54 D0


title: PairedCC_Patient SU10 V4


title: PairedCC_Patient UP50 D0


title: PairedCC_Patient SU09 V2


title: PairedCC_Patient SU09 V3


title: PairedCC_Patient SU10 V2


title: PairedCC_Patient SU07 V2


title: PairedCC_Patient SU08 V2


title: PairedCC_Patient SU06 V1


title: PairedCC_Patient SU05 V3


title: PairedCC_Patient SU06 V2


title: PairedCC_Patient SU08 V1


title: PairedCC_Patient SU05 V2


title: PairedCC_Patient UP53 D7


title: PairedCC_Patient SU04 D30


title: PairedCC_Patient SU04 D0


title: PairedCC_Patient SU03 D0


title: PairedCC_Patient SU02 D60


title: PairedCC_Patient SU02 D30


title: PairedCC_Patient SU01 D0


title: PairedCC_Patient UP52 D0


title: PairedCC_Patient UP51 D7


title: PairedCC_Patient SU01 D14


title: PairedCC_Patient UP51 D0


title: PairedCC_Patient UP50 D7


title: Unpaired_AA_V2_Prototype Patient Positive Control Serum for Ro/SSA


title: PairedCC_Patient SU07 V3


title: Unpaired_AA_V2_Prototype Patient Positive Control Serum for La/SSB


title: PairedCC_Patient SU03 D7


title: Unpaired_AA_V2_Prototype Patient Positive Control Serum for Thyroglobulin


title: Unpaired_AA_V2_Prototype Patient Positive Control Serum for Scl-70


title: Unpaired_AA_V2_Prototype Patient Positive Control Serum for RNP


title: Unpaired_AA_V2_Prototype Patient Positive Control Serum for Mitochondrial


title: Unpaired_AA_V2_Healthy Control HC31


title: Unpaired_AA_V2_Prototype Patient Positive Control Serum for Histone


title: Unpaired_AA_V2_Healthy Control HC29


title: Unpaired_AA_V2_Healthy Control HC26


title: Unpaired_AA_V2_Healthy Control HC23


title: Unpaired_AA_V2_Healthy Control HC21


title: Unpaired_AA_V2_Healthy Control HC22


title: Unpaired_AA_V2_Healthy Control HC17


title: Unpaired_AA_V2_Healthy Control HC24


title: Unpaired_AA_V2_Healthy Control HC13


title: Unpaired_AA_V2_Healthy Control HC19


title: Unpaired_AA_V2_Healthy Control HC18


title: Unpaired_AA_V2_Healthy Control HC15


title: Unpaired_AA_V2_Healthy Control HC12


title: Unpaired_AA_V2_Healthy Control HC20


title: Unpaired_AA_V2_Healthy Control HC14


title: Unpaired_AA_V2_Healthy Control HC16


title: Unpaired_AA_V2_Healthy Control HC11


title: Unpaired_AA_V2_Healthy Control HC10


title: Unpaired_AA_V2_Healthy Control HC28


title: Unpaired_AA_V2_Healthy Control HC30


title: Unpaired_AA_V2_Healthy Control HC25


title: Unpaired_AA_V2_Healthy Control HC09


title: Unpaired_AA_V2_Prototype Patient Positive Control Serum for Centromere


title: Unpaired_AA_V2_Healthy Control HC08


title: Unpaired_AA_V2_Healthy Control HC03


title: Unpaired_AA_V2_Healthy Control HC07


title: Unpaired_AA_V2_Healthy Control HC02


title: Unpaired_AA_V2_Healthy Control HC01


title: Unpaired_AA_V2_Healthy Control HC27


title: Unpaired_AA_V2_Healthy Control HC05


title: Unpaired_AA_V2_Healthy Control HC06


title: Unpaired_AA_V2_Patient UP62 D7


title: Unpaired_AA_V2_Patient UP49 D7


title: Unpaired_AA_V2_Patient UP48 D7


title: Unpaired_AA_V2_Patient UMR19 D6


title: Unpaired_AA_V2_Patient UP47 D7


title: Unpaired_AA_V2_Patient UP46 D7


title: Unpaired_AA_V2_Patient UP44 D7


title: Unpaired_AA_V2_Patient UP42 D7


title: Unpaired_AA_V2_Patient UP36 D0


title: Unpaired_AA_V2_Healthy Control HC04


title: Unpaired_AA_V2_Patient UP38 D0


title: Unpaired_AA_V2_Patient UP35 D0


title: Unpaired_AA_V2_Patient UP41 D7


title: Unpaired_AA_V2_Patient UP37 D0


title: Unpaired_AA_V2_Patient UP32 D0


title: Unpaired_AA_V2_Patient UP40 D0


title: Unpaired_AA_V2_Patient UP33 D0


title: Unpaired_AA_V2_Patient UP34 D0


title: Unpaired_AA_V2_Patient UP30 D0


title: Unpaired_AA_V2_Patient UP24 D0


title: Unpaired_AA_V2_Patient UP25 D0


title: Unpaired_AA_V2_Patient UP27 D0


title: Unpaired_AA_V2_Patient UP43 D7


title: Unpaired_AA_V2_Patient UP29 D0


title: Unpaired_AA_V2_Patient UP28 D0


title: Unpaired_AA_V2_Patient UP39 D0


title: Unpaired_AA_V2_Patient UP26 D0


title: Unpaired_AA_V2_Patient UP31 D0


title: Unpaired_AA_V2_Patient UP21 D0


title: Unpaired_AA_V2_Patient UP20 D0


title: Unpaired_AA_V2_Patient UP22 D0


title: Unpaired_AA_V2_Patient UP18 D0


title: Unpaired_AA_V2_Patient UP13 D0


title: Unpaired_AA_V2_Patient UP12 D0


title: Unpaired_AA_V2_Patient UP14 D0


title: Unpaired_AA_V2_Patient UP17 D0


title: Unpaired_AA_V2_Patient UP16 D0


title: Unpaired_AA_V2_Patient UP15 D0


title: Unpaired_AA_V2_Patient UP11 D0


title: Unpaired_AA_V2_Patient UP08 D0


title: Unpaired_AA_V2_Patient UP10 D0


title: Unpaired_AA_V2_Patient UP05 D0


title: Unpaired_AA_V2_Patient UP06 D0


title: Unpaired_AA_V2_Patient UP23 D0


title: Unpaired_AA_V2_Patient UP01 D0


title: Unpaired_AA_V2_Patient UP04 D0


title: Unpaired_AA_V2_Patient UP03 D0


title: Prototype autoantigen_V2_Patient Positive Control Serum La/SSB


title: Unpaired_AA_V2_Patient UP19 D0


title: Prototype autoantigen_V2_Patient Positive Control Serum Histone


title: Unpaired_AA_V2_Patient UP02 D0


title: Prototype autoantigen_V2_Patient Positive Control Serum Thyroglobulin


title: Prototype autoantigen_V2_Patient Positive Control Serum Ro/SSA


title: Prototype autoantigen_V2_Patient Positive Control Serum RNP


title: Prototype autoantigen_V2_Patient Positive Control Serum Scl-70


title: Prototype autoantigen_V2_Patient Positive Control Serum Centromere


title: Unpaired_AA_V2_Patient UP09 D0


title: autoantigen_V2_Healthy Control HC31


title: Unpaired_AA_V2_Patient UP07 D0


title: Prototype autoantigen_V2_Patient Positive Control Serum Mitochondrial


title: autoantigen_V2_Healthy Control HC30


title: autoantigen_V2_Healthy Control HC26


title: autoantigen_V2_Healthy Control HC29


title: autoantigen_V2_Healthy Control HC28


title: autoantigen_V2_Healthy Control HC24


title: autoantigen_V2_Healthy Control HC27


title: autoantigen_V2_Healthy Control HC21


title: autoantigen_V2_Healthy Control HC20


title: autoantigen_V2_Healthy Control HC23


title: autoantigen_V2_Healthy Control HC22


title: autoantigen_V2_Healthy Control HC17


title: autoantigen_V2_Healthy Control HC18


title: autoantigen_V2_Patient UMR20 D14


title: autoantigen_V2_Patient UMR20 D6


title: autoantigen_V2_Healthy Control HC19


title: autoantigen_V2_Patient UMR10 D20


title: autoantigen_V2_Healthy Control HC16


title: autoantigen_V2_Patient UMR07 D39


title: autoantigen_V2_Patient UMR10 D29


title: autoantigen_V2_Patient UMR07 D2


title: autoantigen_V2_Patient UMR12 D6


title: autoantigen_V2_Patient UMR11 D19


title: autoantigen_V2_Patient UMR13 D3


title: autoantigen_V2_Patient UMR14 D40


title: autoantigen_V2_Patient UMR15 D40


title: autoantigen_V2_Healthy Control HC25


title: autoantigen_V2_Patient UMR13 D1


title: autoantigen_V2_Patient UMR08 D20


title: autoantigen_V2_Patient UMR08 D13


title: autoantigen_V2_Patient UMR09 D21


title: autoantigen_V2_Patient UMR16 D6


title: autoantigen_V2_Patient UMR09 D3


title: autoantigen_V2_Patient UMR16 D8


title: autoantigen_V2_Patient UMR15 D3


title: autoantigen_V2_Patient UMR06 D16


title: autoantigen_V2_Patient UMR06 D52


title: autoantigen_V2_Patient UMR05 D10


title: autoantigen_V2_Patient UMR05 D47


title: autoantigen_V2_Patient UMR11 D47


title: autoantigen_V2_Patient UMR04 D16


title: autoantigen_V2_Patient UMR12 D15


title: autoantigen_V2_Patient UMR03 D9


title: autoantigen_V2_Patient UMR04 D11


title: autoantigen_V2_Patient UMR14 D18


title: autoantigen_V2_Patient UMR03 D26


title: autoantigen_V2_Patient UMR02 D16


title: autoantigen_V2_Patient UMR01 D60


title: autoantigen_V2_Patient UMR02 D29


title: autoantigen_V2_Patient UMR01 D14


title: autoantigen_V2_Patient UP71 D7


title: autoantigen_V2_Patient UP71 D0


title: autoantigen_V2_Patient UP70 D0


title: autoantigen_V2_Patient UP69 D0


title: autoantigen_V2_Patient UP68 D14


title: autoantigen_V2_Patient UP68 D0


title: autoantigen_V2_Patient UP67 D0


title: autoantigen_V2_Patient UP65 D7


title: autoantigen_V2_Patient UP70 D21


title: autoantigen_V2_Patient UP70 D7


title: autoantigen_V2_Patient UP69 D7


title: autoantigen_V2_Patient UP71 D14


title: autoantigen_V2_Patient UP61 D7


title: autoantigen_V2_Patient UP63 D0


title: autoantigen_V2_Patient UP64 D0


title: autoantigen_V2_Patient UP66 D7


title: autoantigen_V2_Patient UP59 D0


title: autoantigen_V2_Patient UP67 D7


title: autoantigen_V2_Patient UP66 D0


title: autoantigen_V2_Patient UP65 D0


title: autoantigen_V2_Patient UP57 D0


title: autoantigen_V2_Patient UP57 D7


title: autoantigen_V2_Patient UP64 D7


title: autoantigen_V2_Patient UP63 D7


title: autoantigen_V2_Patient UP61 D0


title: autoantigen_V2_Patient UP60 D0


title: autoantigen_V2_Patient UP59 D7


title: autoantigen_V2_Patient UP60 D7


title: autoantigen_V2_Patient UP58 D7


title: autoantigen_V2_Patient UP56 D0


title: autoantigen_V2_Patient UP55 D7


title: autoantigen_V2_Patient UP58 D0


title: autoantigen_V2_Patient UP52 D0


title: autoantigen_V2_Patient UP50 D0


title: autoantigen_V2_Patient UP50 D7


title: autoantigen_V2_Patient UP51 D7


title: autoantigen_V2_Patient SU10 V2


title: autoantigen_V2_Patient SU09 V3


title: autoantigen_V2_Patient SU08 V2


title: autoantigen_V2_Patient UP54 D7


title: autoantigen_V2_Patient UP55 D0


title: autoantigen_V2_Patient UP56 D7


title: autoantigen_V2_Patient UP54 D0


title: autoantigen_V2_Patient SU07 V3


title: autoantigen_V2_Patient UP53 D7


title: autoantigen_V2_Patient SU04 D30


title: autoantigen_V2_Patient SU05 V2


title: autoantigen_V2_Patient UP53 D0


title: autoantigen_V2_Patient SU04 D0


title: autoantigen_V2_Patient SU02 D30


title: autoantigen_V2_Patient SU01 D14


title: autoantigen_V2_Patient UP52 D7


title: autoantigen_V2_Patient SU02 D60


title: autoantigen_V1_Prototype Patient Positive Control Serum for La/SSB


title: autoantigen_V2_Patient SU06 V2


title: autoantigen_V2_Patient SU08 V1


title: autoantigen_V2_Patient SU10 V4


title: autoantigen_V2_Patient UP51 D0


title: autoantigen_V1_Prototype Patient Positive Control Serum for Thyroglobulin


title: autoantigen_V2_Patient SU07 V2


title: autoantigen_V2_Patient SU09 V2


title: autoantigen_V2_Patient SU06 V1


title: autoantigen_V1_Prototype Patient Positive Control Serum for Mitochondrial


title: autoantigen_V2_Patient SU05 V3


title: autoantigen_V1_Healthy Control HC40


title: autoantigen_V2_Patient SU03 D7


title: autoantigen_V2_Patient SU03 D0


title: autoantigen_V1_Healthy Control HC38


title: autoantigen_V1_Healthy Control HC37


title: autoantigen_V1_Prototype Patient Positive Control Serum for Ro/SSA


title: autoantigen_V2_Patient SU01 D0


title: autoantigen_V1_Healthy Control HC35


title: autoantigen_V1_Healthy Control HC41


title: autoantigen_V1_Prototype Patient Positive Control Serum for Centromere


title: autoantigen_V1_Prototype Patient Positive Control Serum for Scl-70


title: autoantigen_V1_Prototype Patient Positive Control Serum for RNP


title: autoantigen_V1_Healthy Control HC34


title: autoantigen_V1_Healthy Control HC32


title: autoantigen_V1_Healthy Control HC33


title: autoantigen_V1_Patient KP45


title: autoantigen_V1_Healthy Control HC39


title: autoantigen_V1_Patient KP44


title: autoantigen_V1_Patient KP43


title: autoantigen_V1_Healthy Control HC36


title: autoantigen_V1_Patient KP39


title: autoantigen_V1_Patient KP47


title: autoantigen_V1_Patient KP48


title: autoantigen_V1_Patient KP42


title: autoantigen_V1_Patient KP41


title: autoantigen_V1_Patient KP38


title: autoantigen_V1_Patient KP37


title: autoantigen_V1_Patient KP46


title: autoantigen_V1_Patient KP36


title: autoantigen_V1_Patient KP35


title: autoantigen_V1_Patient KP34


title: autoantigen_V1_Patient KP40


title: autoantigen_V1_Patient KP30


title: autoantigen_V1_Patient KP29


title: autoantigen_V1_Patient KP32


title: autoantigen_V1_Patient KP25


title: autoantigen_V1_Patient KP31


title: autoantigen_V1_Patient KP24


title: autoantigen_V1_Patient KP26


title: autoantigen_V1_Patient KP27


title: autoantigen_V1_Patient KP28


title: autoantigen_V1_Patient KP22


title: autoantigen_V1_Patient KP16


title: autoantigen_V1_Patient KP21


title: autoantigen_V1_Patient KP19


title: autoantigen_V1_Patient KP20


title: autoantigen_V1_Patient KP17


title: autoantigen_V1_Patient KP18


title: autoantigen_V1_Patient KP15


title: autoantigen_V1_Patient KP33


title: autoantigen_V1_Patient KP09


title: autoantigen_V1_Patient KP11


title: autoantigen_V1_Patient KP08


title: autoantigen_V1_Patient KP14


title: autoantigen_V1_Patient KP07


title: autoantigen_V1_Patient KP23


title: autoantigen_V1_Patient KP06


title: autoantigen_V1_Patient KP13


title: autoantigen_V1_Patient KP12


title: autoantigen_V1_Patient KP10


title: autoantigen_V1_Patient KP04


title: autoantigen_V1_Patient KP03


title: autoantigen_V1_Patient KP05


title: autoantigen_V1_Patient KP02


title: autoantigen_V1_Patient KP01


title: Viral_Anti-His

organism: synthetic construct

source_name: Anti-6X-histidine tag antibody (Mouse Monoclonal Antibody)

value: Mouse Monoclonal Antibody

value: Anti-6X-histidine tag antibody


title: Viral_Healthy Control HC28


title: Viral_Healthy Control HC29


title: Viral_Healthy Control HC30


title: Viral_Healthy Control HC21


title: Viral_Patient UMR10 D29


title: Viral_Healthy Control HC22


title: Viral_Healthy Control HC26


title: Viral_Healthy Control HC20


title: Viral_Healthy Control HC24


title: Viral_Healthy Control HC23


title: Viral_Healthy Control HC19


title: Viral_Healthy Control HC25


title: Viral_Healthy Control HC18


title: Viral_Patient UMR07 D39


title: Viral_Healthy Control HC27


title: Viral_Healthy Control HC31


title: Viral_Patient UMR10 D20


title: Viral_Patient UMR12 D15


title: Viral_Patient UMR11 D19


title: Viral_Healthy Control HC16


title: Viral_Patient UMR14 D40


title: Viral_Patient UMR13 D3


title: Viral_Patient UMR12 D6


title: Viral_Patient UMR07 D2


title: Viral_Healthy Control HC17


title: Viral_Patient UMR15 D40


title: Viral_Patient UMR11 D47


title: Viral_Patient UMR15 D3


title: Viral_Patient UMR16 D6


title: Viral_Patient UMR06 D52


title: Viral_Patient UMR08 D20


title: Viral_Patient UMR16 D8


title: Viral_Patient UMR09 D21


title: Viral_Patient UMR09 D3


title: Viral_Patient UMR06 D16


title: Viral_Patient UMR05 D10


title: Viral_Patient UMR04 D16


title: Viral_Patient UMR05 D47


title: Viral_Patient UMR03 D26


title: Viral_Patient UMR02 D29


title: Viral_Patient UMR14 D18


title: Viral_Patient UMR04 D11


title: Viral_Patient UMR03 D9


title: Viral_Patient UMR02 D16


title: Viral_Patient UMR13 D1


title: Viral_Patient UMR01 D60


title: Viral_Patient UMR01 D14


title: Viral_Patient UP71 D14


title: Viral_Patient UP71 D0


title: Viral_Patient UMR08 D13


title: Viral_Patient UP70 D21


title: Viral_Patient UP70 D7


title: Viral_Patient UP69 D0


title: Viral_Patient UP70 D0


title: Viral_Patient UP69 D7


title: Viral_Patient UP68 D14


title: Viral_Patient UP68 D0


title: Viral_Patient UP71 D7


title: Viral_Patient UP66 D7


title: Viral_Patient UP66 D0


title: Viral_Patient UP67 D0


title: Viral_Patient UP67 D7


title: Viral_Patient UP65 D7


title: Viral_Patient UP64 D7


title: acidification replicate-1

city: Busan

first: Seonock

last: Woo

address: Haeyangro 385

institute: Korea Institute of Ocean Science and Technology

description:
ph6.5
acidification stressed soft coral polyp, ph6.5, hybridized with ph8.0 exposed coral polyps (control group).
Total RNA from pooled coral polyps.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: The hybridization images were analyzed by Agilent DNA microarray Scanner (Agilent Technology, USA) and the data quantification was performed using Agilent Feature Extraction software 9.3.2.1 (Agilent Technology, USA). The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpring GX 7.3.1 (Agilent Technology, USA). Genes were filtered with removing flag-out genes in each experiment. Intensity-dependent normalization (LOWESS) was performed, where the ratio was reduced to the residual of the Lowess fit of the intensity vs. ratio curve. The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. The differentially expressed genes were identified using the Single t-test that assumes unequal variances between groups. The criteria of significant genes were P value < 0.05.

organism: Scleronephthya gracillimum

source_name: pH8.0 exposed soft coral polyp (control group)

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: Coral samples collected from sea.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: High temperature (26, 28 degrees) for 24hr exposure, acidification condition exposure (ph6.5, 7.0, 7.5) for 24 hr, high temperature and acidification stress exposure (28degree with ph7.0, 7.5, 7.8) for 24hr.

value: soft coral polyps

source_name: pH6.5 exposed soft coral polyp (experimental group)


title: dual stress 7.5, replicate-1

description:
temp28-ph7.5-rep1
dual stressed soft coral polyp, ph7.5 and 28degree, hybridized with ph8.0, 24degree exposed coral polyps (control group), replicate 1.
Total RNA from pooled coral polyps.

source_name: 24C and pH8.0 exposed soft coral polyp (control group)

value: 24C and pH8.0

source_name: 28C and pH7.5 exposed soft coral polyp (experimental group)

value: 28C and pH7.5


title: 28 degree hyperthermal stress replicate 1

description:
temp28-rep1
28degree hyperthermal stress exposed soft coral polyp, hybridized with 24degree exposed coral polyps (control group), replicate 1.
Total RNA from pooled coral polyps.

source_name: 24C exposed soft coral polyp (control group)

value: temperature 24C

source_name: 28C exposed soft coral polyp (experimental group)

value: temperature 28C


title: dual stress 7.0, replicate-1

description:
temp28-ph7.0-rep1
dual stressed soft coral polyp, ph7.0 and 28degree, hybridized with ph8.0, 24degree exposed coral polyps (control group), replicate 1.
Total RNA from pooled coral polyps.

source_name: 28C and pH7.0 exposed soft coral polyp (experimental group)

value: 28C and pH7.0


title: acidification replicate-2

description:
ph7.0
acidification stressed soft coral polyp, ph7.0, hybridized with ph8.0 exposed coral polyps (control group).
Total RNA from pooled coral polyps.

source_name: pH7.0 exposed soft coral polyp (experimental group)


title: dual stress 7.8, replicate-1

description:
temp28-ph7.8-rep1
dual stressed soft coral polyp, ph7.8 and 28degree, hybridized with ph8.0, 24degree exposed coral polyps (control group), replicate 1.
Total RNA from pooled coral polyps.

source_name: 28C and pH7.8 exposed soft coral polyp (experimental group)

value: 28C and pH7.8


title: acidification replicate-3

description:
ph7.5
acidification stressed soft coral polyp, ph7.5, hybridized with ph8.0 exposed coral polyps (control group).
Total RNA from pooled coral polyps.

source_name: pH7.5 exposed soft coral polyp (experimental group)


title: Viral_Patient UP61 D7


title: Viral_Patient UP65 D0


title: 28 degree hyperthermal stress replicate 2

description:
temp28-rep2
28degree hyperthermal stress exposed soft coral polyp, hybridized with 24degree exposed coral polyps (control group), replicate 2.
Total RNA from pooled coral polyps.


title: dual stress 7.5, replicate-2

description:
temp28-ph7.5-rep2
dual stressed soft coral polyp, ph7.5 and 28degree, hybridized with ph8.0, 24degree exposed coral polyps (control group), replicate 2.
Total RNA from pooled coral polyps.


title: Viral_Patient UP64 D0


title: 22RV1 cells induced with Robustanoids A lncRNA 2

city: Hangzhou

first: Jianxin

last: Han

address: Yuhangtang RD 866#

department: Department of Food Science and Nutrition, School of Biosystems Engineering and Food Science

country: China

institute: Zhejiang University

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information.

source_name: 22RV1 cells induced with Robustanoids A

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 22RV1 cells were plated in 6-well plates followed by treated with 10 μM of Robustanoids A for 48 hr. In the control group, cells received 0.1% DMSO, which was tantamount to the amount in the experimental group.

value: Human prostate cancer cells (22RV1 cells)


title: 22RV1 cells induced with Robustanoids A lncRNA 1


title: dual stress 7.8, replicate-2

description:
temp28-ph7.8-rep2
dual stressed soft coral polyp, ph7.8 and 28degree, hybridized with ph8.0, 24degree exposed coral polyps (control group), replicate 2.
Total RNA from pooled coral polyps.


title: 26 degree hyperthermal stress replicate 1

description:
temp26-rep1
26degree hyperthermal stress exposed soft coral polyp, hybridized with 24degree exposed coral polyps (control group), replicate 1.
Total RNA from pooled coral polyps.

source_name: 26C exposed soft coral polyp (experimental group)

value: temperature 26C


title: 26 degree hyperthermal stress replicate 2

description:
temp26-rep2
26degree hyperthermal stress exposed soft coral polyp, hybridized with 24degree exposed coral polyps (control group), replicate 2.
Total RNA from pooled coral polyps.


title: Viral_Patient UP60 D0


title: Viral_Patient UP60 D7


city: Chicago

first: Hoang Van

last: Phan

state: Illinois

address: 5640 S Ellis Ave

department: Priztker School of Molecular Engineering

institute: The University of Chicago

description: FD-seq of PFA-fixed A549 cells (technical replicate 1)

data_processing:
Base calling was done automatically in Illumina's BaseSpace platform
Single-cell data was processed using Drop-seq tools v2.3.0 and STAR aligner according to the online manual
Single-cell count data was analyzed with Seurat 3
Read mapping metrics were calculated using Picard v2.21.8. Read subsampling was performed with samtools v1.9
Genome_build: GRCh38
Supplementary_files_format_and_content: Single-cell data: tab-delimited text file of UMI counts per single cell

source_name: A549-H2B-Ruby cell line

growth_protocol: A549-H2B-Ruby cells were grown in DMEM with 10% FBS.

extract_protocol:
Single cells were captured and lysed in droplets in a microfluidic chip as per Drop-seq.
The single-cell cDNA was tagmented using Nextera XT kit as per Drop-seq protocol.

value: Human lung epithelial cells

tag: virus type

value: PFA fixation and Triton X permeabilization


description: FD-seq of PFA-fixed A549 cells (technical replicate 2)


title: 22RV1 cells  normal lncRNA 3

source_name: 22RV1 normal cells


title: dual stress 7.0, replicate-2

description:
temp28-ph7.0-rep2
dual stressed soft coral polyp, ph7.0 and 28degree, hybridized with ph8.0, 24degree exposed coral polyps (control group), replicate 2.
Total RNA from pooled coral polyps.


title: 22RV1 cells  normal lncRNA 1


title: Viral_Patient UP59 D7

source_name: Hospitalized COVID-19

value: serum


title: 22RV1 cells induced with Robustanoids A lncRNA 3


title: Viral_Patient UP59 D0


title: MPRA SH-SY5Y Replicate 3 - chimp HAR sequences

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

institute: Boston Children's Hospital

data_processing:
Library strategy: MPRA
To identify HAR barcodes, the sequence immediately preceding the adapter sequence was isolated, and the occurrence of each barcode counted
To compare to the reference 10,690 barcodes, each barcode’s Levenstein distance was calculated with respect to all reference barcodes using the stringdist package, and the minimum value was taken for each barcode
Multiple probes were summarized by taking the mean of each probe
Data was normalized to account for effective logFC differences across uneven library sizes by using the Trimmed Means of M normalization as implemented in the edgeR package
The RNA matrix was created by dividing each sample’s RNA value by the respective plasmid DNA
HARs with significant enhancer activity were identified using a one-sided one-sample T-test of the three biological replicates to identify HARs with log2 mRNA/DNA>0. This T-test was performed independently using the human and chimpanzee orthologs as well as the data from N2A and SH-SY5Y cells, and those with a p-value <0.05 in at least one of these samples were considered to have significant enhancer activity. False discovery rates were also identified by shuffling the MPRA data between HARs and samples and recomputing the p-values, to identify the proportion of enhancers identified at a given p-value threshold that may be the result of a falsely identified enhancer. A two-sided paired T-test was used to identify HARs with significantly different log2(mRNA/DNA) ratios between the human and chimpanzee orthologs.
Supplementary_files_format_and_content: tab-delimited file of normalized reporter expression from human or chimp sequence of each assayed HAR

source_name: cell culture

growth_protocol: Neuro2A/N2A cells (ATCC, CCL-131) were grown in 10% fetal bovine serum, Dulbecco’s Modified Eagle Medium, and 1% Penicillin-Streptomycin. SH-SY5Y cell (ATCC, CRL-2266) medium was 10% fetal bovine serum, Dulbecco’s Modified Eagle Medium/F12, and 1% Penicillin-Streptomycin. Both cell lines were maintained in a 5% CO2 incubator at 37oC.

extract_protocol:
mRNA was isolated using TRIzol reagent (Invitrogen, 15596018)
Resulting Tag-seq amplified cDNA was deep sequenced using the Illumina Hi-Seq X with 150-bp paired-end reads.

treatment_protocol: Molecular Inversion Probes (MIPs) targeting flanking regions of all HAR sequences were designed using the MIPgen program (Boyle et al., 2014) and manufactured as a pool by CustomArray (Bothell, WA). Target genomic sequences from both human (Promega, G1521) and chimpanzee DNA (Coriell, NS03489) were captured as previously described (Cantsilieris et al., 2017) and purified using Agencourt AMPure XP beads at 0.9X concentration (Beckman-Coulter, A63881). The MPRA assay then was conducted as previously described (Melnikov et al., 2014). Briefly, the captures were cloned into modified pMPRA1 vector (Addgene, 49349). The only modification to the pMPRA1 vector was the addition of an AsiSI restriction site used for inserting our captured DNA fragments. The luciferase gene and minimal promoter (pMPRA_donor2, Addgene, 49353) was then cloned into the pMPRA1_Capture construct pool. The transfection of the MPRA libraries was performed with five replicates per condition, and the experiment was conducted in triplicate. The cells (N2A and SH-SY5Y) were grown as adherent cultures for 24hr in 15 cm plates. Then, 20ug of MPRA constructs and 4ug of a fluorescent reporter construct per plate were transfected into cells with Lipofectamine LTX reagent (Thermo Fisher, A12621). The cells were checked for fluorescent reporter expression at 24hr and harvested 48hr post-transfection.

value: SH-SY5Y cells (ATCC, CRL-2266)

tag: mpra species

value: chimp


title: MPRA SH-SY5Y Replicate 3 - human HAR sequences

value: human


title: Viral_Patient UP58 D7

value: Hospitalized COVID-19


title: MPRA SH-SY5Y Replicate 1 - chimp HAR sequences


title: MPRA SH-SY5Y Replicate 2 - chimp HAR sequences


title: Viral_Patient UP58 D0


title: MPRA SH-SY5Y Replicate 1 - human HAR sequences


title: Viral_Patient UP57 D0


title: MPRA SH-SY5Y Replicate 2 - human HAR sequences


title: Viral_Patient UP56 D7


title: Viral_Patient UP61 D0


title: Viral_Patient UP56 D0


title: Viral_Patient UP55 D7


title: Viral_Patient UP55 D0


title: 22RV1 cells  normal lncRNA 2


title: Viral_Patient UP57 D7


title: Viral_Patient UP54 D7


title: Control NoUV_rep3

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

country: Portugal

institute: CESAM & University of Aveiro

hyb_protocol: The cRNA samples were hybridized on the Custom Gene Expression Agilent Microarrays (4 x 44k format) developed for Enchytraeus crypticus. Hybridizations were performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, Palo Alto, CA, USA) and each biological replicate was individually hybridized on one array. The arrays were hybridized at 65ºC with a rotation of 10 rpm, during 17h. After that the microarrays were washed using Agilent Gene Expression Wash Buffer Kit (Agilent Technologies, Palo Alto, CA, USA)

scan_protocol: Scanning was performed using the Agilent DNA microarray scanner G2505B (Agilent Technologies). Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies).

data_processing: Background correction was provided by Agilent Feature Extraction software and only gene probes with good signal quality (flag IsPosAndSignif = True) in all samples were employed in the analyses.

organism: Enchytraeus crypticus

source_name: whole body

label_protocol: Labelling and hybridizations followed the protocol “One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling” from Agilent Technologies (Agilent Technologies, Palo Alto, CA, USA)). Briefly, 500 ng of total RNA was amplified and labelled with Agilent Low Input Quick Amp Labelling Kit (Agilent Technologies, Palo Alto, CA, USA). Positive controls were added with the Agilent one-colour RNA Spike-In Kit (Agilent Technologies, Palo Alto, CA, USA). Purification of the amplified and labelled cRNA was performed with the RNeasy columns (Qiagen, Valencia, CA, USA).

extract_protocol: Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA).The quantity and purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were approximately 2. To verify the integrity of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed.

value: Whole body extracts (40 organisms)

tag: stage of development

value: Adult organisms with well developed clitellum

tag: exposure

value: standard laboratory illumination, in ISO reconstituted water, for 5 days


title: Control NoUV_rep2


title: TFE3-N-67

city: Shanghai

first: Ning

last: He

address: No. 11, Lane 100, Banxia Road, Pudong New Area, Shanghai, China

institute: GloriousMed Technology Co., Ltd.

data_processing:
The raw RNA-sequencing reads were filtered by FastQC, Reads were aligned using STAR v2.7.0f with default parameters to the Ensembl human genome assembly GRCh37.
Gene expression levels were estimated by raw count and TPM (Transcripts Per Kilobase Million).
Annotations of mRNA in the human genome were retrieved from the GENCODE (v19) database.
Paired trimmed/clipped and de-duplicated RNAseq reads were used to identify gene fusion events, and the aligned output was used as input to STAR-Fusion v1.9.1 using the developer-supplied gencode v33 CTAT library from April 6, 2020. Fusion gene supported by at least two reads was selected.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include log2 transfomed TPM values for each Sample

source_name: Renal

extract_protocol:
Total RNA was isolated from each sample using Qiagen RNeasy formalin-fixed paraffin-embedded (FFPE) Kit (Qiagen, Hilden, Germany), following the protocol from manufacturer. Purity and quantity of total RNA were measured by Nanodrop equipment. Integrity of RNA was evaluated using the RNA Nano6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). 1μg RNA of per sample was used as input for the RNA sample preparations.
Strand-specific RNA sequencing libraries were generated using the Whole RNA-seq Lib Prep kit for Illumina (ABclonal, China). Library quality was evaluated on the Agilent Bioanalyzer 2100 system (Agilent, USA). Final libraries were sequenced at the Novogene Bioinformatics Institute (Beijing, China) on an Illumina Hiseq X10 platform by a 150bp paired-end reads.

value: Adjacent normal tissue


title: TFE3-N-59


title: TFE3-N-53


title: TFE3-N-50


title: Viral_Patient UP54 D0


title: TFE3-N-51


title: Control NoUV_rep1


title: Viral_Patient UP53 D7


title: TFE3-N-46


title: TFE3-N-36


title: TFE3-N-35


title: Viral_Patient UP52 D7


title: TFE3-N-44


title: TFE3-N-20


title: Viral_Patient UP52 D0


title: Viral_Patient UP51 D7


title: TFE3-70

value: Renal cell carcinoma

value: male; 2:female):2

tag: tumor size (0

value: <median; 1:≥median):0

tag: t stage (1

tag: n stage (0

tag: m stage (0

tag: os time (months)

tag: OS status


title: TFE3-N-1


title: Viral_Patient UP50 D7


title: Viral_Patient SU10 V2


title: Viral_Patient SU10 V4


title: Viral_Patient UP51 D0


title: Viral_Patient UP50 D0


title: TFE3-67

value: <median; 1:≥median):1


title: Viral_Patient UP53 D0


title: TFE3-65


title: TFE3-69


title: Viral_Patient SU08 V2


title: TFE3-66

value: male; 2:female):1


title: Viral_Patient SU07 V3


title: Viral_Patient SU09 V2


title: TFE3-N-31


title: TFE3-N-19


title: Viral_Patient SU07 V2


title: TFE3-63


title: Viral_Patient SU06 V2


title: TFE3-60


title: TFE3-62


title: TFE3-59


title: TFE3-58


title: TFE3-64


title: Viral_Patient SU06 V1


title: TFE3-56


title: Viral_Patient SU05 V3


title: Viral_Patient SU08 V1


title: Viral_Patient SU04 D0


title: Viral_Patient SU04 D30


title: TFE3-54


title: TFE3-55


title: Viral_Patient SU03 D7


title: Viral_Patient SU02 D60


title: Viral_Patient SU03 D0


title: TFE3-53


title: TFE3-51


title: TFE3-52


title: Viral_Patient SU01 D14


title: Viral_Patient SU01 D0


title: Viral_Patient SU02 D30


title: Viral_Patient SU09 V3


title: Unpaired_CC_Prototype Patient Positive Control Serum AMI_3

source_name: Positive Control Serum

value: Autoimmune Prototype


title: TFE3-46


title: TFE3-48


title: TFE3-50


title: TFE3-57


title: TFE3-43


title: Unpaired_CC_Prototype Patient Positive Control Serum APS-2


title: Unpaired_CC_Prototype Patient Positive Control Serum APS-3


title: TFE3-47


title: Viral_Patient SU05 V2


title: TFE3-40


title: TFE3-42


title: Unpaired_CC_Prototype Patient Positive Control Serum APS-1


title: TFE3-41


title: Unpaired_CC_Prototype Patient Positive Control Serum AMI_2


title: Unpaired_CC_Healthy Control HC30

source_name: Healthy Control

value: Healthy Control


title: TFE3-38


title: Unpaired_CC_Healthy Control HC31


title: Unpaired_CC_Prototype Patient Positive Control Serum PAP


title: Unpaired_CC_Prototype Patient Positive Control Serum AMI_1


title: Sample 12_CD34+ cells Delta1ext-IgG hypoxia bulkRNA rep6

city: Bethesda

first: Daisuke

last: Araki

address: 9000 Rockville Pike

institute: National Institutes of Health

description:
DA4562-18_S41
6th biological replicate

data_processing:
Rigorous quality controls of paired-end reads were assessed using FastQC tools [A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2015), "FastQC," https://qubeshub.org/resources/fastqc].
Reads were aligned to the reference genome using the latest version of HISAT2 [PMID: 31375807], which is a splice-aware aligner that sequentially aligns reads to the known transcriptome and genome.
FeatureCounts [PMID: 24227677] was used for gene level abundance estimation using the GENCODE (v25) [PMID: 22955987] comprehensive gene annotations.
Principal component analysis (PCA) was used to assess outlier samples. Genes were kept in the analysis if they had raw read counts  5 in at least four samples (for each pairwise comparison performed in the differential expression analysis).
Differential expression analysis at the gene levels of summarization were then carried out using open source Limma R package [DOI: https://doi.org/10.1007/0-387-29362-0_23].
Limma-voom [PMID: 24485249, PMID: 25605792], was employed to implement a gene-wise linear modelling which processes the read counts into log2 counts per million (logCPM) with associated precision weights.
The log2CPM values were normalized between samples using trimmed mean of M-values (TMM) [PMID: 20196867].
We adjusted the differential expression analysis by using a covariate indicating paired samples from subjects following the experimental design.
We adjusted for multiple testing by reporting the FDR q-values for each feature [PMID: 26826716].
Genome_build: Gencode v25
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Human CD34+ cells from 6 different healthy donors were thawed and resuspended at a concentration of 5.0 x 105 cells/mL in StemSpanTM Serum-Free Expansion Medium II (STEMCELL Technologies) supplemented with 50 ng/mL of human recombinant Stem Cell Factor (SCF), Fms-like tyrosine kinase 3 ligand (FLT3) and Thrombopoietin (TPO) (PeproTech). Subsequently, cells were ex vivo cultured for 24 hours in vessels coated with Delta1ext-IgG at 10 µg/mL under normoxia and 5 µg/mL under hypoxia.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions. The genomic DNA elimination columns contained in the kit were used to eliminate possible DNA contamination during the extraction.
The sequencing libraries were constructed from 10 pg–10 ng of total RNA using the Takara Bio USA’s SMART-Seq V4 Ultra Low Input RNA Kit for Sequencing (Cat # 634888) following the manufacturer’s instructions. Full-length cDNA synthesis was performed using oligo-dT and SMART oligos, and the Illumina sequencing adaptors and barcodes incorporated into the final library by PCR. The fragment size of the RNAseq libraries was verified using the Agilent 2100 Bioanalyzer (Agilent) and the concentrations determined using the Qubit instrument (Thermo Fisher Scientific). The libraries were loaded onto the Illumina HiSeq 3000 machine (Illumina) for paired end 75 bp read sequencing and generated about 50 M reads per sample. The.fastq files were generated using the bcl2fastq software (Illumina) for further analysis.

tag: cell type

value: G-CSF mobilized human CD34+ cells

value: ex vivo cultured for 24 hours with 5 µg/mL Delta1ext-IgG in hypoxia


title: Sample 11_CD34+ cells Delta1ext-IgG hypoxia bulkRNA rep5

description:
DA4562-17_S40
5th biological replicate


title: Sample 10_CD34+ cells Delta1ext-IgG hypoxia bulkRNA rep4

description:
DA4562-16_S39
4th biological replicate


title: Sample 9_CD34+ cells Delta1ext-IgG hypoxia bulkRNA rep3

description:
DA4562-15_S38
3rd biological replicate


title: TFE3-37


title: TFE3-36


title: Sample 8_CD34+ cells Delta1ext-IgG hypoxia bulkRNA rep2

description:
DA4562-14_S37
2nd biological replicate


title: TFE3-35


title: TFE3-45


title: TFE3-44


title: TFE3-34


title: Sample 7_CD34+ cells Delta1ext-IgG hypoxia bulkRNA rep1

description:
DA4562-13_S36
1st biological replicate


title: Sample 6_CD34+ cells Delta1ext-IgG normoxia bulkRNA rep6

description:
DA4562-12_S35
6th biological replicate

value: ex vivo cultured for 24 hours with 10 µg/mL Delta1ext-IgG in normoxia


title: TFE3-33


title: TFE3-31


title: TFE3-32


title: Sample 5_CD34+ cells Delta1ext-IgG normoxia bulkRNA rep5

description:
DA4562-11_S34
5th biological replicate


title: TFE3-28


title: TFE3-30


title: TFE3-29


title: TFE3-24


title: TFE3-23


title: Sample 3_CD34+ cells Delta1ext-IgG normoxia bulkRNA rep3

description:
DA4562-9_S32
3rd biological replicate


title: Sample 1_CD34+ cells Delta1ext-IgG normoxia bulkRNA rep1

description:
DA4562-7_S30
1st biological replicate


title: TFE3-22


title: Exp120B: CD34+ cells Delta1ext-IgG hypoxia scRNA rep2

description: 2nd technical replicate

data_processing:
De-multiplexed scRNA-seq fastq files were processed using Drop-seq Tools v1.12. Read alignment and generation of the digital gene expression matrix were performed using STAR v2.5.4a with default settings and drop-seq-tools-1.12 in NIH Helix/Biowulf High Performing Computation (HPC) system. From read 1, 5’ bases 1–12 and bases 13–20 with equal or higher than 10 quality score were tagged as cell barcode and unique molecular identifier (UMI), respectively, and then filtered for sequence alignment. Adapter sequence and poly-A tail sequence contamination were removed before sequence alignment.
We used R language within the RStudio IDE throughout our analysis. The digital gene expression matrices for all samples were analyzed using Seurat version 3.2.0 by following standard pipeline listed in the website (https://satijalab.org/seurat/vignettes.html).
Quality control was performed to filter low-quality cells by retaining cells that had more than 500 genes and less than 5% of mapped reads mapping to mitochondrial genes.
Gene expression values were normalized using Seurat’s scTransform to account for technical variation in RNA recovery and sequencing depth with default parameters. The filtered and normalized datasets were integrated via Seurat.
To decrease noise and make downstream computations more tractable, the data were dimensionally reduced by projection onto the top 20 principal components. For clustering and visualization, the data were further dimensionally reduced to two dimensions via Uniform Manifold Approximation and Projection (UMAP), a non-linear dimensional reduction technique founded on the assumptions that the data is uniformly distributed on a connected Riemannian manifold with locally constant metric.
Genome_build: hg19
Supplementary_files_format_and_content: _barcodes.tsv: Cell barcodes.
Supplementary_files_format_and_content: _genes.tsv: Genes.
Supplementary_files_format_and_content: _matrix.mtx: Gene barcode matrices.

source_name: G-CSF mobilized human CD34+ cells

growth_protocol: Human CD34+ cells from one healthy donor were thawed and resuspended at a concentration of 5.0 x 105 cells/mL in StemSpanTM Serum-Free Expansion Medium II (STEMCELL Technologies) supplemented with 50 ng/mL of human recombinant Stem Cell Factor (SCF), Fms-like tyrosine kinase 3 ligand (FLT3) and Thrombopoietin (TPO) (PeproTech). Subsequently, cells were ex vivo cultured for 2 hours in vessels coated with Delta1ext-IgG at 10 µg/mL under normoxia and 5 µg/mL under hypoxia.

extract_protocol:
Harvested cells were resuspended at 1.0 x 105 cells/mL and encapsulated with barcoded Bead SeqB microparticles (Chemgenes) into droplets containing lysis buffer using a PDMS microfluidic device (FlowJem), aiming at capturing 3,000 - 4,000 single cells per technical replicate of each culture condition, two technical replicates were run per culture condition. Following single-cell encapsulation, droplet breakage, reverse transcription, exonuclease I treatment and PCR amplification were all performed following the standard Drop-seq protocol. The amplified cDNA and sequencing libraries were quantified using the Qubit dsDNA High Sensitivity assay (Thermo Fisher Scientific) and sized using a DNA High-sensitivity BioAnalyzer 2100 kit and instrument (Agilent Technologies).
Sequencing libraries were prepared using the Nextera XT DNA sample prep kit (Illumina). The libraries were sequenced on the Illumina HiSeq 3000, with a read length of 20 bp of Read 1 using a custom primer (5’ GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC 3’), 60 bp of Read 2, and 8 bp of index read 1 for sample demultiplexing. Sequencing depth was at least 50,000 raw read pairs per cell.

value: ex vivo cultured for 2 hours with 5 µg/mL Delta1ext-IgG in hypoxia


title: TFE3-27


title: MPRA N2A Replicate 3 - chimp HAR sequences

value: Neuro2A/N2A cells (ATCC, CCL-131)

value: chimp


title: Sample 2_CD34+ cells Delta1ext-IgG normoxia bulkRNA rep2

description:
DA4562-8_S31
2nd biological replicate


title: TFE3-20


title: Exp120A: CD34+ cells Delta1ext-IgG hypoxia scRNA rep1

description: 1st technical replicate


title: Exp103B: CD34+ cells Delta1ext-IgG normoxia scRNA rep2

description: 2nd technical replicate

value: ex vivo cultured for 2 hours with 10 µg/mL Delta1ext-IgG in normoxia


title: Exp103A: CD34+ cells Delta1ext-IgG normoxia scRNA rep1

description: 1st technical replicate


title: MPRA N2A Replicate 3 - human HAR sequences

value: human


title: MPRA N2A Replicate 2 - chimp HAR sequences


title: TFE3-19


title: MPRA N2A Replicate 2 - human HAR sequences


title: TFE3-18


title: Sample 4_CD34+ cells Delta1ext-IgG normoxia bulkRNA rep4

description:
DA4562-10_S33
4th biological replicate


title: TFE3-16


title: TFE3-17


title: MPRA N2A Replicate 1 - chimp HAR sequences


title: MPRA N2A Replicate 1 - human HAR sequences


title: TFE3-15


title: B16 PB-4 2 miRNA

city: Yantai

first: Defang

last: Li

address: No. 346 Guanhai, Laishan District

institute: Binzhou Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) a)10% base quality <15 b) 13% base quality <20 c) 15bp < read length < 30bp.
Utilizing the BWA software, we mapped the clean data to miRBase 22.0 Mus musculus miRNA database and GRCm38 genome.
count counting
genome build:  miRBase 22.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Mouse skin tissue

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: TFE3-11


title: B16 PB-4 3 miRNA


title: B16 ATRA 2 miRNA

value: ATRA


title: TFE3-13


title: B16 ATRA 1 miRNA


title: TFE3-12


title: B16 PB-4 1 miRNA


title: TFE3-8


title: B16 ATRA 3 miRNA


title: B16 Control 3 miRNA

value: Control


title: TFE3-9

value: Renal cell carcinoma


title: B16 PB-4 3 total RNA seq

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
genome build:  mm10_GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: TFE3-7

value: male; 2:female):2


title: TFE3-10

value: <median; 1:≥median):0


title: B16 Control 2 miRNA


title: TFE3-6

value: <median; 1:≥median):1


title: B16 Control 1 miRNA


title: B16 PB-4 1 total RNA seq


title: TFE3-5

value: male; 2:female):1


title: TFE3-14


title: B16 PB-4 2 total RNA seq


title: TFE3-4


title: TFE3-1


title: TFE3-3


title: Mx1Cre-A10f/f_with_Abx

first: Keisuke

middle: Chris

last: Nagao

state: Maryland

address: 9000 Rockville Pike, Bldg 10, Rm12N240B

institute: National Institute of Arthritis and Musculoskeletal and Skin Diseases

data_processing:
Post-processing and quality control were performed using the 10x Cell Ranger pipelines (v2.2.0, 10x Genomics). Reads were aligned to mouse reference genome (mm10) using a STAR aligner to produce the digital gene expression matrix (10x Genomics Cell Ranger).
Genome_build: mm10

source_name: CD45-negative cells

extract_protocol:
Droplet-based scRNA-seq captures were performed with 10x Chromium (10x Genomics) in accordance with the manufacturer protocol.
cDNA libraries were prepared following the recommended protocol for the Chromium Single Cell 3’ Reagent Kit (v2 Chemistry).

treatment_protocol: CD45-negative non-immune cells were sorted from WT, antibiotics non-treated Mx1Cre-Adam10f/f  and antibiotics treated Mx1Cre-Adam10f/f mice 30 days post-induction with poly(I:C). Whole skin cell suspensions were sorted for viable cells based on SYTOXTMRed dead cell stain. Cells were further sorted for CD45-negative cells.

tag: strain

value: skin

tag: experimental group

tag: genotyping


title: B16 ATRA 3 total RNA seq

tag: treatment


title: TFE3-2

tag: tissue


title: B16 ATRA 2 total RNA seq


title: B16 Control 3 total RNA seq


title: Mx1Cre-Rbpjf/f CD45-negative cells

data_processing:
Post-processing and quality control were performed using the 10x Cell Ranger pipelines (v3.0.2, 10x Genomics). Reads were aligned to mouse reference genome (mm10) using a STAR aligner to produce the digital gene expression matrix (10x Genomics Cell Ranger).
Genome_build: mm10

extract_protocol:
Droplet-based scRNA-seq captures were performed with 10x Chromium (10x Genomics) in accordance with the manufacturer protocol.
cDNA libraries were prepared following the recommended protocol for the Chromium Single Cell 3’ Reagent Kit (v3 Chemistry).

treatment_protocol: CD45-negative non-immune cells were sorted from Mx1Cre-Rbpjf/f  mice 30 days post-induction with poly(I:C). Whole skin cell suspensions were sorted for viable cells based on SYTOXTMRed dead cell stain. Cells were further sorted for CD45-negative cells.


title: WT

value: WT


title: WT_Nanopore

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: Nanopore sequencing

library_source: genomic

data_processing:
Library strategy: DNA-seq
Nanopore long reads data was processed using the Nanopype pipeline (v1.1.0). The basecaller Guppy (v4.0.11) was used with the r9.4.1 fast configuration. Quality filtering was disabled for any basecalling.
Genome wide methylation rates were obtained by aligning all reads against reference genome mm9 using NGMLR (v0.2.7) followed by nanopolish (v0.13.2) using default parameters and filtered for CpGs with 15x coverage.
Genome_build: mm9
processed data files format and content: bigWig file of coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

molecule: genomic DNA

source_name: V65 mESC

growth_protocol: mES cells were cultured in Knock Out DMEM media (Gibco) containing 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and 105 U LIF. For ES cell maintenance, dishes were coated with 0.2% gelatin and irradiated CD1 mouse embryonic fibroblasts (MEFs) were plated as a confluent layer of feeder cells. mES cells were seeded at a density of 50,000 cells per well of a six-well plate and were split every 3–4 days.

extract_protocol:
Genomic DNA was isolated from cells through phenol-chloroform extraction
Ligation Sequencing Kit SQK-LSK109 (manufacturer's recommendation)

value: mESC

tag: genotype


title: DKO0_Nanopore

description: Nanopore sequencing

source_name: J1 mESC

extract_protocol:
Genomic DNA was isolated from 16 million cells through phenol-chloroform extraction
Ligation Sequencing Kit SQK-LSK109 (manufacturer's recommendation)

treatment_protocol: Passaged fifteen times after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid

value: Dnmt3a + Dnmt3b KO


title: TKOL_Nanopore

description: Nanopore sequencing

value: Dnmt3a + Dnmt3b KO + Dnmt1 shRNA


title: B16 Control 1 total RNA seq


title: B16 Control 2 total RNA seq


title: Endo_B_cell_sample_15

city: Oxford

first: Jen

last: Southcombe

address: John Radcliffe Hospital, Headington, Oxford OX3 9RR

department: Nuffield Department of Women's and Reproductive Health

country: United Kingdom

institute: University of Oxford

data_processing:
Raw reads of fastq format were firstly processed through Novogene Co., Ltd. in-house  perl scripts. In this step, probability of an incorrect base call 1 in 100 times (Q20),  probability of an incorrect base call 1 in 1000 times (Q30), raw reads number, error  rate and A/T/G/C content distribution were calculated. Accordingly, clean data (clean  reads) were obtained by removing reads containing adapter, reads containing ploy-N and  low quality reads from raw data. Read trimming was also performed to remove bases  towards read ends with high error rate and distorted GC contents. All the downstream  analyses were based on the obtained clean data.
Raw reads were mapped to Ensembl Homo sapiens cDNA database release 94 (http://  ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/cdna/) using TopHat v2.0.12. Appropriate parameters are also set (e.g. the longest intron length). Only  filtered reads were used to analyse mapping status of RNA-seq data to the reference  genome.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. The non-normalised count table generated was then used for downstream  analysis.
Genome_build: Homo sapiens cDNA database release 94 (http://  ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/cdna/)
Supplementary_files_format_and_content: Tab-delimited text file containing normalized abundance measurements for each sample, output from DESeq2
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts for each sample

source_name: endometrium

extract_protocol:
Immediately after sorting, cells were pelleted by centrifugation and re-suspended in RLT  buffer (Qiagen, USA) and RNA was extracted using QIAGEN RNeasy Micro Kits (Qiagen,  USA) according to the manufacturer’s protocol ’Purification of Total RNA from Animal  and Human Cells’. The procedure enriches for mRNA; all RNA molecules longer than  200 nucleotides are purified.
Samples were treated as single cells using Smart-Seq2  protocol for cDNA conversion. The library was prepared using Standard  Nextera Illumina Library Prep kit according to manufacturer’s protocol.

treatment_protocol: Frozen endometrial cell digests were thawed into HS-media (RPMI1640 supplemented with 10%FCS, 1% Human Serum, 2mM glutamine, 100 IU/ml penicillin and 100 ug/ml streptomycin) at 37C and centrifuged at 300 x g. Endometrial cells were re-suspended in HS-Media and transferred to a 25cm2 flask for 30 minutes at 37C/ 5% CO2, then supernatants containing non-adherent cells were further transferred to a fresh flask for an  additional 30 minutes incubation, for stromal and epithelial cell depletion. Supernatants were then removed and transferred onto a lymphoprep layer with centrifugation at 800 x g for 20 minutes. Cells in the interface were washed in PBS and prepared for cell sorting on an Aria III (BD Biosciences, USA) using 85 micrometer nozzle. Briefly, endometrial cells were stained with Zombie AquaTM Viability Dye (Biolegend, USA) then incubated  with antibodies CD3 APC FIRETM750, CD45 BV650TM, CD4 FITC, CD25 PE, CD8 BV711TM, CD19 PE-Cy7 and CD127 APC (all from Biolegend, USA). CD19+ B cells were isolated as singlet cells (FSC-H vs FSC-A), Zombie Aqua-,CD45+, CD19+

value: endometrium

tag: age

value: B cells

tag: menstrual phase

value: mid-luteal


title: Endo_B_cell_sample_14


title: Endo_B_cell_sample_13


title: HumanInfarctMyocardium_scRNA-seq

first: Connor

last: Lantz

state: IL

address: 303 E. Chicago Ave. Ward 4-075

institute: Northwestern University

description: Infarct/scar-associated macrophages from human patients with ischemic cardiomyopathy

data_processing:
cellranger_v2.1.1
Seurat v4.0.0
sctransform v0.3.2
Genome_build: GRCh38
Supplementary_files_format_and_content: Seurat Raw Count Matrix

source_name: Explanted Heart - Infarct Area

extract_protocol:
Single Cells were isolated from explanted heart tissue (> 1 hour explanted) by collagenase & Dnase digestion and processed following the 10x Genomics Pipeline
Libraries were prepared floolowing the 10x Genomics Pipeline for Illumina libraries

tag: disease state

value: Ischemic cardiomyopathy

value: Myocardium (Left Ventricle)


title: PC-3_Palbociclib_H3K27ac_Rep2

city: Rochester

first: Ting

last: Wei

state: MN

address: 507 3rd St SW

institute: Mayo Clinic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7.
Raw sequences were mapped to reference genome (hg38) using BWA (v0.5.9) with default parameters.
Peak calling was performed using MASC2 (v2.0.10).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: prostate

growth_protocol: Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

treatment_protocol: PC-3 cells were treated with vehicle (DMSO) or 5μM Palbociclib for 24 hours.

tag: passages

value: Palbociclib

tag: chip antibody

value: Rabbit monoclonal anti-Acetyl Histone H3 (Lys27) Abcam Cat# ab4729, RRID:AB_2118291anti-STAT2 #72604S, Cell Signaling Technology


title: Mx1Cre-A10f/f_no_Abx


title: lung, homoharringtonine administration H2

city: Daegu

first: Eok-Cheon

last: Kim

address: hyunchung-ro 170

department: Biochemistry and Molecular Biology

institute: College of Medicine, Yeungnam University

description: Gene expression data from lung tissue

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)
Affymetrix Power Tools (affymetrix-power-tools.html) R 3.5.1 (https://www.r-project.org/)

source_name: lung tissue of bleomycin instillation and homoharringtonine administration mouse

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Animals were housed in a light- and temperature-controlled room and had free access to drinking water and standard rodent diet.

treatment_protocol: Male C57BL/6J mice (8 weeks old) were anesthetized and received intratracheal instillation of PBS or 2 U/kg bleomycin. After 5 days, HHT (0.545 mg/kg) or vehicle was administered intraperitoneally 2 times a week for 15 days.

value: lung

tag: gender

value: male

value: 11 weeks old


title: B16 ATRA 1 total RNA seq

value: ATRA


title: Endo_B_cell_sample_12


title: Endo_B_cell_sample_11


title: PC-3_Palbociclib_H3K27ac_Rep1


title: lung, homoharringtonine administration H3

description: Gene expression data from lung tissue

value: bleomycin instillation and homoharringtonine administration


title: lung, bleomycin instillation B2

description: Gene expression data from lung tissue

source_name: lung tissue of bleomycin instillation mouse

value: bleomycin instillation


title: lung, bleomycin instillation B3

description: Gene expression data from lung tissue


title: lung, homoharringtonine administration H1

description: Gene expression data from lung tissue


title: lung, bleomycin instillation B1

description: Gene expression data from lung tissue


title: lung, vehicle treatment C3

description: Gene expression data from lung tissue

source_name: lung tissue of vehicle-treated mouse

value: vehicle-treated


title: Endo_B_cell_sample_10