title: Control 23.3. neuron-1

description:
Control sample biological rep 1
FXS vs Control hiPSC normalized counts, Log2FC FXS vs Control hiPSC

value: wild type


title: GEO-117: secondary_AML

status: Public on May 24 2020

type: SRA

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

country: Germany

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

library_source: transcriptomic

data_processing:
Perfomed adapter clipping with Cutadapt v1.7.1, as well as removing the first 6 bases from the forward reads and 9 bases from the reverse reads
Quality trimming performed with Trimmomatic v0.32 using the "MAXINFO" option (“target read length”: 40, “strictness”: 0.5); orphaned reads were discarded
STAR v2.5.1b used for sequence alignment with the GRCh37 genome build
STAR v2.5.1b used for second pass alignment with the GRCh37 genome build along with splice junction information from all samples (junctions in the mitochondrial sequences were removed) with the default parameters recommended for gene-fusion detection
Picard v1.136.0 used for merging properly paired and discordant paired reads
Salmon v0.9.1 used to create isoform and gene counts (GRCh37)
Raw gene counts: Raw gene counts for all Ensembl genes (GRCh37). Table created with salmon after adapater clipping with Cutadapt and quality trimming with Trimmomatic. Rows correspond to Ensembl gene identifiers and columns to samples.
Raw isoform counts: Raw isoform counts for all Ensembl isoforms (GRCh37). Table created with salmon after adapater clipping with Cutadapt and quality trimming with Trimmomatic. Rows correspond to Ensembl transcript identifiers and columns to samples.
Known splice junction counts: Uniquely aligned reads supporting each known splice junction extracted from the SJ.out.tab-file after two-pass alignment with STAR. Row names correspond to splice junction identifiers (in the form „chromosome:start-end“). An expression filter has been applied and only splice junctions with at least 3 supporting reads in at least 3 samples and at least 10 supporting reads in at least 1 sample are shown. Samples containing SF mutations not in SRSF2, U2AF1 or SF3B1 are not provided in this table as filtering was performed after their exclusion (n=6).
Novel splice junction counts: Uniquely aligned reads supporting each novel splice junction extracted from the SJ.out.tab-file after two-pass alignment with STAR. Row names correspond to splice junction identifiers (in the form chromosome:start-end). An expression filter has been applied and only splice junctions with at least 10 supporting reads in at least 3 samples and at least 30 supporting reads in at least 1 sample are shown. Samples containing SF mutations not in SRSF2, U2AF1 or SF3B1 are not provided in this table as filtering was performed after their exclusion (n=6).
Exon counts: Raw counts for each non-overlapping exonic segment (GRCh37), produced with DEXSeq after adapter clipping, quality trimming and alignment with STAR. First column corresponds to the exon identifier (in the form „gene:exon number“). Chromosome and strand information, as well as exon start and ending positions are provided.
Intron counts: Raw counts for each non-overlapping intronic segment (GRCh37). The table was produced after creating a gtf-file containing introns and counting with DEXSeq. First column corresponds to the intron identifier (in the form „gene:intron number“). Chromosome and strand information, as well as intron start and ending positions are provided.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab delimited text files including gene counts, isoform counts, uniquely aligned reads supporting known and novel splice junctions and counts for each non-overlapping exonic and intronic segment

molecule: polyA RNA

organism: Homo sapiens

source_name: bone marrow or peripheral blood mononuclear cells

extract_protocol:
Mononuclear cells from peripheral blood (PB) or bone marrow (BM) were enriched by Ficoll gradient centrifugation.
RNAseq libraries were prepared using the Sense mRNA Seq Library Prep Kit V2 following the manufractur´s instruction. Between 500-1000 ng total RNA (RNA integrity number [RIN] >7) were used as input material. All sequencing was paired end and performed using polyadenylated-selected and stranded RNA sequencing.

treatment_protocol: Pretreatment bone marrow mononuclear cells from patients with newly diagnosed acute myeloid leukemia (AML)

tag: gender

value: female

tag: study

tag: diagnosis

tag: cytogenetics

value: CN-AML

tag: mrc

value: Intermediate

value: Adverse

tag: fab

tag: ecog

value: alive

tag: relapse

value: YES

value: CRi

tag: wbc

tag: ldh

tag: haemoglobin

tag: platelets

tag: cebpa

value: NO


title: WT_RNA-Seq_CT44_Rep2

city: Houston

first: Huan

last: Meng

state: Texas

address: One Baylor Plaza BCM 130

department: Department of Molecular & Cellular Biology

country: USA

institute: Baylor College of Medicine

description: Total RNA-seq

data_processing:
Fastq files containing raw RNA-seq reads were aligned to the mouse genome (mm10/NCBI38) using HISAT2. RNA-seq quantification was performed with htseq-count (default parameters). Protein-coding genes were quantified by iGenome annotation. Quantification values were normalized with DESeq2, followed by filtering out of zero expression genes in each replicate or time point.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol: These RNA samples (200ng of total RNA for each sample) were converted into strand-specific total mRNA-seq libraries with the Universal Plus mRNA-seq kit (NuGen) per the manufacturer’s protocol. The size selected libraries were analyzed for quality control with High Sensitivity DNA chip on a Bioanalyzer 2100 (Agilent), and the pooled libraries were sequenced with the NovaSeq 6000 (Illumina) using a 100-bp paired-end for an average of 40 million paired-end reads per sample at the University of Houston Sequencing Core.

treatment_protocol: RNA samples were isolated from two biological replicates of mouse liver tissues from circadian time 0 (CT0) every 2 hours for 48 hours with the miRNeasy Mini Kit (Qiagen) per the manufacturer’s instructions.

tag: strain

value: C57BJ/L6 background

tag: genotype

value: Xbp1 flx/flx (WT, wild-type)

value: Male

tag: age

value: 12-16 weeks

tag: tissue

value: Liver

tag: time point


title: Control 23.3. neuron-2

city: Singapore

first: Kagistia

middle: Hana

last: Utami

address: 8A Biomedical Grove

country: Singapore

institute: Translational Laboratory in Genetic Medicine

description:
Control sample biological rep 2
FXS vs Control hiPSC normalized counts, Log2FC FXS vs Control hiPSC

data_processing:
RNA seq quantification directly from the reads with Salmon v0.9.1 19 using hg38 human reference genome.
Data was imported into R using tximport and analyzed for differentially expressed genes with DESeq2
Significant hits were identified using FDR <0.05 cut-off and divided into upregulated (Log2FC >0) and downregulated (Log2FC<0)
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: hiPSC-derived neurons

growth_protocol: neurons were differentiated from human NPCs-derived hiPSC, with a midbrain-patterning differentiation protocol

extract_protocol:
cells were harvested at the last day of differentiation (37 days in culture), total RNA was extracted by RNAeasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell

value: 37 days neurons

tag: Sex

value: male


title: WT_RNA-Seq_CT44_Rep1

description: Total RNA-seq

tag: gender


title: GEO-116: primary_AML

tag: study

tag: diagnosis

tag: cytogenetics

tag: mrc

value: favorable

value: CR


title: Control 11.4 neuron-3

description:
Control sample biological rep 3
FXS vs Control hiPSC normalized counts, Log2FC FXS vs Control hiPSC

value: wild type


title: GEO-115: primary_AML

value: female

value: CN-AML

tag: fab

tag: ecog

value: dead

tag: relapse

tag: wbc


title: Control 11.4 neuron-1


title: WT_RNA-Seq_CT42_Rep2

description: Total RNA-seq


title: FXS 100.2 neuron-2

description:
FXS Disease sample biological rep 2
FXS vs Control hiPSC normalized counts, Log2FC FXS vs Control hiPSC

value: FXS disease


title: Control 11.4 neuron-2


title: PLCG2 KO, Zymosan, 24 hours, rep2

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

description:
dst72_counts.xlsx
DRN-10068

data_processing:
Sequencing adapters were trimmed using skewer (Jiang et al., 2014) (version 0.2.2) with default parameters. Unique molecular identifiers (UMIs) were extracted from each read with the umi2index tool (Lexogen). Quality control of the trimmed reads was performed using FastQC (version 0.11.5: www.bioinformatics.babraham.ac.uk/projects/fastqc). Reads were aligned to the human genome version GRCh38_p12. A STAR index (version 2.5.3a) (Dobin et al., 2013); was built with the --sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release release_28) were provided via the --sjdbGTFfile argument.  STAR alignments were generated with the following parameters: --outFilterType BySJout, --quantMode TranscriptomeSAM, -- outFilterIntronMotifs RemoveNoncanonicalUnannotated, --outSAMstrandField intronMotif, -- outSAMattributes NH HI AS nM MD XS and --outSAMunmapped Within. Alignments were obtained with the following parameters: --readFilesCommand zcat --outFilterType BySJout -- outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 -- outFilterMismatchNmax 999 - outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 -- alignIntronMax 1000000 --alignMatesGapMax 1000000 --quantMode GeneCounts -- outSAMunmapped Within --outSAMattributes NH HI AS nM MD XS –outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --outBAMcompression 6.  Unique molecular identifiers (UMIs) were extracted from each read with the umi2index tool (Lexogen). Gene level counts were obtained using featureCounts from the subread package (version 1.6.2) (Liao et al., 2014).
To calculate normalized counts per million (CPM) TMM normalization was applied across all genes annotated as protein_coding with the edgeR R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel (XLSX) file with sample annotations, raw counts and TMM-normalized counts per million (CPM)

source_name: iPSC-derived microglia

growth_protocol: iPSCs were maintained in mTeSR1 medium (StemCell Technologies, #85857) and routinely passaged as clumps onto Geltrex (Thermo Fisher, #A1413301)-coated plates. For differentiation into microglia, iPSCs were first differentiated into hematopoietic progenitor cells (HPCs) following manufacturer’s instructions using the commercially available STEMdiff Hematopoietic Kit (StemCell Technologies, #05310). HPCs positive for identity markers CD34, CD43, and CD45 were transferred to plates containing primary human astrocytes and co-cultured in Media C adapted from Pandya et al (IMDM, FBS, PenStrep, 20ng/mL each of IL3, GM-CSF, M-CSF) for 14-21 days, during which time HPCs were progressively removed. Media components were obtained from Thermo Fisher and growth factors from Peprotech. Once non-adherent cells in co-culture were predominantly (>80%) mature microglia, the microglia (iMG) were harvested and transferred into homeostatic culture conditions adapted from Muffat et al.33 (MGdM media) for 3-5 days prior to assay, unless otherwise described.

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, #74034) and resuspended in 14 µl nuclease-free water. RNA quantity and quality were assessed with a RNA 6000 Pico chip (Agilent, #5067-1513) on a 2100 Bioanalyzer (Agilent). For qPCR, 6 µl RNA was transcribed into cDNA using SuperScript IV (Thermo Fisher, #18091050).
RNA was processed using the QuantSeq 3' mRNAseq Library Prep Kit FWD for Illumina with unique molecular identifiers (UMIs) (Lexogen), following the ‘low-input’ protocol defined by the manufacturer. Barcoded samples were quantified using the NEBNext Library Quant Kit for Illumina (NEB, #E7630S). All samples were pooled in equimolar ratios into one sequencing library, which was quantified on a Bioanalyzer with a High Sensitivity DNA chip (Agilent, #5067-4626). 50 bp single-end reads were generated in Illumina HiSeq 4000 lane at the UCSF Center for Advanced Technology

treatment_protocol: Gene knockouts were generated using a nucleofection-based RNP approach to introduce Cas9 and sgRNAs against the gene targets into human episomal iPSC line A18945 (Thermo Fisher Scientific). Clones with indels introduced into both alleles were identified and selected for characterization as homozygous knock-out lines.

tag: cell type

value: iPSC-derived microglia

value: PLCG2 -/-

tag: treatment

value: Zymosan

value: ug/ml

value: hours

tag: batch

tag: group


title: WT_RNA-Seq_CT42_Rep1

description: Total RNA-seq

tag: strain

value: C57BJ/L6 background

tag: genotype

value: Xbp1 flx/flx (WT, wild-type)

value: Male

tag: age

tag: tissue


title: PLCG2 KO, Zymosan, 24 hours, rep1

description:
dst72_counts.xlsx
DRN-10067

tag: Sex


title: PLCG2 KO, No treatment, rep2

description:
dst72_counts.xlsx
DRN-10062


title: WT_RNA-Seq_CT40_Rep2

description: Total RNA-seq

tag: gender

value: 12-16 weeks

value: Liver

tag: time point


title: GEO-112: primary_AML

value: male

tag: study

tag: diagnosis

tag: cytogenetics

value: Intermediate

value: Adverse

value: YES

value: CRi

tag: ldh

tag: haemoglobin

tag: platelets

tag: cebpa

value: NO


title: Control 23.3. neuron-3

tag: cell

value: 37 days neurons

value: wild type


title: GEO-113: primary_AML

value: female

value: CN-AML

tag: mrc

tag: fab

tag: ecog

value: dead

tag: relapse

tag: wbc


title: PLCG2 KO, No treatment, rep1

description:
dst72_counts.xlsx
DRN-10061

tag: cell type

value: iPSC-derived microglia

tag: genotype

value: PLCG2 -/-

tag: treatment

value: ug/ml

value: hours

tag: batch

tag: group


title: TREM2 KO, Zymosan, 24 hours, rep2

description:
dst72_counts.xlsx
DRN-10056

value: TREM2 -/-

value: Zymosan

tag: Sex


title: TREM2 KO, Zymosan, 24 hours, rep1

description:
dst72_counts.xlsx
DRN-10055


title: TREM2 KO, No treatment, rep2

description:
dst72_counts.xlsx
DRN-10052


title: GEO-111: primary_AML

tag: gender

tag: study

tag: diagnosis

tag: cytogenetics

value: del(7q)/monosomy 7


title: WT_RNA-Seq_CT40_Rep1

description: Total RNA-seq

tag: strain

value: C57BJ/L6 background

value: Xbp1 flx/flx (WT, wild-type)

value: Male

tag: age

value: 12-16 weeks

tag: tissue

value: Liver

tag: time point


title: GEO-110: primary_AML

tag: mrc

value: Intermediate

value: Adverse

tag: fab

tag: ecog

value: YES

value: CR

tag: ldh

tag: haemoglobin

tag: platelets

value: NO

tag: cebpa


title: TREM2 KO, No treatment, rep1

description:
dst72_counts.xlsx
DRN-10051

tag: cell type

value: iPSC-derived microglia

tag: genotype

tag: treatment

value: female

tag: batch

tag: group


title: GEO-109: treatment-associated_AML

tag: gender

tag: study

tag: diagnosis

tag: cytogenetics

value: CN-AML

value: dead

tag: relapse

value: CRi

tag: wbc


title: iPSC-1, Zymosan, 24 hours, rep1

description:
dst72_counts.xlsx
DRN-10045

value: WT

value: Zymosan

value: ug/ml

value: hours

tag: Sex


title: iPSC-1, No treatment, rep4

description:
dst72_counts.xlsx
DRN-10030


title: iPSC-1, No treatment, rep3

description:
dst72_counts.xlsx
DRN-10029


title: GEO-114: primary_AML

value: del(7q)/monosomy 7

tag: mrc

tag: fab

tag: ecog


title: WT_RNA-Seq_CT38_Rep1

description: Total RNA-seq

tag: strain

value: C57BJ/L6 background

value: Xbp1 flx/flx (WT, wild-type)

value: Male

tag: age

value: 12-16 weeks

tag: tissue

tag: time point


title: GEO-108: primary_AML

value: male

value: Various

value: Intermediate

value: alive

tag: ldh

tag: haemoglobin

tag: platelets

tag: cebpa


title: WT_RNA-Seq_CT36_Rep1

description: Total RNA-seq

tag: genotype

tag: gender

value: Liver


title: iPSC-1, No treatment, rep2

description:
dst72_counts.xlsx
DRN-10028

tag: cell type

value: iPSC-derived microglia

tag: treatment

value: female

tag: batch

tag: group


title: GEO-107: primary_AML

tag: study

tag: diagnosis

tag: cytogenetics

value: CN-AML

tag: mrc

tag: relapse

value: NO

value: CR

tag: wbc

value: YES


title: iPSC-1, No treatment, rep1

description:
dst72_counts.xlsx
DRN-9954

value: WT

value: ug/ml

value: hours

tag: Sex


title: WT_RNA-Seq_CT34_Rep2

description: Total RNA-seq

tag: strain

value: C57BJ/L6 background

value: Xbp1 flx/flx (WT, wild-type)

tag: age

tag: tissue

tag: time point


title: FMR1 Knockout sample biological rep 4

source_name: hESC-derived neurons

growth_protocol: neurons were differentiated from human NPCs-derived hESC, with a midbrain-patterning differentiation protocol

tag: cell

value: 37 days neurons

tag: genotype

value: knockout


title: FMR1 Knockout sample biological rep 3

value: male


title: FMR1 Knockout sample biological rep 2


title: GEO-105: treatment-associated_AML

tag: gender

value: Intermediate

tag: fab

tag: ecog

value: dead

tag: ldh

tag: haemoglobin

tag: platelets

tag: cebpa


title: GEO-104: primary_AML

tag: study

tag: diagnosis

tag: cytogenetics

value: del(7q)/monosomy 7

tag: mrc

value: Adverse


title: WT_RNA-Seq_CT38_Rep2

description: Total RNA-seq

tag: strain

value: Male

value: 12-16 weeks

value: Liver


title: FMR1 Knockout sample biological rep 1

tag: Sex


title: WT_RNA-Seq_CT34_Rep1

description: Total RNA-seq

tag: age

tag: tissue


title: iPSC-1, Zymosan, 24 hours, rep2

description:
dst72_counts.xlsx
DRN-10046

tag: cell type

value: iPSC-derived microglia

tag: treatment

value: Zymosan

value: female

tag: batch

tag: group


title: FXS Disease sample biological rep 4

tag: cell

tag: genotype

value: FXS disease


title: GEO-103: secondary_AML

tag: gender

value: CN-AML

value: favorable

tag: fab

tag: ecog

tag: relapse

value: YES

value: CR

tag: wbc

tag: ldh

tag: haemoglobin

value: NO


title: WT_RNA-Seq_CT32_Rep1

description: Total RNA-seq

tag: strain

value: C57BJ/L6 background

value: Xbp1 flx/flx (WT, wild-type)

tag: time point


title: WT_RNA-Seq_CT36_Rep2

description: Total RNA-seq

tag: age


title: FXS Disease sample biological rep 3

value: 37 days neurons

tag: Sex

value: male


title: GEO-101: primary_AML

tag: study

tag: diagnosis

tag: cytogenetics

tag: mrc

value: Intermediate

value: alive

tag: platelets

tag: cebpa


title: WT_RNA-Seq_CT30_Rep2

description: Total RNA-seq

tag: genotype

tag: gender

value: Male

value: 12-16 weeks

tag: tissue


title: WT_RNA-Seq_CT30_Rep1

description: Total RNA-seq

value: Liver


title: FXS Disease sample biological rep 2

tag: cell


title: Control sample biological rep 4

value: wild type


title: FXS Disease sample biological rep 1


title: GEO-100: secondary_AML

value: female

value: Adverse

tag: fab

tag: ecog

value: dead

tag: relapse

tag: wbc


title: WT_RNA-Seq_CT28_Rep2

description: Total RNA-seq

tag: strain

tag: time point


title: Control sample biological rep 3

tag: Sex


title: WT_ES_Rep2

city: Guangzhou

first: Zhijun

last: Ren

address: 74 Zhongshan Rd.2

country: China

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.4.
RNA-seq reads were aligned to the mm10 genome assembly using HISAT2 (v2.1.0).
The PCR duplicates were removed using SAMtools (v1.9).
FPKMs (fragments per kilobase of transcript per million mapped reads) were calculated using Cufflinks (v2.1.1). The genes with maximum FPKM>1 and fold change>2 were considered as differentially expressed.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *bw: Normalized read signal was generated by bamcoverage program in deeptools with the parameters --normalizeUsing RPKM --extendRead 200 to bigwig for visualize.

source_name: embryo-derived ESC

extract_protocol:
Mouse ES cell and day 4 EB total RNA of WT and Mst KO samples were harvested by the Trizol (Invitrogen). Contaminant DNA was removed by the RNase-Free DNase (NEB).
RNA-Seq libraries for deep-sequencing were prepared using Dynabeads mRNA purification kit (Ambion) and Illumina TruSeq Standard kit (Illumina). Sequencing was carried out with Illumina HiSeq 2000.

tag: cell type

value: Embryonic stem cells

tag: passages

tag: strain/background

tag: genotype/variation

value: Wild type


title: WT_RNA-Seq_CT28_Rep1

description: Total RNA-seq

tag: age


title: Control sample biological rep 2


title: WT_ES_Rep1


title: WT_RNA-Seq_CT26_Rep2

description: Total RNA-seq


title: WT_RNA-Seq_CT32_Rep2

description: Total RNA-seq


title: WT_EB_Rep2

value: Embryoid bodies, day 4


title: WT_RNA-Seq_CT24_Rep2

description: Total RNA-seq


title: RBC_SH9

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
results.rbc.N2vsHS1.csv.gz
results.rbc.N2vsHS2.csv.gz

library_source: genomic

data_processing:
Basic read quality was verified using summaries produced by FastQC. Raw reads were trimmed and filtered by quality characteristics using Trimmomatic.
The reads for each sample were mapped to the NCBI RefSeq provided Omyk_1.0 reference genome using Bowtie2.
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than 1e-5 were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
Genome_build: Omyk_1.0 (RefSeq)
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

molecule: genomic DNA

organism: Oncorhynchus mykiss

source_name: RBC

growth_protocol: A brood stock hatchery operation (Winthrop National Fish Hatchery, WNFH, US Fish and Wildlife Service) on the Methow River in Washington State, USA was selected to compare wild natural-origin populations and hatchery populations of steelhead trout. This hatchery used hatchery-reared steelhead crossed with natural-origin fish from the same river as broodstock to produce offspring that were raised in hatcheries until the time of release as smolts, at which point they can migrate downstream to the ocean. After returning from the ocean (during spring migration), fast- growth (S1), slow-growth (S2), and natural origin (N) fish were collected and sampled.

extract_protocol:
Genomic DNA from sperm was prepared as follows: Five μl of steelhead sperm suspension was used and adjusted to 100 μl with 1 x Phosphate Buffered Saline (PBS), then mixed well. Then 820 μl DNA extraction buffer (50mM Tris pH8, 10mM EDTA pH8, 0.5% SDS, TE buffer) and 80 μl 0.1 M dithiothreitol (DTT) were added, and the sample was incubated at 65 C for 15 minutes. Then 80 μl Proteinase K (20 mg/ml) was added, and the sample was incubated on a rotator at 55 C for 2 hours. After incubation, 300 μl of protein precipitation solution (Promega, A795A) was added, the sample was mixed and incubated on ice for 15 minutes, then spun at 4 C at 13,000 xg for 20 minutes. The supernatant was transferred to a fresh tube, then precipitated overnight with the same volume 100% isopropanol and 2 μl glycoblue at -20 C. The sample was then centrifuged and the pellet washed with 75% ethanol, then air-dried and resuspended in 100 μl H2O. DNA concentration was measured using the Nanodrop (Thermo Fisher). Genomic DNA from Steelhead red blood cells (RBC) was prepared using the Qiagen DNAeasy Blood and Tissue Kit (Qiagen). A 2.5 μl aliquot of well mixed RBC was used, and the manufacturer’s instructions for nucleated blood samples were followed, but in the final DNA elution step 100 μl H2O was used instead of the buffer provided in the kit. Methylated DNA Immunoprecipitation (MeDIP) from genomic DNA was performed as follows: for the sperm samples 6 μg of each individual or pooled (3-5 individuals) genomic DNA was diluted to 150 μl with 1x Tris-EDTA (TE, 10mM Tris, 1 mM EDTA) and sonicated with a probe sonicator using 5 x 20 pulses at 20% amplitude, or fragmented using the Covaris M22 with 300 bp program. Fragment size (200-800 bp) was verified on 1.5% agarose gel. Sonicated DNA was diluted to 400 μl with 1xTE buffer and heated to 95 C for 10 minutes, then shocked in ice water for 10 minutes. Then 100 μl of 5 x IP buffer (50mM Sodium Phosphate pH7, 700mM NaCl, 0.25% Triton X-100) and 5 μg of 5-mC monoclonal antibody (Diagenode, C15200006-500) were added, and the sample was incubated on a rotator at 4 C overnight. The next day for N-1 and H-1 samples Protein A/G Agarose Beads from Santa Cruz were prewashed with 1xPBS/0.1% BSA and resuspended in 1 x IP buffer. Eighty μl of the bead slurry were added to each sample and then incubated at 4 C for 2 hours on a rotator. The bead-DNA-antibody complex was washed 3 times with 1 x IP buffer by centrifuging at 6,000 xg for 2 minutes and resuspending in 1 x IP buffer. For the other samples magnetic beads were used (Dynabeads M280 sheep anti-mouse IgG;11201D). After the last wash, the bead-complex was resuspended in 250μl of digestion buffer (50mM Tris pH8, 10mM EDTA pH8, 0.5% SDS) with 3.5 μl Proteinase K (20mg/ml) per sample and incubated on a rotator at 55 C for 2 hours. After incubation, DNA was extracted with same volume of Phenol-Chloroform- Isoamyalcohol and then with same volume chloroform. To supernatant from chloroform extraction 2 μl glycoblue, 20 μl 5M Sodium Chloride and 500 μl 100% cold ethanol were added. DNA was precipitated at -20 C overnight, and then spun for 20 minutes at 13,000 rpm at 4 C, washed with 75% ethanol and air-dried. Dry pellet was resuspended in 20 μl H2O, and the concentration was measured in Qubit using the Qubit ssDNA Assay Kit (Life Technologies, Carlsbad, CA). For the RBC samples, the MeDIP procedures used were the same as described above, except that genomic DNA was pooled using 3-5 individuals per pool with equal amounts of DNA from each individual, making 6 μg of total DNA per pool.
Sperm and RBC MeDIP pools were used to create libraries for NGS at the University of Reno, NV, Genomics Core Laboratory or Genomics Core at WSU Spokane with an Illumina platform. All the pools consisted of 3-5 individuals for the sperm and RBC, with 3 pools each for the wild natural versus the hatchery populations. For library preparation the NEBNext Ultra RNA Library Prep Kit for Illumina was used, starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step, the manufacturer’s protocol was followed. Each pool received a separate index primer.

treatment_protocol: Some steelhead were placed on a high plane of nutrition and reached smolt stage within one year (fast growth), at which time they were released. Others were placed on a lower plane of nutrition, and took two years to reach smolt stage (slow growth) prior to release. Natural-origin steelhead trout generally take two years to reach smolt stage in this river system.

value: RBC

tag: source

value: Natural

tag: growth


title: WT_EB_Rep1


title: MstKO_ES_Rep2

value: MstKO


title: WT_RNA-Seq_CT26_Rep1

description: Total RNA-seq

value: C57BJ/L6 background

tag: genotype

value: Xbp1 flx/flx (WT, wild-type)

tag: gender


title: Control sample biological rep 1

tag: cell

value: 37 days neurons

value: male


title: GEO-102: primary_AML

tag: study

tag: diagnosis

tag: cytogenetics

value: CN-AML

tag: mrc

value: Intermediate

tag: fab

value: alive

value: NO

value: CR

tag: ldh

tag: haemoglobin

tag: platelets

tag: cebpa


title: XBP1_LKO_ChIP_seq_XBP1sChIP

data_processing:
ChIP-seq sequencing reads were mapped to the mouse genome (mm10/NCBI38) with BOWTIE2. The mapping allowed a maximum of two mismatches and removed duplicated reads to ensure only “unique” reads were allowed for output to the bam file. Unique reads with mapping scores higher than 15 were kept for subsequent ChIP-seq analysis. To comprehensively determine the XBP1 oscillating cistrome in a unbiased manner, MACS2 version 2.1.1.20160309 was used to perform the peak calling at CT0 and CT8 against their respective input for each replicate individually, and only intersecting peaks between the two biological replicates at each time point were determined as high-confidence peaks. For the CT0 to CT36 4-hour interval ChIP-seqs, duplicates at each time point were pooled, and heatmap and enrichment plotting were carried out against the ChIP-seq of the AlbCre;Xbp1flx/flx mice. In all the sequencing analysis, the differential sequencing reads were “down-sampled” to the lowest number of uniquely mapped reads for the normalization of sequencing depth. The ChIP-seq peak annotations and motif analysis from the high-confidence peaks were determined using HOMER with default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

extract_protocol: The comprehensive CT0 and CT8 DNA libraries were prepared at the MD Anderson Cancer Center, which generated ~40 million 75 bp paired-end reads per samples. The CT0 to CT36 time point DNA libraries were prepared at the University of Houston Sequencing Core and generated ~30 million 75 bp single-end reads per sample. DNA libraries generated from 1ng input DNA were prepared with KAPA Hyper Prep Kit (KAPABIOSYSTEMS) for the comprehensive CT0 and CT8 DNA libraries and with Ovation® Ultralow V2 DNA-Seq library preparation kit (NuGen) for the CT0 to CT36 time point DNA libraries. The size selection was performed using SPRIselect beads (Beckman Coulter), followed by quality control analyzed using the High Sensitivity DNA chip on Bioanalyzer 2100 (Agilent). The DNA libraries were pooled and sequenced using NextSeq 500 (Illumina).

treatment_protocol: Mouse liver chromatin was prepared with the ChIP-IT Kit (Active Motif) per the manufacturer’s instruction with the following modifications. Briefly, mouse liver samples were dissected into small pieces in PBS containing 1% formaldehyde and incubated for 15 min at room temperature, followed by the addition of 0.125 M glycine to stop the reaction. The formaldehyde-fixed samples were then washed in PBS, followed by homogenization in lysis buffer. The released nuclei were pelleted and resuspended in digestion buffer for 5 minutes at 37°C. An appropriate amount of Micrococcal nuclease (MNase) (NEB) was then added to enzymatically digest the chromatin. The optimal amount of incubation time was pre-determined to shear the chromatin into a 150-1000bp banded pattern, and the reaction was stopped by 0.5 M EDTA, followed by chilling on ice for 10 minutes. Following chromatin quantification, an aliquot of 100ug of mouse liver chromatin and 10ug of anti-XBP1s antibody (Biolegend Poly6195) was used for the two CT0 and CT8 time points, with appropriate input genomic DNA saved for the comprehensive analysis. For the set of XBP1s ChIP-seq from CT0 every 4 hours for three complete 12-hour cycles, an aliquot of 30ug chromatin and 4ug anti-XBP1s antibody was used. The co-immunoprecipitated complexes were then washed and eluted with elution buffer. The genomic DNA input and ChIP DNA fragments were reverse crosslinked at 65°C overnight, and treated with RNaseA and proteinase K, and then purified by phenol-chloroform extraction and ethanol precipitation.

tag: strain

value: AlbCre;Xbp1 flx/flx (XBP1 LKO, liver-specific knockout)

value: Male

value: 12-16 weeks

tag: tissue

value: Liver

tag: antibody

value: anti-XBP1s (Biolegend Poly6195)


title: XBP1_LKO_ChIP_seq_Input

tag: age


title: WT_RNA-Seq_CT22_Rep2

description: Total RNA-seq

tag: time point


title: RBC_SH7

value: RBC

tag: Sex

tag: source

tag: growth


title: MstKO_EB_Rep2

tag: cell type

value: Embryoid bodies, day 4

tag: passages

tag: strain/background

tag: genotype/variation


title: XBP1_WT_CT8_ChIP_seq_XBP1sChIP

tag: genotype

tag: gender


title: XBP1_WT_CT8_ChIP_seq_Input


title: WT_RNA-Seq_CT22_Rep1

description: Total RNA-seq


title: MstKO_EB_Rep1

value: MstKO


title: RBC_SH6

description:
results.rbc.N2vsHS2.csv.gz
results.rbc.HS1vsHS2.csv.gz

value: Hatchery

value: Slow


title: GEO-146: secondary_AML

tag: study

tag: diagnosis

tag: cytogenetics

tag: mrc

value: favorable

tag: fab

tag: ecog

value: dead

tag: relapse

value: YES

tag: wbc

tag: ldh

tag: haemoglobin


title: RBC_SH5

tag: tissue

tag: Sex

value: male

tag: source

tag: growth


title: XBP1_WT_CT0_ChIP_seq_XBP1sChIP

tag: strain

value: C57BJ/L6 background

value: Xbp1 flx/flx (WT, wild-type)

tag: age

tag: time point

tag: antibody


title: WT_RNA-Seq_CT20_Rep2

description: Total RNA-seq

tag: genotype

tag: gender


title: RBC_SH4


title: Mst_MstKO_Input_ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 (v2.3.5).
The PCR duplicates were removed using SAMtools (v1.9).
MACS2 program (v 2.2.4) was used to call peaks of each ChIP-seq library with the corresponding input data as control. To call ChIP-seq peaks, the default parameters were adopted except for H3K36me3 and H3K27me3, for which the broad peak-calling algorithm was used.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *bw: Normalized read signal was generated by bamcoverage program in deeptools with the parameters --normalizeUsing RPKM --extendRead 200 to bigwig for visualize.

growth_protocol: DMEM/F12 medium supplemented with 0.4μM MEK inhibitor PD0325901 (Stemgent), 3μM GSK3β inhibitor CHIR99021 (Stemgent) and 1000U/ml Leukemia inhibitory factor (LIF, Millipore) in 5% CO2 incubator at 37℃.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
5ng-10ng of ChIP DNA and Input DNA were used separately to prepare DNA library for Illumina sequencing. Firstly, DNA fragments were repaired to blunt ends by Klenow fragments enzyme, T4 DNA polymerase and a phosphate group was added to the 5’-ends of DNA fragment by T4 PNK. Next, a single ‘A’ base was added to the repaired 3’-end with Klenow (3’→5’ exo-) for adaptor ligation. Subsequently, a pair of barcoded TruSeq adapters with 3’-end ‘T’ overhang was ligated to both ends of A-tailed DNA fragment with T4 DNA ligase. Eventually, the ligation products were subjected to amplification by using adaptor primers, the resultant library with size of 250bp-500bp was gel purified by QIAGEN kit to remove adaptor dimers and other contamination. After quantification and quality control, the purified library was used for pair-end sequencing on Illumina Hiseq 2000 platform.

tag: cell type

value: Embryonic stem cells

tag: passages

tag: strain/background

tag: genotype/variation

tag: chip antibody


title: WT_RNA-Seq_CT20_Rep1

description: Total RNA-seq


title: XBP1_WT_CT0_ChIP_seq_Input


title: RBC_SH8

value: Natural


title: Mst_MstKO2_H3K27Ac_IP_ChIP-seq


title: XBP1s_ChIP_LKO

value: AlbCre;Xbp1 flx/flx (XBP1 LKO, liver-specific knockout)

value: Male


title: RBC_SH3

description:
results.rbc.N2vsHS1.csv.gz
results.rbc.HS1vsHS2.csv.gz

value: Fast


title: RBC_SH2


title: WT_RNA-Seq_CT18_Rep1

description: Total RNA-seq

value: 12-16 weeks

value: Liver


title: Mst_MstKO1_H3K27Ac_IP_ChIP-seq


title: WT_RNA-Seq_CT18_Rep2

description: Total RNA-seq


title: RBC_SH1

value: RBC


title: WT_RNA-Seq_CT24_Rep1

description: Total RNA-seq


title: Mst_H3K27Ac_sg2-39_ChIP-seq

description: "sg1" and "sg2" represent two different sg-RNA, which can guide CRISPR-Cas9 KO Yap.

value: MstKO and YapKO


title: WT_RNA-Seq_CT16_Rep2

description: Total RNA-seq


title: XBP1s_ChIP_CT32

value: anti-XBP1s (Biolegend Poly6195)


title: Mst_H3K27Ac_sg2-17_ChIP-seq


title: WT_RNA-Seq_CT16_Rep1

description: Total RNA-seq


title: XBP1s_ChIP_CT28


title: WT_RNA-Seq_CT14_Rep2

description: Total RNA-seq


title: Sperm_SH8

description:
results.sperm.N2vsHS1.csv.gz
results.sperm.N2vsHS2.csv.gz

source_name: Sperm

value: Sperm


title: XBP1s_ChIP_CT20


title: Sperm_SH7


title: Mst_H3K27Ac_sg1-66_ChIP-seq


title: Mst_H3K27Ac_sg1-76_ChIP-seq


title: WT_YAP_ChIP-seq

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
5ng-10ng of ChIP DNA and Input DNA were used separately to prepare DNA library for Illumina sequencing. Firstly, DNA fragments were repaired to blunt ends by Klenow fragments enzyme, T4 DNA polymerase and a phosphate group was added to the 5’-ends of DNA fragment by T4 PNK. Next, a single ‘A’ base was added to the repaired 3’-end with Klenow (3’→5’ exo-) for adaptor ligation. Subsequently, a pair of barcoded TruSeq adapters with 3’-end ‘T’ overhang was ligated to both ends of A-tailed DNA fragment with T4 DNA ligase. Eventually, the ligation products were subjected to amplification by using adaptor primers, the resultant library with size of 250bp-500bp was gel purified by QIAGEN kit to remove adaptor dimers and other contamination. After quantification and quality control, the purified library was used for pair-end sequencing on Illumina HiSeq 2000 platform.

value: Wild type

value: YAP


title: WT_RNA-Seq_CT14_Rep1

description: Total RNA-seq


title: XBP1s_ChIP_CT16


title: WT_RNA-Seq_CT12_Rep2

description: Total RNA-seq


title: XBP1s_ChIP_CT36


title: WT_sox2_ChIP-seq


title: WT_RNA-Seq_CT12_Rep1

description: Total RNA-seq


title: Sperm_SH5

description:
results.sperm.N2vsHS2.csv.gz
results.sperm.HS1vsHS2.csv.gz

value: Hatchery

value: Slow


title: WT_OCT4_ChIP-seq


title: XBP1s_ChIP_CT12

value: C57BJ/L6 background


title: MstKO_ES_Rep1

value: MstKO


title: Sperm_SH4

value: male


title: Sperm_SH9

value: Natural


title: WT_RNA-Seq_CT10_Rep1

description: Total RNA-seq

value: Xbp1 flx/flx (WT, wild-type)


title: XBP1s_ChIP_CT04

value: Male


title: WT_RNA-Seq_CT10_Rep2

description: Total RNA-seq


title: XBP1s_ChIP_CT08


title: WT_Nanog_ChIP-seq

value: Embryonic stem cells

value: Nanog


title: XBP1s_ChIP_CT24

value: 12-16 weeks

value: Liver


title: Sperm_SH3

description:
results.sperm.N2vsHS1.csv.gz
results.sperm.HS1vsHS2.csv.gz

value: Fast


title: WT_input_ChIP-seq


title: WT_RNA-Seq_CT08_Rep2

description: Total RNA-seq


title: Sperm_SH2


title: XBP1s_ChIP_CT00

value: anti-XBP1s (Biolegend Poly6195)


title: WT_H3K4Me3_ChIP-seq


title: Sperm_SH6

value: Sperm


title: WT_H3K36Me3_ChIP-seq

value: Wild type


title: Sperm_SH1


title: WT_RNA-Seq_CT06_Rep2

description: Total RNA-seq


title: WT_H3K27Me3_ChIP-seq


title: LX-2_3

city: suzhou

first: shouli

last: wang

address: renai road 199, suzhou industrial park

department: pathology

institute: soochow university school of medicine

description: microRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg18
Supplementary_files_format_and_content: excel format: enriched peaks

source_name: Hepatic stellate cells

growth_protocol: Cells were cultured in a 6-well plastic cell plate with 1.5 ml hUC-MSCs (1 × 105 cells) in the upper semi-permeable membrane (Transwell insert) and with 2 ml HSCs (1 × 105 cells) in the lower membrane layer.

extract_protocol:
RNA was harvested using Trizol reagent.
miRNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: treatment

value: stimulated with TGF-β1 for 24h

tag: co-culture


title: LX-2+MSC_2

description: microRNA

value: hUC-MSCs


title: LX-2+MSC_3

description: microRNA


title: LX-2+MSC_1

description: microRNA


title: Sperm_N2

tag: tissue

tag: Sex


title: WT_RNA-Seq_CT06_Rep1

description: Total RNA-seq


title: WT_RNA-Seq_CT04_Rep1

description: Total RNA-seq


title: WT_RNA-Seq_CT04_Rep2

description: Total RNA-seq


title: Mst_YAP_ChIP-seq

value: YAP


title: Mst_sox2_ChIP-seq


title: Sperm_H3

tag: source

value: Hatchery

tag: growth

value: Standard


title: Sperm_H2

value: male


title: LX-2_2

description: microRNA


title: LX-2_1

description: microRNA


title: WT_H3K27Ac_ChIP-seq


title: Mst_OCT4_ChIP-seq

value: MstKO


title: WT_RNA-Seq_CT02_Rep2

description: Total RNA-seq

tag: strain

value: C57BJ/L6 background

value: Xbp1 flx/flx (WT, wild-type)

tag: age


title: WT_RNA-Seq_CT02_Rep1

description: Total RNA-seq

value: Male

tag: time point


title: Mst_Nanog_ChIP-seq

value: Embryonic stem cells

value: Nanog


title: WT_RNA-Seq_CT08_Rep1

description: Total RNA-seq

tag: genotype

value: 12-16 weeks

value: Liver


title: RBC_H3

value: RBC


title: WT_RNA-Seq_CT00_Rep2

description: Total RNA-seq

tag: gender


title: Sperm_N3

value: Sperm

value: Natural


title: Mst_input_ChIP-seq

tag: cell type


title: Mst_H3K4Me3_ChIP-seq

tag: passages


title: WT_RNA-Seq_CT00_Rep1

description: Total RNA-seq


title: Mst_H3K36Me3_ChIP-seq

tag: strain/background


title: 108953_Fe_deplete_2

city: Ann Arbor

first: Danelle

middle: Rae

last: Weakland

state: MI

address: 1150 West Medical Center Dr.

department: Microbiology and Immunology

institute: University of Michigan Medical School

data_processing:
Adapter sequences and low qaulity ends were trimmed off the reads using Trimmomatic v0.36
EDGE-pro was used to align reads to the reference genome for Serratia marcescens UMH9 (Genbank: https://www.ncbi.nlm.nih.gov/nuccore/1217739760)
Gene-level read count data was processed using edgeR package in R for normalization and differential expression testing between the two groups
Differentially expressed genes were identified by requiring FDR<=0.05 and FC>=1.5
Genome_build: NCBI Reference Sequence: NZ_CP018923.1
Supplementary_files_format_and_content: Excel file with RPKM values for each sample with logFC calculated comparing genes differentially expressed in iron replete and depleted conditions

organism: Serratia marcescens

source_name: bacterial cells_Fe_deplete

extract_protocol:
RNA was stabilized using RNAprotect. Baceria were lysed using lysozyme and Proteinase K. The RNAeasy minikit from Qiagen was used to purify RNA according to the manufacture's directions. Turbo Dnase (Thermo Fisher) was used to deplete genomic DNA.
A cDNA stranded library was prepared using the ScriptSeq RNA-seq Library Prep Kit (SSV21124) from Illumnia per the manufacturer's directions.

treatment_protocol: Cultures were depleted of iron or supplemented with 36µM FeSO4

tag: iron/culture condition

value: iron deplete


title: Sperm_N1


title: RBC_H1


title: 108952_Fe_replete_2

source_name: bacterial cells_Fe_replete

value: iron replete; supplemented with 36µM FeSO4


title: 108951_Fe_deplete_1


title: RBC_N2


title: Sperm_H1


title: RBC_N1


title: 108950_Fe_replete_1


title: RBC_N3


title: Mst_H3K27Ac_ChIP-seq

tag: genotype/variation

tag: chip antibody


title: RBC_H2


title: CD_rep2

type: RNA

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

description:
CD17
Gene expression profile in mouse mammary epithelial cells exposed to control diet.
Replicate 2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Whole Mouse Genome microarray 4x44K Ver. 2.0 (G2519F #26655, Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_GX_1Color and Grid: 026655_D_F_20121126) to obtain background subtracted and spatially detrended Processed Signal.
Data were normalized and filtered with three filters with GeneSpring software 12.1 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than 20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was excluded. In the last filter, when the value (log scale) of CV was over 50 percent in both conditions, the probe was excluded. After filtering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: mouse mammary glands isolated from 8-week-old female Trp-53 knockout mice that had been fed with CD for five weeks

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

extract_protocol:
Mouse mammary glands were isolated from 8-week-old female Trp-53 knockout mice that had been fed with HFD or CD for five weeks.
Total RNA was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Trp53-/- female mice were randomly assigned to a specific diet: CD or HFD. They were fed from three weeks of age to eight weeks of age (diet exposure is 5 weeks).

value: Trp-53 knockout

value: Mammary glands

value: Female

value: 8 weeks

tag: treatment

value: Control diet


title: CD_rep3

description:
CD18
Gene expression profile in mouse mammary epithelial cells exposed to control diet.
Replicate 3


title: HFD_rep3

description:
HFD16
Gene expression profile in mouse mammary epithelial cells exposed to high-fat diet.
Replicate 3

source_name: mouse mammary glands isolated from 8-week-old female Trp-53 knockout mice that had been fed with HFD for five weeks

value: High-fat diet


title: CD_rep1

description:
CD12
Gene expression profile in mouse mammary epithelial cells exposed to control diet.
Replicate 1


title: HFD_rep2

description:
HFD15
Gene expression profile in mouse mammary epithelial cells exposed to high-fat diet.
Replicate 2


title: SCNT 2-cell Rep2

status: Public on May 23 2020

city: Seongnam-si

first: Dong Ryul

last: Lee

state: Gyeonggi-do

address: 335, Pangyo-ro

country: South Korea

institute: CHA University

data_processing:
Paired-end sequencing reads were mapped to mm9 mouse genome using STAR tool(v2.5.2b).
After mapping, fragments per kilobase million (FPKM) was calculated by Cufflinks (v2.2.1) tool using the following strand-specific Cuffnorm option: --library-type=fr-second strand.
Functional annotation of differentially expressed genes (DEGs) and enrichment analyses were performed using DAVID (v6.8) and Gene Set Enrichment Analysis (GSEA, v2.2.4), respectively, and genes were considered differentially expressed at the fold change > 3 and FPKM > 3. R (v3.3.2) package was used for statistical analyses and scatter plot generation, and RNA-Seq results were visualized using Integrative Genomics Viewer (IGV).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: SCNT 2-cell embryos

growth_protocol: All MII stage oocytes with distinct first polar bodies were enucleated in M2 medium containing 5 µg/ml cytochalasin B. For nuclear transfer, cumulus cells were injected into enucleated oocytes in M2 medium using a PIEZO-driven micromanipulator (Primetech, Tsuchiura-shi, Japan). After nuclear transfer, the reconstructed oocytes were incubated in KSOM medium for 1-2 hours before activation. Activation was performed by incubation in M16 (Millipore) medium containing 10 mM SrCl2, 2 mM EGTA, and 5 µg/ml cytochalasin B for 6 hours and then the oocytes were cultured in KSOM in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
For the RNA-Seq analysis, the DriveMapTM library preparation method (Celecta) was used.
RNA-Seq data were analyzed by using either the ROSALIND tool (OnRamp) or public resources.

treatment_protocol: During activation, the treated groups were supplemented with RAD51-stimulatory compound 1 (RS-1), which was continued for 22 hours after activation, until the 2-cell stage. After activation, Kdm4a mRNA is injected into SCNT embryos.

tag: method

value: SCNT

value: preimplantation embryo

value: Wild type


title: SCNT 2-cell RS-1 Rep2

source_name: SCNT 2-cell embryo treated with RS-1

value: SCNT with RS-1

tag: tissue


title: SCNT 2-cell Rep1


title: IVF 2-cell Rep1

source_name: IVF 2-cell embryos

value: IVF


title: IVF 2-cell Rep2


title: NCC24_H3K9me3_rep2

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

data_processing:
BCL2FASTQ version1.8.4 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie1.0.1.
Duplication reads were removed from aligned file by using picard-tools-1.119.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: Gastric cancer cell line

growth_protocol: These cells were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO) at 37 °C in 5% CO2 incubator.

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol.

value: Gastric cancer cell line

value: H3K9me3_ChIP (abcam, ab8895, lot GR114265-2)


title: NCC24_H3K27ac_rep2


title: NCC24_H3K27me3_rep2


title: NCC24_H3K4me3_rep2

value: H3K4me3_ChIP (Active Motif, 39159, lot 25817005)


title: SNU719_H3K9me3_rep2


title: SNU719_H3K27ac_rep2


title: HFD_rep1

description:
HFD7
Gene expression profile in mouse mammary epithelial cells exposed to high-fat diet.
Replicate 1

tag: Sex


title: SNU719_H3K27me3_rep2


title: SCNT 2-cell RS-1 Rep1


title: NCC24_H3K4me1_rep2

value: H3K4me1_ChIP (CST, 5326S, lot 3)


title: SNU719_H3K4me3_rep2


title: SNU719_H3K4me1_rep2


title: Mst_H3K27Me3_ChIP-seq

value: Embryonic stem cells

value: MstKO


title: single cell SCNT-RS1 10


title: single cell SCNT-RS1 13


title: single cell SCNT-RS1 11


title: single cell SCNT-RS1 7


title: single cell SCNT-RS1 8


title: single cell SCNT-RS1 9


title: single cell SCNT-RS1 5


title: single cell SCNT-RS1 12


title: single cell SCNT-RS1 6


title: single cell SCNT-RS1 3


title: single cell SCNT 11


title: single cell SCNT 10


title: single cell SCNT 8


title: single cell SCNT-RS1 4


title: single cell SCNT-RS1 2


title: single cell SCNT 4


title: single cell SCNT 1


title: single cell SCNT 5


title: single cell SCNT-RS1 1


title: single cell IVF 15


title: single cell SCNT 6


title: single cell SCNT 7


title: single cell IVF 16


title: single cell IVF 14


title: single cell IVF 12


title: single cell IVF 13


title: single cell IVF 11


title: single cell IVF 9


title: single cell IVF 5


title: single cell IVF 6


title: single cell IVF 10


title: single cell IVF 4


title: single cell IVF 7


title: single cell SCNT 2


title: single cell IVF 2


title: single cell IVF 1


title: single cell IVF 3


title: single cell IVF 8


title: Mouse E16 small intestine organoids 3

city: Wuerzburg

first: Ozge

last: Kayisoglu

address: Josef-Schneider-Str. 2/D15

institute: Research Center for Infectious Diseases (ZINF)

data_processing:
Raw reads were trimmed and clipped for quality control using cutadapt 1.16 with Python 3.6.4.
Read quality was checked for each sample using FastQC version 0.11.7.
Genomic mapping to human GRCh38 and mouse GRCm38 genomes were performed using READemption (version 0.4.3).
The number of genes per gene was determined by using htseq-count.
Genome_build: GRCh38; GRCm38
Supplementary_files_format_and_content: read counts

source_name: Proximal intestine organoids

growth_protocol: Human and mouse organoids were generated from isolated gastric glands, small intestine and colon crypts to be maintained in culture as described previously (Sato et al., 2009; Sato et al., 2011; Barker et al., 2010; Bartfeld et al., 2015)  and kept at 37°C, 5% CO2 in a humidified incubator.

extract_protocol:
Organoids were removed from Matrigel and resuspended in RTL buffer (Qiagen). RNA was extracted from the organoids using the RNeasy Mini RNA Extraction Kit (Qiagen).
Illumina TruSeq Stranded mRNA Library Prep Kit (Cat#20020594) was used with 500 ng of total RNA for the construction of sequencing libraries. Libraries were prepared for sequencing according to the manufacturer's protocol using 11 PCR cycles.

value: Proximal intestine organoids

tag: developmental stage


title: Mouse E16 small intestine organoids 1


title: Mouse E16 small intestine organoids 2


title: single cell SCNT 9


title: Mouse proximal colon organoids 1

source_name: Colon organoids

value: Colon organoids

value: adult


title: Mouse jejunum organoids 3

source_name: Jejunum organoids

value: Jejunum organoids


title: Mouse proximal colon organoids 2


title: Mouse ileum organoids 1

source_name: Ileum organoids

value: Ileum organoids


title: Mouse ileum organoids 2


title: single cell SCNT 3


title: Mouse E16 stomach organoids 2

source_name: Stomach organoids

value: Stomach organoids


title: Mouse duodenum organoids 3

source_name: Duodenum organoids

value: Duodenum organoids


title: Mouse proximal colon organoids 3


title: Mouse jejunum organoids 2


title: Mouse jejunum organoids 1


title: Mouse duodenum organoids 2


title: Mouse duodenum organoids 1


title: Mouse pylorus organoids 1

source_name: Stomach pylorus organoids

value: Stomach pylorus organoids


title: Mouse corpus organoids 3

source_name: Stomach corpus organoids

value: Stomach corpus organoids


title: Mouse corpus organoids 2


title: Mouse pylorus organoids 2


title: Mouse pylorus organoids 3


title: MKN7_WT_episomalVec_H3K9me3_rep2

value: uninfected control cell


title: Mouse corpus organoids 1


title: Mouse ileum organoids 3


title: Mouse E16 stomach organoids 1


title: MKN7_WT_EBNA1_H3K9me3_rep2


title: MKN7_WT_H3K9me3_rep2


title: MKN7_WT_Mock_H3K9me3_rep2


title: MKN7_WT_episomalVec_H3K27ac_rep2

value: H3K27ac_ChIP (Active Motif, 91193, lot 01518001)


title: MKN7_WT_H3K27ac_rep2


title: MKN7_EBVi_mCherry_H3K9me3_rep2

value: EBV infected cell


title: MKN7_EBVi_mtEBNA1_H3K9me3_rep2

value: H3K9me3_ChIP (abcam, ab8895, lot GR114265-2)


title: MKN7_WT_Mock_H3K27ac_rep2


title: MKN7_EBVi_DMSO_H3K9me3_rep2


title: MKN7_WT_episomalVec_H3K9me3_rep1


title: MKN7_EBVi_NCDM-32b_H3K9me3_rep2


title: MKN7_EBVi_C646_H3K27ac_rep2


title: MKN7_WT_EBNA1_H3K27ac_rep2


title: MKN7_EBVi_IOX1_H3K9me3_rep2


title: MKN7_EBVi_Garcinol_H3K27ac_rep2


title: MKN7_WT_H3K9me3_rep1


title: MKN7_WT_EBNA1_H3K9me3_rep1


title: MKN7_WT_episomalVec_H3K27ac_rep1


title: MKN7_WT_Mock_H3K9me3_rep1


title: MKN7_WT_H3K27ac_rep1


title: MKN7_EBVi_mtEBNA1_H3K9me3_rep1


title: MKN7_EBVi_mCherry_H3K27ac_rep1


title: MKN7_EBVi_mCherry_H3K9me3_rep1


title: MKN7_EBVi_mtEBNA1_H3K27ac_rep1


title: MKN7_EBVi_NCDM-32b_H3K9me3_rep1


title: MKN7_EBVi_mtEBNA1_H3K27ac_rep2


title: MKN7_EBVi_IOX1_H3K9me3_rep1


title: MKN7_EBVi_Garcinol_H3K27ac_rep1


title: MKN7_EBVi_mCherry_H3K27ac_rep2


title: MKN7_EBVi_C646_H3K27ac_rep1


title: MKN7_EBVi_DMSO_H3K27ac_rep1


title: GES1_EBVi_K27me3_rep2

source_name: Normal gastric epithelial cell


title: MKN7_EBVi_DMSO_H3K27ac_rep2


title: GES1_EBVi_K27ac_rep2


title: GES1_EBVi_K9me3_rep2


title: GES1_EBVi_K4me3_rep2

value: H3K4me3_ChIP (Active Motif, 39159, lot 25817005)


title: GES1_WT_K9me3_rep2


title: GES1_WT_K4me3_rep2


title: GES1_WT_K27ac_rep2


title: GES1_EBVi_K4me1_rep2

value: H3K4me1_ChIP (CST, 5326S, lot 3)


title: GES1_EBVi_K9me3_rep1


title: GES1_WT_K4me1_rep2


title: GES1_EBVi_K27me3_rep1


title: GES1_EBVi_K27ac_rep1


title: MKN7_WT_EBNA1_H3K27ac_rep1


title: GES1_EBVi_K4me1_rep1


title: MKN7_WT_Mock_H3K27ac_rep1


title: GES1_WT_K9me3_rep1


title: GES1_WT_K27ac_rep1


title: GES1_WT_K4me3_rep1


title: YCC10_H3K9me3_rep2

value: Gastric cancer cell line


title: GES1_WT_K27me3_rep1


title: MKN7_EBVi_DMSO_H3K9me3_rep1


title: YCC10_H3K27ac_rep2


title: GES1_WT_K4me1_rep1


title: YCC10_H3K9me3_rep1


title: YCC10_H3K4me1_rep2


title: YCC10_H3K27me3_rep1


title: YCC10_H3K27ac_rep1


title: YCC10_H3K4me1_rep1


title: GES1_WT_K27me3_rep2


title: YCC10_H3K27me3_rep2


title: YCC10_H3K4me3_rep2


title: 4Cseq_PGRMC2_enhancer1_GES1_EBVi

data_processing:
BCL2FASTQ version1.8.4 software was used for basecalling.
4C-seq reads were processed using w4Cseq.
fastq files for each sample were extracted from pooled fastq files by w4Cseq using bait region sequence.
bigwig files were generated by w4Cseq.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: Normal gastric epithelial cells

extract_protocol: Chromosome conformation capture (3C) template was prepared from fixed chromatin following Splinter et al., 2012 (PMID: 22609568). The template was amplified with Expand Long Template Polymerase (Roche #11759060001) using a 4C library construction primers which designed at each bait region.


title: 4Cseq_PGRMC2_enhancer1_GES1_WT

value: Control uninfected cells


title: 4Cseq_PGRMC2_enhancer2_GES1_WT


title: GES1_EBVi_K4me3_rep1


title: 4Cseq_PGRMC2_enhancer2_GES1_EBVi


title: 4Cseq_TGFBR2_TSS_MKN7_WT


title: 4Cseq_TGFBR2_TSS_MKN7_EBVi


title: 4Cseq_episomalVec_2_MKN7_WT

value: episomal vector introduced cells


title: G_CD14_2

city: London

first: Kristine

last: Vaivode

address: CIBCI, First Floor, New Hunt's House, Great Maze Pond

department: Centre for Inflammation Biology and Cancer Immunology

country: United Kingdom

institute: King's College London

data_processing:
Base-calling was performed on Illumina bcl2fastq v2.19.1.403
The raw sequencing data was initially processed using open source, web-based platform Galaxy (version 18.05.rc1).
Reads were filtered for quality with more than 80% of the sequence having quality score > 33 using FastQC tool.
Mapping against reference genome was performed with Hisat2 v2.1.0 to the hg38 human genome.
Adapter sequences were detected automatically with TrimGalore!. Reads under 20bp were discarded.
All processed sequencing files were imported in Partek® Flow® software (Partek Inc., build 7.0.18.0514) and the gene count data was normalised using FPKM.
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated value file with FPKM values for each sample

source_name: Cord blood HSPC derived  mononuclear phagocytes

growth_protocol: CD34+ hematopoietic progenitors isolated from human cord blood were differentiated in vitro by culturing them with engineered mesenchymal stromal cells expressing human transmembrane FLT3L, SCF and soluble CXCL12 (MS5_FS12) or human GM-CSF (MS5_GM) for 14 days.

extract_protocol:
in vitro differentiated cells were FACS sorted in 96-well plates (100 cells/well) containing lysis buffer (RLT).
RNA-seq libraries were prepared using Labcyte Echo 525 contactless liquid handling system (Labcyte Inc). In brief, ERCC mix (Thermo Fisher) was added to each sample and first strand full length cDNA was generated with a modified protocol of the SMARTseq v4 Ultra Low Input RNA Kit (Takara Clontech) using poly dT primers and a template switching oligo. Full length cDNA was amplified using SeqAmp™ DNA Polymerase (Takara Clontech). 12 ng of amplified cDNA from each sample was used to generate non-stranded RNA libraries using a modified protocol of the Ovation Ultralow System V2 1-96 kit (NuGEN). In brief, amplified cDNA was fragmented through sonication on Covaris E220 (Covaris Inc), repaired and polished followed by ligation of indexed adapters. Adapter ligated cDNA were pooled before final amplification to add flow cell primers. Libraries were sequenced on HiSeq2500 (Illumina Cambridge) for 100 cycles PE in Rapid mode.

tag: protocol

value: In vitro differentiated cells

tag: donor

value: CD1c-CD14+ cells

tag: culture conditions

value: Co-cultured with MS5_GM


title: 4Cseq_episomalVec_1_MKN7_WT


title: G_CD14_1


title: G_CD1c_CD206_3

value: CD1c+ CD206+ cells


title: G_CD1c_CD206_2


title: HepG2-nop53-mRNA-seq rep 2

city: chengdu

first: yin

last: zhang

address: Jinniu District

institute: southwest jiaotong university

data_processing:
Raw reads were trimmed for adaptor sequence with cutadapter
then mapped to the human reference genome (hg38) using HISAT2
The number of reads that were mapped to each gene was counted by using HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each Sample ...

source_name: Hepatocellular carcinoma cells

growth_protocol: HepG2 were cultured with DMEM with 10% FBS,100 IU/ml penicillin and 100 µg/ml streptomycin solution.Cell cultures were maintained at 37°C and at 5% CO2.

extract_protocol:
Total RNA was extracted from the cultured cells using Trizol Reagent (Invitrogen) according to the manufacturer’s instructions.mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, and double stranded cDNA synthesized using random hexamers  cDNA was synthesized using random hexamers, M-MuLV Reverse Transcriptase (RNase H), and DNA Polymerase I.The library fragments are purified with AMPure XP system
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HepG2 cells were treated with doxorubicin (1µg/ml) for 24 hours to induce the expression of p53.

value: Hepatocellular carcinoma cells

tag: cell line

value: untreated


title: HepG2-p53-mRNA-seq rep 2


title: 4Cseq_Bait2_GES1_EBVi


title: YCC10_H3K4me3_rep1


title: 4Cseq_Bait1_GES1_EBVi


title: HepG2-p53-mRNA-seq rep 1


title: G_CD1c_CD206_1


title: 4Cseq_Bait1_YCC10

value: EBV(+) Gastric cancer cell line


title: 4Cseq_Bait2_YCC10


title: G_CD1c_CD14_3

value: CD1c+CD14+ cells


title: HepG2-nop53-mRNA-seq rep 1


title: G_CD14_CD16_2

value: CD14+CD16+ cells


title: G_CD14_CD16_1


title: G_DC2_1

value: CD1c+ cells


title: G_CD1c_CD14_2


title: GES1_EBVi_RNAseq_rep2

data_processing:
BCL2FASTQ version1.8.4 software was used for basecalling.
Reads were aligned to hg19 genome assembly with Hisat v2.2.1.0 for RNA-Seq.
Reads with more than two mismatches were removed form aligned reads for RNA-Seq.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1for RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was extracted using the TRIzol Reagent (Termo Fisher) and the Direct-zol RNA MiniPrep Kit (Zymo Research) following the manufacturer’s protocol
Libraries were prepared TruSeq Stranded mRNA Sample Prep Kit (Illumina).

value: Normal gastric epithelial cell line

value: EBV infection


title: G_DC1_3

value: Clec9A+CD141+ cells


title: G_CD1c_CD14_1


title: SNU719_RNAseq_rep2


title: NCC24_RNAseq_rep2


title: GES1_WT_RNAseq_rep2


title: YCC10_RNAseq_rep1


title: NCC24_RNAseq_rep1


title: SNU719_RNAseq_rep1


title: G_DC1_2


title: YCC10_RNAseq_rep2


title: GES1_EBVi_RNAseq_rep1


title: GES1_WT_RNAseq_rep1


title: G_DC2_3


title: G_CD14_CD16_3


title: NCC24_H3K27me3


title: NCC24_H3K9me3

value: H3K9me3_ChIP (abcam, ab8895, lot GR114265-2)


title: F_CD14_1

value: Co-cultured with MS5_FS12


title: F_CD14_2


title: NCC24_H3K4me3

value: Gastric cancer cell line

value: H3K4me3_ChIP (Active Motif, 39159, lot 25817005)


title: NCC24_H3K27ac


title: F_CD14_CD16_3

value: In vitro differentiated cells


title: F_CD14_CD16_2


title: F_CD14_3

value: CD1c-CD14+ cells


title: F_CD14_CD16_1


title: G_CD14_3

value: Co-cultured with MS5_GM


title: G_DC2_2


title: G_DC1_1


title: NCC24_H3K4me1

value: H3K4me1_ChIP (CST, 5326S, lot 3)


title: F_CD1c_CD14_3


title: CD103pos_Tcells_3

description:
PG_Bulk_Blood_raw_counts.csv
CD103pos-d3

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the the human reference genome using STAR aligner (v2.5.3a).
Raw read counts matrix made also with STAR (using the parameter --quantMode GeneCounts).
The read counts matrix was imported in Rstudio Version 1.2.5033 with  R version 3.6.1.
Dataset was processed using DESeq2 R package (version 1.24.0) functions.
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated value file with raw data values for each sample

source_name: Naïve blood CD8+ T cells

growth_protocol: Naïve CD8+ T cells from healthy blood donor were cocultured, for 5 days, with mismatched DC3 from healthy blood donor in presence of superantigen (Cytostim).

extract_protocol:
Cells were FACS sorted in in 1.5ml Eppendorf tubes (100-1000 cells/tube) containing Trizol
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA). RNA library preparations, sequencing reactions, and initial bioinformatics analysis were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). The SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA) as per manufacturer’s protocol. Illumina Nextera XT library was used for library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. Final libraries were analyzed on the Agilent TapeStation for library sizing and quantified using the Qubit dsDNA HS Assay Kit and by qPCR using the KAPA Library Quantification Kit. The sequencing libraries were multiplexed and clustered on four lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Paired End (PE) configuration.

treatment_protocol: Blood Monocytes, DC2 and DC3 were stimulated ex vivo with a TLR agonist cocktail (LPS, Poly I:C, R848) for 16h.

value: CXCR3+ CD103+ CD8+ T


title: SNU719_H3K27me3


title: SNU719_H3K4me3


title: SNU719_H3K27ac


title: SNU719_H3K4me1


title: F_CD1c_CD14_2


title: CD103pos_Tcells_2

description:
PG_Bulk_Blood_raw_counts.csv
CD103pos-d2


title: 4Cseq_MZT1e_MKN7_EBVi

value: EBV infected cell


title: SNU719_H3K9me3


title: F_CD1c_CD14_1


title: 4Cseq_MZT1p_NCC24

value: EBV(+) Gastric cancer cell line


title: 4Cseq_MZT1p_MKN7_EBVi


title: 4Cseq_MZT1e_MKN7_WT

value: EBV(-) Gastric cancer cell line


title: 4Cseq_MZT1p_SNU719


title: CD103neg_Tcells_2

description:
PG_Bulk_Blood_raw_counts.csv
CD103neg-d2

value: CXCR3+ CD103- CD8+ T


title: CD103pos_Tcells_1

description:
PG_Bulk_Blood_raw_counts.csv
CD103pos-d1


title: 4Cseq_Bait1_MKN7_EBVi


title: Naïve_Tcells_3

description:
PG_Bulk_Blood_raw_counts.csv
Naive-d3

value: Peripheral blood

value: CD3+ CD45RO+ CD8+ T cells


title: CD103neg_Tcells_1

description:
PG_Bulk_Blood_raw_counts.csv
CD103neg-d1


title: Naïve_Tcells_2

description:
PG_Bulk_Blood_raw_counts.csv
Naive-d2


title: Mono_TLR_4

description:
PG_Bulk_Blood_raw_counts.csv
Mono-CD88pos-S-d4

source_name: In vitro TLR agonist activated  human periferal blood mononuclear phagocytes

value: CD88+ cells


title: Mono_TLR_3

description:
PG_Bulk_Blood_raw_counts.csv
Mono-CD88pos-S-d3


title: MG_NR14

city: Milan

first: Paola

last: Cavalcante

address: Via Celoria 11

department: Neurology IV

country: Italy

institute: Fondazione IRCCS Istituto Neurologico Carlo Besta

description: Rawcounts_MiRNA_MG R_NR

data_processing:
bcl2fastq software (Illumina) was used for basecalling .
After sequencing adapters were trimmed off as part of the base calling, using an Exiqon in-house software. Trimming of adapters from the dataset revealed one distinct peak representing microRNA (~18-23nt).
After quality control, reads were mapped with botwie2 v. 2.2.6 to miRBase 20.
MiRNA counting was performed on files including only uniquely mapped fragments using an Exiqon in-house software.
Genome_build: GRCh37
Supplementary_files_format_and_content: excel file including raw counts for each sample (columns) across 2578 miRNAs (rows) [counts matrix]

source_name: blood

extract_protocol:
Whole blood from MG patients was collected in PAXgene Blood RNA Tube and frozen at -20 °C. Total RNA was isolated from blood samples using the PAXgene Blood RNA Kit. A total of 100 ng of total RNA was converted into microRNA NGS libraries.
MicroRNA libraries were prepared using the NEBNext® Small RNA Library preparation kit (New England Biolabs).

tag: disease

value: MG

tag: age at blood collection

value: F

tag: phenotypes

value: Non-responder


title: MG_NR15

description: Rawcounts_MiRNA_MG R_NR


title: MG_NR13

description: Rawcounts_MiRNA_MG R_NR

value: M


title: DC3_TLR_4

description:
PG_Bulk_Blood_raw_counts.csv
DC3-CD163-S-d4

tag: cell type

value: CD1c+CD163+ cells


title: Mono_TLR_1

description:
PG_Bulk_Blood_raw_counts.csv
Mono-CD88pos-S-d1


title: CD103neg_Tcells_3

description:
PG_Bulk_Blood_raw_counts.csv
CD103neg-d3

value: In vitro differentiated cells


title: MG_NR9

description: Rawcounts_MiRNA_MG R_NR


title: DC3_TLR_1

description:
PG_Bulk_Blood_raw_counts.csv
DC3-CD163-S-d1


title: MG_NR10

description: Rawcounts_MiRNA_MG R_NR


title: MG_NR8

description: Rawcounts_MiRNA_MG R_NR


title: DC3_TLR_3

description:
PG_Bulk_Blood_raw_counts.csv
DC3-CD163-S-d3


title: MG_NR7

description: Rawcounts_MiRNA_MG R_NR


title: MG_NR5

description: Rawcounts_MiRNA_MG R_NR


title: AS_DC_1

description:
PG_Bulk_Blood_raw_counts.csv
AS-DC-d1

source_name: Sorted human periferal blood mononuclear phagocytes

value: CD123+CD45RA+AXL+Siglec6+ cells


title: DC2_TLR_1

description:
PG_Bulk_Blood_raw_counts.csv
DC2-BTLA-S-d1

value: CD1c+BTLA+ cells


title: AS_DC_3

description:
PG_Bulk_Blood_raw_counts.csv
AS-DC-d3


title: DC2_TLR_4

description:
PG_Bulk_Blood_raw_counts.csv
DC2-BTLA-S-d4


title: AS_DC_4

description:
PG_Bulk_Blood_raw_counts.csv
AS-DC-d4


title: MG_NR6

description: Rawcounts_MiRNA_MG R_NR


title: MG_NR2

description: Rawcounts_MiRNA_MG R_NR


title: MG_NR4

description: Rawcounts_MiRNA_MG R_NR


title: Naïve_Tcells_1

description:
PG_Bulk_Blood_raw_counts.csv
Naive-d1


title: MG_NR3

description: Rawcounts_MiRNA_MG R_NR


title: pDC_1

description:
PG_Bulk_Blood_raw_counts.csv
pDC-d1

value: CD123+CD45RA+AXL-Siglec6- cells


title: Mono_CD88neg_4

description:
PG_Bulk_Blood_raw_counts.csv
Mono-CD88neg-d4

value: CD88- cells


title: pDC_3

description:
PG_Bulk_Blood_raw_counts.csv
pDC-d3


title: MG_R14

description: Rawcounts_MiRNA_MG R_NR

value: Responder


title: MG_NR11

description: Rawcounts_MiRNA_MG R_NR


title: DC2_TLR_3

description:
PG_Bulk_Blood_raw_counts.csv
DC2-BTLA-S-d3


title: MG_NR1

description: Rawcounts_MiRNA_MG R_NR


title: MG_R13

description: Rawcounts_MiRNA_MG R_NR


title: MG_NR12

description: Rawcounts_MiRNA_MG R_NR


title: Mono_CD88neg_3

description:
PG_Bulk_Blood_raw_counts.csv
Mono-CD88neg-d3


title: MG_R15

description: Rawcounts_MiRNA_MG R_NR


title: Mono_CD88neg_2

description:
PG_Bulk_Blood_raw_counts.csv
Mono-CD88neg-d2


title: Mono_CD88neg_1

description:
PG_Bulk_Blood_raw_counts.csv
Mono-CD88neg-d1


title: MG_R12

description: Rawcounts_MiRNA_MG R_NR


title: MG_R10

description: Rawcounts_MiRNA_MG R_NR


title: MG_R9

description: Rawcounts_MiRNA_MG R_NR


title: Mono_CD88pos_4

description:
PG_Bulk_Blood_raw_counts.csv
Mono-CD88pos-d4


title: MG_R11

description: Rawcounts_MiRNA_MG R_NR


title: MG_R8

description: Rawcounts_MiRNA_MG R_NR


title: Mono_CD88pos_2

description:
PG_Bulk_Blood_raw_counts.csv
Mono-CD88pos-d2


title: MG_R7

description: Rawcounts_MiRNA_MG R_NR


title: Mono_CD88pos_1

description:
PG_Bulk_Blood_raw_counts.csv
Mono-CD88pos-d1


title: Mono_CD88pos_3

description:
PG_Bulk_Blood_raw_counts.csv
Mono-CD88pos-d3


title: DC3_4

description:
PG_Bulk_Blood_raw_counts.csv
DC3-d4


title: DC3_3

description:
PG_Bulk_Blood_raw_counts.csv
DC3-d3


title: pDC+NK_mock_indB

city: Uppsala

first: Pascal

last: Pucholt

address: Dag Hammarskjölds väg 20

department: Medical Science

country: Sweden

institute: Uppsala University

hyb_protocol: 600 ng Cy3-labeled fragmented cRNA was hybridized for 17 hours, at 65°C to Agilent Whole Human Genome Oligo Microarrays 8x60K, and the fluorescence signals of the hybridized probes were scanned.

scan_protocol: standard Agilent Protocol

data_processing: For readout and processing of the microarray image files, the Agilent Feature Extraction Software (FES) was used

source_name: Peripheral blood plasmacytoid dendritic cells and NK cells mock stimulated individual B

label_protocol: 50ng RNA per sample was used to produce Cy3-labeled cRNA

extract_protocol: RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel) after 6 hours according to manufacturer’s instructions.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were prepared by Ficoll-Hypaque (GE-Healthcare) density-gradient centrifugation of buffy coats from healthy blood donors. pDCs, NK and B cells were isolated from PBMCs by negative selection, using pDC isolation kit II, NK Cell Isolation Kit and B cell isolation kit II (Miltenyi Biotec), pDCs (25000/well), NK cells (50000/well) or B-cells (50000 /well), were cultivated in a total volume of 100 µl/well, in flat-bottomed 96-well plates (Nunclon) at 37°C with 5 % CO2

tag: individual

value: B

tag: affection status

value: healthy

tag: cell types

value: pDC + NK cells

value: mock


title: pDC+NK_IC_indB

source_name: Peripheral blood plasmacytoid dendritic cells and NK cells immune complex stimulated individual B

value: immune complex


title: NK_mock_indB

source_name: Peripheral blood NK cells mock stimulated individual B

value: NK cells


title: NK_IC_indB

source_name: Peripheral blood NK cells immune complex stimulated individual B


title: pDC+B_IC_indB

source_name: Peripheral blood plasmacytoid dendritic cells and B cells immune complex stimulated individual B

value: pDC + B cells


title: B_IC_indB

source_name: Peripheral blood B cells immune complex stimulated individual B

value: B cells


title: B_mock_indB

source_name: Peripheral blood B cells mock stimulated individual B


title: pDC_mock_indB

source_name: Peripheral blood plasmacytoid dendritic cells mock stimulated individual B

value: plasmacytoid DC (pDC)


title: pDC_IC_indB

source_name: Peripheral blood plasmacytoid dendritic cells immune complex stimulated individual B


title: pDC+NK_IC_indA

source_name: Peripheral blood plasmacytoid dendritic cells and NK cells immune complex stimulated individual A

value: A


title: pDC+NK_mock_indA

source_name: Peripheral blood plasmacytoid dendritic cells and NK cells mock stimulated individual A


title: pDC+B_mock_indB

source_name: Peripheral blood plasmacytoid dendritic cells and B cells mock stimulated individual B


title: MG_R4

description: Rawcounts_MiRNA_MG R_NR

value: MG

value: M


title: DC3_2

description:
PG_Bulk_Blood_raw_counts.csv
DC3-d2

value: Peripheral blood

value: CD1c+CD163+ cells


title: pDC+B_mock_indA

source_name: Peripheral blood plasmacytoid dendritic cells and B cells mock stimulated individual A


title: pDC+B_IC_indA

source_name: Peripheral blood plasmacytoid dendritic cells and B cells immune complex stimulated individual A

value: pDC + B celss


title: NK_IC_indA

source_name: Peripheral blood NK cells immune complex stimulated individual A


title: MG_R3

description: Rawcounts_MiRNA_MG R_NR

source_name: blood

value: F


title: MG_R6

description: Rawcounts_MiRNA_MG R_NR

value: Responder


title: DC3_1

description:
PG_Bulk_Blood_raw_counts.csv
DC3-d1

source_name: Sorted human periferal blood mononuclear phagocytes


title: MG_R5

description: Rawcounts_MiRNA_MG R_NR


title: pDC_IC_indA

source_name: Peripheral blood plasmacytoid dendritic cells immune complex stimulated individual A


title: B_mock_indA

source_name: Peripheral blood B cells mock stimulated individual A


title: DC2_CD5pos_4

description:
PG_Bulk_Blood_raw_counts.csv
DC2-CD5pos-d4

value: CD1c+CD5+  cells


title: MG_R2

description: Rawcounts_MiRNA_MG R_NR


title: MG_R1

description: Rawcounts_MiRNA_MG R_NR


title: HiC_MKN7_EBVi

data_processing:
BCL2FASTQ version1.8.4 software was used for basecalling.
Hi-C reads were processed using HiC-Pro or Juicer
Genome_build: hg19+NC007605.1
Supplementary_files_format_and_content: .hic

source_name: Gastric cancer cell line

extract_protocol: Hi-C experiment were conducted in biological replicates using NlaIII, according to the protocol published by Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).  DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).

value: Gastric cancer cell line MKN7

value: EBV-infected cell


title: DC2_CD5pos_3

description:
PG_Bulk_Blood_raw_counts.csv
DC2-CD5pos-d3


title: B_IC_indA

source_name: Peripheral blood B cells immune complex stimulated individual A

value: healthy


title: NK_mock_indA

source_name: Peripheral blood NK cells mock stimulated individual A

value: mock


title: 4Cseq_MZT1p_MKN7_WT

value: EBV(-) Gastric cancer cell line


title: pDC_mock_indA

source_name: Peripheral blood plasmacytoid dendritic cells mock stimulated individual A


title: 4Cseq_TGFBR2e_MKN7_EBVi

value: EBV infected cell


title: 4Cseq_TGFBR2e_MKN7_WT


title: Human colon organoids 3

source_name: Colon organoids

value: Colon organoids


title: DC2_CD5pos_2

description:
PG_Bulk_Blood_raw_counts.csv
DC2-CD5pos-d2


title: Human colon organoids 2


title: DC2_CD5pos_1

description:
PG_Bulk_Blood_raw_counts.csv
DC2-CD5pos-d1


title: YAPcKO soft replicate 1

city: Los Angeles

first: Manish

middle: J

last: Butte

state: CA

address: 10833 Le Conte Ave, MDCC Building Room 12-430

institute: UCLA

data_processing:
Basecalls performed using CASAVA version 1.4
Filtering with custom R
STAR 2.5 mismatch=2
HTSeq 0.6.1 -m union
Deseq2 2.163 padj<0.05
Genome_build: mm10
Supplementary_files_format_and_content: read counts

source_name: CD4+ T cells

extract_protocol:
Library for RNA-Seq was prepared according to KAPA Stranded mRNA-Seq poly(A) selected kit (KAPA Biosystems, Wilmington, MA) using 250 ng total RNAs as input.
Illumina

tag: strain

value: YAPcKO

tag: stiff

value: 4 kPa

tag: replicate


title: YAPcKO stiff replicate 1

value: 40 kPa


title: WT stiff replicate 1

value: WT


title: WT soft replicate 1


title: HiC_MKN7_WT

tag: treatment

value: uninfected control cell


title: 4Cseq_Bait2_NCC24_Rep3

value: EBV(+) Gastric cancer cell line


title: DC2_CD5neg_4

description:
PG_Bulk_Blood_raw_counts.csv
DC2-CD5neg-d4

tag: tissue

value: Peripheral blood

value: CD1c+CD5-  cells


title: Human colon organoids 1


title: 4Cseq_Bait2_NCC24_Rep2


title: DC2_CD5neg_3

description:
PG_Bulk_Blood_raw_counts.csv
DC2-CD5neg-d3


title: 4Cseq_Bait2_NCC24_Rep1


title: Human ileum organoids 3

source_name: Ileum organoids

value: Ileum organoids


title: 4Cseq_Bait1_NCC24_Rep3


title: Vec2 7/1

city: Frederick

first: Jack

last: Chen

state: MD

address: SAIC-Frederick Miller Dr

institute: NIH

data_processing:
Sequencing analysis was done using raw sequencing reads produced by the Illumina sequencer were quality checked for potential sequencing issues and contaminants using FastQC and FastQ Screen . Adapter sequences and primers were trimmed from the sequencing reads using trimmomatic then followed by removing polyA tail, polyN, and read portions with quality score of Q30 using PRINSEQ. Reads with a remaining length of fewer than 20 bp after trimming were discarded. A second round of quality check with FastQC was made to compare read quality before and after trimming. The sequencing reads aligned to RefSeq by STAR and annotated genes were quantified using RSEM
Genome_build: hg19
Supplementary_files_format_and_content: RSEM raw counts

source_name: cells grown in culture

growth_protocol: cells were grown on ultra-low attachment surface plates (Corning). Cells were incubated for 22 h, stained for 30 mins with crystal violet (Sigma-Aldrich), washed twice then resuspended in phosphate buffered saline (PBS). LMB-100 immunotoxin was manufactured by Roche and provided for these studies through a Collaborative Research and Development Agreement

extract_protocol:
Total RNA from triplicate samples of MSLN WT and KO cells grown in culture and IP tumors tissues was extracted using RNeasy Mini Kit (Qiagen). On-column DNase I digestion was done using the RNase-Free DNase Set (Qiagen). BioAnalysis quality control and RNA-seq were conducted by the Sequencing Facility-Illumina-Center for Cancer using a HiSeq 2500 Next Generation Sequencing instrument.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-deep Seq

value: cells grown in culture

tag: genotype

value: Mock (MSLN+, monoclonal)


title: DC2_CD5neg_2

description:
PG_Bulk_Blood_raw_counts.csv
DC2-CD5neg-d2


title: Vec2 6/24


title: Human ileum organoids 2


title: 4Cseq_Bait1_NCC24_Rep2


title: DC2_CD5neg_1

description:
PG_Bulk_Blood_raw_counts.csv
DC2-CD5neg-d1


title: Human ileum organoids 1


title: 4Cseq_Bait1_NCC24_Rep1


title: Vec2 6/20


title: CD14_4

data_processing:
Transcriptomic data were aligned using STAR (version 2.5.0a) on hg19 and RefSeq gene annotation. Sequencing read coverage per gene was determined using HTSeq (version 0.6.1p1) using these parameters: --stranded no --idattr gene_id --mode intersection-nonempty --format bam --type exon (all others are the default parameters).
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated value file with raw data values for each sample

source_name: Human breast cancer iLN mononuclear phagocytes

extract_protocol:
Tumor-draining lymph nodes (tdLN) and primary tumors were collected in CO2 independent medium (Gibco) within few hours after the primary surgery. Tissue were cut into small fragments and submitted to enzymatic digestion using 0.1 mg/ml of Liberase TL (Roche) and 0.1 mg/ml of DNase (Roche) for 30 min. Cells were filtered on 40-μm cell strainer (BD), washed using CO2 independent medium (Gibco) containing 0.4g/ml of human albumin and resuspended for cell counting.
T and B lymphocytes, NK cells, erythrocytes and myelomonocytic cells were depleted using monoclonal antibodies against: CD3, CD19, CD56, CD235a and CD15, respectively. Subsequently, cell suspensions were stained for 30 min with antibody-conjugated as the following: HLA-DR, CD11c, CD14, CD1c, CD304, CD1a, CD206, CD141. Around 1,000 cells of each DC subset were sorted by flow cytometry using BD FACS ARIA II cell sorter, (purity > 98%). Cells were centrifuged and lysed with TCL buffer (Qiagen) containing 1% of beta-mercaptoethanol before storage at -80°C. RNA were extracted and isolated using the Single Cell RNA purification kit (Norgen)  according to the manufacturer’s instructions and the RNA integrity number was evaluated with an Agilent RNA 6000 pico kit.

value: Breast cancer iLN

value: CD11c+HLADR+CD1a-CD1c-CD14+ cells


title: Human jejunum organoids 3

source_name: Jejunum organoids

value: Jejunum organoids


title: INFDC_4

value: CD11c+HLADR+CD1a-CD1c+CD14+ cells


title: 4Cseq_Bait2_SNU719_Rep3


title: E10 7/1

value: KO#2 (MSLN-, CRISPR/Cas9 deletion, monoclonal)


title: 4Cseq_Bait2_SNU719_Rep2


title: BDCA1_4

value: CD11c+HLADR+CD14-CD1a-CD206-CD1c+ cells


title: 4Cseq_Bait2_SNU719_Rep1


title: pDC_4

description:
PG_Bulk_Blood_raw_counts.csv
pDC-d4

value: CD123+CD45RA+AXL-Siglec6- cells


title: E10 6/24


title: INFDC_2


title: Human jejunum organoids 2


title: E10 6/20


title: E8 7/1

value: KO#1 (MSLN- CRISPR/Cas9 deletion, monoclonal)


title: Human duodenum organoids 3

source_name: Duodenum organoids

value: Duodenum organoids


title: E8 6/24


title: 4Cseq_Bait1_SNU719_Rep3


title: CD14_2


title: 4Cseq_Bait1_SNU719_Rep2


title: BDCA1_2


title: Human duodenum organoids 1


title: Human duodenum organoids 2


title: E10 711

source_name: IP tumor tissue

value: IP tumor tissue


title: 4Cseq_Bait2_MKN7_EBVi

value: EBV infected cell


title: INFDC_1


title: CD14_1


title: Human jejunum organoids 1


title: Human pylorus organoids 3

source_name: Stomach pylorus organoids

value: Stomach pylorus organoids


title: E10 707


title: Human pylorus organoids 2


title: E10 704


title: E10 702


title: BDCA1_1


title: Δsbp1 NaN3 treated Rep 2

city: Bangalore

first: Purusharth

middle: I

last: Rajyaguru

state: Karnataka

address: Lab No FE-16, Dept. of Biochemistry, IISc

department: Biochemistry

country: India

institute: Indian Institute of Science

data_processing:
The QC passed reads were mapped onto indexed Saccharomyces Cerevisiae reference genome (S288c) using STAR v2 aligner. The PCR and optical duplicates were marked and removed using Picard tools. Gene level expression values were obtained as read counts using featureCounts program. Differential expression analysis was carried out using edgeR package after normalizing the data based on trimmed mean of M (TMM) values. After normalization 248 features (3.76%) have been removed from the analysis because they did not have at least 1 counts-per-million in at least 2 samples.
UpSetR R package was used to generate plot showing overlapping significant genes between conditions.
Supplementary_files_format_and_content: txt files containing differential expression data

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown until OD600 0.4-0.5 in YEPD media followed by treatment with 0.5% Sodium azide for 30 minutes.

extract_protocol:
RNA was isolated using the hot-phenol method.
Library was prepared using NEB Next RNA II library preparation kit for Illumina (NEB). The library quality and quantity was checked used Bioanalyzer DNA 1000 kit (Agilent Technologies) and Qubit DNA HS kit (Thermo Fisher Scientific)

treatment_protocol: Cells were treated with 0.5% sodium azide for 30 minutes.

value: SBP1 deletion


title: Human pylorus organoids 1


title: Human corpus organoids 3

source_name: Stomach corpus organoids

value: Stomach corpus organoids


title: Δsbp1 NaN3 treated Rep 1


title: Δsbp1 untreated Rep 2


title: pDCs from Individual ME5

data_processing:
Sequence data was transformed and demultiplexed using the “UMIs” (unique molecular identifier) command line tool
expression levels of genes per cell were estimated using Kallisto with the GRCh38 gene set as reference
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-separated text files include normalized read counts for each cell barcode

source_name: pDC

extract_protocol:
Cells were encapsulated in droplets and analyzed using the ddSEQ™ Single-Cell Isolator (Biorad)
A total of 1200 cells were encapsulated in droplets and barcoded sequencing libraries were prepared using the ddSEQ™ Single-Cell Isolator (Biorad) and sequenced on an Illumina Hiseq 2500.

treatment_protocol: PDCs from two healthy blood donors (50 x 103cells/well) were stimulated with RNA-IC together with IFN-α2b (500 IU/ml) and IL-3 (1 ng/ml). Cell purity was >95% as determined by flow cytometry staining of BDCA2. After 6 h, cells were pooled and washed with cold phosphate buffered saline (PBS) and 0.1% human serum albumin.

tag: disease state

value: healthy


title: Human corpus organoids 1


title: Vec2 725


title: pDCs from Individual ME6


title: Δsbp1 untreated Rep 1


title: Human corpus organoids 2


title: Vec2 724


title: Vec2 723


title: E8 6/20

value: cells grown in culture


title: Δscd6 NaN3 treated Rep 1

value: SCD6 deletion


title: 4Cseq_Bait1_SNU719_Rep1

value: EBV(+) Gastric cancer cell line


title: Vec2 721

value: Mock (MSLN+, monoclonal)


title: ntp4-1-rep3

city: Shenzhen

first: Wenwen

last: Kong

state: Guangdong

address: 1066 Xueyuan Avenue, Nanshan District

department: College of Life Sciencesand Oceanography

institute: Shenzhen University

data_processing:
All the data were analized with the pipeline pRNASeqTools (https://github.com/grubbybio/pRNASeqTools).
Genome_build: Araport11 genome
Supplementary_files_format_and_content: Processed data were combined into excel file which contained all the RPM value from each sample.

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Plants were grown under long photoperiod conditions (16-h light/8-h dark; white light; light intensity, 120 mmol m22 s21) at 22°C.

extract_protocol:
Total RNAs were extracted from Arabidopsis inflorescence with TRIzol reagent (Ambion) and treated with DNase I (NEB).
Manufacturer of NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300)

treatment_protocol: No treatment

tag: ecotype


title: ntp4-1-rep2


title: E8713


title: E8714


title: Δscd6 untreated Rep 1


title: Δscd6 untreated Rep 2


title: ntp4-1-rep1


title: urt1-1-rep3


title: urt1-1-rep2


title: EB711


title: E8712


title: urt1-1-rep1


title: BY4741 untreated Rep 1

value: Wild type


title: Δscd6 NaN3 treated Rep 2


title: BY4741 NaN3 treated Rep 1


title: KLM737

value: Parent KLM1 human pancreatic line (MSLN+, polyclonal)


title: KLM736


title: heso1-1-rep1


title: heso1-1-rep3


title: BY4741 untreated Rep 2


title: KLM734


title: KLM740


title: hPBMCs_day0

data_processing:
Demultiplexing to generate fastq files has been done using cellranger mkfastq from Cellranger v.2.1.1.
Alignment, cell-calling and quality controls to generate count matrix have been done using cellranger count from Cellranger v.2.1.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx, genes.tsv, barcodes.tsv

source_name: Blood phagocytes

extract_protocol:
Total blood cells were submitted to ficool-gradient to obtain PBMCs. Subsequently, cells were further washed in PBS1X twice, stained with specific mAb and submitted to FACS-sorting. After sorting, cells were collected in PBS+0.04% BSA and counted before being submitted to 10x Genomics single-cell RNAseq protocol using 3'Reagents Kit as the following: Single cells were included and barcoded into droplets together with gel beads coated with unique barcodes, unique molecular identifiers (UMI), and poly(dT) sequences, followed by in droplet reverse transcription to generate barcoded full-length cDNA. cDNA was subsequently recovered from droplets, then cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific), then amplified with the following protocol: 98 C - 3 min; 12x (98 C - 15 s, 67 C - 20 s, 72 C - 1 min); held at 4 C. Amplified cDNA product was cleaned up using the SPRI select Reagent Kit (Beckman Coulter).
Indexed libraries were constructed following these steps: (1) fragmentation, end repair and A-tailing; (2) size selection with SPRI select beads; (3) adaptor ligation; (4) post-ligation cleanup with SPRI select beads; (5) sample index PCR and final cleanup with SPRI select beads. Library quantification and quality assessment were achieved using a dsDNA High Sensitivity Assay Kit and Bioanalyzer Agilent 2100 System. Indexed libraries were tested for quality, equimolarly pooled and sequenced on Illumina Novaseq 6000 S1 using paired-end 26x91bp as sequencing mode, targeting at least 50 000 reads per cell.
Libraries were prepared using a Single Cell 30 Reagent Kit (V2 chemistry, 10X Genomics) according to the manufacturer’s protocol

value: healthy donor

value: blood

value: CD11c+HLADR+CD1c+CD14+, CD11c+HLADR+CD1cnegCD14+ and CD11c+HLADR+CD1c+CD14neg cells


title: hPBMCs_mice_GM-CSFpos

data_processing:
Demultiplexing to generate fastq files has been done using cellranger mkfastq from Cellranger v.2.1.1.
Alignment, cell-calling and quality controls to generate count matrix have been done using cellranger count from Cellranger v.2.1.1. We used the parameter "--force-cells" to conserve the information of 300 cells.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx, genes.tsv, barcodes.tsv

source_name: Lung from humanized mice

extract_protocol:
PDX tumors were collected in CO2 independent medium (Gibco) within few hours after resection. Tissue were cut into small fragments and submitted to enzymatic digestion using 0.1 mg/ml of Liberase TL (Roche) and 0.1 mg/ml of DNase (Roche) for 30 min. Cells were filtered on 40-μm cell strainer (BD), washed using CO2 independent medium (Gibco) containing 0.4g/ml of human albumin and resuspended for cell counting. Cells were further washed in PBS and stained with specific mAb and submitted to FACS-sorting. After sorting, cells were collected in PBS+0.04% BSA and counted before being submitted to 10x Genomics single-cell RNAseq protocol using 3'Reagents Kit as the following: Single cells were included and barcoded into droplets together with gel beads coated with unique barcodes, unique molecular identifiers (UMI), and poly(dT) sequences, followed by in droplet reverse transcription to generate barcoded full-length cDNA. cDNA was subsequently recovered from droplets, then cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific), then amplified with the following protocol: 98 C - 3 min; 12x (98 C - 15 s, 67 C - 20 s, 72 C - 1 min); held at 4 C. Amplified cDNA product was cleaned up using the SPRI select Reagent Kit (Beckman Coulter).
Indexed libraries were constructed following these steps: (1) fragmentation, end repair and A-tailing; (2) size selection with SPRI select beads; (3) adaptor ligation; (4) post-ligation cleanup with SPRI select beads; (5) sample index PCR and final cleanup with SPRI select beads. Library quantification and quality assessment were achieved using a dsDNA High Sensitivity Assay Kit and Bioanalyzer Agilent 2100 System. Indexed libraries were tested for quality, equimolarly pooled and sequenced on Illumina Novaseq 6000 S1 using paired-end 26x91bp as sequencing mode, targeting at least 50 000 reads per cell.
Libraries were prepared using a Single Cell 30 Reagent Kit (V2 chemistry, 10X Genomics) according to the manufacturer’s protocol

value: lung from humanized mice


title: Col-0-rep3

value: wildtype


title: heso1-1-rep2


title: NIL_PRL5APO1_YP_3

city: Nagoya

first: Tokunori

last: Hobo

address: Furo-cho, Chikusa-ku

institute: Nagoya University

data_processing:
convert .bcl files to .fastq using bcl2fastq
mask bases with QV < 25 using original script
align reads to cDNA reference provided from IRGSP1using bowtie with options "--all --best --strata"
count reads using linux commands (sort and uniq)
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.csv

organism: Oryza sativa

source_name: Oryza sativa

extract_protocol:
RNA was extracted from young panicle as described by Sambrook et al. (Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning: a laboratory manual. Mol. cloning a Lab. manual. (1989).)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Young panicles

value: Prl5 and Pbl6 [APO1]


title: BY4741 NaN3 treated Rep 2


title: 1003_B23_Tumor

city: Auburn

middle: W

last: Greene

state: AL

address: 260 Lem Morrison Dr

department: Nutrition

institute: Auburn University

description: in vivo subcutaneously grown PDX CRC tumor, batch 23

data_processing:
Sequencing reads were aligned to the human GRCh38 reference genome and counted with STAR using aRNApipe, a RNA-seq analysis pipeline developed at the HusdonAlpha Institute for Biotechnology
Human mapped raw counts obtained from STAR were used for differential expression analysis with the R package DESeq2. False discovery rates (FDR) p value less than 0.05 were considered significantly differentially expressed and genes with log2 fold change greater than 1.5 were used for downstream gene set analyses.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file with htseq gene counts for each Sample.

source_name: PDX tumor

extract_protocol:
3D engineered CRC tissues and in vivo tumors were flash frozen in liquid nitrogen, and then stored at -80C.  RNA was isolated using RNeasy Plus Micro Kit (Qiagen). Illumina TruSeq RNA Stranded RNA Kit with Ribo-Zero Gold was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina NovaSeq protocols

tag: pdx model

value: In vivo

tag: crc stage

value: Stage II

tag: consensus molecular subtype

tag: batch

value: batch 23


title: 1003_B20_4614

description: in vivo subcutaneously grown PDX CRC tumor, batch 20

value: batch 20