title: genomic DNA from distal femur trabecular bone Cjac01 (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 Cjac03 (nhp850K)

status: Public on Mar 15 2020

type: genomic

city: Chicago

first: Genevieve

last: Housman

state: IL

address: 920 East 58th Street, CLSC 317

department: Genetic Medicine

country: USA

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: Papio anubis, Macaca mulatta, Chlorocebus          aethiops, Pan troglodytes, and Callithrix jacchus > only probes that          overlapped across all examined species were retained

label: Cy5 and Cy3

molecule: genomic DNA

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

tag: taxon

value: marmoset

tag: group

value: nwm

tag: Sex

value: female

tag: age (years)

tag: steady state weight (kg)

value: bone

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: B1489-2: GastricLowGradeIntraepithelialNeoplasia

type: RNA

city: Beijing

first: Yajing

last: Zhang

state: Beijing

address: no.17 Panjiayuan Nanli

country: China

institute: Peking Union Medical College

description: LGIN

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.

molecule: total RNA

organism: Homo sapiens

source_name: GastricLowGradeIntraepithelialNeoplasia

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.

tag: tissue

value: gastric

tag: gender

value: Female

tag: age


title: B1366-1: Gastritis

description: paired control sample of B1366-2

source_name: Gastritis

value: Male


title: B1272-2: IntestinalGastricCancer

description: EGC

source_name: IntestinalGastricCancer


title: genomic DNA from distal femur trabecular bone Mmul05 (nhp850K)

description: medial condyle distal femur trabecular bone from macaque

organism: Macaca mulatta

tag: taxon

value: macaque

tag: group

value: owm

tag: Sex

value: male

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 Mmul03 (nhp850K)

source_name: distal femur trabecular bone from macaque

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: B1170-1: Gastritis

description: paired control sample of B1170-2

tag: gender

tag: age


title: B1115-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN

tag: tissue


title: B1115-1: Gastritis

description: paired control sample of B1115-2


title: genomic DNA from distal femur trabecular bone Mmul08 (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: B0358-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN

tag: tissue

tag: gender

tag: age


title: genomic DNA from distal femur trabecular bone Mmul06 (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: B1064-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN

tag: tissue

tag: gender

tag: age


title: genomic DNA from distal femur trabecular bone Mmul10 (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 Mmul07 (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: B0344-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN

tag: gender

tag: age


title: B1047-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN

tag: tissue


title: genomic DNA from distal femur trabecular bone Mmul01 (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: B0358-1: Gastritis

description: paired control sample of B0358-2

tag: tissue

tag: gender

tag: age


title: B1064-1: Gastritis

description: paired control sample of B1064-2


title: B1047-1: Gastritis

description: paired control sample of B1047-2


title: genomic DNA from distal femur trabecular bone Ptro04 (nhp850K)

description: medial condyle distal femur trabecular bone from chimpanzee

organism: Pan troglodytes

tag: taxon

value: chimpanzee

tag: group

value: ape

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: B0344-1: Gastritis

description: paired control sample of B0344-2

tag: tissue

tag: gender

tag: age


title: genomic DNA from distal femur trabecular bone Ptro02 (nhp850K)

source_name: distal femur trabecular bone from chimpanzee

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: B0331-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN

tag: tissue

tag: gender

tag: age


title: genomic DNA from distal femur trabecular bone Ptro03 (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 healthy adult distal femur trabecular bone Panu49_B (nhp850K)

description: medial condyle healthy adult distal femur trabecular bone from baboon

organism: Papio sp.

tag: taxon

value: baboon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

value: adult

tag: disease state

value: healthy

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: B0331-1: Gastritis

description: paired control sample of B0331-2

tag: gender

tag: age


title: genomic DNA from distal femur trabecular bone Mmul04 (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

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 Ptro01 (nhp850K)

tag: taxon

tag: group

tag: Sex

value: unknown

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: B0294-2: GastricLowGradeIntraepithelialNeoplasia

description: LGIN

tag: gender

tag: age


title: genomic DNA from healthy adult distal femur trabecular bone Panu50_B (nhp850K)

source_name: healthy adult distal femur trabecular bone from baboon

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

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 healthy adult distal femur trabecular bone Panu36_B (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 healthy adult distal femur trabecular bone Panu40_B (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: B0294-1: Gastritis

description: paired control sample of B0294-2

tag: tissue

tag: gender

tag: age


title: WM793B NL4si rep 3

city: Wien

first: David

last: Schörghofer

address: Währingerstraße 10

department: Department for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

description: Gene expression data from knockdown WM793B cells

hyb_protocol: Affymetrix GeneChip® Human PrimeView arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Plus Reagent Kit User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

label: biotin

source_name: WM793B melanoma cells treated with NLGN4X siRNA

label_protocol: 100ng of total RNA were amplified and labeled using the Affymetrix 3` IVT Plus Reagent Kit (Catalog Number 902416), Affymetrix, Santa Clara, CA)

growth_protocol: Melanoma cells were cultured in MIM medium supplemented with 2 % FCS containing: 80 % MCDB153, 20 % Leibovitz`s l15, 5 µg/ml Insuline, bovine, 0.5 ng/ml Epidermal Growth Factor (EGF), 1.68 mM CaCl2, 100 IU/ml Penicillin, 100 µg/ml Streptomycin and 2 µg/ml Ciprofloxacin at 37°C at 5% CO2

extract_protocol: Total RNA was isolated using peqGold total RNA kit (Peqlab, Erlangen, Germany) according to the manufacturer’s instructions.

treatment_protocol: Melanoma cells cultivated in antibiotic free 2 % MIM were transfected as soon as the cells reached 60-70 % confluency. 5 µM siRNA was diluted 1:20 in serum free MIM, DharmaFECT (Thermo Fisher Scientific) was diluted 1:50 in serum free MIM. After 5 min incubation time at RT, both reactions were mixed and incubated for 20 min at RT. Mixtures were added to the cells in a ratio 1:5 in antibiotic free 2 % MIM medium to a final siRNA concentration of 25 nM. Cells were incubated for 24 h at 37 °C in 5 % CO2.

tag: cell line

tag: cell type

value: melanoma

tag: treatment

value: NLGN4X siRNA


title: WM793B NL4si rep 2


title: WM793B Ctrl rep 1

description: Gene expression data from control WM793B cells

source_name: WM793B melanoma cells treated with non-targeting siRNA

value: non-targeting siRNA


title: genomic DNA from healthy adult distal femur trabecular bone Panu06_B (nhp850K)

tag: taxon

tag: group

tag: Sex

value: female

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)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)


title: genomic DNA from healthy adult distal femur trabecular bone Panu44_B (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

value: bone

tag: age cohort

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (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: MCM1G NL4si rep 2

description: Gene expression data from knockdown MCM1G cells

source_name: MCM1G melanoma cells treated with NLGN4X siRNA

tag: cell line

tag: cell type

tag: gender

tag: treatment


title: genomic DNA from healthy adult distal femur trabecular bone Panu47_B (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

tag: disease state

tag: 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)


title: WM793B Ctrl rep 2

tag: cell line

tag: cell type

tag: gender

tag: treatment


title: MCM1G Ctrl rep 3

description: Gene expression data from control MCM1G cells

source_name: MCM1G melanoma cells treated with non-targeting siRNA


title: genomic DNA from healthy adult distal femur trabecular bone Panu18_B (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

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: 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 healthy adult distal femur trabecular bone Panu37_B (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

tag: disease state

tag: femur length (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)


title: WM793B NL4si rep 1

tag: cell line

tag: cell type

tag: gender

tag: treatment


title: MCM1G NL4si rep 3


title: genomic DNA from healthy adult distal femur trabecular bone Panu34_B (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

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: 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: Sick group rep23 (barrow)

type: SRA

city: Edmonton

first: Graham

last: Plastow

country: Canada

institute: University of Alberta

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads were aligned to pig reference genome sequence assembly (Sscrofa10.2)  using Tophat 2.0.2 with default parameters which included: enable use of GTF file, set minimum anchor length of 8, accept zero mismatches in the anchor region, allow intron length between 50 and 500,000, and allow up to 20 alignments to the reference for a given read. For annotation of genes, we used the GTF file for Sscrofa10.2 from Ensembl version 67
The number of reads uniquely mapped to each gene was determined using Htseq-count (v0.5.3.p3).
Genome_build: Ssc10.2

organism: Sus scrofa

source_name: Peripheral blood

extract_protocol:
Total RNA was isolated from blood samples using the Total RNA Purification Kit (Norgen, Biotek Corp.) following the manufacturer’s protocol. An in-solution DNase I digestion step was employed to remove the contaminant DNA as recommended. RNA was then recovered by the RNeasy MinElute Cleanup kit (Qiagen, Hilden, Germany) and quantified using the Nanodrop 2000 spectrophotometer (Thermo Scientific, Wilmington, USA). The purity and integrity of total RNA were assessed with the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). RNA samples with integrity number larger than 6.0 were then subjected to a globin depletion protocol to remove the majority of globin transcripts.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Duroc

tag: group

value: sick


title: genomic DNA from healthy adult distal femur trabecular bone Panu10_B (nhp850K)

tag: taxon

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (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)


title: genomic DNA from healthy adult distal femur trabecular bone Panu13_B (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (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: Sick group rep21 (gilt)

tag: breed

tag: group


title: MCM1G Ctrl rep 2

tag: cell line

tag: cell type

tag: gender

tag: treatment


title: genomic DNA from healthy adult distal femur trabecular bone Panu48_B (nhp850K)

tag: taxon

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

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)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)


title: MCM1G Ctrl rep 1

tag: cell line

tag: cell type

tag: gender

tag: treatment


title: genomic DNA from healthy adult distal femur trabecular bone Panu03_B (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

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: 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 healthy adult distal femur trabecular bone Panu29_B (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

tag: disease state

tag: femur length (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)


title: genomic DNA from healthy adult distal femur trabecular bone Panu46_B (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

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: 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: WM793B Ctrl rep 3

tag: cell line

tag: cell type

tag: gender

tag: treatment


title: genomic DNA from healthy adult distal femur trabecular bone Panu56_B (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

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: 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)


title: Healthy group rep23 (gilt)

tag: breed

tag: group


title: Healthy group rep22 (gilt)


title: Sick group rep20 (gilt)


title: genomic DNA from healthy adult distal femur trabecular bone Panu42_B (nhp850K)

tag: taxon

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (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: Healthy group rep21 (barrow)

tag: breed

tag: group


title: Sick group rep19 (barrow)


title: Sick group rep22 (barrow)


title: Entry group rep18 (barrow)

value: entry


title: Entry group rep17 (gilt)


title: Sick group rep17 (barrow)


title: Fast Blue LPS Positive group 1

city: Durham

first: Melanie

middle: Maya

last: Kaelberer

address: 203 Research Drive

institute: Duke University

data_processing:
Reads were aligned to genome using TopHat
Transcripts were mapped to the mm9 reference genome using Cufflinks
Differential expression was determined using Cuffdiff and manually using Matlab
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and comparison p-values determined by Cuffdiff

organism: Mus musculus

source_name: sorted vagal ganglia of 5 mice pooled

extract_protocol:
ganglia from 5 mice were dissociated and pooled together, neurons were FAC sorted into Fast Blue positive and negative samples. RNA was extracted using the Rneasy Micro Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: treatment

value: LPS

tag: sorted cells

value: positive


title: Entry group rep16 (barrow)


title: Healthy group rep20 (barrow)


title: Fast Blue LPS Positive group 2


title: Sick group rep16 (barrow)


title: Healthy group rep19 (barrow)


title: Fast Blue Vehicle Positive group 2

value: vehicle


title: Sick group rep18 (gilt)


title: Fast Blue Vehicle Positive group 1


title: genomic DNA from healthy adult distal femur trabecular bone Panu21_B (nhp850K)

tag: taxon

value: owm

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

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: 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)


title: Fast Blue LPS Negative group 1

tag: strain

tag: treatment

tag: sorted cells

value: negative


title: Fast Blue Vehicle Negative group 2


title: Sick group rep15 (gilt)

tag: breed

tag: group


title: Sick group rep14 (barrow)


title: Entry group rep14 (barrow)


title: Entry group rep15 (gilt)


title: genomic DNA from healthy adult distal femur trabecular bone Panu33_B (nhp850K)

tag: taxon

value: baboon

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

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: 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 healthy adult distal femur trabecular bone Panu19_B (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

value: adult

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (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)


title: Sick group rep13 (barrow)

tag: breed

tag: group


title: genomic DNA from healthy adult distal femur trabecular bone Panu53_B (nhp850K)

tag: taxon

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

value: healthy

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: 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: MCM1G NL4si rep 1

tag: cell line

tag: cell type

tag: gender

value: male

tag: treatment


title: Healthy group rep18 (barrow)

tag: breed

tag: group


title: genomic DNA from healthy adult distal femur trabecular bone Panu41_B (nhp850K)

tag: taxon

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

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)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)


title: Sick group rep12 (gilt)

tag: breed

tag: group


title: Fast Blue Vehicle Negative group 1

tag: strain

tag: treatment

tag: sorted cells


title: genomic DNA from healthy adult distal femur trabecular bone Panu45_B (nhp850K)

tag: taxon

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

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: 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 healthy adult distal femur trabecular bone Panu39_B (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (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)


title: genomic DNA from healthy adult distal femur trabecular bone Panu08_B (nhp850K)

tag: taxon

tag: group

tag: Sex

tag: age (years)

tag: steady state weight (kg)

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: 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: TG 2

description:
2-drg-tg_genes.txt
3-jnc-tg_genes.txt

source_name: trigeminal ganglia

extract_protocol:
ganglia were removed, flash frozen oin liquid nitrogen, and RNA was harvested using Rneasy Micro Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: trigeminal ganglia


title: Entry group rep12 (barrow)

tag: breed

tag: group


title: TG 3

description:
2-drg-tg_genes.txt
3-jnc-tg_genes.txt


title: Healthy group rep17 (gilt)


title: Fast Blue LPS Negative group 2

tag: treatment

tag: sorted cells


title: TG 1

description:
2-drg-tg_genes.txt
3-jnc-tg_genes.txt


title: Entry group rep13 (gilt)


title: DRG 2

description:
1-jnc-drg_genes.txt
2-drg-tg_genes.txt

source_name: dorsal root ganglia

value: dorsal root ganglia


title: genomic DNA from healthy adult distal femur trabecular bone Panu55_B (nhp850K)

tag: taxon

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)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)


title: DRG 3

description:
1-jnc-drg_genes.txt
2-drg-tg_genes.txt

tag: strain

tag: tissue


title: DRG 1

description:
1-jnc-drg_genes.txt
2-drg-tg_genes.txt


title: JNC 2

description:
1-jnc-drg_genes.txt
3-jnc-tg_genes.txt

source_name: vagal ganglia

value: vagal ganglia


title: Entry group rep11 (barrow)

tag: breed

tag: group


title: Entry group rep10 (gilt)


title: JNC 1

description:
1-jnc-drg_genes.txt
3-jnc-tg_genes.txt


title: Mesenchymal stromal cells, ENU3

first: Angela

last: Stoddart

address: 900 E. 57th Street, Lab 5220A

department: Pathology

data_processing:
Illumina's bcl2fastq was used for basecalling
Fastqc was used for quality check
Reads were aligned to mm10 with Tophat
Samtools were used to  filter out reads with a quality score less than 30.
EdgeR was used to correct for batch effects and multiple testing.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cpm (counts per million) values for each sample

source_name: mesenchymal stromal cell

growth_protocol: Bone marrow, isolated from Egr1+/-, Apc del/+ mice, was transduced with a shRNA specific for luciferase (control) or Trp53 and  transplanted into WT recipient mice.  Donor and/or recipient were ENU-treated where indicated.  LSK (Lin-, Sca1+, Kit+) hematopoietic stem and progenitor cells were sorted from the bone marrow about 2 months after transplant before myeloid disease, or  RNA was isolated from bone marrow after mice developed MDS or AML.MSCs were isolated from compact bone using collagenase, from mice mock or ENU treated one month earlier. MSCs were grown using MesenCult media (Stem cell technologies) to passage 1 or 2, and then RNA was isolated.

extract_protocol:
RNA was isolated from bone marrow cells with Trizol
RNA libraries were constructed using Illumina's TruSeq Stranded mRNA kit.

treatment_protocol: Mice were treated with ENU as indicated.

tag: tumor stage

value: no disease

tag: haploinsufficiency

tag: shRNA

tag: treatment

value: 100 mg/kg ENU

tag: transplant

value: WT BM, no transplant

tag: mouse tag number

tag: cell type

value: mesenchymal stromal cell


title: Healthy group rep16 (barrow)

value: Duroc


title: LPS 5

value: LPS


title: Sick group rep11 (gilt)

value: sick


title: Healthy group rep15 (barrow)


title: Mesenchymal stromal cells, ENU2

value: WT BM_no transplant


title: Mesenchymal stromal cells, ENU1


title: Mesenchymal stromal cells, C2

value: 10% ethanol


title: Mesenchymal stromal cells, C3


title: LPS 4


title: genomic DNA from distal femur trabecular bone Mmul09 (nhp850K)

tag: taxon

value: macaque

value: owm

tag: Sex

value: female

tag: age (years)

tag: steady state weight (kg)

value: bone

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: 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: LPS 3

tag: strain

tag: treatment


title: LPS 2


title: Entry group rep9 (barrow)

tag: breed

tag: group

value: entry


title: Bone marrow, AML_5

source_name: bone marrow

tag: tumor stage

value: AML

tag: haploinsufficiency

value: Egr1, Apc

tag: shRNA

value: ENU-both donor and recipient

tag: transplant

value: Egr1+/-, Apc del/+, Trp53 shRNA BM transplanted into WT recipient

tag: mouse tag number

tag: tissue

value: bone marrow


title: Bone marrow, AML_6

value: ENU- recipient


title: Mesenchymal stromal cells, C1

value: no disease

value: WT BM, no transplant

tag: cell type

value: mesenchymal stromal cell


title: Sick group rep10 (barrow)

value: Duroc

value: sick


title: Bone marrow, AML_4


title: Healthy group rep14 (gilt)

value: healthy


title: JNC 3

description:
1-jnc-drg_genes.txt
3-jnc-tg_genes.txt

value: vagal ganglia


title: Bone marrow, AML_1


title: Bone marrow, AML_3

value: no ENU


title: Sick group rep9 (barrow)


title: Bone marrow, AML_2


title: LPS 1

value: LPS


title: Bone marrow, MDS_6

value: MDS

value: Luciferase

value: Egr1+/-, Apc del/+, Luc shRNA BM transplanted into WT recipient


title: Veh 5

value: vehicle


title: Bone marrow, MDS_5

value: Egr1, Apc

value: ENU-both donor and recipient


title: Bone marrow, MDS_3

value: bone marrow


title: Veh 2


title: genomic DNA from healthy adult distal femur trabecular bone Panu43_B (nhp850K)

tag: taxon

value: baboon

value: owm

tag: Sex

value: female

tag: age (years)

tag: steady state weight (kg)

value: bone

tag: age cohort

value: adult

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)

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)


title: Veh 4

tag: strain

tag: treatment


title: Bone marrow, MDS_4

tag: tumor stage

tag: haploinsufficiency

tag: shRNA

tag: transplant

tag: mouse tag number

tag: tissue


title: Veh 3


title: Healthy group rep13 (barrow)

tag: breed

value: Duroc

tag: group


title: Sick group rep8 (barrow)

value: sick


title: habenula, sample 2

city: Boston

first: Michael

middle: L

last: Wallace

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

description: Contains libraries Hab161102.1 and Hab161102.2 Please see README file containing library barcodes for demultiplexing.

data_processing:
All processing steps performed on sequencing fastq files to generate count matrices were performed using a custom pipeline for inDrops data analysis available at https://github.com/indrops/indrops (Klein et al., 2015).
Reads were filtered by expected structure and sorted by the corresponding library index. Valid reads were then trimmed (Trimmomatic version 0.33; parameters: LEADING: "28" SLIDINGWINDOW: "4:20" MINLEN: "16") before demultiplexing and sorting by cell barcodes.
Reads were aligned to a reference mouse transcriptome (Ensembl GRCm38 release 87) using Bowtie 1.1.1 (m = 200, n = 1, l = 15, e = 1000).
Aligned reads were then quantified as UMI-filtered mapped read (UMIFM) counts. UMIFM counts and quantification metrics for each cell were combined into a single file sorted by library and exported as a gunzipped TSV file.
Genome_build: GRCm38.87
Supplementary_files_format_and_content: The processed files are compressed TSV files containing UMIFM count matrices from a single library.

molecule: polyA RNA

source_name: Microdissected brain tissue containing habenula

growth_protocol: Mice were pair-housed in standard 12:12 light-dark cycles (7:00 AM - 7:00 PM) with ad-libitum food and water.

extract_protocol:
Mice were transcardially perfused with an ice-cold choline cutting solution (110 mM choline chloride, 25 mM sodium bicarbonate, 12 mM D-glucose, 11.6 mM sodium L-ascorbate, 10 mM HEPES, 7.5 mM magnesium chloride, 3.1 mM sodium pyruvate, 2.5 mM potassium chloride, 1.25 mM sodium phosphate monobasic, saturated with bubbling 95% oxygen/5% carbon dioxide, pH adjusted to 7.4 using sodium hydroxide). Brains were rapidly dissected out and sliced into 200 µm thick coronal sections on a vibratome (Leica Biosystems, VT1000) with a chilled cutting chamber filled with choline cutting solution. Coronal slices containing the habenula were then transferred to a chilled dissection dish containing a choline-based cutting solution for microdissection. Dissected tissue chunks were transferred to cold HBSS-based dissociation media (Thermo Fisher Scientific Cat. # 14170112, supplemented to final content concentrations: 138 mM sodium chloride, 11 mM D-glucose, 10 mM HEPES, 5.33 mM potassium chloride, 4.17 mM sodium bicarbonate, 2.12 mM magnesium chloride, 0.441 mM potassium phosphate monobasic, 0.338 mM sodium phosphate monobasic, saturated with bubbling 95% oxygen/5% carbon dioxide, pH adjusted to 7.35 using sodium hydroxide) and kept on ice until dissections were completed.  Dissected tissue chunks for each sample were pooled for each hemisphere for the subsequent dissociation steps. Tissue chunks were first mixed with a digestion cocktail (dissociation media, supplemented to working concentrations: 20 U/ml papain, 0.05 mg/mL DNAse I) and incubated at 34 °C for 90 min with gentle rocking. The digestion was quenched by adding dissociation media supplemented with 0.2% BSA and 10 mg/ml ovomucoid inhibitor (Worthington Cat. # LK003128), and samples were kept chilled for the rest of the dissociation procedure. Digested tissue was collected by brief centrifugation (5 min, 300 g), re-suspended in dissociation media supplemented with 0.2% BSA, 1 mg/ml ovomucoid inhibitor, and 0.05 mg/mL DNAse I. Tissue chunks were then mechanically triturated using fine-tip plastic micropipette tips of progressively decreasing size. The triturated cell suspension was filtered through a 40 µm cell strainer (Corning 352340) and washed in two repeated centrifugation (5 min, 300 g) and re-suspension steps to remove debris before a final re-suspension in dissociation media containing 0.04% BSA and 15% OptiPrep (Sigma D1556). Cell density was calculated based on hemocytometer counts and adjusted to approximately 100,000 cells/ml. Single-cell encapsulation and RNA capture on the InDrop platform was performed at the Harvard Medical School ICCB Single Cell Core using v3 chemistry hydrogels based on previously described protocols (Zilionis et al., 2017). Suspensions were kept chilled until the cells were flowed into the microfluidic device. Libraries were prepared and indexed following the protocols referenced above, and sequencing-ready libraries were stored at -80 °C. Libraries from different samples were pooled and sequenced on an Illumina NextSeq 500 (High Output v2 kits).
Libraries were constructed following the protocols described in Zillionis et al. (2017) for inDrop v3 hydrogels. 2 libraries were pooled for sequencing and demultiplexed using library barcodes (see README file). R1 is the biological read, R2 is the first half of the hydrogel barcode, R3 is the library index, and R4 contains the second half of the hydrogel barcode, UMI, and fraction of the polyA tail.

tag: age

value: 8-10 weeks

tag: Sex

value: Male

value: habenula

tag: hemisphere

value: left and right mixed samples (non-demultiplexed)


title: Healthy group rep12 (gilt)

value: healthy


title: habenula, sample 3

description: Contains libraries Hab161103.1 and Hab161103.2 Please see README file containing library barcodes for demultiplexing.


title: habenula, sample 4

description: Contains libraries Hab161105.1 and Hab161105.2 Please see README file containing library barcodes for demultiplexing.


title: Healthy group rep11 (barrow)


title: Entry group rep8 (gilt)

value: entry


title: Bone marrow, MDS_2

value: MDS

value: Luciferase

value: Egr1+/-, Apc del/+, Luc shRNA BM transplanted into WT recipient


title: Veh 1

value: vehicle


title: Entry group rep7 (gilt)


title: Bone marrow, MDS_1

value: Egr1, Apc

value: ENU-both donor and recipient

value: bone marrow


title: 786-O-VectorControl_rep3

city: Guangzhou

first: Yifeng

last: Luo

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Institute of Respiratory Diseases of Sun Yat-sen University

institute: The First Affiliated Hospital of Sun Yat-sen University

description: Gene expression of Kidney cancer

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the GRCh38 genome assembly using Hisat2 version 2.1.0 with default parameters
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR function package in R program version 3.4.3
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: 786-O Cell Line

growth_protocol: All cells were cultured in their paired medium and incubated at 37°C in 5% CO2

extract_protocol:
Total RNA from lung  cancer and kidney cancer cells (includingA549-NC, A549-OE-GPD1; 786-O-NC, 786-O-OE-GPD1) were isolated by  using a RNeasy mini kit (Qiagen, Germany) and extracted by chloroform. RNA degradation and contamination were monitored on 1% agarose gels and purity was checked by the NanoPhotometer spectrophotometer (IMPLEN, CA USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer(Life Technologies, CA, USA) and integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzeer 2100 system (Agilent Technologies, CA, USA ).
Sequencing libraries were generated using NEBNest UltraTM RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: A549 and 786-O cell line were transfected with GPD1-overexpression lentivirus or blank ventor lentivirus as control group. In metform treatment group, cells were treated with the medium contains 10mM metformin.

tag: cell line

tag: genotype/variation

value: Vector Control

tag: cancer type

value: Kidney cancer


title: KO5 I

city: Montréal

first: Tarik

last: Moroy

state: Québec

address: 110 Avenue des Pins

institute: Institut de recherches cliniques de Montréal (IRCM)

description: KO5 I

data_processing:
Trimming: Trimmomatic v0.36 with TRAILING:30, SLIDINGWINDOW:4:20 and MINLEN:30
Pseudoalignment: Kallisto quant v0.44 with default parameters values
Differential expression: DESeq2 v1.20.0 with R v3.5.0 and Bioc 3.7
Genome_build: Mus musculus Ensembl v94
Supplementary_files_format_and_content: Excel files containing raw counts and TPM.
Supplementary_files_format_and_content: Differential expression results

source_name: Peritoneal macrophages

growth_protocol: Peritoneal macrophages were extracted from both WT and  HIF-1ɑ-/- mice and plated for 4 hours, prior to infection. Then, non-adherent cells were removed by washing with warm media and cells were infected with L. donovani promastigotes for 6 hours, at a ratio of 10:1.

extract_protocol: The NEBNext Ultra II directional RNA library prep kit for Illumina (New Englands Biolabs Inc., Ipswich, MA, USA) was used to prepare total RNA sequencing libraries, according to manufacturer’s instruction. Briefly, 100 ng of total RNA was used. Ribosomal RNA (rRNA) including both cytoplasmic and mitochondrial rRNA was removed using RNaseH-based method (NEBNext rRNA depletion kit; New Englands Biolabs Inc., Ipswich, MA, USA). Following purification with Agencourt RNAClean XP beads (Beckman Coutler, Missisauga, Ontario, Canada), the RNA was fragmented using divalent cations under elevated temperature. The fragmented RNA was used as a template for cDNA synthesis by reverse transcriptase with random primers. The specificity of the strand was obtained by replacing the dTTP with the dUTP. This cDNA was subsequently converted to double-stranded DNA and end-repaired. Ligation of adaptors was followed by a purification step with AxyPrep Mag PCR Clean-up kit (Axygen, Big Flats, NY, USA), by an excision of the strands containing the dUTPs and finally, by a PCR enrichment step of 11 cycles to incorporate specific indexed adapters for the multiplexing. The quality of final amplified libraries was examined with a DNA screentape D1000 on a TapeStation 2200 and the quantification was done on the QBit 3.0 fluorometer (ThermoFisher Scientific, Canada). Subsequently, total RNA-seq librairies with unique index were pooled together in equimolar ratio and sequenced for paired-end 125 pb sequencing using one lane of a high ouput flowcell on an HiSeq 2500 V4 system at the Next-Generation Sequencing Plateform, Genomics Center, CHU de Québec-Université Laval Research Center, Québec City, Canada.

treatment_protocol: At the desired time point (6 hours post-infection), non-phagocytosed parasites were removed by washing adherent cells with warm media and RNA was preserved by adding TRI reagent to each well (500 ul/well).

tag: infection

value: Infected

tag: genotype


title: LSK bone marrow cells, EAP_E3

source_name: LSK (Lin-, Sca1+, Kit+) bone marrow cells

tag: strain

value: prior to myeloid disease

tag: treatment

value: Egr1+/-, Apc del/+, Trp53 shRNA BM transplanted into WT recipient

tag: cell type


title: 786-O-VectorControl_rep2

description: Gene expression of Kidney cancer


title: KO4 I

description: KO4 I


title: KO3 I

description: KO3 I


title: 786-O-VectorControl_rep1

description: Gene expression of Kidney cancer


title: LSK bone marrow cells, EAP_E1

tag: tumor stage

tag: haploinsufficiency

tag: shRNA

value: LSK (Lin-, Sca1+, Kit+) bone marrow cells


title: Sick group rep7 (gilt)

value: Duroc

value: sick


title: LSK bone marrow cells, EAP_E2

tag: transplant

tag: mouse tag number


title: Healthy group rep10 (gilt)

tag: breed

tag: group

value: healthy


title: KO2 I

description: KO2 I


title: 786-O-VectorControl_Metformin-rep3

description: Gene expression of Kidney cancer

value: metformin


title: LSK bone marrow cells, EAP_3

value: no ENU


title: Sick group rep6 (gilt)


title: LSK bone marrow cells, EAP_2


title: KO1 I

description: KO1 I


title: habenula, sample 1

description: Contains libraries Hab160822.1 and Hab160822.2 Please see README file containing library barcodes for demultiplexing.

tag: age

value: 8-10 weeks

tag: Sex

value: Male

tag: tissue

value: habenula

value: left and right mixed samples (non-demultiplexed)


title: WT5 I

description: WT5 I

value: Wild type


title: Healthy group rep9 (gilt)


title: 786-O-VectorControl_Metformin-rep2

description: Gene expression of Kidney cancer

tag: cell line

tag: genotype/variation


title: WT4 I

description: WT4 I

tag: infection


title: Entry group rep6 (gilt)

value: entry


title: LSK bone marrow cells, EAP_1

value: Egr1, Apc

value: WT BM_transplanted into WT recipient


title: Healthy group rep8 (gilt)


title: 786-O-GPD1_rep2

description: Gene expression of Kidney cancer

value: GPD1 Overexpression

tag: cancer type

value: Kidney cancer


title: 786-O-GPD1_rep1

description: Gene expression of Kidney cancer


title: WT3 I

description: WT3 I

value: Infected

tag: genotype

tag: strain


title: Sick group rep5 (gilt)


title: 786-O-VectorControl_Metformin-rep1

description: Gene expression of Kidney cancer

value: Vector Control

tag: treatment


title: LSK bone marrow cells, WT_X2

tag: tumor stage

value: prior to myeloid disease

value: Luciferase

tag: cell type

value: LSK (Lin-, Sca1+, Kit+) bone marrow cells


title: WT2 I

description: WT2 I


title: Sick group rep4 (gilt)

value: Duroc

value: sick


title: LSK bone marrow cells, WT_X1

tag: haploinsufficiency

tag: shRNA

value: no ENU


title: 786-O-GPD1_Metformin-rep3

description: Gene expression of Kidney cancer

value: metformin


title: Healthy group rep7 (gilt)

value: healthy


title: 786-O-GPD1_Metformin-rep2

description: Gene expression of Kidney cancer


title: LSK bone marrow cells, WT_3

tag: transplant

value: WT BM, no transplant

tag: mouse tag number


title: LSK bone marrow cells, WT_2


title: KO4 U

description: KO4 U

value: Uninfected


title: 786-O-GPD1_rep3

description: Gene expression of Kidney cancer


title: 786-O-GPD1_Metformin-rep1

description: Gene expression of Kidney cancer


title: LSK bone marrow cells, WT_1

value: WT BM_no transplant


title: Healthy group rep6 (gilt)

tag: breed

tag: group


title: A549-VectorControl_rep2

description: Gene expression of Lung cancer

source_name: A549 Cell Line

value: Lung cancer


title: WT5 U

description: WT5 U

value: Wild type


title: LSK bone marrow cells, WT_X3

value: WT BM_transplanted into WT recipient


title: KO1 U

description: KO1 U


title: Sick group rep3 (gilt)


title: HT29-Furin-KO- replicate2

city: Leuven

first: Zongsheng

last: He

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Base calling was made with Illumina's bcl2fast package,
Adapters were filtered with ea-utils,
Alignment was performed with Tophat2,
Read count per genes was done with HT-Seq count,
Differential expression analysis was performed with R-package deseq,
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts values for each Sample ...

source_name: Colorectal cancer cells

growth_protocol: DLD1 and HCA7 cell lines were grown in DMEM/F12 medium supplemented with 10% FCS, 100 units/ml penicillin and 100µg/ml streptomycin. HT29 cell line was grown in McCoy's 5A (Modified) medium supplemented with 10% FCS, 100 units/ml penicillin and 100µg/ml streptomycin.

extract_protocol:
Cells were harvested, and RNA was isolated using NucleoSpin® RNA kit.
1µg of total RNA were used for library generation using Illumina TruSeq Stranded mRNA HT Sample Prep Kit strictly following the manufacturer's protocol.

treatment_protocol: No treatment

value: Colorectal

value: Furin-KO


title: WT4 U

description: WT4 U


title: HT29-Furin-KO- replicate1


title: A549-VectorControl_Metformin-rep3

description: Gene expression of Lung cancer

value: Vector Control


title: HT29-WT - replicate2


title: A549-VectorControl_rep1

description: Gene expression of Lung cancer


title: WT3 U

description: WT3 U


title: KO5 U

description: KO5 U


title: Healthy group rep4 (barrow)


title: A549-VectorControl_Metformin-rep2

description: Gene expression of Lung cancer


title: Entry group rep5 (gilt)

value: entry


title: WT2 U

description: WT2 U


title: KO3 U

description: KO3 U


title: HCA7-Furin-KO- replicate2


title: Entry group rep4 (gilt)


title: Entry group rep3 (barrow)


title: A549-VectorControl_rep3

description: Gene expression of Lung cancer


title: Healthy group rep3 (barrow)


title: HCA7-Furin-KO- replicate1


title: A549-GPD1_rep3

description: Gene expression of Lung cancer

value: GPD1 Overexpression


title: Entry group rep2 (barrow)


title: Healthy group rep5 (barrow)


title: A549-GPD1_rep2

description: Gene expression of Lung cancer


title: HCA7-WT - replicate1


title: HCA7-WT - replicate2


title: HT29-WT - replicate1


title: A549-GPD1_Metformin-rep3

description: Gene expression of Lung cancer


title: DLD1-Furin-KO- replicate2


title: ACHN-sunitinib resistant Clone3

city: Shenyang

first: Yunhong

last: Zhan

address: No. 36 Sanhao Street

institute: Shengjing Hospital of China Medical University

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions, Analysis tool for nrStar™ Human Functional LncRNA PCR Array (v1.02).
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1, RPLP0.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The analytical tool automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: ACHN-sunitinib resistant Clone3

label_protocol: 200ng RNA was reverse transcribed to cDNA in 20μl system by SuperScriptTM reverse transcriptase kit (Thermo Fisher Scientific).  Real-time PCR was performed using the Mx3000P real-time PCR system (Thermo Fisher Scientific, Waltham, MA, USA). PCR was carried out as follows: 40 cycles of 94 °C for 15s, 60 °C for 10s and 72 °C for 20s.

growth_protocol: Human renal carcinoma cell lines ACHN was obtained from Cell Bank of the Chinese Academy of Sciences  (Shanghai, China) and was exposed to stepwise increasing sunitinib for over 10 months. The survival cells were subsequently passaged and grew under the same conditions for more than 12 passages with 0.02μM sunitinib. The sunitinib-adapted cells were termed ACHN-SR. Cells were cultureed in DMEM, supplemented with 10% FBS. All cell lines were maintained in a humidified incubator with 5% of CO2 and 95% air at 37°C.

extract_protocol: Total RNA was extracted by 1ml TRIzolTM Plus RNA Purification Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s protocol.

tag: sample type

value: renal cell carcinoma cell

value: sunitinib-resistant subline

tag: passage


title: A549-VectorControl_Metformin-rep1

description: Gene expression of Lung cancer

tag: cell line


title: Entry group rep1 (gilt)

value: Duroc


title: Sick group rep2 (barrow)

value: sick


title: A549-GPD1_Metformin-rep2

description: Gene expression of Lung cancer

tag: genotype/variation

value: metformin


title: ACHN-sunitinib resistant

description: Test

source_name: ACHN-sunitinib resistant


title: DLD1-WT - replicate2

tag: tissue


title: ACHN Clone2

description: Control

source_name: ACHN Clone2

value: parental cell line


title: ACHN Clone3

description: Control

source_name: ACHN Clone3


title: WT1 U

description: WT1 U

tag: infection


title: A549-GPD1_Metformin-rep1

description: Gene expression of Lung cancer

tag: cancer type


title: Healthy group rep2 (gilt)

source_name: Peripheral blood

value: healthy


title: Healthy group rep1 (barrow)


title: DLD1-WT - replicate1

tag: genotype


title: ACHN-sunitinib resistant Clone2

description: Test

source_name: ACHN-sunitinib resistant Clone2


title: ACHN Clone1

description: Control

source_name: ACHN Clone1


title: Mouse melanocytes flow sorted  E17.5 pc, rep3

status: Public on Mar 14 2020

city: Bethesda

first: Paul

last: Meltzer

address: 9100 Rockville Pike

institute: NCI/NIH

hyb_protocol: Per manufacturer recommendation.

scan_protocol: Per manufacturer recommendation.

data_processing: A variance stabilization transformation followed by quantile normalization and quality assessment were performed using the lumi bioconductor package.

label_protocol: Per manufacturer recommendation.

growth_protocol: A double homozygous Dct-rtTA/TRE-H2BGFP transgenic mouse line (Dct-GFP) was established in the albino FVB/N background, and males were crossed with wildtype FVB/N females to produce litters that were 100% Dct-GFP double heterozygous.

extract_protocol: Melanocytes were isolated from the dorsal skin of Dct-GFP mouse pups irradiated at P1 with either UVB or UVA. Doxycycline-induced GFP-labeled melanocytes were isolated via fluorescence-activated cell sorting (FACS) at 1 day, 6 days, and 21 days post irradiation. Following FACS collection of cells into PBS+1% BSA solution, the cells were centrifuged at 4C. Total RNA was isolated from the pelleted cells by Trizol (Invitrogen) organic extraction, followed by the RNeasy Micro Kit (Qiagen Sciences, MD, USA) procedure.

treatment_protocol: Precisely defined wideband wavelengths and physiologically relevant doses of UVB (output peak = 308 nm; total dose = 6 kJ/m2; equivalent to 15 times the Standard Erythemal Dose) and UVA (output peak = 375 nm; total dose = 150 kJ/m2) were used to irradiate Dct-GFP neonatal mice at postnatal day 1 (P1). To avoid potential complications of GFP expression, including toxicity associated with chronic expression and UV absorption, GFP was routinely induced by doxycycline administration only after UV irradiation, 24 hours prior to skin harvest.

tag: strain/background

value: FVB/N

value: double heterozygous Dct-rtTA/TRE-H2BGFP (Dct-GFP)

tag: developmental stage

value: embryo

value: melanocytes

tag: uv treatment

tag: days to harvest of cells

value: no UV


title: A549-GPD1_rep1

description: Gene expression of Lung cancer

value: Lung cancer

tag: treatment


title: Sick group rep1 (barrow)


title: Mouse melanocytes flow sorted  E17.5 pc, rep1

tag: cell type


title: Mouse melanocytes flow sorted  E17.5 pc, rep2


title: DLD1-Furin-KO- replicate1

value: Colorectal

value: Furin-KO


title: Total_III

city: New York

first: Kateri

last: Moore

address: One Gustave L. Levy Place, Box 1496

department: Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The reads were then mapped to the mouse Ensembl GRCm38 cDNA reference and quantified using Kallisto v0.43.0 with parameters -t 8 -s 5 -l 100 --single -o.
Reads were normalized across samples using quantile normalization to generate normalized abundance measurements.  Zeros were further eliminated by increasing all values by 1.1, and then log2 transforming the data.
Genome_build: GRCm38
Supplementary_files_format_and_content: File contains qunatile normalized reads in transcripts per kilobase million (TPM), shifted to eliminate zeros and log2 transformed

extract_protocol:
Bone marrow from the tibia, femur, pelvic bones, sternum, and spine was harvested by crushing the bones with a mortar and pestle in a PBS buffer supplemented with 5% new born calf serum. Cells were triturated to obtain a single cell suspension, and bone debris was removed by filtering through a 70μm cell strainer. Red cells were lysed with an ammonium chloride lysis buffer. Cells were first stained with biotin-conjugated lineage marker's anti-CD48, and anti-Flk2, followed by anti-biotin superparamagnetic beads (Dynabeads® Biotin Binder, Life technologies), and lineage marker expressing cells were depleted via magnetic separation. The fraction enriched for Lineage-/low cells was further incubated with antibodies against CD150, c-Kit, Sca1, and fluorophore-conjugated streptavidin. HSCs were sorted as LSK/CD48-/Flk2-/CD150+ cells, and the HSC population were sorted into subpopulations based on label retention of H2BGFP. Cells were sorted into PBS with 5% newborn calf serum, pelleted, and resuspended in Trizol for RNA extraction. Glycoblue (15ug/ml) was added prior to RNA precipitation.
Libraries were prepared according to manufactures instructions (Clontech, SMART-Seq v4 Ultra Low Input RNA Kit). Briefly, up to 1ng of Total RNA from each sample was taken for library cDNA synthesis. The resulting cDNA was quantified using Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen), and thecDNA integrity was assessed by Bioanalyzer.  100-300pg of cDNA was used for further library preparation uwing Nextera XT DNA Sample Preparation Kit (Illumina). Barcoded library concentrations and quality were assessed by Qbit (Invitrogen) and Bioanalyzer (Agilent).

treatment_protocol: hCD34xH2BGFP mice were placed and maintained dox (1mg/ml in the drinking water, changed weekly) starting at 2-4 months of age until tissue harvest.

tag: strain

value: hCD34-tTA x TetO-H2BGFP

tag: age

value: 6.5 months

value: bone marrow-derived hematopoietic stem cells (HSCs)

tag: dox treatment length

value: 16 weeks


title: Total_II

value: 5.5 months

value: 14 weeks


title: GFP1_II


title: GFP1_III


title: GFP2_II


title: GFP2_III


title: GFP2_I

value: 5 months

value: 12 weeks


title: GFP3_III


title: GFP3_II


title: GFP4_III


title: GFP4_II


title: GFP3_I


title: GFP1_I


title: NS-SV-DC

city: Tokushima

first: noriko

last: mizusawa

address: 3-18-15 Kuramoto-cho

department: Department of Medical Pharmacology

country: Japan

institute: The University of Tokushima Graduate School, Institute of Health Biosciences

hyb_protocol: Approximately 1.85 μg of fragmented and labeled DNA target was hybridized to the Affimetrix GeneChip® Human Gene 1.0 ST Array at 45˚C for 17 h on a GeneChip® Hibridization Oven 640 (Affimetrix) according to the manufacture’s recommendation.

scan_protocol: GeneChip® Scanner 3000 7G (Affimetrix)

data_processing: Signals were estimated by RMA16 from GeneSpring software version 12

source_name: NS-SV-DC (human submandibular gland cell lines, duct-like)

label_protocol: First strand cDNA was synthesized from 400 ng of total RNA by using GeneChip® Whole Transcript (WT) cDNA Synthesis and Amplification Kit (Affimetrix) accoding to the manufacturer’s instructions. Ten μg of cDNA were input into the second-cycle cDNA reaction. cDBA was fragmented and end-labeled with the GeneChip® WT Terminal Labeling Kit (Affimetrix).

extract_protocol: Total RNA was extracted from NS-SV-AC and NS-SV-DC cells using a mirVana PARIS kit (Ambion, Austin, TX, USA).  Relative purity was examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: NS-SV-AC and NS-SV-DC cells were cultured at 37°C in SFKM (Gibco BRL, Grand Island, NY, USA) in an incubator with an atmosphere containing 5% CO2.

value: NS-SV-DC

value: human submandibular gland (duct-like) cell line


title: Total_I


title: NS-SV-AC

source_name: NS-SV-AC (human submandibular gland cell lines, acinar-like)

value: NS-SV-AC

value: human submandibular gland (acinar-like) cell line


title: GFP4_I


title: genomic DNA from healthy adult distal femur trabecular bonePanu34_B (baboon_intraspecific)

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

source_name: healthy adult distal femur trabecular bone from baboon

tag: Sex

value: female

tag: age (years)

tag: steady state weight (kg)

value: bone

tag: age cohort

value: adult

tag: disease state

value: healthy

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 Caet10 (vervet_intraspecific)

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: Chlorocebus aethiops

organism: Chlorocebus aethiops

tag: Sex

value: male

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: genomic DNA from healthy adult distal femur trabecular bonePanu29_B (baboon_intraspecific)

tag: steady state weight (kg)

tag: age cohort

tag: disease state

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 healthy adult distal femur trabecular bonePanu50_B (baboon_intraspecific)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

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)


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

source_name: distal femur trabecular bone from vervet

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: genomic DNA from distal femur trabecular bone Caet02 (vervet_intraspecific)

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: genomic DNA from healthy adult distal femur trabecular bonePanu37_B (baboon_intraspecific)

tag: steady state weight (kg)

tag: age cohort

tag: disease state

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 Caet08 (vervet_intraspecific)

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: genomic DNA from healthy adult distal femur trabecular bonePanu36_B (baboon_intraspecific)

tag: steady state weight (kg)

tag: age cohort

tag: disease state

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 Caet09 (vervet_intraspecific)

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: genomic DNA from healthy adult distal femur trabecular bonePanu06_B (baboon_intraspecific)

tag: steady state weight (kg)

tag: age cohort

tag: disease state

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 healthy adult distal femur trabecular bonePanu13_B (baboon_intraspecific)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

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)


title: genomic DNA from healthy adult distal femur trabecular bonePanu49_B (baboon_intraspecific)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

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: C09

city: Cambridge

first: Martin

middle: Lee

last: Miller

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description: Gene expression data

hyb_protocol: Hybridization was performed using the following protocol: "GeneChip WT Pico Reagent Kit Manual Target Preparation for GeneChip Whole-Transcript Expression Arrays".

scan_protocol: The Affymetrix GCS3000 scanner was used along with Affymetrix GeneChip Command Console software for imaging processing.

data_processing: Affymetrix Expression Console software version 1.4.1.46 was used for primary analysis, and SST-RMA was used as the processing algorithm. To define whether a gene was expressed or not we used the Affymetrix Transcriptome Analysis Console version 3.1.0.5 and implemented an alternative-splicing analysis, which gives an Expressed column with True or False values. For genes for which this approach gives an ambiguous result (e.g. since some genes have more than one probe aligning to it, if one probe gives True and the other False), then we used the median expression level (accross probes) of the SRY gene for each sample as a threshold for that tumor sample. For indivdual gene expression level analysis, we first filtered the probes that hybridize with protein coding genes. Then we assigned the median gene expression value for each gene, and we normalized the gene expression values using the "normalize.loess" function of the R package "affy". We selected the distributions that were not significantly different between them. The gene expression levels obtained were then compared between samples. Here we provide the CHP files and gene level values after the SST-RMA normalization only, but we can provide the SST-RMA+loess normalized gene expression values upon request. The HeLa cell lines were used only by Affymetrix as their internal controls and were not incorporated in any analysis in the study.

source_name: Pouch of Douglas

label_protocol: Labeling was performed using the following protocol: "GeneChip WT Pico Reagent Kit Manual Target Preparation for GeneChip Whole-Trascript Expression Arrays".

extract_protocol: RNA was extracted from FFPE samples using the RecoverAll Total Nucleic Acid Isolation from Thermo Fisher Scientific (Catalog Number: AM1975).

tag: subject id

tag: gender

value: Female

tag: tissue

value: Pouch of Douglas

tag: condition

value: Malignant

tag: tumor type

value: High grade serous ovarian cancer

tag: tumor stage

value: IV

tag: sample type

value: FFPE


title: genomic DNA from healthy adult distal femur trabecular bonePanu18_B (baboon_intraspecific)

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)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)


title: C12

description: Gene expression data

source_name: Omentum

tag: subject id

tag: gender

tag: tissue

value: Omentum

tag: condition

tag: tumor type

tag: tumor stage

value: IIIC

tag: sample type


title: D02

description: Gene expression data

source_name: Serosa

value: Serosa


title: genomic DNA from healthy adult distal femur trabecular bonePanu44_B (baboon_intraspecific)

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: 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 Caet06 (vervet_intraspecific)

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: 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)


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

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: 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: D01

description: Gene expression data

tag: subject id

tag: gender

tag: tissue

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: C10

description: Gene expression data

source_name: Right psoas

value: Right psoas


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

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)


title: D03

description: Gene expression data

source_name: Ovary

tag: subject id

tag: gender

tag: tissue

value: Ovary

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: genomic DNA from healthy adult distal femur trabecular bonePanu40_B (baboon_intraspecific)

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: 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 Caet03 (vervet_intraspecific)

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: 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)


title: C08

description: Gene expression data

tag: subject id

tag: gender

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: genomic DNA from healthy adult distal femur trabecular bonePanu10_B (baboon_intraspecific)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

tag: age cohort

tag: disease state

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (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: 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)