title: HAIRM_DMSO_8_hrs_Rep_3

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: Cell line treated with DMSO for 8 hours, replicate 3

data_processing:
Illumina Casava 1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to HG38 whole genome using STAR v2.5.2b in "Gene_counts" mode
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each gene reported in gencode v22.

source_name: HAIR-M cell line

growth_protocol: Cell lines derived from HAIR-M were used. All media were supplemented with fetal bovine serum (10%), Penicillin-Streptomycin- Neomycin (~5,000 units penicillin, 5 mg streptomycin and 10 mg neomycin/mL, Sigma) and L-glutamine (1%). Cell identity was authenticated by short tandem repeat (STR) DNA profiling (IDEXX BioResearch, Ludwigsburg, Germany).

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We exposed the MZL cell line HAIR-M to DMSO or copanlisib (5nM, for 4, 8 and 12 h).

value: HAIR-M

value: DMSO

tag: time point

value: 8 hours

tag: replicate


title: W9_0.01_8hr_Rep3

status: Public on Mar 16 2020

type: SRA

city: Boston

first: Stephanie

middle: Sarah

last: Pavlovich

state: Massachusetts

address: 700 Albany St, W508D

department: Microbiology

country: USA

institute: Boston University School of Medicine

library_source: transcriptomic

data_processing:
Sequencing, base-calling, and de-multiplexing was done by Tufts Genomics Center
5’ adapter sequences were trimmed using cutadapt v1.5. Reads shorter than 50 bp were discarded
Trimmed reads were mapped to the Raegyp2.0 genome with hisat2 v2.1.0
Count tables of uniquely mapped reads were tabulated with HTSeq v0.6.1p1
Count tables were used for pairwise differential expression analysis with edgeR (v3.20.9) within the R environment (R version 3.4.3)
Genome_build: Raegyp2.0 genome (RefSeq accession: GCF_001466805.2)
Supplementary_files_format_and_content: tab-delimited text file with counts for each gene

molecule: polyA RNA

organism: Rousettus aegyptiacus

source_name: kidney

extract_protocol:
RNA was harvested in RNAzol RT and frozen at -80°C prior to extraction by pelleting out of DNA and proteins and then precipitation with isopropanol.
RNA libraries were prepared with the Illumina TruSeq® Stranded mRNA Library Prep kit. Pooled libraries underwent pippin size selection.

tag: cell type

value: kidney fibroblasts

tag: cell line

value: RoNi/7.1 cells

tag: tissue

value: kidney

tag: treatment

value: recombinant interferon omega9 0.01ng/mL for 8 hrs


title: W9_0.01_8hr_Rep2


title: 222C

city: San Francisco

first: Tatsuya

last: Tsukui

state: CA

address: 555 Mission Bay Blvd South, 282

department: Medicine

institute: UCSF

data_processing:
Demultiplex and basecall to fastq with cellranger mkfastq
Trimming of Read 2 for TSO and poly(A) with cutadapt
filtering, alligning, and barcode collapsing with zUMIs 2.0 (STAR 2.6.0 for alignment)
Cells filtered with > 12% of transcriptome from intron-spanning reads; < 20% mitochondrial origin; at least 1000 unique genes
ensembl gene IDs translated to HGNC only when a 1:1 translation was feasible using the R package biomaRt with the "Oct 2018" ensembl archive
All cells were removed that belonged to immune (PTPRC+), epithelial (EPCAM+) and entothelial populations (PECAM1+). Only collagen expressing mesenchymal cell populations remain
Genome_build: GRCh38 Release 91
Supplementary_files_format_and_content: RawCounts_triples.txt: Gene expression UMI counts of all intron and exon spanning transcripts. Data is a tab delimited text file in triples format. Three columns: "row" is the gene, "col" is the cell barcode, and "UMI_Counts" is the associated non-zero raw UMI count
Supplementary_files_format_and_content: Cell_MetaData.txt: MetaData to describe all 6,607 cells; including subject and  disease status. Each row represents a different cell barcode, columns are metadata including subject, library and disease status

molecule: total RNA

organism: Homo sapiens

source_name: Whole Lung Dissociate; Collagen expressing mesenchymal cells only

extract_protocol:
Thawed Cells were rinsed with 10% FBS; passed through 40 uM strainer
10X Genomics 3 prime v2

treatment_protocol: Enzymatic and Mechanical Digestion; Cryopreservation in 10% DMSO

tag: disease

value: Control

tag: Sex

value: M

tag: age


title: HAIRM_DMSO_8_hrs_Rep_2

description: Cell line treated with DMSO for 8 hours, replicate 2


title: 208C


title: W9_0.01_8hr_Rep1


title: HAIRM_DMSO_8_hrs_Rep_1

description: Cell line treated with DMSO for 8 hours, replicate 1


title: 388C


title: W4_100_8hr_Rep3

value: recombinant interferon omega4 100ng/mL for 8 hrs


title: W4_100_8hr_Rep2


title: HAIRM_DMSO_4_hrs_Rep_3

description: Cell line treated with DMSO for 4 hours, replicate 3

value: 4 hours


title: D1_1_8hr_Rep1

value: recombinant D1 peptide 1ng/mL for 8 hrs


title: HAIRM_DMSO_4_hrs_Rep_2

description: Cell line treated with DMSO for 4 hours, replicate 2


title: HAIRM_DMSO_4_hrs_Rep_1

description: Cell line treated with DMSO for 4 hours, replicate 1


title: Tot fraction of patient 276 (ME)

type: genomic

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL276-Tot

hyb_protocol: We used the EZ DNA Methylation kit (Zymo Research) for bisulfite conversion of 500 ng of genomic DNA obtained from at least 0.5 x 10e6 cells of each fractionated CLL sample. Further sample processing and hybridization was carried out according to Illumina's suggested guidelines.

scan_protocol: Arrays were imaged using iScan using standard manufacturer recommended scanner settings.

data_processing: The intensities of the images were extracted using GenomeStudio Methylation module software and processed in R/Bioconductor using the ‘ChAMP’ package and custom scripts. Briefly, we used default settings to filter out probes by detection p < 0.01 using the minfi method, discarded probes with < 3 beads in at least 5% of samples, performed BMIQ normalization to adjust for technical bias, followed by batch correction between slides using comBat from the ‘sva’ package, which resulted in improved correlation and tighter clustering of replicate samples. In addition, probes near SNPs and cross-hybridizing probes were removed using the rmSNPandCH function from the ‘DMRcate’ package. Only samples having Dim, Int, Br and Tot fractions and matching gene expression were used in the linked publication, the other samples were included in the normalization procedure, and the duplicate samples were used to assess performance of batch correction. We used limma to identify differentially methylated CpGs (DMC) using the M-values (logit-transformed beta-values) of the normalized, filtered methylation data.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: sorted CLL PBMCs

label_protocol: Methylation high-density profiling was carried out by using the Illumina Infinium HD Human Methylation 450K BeadChip according to manufacturer’s instructions.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were separated by Ficoll-Paque density gradient centrifugation from heparinized venous blood obtained 3 months before, during or 3 months after the 6 week 2H2O labeling period, and cryopreserved. Before sorting, CLL PBMCs were thawed and incubated with murine anti-human monoclonal antibodies CD5-PECy7, CXCR4-PE, and CD19-Pacific Blue (BD Biosciences). After gating on CD19+CD5+ cells, equal numbers of viable cells falling into proliferative (“Dim”; CXCR4DimCD5Bright), intermediate (“Int”, CXCR4IntCD5Int, IF), resting (“Br”; CXCR4BrightCD5Dim), or Dbr (CXCR4BrightCD5Bright) based on reciprocal densities of CXCR4 and CD5 (~5% of the clone for each fraction) were sorted with a BD FACSAria. After sorting, cells were washed, pelleted, and stored at -80º until DNA extraction was performed.

tag: patient

tag: fraction

value: Tot

tag: ighv

tag: birthrate (% cells/day)

value: sorted CLL PBMCs


title: DBr fraction of patient 276 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL276-Dbri

extract_protocol: We used the EZ DNA Methylation kit (Zymo Research) for bisulfite conversion of 500 ng of genomic DNA obtained from at least 0.5 x 10e6 cells of each fractionated CLL sample.

value: DBr


title: W4_1_8hr_Rep3

value: recombinant interferon omega4 1ng/mL for 8 hrs


title: Br fraction of patient 276 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL276-Br

value: Br


title: W4_1_8hr_Rep2


title: HAIRM_DMSO_12_hrs_Rep_2

description: Cell line treated with DMSO for 12 hours, replicate 2

value: HAIR-M

value: 12 hours


title: HAIRM_DMSO_12_hrs_Rep_3

description: Cell line treated with DMSO for 12 hours, replicate 3

value: DMSO


title: W4_1_8hr_Rep1

value: kidney fibroblasts


title: HAIRM_DMSO_12_hrs_Rep_1

description: Cell line treated with DMSO for 12 hours, replicate 1


title: DBr fraction of patient 1127 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1127-DBr


title: 244C


title: 296C

value: F


title: 396C


title: 226C


title: 098C


title: 465C


title: 218C


title: HAIRM_Copanlisib_8_hrs_Rep_3

description: Cell line treated with Copanlisib for 8 hours, replicate 3

value: Copanlisib

value: 8 hours


title: Dim fraction of patient 276 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL276-Dim

value: Dim


title: W4_0.01_8hr_Rep3

value: RoNi/7.1 cells

value: kidney

value: recombinant interferon omega4 0.01ng/mL for 8 hrs


title: HAIRM_Copanlisib_8_hrs_Rep_2

description: Cell line treated with Copanlisib for 8 hours, replicate 2


title: 034C

value: Control

value: M


title: Mouse  FIP200 knockout RAW macrophages ,  10^7 cells, no treatment

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

data_processing:
The qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume
Paired-end reads were directionally mapped to the genomic loci of mouse genome (GRCm38.p6) by TopHat2.
Cufflinks/Cuffdiff analysis was run to identify the dysregulated RNAs
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Gene expression file generated by cuffdiff analysis

organism: Mus musculus

source_name: FIP200 knockout RAW macrophages

extract_protocol:
Total RNA was isolated from  RAW macrophages by using Qiagen kit
Libraries were prepared with the Illumina mRNA Library Preparation kit. mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

value: macrophage cell line RAW24.7

tag: genotype

value: FIP200 knockout

value: untreated


title: Mouse  FIP200 knockout RAW macrophages , 10^7 cells, poly(I:C) for 6 h


title: Br fraction of patient 1127 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1127-Br

value: Br

value: sorted CLL PBMCs


title: 1372C


title: Tot fraction of patient 1127 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1127-Tot

value: Tot


title: W4_0.01_8hr_Rep2


title: W4_0.01_8hr_Rep1


title: 133C


title: HAIRM_Copanlisib_8_hrs_Rep_1

description: Cell line treated with Copanlisib for 8 hours, replicate 1

value: HAIR-M


title: HAIRM_Copanlisib_4_hrs_Rep_3

description: Cell line treated with Copanlisib for 4 hours, replicate 3

value: 4 hours


title: Mock_8hr_Rep3

value: kidney fibroblasts

value: RoNi media for 8 hrs


title: Mouse  RAW macrophages, 10^7 cells, poly(I:C) for 6 h

source_name: RAW macrophages

value: control


title: HAIRM_Copanlisib_4_hrs_Rep_2

description: Cell line treated with Copanlisib for 4 hours, replicate 2

value: Copanlisib


title: Mock_8hr_Rep2

value: RoNi/7.1 cells


title: Agrp_neurons_RNA_seq_Phf6_cKO-5_Fasted_condition

city: Shanghai

first: Qian

last: Li

address: 280 South Chongqing Road, Building No.5, Room 408

department: Department of Anatomy and Physiology

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
RNA-seq Reads were trimmed by Trimmomatic (version 0.36) and then aligned to the mouse reference genome (GRCm38/mm10, downloaded from UCSC, http://genome.ucsc.edu/) using Hisat2 (version 2.1.0).
Next, raw counts of genes were quantified using featureCounts from Subread package (version 1.6.2). Normalized counts were obtained by normalizing raw counts with size factors using the "median ratio method" in DESeq2 1.20.0 package.
Subsequent differentiated expressed gene analysis was performed using DESeq2 with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing raw counts and normalized counts obtained from DESeq2 package

source_name: Agrp neurons

growth_protocol: AGRP neurons were obtained by sorting tdTomato+ red fluorescent neurons from the hypothalamus of P25-P30 Phf6cKO mice (Phf6 flox/y; AgRP-Cre/+; Ai9/+) and Phf6WT mice (AgRP-Cre/+; Ai9/+) littermate mice.

extract_protocol:
Mice were sacrificed and around 1 mm3 hypothalamic tissue from each mouse was obtained with 1 mm-diatmeter micro punch in ice-cold dissection solution (1xHBSS with 10 mM HEPES and 23 mM D-glucose). Cell dissociation was conducted using Papain Dissociation System kit (Worthington-Biochem: #LK003150), and the cell dissociation procedure was conducted under the guidance of the kit.
1000 tdTomato+ AgRP neurons in 10 ml RNAseq lysis buffer with RNase inhibitor per sample were submitted for cDNA synthesis by using SMART-seq v4 Ultra Low Input RNA kit (Clontech). First-strand cDNA synthesis was primed by the 3’ SMART-Seq CDS Primer II A and used the SMART-Seq v4 oligonucleotide for template switching at the 5’ end of the transcript. cDNAs were amplified by LD PCR.  PCR II A amplified cDNA from the SMART sequences introduced by 3’ SMART-Seq CDS Primer II A and the SMART-Seq v4 oligonucleotide for 15 cycles. PCR-amplified cDNA was purified by immobilization on AMPure XP beads. The beads were then washed with 80% ethonal and cDNA is eluted with elution buffer. Amplified cDNAs were then validated using the Agilent 2100 Bioanalyzer and Agilent’s High Sensitivity DNA kit. 5 ng full-length cDNA output for next-generation sequencing was processed with the Nextera XT DNA library preparation kit (Illumina). Libraries were sequenced on the Illumina HiSeq X Ten.

treatment_protocol: For mice in overnight fasted condition, food deprivation was started from 5 pm the day before experiment, and only water was provided.

value: Agrp neurons

tag: strain

value: Phf6 cKO

tag: feeding condition

value: Fasted


title: Mouse RAW macrophages, 10^7 cells, no treatment


title: C-L20-1

city: Bellaterra

first: Blanca

last: San Segundo

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Plant Responses to Stress

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

data_processing:
Raw reads were checked for quality by using FastQC v0.11.3
Trimming and removal of adapters involved using Trimmomatic v0.33 (minimum quality score 35, minimum length 25).
The obtained reads were mapped against the Oryza sativa reference genome (MSU 7.0) by using STAR (v2.4.0j)
Alignment files were filtered to remove reads with mapping quality (MAPQ) <30. FeatureCounts (v1.4.5-p1)
Statistical analysis of read counts was performed with R, with the HTSFilter package to remove low-expressed genes and the edge R package
Genome_build: MSU 7.0
Supplementary_files_format_and_content: TXT

organism: Oryza sativa

source_name: miR399f overexpressing line L20

growth_protocol: Rice plants were grown at 28ºC with a 14 h/10 h light/dark cycle. The fungus M. oryzae was grown in Complete Media Agar (CMA, 9 cm plates, containing 30 mg/L chloramfenicol) for 15 days at 28ºC under a 16 h/8 h light/dark photoperiod condition.

extract_protocol:
Total RNA was extracted with the Maxwell 16 LEV Plant RNA Kit (Promega) following manufacturer's instructions.
Indexed libraries prepared from 1ug purified RNA with TruSeq Stranded mRNA Sample Prep Kit (Illumina). Samples pooled; each index-tagged sample present in equimolar amounts (final concentration of pooled samples at 2nm). Pooled samples subjected to cluster generation and sequencing using Illumina Hseq 2500. 2x100 paired-ennd at final concentration of 8pmol.

treatment_protocol: Soil-grown plants (3-4 leaf stage) were mock-inoculated or inoculated with M. oryzae spores for 48hours . Inoculation was done by spraying whole rice plants with a M. oryzae spore suspension (10E5 spores/ml; 0.2 ml/plant) by using an aerograph at 2 atmospheres of pressure

value: leaf

tag: rice cultivar

value: Tainung67 (japonica)


title: UIFN_4hr_Rep3

value: kidney

value: Universal interferon for 4 hrs


title: C-L20-2


title: Int fraction of patient 1127 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1127-Int

value: Int

value: M


title: Tot fraction of patient 1026 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1026-Tot

value: Tot

value: F

value: sorted CLL PBMCs


title: HAIRM_Copanlisib_12_hrs_Rep_3

description: Cell line treated with Copanlisib for 12 hours, replicate 3

value: HAIR-M

tag: time point

value: 12 hours


title: Agrp_neurons_RNA_seq_Phf6_cKO-3_Fasted_condition


title: Mock_8hr_Rep1

value: kidney fibroblasts

value: RoNi media for 8 hrs


title: C-L4-1

source_name: miR399f overexpressing line L4


title: UIFN_4hr_Rep2

value: RoNi/7.1 cells


title: HAIRM_Copanlisib_4_hrs_Rep_1

description: Cell line treated with Copanlisib for 4 hours, replicate 1

value: Copanlisib

value: 4 hours

tag: replicate


title: Agrp_neurons_RNA_seq_Phf6_cKO-4_Fasted_condition

tag: cell type

value: Agrp neurons

value: Phf6 cKO

value: Fasted


title: Tot fraction of patient 1039 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1039-Tot


title: Br fraction of patient 1078 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1078-Br

value: Br

value: U


title: W4_100_8hr_Rep1

tag: cell line

value: kidney

value: recombinant interferon omega4 100ng/mL for 8 hrs


title: Tot fraction of patient 1078 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1078-Tot

value: Tot


title: C-L4-2

tag: tissue

value: leaf

value: Tainung67 (japonica)


title: Int fraction of patient 1039 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1039-Int

value: Int

value: M

value: F

value: sorted CLL PBMCs


title: Agrp_neurons_RNA_seq_Phf6_cKO-2_Fasted_condition


title: UIFN_4hr_Rep1

value: kidney fibroblasts

value: RoNi/7.1 cells

tag: treatment

value: Universal interferon for 4 hrs


title: HAIRM_Copanlisib_12_hrs_Rep-1

description: Cell line treated with Copanlisib for 12 hours, replicate 1

value: HAIR-M

value: Copanlisib

value: 12 hours


title: D1_100_4hr_Rep3

value: recombinant D1 peptide 100ng/mL for 4 hrs


title: C-WT-2

source_name: Wild-type Rice


title: D1_100_4hr_Rep2


title: Gradient_f21

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

country: Germany

institute: Philipps-Universität Marburg

description: Glycerol gradient, fraction 21

data_processing:
RTA version 1.18.66.4 was used for basecalling
bcl2fastq version 1.8.4. was used for demultiplexing
Reads were mapped using the CLC genomics workbench version 10.01 and the GRCh38 human genome annotation with standard settings: mismatch cost = 2; insertion cost = 3; deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8.
RPKMs were calculated based on uniqely mapped read numbers reported by the CLC genomics worbench version 10.01
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text-files including ENSEMBL gene ID, gene alias, chromosome, genomic position, unique gene reads, RPKM (samples Gradient_f1-f22: spike-in normalized RPKMs)

source_name: Peripheral blood leukocytes

growth_protocol: peripheral blood derived CD14+ monocytes (MACS enrichement) were differentiated in cell culture plastic multi-well plates (4*10e5 cell per 12-well, 1 ml of medium per well) using X-Vivo-15 medium supplemented with 5 % FCS and 20 ng / ml of recombinant human GM-CSF for 8 days

extract_protocol:
Cells were washed once with PBS and RNA was extracted with Trizol. For subcellular fractionation cells were lysed with mild detergent buffer and nuclei and cytosol were seperated by centrifugation at low speed. Cytosol was cleared from remaining nuclei by high speed centrifugation and nuclear fraction was carefully washed twice with mild detergent buffer before RNA-Extraction with Trizol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit according to the manufacturer's protocol or an in-house total RNA strand-specific library protocol from Vertis Biotech AG (Freising, Germany)

treatment_protocol: cells were stimulated with Escherichia coli LPS at a concentration of 100 ng / ml for 8 h. Samples 1-8: Cells were pre-incubated with DMSO or inhibitors for 2 h prior to LPS-stimulation

value: D8 GM-CSF macrophage

tag: precursor

value: CD14+ monocyte

tag: donor

value: healthy, caucasian

tag: agent

value: Glycerol gradient, fraction 21


title: Agrp_neurons_RNA_seq_Phf6_cKO-1_Fasted_condition

value: Agrp neurons

tag: age

value: Phf6 cKO

value: Fasted


title: Gradient_f22

description: Glycerol gradient, fraction 22

value: Glycerol gradient, fraction 22


title: Int fraction of patient 1026 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1026-Int

tag: patient

tag: fraction

value: Int

value: M

tag: Sex

value: F


title: DBr fraction of patient 1039 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1039-DBr

value: DBr

tag: ighv

tag: birthrate (% cells/day)

value: sorted CLL PBMCs


title: Dim fraction of patient 1127 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1127-Dim

value: Dim


title: Dim fraction of patient 1039 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1039-Dim


title: Agrp_neurons_RNA_seq_WT-5_Fasted_condition

tag: strain

tag: genotype

value: wild type

tag: feeding condition


title: Br fraction of patient 1026 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1026-Br

value: Br


title: Fertilized egg ATAC-Seq at SRPK1 knock-down condition replicate2

city: San Diego

first: Yajing

last: Hao

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

library_source: genomic

data_processing:
Clean reads were mapped to the reference Mus musculus genome (mm10) using Bowtie2.
Enriched peaks were detected by MACS2 with input data as control using the parameters -f BAMPE --nomodel --broad -g mm.
The wig files of each chromatin mark ChIP-seq dataset was obtained by using bamCoverage tools from Deeptools with the parameters: --binSize 100 --normalizeUsing RPKM --smoothLength 1000 --extendReads --ignoreDuplicates and --ignoreForNormalization chrM.
Genome_build: mm10

source_name: Fertilized egg

extract_protocol: After removing the zona pellucida, fertilized eggs were washed with PBS. ATAC-seq libraries were generated using omni-ATAC-seq developed by Corces et al. with some modifications. Briefly, fertilized zygotes were incubated in cold resuspension buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, and 3 mM MgCl2) containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin on ice for 3 min and then washed with cold resuspension buffer containing 0.1% Tween-20. Tagmentation was next performed with Tn5 transposon enzyme (Illumina) in tagmentation buffer (20 mM Tris-Cl pH 7.4, 10 mM MgCl2, 20% dimethyl foramide, 0.1% Tween-20, and 0.01% digitonin) for 30 min at 37°C in a thermomixer with shaking at 1,000 rpm. Tagmentated DNA was purified using DNA Clean & Concentrator-5 Kit (Zymo Research). PCR was performed to amplify each library for 14 cycles.

treatment_protocol: Sperm were harvested from caudal epididymides in the BALB/cJ background. MII oocytes for insemination were obtained through an in vitro culture of growing oocytes(isolated from C57BL/6 females), which were injected with SRPK1 siRNA or Control siRNA.  Five hours post insemination, fertilized eggs (confirmed by pronucleus formation under microscope) were harvested for ATAC-seq

value: C57BL/6 (female)  x BALB/cJ (male)

tag: passages

value: 1-cell (5 h post insemination, between pronucleus (PN) stage II and early stage III)

value: SRPK1 knock-down


title: Fertilized egg ATAC-Seq at SRPK1 knock-down condition replicate1


title: HAIRM_Copanlisib_12_hrs_Rep_2

description: Cell line treated with Copanlisib for 12 hours, replicate 2

value: HAIR-M

value: Copanlisib

tag: time point

value: 12 hours

tag: replicate


title: DBr fraction of patient 1026 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1026-DBr

tag: cell type


title: Dim fraction of patient 1026 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1026-Dim


title: D1_1_4hr_Rep3

value: kidney fibroblasts

tag: cell line

value: RoNi/7.1 cells

tag: tissue

value: kidney

tag: treatment

value: recombinant D1 peptide 1ng/mL for 4 hrs


title: D1_100_4hr_Rep1

value: recombinant D1 peptide 100ng/mL for 4 hrs


title: Gradient_f20

description: Glycerol gradient, fraction 20

value: D8 GM-CSF macrophage

tag: precursor

value: CD14+ monocyte

tag: donor

value: healthy, caucasian

tag: agent

value: Glycerol gradient, fraction 20


title: Int fraction of patient 276 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL276-Int

tag: patient

tag: fraction

value: Int

value: M

value: sorted CLL PBMCs


title: Agrp_neurons_RNA_seq_WT-3_Fasted_condition

value: Agrp neurons

tag: age

value: wild type

value: Fasted


title: Fertilized egg ATAC-Seq at wild-type condition replicate2_1

value: C57BL/6 (female)  x BALB/cJ (male)

value: 1-cell (5 h post insemination, between pronucleus (PN) stage II and early stage III)

value: wild-type


title: Fertilized egg ATAC-Seq at wild-type condition replicate1_1


title: Agrp_neurons_RNA_seq_WT-2_Fasted_condition


title: Gradient_f18

description: Glycerol gradient, fraction 18

value: Glycerol gradient, fraction 18


title: Br fraction of patient 1039 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL1039-Br

value: Br

tag: ighv

tag: Sex

value: F

tag: birthrate (% cells/day)


title: Gradient_f19

description: Glycerol gradient, fraction 19

value: Glycerol gradient, fraction 19


title: Agrp_neurons_RNA_seq_WT-1_Fasted_condition

tag: strain

tag: genotype

tag: feeding condition


title: Fertilized egg ATAC-Seq at Double Mutation condition replicate2

data_processing:
Clean reads were mapped to the reference Mus musculus genome (mm10) using Bowtie2.
Enriched peaks were detected by MACS2 with input data as control using the parameters -f BAMPE --nomodel --broad -g mm.
The wig files of each chromatin mark ChIP-seq dataset was obtained by using bamCoverage tools from Deeptools with the parameters: --binSize 100 --normalizeUsing RPKM --smoothLength 1000 --extendReads --ignoreDuplicates and --ignoreForNormalization chrM.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

treatment_protocol: Sperm were harvested from caudal epididymides of wild-type or knock-in male mice in the C57BL/6 background. MII oocytes for insemination were isolated from superovulated BALB/cJ females. Five hours post insemination, fertilized eggs (confirmed by pronucleus formation under microscope) were harvested for ATAC-seq

value: C57BL/6 (male)  x BALB/cJ (female)

value: Double Mutation condition

value: fertilized egg (1-cell (5 h post insemination, between pronucleus (PN) stage II and early stage III))


title: D1_1_4hr_Rep2

value: kidney fibroblasts

value: RoNi/7.1 cells

value: kidney

value: recombinant D1 peptide 1ng/mL for 4 hrs


title: Agrp_neurons_RNA_seq_Phf6_cKO-5_Fed_condition

value: Agrp neurons

value: Phf6 cKO

value: Fed


title: Gradient_f17

description: Glycerol gradient, fraction 17

value: D8 GM-CSF macrophage

value: CD14+ monocyte

value: healthy, caucasian

value: Glycerol gradient, fraction 17


title: Fertilized egg ATAC-Seq at S43A condition replicate2

value: S43A condition


title: D1_0.01_4hr_Rep3

value: recombinant D1 peptide 0.01ng/mL for 4 hrs


title: D1_1_4hr_Rep1


title: Gradient_f16

description: Glycerol gradient, fraction 16

value: Glycerol gradient, fraction 16


title: Fertilized egg ATAC-Seq at S9A condition replicate2

value: C57BL/6 (male)  x BALB/cJ (female)

value: S9A condition


title: Agrp_neurons_RNA_seq_Phf6_cKO-3_Fed_condition


title: D1_0.01_4hr_Rep2


title: Gradient_f15

description: Glycerol gradient, fraction 15

value: Glycerol gradient, fraction 15


title: Fertilized egg ATAC-Seq at wild-type condition replicate2

value: wild-type condition

value: fertilized egg (1-cell (5 h post insemination, between pronucleus (PN) stage II and early stage III))


title: Gradient_f14

description: Glycerol gradient, fraction 14

value: Glycerol gradient, fraction 14


title: Fertilized egg ATAC-Seq at Double Mutation condition replicate1

value: Double Mutation condition


title: Gradient_f13

description: Glycerol gradient, fraction 13

value: Glycerol gradient, fraction 13


title: Agrp_neurons_RNA_seq_Phf6_cKO-1_Fed_condition

value: Agrp neurons

value: Phf6 cKO


title: Agrp_neurons_RNA_seq_WT-5_Fed_condition

value: wild type

value: Fed


title: W9_100_4hr_Rep3

value: kidney fibroblasts

value: RoNi/7.1 cells

value: kidney

value: recombinant interferon omega9 100ng/mL for 4 hrs


title: Fertilized egg ATAC-Seq at S43A condition replicate1

value: S43A condition


title: Agrp_neurons_RNA_seq_Phf6_cKO-2_Fed_condition


title: W9_100_4hr_Rep2


title: Fertilized egg ATAC-Seq at S9A condition replicate1

value: C57BL/6 (male)  x BALB/cJ (female)


title: Fertilized egg ATAC-Seq at wild-type condition replicate1


title: W9_100_4hr_Rep1


title: Agrp_neurons_RNA_seq_WT-4_Fed_condition


title: Gradient_f11

description: Glycerol gradient, fraction 11

value: D8 GM-CSF macrophage

value: CD14+ monocyte

value: healthy, caucasian

value: Glycerol gradient, fraction 11


title: Agrp_neurons_RNA_seq_Phf6_cKO-4_Fed_condition


title: W9_1_4hr_Rep3

value: recombinant interferon omega9 1ng/mL for 4 hrs


title: Sperm ATAC-Seq at Double Mutation condition

source_name: Sperm

extract_protocol: ATAC-seq libraries were generated using omni-ATAC-seq developed by Corces et al. with some modifications. Briefly, sperms were incubated in cold resuspension buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, and 3 mM MgCl2) containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin on ice for 3 min and then washed with cold resuspension buffer containing 0.1% Tween-20. Tagmentation was next performed with Tn5 transposon enzyme (Illumina) in tagmentation buffer (20 mM Tris-Cl pH 7.4, 10 mM MgCl2, 20% dimethyl foramide, 0.1% Tween-20, and 0.01% digitonin) for 30 min at 37°C in a thermomixer with shaking at 1,000 rpm. Tagmentated DNA was purified using DNA Clean & Concentrator-5 Kit (Zymo Research). PCR was performed to amplify each library for 14 cycles.

value: Double Mutation condition

value: sperm


title: Agrp_neurons_RNA_seq_WT-3_Fed_condition

value: Agrp neurons


title: Gradient_f9

description: Glycerol gradient, fraction 9

value: Glycerol gradient, fraction 9


title: Agrp_neurons_RNA_seq_WT-2_Fed_condition

value: wild type


title: Gradient_f10

description: Glycerol gradient, fraction 10

value: Glycerol gradient, fraction 10


title: W9_1_4hr_Rep1

value: kidney fibroblasts


title: Sperm ATAC-Seq at S43A condition


title: Gradient_f12

description: Glycerol gradient, fraction 12

value: Glycerol gradient, fraction 12


title: Gradient_f8

description: Glycerol gradient, fraction 8

value: Glycerol gradient, fraction 8


title: Sperm ATAC-Seq at S9A condition

value: S9A condition


title: W9_0.01_4hr_Rep3

value: RoNi/7.1 cells

value: kidney

value: recombinant interferon omega9 0.01ng/mL for 4 hrs


title: Gradient_f7

description: Glycerol gradient, fraction 7

value: D8 GM-CSF macrophage

value: CD14+ monocyte

value: Glycerol gradient, fraction 7


title: Sham heart 3

city: Nottingham

first: Chrysostomos

last: Perdios

state: Nottinghamshire

address: Queen's Medical Centre, Derby Road

department: Medical School

country: United Kingdom

institute: The University of Nottingham

data_processing:
Base-calling done with cl2fastq, Illumina standard processing
Compressed FASTQ files were trimmed to filter reads for adapter and low quality bases, then mapped to galGal4 reference genome using Tophat (https://ccb.jhu.edu/ software/tophat/index.shtml) to known gene exon coordinates
Alignment counts were recorded in BAM format with only uniquely mapped read alignment hits (47-90 x 106) having a quality score of MAPQ ≥ 20 used. Htseq-count was used for generation of count tables.
Read counts were then normalised using FPKM.Genes with average FPKM values <1 were filtered from the FPKM data before gene regulation was assessed using DESeq adjusted p-values (FDRs).
Genome_build: galGal4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample...

organism: Gallus gallus

source_name: Heart

extract_protocol:
Hearts were removed, flash frozen in liqid nitrogen, and RNA was harvested using Trizol reagent. NEBNext Ultra directional RNA library Prep Kit for Illumina (NEB#E7420S/L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols for paired end sequencing

value: Heart

tag: sample type

value: sham


title: D1_0.01_4hr_Rep1

tag: cell type

value: recombinant D1 peptide 0.01ng/mL for 4 hrs


title: Agrp_neurons_RNA_seq_WT-1_Fed_condition

value: Agrp neurons

value: Fed


title: W9_0.01_4hr_Rep2

tag: cell line


title: Gradient_f6

description: Glycerol gradient, fraction 6

value: healthy, caucasian

value: Glycerol gradient, fraction 6


title: W9_0.01_4hr_Rep1

value: kidney fibroblasts

tag: tissue


title: Gradient_f5

description: Glycerol gradient, fraction 5

value: Glycerol gradient, fraction 5


title: Sham heart 2


title: B16_3

city: BeiJing

first: Yidong

last: Chen

address: Yiheyuan Road

institute: Peking University

data_processing:
All RNA-seq raw data were first to remove Illumina adaptor sequences, amplification primer, polyA tail sequences and reads of low-quality bases (N>10%). Then, the processed sequences were aligned to the mm9 mouse reference genome (UCSC) using TopHat (version 2.0.12). Subsequently, the expression level of each gene was calculated using cufflinks (version 2.2.1). Expression levels of each gene were converted to log2 (fpkm+1) for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: txt files which include the FPKM values of RefSeq genes.

source_name: Mouse Lymphatic Endothelial Cells

growth_protocol: Using a 30-gauge Hamilton syringe, 1× 105 GL261 or B16 cells in a volume of 5µL PBS were injected into CSF-filled cisterna magna of mice aged 7-8 weeks, and same volume of PBS was injected as control. Mice bearing with GL261 were sacrificed after ~3 weeks, and mice bearing with B16 were sacrificed after ~2 weeks for meningeal lymphatic endothelial cells collection.

extract_protocol:
Smart-seq2 protocol was applied. After 10 lymphatic endothelial cells were placed into the lysis buffer by mouth pipette, in reverse transcription reaction, a poly(T) tail was added to the 5’ end of the first-strand cDNAs.
After the first-strand reaction, the cDNAs were amplified by 18 cycles for the library construction. The amplified cDNA was fragmented to approximately 300bp by Covaris S2, and KAPA Hyper Prep Kit was used to generate sequence libraries. Paired-end 150 bp sequencing was further performed on an Illumina HiSeq 4000 platform (sequenced by Novogene).

treatment_protocol: Briefly, isolated meninges were incubated in Ca2+-PBS containing 0.2% type I and 0.2% type II collagenase at 37℃ for 45 min (n = 3 biological replicates per group, each pooled from 6 individual mice). At the end of incubation, the tissue fragments were passed through 70-μm nylon mesh cell strainers after neutralization with 10% FBS DMEM. The cells were then centrifuged at 2000 rpm at 4℃ for 10 min, the supernatant was removed, and the cells were re-suspended in ice-cold FACS solution (pH 7.4, 0.1 M PBS, 1 mM EDTA, 1% BSA). Further, cells were stained with CD31-PE-CY7, CD45-FITC, LYVE-1-eFluor 660 and fixable viability stain 510. After washing twice with PBS containing 1% BSA, cells were analyzed and sorted by flow cytometry. After FACS purification, 10 lymphatic endothelial cells were placed into the lysis buffer by mouth pipette.

tag: gender

value: male


title: Gradient_f4

description: Glycerol gradient, fraction 4

tag: precursor

value: Glycerol gradient, fraction 4


title: Sham heart 1


title: W4_100_4hr_Rep3

value: RoNi/7.1 cells

tag: treatment

value: recombinant interferon omega4 100ng/mL for 4 hrs


title: W9_1_4hr_Rep2

value: kidney

value: recombinant interferon omega9 1ng/mL for 4 hrs


title: B16_2


title: OFT-banded heart 3

value: outflow tract


title: C-WT-1

value: leaf

tag: rice cultivar

value: Tainung67 (japonica)


title: Gradient_f3

description: Glycerol gradient, fraction 3

value: D8 GM-CSF macrophage

value: CD14+ monocyte

tag: donor

tag: agent

value: Glycerol gradient, fraction 3


title: OFT-banded heart 2

value: Heart

tag: age


title: W4_100_4hr_Rep2


title: GL261_3


title: Gradient_f2

description: Glycerol gradient, fraction 2

value: healthy, caucasian

value: Glycerol gradient, fraction 2


title: W4_100_4hr_Rep1

value: kidney fibroblasts


title: OFT-banded heart 1


title: Sperm ATAC-Seq at wild-type condition

value: wild-type condition

value: sperm


title: GL261_2

value: male


title: I-L20-2

organism:
Oryza sativa
Pyricularia oryzae

source_name: miR399f overexpressing line L20 infected with Magnaporthe oryzae 48 hpi

tag: m. oryzae strain


title: W4_1_4hr_Rep3

value: RoNi/7.1 cells

value: recombinant interferon omega4 1ng/mL for 4 hrs


title: GL261_1


title: Agrp_neurons_RNA_seq_WT-4_Fasted_condition

value: Agrp neurons

value: wild type

value: Fasted


title: I-L20-1

value: leaf


title: IRBB5-0h

city: Beijing

first: yanfeng

last: jia

address: Beijing Beijing Chaoyang District Beichen West Road

institute: Institute of genetics and developmental biology, Chinese academy of science

data_processing:
By removing adaptor sequences and low quality reads, clean reads aligned to Oryza sativa transcriptome data were applied to identify potentially cleaved targets and categorized by CleaveL and 3.0 pipeline.
The target genes corresponding to miRNAs were further deepen by overlapping the mRNA predicted by Targetfinder software.
According to peak classification and value of sliced target sites, T-plot ﬁgures were built to analyze the reliability of the potential miRNA targets.
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/Oryza_sativa_Japonica_Group/

organism: Oryza sativa Japonica Group

source_name: Leaves

growth_protocol: The Indica rice (Oryza sativa L.) cultivars, IR24 and IRBB5, were cultivated in the experimental fields in Beijing

extract_protocol:
Two degradome libraries, IRBB5-D (including IRBB5-0 h, IRBB5-8 h and IRBB5-24 h) and IR24-D (including IR24-0 h, IR24-8 h and IR24-24 h), were generated with some modification from previously described (Addo-Quaye et al., 2008).
Briefly, 5′RNA adapters were ligated to the 5′-phosphate of degraded mRNA fragments enriched by oligo d(T) magnetic beads, then reverse transcription were achieved with purified ligated products and biotinylated random primers. The libraries were completed via PCR-based amplification and sequenced using the Illumina HiSeq 2000/2500.

treatment_protocol: Leaves were inoculated with Xoo strain PXO86 at the tillering stage by the leaf-clipping method. And leaf tissues loci were collected at 0, 8, 24 hpi, respectively.

tag: cultivar

value: Leaf

tag: Stage

value: at the tillering stage


title: Gradient_f1

description: Glycerol gradient, fraction 1

value: D8 GM-CSF macrophage

value: CD14+ monocyte

value: Glycerol gradient, fraction 1


title: W4_1_4hr_Rep2

value: kidney


title: Control_3

value: control


title: I-L4-2

source_name: miR399f overexpressing line L4 infected with Magnaporthe oryzae 48 hpi

value: Tainung67 (japonica)


title: W4_1_4hr_Rep1

source_name: kidney

value: kidney fibroblasts


title: Control_2


title: B16_1


title: Control_1


title: osnrpd1ab_base_sRNA180209_rep3

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

data_processing:
For whole-genome bisulfite sequencing, reads were mapped and analyzed with BRAT-BW (Harris et al., 2012). For small RNA sequencing, reads were mapped with Bowtie and analyzed by in-house PERL scripts. For RNA sequencing, reads were mapped with Tophat and differentially expressed genes were identified with DESeq2.
Genome_build: RGAP7
Supplementary_files_format_and_content: bigwig for whole-genome bisulfite sequencing; expression matrix for RNA sequencing; raw read counts for small RNA sequencing

source_name: shoot base of seedling

growth_protocol: Seedlings of WT and transgenic lines were grown in the green chambers at 70% humidity, under conditions with daily cycles of 12 h of light at 30 °C and 12 h of dark at 25 °C.

extract_protocol:
For whole-genome bisulfite sequencing, genomic DNA was purified from the shoot base of 4-week-old seedlings using the DNeasy Plant Mini Kit (QIAGEN, 69104). For RNA sequencing, total RNA was purified from the shoot base of 4-week-old seedlings using the RNeasy Plant Mini Kit (QIAGEN, 74904). For small RNA sequencing, total RNA was purified from the shoot base of 4-week-old seedlings using TRIzol reagent (Invitrogen, 15596026). Large RNAs were selectively precipitated using 5% PEG8000 (Sigma, P5413) and 0.5 M NaCl (Sigma, S3014). Small RNAs were recovered from the supernatant by ethanol precipitation and then separated by electrophoresis using a 15% denaturing PAGE gel.
Paired-end bisulfite sequencing libraries were generated using the NEXTflex Bisulfite-Seq kit (BIOO SCIENTIFIC, NOVA-511911). Briefly, genomic DNA was sonicated to ~300 bp, end repaired and 3’ adenylated. The products were ligated with methylated adapters and then subject to size selection using Ampure XP purification beads (Beckman, A63881). Bisulfite treatment was carried out using the EZ DNA Methylation-Gold kit (ZYMO Research, D5005) according to the manufacturer’s instructions. Bisulfite-converted DNA products were amplified by PCR for 15 cycles using EX Taq DNA polymerase (Takara, RR001C). The PCR products were cleaned up using Ampure XP purification beads (Beckman, A63881). The constructed libraries were validated using the Agilent 2100 Bioanalyzer and paired-end sequenced in 150-bp on an Illumina X-Ten platform. Libraries for RNA sequencing were generated using NEXTflex RNA-Seq Kit (Bioo Scientific) according to the manufacturer’s instructions. Libraries for small RNA sequencing were generated using NEBNext Small RNA Library Prep Set for Illumina (NEB).

value: shoot base

tag: substrate

value: nutrient soil


title: W4_0.01_4hr_Rep3

value: RoNi/7.1 cells

value: recombinant interferon omega4 0.01ng/mL for 4 hrs


title: IR24-0h


title: osnrpd1ab_base_sRNA180209_rep2


title: I-L4-1


title: W4_0.01_4hr_Rep2


title: Wild-type Rep2 (MethylC-seq)

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
HZ10089
Total DNA from inhibitory neurons sorted from the striatum of a male wild-type mouse

data_processing:
Adaptor sequences were trimmed from sequencing reads using Cutadapt 1.11 with parameters -f fastq -q 20 m 50 -a AGATCGGAAGAGCACACGTCTGAAC -A AGATCGGAAGAGCGTCGTGTAGGGA. We further trimmed 10 bp from both 5’- and 3’- ends of both R1 and R2 reads with parameters -f fastq -u 10 u −10 m 30. Trimmed R1 and R2 reads were mapped to the mm10 reference genome as single-end reads using bismark 0.14.4 with parameter --bowtie2. --pbat option was used for mapping R1 reads. Mapped reads were sorted using Samtools 1.3 followed by removing duplicate reads using Picard 1.141 MarkDuplicates with parameter REMOVE_DUPLICATES = true. Reads were further filtered by MAPQ > 20 using samtools view with parameter -bhq20. Methylation level at each cytosine was summarized using call_methylated_sites from Methylpy package (https://github.com/yupenghe/methylpy/).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)

source_name: Wild-type mouse #2

growth_protocol: standard animal house conditions

extract_protocol:
DNeasy Blood & Tissue Kit from Qiagen
Modified snmC-seq method adapted for bulk DNA samples

value: male

tag: strain

value: whole striatum

value: inhibitory neurons

tag: genotype

value: R26-CAG-LSL-sfGFP-Myc+/-; Viaat-Cre+/-


title: I-WT-2

source_name: Wild-type Rice infected with Magnaporthe oryzae 48 hpi

value: leaf


title: I-WT-1


title: W4_0.01_4hr_Rep1


title: osnrpd1ab_base_sRNA180209_rep1


title: Mock_4hr_Rep3

value: RoNi media for 4 hrs


title: WT_base_sRNA180209_rep3


title: Wild-type Rep1 (MethylC-seq)

description:
HZ10088
Total DNA from inhibitory neurons sorted from the striatum of a male wild-type mouse

source_name: Wild-type mouse #1


title: Mock_4hr_Rep2


title: Dnmt3a cKO Rep2 (MethylC-seq)

description:
HZ10085
Total DNA from inhibitory neurons sorted from the striatum of a male Dnmt3a cKO mouse

source_name: Dnmt3a cKO mouse #2


title: IRBB5_24h_3

data_processing:
Raw reads were processed into clean reads by trimming adapter sequence and the low-quality reads.
Then, clean reads were classified by aligning to rice genome(http://rise2.genomics.org.cn/page/rice/download.jsp) and non-coding RNA(http://rfam.janelia.org) using AASRA and cmsearch software, respectively.
Reads  matching mature miRNA sequence in the miRBase Database (v20.0) were identiﬁed as known miRNAs, and novel miRNAs were predicted using ‘MIREAP’(https://sourceforge.net/projects/mireap/) in terms of the characteristic fold-back structure (Blake et al., 2008), and other small non-coding RNAs were also sorted out with related database.
MiRNAs with at least 20 M clean reads in three biological replicates were chosen to perform expression analysis, and the expression levels were quantified using the mean value. The criterion of DE miRNAs was set as |log2(fold change ratio)| ≥1.5.
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/Oryza_sativa_Japonica_Group/
Supplementary_files_format_and_content: abundance measurements

extract_protocol:
Every sample was pooled with infected leaves collected from twenty plants in one plot to diminish the individual environment differences.Total RNA were extracted from the mentioned samples using Trizol reagent (Invitrogen, USA) according to the manufacturer’s recommendation.
Small RNAs with 18~30 nt in length were isolated from the total RNA using a polyacrylamide gel electrophoresis gel, and then were sequenced by the BGISEQ-500.

tag: developmental stage

value: at the tillering stage

tag: treatment/infection

value: Xoo strain PXO86 infection

tag: time point

value: 24 hpi

value: Leaf


title: IRBB5_24h_2

tag: tissue


title: Mock_4hr_Rep1

tag: cell type

tag: cell line

value: kidney


title: Dnmt3a cKO Rep1 (MethylC-seq)

description:
HZ10084
Total DNA from inhibitory neurons sorted from the striatum of a male Dnmt3a cKO mouse

source_name: Dnmt3a cKO mouse #1

tag: gender


title: MeCP2 cKO Rep2 (MethylC-seq)

description:
HZ10081
Total DNA from inhibitory neurons sorted from the striatum of a male MeCP2 cKO mouse

source_name: MeCP2 cKO mouse #2


title: WT_base_sRNA180209_rep1

tag: treatment


title: IRBB5_24h_1


title: IRBB5_8h_3

value: 8 hpi


title: mESC, UV5I

city: Boulder

first: Desmond

middle: J

last: Hamilton

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: CU Boulder

data_processing:
R1: biological read
R2: technical (umi) read
R3: biological read
Reads were aligned to mm10 genome using STAR, with the gene annotation obtained from GENCODE (vM16).
The unique molecular identifiers (UMIs) associated with uniquely-mapped reads were counted for genes in the annotation.
Genome_build: mm10
Supplementary_files_format_and_content: The provided text file includes the numbers of UMIs for every gene in every sample.

source_name: mESC

growth_protocol: Male mouse ESCs were maintained on 0.1% gelatin (EmbryoMax, ES-006-B) coated plates in mESC media (KnockOut DMEM (gibco), 12.6% FBS (EmbryoMax, ES-009-B), MEM non-essential amino acids, 1x (gibco), GlutaMAX supplement, 1x (gibco), Penicillin/streptomycin, 100.7 units/mL-100.7 ug/mL (gibco), 2-mercaptoethanol (gibco), 1000 U/mL LIF (ESGRO), PD0325901, 1 uM (sigma, PZ0162), and CHIR99021, 3 uM (sigma, SML1046)) to maintain pluripotency. Media was changed daily and passaged every 2-3 days.

extract_protocol:
Crosslinked cells were collected by scrapping, lysed by sonication, and Sox2-RNA complexes were immunoprecipated with magnetic beads. Sox2-RNA complexes were disrupted by reverase crosslinking and proteinase K treatment, RNA was isolated using Trizol, treated with DNAse, and purified with Qiagen Rneasy MinElute Cleanup kit.
The commerical kit (Kapa RNA HyperPrep with RiboErase, KK8560) was used with IDT xGen dual index UMI adaptors.
Ribosomal RNA was depleted followed by cDNA synthesis.

treatment_protocol: Either formaldehyde or UV was used to crosslink mESCs.

tag: Sex

tag: crosslinker

value: UV

tag: pulldown

value: Input

value: mESC


title: mESC, UV6B

value: IP


title: mESC, UV6I


title: Neutrophils, Control 6

city: Amsterdam

first: Evelien

last: Sprenkeler

address: Plesmanlaan 125

department: Department of Blood Cell Research

country: Netherlands

institute: Sanquin Research

data_processing:
The data were analyzed by the RNAseq plugin from the Torrent Suite software
The RNA output was analyzed in Rstudio 1.0.456/R version 3.5.3. using limma-voom
Moderated t-tests were performed taking into account biological and technical replicates;
Benjamini-Hochberg multiple comparison adjusted p <0.05 and a log fold change ≥1 was considered significant and relevant. The median of technical replicates per experimental condition were used for visualization in a heatmap using the Complexheatmap package
Genome_build: hg19
Supplementary_files_format_and_content: read counts

source_name: venous blood

extract_protocol:
Neutrophils were isolated by percoll gradient and 1-3 x 106 freshly purified neutrophils were suspended in RNAlater (RLT) lysis buffer. From this lysate RNA was purified using the QIAamp RNA Blood Mini Kit (Qiagen, Hilden, Germany).
cDNA was synthesized with SuperScript™ VILO™ cDNA Synthesis Kit (Thermofisher Scientific, Waltham, Massachusetts, USA) in an Ampliseq plate from the Ion AmpliSeq™ Kit for Chef DL8 (Thermofisher Scientific). The Ion AmpliSeq™ Transcriptome Human Gene Expression Panel, Chef Ready Kit (Thermofisher Scientific) was used to produce amplicons from 20,000 RefSeq genesLibrary preparation was done on the Ion Chef sytem (Thermofisher Scientific) . Libraries were sequenced on the Genestudio S5 (Thermofisher Scientific).
Targeted RNA-seq

value: neutrophil

value: control


title: miR-483 mimic 1

city: Xi'an

first: Jin

last: Zhang

state: Shaanxi

address: Yanta West Road No.76

institute: Xi'an Jiaotong University

data_processing:
Basecalling were performed using Illumina Casava1.7 software.
Raw sequencing data (reads) in fastq format were processed with custom made perl scripts that removed reads containing adaptor poly-N and low-quality sequences.
Clean data were then mapped to the hg19 whole genome by using Hisat2 v2.0.5
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Then reads per kilobase of exon per megabase of library size (RPKM) were calculated based on the length of the gene and reads count mapped to this gene
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

growth_protocol: Human pulmonary arterial endothelial cells (hPAECs) between 5-6 passages were grown in EGM-2 Bulletkit medium.

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen).
RNA libraries were prepared by using the NEBNex Ultra RNA library Pre Kit (Illumina) according to the manufacturer's protocols.

treatment_protocol: hPAECs were grown to 70% confluency and transfected with an equimolar of miR-483-3p and -5p mimic or control mimic (10 nM) for 36 hours.

value: Pulmonary arterial endothelial cells

tag: passage


title: miR-483 mimic 2

source_name: Human pulmonary arterial endothelial cells


title: Neutrophils, Control 5


title: Control mimic 2


title: Neutrophils, Control 4


title: IRBB5_8h_1

tag: cultivar


title: IRBB5_8h_2


title: IRBB5_0h_3

value: 0 hpi


title: mESC, UV4I

value: male


title: IRBB5_0h_2


title: Control mimic 1


title: Neutrophils, Control 3B

description: duplo sample 6 (different run)


title: WT_base_sRNA180209_rep2

value: shoot base

tag: age

value: nutrient soil


title: IRBB5_0h_1

value: at the tillering stage


title: Neutrophils, Control 3A


title: mESC, UV3I


title: MeCP2 cKO Rep1 (MethylC-seq)

description:
HZ10080
Total DNA from inhibitory neurons sorted from the striatum of a male MeCP2 cKO mouse

source_name: MeCP2 cKO mouse #1

value: whole striatum

value: inhibitory neurons


title: IR24_24h_3

value: Xoo strain PXO86 infection

value: 24 hpi

value: Leaf


title: Neutrophils, Control 1


title: mESC, UV3B

value: UV


title: IR24_24h_2


title: mESC, F6I

value: Formaldehyde

value: Input


title: mESC, UV5B

value: IP

value: mESC


title: Neutrophils, MKL1 pt 2

value: neutrophil


title: IR24_24h_1


title: mESC, F6B


title: mESC, F5I


title: IR24_8h_3

value: 8 hpi


title: Neutrophils, MKL1 pt 1B

description: duplo sample 1 (different run)


title: mESC, UV4B


title: IR24_8h_2


title: mESC, F5B


title: IR24_8h_1


title: s678_ChIPSeq_Rep2

first: Jiayang

address: West Beichen Road

institute: Institute of Genetics and Developmental Biology, CAS

description: processed data file: s678_SMXL6HA_Rep2_vs_s678_Rep2_peaks.bed

data_processing:
All ChIP-seq reads were mapped to the Arabidopsis genome TAIR10 using BWA (version 0.7.10-r789) software with default parameters.
Duplicated reads and reads with low mapping quality were discarded using SAMtools (version 0.1.19-44428cd) with default parameters.
Peaks for SMXL6-HA were identified by the model-based analysis software (MACS version 1.4.2) in comparison with smxl6/7/8 with the parameters '--mfold=10, 30' and fold enrichment equal or larger than 2 using DNA enriched from the smxl6/7/8 mutant as a control.
Genome_build: Arabidopsis genome TAIR10
Supplementary_files_format_and_content: wig, bed files

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Arabidopsis seeds were surface sterilized, vernalized at 4 ºC for 2-4 days, germinated and grown on the 0.5× Murashige and Skoog (MS) medium containing 1.0% sucrose and 0.7% agar under a long day photoperiod (16-h light, 8-h dark cycle) with a light intensity of 60-80 μE m−2 sec−1 at 21 ºC.

extract_protocol:
Two-week-old seedlings were frozen and ground into powder in liquid nitrogen, then fixed in formaldehyde solution to cross-link protein-DNA complexes. The protein-DNA complexes were extracted from nuclei, underwent subsequent sonication, and immune precipitation with an anti-HA polyclonal antibody.
DNA libraries were prepared for sequencing according to Illumina's instructions accompanying the NextflexTM Rapid DNA-seq Kit (Bioo Scientific, 5144-02).

value: two weeks

value: whole seedlings

tag: chip antibody

value: anti-HA polyclonal antibody (Sigma, H6908)


title: IR24_0h_3

value: 0 hpi


title: IR24_0h_2

value: at the tillering stage


title: s678 SMXL6HA_ChIPSeq_Rep2

description:
pSMXL6:SMXL6-HA transgenic line
processed data file: s678_SMXL6HA_Rep2_vs_s678_Rep2_peaks.bed

value: smxl6/7/8 pSMXL6:SMXL6-HA


title: Neutrophils, MKL1 pt 1A


title: s678_ChIPSeq_Rep1

description: processed data file: s678_SMXL6HA_Rep1_vs_s678_Rep1_peaks.bed


title: mESC, F4I

value: male


title: mESC, F3I


title: Neutrophils, Control 2

value: control


title: IR24_0h_1

value: Xoo strain PXO86 infection


title: s678 SMXL6HA_ChIPSeq_Rep1

description:
pSMXL6:SMXL6-HA transgenic line
processed data file: s678_SMXL6HA_Rep1_vs_s678_Rep1_peaks.bed


title: mESC, F3B


title: mESC, F4B


title: B2524-2: IntestinalGastricCancer

status: Public on Mar 15 2020

type: RNA

state: Beijing

address: no.17 Panjiayuan Nanli

institute: Peking Union Medical College

description: EGC

hyb_protocol: 600 ng of CTP-Cy3-labelled cRNA (specific activity > 10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 µl containing 25 x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2 x Agilent hybridization buffer were added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 min with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief passage in acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides: scan area was 61x21.6 mm, scan resolution 3 µm, dye channel was set to Green, Tiff file dynamic range was 20 bits and Green PMT was set to 100 %.

data_processing: The raw data were normalized using GeneSpring GX software, version 11.5 (Silicon Genetics, Redwood City, CA, USA). The expression value for a particular gene was determined as the median value of all probes mapping to this gene.

source_name: IntestinalGastricCancer

label_protocol: CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent, version 6.6) according to manufacturer's instructions, followed by RNeasy column purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (Nanodrop ND1000, Labtech) and with the Agilent 2100 Bioanalyser.

extract_protocol: Total RNA was extracted from frozen tissues using the RNeasy Mini Kit (Cat No. 74106, Qiagen, Germany) according to the manufacturer’s instructions. RNA concentrations were determined using a NanoDrop ND-2000 Spectrophotometer (NanoDrop Technologies, Wilmington, USA), and RNA integrity was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Biopsy forceps were used to clamp the tissue from the suspected gastric mucosa and adjacent normal gastric mucosa that were at least 5 cm from the lesion location. Gastroscopic biopsy tissues were rapidly immersed in RNA later after being isolated and transferred to a -80° C refrigerator for long-term storage after overnight storage at 4° C.

value: gastric

value: Male


title: B2461-1: Gastritis

description: paired control sample of B2461-2

source_name: Gastritis


title: B2461-2: IntestinalGastricCancer

description: EGC


title: Intestine_YA_RNA_pe_rep2

city: Cambridge

first: Julie

last: Ahringer

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

data_processing:
Reads were trimmed using fastx_trimmer and aligned using bwa.
Low-quality (q<10), mitochondrial, and modENCODE-blacklisted reads were discarded.
Strand-specific normalised coverage was calculated using bedtools genomecov -ibam stdin -bg -scale NBFRAGS -pc -strand STRAND.
Tissue-specific stranded RNA-seq tracks were computed by averaging biological replicates.
Genome_build: WBcel235/ce11
Supplementary_files_format_and_content: Tissue-specific genome-wide nuclear RNA-seq profiles.

organism: Caenorhabditis elegans

source_name: Intestine nuclei

growth_protocol: Worms were grown at 25°C in liquid culture to the adult stage using standard S-basal medium with HB101 bacteria, animals bleached to obtain embryos, and the embryos hatched without food in M9 buffer for 24 hrs at 25°C to obtain synchronized starved L1 larvae. L1 larvae were grown in a further liquid culture at 25°C to the desired stage, then collected, washed in M9, floated on sucrose, washed again in M9, then frozen into "popcorn" by dripping embryo or worm slurry into liquid nitrogen. Popcorn were stored at -80°C until use. Times of growth were 4h (L1), 30h (L3) and 46-50h (YA) post-bleaching.

extract_protocol:
Frozen worms were broken by smashing using a Biopulverizer then the frozen powder was thawed in 8 ml Egg buffer (25 mM HEPES pH 7.3, 118 mM NaCl, 48 mM KCl, 2 mM CaCl2, 2 mM MgCl2). Ground worms were pelleted by spinning at 800 g for 3 min, then resuspended in 8 ml of Buffer A (0.3 M sucrose, 10 mM Tris pH 7.5, 10 mM MgCl2, 1 mM DTT, 0.5 mM spermidine 0.15 mM spermine, protease inhibitors (Roche complete, EDTA free) and 0.025 % IGEPAL CA-630). The sample was dounced (two strokes) in a 14-ml stainless steel tissue grinder (VWR), then the sample spun 100 g for 6 min to pellet remaining worm fragments. The supernatant was kept (nuclei batch 1) and the pellet resuspended in a further 7 ml of Buffer A and dounced for 30 strokes. This was spun 100 g for 6 min to pellet debris and the supernatant was kept (nuclei batch 2). This way, we found that the first fraction was already enriched for germline nuclei while the second fraction was enriched for somatic nuclei. At this stage, nuclei quality was assessed by microscopy before proceeded to immuno-staining. Nuclei immuno-staining was performed on the appropriate fraction of nuclei (first fraction to purify germline nuclei or second fraction to purify nuclei from any somatic tissue) as follows: Phycoerythrin-coupled anti-GFP antibody (Biolegend # 338003) was added to clarified nuclei in 7 to 8 ml of buffer A at 1:200 dilution. 280 units of murine RNAse inhibitor (M0314S) was added to protect RNA from being degraded. Nuclei were incubated in dark for 1 h or up to 16h at 4 C slowly rotating. Nuclei were clarified again after incubation (100 g for 6 min at 4 C) then pelleted (2000 g for 20 min at 4 C). Pelleted nuclei were then washed in 6 ml of buffer A and resuspended in 6 ml of buffer A + 1:500 of murine RNAse inhibitor and filtered on 30 µm mesh (CellTrics 04-0042-2316). Nuclei were stained with 0.025 µg/ml DAPI and their quality was assessed immediately before sorting by observation at 40X magnification. Nuclei sorting was performed using a Sony SH800Z sorter fitted with a 100 µm sorting chip and auto-calibrated. The nuclei were kept at 4 C during and after sorting. Background noise and debris were discarded by using the DAPI intensity signal as detection threshold. 2N single nuclei were gated using the DAPI signal and PE-positive nuclei were gated using PE-H / BSC-A signal. A recording speed > 15,000 nuclei per second ensured a sorting efficiency higher than 80 %, and nuclei were sorted in batches of one million and then processed for downstream applications immediately to limit the time they sit in buffer post-sorting. Nuclei were sorted into 15 ml Falcon tubes coated and filled with 500 µl of buffer A + 2 % RNAse-free BSA + 1:50 murine RNAse inhibitor (10 µl). Sorting purity was assessed before sorting large batches of nuclei and immediately after sorting for each batch, by microscopy and by recording sorted nuclei in a second pass in the sorter. A purity higher than 95 % was considered satisfactory.
RNA was extracted from batches of one million sorted nuclei by pelleting nuclei (2000 g for 20 min at 4 C), washing them in 1 ml of buffer A, then adding 500 µl of Trizol to pelleted nuclei. 100 µl of Chloroform were added and samples were shaken vigorously for 15 s. Samples were then spun at 12,000 g for 15 min at 4 C and the aqueous phase was transferred into one volume of ice-cold Isopropanol. 0.5 µl of GlycoBlue (AM9515) was added and RNA was left to precipitate overnight at -20 C. Once precipitated, RNA was pelleted (12,000 g for 30 min at 4 C), washed in 1 ml of ice-cold 80% Ethanol and resuspended in 12 µl of RNAse-free water. Concentration was estimated using Qubit. A minimum of 20 ng of total nuclear RNA was used to make long nuclear RNA-seq libraries. Long nuclear RNA (>200 nt) was isolated using Zymo Clean and Concentrate columns (#R1013) and stranded libraries were prepared using the NEB Next Ultra Directional RNA Library Prep Kit (#E7420S) after removing rRNA using the Ribo-Zero rRNA removal kit (MRZH11124). Long nuclear RNA-seq libraries were made from two biological replicates for each tissue.

tag: strain

tag: Stage

value: YA

tag: sequencing

value: paired-end


title: Muscle_YA_RNA_pe_rep2

source_name: Muscle nuclei


title: Neurons_YA_RNA_pe_rep2

source_name: Neurons nuclei


title: Hypodermis_YA_RNA_pe_rep2

source_name: Hypodermis nuclei


title: B2920-1: Gastritis

description: paired control sample of B2920-2

value: Female


title: B2516-2: IntestinalGastricCancer

description: EGC


title: B2944-2: IntestinalGastricCancer

description: EGC


title: Q0438-1: Gastritis

description: paired control sample of Q0438-2


title: Q0479-2: IntestinalGastricCancer

description: EGC


title: B2944-1: Gastritis

description: paired control sample of B2944-2


title: Q0479-1: Gastritis

description: paired control sample of Q0479-2


title: B2809-1: Gastritis

description: paired control sample of B2809-2


title: Q0500-2: IntestinalGastricCancer

description: EGC


title: B2920-2: IntestinalGastricCancer

description: EGC


title: B2524-1: Gastritis

description: paired control sample of B2524-2


title: B2516-1: Gastritis

description: paired control sample of B2516-2


title: Q0514-2: IntestinalGastricCancer

description: EGC


title: Q0500-1: Gastritis

description: paired control sample of Q0500-2


title: Q0423-1: Gastritis

description: paired control sample of Q0423-2


title: Q0452-2: IntestinalGastricCancer

description: EGC


title: B1326-2: IntestinalGastricCancer

description: EGC


title: Q0423-2: IntestinalGastricCancer

description: EGC


title: Germline_YA_RNA_pe_rep2

source_name: Germline nuclei


title: Intestine_YA_RNA_pe_rep1


title: Q0438-2: IntestinalGastricCancer

description: EGC


title: Q0452-1: Gastritis

description: paired control sample of Q0452-2


title: Muscle_YA_RNA_pe_rep1


title: B2809-2: IntestinalGastricCancer

description: EGC


title: Neurons_YA_RNA_pe_rep1


title: Q0514-1: Gastritis

description: paired control sample of Q0514-2


title: B1272-1: Gastritis

description: paired control sample of B1272-2


title: Germline_L3_ATAC_se_rep1

data_processing:
Reads were trimmed using fastx_trimmer and aligned using bwa.
Low-quality (q<10), mitochondrial, and modENCODE-blacklisted reads were discarded.
Normalised coverage was calculated using MACS2: --format BAM --bdg --SPMR --gsize ce --nolambda --nomodel --extsize 150 --shift -75 --keep-dup all
Tissue-specific accessibility was calculated by averaging across biological replicates
Genome_build: WBcel235/ce11
Supplementary_files_format_and_content: Tissue-specific genome-wide accessibility profiles.

extract_protocol:
Frozen worms were broken by smashing using a Biopulverizer then the frozen powder was thawed in 8 ml Egg buffer (25 mM HEPES pH 7.3, 118 mM NaCl, 48 mM KCl, 2 mM CaCl2, 2 mM MgCl2). Ground worms were pelleted by spinning at 800 g for 3 min, then resuspended in 8 ml of Buffer A (0.3 M sucrose, 10 mM Tris pH 7.5, 10 mM MgCl2, 1 mM DTT, 0.5 mM spermidine 0.15 mM spermine, protease inhibitors (Roche complete, EDTA free) and 0.025 % IGEPAL CA-630). The sample was dounced (two strokes) in a 14-ml stainless steel tissue grinder (VWR), then the sample spun 100 g for 6 min to pellet remaining worm fragments. The supernatant was kept (nuclei batch 1) and the pellet resuspended in a further 7 ml of Buffer A and dounced for 30 strokes. This was spun 100 g for 6 min to pellet debris and the supernatant was kept (nuclei batch 2). This way, we found that the first fraction was already enriched for germline nuclei while the second fraction was enriched for somatic nuclei. At this stage, nuclei quality was assessed by microscopy before proceeded to immuno-staining. Nuclei immuno-staining was performed on the appropriate fraction of nuclei (first fraction to purify germline nuclei or second fraction to purify nuclei from any somatic tissue) as follows: Phycoerythrin-coupled anti-GFP antibody (Biolegend # 338003) was added to clarified nuclei in 7 to 8 ml of buffer A at 1:200 dilution. 280 units of murine RNAse inhibitor (M0314S) was added to protect RNA from being degraded. Nuclei were incubated in dark for 1 h or up to 16h at 4 C slowly rotating. Nuclei were clarified again after incubation (100 g for 6 min at 4 C) then pelleted (2000 g for 20 min at 4 C). Pelleted nuclei were then washed in 6 ml of buffer A and resuspended in 6 ml of buffer A + 1:500 of murine RNAse inhibitor and filtered on 30 µm mesh (CellTrics 04-0042-2316). Nuclei were stained with 0.025 µg/ml DAPI and their quality was assessed immediately before sorting by observation at 40X magnification. Nuclei sorting was performed using a Sony SH800Z sorter fitted with a 100 µm sorting chip and auto-calibrated. The nuclei were kept at 4 C during and after sorting. Background noise and debris were discarded by using the DAPI intensity signal as detection threshold. 2N single nuclei were gated using the DAPI signal and PE-positive nuclei were gated using PE-H / BSC-A signal. A recording speed > 15,000 nuclei per second ensured a sorting efficiency higher than 80 %, and nuclei were sorted in batches of one million and then processed for downstream applications immediately to limit the time they sit in buffer post-sorting. Nuclei were sorted into 15 ml Falcon tubes coated and filled with 500 µl of buffer A + 2 % RNAse-free BSA + 1:50 murine RNAse inhibitor (10 µl). Sorting purity was assessed before sorting large batches of nuclei and immediately after sorting for each batch, by microscopy and by recording sorted nuclei in a second pass in the sorter. A purity higher than 95 % was considered satisfactory.
A batch of one million sorted nuclei was pelleted (2000 g for 20 min at 4 C) and resuspended in 10 µl of buffer A and topped up to 200 µl with 1X Tn5 Buffer (10mM Tris pH 8, 5mM MgCl2, 10% DMF). 47.5 µl of nuclei suspension were then aliquoted and 2.5 µl of Tn5 were added to the suspension. The mix was incubated for 30 min at 37 C while mixing at 400 rpm. Tagmented DNA was purified using a MinElute column (Qiagen) and converted into a library using the Nextera kit protocol. Typically, libraries were amplified using 12-16 PCR cycles. Libraries were then cleaned up using 0.6 volumes of beads. Beads bound by large fragments of DNA (> 700bp) were discarded and DNA recovered from the supernatant by adding 1.2 volumes of beads. DNA was eluted in 50 µl water and 0.9 volumes of beads were used to bind the library, leaving adaptor dimers in the supernatant. DNA was eluted in 20 µl water, quantified using a Qubit, and analyzed using an Agilent Tapestation. ATAC-seq libraries were made from two biological replicates for each tissue and sequenced in both single-end and paired-end modes.


title: Muscle_L3_ATAC_se_rep1

value: single-end


title: Germline_YA_RNA_pe_rep1


title: Muscle_L1_ATAC_se_rep1

value: fed L1


title: Hypodermis_YA_RNA_pe_rep1


title: Intestine_YA_ATAC_pe_rep2


title: B1019-2: IntestinalGastricCancer

description: EGC


title: B1090-2: IntestinalGastricCancer

description: EGC


title: B1090-1: Gastritis

description: paired control sample of B1090-2


title: Hypodermis_YA_ATAC_pe_rep2


title: Muscle_YA_ATAC_pe_rep2


title: Q0469-1: Gastritis

description: paired control sample of Q0469-2


title: Q0469-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN


title: Q0465-1: Gastritis

description: paired control sample of Q0465-2


title: Intestine_YA_ATAC_pe_rep1


title: Hypodermis_YA_ATAC_pe_rep1


title: Neurons_YA_ATAC_pe_rep2


title: Muscle_YA_ATAC_pe_rep1


title: Neurons_YA_ATAC_pe_rep1


title: B1019-1: Gastritis

description: paired control sample of B1019-2


title: Germline_YA_ATAC_pe_rep2


title: Intestine_YA_ATAC_se_rep2


title: Muscle_YA_ATAC_se_rep2


title: Hypodermis_YA_ATAC_se_rep2


title: B1682-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN


title: Neurons_YA_ATAC_se_rep2


title: B1632-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN


title: B1703-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN


title: B1682-1: Gastritis

description: paired control sample of B1682-2


title: B1632-1: Gastritis

description: paired control sample of B1632-2


title: B1322-1: Gastritis

description: paired control sample of B1322-2


title: B1559-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN


title: B1703-1: Gastritis

description: paired control sample of B1703-2


title: Q0465-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN


title: B1322-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN


title: Germline_YA_ATAC_pe_rep1


title: B1559-1: Gastritis

description: paired control sample of B1559-2


title: B1244-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN


title: Germline_YA_ATAC_se_rep2


title: Hypodermis_YA_ATAC_se_rep1


title: Intestine_YA_ATAC_se_rep1


title: Muscle_YA_ATAC_se_rep1


title: Neurons_YA_ATAC_se_rep1


title: Germline_YA_ATAC_se_rep1


title: B1168-1: Gastritis

description: paired control sample of B1168-2


title: B1168-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN


title: B1326-1: Gastritis

description: paired control sample of B1326-2


title: B1244-1: Gastritis

description: paired control sample of B1244-2


title: B0420-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN


title: B0362-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN


title: B1025-1: Gastritis

description: paired control sample of B1025-2


title: B0420-1: Gastritis

description: paired control sample of B0420-2


title: B1025-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN


title: genomic DNA from distal femur trabecular bone Cjac03 (marmoset_intraspecific)

city: Chicago

first: Genevieve

last: Housman

state: IL

address: 920 East 58th Street, CLSC 317

department: Genetic Medicine

institute: University of Chicago

description: medial condyle distal femur trabecular bone from marmoset

hyb_protocol: Infinium MethylationEPIC array

scan_protocol: standard illumina scanner

data_processing:
Raw fluorescent data were normalized using the Noob background correction    method with dye-bias normalization followed with a between-array    normalization method (functional normalization) as implemented in the R    package minfi. After normalization, methylation values (beta values) for    each site were calculated as the ratio of methylated probe signal intensity    to the sum of both methylated and unmethylated probe signal intensities.
Those probes with failed detection levels (p-value > 0.05) in greater than    10% of samples were removed. Cross-reactive probes, probes containing SNPs    at the CpG site, probes detecting SNP information, probes detecting    methylation at non-CpG sites, and probes targeting sites within the sex    chromosomes were also removed using the minfi package in R.
Lastly, probes that were determined to be non-specific to each nonhuman    primate genome were also removed. Filtering for these files was based    on Hernando-Herraez  et al. (2013). Briefly, all 485,512 probes were mapped to the appropriate    nonhuman primate genome, and only those probes that successfully mapped to    the genome, had only 1 unique hit, and targeted CpG sites were retained.    Additionally, probes were kept for subsequent analyses only if they had 0    mismatches in 5bp closest to and including the CpG site, and had 0-2    mismatches in 45bp not including the CpG site.
- Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M,       Heyn H, Hvilsom C, et al. Dynamics of DNA methylation in recent human and       great ape evolution. PLOS Genet 2013;9:e1003763.
Nonhuman Primate Genome: Callithrix jacchus

organism: Callithrix jacchus

label_protocol: 400ng of DNA was bisulphite converted using the EZ DNA methylation kit (Zymo Research)

extract_protocol: genomic DNA was extracted from pulverized trabecular bone using a phenol-cholorform protocol

value: female

tag: age (years)

value: bone

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: genomic DNA from distal femur trabecular bone Cjac06 (marmoset_intraspecific)

source_name: distal femur trabecular bone from marmoset

tag: Sex

tag: age (years)

tag: tissue

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)


title: B0249-1: Gastritis

description: paired control sample of B0249-2

tag: gender

tag: age


title: genomic DNA from distal femur trabecular bone Cjac04 (marmoset_intraspecific)

tag: Sex

tag: age (years)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: B0216-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN

tag: tissue

tag: gender

tag: age


title: genomic DNA from distal femur trabecular bone Caet10 (nhp850K)

description: medial condyle distal femur trabecular bone from vervet

data_processing:
Raw fluorescent data were normalized using the Noob background correction    method with dye-bias normalization followed with a between-array    normalization method (functional normalization) as implemented in the R    package minfi. After normalization, methylation values (beta values) for    each site were calculated as the ratio of methylated probe signal intensity    to the sum of both methylated and unmethylated probe signal intensities.
Those probes with failed detection levels (p-value > 0.05) in greater than    10% of samples were removed. Cross-reactive probes, probes containing SNPs    at the CpG site, probes detecting SNP information, probes detecting    methylation at non-CpG sites, and probes targeting sites within the sex    chromosomes were also removed using the minfi package in R.
Lastly, probes that were determined to be non-specific to each nonhuman    primate genome were also removed. Filtering for these files was based    on Hernando-Herraez  et al. (2013). Briefly, all 485,512 probes were mapped to the appropriate    nonhuman primate genome, and only those probes that successfully mapped to    the genome, had only 1 unique hit, and targeted CpG sites were retained.    Additionally, probes were kept for subsequent analyses only if they had 0    mismatches in 5bp closest to and including the CpG site, and had 0-2    mismatches in 45bp not including the CpG site.
- Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M,       Heyn H, Hvilsom C, et al. Dynamics of DNA methylation in recent human and       great ape evolution. PLOS Genet 2013;9:e1003763.
Nonhuman Primate Genome: Papio anubis, Macaca mulatta, Chlorocebus          aethiops, Pan troglodytes, and Callithrix jacchus > only probes that          overlapped across all examined species were retained

organism: Chlorocebus aethiops

tag: taxon

value: vervet

tag: group

value: owm

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)


title: B1476-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN

source_name: GastricLowGradeIntraepithelialNeoplasia

tag: tissue

tag: gender

tag: age


title: B0362-1: Gastritis

description: paired control sample of B0362-2


title: B2330-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN


title: genomic DNA from distal femur trabecular bone Cjac02 (marmoset_intraspecific)

tag: Sex

tag: age (years)

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: B0216-1: Gastritis

description: paired control sample of B0216-2

tag: tissue

tag: gender

tag: age


title: B1476-1: Gastritis

description: paired control sample of B1476-2


title: genomic DNA from distal femur trabecular bone Cjac05 (marmoset_intraspecific)

tag: Sex

tag: age (years)

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)


title: genomic DNA from distal femur trabecular bone Caet03 (nhp850K)

source_name: distal femur trabecular bone from vervet

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

tag: disease state

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: genomic DNA from distal femur trabecular bone Cjac01 (marmoset_intraspecific)

tag: Sex

tag: age (years)

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)


title: B0249-2: GastricHighGradeIntraepithelialNeoplasia

description: HGIN

tag: tissue

tag: gender

tag: age


title: genomic DNA from distal femur trabecular bone Caet07 (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: genomic DNA from distal femur trabecular bone Caet09 (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

tag: disease state

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)


title: genomic DNA from distal femur trabecular bone Caet08 (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: B1514-1: Gastritis

description: paired control sample of B1514-2

tag: tissue

tag: gender

tag: age


title: B1514-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN


title: genomic DNA from distal femur trabecular bone Caet02 (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)


title: B1666-1: Gastritis

description: paired control sample of B1666-2

tag: tissue

tag: gender

tag: age


title: B1834-1: Gastritis

description: paired control sample of B1834-2


title: B1834-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN


title: B2330-1: Gastritis

description: paired control sample of B2330-2


title: genomic DNA from distal femur trabecular bone Cjac04 (nhp850K)

tag: taxon

value: marmoset

tag: group

value: nwm

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: genomic DNA from distal femur trabecular bone Caet05 (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

tag: disease state

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)


title: genomic DNA from distal femur trabecular bone Cjac06 (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: B1505-1: Gastritis

description: paired control sample of B1505-2

tag: tissue

tag: gender

tag: age


title: genomic DNA from distal femur trabecular bone Caet04 (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)


title: genomic DNA from distal femur trabecular bone Caet06 (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

tag: disease state

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: genomic DNA from distal femur trabecular bone Cjac05 (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)


title: B1505-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN

tag: tissue

tag: gender

tag: age


title: genomic DNA from distal femur trabecular bone Caet01 (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: B1489-1: Gastritis

description: paired control sample of B1489-2

tag: tissue

tag: gender

tag: age


title: B1364-1: Gastritis

description: paired control sample of B1364-2


title: B1366-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN


title: genomic DNA from distal femur trabecular bone Cjac02 (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)


title: B1364-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN

tag: tissue

tag: gender

tag: age


title: B1666-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN


title: B1170-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN


title: genomic DNA from distal femur trabecular bone Mmul02 (nhp850K)

description: medial condyle distal femur trabecular bone from macaque

organism: Macaca mulatta

tag: taxon

value: macaque

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)