title: C11

description: Gene expression data

tag: subject id

tag: gender

tag: tissue

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


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

status: Public on Mar 14 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 vervet

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: Chlorocebus aethiops

label: Cy5 and Cy3

molecule: genomic DNA

organism: Chlorocebus aethiops

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: Sex

value: female

tag: age (years)

value: bone

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: genomic DNA from healthy adult distal femur trabecular bonePanu43_B (baboon_intraspecific)

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

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

organism: Papio sp.

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue

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)


title: genomic DNA from healthy adult distal femur trabecular bonePanu48_B (baboon_intraspecific)

source_name: healthy adult distal femur trabecular bone from baboon

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: genomic DNA from healthy adult distal femur trabecular bonePanu56_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 bonePanu21_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: C04

type: RNA

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.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Ovary

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: Ovary

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 bonePanu42_B (baboon_intraspecific)

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)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)


title: C03

description: Gene expression data

tag: subject id

tag: gender

tag: tissue

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: genomic DNA from healthy adult distal femur trabecular bonePanu45_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: C01

description: Gene expression data

source_name: Omentum

tag: subject id

tag: gender

tag: tissue

value: Omentum

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: B10

description: Gene expression data

value: IVB


title: B12

description: Gene expression data

source_name: Adnexal surface

value: Adnexal surface


title: B08

description: Gene expression data

value: IIIC


title: B11

description: Gene expression data


title: B07

description: Gene expression data


title: genomic DNA from healthy adult distal femur trabecular bonePanu33_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: genomic DNA from healthy adult distal femur trabecular bonePanu53_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: 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: B06

description: Gene expression data

tag: subject id

tag: gender

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: C02

description: Gene expression data

tag: tissue


title: C06

description: Gene expression data


title: C05

description: Gene expression data


title: B09

description: Gene expression data


title: B05

description: Gene expression data


title: genomic DNA from healthy adult distal femur trabecular bonePanu03_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: genomic DNA from healthy adult distal femur trabecular bonePanu41_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: 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 bonePanu39_B (baboon_intraspecific)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

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: B04

description: Gene expression data

tag: subject id

tag: gender

tag: tissue

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: genomic DNA from healthy adult distal femur trabecular bonePanu08_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 healthy adult distal femur trabecular bonePanu46_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: 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 healthy adult distal femur trabecular bonePanu19_B (baboon_intraspecific)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

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: B03

description: Gene expression data

tag: subject id

tag: gender

tag: tissue

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: 40T: 22 month old tricep muscle rep10

type: SRA

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

library_source: transcriptomic

data_processing:
Illumina Casava 1.8 software used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and mapped to Rnor 6.0 whole genome using RNA-STAR v2.3.0e with parameters --genomeLoad NoSharedMemory --runThreadN 12
Counts within genes were generated using HTSeq, mode union, strand no, annotation file Rattus_norvegicus.Rnor_6.0.80.gtf
Genome_build: RGSC 6.0
Supplementary_files_format_and_content: tab-delimited text file including counts per gene for each sample quantified by HTSeq

molecule: polyA RNA

organism: Rattus norvegicus

source_name: tricep muscle

extract_protocol:
mRNA was extracted using the miRNeasy kit from Qiagen, following the manufacturer's instructions.
TruSeq RNA Library Preparation Kit v2

tag: strain

value: Wistar

value: tricep muscle

tag: age (month)

tag: animal id


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

description: medial condyle distal femur trabecular bone from macaque

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: Macaca mulatta

organism: Macaca mulatta

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)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)


title: genomic DNA from healthy adult distal femur trabecular bonePanu55_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: 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: 40G: 22 month old gastrocnemius muscle rep10

source_name: gastrocnemius muscle

tag: strain

tag: gender

value: gastrocnemius muscle

tag: age (month)

tag: animal id


title: 39T: 22 month old tricep muscle rep9

tag: tissue


title: A08

description: Gene expression data

tag: subject id

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: B01

description: Gene expression data


title: A06

description: Gene expression data


title: 39G: 22 month old gastrocnemius muscle rep9


title: genomic DNA from distal femur trabecular bone Mmul06 (macaque_intraspecific)

source_name: distal femur trabecular bone from macaque

tag: Sex

value: female

tag: age (years)

value: bone

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)


title: genomic DNA from distal femur trabecular bone Mmul02 (macaque_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: 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: A09

description: Gene expression data

tag: subject id

tag: gender

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: genomic DNA from distal femur trabecular bone Mmul07 (macaque_intraspecific)

tag: Sex

tag: age (years)

tag: tissue

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)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)


title: genomic DNA from distal femur trabecular bone Mmul10 (macaque_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: 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 Mmul03 (macaque_intraspecific)

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)


title: A10

description: Gene expression data

tag: subject id

tag: gender

tag: tissue

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: genomic DNA from distal femur trabecular bone Mmul09 (macaque_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: 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: B02

description: Gene expression data

tag: subject id

tag: gender

tag: tissue

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: genomic DNA from distal femur trabecular bone Mmul01 (macaque_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: 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)


title: C07

description: Gene expression data

tag: subject id

tag: gender

tag: tissue

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: A04

description: Gene expression data


title: 37T: 22 month old tricep muscle rep7

tag: strain

tag: age (month)

tag: animal id


title: genomic DNA from distal femur trabecular bone Mmul08 (macaque_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: 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: A11

description: Gene expression data

tag: subject id

tag: gender

tag: tissue

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: 36T: 22 month old tricep muscle rep6

tag: strain

tag: age (month)

tag: animal id


title: 36G: 22 month old gastrocnemius muscle rep6


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

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)


title: A03

description: Gene expression data

source_name: Paracolic gutter

tag: subject id

tag: gender

tag: tissue

value: Paracolic gutter

tag: condition

tag: tumor type

tag: tumor stage

tag: sample type


title: 35T: 22 month old tricep muscle rep5

tag: strain

tag: age (month)

tag: animal id


title: 35G: 22 month old gastrocnemius muscle rep5


title: 38T: 22 month old tricep muscle rep8


title: 34T: 22 month old tricep muscle rep4


title: 34G: 22 month old gastrocnemius muscle rep4


title: A07

description: Gene expression data

value: Female


title: A05

description: Gene expression data

value: Ovary


title: A02

description: Gene expression data

value: Malignant


title: 38G: 22 month old gastrocnemius muscle rep8


title: 33G: 22 month old gastrocnemius muscle rep3


title: 33T: 22 month old tricep muscle rep3


title: 32T: 22 month old tricep muscle rep2


title: 32G: 22 month old gastrocnemius muscle rep2


title: NAC39B

description: Gene expression data

treatment_protocol: Samples with A suffix did not receive any treatment. Samples with the B suffix, were collected after patients were treated with neoadjuvant chemotherapy (cisplatin + taxane) as the standard of cancer in HGSOC requires.

tag: treatment status

value: post-treatement

value: High grade serous ovarian cancer


title: 31T: 22 month old tricep muscle rep1


title: A01

description: Gene expression data

value: FFPE


title: lidocaine_2 [DRG tissue]

city: Shanghai

first: Qianqian

last: YIN

address: Chongqing South Road

department: Institute of Immunology

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina bcl2fastq software was used for base-calling
STAR(2.5.3a) software was used for read alignment, parameter setting as follows:—twopassMode Basic|--outSAMstrandField intronMotif|--alignSJstitchMismatchNmax 5 -1 5 5
FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) was calculated, and then normalized with TMM standard; DESeq2 software was used to filter differentially expressed genes, according to the standard that |log2(fold change)|>=1 and P value <=0.05
Genome_build: rno6
Supplementary_files_format_and_content: xls

source_name: DRG tissue

growth_protocol: SD rats of 250g body weight were kept in the SPF condition.

extract_protocol:
Rats were sacrificed and DRG tissues were collected. DRG tissues were freezed quickly in liquid nitroge and grind up in the tissue lyser. Total RNA was extracted using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats were divided into 3 groups: 1. WT group: WT rats without any treatment; 2. IMQ group:  rats treated with IMQ-induction on the back skin for consecutive 6 days; 3. lidocaine group: rats treated with IMQ-induction for consecutive 6 days in addition to 4 days' epidural injection of 1% lidocaine from day 3 of IMQ induction.

value: Sprague Dawley

value: DRG tissue

tag: weight

tag: genotype

value: imiquimod(IMQ)-induced psoraisis-like rat model with epidural injection of 1percent lidocaine


title: NAC23B

description: Gene expression data

value: Omentum

value: IV


title: NAC32A

description: Gene expression data

source_name: Pleural box

value: pre-treatment

value: Pleural box


title: 37G: 22 month old gastrocnemius muscle rep7

value: Wistar

value: male

value: gastrocnemius muscle


title: 31G: 22 month old gastrocnemius muscle rep1


title: IMQ_2 [DRG tissue]

value: imiquimod(IMQ)-induced psoraisis-like rat model


title: NAC34B

description: Gene expression data

value: Female


title: NAC34A

description: Gene expression data

source_name: Umbilical hernia

value: Umbilical hernia


title: NAC23A

description: Gene expression data

source_name: Peritoneal box

value: Peritoneal box

value: Malignant


title: 30T: 20 month old tricep muscle rep10

value: tricep muscle


title: NAC39A

description: Gene expression data

source_name: Pelvic box

value: Pelvic box

value: High grade serous ovarian cancer

value: FFPE


title: NAC24B

description: Gene expression data

value: post-treatement

value: Ovary

value: IIIC


title: NAC33B

description: Gene expression data

value: IV


title: 30G: 20 month old gastrocnemius muscle rep10


title: lidocaine_1 [DRG tissue]

value: Sprague Dawley

value: DRG tissue

value: imiquimod(IMQ)-induced psoraisis-like rat model with epidural injection of 1percent lidocaine


title: genomic DNA from healthy adult distal femur trabecular bonePanu47_B (baboon_intraspecific)

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: 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: WT_3 [DRG tissue]

tag: strain

tag: tissue

tag: weight

tag: genotype

value: Wild type


title: NAC22B

description: Gene expression data

tag: treatment status

tag: gender

value: Female

tag: condition

value: Malignant

tag: tumor type

tag: tumor stage

tag: sample type


title: NAC33A

description: Gene expression data

source_name: Anterior abdominal wall

value: pre-treatment

value: Anterior abdominal wall


title: NAC32B

description: Gene expression data

value: High grade serous ovarian cancer

value: FFPE


title: WT_2 [DRG tissue]


title: IMQ_1 [DRG tissue]

value: imiquimod(IMQ)-induced psoraisis-like rat model


title: 29T: 20 month old tricep muscle rep9

value: Wistar

value: male

value: tricep muscle

tag: age (month)

tag: animal id


title: NAC36B

description: Gene expression data

value: post-treatement

value: Ovary

value: IV


title: NAC22A

description: Gene expression data

source_name: Pelvic peritoneum

value: Pelvic peritoneum

value: IIIC


title: WT_1 [DRG tissue]

value: Sprague Dawley

value: DRG tissue


title: 29G: 20 month old gastrocnemius muscle rep9

value: gastrocnemius muscle


title: NAC24A

description: Gene expression data

value: Female

value: Peritoneal box

value: Malignant


title: Cardiomyocyte RNA-seq, no drug treatment, replicate 3

city: Dallas

first: Jin

last: Chen

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description:
rRNA-depleted total RNA
RNA_CM_fw.wig
RNA_CM_rc.wig

data_processing:
3' linker sequences were removed from reads and samples were de-multiplexed using FASTX-clipper and -barcode splitter, respectively.
Unique molecular identifiers (UMIs) and sample barcodes were removed from the reads using a custom Python script. UMIs were appended to the FASTQ header of each read immediately following the cluster y-coordinate (e.g. if UMI=AGTAG, header will resemble @K00153:418:HKMLHBBXX:1:1101:3437:1191_AGTAG ...).
Bowtie v1.1.2 was used to filter out reads aligning to rRNAs, tRNAs, and other contaminants. All surviving reads were aligned to a custom human transcriptome using tophat v2.1.1.
The ORF-RATER pipeline was applied to aligned reads to identify high-confidence sites of translation
Genome_build: hg19
Supplementary_files_format_and_content: WIG files to visualize aligned reads, as well as a BED file (orfratings.bed) incorporating the results from ORF-RATER

source_name: cell lysate

growth_protocol: WTC iPSCs (Coriell Biorepository #GM25256) were maintained under feeder-free conditions on growth factor-reduced Matrigel (Corning) in mTeSR medium (STEMCELL Technologies). Accutase (STEMCELL Technologies) was used to enzymatically dissociate iPSCs into single cells to passage. To promote cell survival during enzymatic passaging, cells were passaged with 10 uM p160-Rho-associated coiled-coil kinase (ROCK) inhibitor Y-27632 (Selleckchem). iPSCs were differentiated into iPS-derived cardiomyocytes using the WNT modulation-differentiation method following previously published protocols (Mandegar M.A., et al, 2016, Cell Stem Cell and Lian X., et al, 2012, PNAS)

extract_protocol:
Cells were lysed and lysates were clarified by centrifugation at 20,000×g for 10 min.  The lysate is used to prepare RNA-seq libraries, as well as treated with RNase I to  digest RNA not protected by ribosomes for ribosome profiling. For ribosome profiling, high molecular weight species were then isolated by centrifuging lysates through a 34% sucrose cushion at 200,000×g for 4 hours at 4°C. Pellets were resuspended in Trizol (Life Technologies) and the RNA fraction isolated.
Ribosome profiling and RNA-seq libraries were generated essentially as described in MGlincy, N.J. and Ingolia, N.T., 2017, Methods.

tag: cell type

value: iPSC-derived cardiomyocytes

tag: cell line

tag: drug treatment

value: no drug


title: NAC36A

description: Gene expression data

source_name: Pelvic mass

value: pre-treatment

value: Pelvic mass

value: High grade serous ovarian cancer

value: FFPE


title: 28G: 20 month old gastrocnemius muscle rep8

value: Wistar

value: male


title: Cardiomyocyte RNA-seq, no drug treatment, replicate 2


title: iPSC RNA-seq, no drug treatment, replicate 3

description:
rRNA-depleted total RNA
RNA_iPSC_fw.wig
RNA_iPSC_rc.wig

value: iPSC


title: 27T: 20 month old tricep muscle rep7

value: tricep muscle


title: Cardiomyocyte RNA-seq, no drug treatment, replicate 1


title: iPSC RNA-seq, no drug treatment, replicate 2


title: 26G: 20 month old gastrocnemius muscle rep6


title: 26T: 20 month old tricep muscle rep6


title: 28T: 20 month old tricep muscle rep8


title: iPSC RNA-seq, no drug treatment, replicate 1


title: 25T: 20 month old tricep muscle rep5


title: Cardiomyocyte ribosome profiling, no drug treatment, replicate 3

description:
Ribosome protected mRNA fragment
RP_CM_ND_fw.wig
RP_CM_ND_rc.wig

data_processing:
Library strategy: Ribo-Seq
3' linker sequences were removed from reads and samples were de-multiplexed using FASTX-clipper and -barcode splitter, respectively.
Unique molecular identifiers (UMIs) and sample barcodes were removed from the reads using a custom Python script. UMIs were appended to the FASTQ header of each read immediately following the cluster y-coordinate (e.g. if UMI=AGTAG, header will resemble @K00153:418:HKMLHBBXX:1:1101:3437:1191_AGTAG ...).
Bowtie v1.1.2 was used to filter out reads aligning to rRNAs, tRNAs, and other contaminants. All surviving reads were aligned to a custom human transcriptome using tophat v2.1.1.
The ORF-RATER pipeline was applied to aligned reads to identify high-confidence sites of translation
Genome_build: hg19
Supplementary_files_format_and_content: WIG files to visualize aligned reads, as well as a BED file (orfratings.bed) incorporating the results from ORF-RATER


title: 25G: 20 month old gastrocnemius muscle rep5


title: Cardiomyocyte ribosome profiling, no drug treatment, replicate 2


title: NAC28B

description: Gene expression data

value: post-treatement

value: Ovary

value: IV


title: 27G: 20 month old gastrocnemius muscle rep7

value: gastrocnemius muscle


title: NAC31B

description: Gene expression data

value: Female

value: IIIC


title: NAC31A

description: Gene expression data

value: Peritoneal box

value: Malignant


title: Cardiomyocyte ribosome profiling, no drug treatment, replicate 1

value: iPSC-derived cardiomyocytes

value: no drug


title: 24T: 20 month old tricep muscle rep4


title: NAC28A

description: Gene expression data

value: pre-treatment

value: Pleural box


title: NAC17B

description: Gene expression data

value: High grade serous ovarian cancer

value: FFPE


title: NAC19B

description: Gene expression data

source_name: Left ovary

value: Left ovary


title: NAC17A

description: Gene expression data

value: Pelvic box


title: iPSC ribosome profiling, no drug treatment, replicate 3

description:
Ribosome protected mRNA fragment
RP_iPSC_ND_fw.wig
RP_iPSC_ND_rc.wig

value: iPSC


title: iPSC ribosome profiling, no drug treatment, replicate 2


title: 24G: 20 month old gastrocnemius muscle rep4

value: Wistar

value: male


title: 23G: 20 month old gastrocnemius muscle rep3


title: NAC40B

description: Gene expression data

source_name: Ovary

value: post-treatement

value: Ovary


title: iPSC ribosome profiling, no drug treatment, replicate 1


title: 22T: 20 month old tricep muscle rep2

value: tricep muscle


title: NAC38B

description: Gene expression data

source_name: Fallopian tube

value: Female

value: Fallopian tube

value: IIIC


title: NAC19A

description: Gene expression data

value: Peritoneal box

value: Malignant


title: Cardiomyocyte ribosome profiling, harringtonine-treated

description:
Ribosome protected mRNA fragment
RP_CM_Harr_fw.wig
RP_CM_Harr_rc.wig

value: iPSC-derived cardiomyocytes

value: harringtonine


title: 22G: 20 month old gastrocnemius muscle rep2

value: gastrocnemius muscle


title: NAC38A

description: Gene expression data

source_name: Groin box

value: pre-treatment

value: Groin box

value: High grade serous ovarian cancer

value: FFPE


title: iPSC ribosome profiling, harringtonine-treated

description:
Ribosome protected mRNA fragment
RP_iPSC_Harr_fw.wig
RP_iPSC_Harr_rc.wig

value: iPSC


title: 21G: 20 month old gastrocnemius muscle rep1

value: Wistar

value: male


title: NAC35B

description: Gene expression data

value: post-treatement

value: Ovary

value: IV


title: 21T: 20 month old tricep muscle rep1

source_name: tricep muscle

value: tricep muscle


title: NAC27B

description: Gene expression data

source_name: Right ovary area

value: Female

value: Right ovary area

value: IIIC


title: OGTWT rep4 [OGF373-05.FPKM]

city: La Jolla

first: Yongxin

last: Mu

state: CA

address: 9500 Gilman Drive

department: medicine

institute: University of California SD

description:
wt04-OGF373_7_S5_L004
OGF373-05.FPKM

data_processing:
We used Illumia basespace online Tophat App (version 1.0.0), witch runs Bowtie2, TopHat2, the Isaac Variant Caller, and Cufflinks2 to map and align reads to mouse reference genome mm10, and calculated the FPKM for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Mus musculus

extract_protocol:
whole hearts were dissected from 11.5 embryos and snap frozen in liquid nitrogen and stored at -80oC until use.   Trizol was used to isolated total RNAand mRNA was selected using oligoT column. Then about 1ug total RNA was used for library construction using Illumina True seq kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Comparison between control and knockout embryo hearts

tag: strain background

tag: developmenal stage

value: embryonic day 11.5

tag: genotype/variation

value: control

value: heart


title: OGTKO rep2 [OGF373-02.FPKM]

description:
KO02-OGF373_3_S2_L004
OGF373-02.FPKM

value: OGT cadiomyocytes specific knockout using TnT Cre

tag: tissue


title: OGTKO rep1 [OGF373-08.FPKM]

description:
KO01-OGF355_8_S8_L004
OGF373-08.FPKM


title: OGTWT rep3 [OGF373-01.FPKM]

description:
wt03-OGF373_1_S1_L004
OGF373-01.FPKM


title: OGTKO rep3 [OGF373-03.FPKM]

description:
KO03-OGF373_4_S3_L004
OGF373-03.FPKM


title: OGTWT rep2 [OGF373-07.FPKM]

description:
wt02-OGF355_4_S7_L004
OGF373-07.FPKM


title: OGTKO rep4 [OGF37304.FPKM]

description:
KO04-OGF373_5_S4_L004
OGF37304.FPKM


title: CTB-Control, rep3

city: Tampa

first: Ozlem

last: Guzeloglu Kayisli

state: FL

address: 12901 Bruce B Down Blvd

department: Ob and Gyn

institute: University of South Florida

description:
77CT
Gene expression data from CTB treated with vehicle-control.

hyb_protocol: Amplified RNA was hybridized to HumanHT-12 v4 Expression BeadChip using Illumina's Whole-Genome Gene Expression Direct Hybridization Assay Guide. Hybridized samples were washed using same Hybridization Assay Guide and stained with Amersham Cy3-Streptavidin (GE Healthcare PA43001).

scan_protocol: BeadChips were scanned using the Illumina HiScan System.

data_processing: The data were normalised 75th percentile shift and transforming the baseline to the median of all samples with GX 12.6.1 software.

label: Biotin

source_name: Cytotrophoblast cells, control

label_protocol: Total RNA samples were normalized to 500ng using Thermo Scientific NanoDrop concentration readings. Samples were then amplified using Ambion's Illumina TotalPrep RNA Amplification Kit (P/N AMIL1791) following Ambion's protocol. Amplified RNA samples were measured for their concentration using the Thermoscientific NanoDrop and normalized to 750ng.

growth_protocol:
After written Institutional Review Board approval and informed consent, term decidual cells (TDC) were prepared from the decidua obtained from uncomplicated term pregnancies. The decidua was minced, and incubated with 25 mg/ml of collagenase (200 U/mg) (Worthington Biochemical) and 6.25 U/ml of DNase (Sigma-Aldrich). Cell clusters in the final digestate were further disrupted by passage through a 23-gauge needle. The cells were enriched by centrifugation through discontinuous Percoll gradients, and then cultivated over three passages until >99% free of CD45+ leukocytes in basal medium, a phenol red-free 1:1 vol/vol mix of Dulbecco's Modified Eagle Medium (DMEM)/Ham’s F-12 (Life Technologies) with 100 U/ml penicillin, 100 µg/ml streptomycin, 0.25 µg/ml amphotericin B supplemented with 10% charcoal stripped calf serum (SCS). Passaged, confluent, leukocyte-free decidual cells were primed for 13 days in basal medium supplemented with SCS containing 10-8 M 17β-estradiol (E2; Sigma-Aldrich) and 10-7 M medroxyprogesterone acetate (MPA; Sigma-Aldrich). The cultures were then washed twice with PBS and switched to a defined medium consisting of basal medium (without the addition of SCS) plus ITS+ Premix (BD Biosciences), 5 μM FeSO4, 0.5 μM ZnSO4, 1 nM CuSO4 (Sigma-Aldrich), 50 μg/ml ascorbic acid (Sigma-Aldrich) for 24h.
Cytotrophoblasts (CTB) were isolated from human villous tissue at term following trypsin digestion and centrifugation on Percoll gradients. Placental tissue fragments were finely chopped, washed with saline, and treated with trypsin and DNase. The digestate was poured through wire-mesh sieves. The effluent was collected and centrifuged at 500·g for 5 min. The cell pellets were re-suspended for centrifugation on a continuous Percoll gradient. The CTBs sedimenting as a ring of cells at a density of approximately 1.05 g/mL were washed and re suspended in basal medium supplemented with 10% heat-inactivated fetal calf serum (FCS; Hyclone Laboratories, Logan, UT, USA), 2 mml-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 0.25 µg/ml amphotericin B. Immunopurification was carried out to remove other cells using immunomagnetic microspheres conjugated to mouse anti-human CD-45 (immune cell marker) and CD-9 (fibroblast and extravillous trophoblast marker) obtained from Clemente Associates Inc. (Madison, CT) were added to approximately 3 X 10e8 cells. The mixture was then incubated on ice for 30 min with intermittent mixing. Magnetic microparticles were removed using a magnet, and the supernatant was subjected to a second round of immunopurification. Immunopurified CTBs were washed and used to either primary CTBs culture or to generate STBs culture. STBs were generated by culturing CTBs for 72 h in FCS medium. Under these conditions CTBs spontaneously differentiate into STBs. The CTB and STB cultures were then washed twice with PBS and switched to a defined medium consisting of basal medium (without serum) plus ITS+ Premix (BD Biosciences), 5 μM FeSO4, 0.5 μM ZnSO4, 1 nM CuSO4 (Sigma-Aldrich), 50 μg/ml ascorbic acid (Sigma-Aldrich) for 24h.

extract_protocol: Total RNA was isolated using Qiagen miRNeasy Mini Kit (Qiagen, Valencia, CA) and RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: TDC, CTB and STB cells were incubated in define media with ITS without serum for 24 h.

value: villous tissue obtained from term placenta

value: cultured cytotrophoblast

value: female

tag: gestational stage

value: term-uncomplicated pregnancy

tag: treatment

value: vehicle-control


title: 23T: 20 month old tricep muscle rep3

tag: strain

value: Wistar

value: male


title: NAC21B

description: Gene expression data

tag: treatment status

value: post-treatement

tag: gender

value: Ovary

value: Malignant

value: High grade serous ovarian cancer

value: FFPE


title: OGTWT rep1 [OGF373-0602.FPKM]

description:
wt01-OGF355_3_S6_L004
OGF373-0602.FPKM


title: NAC21A

description: Gene expression data

source_name: Pelvic nodule box

value: pre-treatment

value: Female

value: Pelvic nodule box

tag: condition

tag: tumor type

value: IIIC


title: STB-Control, rep3

description:
83ST
Gene expression data from STB treated with vehicle-control.

source_name: Syncytotrophoblast cells, control

value: cultured syncytotrophoblast


title: NAC25B

description: Gene expression data

tag: tumor stage

value: IV

tag: sample type


title: NAC20B

description: Gene expression data


title: NAC20A

description: Gene expression data

source_name: Cul-de-sac box

value: Cul-de-sac box


title: STB-Control, rep1

description:
81ST
Gene expression data from STB treated with vehicle-control.

value: villous tissue obtained from term placenta

value: female


title: TNF_CD45+ cortical cells

first: Johannes

middle: Carolus Magnus

last: Schlachetzki

address: 9500 Gilman Drive  #0651

department: Cellular and Molecular Medicine

institute: UCSD

description:
polyA RNA-single cell
scRNA-Seq generated using 10x genomics Single Cell 3’ Reagent Kits V3.0

data_processing:
Data was mapped using Cell Ranger (10X Genomics) to mm10 and analyzed using the Seurat R toolkit for single cell genomics (Satija et al., 2015).
Genome_build: mm10

source_name: TNFtg

extract_protocol:
Mechanical dissociation of myeloid cells from cortical tissue based on Gosselin et al., Cell 2014. Briefly, the cortex of wt and TNFtg (n=2 per experimental group) were dissected and homogenized by gentle mechanical dissociation at 4°C. Myeloid cells were then enriched by Percoll gradient, washed and then stained for DAPI and with anti-CD11b and anti-CD45 antibody. Life CD11b+CD45+DAPI- cells (containing CD45hi and CD45low/int cells) were sorted into PBS containing 0.04 % BSA.
Using the 10X GemCode technology, single cells were captured with barcoded beads in a droplet emulsion for the RT reaction (10X Genomics®). Libraries were prepared following the standard protocol of 10X Single Cell 3’ v3.0 and sequenced on the Hi-Seq 4000 (Illumina).
10X Single Cell 3’ v3.0

tag: straiin

value: Mus musculus (C57Bl6)

value: Brain Cortex

tag: time

value: 14 weeks

value: myeloid cells (live CD45+)


title: IMQ_3 [DRG tissue]

source_name: DRG tissue

value: Sprague Dawley

value: DRG tissue

tag: weight

tag: genotype

value: imiquimod(IMQ)-induced psoraisis-like rat model


title: Tet1cKO_LPC_3

city: New York

first: Sarah

last: Moyon

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: CUNY ASRC

data_processing:
10 ng of total RNA per sample were used for library construction with the Ultra-Low-RNA-Seq Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 4000 instrument according to the manufacturer's instructions for 100 bp paired end read runs.
Samples were multiplexed. The raw data produced from the runs were demultiplexed using indexes into fatsq fikes. The fastq files for a sample were then aggregated for alignment.
High-quality reads were aligned to the mouse reference genome (mm10)using the STAR aligner. The read count for each RefSeq transcript was extracted using uniquely aligned reads to exon and splice-junction regions for each transcript.
The raw read counts were inputted into DESeq2 v1.2.5 (Anders and Huber, 2010) for calculation of normalized signal for each transcript and to ascertain differential gene expression with associated p-values.
Differentially expressed genes were selected at a p-valu<0.01 and q-value < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: counts, .txt file

source_name: 4-day-post-lesion oligodendroglial-enriched spinal cord from Tet1 mutant mouse

extract_protocol:
Total RNAs were obtained from oligodendroglial-enriched cell suspensions, isolated from P60 spinal cords tissues, either from control or Tet1 mutant mice, either from unlesioned or lesioned tissues. We used AllPrep RNAeasy Mini Kit (Qiagen), with on-column DNase treatment during the RNA isolation, in accordance with the manufacturer’s protocol, to isolate RNA. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop, and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols at the Cornell Genomic core.

tag: developmental stage

value: spinal cord

tag: enrichment method

value: oligodendroglial-enriched by percoll gradient

value: Tet1 cKO


title: Tet1cKO_SC_3

source_name: Unlesioned oligodendroglial-enriched spinal cord from Tet1 mutant mouse

value: unlesioned


title: Tet1cKO_LPC_2


title: 7Y3

city: Beijing

first: Bo

last: Zhang

address: No. 2 Yuanmingyuan West Road, College Animal Science & Technology, China Agriculture University, Beijing

institute: China Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
The reference genome index was built using Bowtie2 v2.2.3 and the clean data were then aligned to the reference genome using TopHat2
Reads for each gene was counted using HTSeq v0.6.0, and the expression levels of genes per sample were calculated by fragments per kilobase million mapped reads (FPKM) based on sequence lengths and on the read counts mapped to them
Genome_build: ftp://ftp.ensembl.org/pub/release-96/fasta/gallus_gallus/dna/ Gallus_gallus.GRCg6a.dna.toplevel.fa
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Gallus gallus

source_name: feather follicles

extract_protocol:
The feather follicles were cut off 2 mm from bottom end of the feather, and total RNA was extracted from the feather follicles using an RNAprep pure Tissue Kit (Tiangen, Dalian, China)
The sequencing libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)

value: F3 of Huiyang Bearded X White Leghorn

value: feather follicles

tag: feather colour

value: yellow

tag: sampling age

value: 7-week age

tag: sampling postion

value: nape


title: 7Y4

tag: tissue


title: 7Y1

tag: strain


title: 7W3

value: white


title: Tet1cKO_LPC_1

tag: treatment


title: NAC35A

description: Gene expression data

source_name: Pleural box

tag: treatment status

value: pre-treatment

tag: gender

value: Female

value: Pleural box

value: Malignant

value: High grade serous ovarian cancer

value: IV

value: FFPE


title: Insertion-site-mapping-Clone21

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

description: Target-enriched seqeuencing

library_source: genomic

data_processing:
Library strategy: DNA-seq
Demultiplexed Illumina sequencing reads underwent adapter trimming, with read pairs removed if both reads mapped to the Inversed Repeat. Read1 of the remaining read pairs were further filtered to those that had a partial match to the Inversed Repeats, with right-trimming performed to remove these Inverse Repeats sequence fragments. All these steps were carried out using the BBDuk tool (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/). Adapter- and Inverse Repeats-trimmed sequence fragments were then mapped to hg19 using Bowtie 2. Resulting SAM files were converted to BAM files, which were then sorted, both using SAMtools. Genome-wide coverage was then obtained using BEDTools. Genome coordinates with >25X coverage were visualized as peaks, and the insertion sites were identified to be between the two bases with the highest coverage in each peak. Each insertion site was subsequently validated using targeted PCRs.
Genome_build: hg19
Supplementary_files_format_and_content: .txt with bedgraph format

growth_protocol: HAP1 cells (Carette et al., Nature 477, 340-343 (2011)), derived from KBM7 cells, a chronic myelogenous leukemia cell line, were cultured in IMDM with 10% FBS and 1% penicillin/streptomycin at 37°C with 5% CO2 (as described in Carette et al., 2011).

extract_protocol: Capture using biotinylated oligos and pull-down with streptavidin beads were used to map transposon insertion sites. Specifically, for Clone 21 and Clone 25, 8µg of gDNA, prepared with PureLink™ Genomic DNA Mini Kit (Thermo Fisher, K182001), was sonicated at 100% amplitude, 30 seconds on/30 seconds off, for 40 minutes, in a bath sonicator (QSonica Q800R3). Sonicated DNA was cleaned up using AMPure XP beads (Beckman Coulter), End Repaired, dA-Tailed (NEBNext® Ultra™), adaptor ligated, indexed (NEBNext® Multiplex Oligos for Illumina®), and P5/P7 amplified (NEBNext® Q5® Hot Start HiFi PCR Master Mix). This library prepared DNA, dried in a PCR machine with the tube cap open, was resuspended in 7.5µL NimbleGen 2X Hybridization buffer, 3µL NimbleGen Hybridization Component A, and 2.5µL nuclease-free water, and incubated for 10 minutes at room temperature. Resuspended DNA was then denatured at 95°C in a PCR machine for 10 minutes. 2µL 1.5µM 5’ biotinylated hybridization oligo, which targets the Inversed Repeat regions immediately proximal to the endogenous genome, was subsequently added. After vortexing for a few seconds and spinning down, the mixture was incubated in a PCR machine at 47°C (lid temperature 57°C) overnight. Each mixed library DNA and biotinylated hybridization oligo was then added to 40µL washed Dynabeads™ MyOne™ Streptavidin C1 (Thermo Fisher 65001) at 47°C in a thermomixer for 1 hour. With 100µL pre-heated 1X Wash Buffer I added to the beads-DNA mixture, the tubes were vortexed and placed on a magnetic stand, with the supernatant containing unbound DNA subsequently removed. DNA-bound streptavidin beads were then washed twice with Stringent Wash Buffer, followed by one wash each with Wash Buffers I, II and III (all Wash Buffers, together with NimbleGen 2X Hybridization buffer and Nimblegen Hybridization Component A, were supplied in the SeqCap EZ Hybridization and Wash Kits, Roche NimbleGen, 05634261001). Hybridized DNA was eluted off the beads with 25µL 0.125M NaOH, neutralized with 25µL 1M Tris-HCl, pH 8.8, followed by AMPure XP beads cleanup. Eluted DNA was then enriched with PCR using P5/P7 primers (NEBNext® Q5® Hot Start HiFi PCR Master Mix), for 12 cycles. PCR-enriched pulldown DNA underwent an additional round of biotinylated oligo hybridization and streptavidin beads pulldown as described above. Pulldown enrichment was confirmed using qPCR prior to Illumina sequencing.

treatment_protocol: HAP1 cells were co-transfected with the two components of the Sleeping Beauty transposon system: pSA-MCS-2kb, the transposon vector with the 2kb insert containing a CTCF binding site and the TSS of PARL gene, and the transposase vector, pCMV(CAT)T7-SB100. Clonal lines were established following transposon genome editing. Hi-C was then performed for two clones (Clone 21 and Clone 25) with the highest numbers of insertions. Where indicated, CRISPR editing using a gRNA targeting the CTCF binding site within ectopic insertions was performed, and Capture-C was used to characterize effects upon CTCF binding site disruption.

tag: cell type

value: KBM7-derived near haploid cells


title: NAC25A

description: Gene expression data

source_name: Anterior abdominal wall

value: Anterior abdominal wall

tag: condition

tag: tumor type

tag: tumor stage


title: Insertion-site-mapping-Clone25

description: Target-enriched seqeuencing


title: CTB-Control, rep2

description:
76CT
Gene expression data from CTB treated with vehicle-control.

value: villous tissue obtained from term placenta

value: cultured cytotrophoblast

value: female

tag: gestational stage

value: term-uncomplicated pregnancy

value: vehicle-control


title: WT_CD45+ cortical cells

source_name: WT

tag: straiin

value: Mus musculus (C57Bl6)

value: Brain Cortex

tag: time

value: 14 weeks

value: myeloid cells (live CD45+)


title: Tet1cKO_SC_2

tag: developmental stage

value: spinal cord

value: oligodendroglial-enriched by percoll gradient

tag: genotype

value: Tet1 cKO

value: unlesioned


title: 7W2

value: F3 of Huiyang Bearded X White Leghorn

value: feather follicles

tag: feather colour

value: white

value: 7-week age

value: nape


title: NAC40A

description: Gene expression data

source_name: Pelvic box

value: pre-treatment

value: Female

value: Pelvic box

value: Malignant

value: High grade serous ovarian cancer

value: IIIC

tag: sample type

value: FFPE


title: NAC13A

description: Gene expression data

source_name: Omentum

value: Omentum


title: NAC27A

description: Gene expression data

source_name: Right diaphragm

value: Right diaphragm


title: CTB-Control, rep1

description:
75CT
Gene expression data from CTB treated with vehicle-control.

value: villous tissue obtained from term placenta

value: cultured cytotrophoblast

value: female

value: term-uncomplicated pregnancy

value: vehicle-control


title: Tet1cKO_SC_1

value: spinal cord

tag: enrichment method

value: oligodendroglial-enriched by percoll gradient

value: Tet1 cKO

value: unlesioned


title: TDC-Control, rep2

description:
68TDC
Gene expression data from TDC treated with vehicle-control.

source_name: Term decidual cells, control

tag: tissue

value: decidual tissue obtained from term placenta

value: cultured term decidual cells


title: 7W1

tag: strain

value: F3 of Huiyang Bearded X White Leghorn

value: feather follicles

value: white

tag: sampling age

value: 7-week age

tag: sampling postion

value: nape


title: STB-Control, rep2

description:
82ST
Gene expression data from STB treated with vehicle-control.

value: cultured syncytotrophoblast

tag: gender

tag: treatment


title: Tet1Control_LPC_3

source_name: 4-day-post-lesion oligodendroglial-enriched spinal cord from control mouse

value: wildtype


title: NAC10B

description: Gene expression data

tag: treatment status

value: post-treatement

value: Female

value: Omentum

tag: condition

value: Malignant

value: High grade serous ovarian cancer

value: IIIC

value: FFPE


title: TDC-Control, rep3

description:
72TDC
Gene expression data from TDC treated with vehicle-control.

tag: cell type

value: female

value: term-uncomplicated pregnancy

value: vehicle-control


title: NAC37A

description: Gene expression data

source_name: Ovary

value: pre-treatment

value: Ovary

tag: tumor type

tag: tumor stage


title: NAC7A

description: Gene expression data

value: Anterior abdominal wall

value: IV


title: NAC11A

description: Gene expression data


title: Tet1Control_LPC_2

value: spinal cord

value: oligodendroglial-enriched by percoll gradient


title: TDC-Control, rep1

description:
66TDC
Gene expression data from TDC treated with vehicle-control.

value: decidual tissue obtained from term placenta

value: cultured term decidual cells

tag: gestational stage


title: NAC7B

description: Gene expression data

value: post-treatement

value: Female


title: NAC13B

description: Gene expression data

value: Omentum

value: Malignant


title: NAC11B

description: Gene expression data

value: High grade serous ovarian cancer

value: IIIC


title: 1Y3

value: F3 of Huiyang Bearded X White Leghorn

value: feather follicles

value: yellow

value: 11-week age

value: nape


title: NAC37B

description: Gene expression data

value: Ovary

value: FFPE


title: NAC5A

description: Gene expression data

source_name: Bladder peritoneum

value: pre-treatment

value: Bladder peritoneum


title: 1Y4


title: anti-TIE1 treated, biological replicate 4

city: Mannheim

first: Mahak

last: Singhal

address: Ludolf-Krehl-Straße 13-17

country: Germany

institute: European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University

hyb_protocol: (according to user manual Affymetrix 3’ IVT Pico Reagent Kit) 6,6 ug of fragmented and labeled ds-cDNA were hybridized for 17 hr at 45°C on Affymetrix Mouse Clariom S Arrays.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays

data_processing: All intensity data were quarantile normalized.

source_name: mouse lung

label_protocol: The Affymetrix 3’ IVT Pico Reagent Kit is used to generate labeled single-stranded cRNA from input amounts of 100pg total RNA. Label: Biotin

growth_protocol: LLC cells were subcutaneously injected in 8 wk old mice. Mice were treated either with IgG or TIE1-blocking antibody intraperitoneally twice a week. Lungs from primary tumor-bearing mice were isolated and lung EC were FACS-sorted for further processing.

extract_protocol: Total RNA were isolated using Arcturus PicoPure RNA isolation kit according to the manufacturer described protocol.

treatment_protocol: Mice were euthanized and liver tissue was collected. Briefly, minced liver tissue was incubated in collagenase (Liberase, Rche) solution for 30 mins. Next, erythrocytes were lysed with ACK-lysis buffer. Afterward, the single cells were stained with an antibody cocktail (CD45, Ter119, LYVE1, PDPN, CD31) for 20 mins on ice. Liver endothelial cells (EC) were isolated by FACS using CD31+ CD45- LYVE1- PDPN- Ter119- DAPI- surface marker profile.

tag: antibody

tag: sorted cells

value: CD31+ CD45- LYVE1- PDPN- Ter119- DAPI-


title: NAC10A

description: Gene expression data


title: 1W4

tag: feather colour

value: white


title: Tet1Control_SC_2

source_name: Unlesioned oligodendroglial-enriched spinal cord from control mouse

tag: developmental stage

value: spinal cord

value: oligodendroglial-enriched by percoll gradient

tag: genotype

value: wildtype

value: unlesioned


title: anti-TIE1 treated, biological replicate 3


title: NAC4B

description: Gene expression data

value: post-treatement

value: Female

tag: tissue

value: Malignant

value: High grade serous ovarian cancer

tag: sample type


title: 1Y1

tag: strain

value: F3 of Huiyang Bearded X White Leghorn

value: feather follicles

value: yellow

tag: sampling age


title: 1W1

value: 11-week age

tag: sampling postion

value: nape


title: Dm_S2cell_RNAseq_RiboZero_DMSO_4h_rep3

status: Public on Mar 13 2020

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
dBRD4= fs(1)h, dBRD4-L indicating long isoform of dBRD4
processed data file:
Dm_S2cell_RibozeroRNA-seq_DESeq2.counts_ERCCnormalized_DMSOvs4h_JQ1.tsv

data_processing:
Reads were mapped to dm6 using subreads and were mapped to ERCC spikes using STAR,
transcripts were counted using htseq, ERCC spikes were counted using featureCounts
For differential expression analysis DESeq2 was used, using ERCC spikes for normalization
Genome_build: dm6
Supplementary_files_format_and_content: DESeq2 ERCC normalized counts table

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells (Invitrogen) were cultured in Express Five SFM media (Thermo Fisher) supplemented with 10% (v/v) Glutamax (Thermo Fisher). Cultures were maintained adherent or in shaking incubators at 27ºC at a speed of 80

extract_protocol:
RNA was isolated using a Trizol based RNA extraction kit ( Directzol, Zymoresearch)
TruSeq Stranded Total RNA Library Prep (Illumina)

treatment_protocol: for RNAi: dsRNA was added to the cell culture medium, 10µg dsRNA per 1mio cells, cells were harvested after 4 days of RNAi, for dBRD4 inhibitor treatments: DMSO or inhibitor was added to the cell culture medium

tag: cell line

value: S2 cells

tag: knockdown/inhibitor treatment

value: 4h DMSO treatment

tag: tag


title: Small RNA ddm1 inflorescence

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

data_processing:
RNA-seq: FASTQ files were processed for adaptor trimming using cutadapt. Tophat v2.0.12 was used for mapping. Cuffnorm was used to obtain FPKM values from bam files.
Small RNA-seq: After trimming the 3’ adapter and filtering collapsed reads according to length and quality, filtered reads were mapped with bowtie reporting all multi-mappers. Only perfect match reads were used for down-stream analysis, and reads mapped to multiple genomic locations where normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30nt) and perfectly mapped reads.
Short read VLP DNA-seq: Adapters were trimmed from raw reads with Skewer in paired-end mode and read pairs with both mates longer than 25 nt were retained.
Short read VLP DNA-seq: Reads were aligned to the TAIR10 genome with STAR in two-pass mode to improve spliced alignment at unannotated introns. Reads mapping equally well to multiple locations were randomly assigned, and chimeric/split read alignments were output separately from concordant alignments. Optical and PCR duplicates were removed from the alignments with picard-tools (http://broadinstitute.github.io/picard). Genome-wide coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped. Pairwise differential expression at TAIR10 transposon loci was tested across three wild-type, two ddm1, and three ddm1rdr6 replicates using quasi-likelihood F-tests in edgeR, controlling FDR at 5% and a log2(fold-change) threshold of 2.
Long read VLP DNA-seq: Basecalling was performed offline with Guppy v2.3.1 using the default model. Using porechop (https://github.com/rrwick/Porechop), ONT sequencing adapters were trimmed from 5’ ends, 3’ ends, and the middle of raw reads. Reads with middle adapters were split.
Long read VLP DNA-seq: Remaining reads longer than 100 bp were aligned to the TAIR10 reference with minimap2 for coverage and read alignment plots. Structural variants were called on NGMLR alignments using Sniffles with default parameters, except minimum read support was reduced to 3. RPM-normalized coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped.
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values are shown for each gene identification (ID)
Supplementary_files_format_and_content: Small RNA-seq: txt files with 18-30nt reads and counts, and RPM of 20-24nt reads mapped to TAIR10 features
Supplementary_files_format_and_content: Short read VLP DNA-seq: bigWig
Supplementary_files_format_and_content: Long read VLP DNA-seq: bigWig, vcf (Structural variant calls produced by Sniffles on nanopore long-read alignments to the TAIR10 genome. The number of reads supporting each SV call is given in the RE tag.)

organism: Arabidopsis thaliana

source_name: Inflorescence tissues

growth_protocol: Plants were grown under long day conditions at 22 °C. Seeds were grown on ½ Murashige and Skoog (MS) medium and seedlings were transplanted to soil 7 day after germination.

extract_protocol:
Total RNA was isolated using Trizol reagent. 18 to 30-nt small RNA was size-selected using 15% polyacrylamide gel.
TruSeq small RNA sample preparation kit (Illumina)

tag: ecotype

value: Inflorescence tissues

tag: fraction

value: Small RNA


title: Small RNA wild-type inflorescence

value: wild-type


title: IgG-treated, biological replicate 4

value: IgG

value: CD31+ CD45- LYVE1- PDPN- Ter119- DAPI-


title: Tet1Control_SC_1

value: spinal cord

tag: enrichment method

value: oligodendroglial-enriched by percoll gradient

value: wildtype

tag: treatment

value: unlesioned


title: Dm_S2cell_RNAseq_RiboZero_DMSO_1h_rep3

description:
dBRD4= fs(1)h, dBRD4-L indicating long isoform of dBRD4
processed data file:
Dm_S2cell_RibozeroRNA-seq_DESeq2.counts_ERCCnormalized_DMSOvs1h_JQ1.tsv

value: 1h DMSO treatment


title: Dm_S2cell_RNAseq_RiboZero_JQ1_1h_rep3

value: 1h JQ1 treatment, 5µM (Cayman Chemicals, 1187)


title: NAC4A

description: Gene expression data

tag: treatment status

value: pre-treatment

tag: gender

value: Female

value: Ovary

tag: condition

value: Malignant

tag: tumor type

value: High grade serous ovarian cancer

tag: tumor stage

value: IIIC

value: FFPE


title: IgG-treated, biological replicate 2

tag: antibody

tag: sorted cells


title: Dm_S2cell_RNAseq_RiboZero_DMSO_1h_rep2

value: S2 cells


title: Dm_S2cell_RNAseq_RiboZero_JQ1_4h_rep2

value: 4h JQ1 treatment, 5µM (Cayman Chemicals, 1187)


title: anti-TIE1 treated, biological replicate 2

tag: strain


title: Dm_S2cell_RNAseq_RiboZero_JQ1_1h_rep2


title: NAC3A

description: Gene expression data

tag: tissue

value: Right diaphragm

value: IV

tag: sample type


title: NAC5B

description: Gene expression data

value: post-treatement

value: Bladder peritoneum


title: anti-TIE1 treated, biological replicate 1

value: CD31+ CD45- LYVE1- PDPN- Ter119- DAPI-


title: IgG-treated, biological replicate 3

value: IgG


title: Dm_S2cell_RNAseq_RiboZero_DMSO_4h_rep1

tag: cell line

value: 4h DMSO treatment


title: IgG-treated, biological replicate 1


title: Dm_S2cell_RNAseq_RiboZero_DMSO_1h_rep1

tag: knockdown/inhibitor treatment

value: 1h DMSO treatment


title: Dm_S2cell_RNAseq_RiboZero_JQ1_4h_rep1

tag: tag


title: Dm_S2cell_RNAseq_RiboZero_JQ1_4h_rep3


title: Non-transgenic_IgG_control_ChIPseq_sample3

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: ChIPSeq_Sample 45

data_processing:
base-calling using RTA 2.7.7
Reads were aligned by bowtie2 v2.0.5 using only the first 65 bases against the Arabidopsis thaliana TAIR10 reference genome.
Shiftsize was calculated using phantompeakqualtools and default parameters
Peaks called with MACS2 version 2.0.10 with parameters "callpeak -c --format=SAM --gsize=1.19e8 -p 99e-2 --nomodel --shiftsize=[from phantompeakqualtools] --down-sample --call-summits". A concatenated file of all non-transgenic control IP reads was used as the control in peak calling
ChIPPeakAnno was used for annotation. gene ontology enrichment was assessed using clusterProfiler
Genome_build: TAIR10
Supplementary_files_format_and_content: Summit region output created by MACS2 in bed format.

source_name: Three day old etiolated seedlings

growth_protocol: Seeds were sterilised using bleach then plated on 1.2% agar Linsmaier and Skoog medium plates. Stratification was at 4 celsius in the dark for three days. Plates were exposed to the light at room temperature for 2 h to induce germinaiton, then returned to the dark at 22 celsius. Plates were incubated for three days, after which treatments were conducted.

extract_protocol:
Conducted as described in O'Malley et al. 2016 (doi: 10.1016/j.cell.2016.04.038) and Chang et al. 2013 (10.7554/eLife.00675). Harvested seedlings were crosslinked with 1% formaldehyde under vacuum for 20 minutes then snap-frozen in liquid nitrogen. Nuclei were extracted from frozen, ground seedlings according to Qiao et al. 2016 (10.1126/science.1225974) then sonicated according to Chang et al .2016 using a Diagenode bioruptor to yield an average DNA fragment size of approximately 150-300 bases. Transcription-factor DNA complexes were isolated by immunoprecipitation with polyclonal anti-GFP raised in goat from David Dreschel (Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany) or, for non-transgenic controls, IgG from goat. These complexes were then retrieved using Protein G Dynabeads (Life Technologies).
Conducted as described in Chang et al. 2013 (10.7554/eLife.00675) with one modification. Size selection was performed on SPRI beads, instead of on gels, with upper and lower cut-offs to yield a fragment size-range of 150-500 nucleotides. Sequencing was conducted on the Illumina HiSeq 2500 platform.

treatment_protocol: Air or JA treated for 2h

value: Three day old etiolated seedlings

tag: genotype

value: Air treatment for 2h

tag: chip antibody

value: Goat IgG whole molecule (Jackson ImmunoResearch, 005-000-003)


title: NAC1A

description: Gene expression data

source_name: Perihepatic mass

value: pre-treatment

value: Female

value: Perihepatic mass

value: Malignant


title: Dm_S2cell_RNAseq_RiboZero_JQ1_1h_rep1

value: S2 cells

value: 1h JQ1 treatment, 5µM (Cayman Chemicals, 1187)


title: NAC1B

description: Gene expression data

value: High grade serous ovarian cancer

value: IIIC

value: FFPE


title: Dm_S2cell_RNAseq_RiboZero_dBRD4_RNAi_rep3

description:
dBRD4= fs(1)h, dBRD4-L indicating long isoform of dBRD4
processed data file:
Dm_S2cell_RibozeroRNA-seq_DESeq2.counts_ERCCnormalized_GSTvsdBRD4_RNAi.tsv

value: dBRD4 RNAi


title: NAC3B

description: Gene expression data

value: post-treatement

value: Right diaphragm

value: IV


title: Dm_S2cell_RNAseq_RiboZero_NSL3_RNAi_rep3

description:
dBRD4= fs(1)h, dBRD4-L indicating long isoform of dBRD4
processed data file:
Dm_S2cell_RibozeroRNA-seq_DESeq2.counts_ERCCnormalized_GSTvsNSL3_RNAi.tsv

value: NSL3 RNAi


title: Dm_S2cell_RNAseq_RiboZero_NSL1_RNAi_rep3

description:
dBRD4= fs(1)h, dBRD4-L indicating long isoform of dBRD4
processed data file:
Dm_S2cell_RibozeroRNA-seq_DESeq2.counts_ERCCnormalized_GSTvsNSL1_RNAi.tsv

value: NSL1 RNAi


title: Dm_S2cell_RNAseq_RiboZero_dBRD4-L_RNAi_rep2

description:
dBRD4= fs(1)h, dBRD4-L indicating long isoform of dBRD4
processed data file:
Dm_S2cell_RibozeroRNA-seq_DESeq2.counts_ERCCnormalized_GSTvsdBRD4-L_RNAi.tsv

value: dBRD4-L RNAi


title: Dm_S2cell_RNAseq_RiboZero_NSL3_RNAi_rep2


title: Dm_S2cell_RNAseq_RiboZero_dBRD4_RNAi_rep2


title: Dm_S2cell_RNAseq_RiboZero_GST_RNAi_rep2

value: control RNAi (GST)


title: Dm_S2cell_RNAseq_RiboZero_NSL1_RNAi_rep2


title: Dm_S2cell_RNAseq_RiboZero_dBRD4_RNAi_rep1


title: Dm_S2cell_RNAseq_RiboZero_NSL3_RNAi_rep1


title: Dm_S2cell_RNAseq_RiboZero_GST_RNAi_rep1


title: Dm_S2cell_RNAseq_RiboZero_GST_RNAi_rep3


title: Dm_S2cell_RNAseq_RiboZero_dBRD4-L_RNAi_rep3


title: OK6_con2

city: Toronto

first: Oliver

last: Kent

state: ON

address: 101 College Street TMDT12-701

country: Canada

institute: University Health Network

description: Genomic control for ChIP RREB1 replicate 2

data_processing:
Raw reads were aligned to hg19 using bwa (version 0.7.15)
sam files are converted to bam with samtools (version 1.8)
MACS2 was used to call peak on the bam files
bedGraph files containing signal per million reads produced from MACS2 was converted to bigwig files with ucsctool kit (315)
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig and narrowPeak files containing normalized signal and peak intervals

growth_protocol: The HEK293 cells were grown in DMEM 10% FBS growth media.

extract_protocol: Libraries construction was performed using ThruPLEX DNA-seq 48D Kit (Rubicon Genomics)

treatment_protocol: None.

value: input


title: OK6_con1

description: Genomic control for ChIP RREB1 replicate 1


title: OK6_rep1_RREB1

description: ChIP RREB1 replicate 1

value: M2-FLAG (Sigma)


title: OK6_rep3_RREB1

description: ChIP RREB1 replicate 3


title: MSS, tumor 5 tissue.

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR-2.6.1 aligner
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: Endometrial

extract_protocol:
Patient FFPE blocks were obtained from our tissue registry and after a pathologist review, samples with sufficient amounts of tissue were selected for RNA extraction from tumor and paired normal tissue.
Total RNA was quantitated using the Qubit RNA BR assay (Invitrogen) and quality was assessed using the DV200 value (the percentage of RNA fragments greater than 200 bases in length) as determined by the Agilent 2100 Bioanalyzer RNA Nano kit.  For samples with a DV200>30% the RNA input for RNA-seq analysis was 200 ng.  For samples with a DV200 score between 20-30% the amount of RNA used was increased to 400 ng to compensate for RNA degradation.  Samples with a DV200 score below 20% were not used in the study since previous studies in our lab have shown that these rarely provide acceptable results.

tag: phenotype (msi-h or mss)

value: MSS

tag: genetics of msi-h

tag: phenotype(normal/tumor)

value: tumor


title: MSS, tumor 8 tissue.

source_name: Colorectal


title: MSS, tumor 7 tissue.


title: Dm_S2cell_RNAseq_RiboZero_dBRD4-L_RNAi_rep1

value: S2 cells


title: MSS, tumor 4 tissue.


title: MSS, tumor 6 tissue.


title: MSS, tumor 18 tissue.


title: MSS, tumor 19 tissue.


title: MSS, tumor 16 tissue.


title: MSS, tumor 14 tissue.


title: OK6_con3

description: Genomic control for ChIP RREB1 replicate 3


title: MSS, tumor 3 tissue.


title: MSS, tumor 13 tissue.


title: OK6_rep2_RREB1

description: ChIP RREB1 replicate 2


title: MSS, tumor 11 tissue.


title: MSS, tumor 2 tissue.


title: MSS, tumor 17 tissue.


title: MSS, tumor 20 tissue.


title: MSS, tumor 1 tissue.


title: MSS, sample 8 normal tissue.

value: normal


title: MSS, sample 7 normal tissue.


title: MSS, sample 6 normal tissue.


title: MSS, tumor 10 tissue.


title: MSS, tumor 15 tissue.


title: MSS, sample 19 normal tissue.


title: MSS, sample 5 normal tissue.


title: MSS, sample 2 normal tissue.


title: MSS, sample 17 normal tissue.


title: MSS, sample 18 normal tissue.


title: MSS, sample 16 normal tissue.


title: MSS, sample 20 normal tissue.


title: MSS, tumor 12 tissue.


title: MSS, sample 4 normal tissue.


title: Dm_S2cell_RNAseq_RiboZero_NSL1_RNAi_rep1


title: MSS, sample 15 normal tissue.


title: MSS, sample 10 normal tissue.


title: MSS, sample 1 normal tissue.


title: MSS, sample 12 normal tissue.


title: MSS, sample 13 normal tissue.


title: MSS, sample 14 normal tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 8 tumor tissue.

value: MSI


title: MSI-H, likely Lynch due to PMS2 germline,sample 9 tumor tissue.


title: 1W3

source_name: feather follicles

value: F3 of Huiyang Bearded X White Leghorn

value: feather follicles

tag: feather colour

value: white

tag: sampling age

value: 11-week age

tag: sampling postion

value: nape


title: MSI-H, likely Lynch due to PMS2 germline,sample 7 tumor tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 6 tumor tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 4 tumor tissue.


title: Dm_S2cell_RNAseq_RiboZero_DMSO_4h_rep2

value: 4h DMSO treatment


title: MSI-H, likely Lynch due to PMS2 germline,sample 5 tumor tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 3 tumor tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 2 tumor tissue.


title: MSS, sample 11 normal tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 11 tumor tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 14 tumor tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 9 normal tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 6 normal tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 10 tumor tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 13 tumor tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 7 normal tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 16 tumor tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 3 normal tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 1 tumor tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 16 normal tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 15 normal tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 2 normal tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 13 normal tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 11 normal tissue.


title: Tet1Control_LPC_1

tag: developmental stage

value: spinal cord

tag: enrichment method

value: oligodendroglial-enriched by percoll gradient

value: wildtype

tag: treatment


title: MSI-H, likely Lynch due to PMS2 germline,sample 15 tumor tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 5 normal tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 10 normal tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 5 normal tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 8 tumor tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 9 tumor tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 4 normal tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 14 normal tissue.


title: Tet1Control_SC_3

value: unlesioned


title: MSI-H, likely Lynch due to MSH6 germline, sample 5 tumor tissue.


title: MSI-H, likely Lynch due to PMS2 germline,sample 1 normal tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 11 normal tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 12 normal tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 3 normal tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 8 normal tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 9 tumor tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 7 normal tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 11 tumor tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 2 normal tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 6 tumor tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 6 normal tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 4 tumor tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 4 normal tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 7 tumor tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 3 tumor tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 1 tumor tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 10 tumor tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 10 normal tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 7 tumor tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 8 tumor tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 6 tumor tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 5 tumor tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 4 tumor tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 12 tumor tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 2 tumor tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 3 tumor tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 2 tumor tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 12 tumor tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 11 tumor tissue.


title: MSI-H, likely Lynch due to MSH6 germline, sample 1 normal tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 10 tumor tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 9 normal tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 1 tumor tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 11 normal tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 6 normal tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 5 normal tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 4 normal tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 12 normal tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 2 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 19 tumor tissue.


title: MSI-H, MLH1 hypermethylation, sample 3 tumor tissue.


title: MSI-H, MLH1 hypermethylation, sample 8 tumor tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 1 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 6 tumor tissue.


title: MSI-H, MLH1 hypermethylation, sample 5 tumor tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 7 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 18 tumor tissue.


title: MSI-H, likely Lynch due MLH1 germline sample 1 tumor tissue.


title: MSI-H, likely Lynch due to MSH2 germline, sample 10 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 16 tumor tissue.


title: MSI-H, MLH1 hypermethylation, sample 20 tumor tissue.


title: MSI-H, MLH1 hypermethylation, sample 4 tumor tissue.


title: MSI-H, MLH1 hypermethylation, sample 13 tumor tissue.


title: MSI-H, MLH1 hypermethylation, sample 9 tumor tissue.


title: MSI-H, MLH1 hypermethylation, sample 12 tumor tissue.


title: MSI-H, MLH1 hypermethylation, sample 7 tumor tissue.


title: MSI-H, MLH1 hypermethylation, sample 11 tumor tissue.


title: MSI-H, MLH1 hypermethylation, sample 1 tumor tissue.


title: MSI-H, MLH1 hypermethylation, sample 8 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 9 normal tissue.


title: MSI-H, likely Lynch due MLH1 germline sample 1 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 20 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 4 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 7 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 15 tumor tissue.


title: MSI-H, MLH1 hypermethylation, sample 6 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 3 normal tissue.


title: Nsd2KO_K27me3_S2

city: Philadelphia

first: Salina

last: Yuan

address: 421 Curie Blvd

department: Medicine

institute: University of Pennsylvania

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were aligned to the mouse (GRCm38, May 23 2014) and the Drosophila melanogaster (dm6, August 2014) reference genomes using STAR (v2.5.1) with default settings.
Duplicate and low-quality reads (PHRED score <30) were removed using SAMtools.
Peaks were called with MACS2 with default settings (H3K27ac and H3K4me1) and broad settings (H3K36me2 and H3K27me3). Blacklisted peaks (https://sites.google.com/site/anshulkundaje/projects/blacklists) were excluded in all subsequent analysis.
Genome_build: mm10 (GRCm38) + dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: ChIPRX-normalized bigwig files were generated from bam files using deepTools.

source_name: pancreatic cancer cells

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum, 10% glutamine, and 150 µg/mL gentamicin at 37°C, 5% CO2, 21% O2, and 100% humidity.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Details in Methods section.
Libraries were prepared according to the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) protocol.

treatment_protocol: No treatment was applied.

tag: genotype/variation

tag: cell type

value: Pancreatic cancer cells

tag: spike-in genome

value: Drosophila melanogaster genomic DNA


title: WT_K4me1_S2

value: H3K4me1 (Abcam, ab8895)


title: Nsd2KO_K27ac_S2

value: H3K27ac (Abcam, ab4729)


title: Nsd2KO_K4me1_S1


title: WT_K27ac_S2


title: WT_K4me1_S1


title: MSI-H, MLH1 hypermethylation, sample 5 normal tissue.


title: Nsd2KO_K27ac_S1


title: Nsd2KO_K4me1_S2


title: MSI-H, MLH1 hypermethylation, sample 2 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 19 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 18 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 10 tumor tissue.

value: tumor


title: Nsd2KO_input

value: none (input)


title: WT_K27me3_S1


title: MSI-H, MLH1 hypermethylation, sample 17 normal tissue.

value: MSI

value: normal


title: WT_input


title: MSI-H, MLH1 hypermethylation, sample 16 normal tissue.


title: Nsd2KO_K27me3_S1


title: WT_K27me3_S2


title: MSI-H, MLH1 hypermethylation, sample 15 normal tissue.


title: MSI-H, MLH1 hypermethylation, sample 13 normal tissue.


title: Nsd2KO_K36me2_S2

value: H3K36me2 (Abcam, ab9049)


title: MSI-H, MLH1 hypermethylation, sample 12 normal tissue.


title: WT_K36me2_S1


title: WT_K36me2_S2


title: MSI-H, MLH1 hypermethylation, sample 10 normal tissue.


title: m_TAC8W_1

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

description:
TAC heart tissue
mouse_TAC_bulk_CM_readCount.csv

data_processing:
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC mm10 or hg38 genome via STAR v2.5.2b
Then assigned by featureCounts (subread-1.4.6-p1 command line)
Genome_build: mm9
Genome_build: hg38
Supplementary_files_format_and_content: csv, read/UMI matrix
16W_20W_total_cell_umi.csv (column header format: SC(singlecell)_ChIP ID_rowID_colID)

source_name: TAC8W CM

extract_protocol:
Selected cells were removed from low temperature and reversed to get cDNA by a reaction including 5M Betaine Solution (Sigma B0300-1VL) 56 uL, 25 mM dNTP mix (Clontech 639132) 24 uL, 1M MgCl2 (Thermo Fisher Scientific AM9530G) 3.2 uL, 100 mM DTT (Sigma 43816-10ML) 8.8 uL, SMARTScribeTM 5X First-Strand Buffer (Clontech 639537) 61.9 uL, SeqAmpTM 2X PCR Buffer (Clontech 638504) 33.3 uL, 100 uM RT E5 Oligo (WaferGen 430-000240-0001) 4.0 uL, Amp Primer (WaferGen 430-000241-0001) and 100% Triton X-100 (Sigma T8787) 1.6 uL.
The library were prepared by using Nextera XT Library Prep Kit (illumina, 15032350) with some modification.

treatment_protocol: Tissues were cut into slices by using Vibrating-blade Microtome (Leica, VT1200S) and homogenized in low temperature and then the tissues were digested using XXIV protease (Sigma, P8038-250) and Collagenase II (Worthington LS004176) to enrich myocites; tissues were  homogenized and  digested using Cardiomyocyte Isolation Enzyme 1 (with papain) for Pierce Primary Cell Isolation Kits (Thermo 88288) to enrich non-cadiomyocites.

tag: gender

value: male

tag: tissue

value: TAC heart tissue


title: m_TAC5W_1

source_name: TAC5W CM


title: MSI-H, MLH1 hypermethylation, sample 1 normal tissue.


title: MSI-H, likely Lynch due MLH1 germline sample 8 tumor tissue.


title: m_TAC8W_2


title: MSI-H, likely Lynch due MLH1 germline sample 7 tumor tissue.


title: m_TAC5W_2


title: MSI-H, likely Lynch due MLH1 germline sample 6 tumor tissue.


title: m_TAC2W_2

source_name: TAC2W CM