title: AL_mouse_liver

city: Beijing

first: De-Pei

last: Liu

address: Dong Dan San Tiao 5, Dongcheng District

country: China

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

description: Gene expression data from mouse livers

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner.

data_processing: We used 'RMA' processing algorithm on 'R/Bioconductor'.

source_name: livers of mice fed ad libitum

growth_protocol: Eight-week-old male WT C57BL/6J mice were housed individually. The mice were housed in a temperature-controlled environment with a 12-h light:12-h dark cycle and were allowed free access to water.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Three RNA samples in the same group were pooled together in equal amounts.

treatment_protocol: The mice were randomly allocated into 2 groups. AL mice were fed AL food ad libitum for 12 weeks. CR mice were fed a 20% restricted diet for the first week and a 40% restricted diet for the remaining 11 weeks of the CR diet.

value: Male

value: Liver

value: 5 months old

tag: food regimen

value: Ad libitum


title: Ca_DAY25_pH4_3

status: Public on Jan 18 2018

type: SRA

city: Grenoble Cedex 9

first: Cécile

last: Garnaud

country: France

institute: CHU Grenoble Alpes

description: rim101-/- mutant, pH 4, replicate 3

library_source: transcriptomic

data_processing:
Reads were quality-checked using FastQC before and after cleaning by Trimmomatic applying default parameters (Bolger et al., 2014).
Reads were then aligned to the C. albicans SC5314 Assembly22 genome (C_albicans_SC5314_A22-s05-m05-r18_haploid, Candida Genome Database, www.candidagenome.org) using Bowtie2 (Langmead and Salzberg, 2012).
Raw read counts for each gene were calculated using HTSeqCount (Anders et al., 2015).
Read count data were analyzed using standard differential analysis pipeline proposed by the DESeq2 R-package.
Genome_build: C_albicans_SC5314_A22-s05-m05-r18_haploid (Candida Genome Database, www.candidagenome.org)
Supplementary_files_format_and_content: Tab-delimited text files. Include raw read counts for each gene calculated using HTSeqCount

molecule: total RNA

organism: Candida albicans

growth_protocol: Each strain (SC5314, DAY25 and CGY1) was precultured overnight in liquid YPD medium at 30°C with agitation and then diluted to an OD600 of 0.1 in SC medium buffered at pH 7.6 or pH 4 with HEPES or citrate buffer,respectively. Cells were incubated at 30°C with agitation until an OD600 of 0.6 to 0.8 was reached and then were collected by centrifugation

extract_protocol:
MasterPure Yeast RNA purification kit (Epicentre) according to the manufacturer’s instructions.
standard RNA-Seq methods and Illumina technology

tag: strain

tag: genotype/variation

value: rim101-/- disrupted

tag: ph


title: O IDH, sample 2 [validation set]

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description:
SAMPLE 2
Methylation data from brain tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'.

label: biotin/DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: brain tumor

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

tag: tissue

value: brain tumor

tag: methylation class

value: O IDH

tag: material


title: CR_mouse_liver

type: RNA

description: Gene expression data from mouse livers

label: biotin

organism: Mus musculus

source_name: livers of calorie-restricted mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

tag: gender

tag: age

value: 12-week calorie restriction


title: Ca_DAY25_pH7.6_2

description: rim101-/- mutant, pH 7.6, replicate 2


title: Ca_DAY25_pH7.6_1

description: rim101-/- mutant, pH 7.6, replicate 1


title: SIRT3 KO MEF rep 1

city: Boston

first: Karina

middle: Noemi

last: Gonzalez Herrera

state: MA

address: 240 Longwood Avenue, LHRRB, Haigis Lab, Room 301

department: Cell Biology

country: USA

institute: Harvard Medical School

data_processing:
Alignment using STAR
Genome build mm10
DESeq2 for normalized reads
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files contain RPKM values for each sample.

source_name: mouse embryonic fibroblasts

extract_protocol:
Total RNA was isolated by a TRIzol (Invitrogen) extraction followed by a Direct-zol RNA MiniPrep Kit (Zymo Research) purification, and 2 μg of total RNA was used for the construction of sequencing libraries.
Briefly, 2 mg RNA was incubated with poly-T oligo beads and unbound RNA was washed two times to remove ribosomal RNA and enrich for mRNA transcript pools. The Superscript III First-Strand Synthesis System (Invitrogen, Carlsbad, CA) was used to synthesize cDNA, and cDNA libraries were generated using Nextera XT DNA sample preparation kit. Libraries were sequenced on the Illumina NextSeq.

tag: cell type

value: immortalized mouse embryonic fibroblasts

tag: genotype

value: SIRT3 -/-


title: SIRT3 KO MEF rep 2


title: SIRT3 WT MEF rep 3

value: wild type


title: SIRT3 WT MEF rep 1


title: SIRT3 WT MEF rep 2


title: Ca_DAY25_pH4_1

description: rim101-/- mutant, pH 4, replicate 1


title: Ca_DAY25_pH4_2

description: rim101-/- mutant, pH 4, replicate 2


title: Ca_WT_pH7.6_1

description: WT, pH 7.6, replicate 1


title: Ca_WT_pH4_3

description: WT, pH 4, replicate 3


title: Ca_WT_pH7.6_2

description: WT, pH 7.6, replicate 2


title: Ca_WT_pH4_2

description: WT, pH 4, replicate 2


title: Ca_WT_pH4_1

description: WT, pH 4, replicate 1


title: Ca_WT_pH7.6_3

description: WT, pH 7.6, replicate 3


title: ESC_H04_NOMe-seq

status: Public on Jan 17 2018

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: Single-cell methylation and accessibility data obtained using NOMe-seq

library_source: genomic

data_processing:
Libraries were sequenced on the Illumina HiSeq or NextSeq platform using the default RTA analysis software.
Raw sequence reads had the first 6 base pairs clipped off the 5' end to remove the 6N  random priming portion of the reads, and were also trimmed to remove both poor quality calls and adapters using Trim Galore (v0.4.3, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, parameters: --clip_r1 6). Remaining sequences were then aligned to the mouse genome (build GRCm38) with Bismark (v0.17.1) in single-end mode (parameters: --non_directional). Methylation calls were extracted after duplicate sequences had been excluded. Regions that were covered by a disproportionally high read number and were most likely mapping artefacts were excluded from subsequent analysis.
genome build: GRCm38
Supplementary_files_format_and_content: The genome-wide CpG/GpC methylation/accessibility reports are tab-delimited, use 1-based genomic coordinates Supplementary_files_format_and_content:: and are in the following format: <chromosome>  <position>  <methylation rate>

source_name: Embryonic stem cell NMT-seq

growth_protocol: ESCs were cultured in serum/LIF conditions as described previously (Ficz et al., Cell Stem Cell 13, 351–359)

extract_protocol:
DNA and mRNA were seperately purified from single cells using the G&T-seq protocol described previously (Macaulay et al., Nature Protocols, 2016)
Libraries were prepared using scBS-seq protocol described previously (Clark et al., Nature Protocols 2017)

tag: cell line

value: El16 embyonic stem cell


title: ESC_G09_NOMe-seq


title: ESC_H02_NOMe-seq


title: ESC_G04_NOMe-seq


title: ESC_H06_NOMe-seq


title: ESC_H08_NOMe-seq


title: ESC_G03_NOMe-seq


title: ESC_H07_NOMe-seq


title: ESC_G05_NOMe-seq


title: ESC_H09_NOMe-seq


title: ESC_F04_NOMe-seq


title: ESC_H03_NOMe-seq


title: ESC_G07_NOMe-seq


title: ESC_F07_NOMe-seq


title: ESC_F09_NOMe-seq


title: ESC_F08_NOMe-seq


title: ESC_G02_NOMe-seq


title: ESC_F05_NOMe-seq


title: ESC_F02_NOMe-seq


title: ESC_H05_NOMe-seq


title: ESC_F01_NOMe-seq


title: ESC_G08_NOMe-seq


title: ESC_G06_NOMe-seq


title: ESC_E09_NOMe-seq


title: ESC_F03_NOMe-seq


title: ESC_G01_NOMe-seq


title: ESC_F06_NOMe-seq


title: Ca_CGY1_pH7.6_2

description: RIM101 overexpression strain, pH 7.6, replicate 2

value: overexpressing RIM101


title: ESC_E05_NOMe-seq


title: ESC_E06_NOMe-seq


title: ESC_E01_NOMe-seq


title: ESC_D08_NOMe-seq


title: ESC_E07_NOMe-seq


title: ESC_D09_NOMe-seq


title: ESC_E02_NOMe-seq


title: ESC_E03_NOMe-seq


title: ESC_D06_NOMe-seq


title: ESC_E04_NOMe-seq


title: ESC_D07_NOMe-seq


title: ESC_D03_NOMe-seq


title: ESC_D02_NOMe-seq


title: ESC_D05_NOMe-seq


title: ESC_D01_NOMe-seq


title: ESC_control_D12_NOMe-seq

source_name: Embryonic stem cell methylase control


title: ESC_E08_NOMe-seq


title: ESC_B09_NOMe-seq


title: ESC_C08_NOMe-seq


title: ESC_C02_NOMe-seq


title: ESC_C03_NOMe-seq


title: ESC_control_C12_NOMe-seq


title: ESC_C06_NOMe-seq


title: ESC_C04_NOMe-seq


title: ESC_B08_NOMe-seq


title: ESC_C09_NOMe-seq


title: ESC_C01_NOMe-seq


title: ESC_C05_NOMe-seq


title: ESC_control_B12_NOMe-seq


title: ESC_B07_NOMe-seq


title: ESC_B06_NOMe-seq


title: ESC_B03_NOMe-seq


title: ESC_B04_NOMe-seq


title: ESC_B05_NOMe-seq


title: ESC_B02_NOMe-seq


title: ESC_A03_NOMe-seq


title: ESC_H09_RNA-seq

description:
Single-cell RNA-seq
ESC_RNA_counts.txt.gz

data_processing:
Libraries were sequenced on the Illumina HiSeq or NextSeq platform using the default RTA analysis software.
Raw sequences were trimmed with Trim Galore (v0.4.3; Cutadapt v1.9.1) and aligned to the GRCm38 genome with HISAT2 (v2.0.5; options --dta --sp 1000,1000 to disallow soft-clipping). Gene expression counts were quantified from the mapped reads using featureCounts within the R package Rsubread. Gene annotations were obtained from Ensembl version 87. Only protein-coding genes matching canonical chromosomes were considered.
genome build: GRCm38
Supplementary_files_format_and_content: RNA-Seq reports contain raw counts per gene, with one row per gene (Ensembl Gene ID) and one column for each sample.

molecule: polyA RNA

extract_protocol:
DNA and mRNA were seperately purified from single cells using the G&T-seq protocol described previously (Macaulay et al., Nature Protocols, 2016)
Libraries were prepared using  the G&T-seq protocol described previously (Macaulay et al., Nature Protocols 2016)


title: ESC_A06_NOMe-seq


title: ESC_B01_NOMe-seq


title: ESC_A07_NOMe-seq


title: ESC_A08_NOMe-seq


title: ESC_A02_NOMe-seq


title: ESC_A04_NOMe-seq


title: ESC_A09_NOMe-seq


title: ESC_H08_RNA-seq


title: ESC_H04_RNA-seq


title: ESC_H06_RNA-seq


title: ESC_A05_NOMe-seq


title: ESC_H05_RNA-seq


title: ESC_G06_RNA-seq


title: ESC_G02_RNA-seq


title: ESC_H03_RNA-seq


title: ESC_G09_RNA-seq


title: ESC_F04_RNA-seq


title: ESC_E08_RNA-seq


title: ESC_G01_RNA-seq


title: ESC_F01_RNA-seq


title: ESC_F09_RNA-seq


title: ESC_H02_RNA-seq


title: ESC_F06_RNA-seq


title: ESC_G05_RNA-seq


title: ESC_H07_RNA-seq


title: ESC_C07_NOMe-seq


title: ESC_G07_RNA-seq


title: ESC_G04_RNA-seq


title: ESC_E06_RNA-seq


title: ESC_G03_RNA-seq


title: ESC_F07_RNA-seq


title: ESC_F02_RNA-seq


title: ESC_F08_RNA-seq


title: ESC_E04_RNA-seq


title: ESC_E02_RNA-seq


title: ESC_E09_RNA-seq


title: ESC_F05_RNA-seq


title: ESC_D08_RNA-seq


title: ESC_D06_RNA-seq


title: ESC_D02_RNA-seq


title: ESC_D01_RNA-seq


title: ESC_E07_RNA-seq


title: ESC_D09_RNA-seq


title: ESC_C06_RNA-seq


title: ESC_F03_RNA-seq


title: ESC_E03_RNA-seq


title: ESC_G08_RNA-seq


title: ESC_control_RNA-seq_C12

description: Single-cell RNA-seq


title: ESC_control_RNA-seq_B12

description: Single-cell RNA-seq


title: ESC_D04_RNA-seq


title: ESC_E01_RNA-seq


title: ESC_B08_RNA-seq


title: ESC_D03_RNA-seq


title: ESC_control_RNA-seq_D12

description: Single-cell RNA-seq


title: ESC_D07_RNA-seq


title: ESC_D05_RNA-seq


title: ESC_C07_RNA-seq


title: ESC_C09_RNA-seq


title: ESC_C02_RNA-seq


title: ESC_C05_RNA-seq


title: ESC_C03_RNA-seq


title: ESC_B09_RNA-seq


title: ESC_B01_RNA-seq


title: ESC_C08_RNA-seq


title: ESC_B05_RNA-seq


title: ESC_A09_RNA-seq


title: ESC_C01_RNA-seq


title: ESC_B06_RNA-seq


title: ESC_B04_RNA-seq


title: ESC_A04_RNA-seq


title: ESC_B02_RNA-seq


title: ESC_C04_RNA-seq


title: ESC_B03_RNA-seq


title: ESC_A02_RNA-seq


title: ESC_E05_RNA-seq


title: ESC_A06_RNA-seq


title: ESC_A08_RNA-seq


title: ESC_B07_RNA-seq


title: 853_2: miR-301aKO spleen

city: Guangzhou

first: Xiaodong

last: Ma

state: Guangdong

address: Rm406,Building 29, South China Normal University

institute: South China Normal University

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

source_name: spleen

extract_protocol:
Lung and spleen were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Poly(A) RNAs were purified by using the Dynabeads mRNA purification kit and Poly(A) RNAs were fragmented at 94C for 5 min before reverse transcribed to cDNA with random primers. cDNA fragments were blunted and ligated to sequencing adaptors. Libraries were sequenced with the High-Seq 2000 Illumina sequencing platform
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT, miR-301a KO, KrasLA2, miR-301aKO-KrasLA2 mice (22-25g, age 9 weeks) were sacrificed and lung and spleen tissue were obtained.

value: spleen

value: 9 weeks


title: ESC_A05_RNA-seq


title: 851_2: miR-301aKO Kras spleen


title: 358_2: Kras spleen


title: 400_1: miR301aKO Kras lung

source_name: lung

value: lung


title: ESC_A07_RNA-seq


title: 807_2: WT spleen


title: ESC_A03_RNA-seq


title: 851_1: miR301aKO Kras lung


title: 358_1: Kras lung


title: 807_1: WT lung


title: 853_1: miR-301aKO lung


title: EB_P1H09_RNA-seq

description:
Single-cell RNA-seq
EB_RNA_counts.txt.gz

source_name: Embryoid body NMT-seq cell

value: E14 embyonic stem cell derived


title: EB_P2G05_RNA-seq


title: T19

city: Poznan

first: Magdalena

last: Żurawek

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics PAS

description: miRNA expression analysis from  pediatric T1D patient

hyb_protocol: Preparation steps: hybrydyzation, wash and stain were performed with Affymetrix Hybrydyzation, Wash&Stain Kit, Fluidics Protocol FS450_0002 on the on the GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: The primary analysis of raw data were performed using Robust Multi-array Average (RMA) algorithm and Affymetrix Expression Console v1.x software

source_name: PBMC of pediatric T1D patient 19

label_protocol: Biotynylated RNA were perfomed with Affymetrix FlashTag Biotin HSR RNA Labeling Kit according to manufacturer`s protocol

growth_protocol: 4 ml of peripheral blood was collected from pediatric T1D patients and pediatric non-diabetic controls

extract_protocol: Total RNA was extracted with TRI Reagent following the manufacturer`s protocol

treatment_protocol: PBMCs were isolated from human peripheral blood by density gradient centrifugation in Histopaque-1077

value: Peripheral blood mononuclear cells

tag: disease state

value: pediatric T1D

value: male


title: EB_P1H07_RNA-seq


title: T13

source_name: PBMC of pediatric T1D patient 13


title: T21

source_name: PBMC of pediatric T1D patient 21


title: T20

source_name: PBMC of pediatric T1D patient 20


title: EB_P2F02_RNA-seq


title: T15

description: miRNA expression analysis from pediatric T1D patient

source_name: PBMC of pediatric T1D patient 15


title: EB_P1H06_RNA-seq


title: T17

source_name: PBMC of pediatric T1D patient 17


title: T10

source_name: PBMC of pediatric T1D patient 10


title: EB_P2G07_RNA-seq


title: T1

source_name: PBMC of pediatric T1D patient 1


title: T2

source_name: PBMC of pediatric T1D patient 2


title: T9

source_name: PBMC of pediatric T1D patient 9


title: T7

source_name: PBMC of pediatric T1D patient 7


title: T3

source_name: PBMC of pediatric T1D patient 3


title: T6

source_name: PBMC of pediatric T1D patient 6


title: SUP-B15 untreated 3

city: Philadelphia

first: Marco

last: De Dominici

state: Pennsylvania

department: Cancer Biology

institute: Thomas Jefferson University

hyb_protocol: cDNA from BV173 cells was hybridized onto Human Clariom S Assay (Affymetrix) and cDNA from SUP-B15 was hybridized onto Human Gene 1.0 ST Array (Affymetrix) folowing the manifacturer instructions.

scan_protocol: Arrays were scanned by using the Affymetrix Gene Chip Scanner 3000 using the Command Console Software.

data_processing: Microarray data was analyzed by Expression Console, Transcriptom Analysis Console (Thermo Fisher Scientific) and GeneSpring Software (Agilent).

source_name: cell line SUP-B15

label_protocol: biotin labeled cDNA was sythesized using the Affymetrix WT Plus Kit (Thermo Fisher Scientific) for BV173 cells or the Ovation PICO WTA-system V2 and the FL-Ovation 8 cDNA biodin module (NuGen Technologie) for SUP-B15 cells

growth_protocol: Cells were expanded in Iscove's modified DMEM supplemented with 10% featl bovine serum, 100 U/mL penicicllin/streptomycin and 2 mM L-glutamine

extract_protocol: RNA was extracted from 4-5 millions of cells by using the RNeasy Plus Mini-Kit (Qiagen #74134)

treatment_protocol: Cells were plated at 250,000/mL with (DOX) or without (CTRL) doxycycline 1 mg/L for 24 hours


title: SUP-B15 doxycycline 3


title: SUP-B15 untreated 2


title: SUP-B15 untreated 1


title: EB_P1H05_RNA-seq


title: SUP-B15 doxycycline 1


title: SUP-B15 doxycycline 2


title: T14

source_name: PBMC of pediatric T1D patient 14


title: T4

source_name: PBMC of pediatric T1D patient 4


title: EB_P1G09_RNA-seq

source_name: Embryoid body NMT-seq cell


title: EB_P1G06_RNA-seq


title: EB_P1G03_RNA-seq


title: EB_P1G02_RNA-seq


title: C4

description: miRNA expression analysis from non-diabetic pediatric control

source_name: PBMC of healthy pediatric control 4

value: healthy


title: EB_P1G01_RNA-seq


title: C3

source_name: PBMC of healthy pediatric control 3


title: EB_P1F09_RNA-seq


title: EB_P1G04_RNA-seq


title: EB_P1H02_RNA-seq


title: EB_P1F06_RNA-seq


title: EB_P1F08_RNA-seq


title: EB_P1G08_RNA-seq


title: EB_P1E11_RNA-seq


title: EB_P1F03_RNA-seq


title: C2

source_name: PBMC of healthy pediatric control 2


title: EB_P1G07_RNA-seq


title: EB_P1E07_RNA-seq


title: EB_P1F02_RNA-seq


title: EB_P1F07_RNA-seq


title: EB_P1F01_RNA-seq


title: EB_P1E08_RNA-seq


title: EB_P1E05_RNA-seq


title: EB_P1E02_RNA-seq


title: EB_P1D08_RNA-seq


title: EB_P1D11_RNA-seq


title: PBMC_Control_Subject2

city: Stanford

first: Vandana

last: Kaul

state: CA

address: 1201 Welch Rd., MSLS P328

department: Surgery

institute: Stanford University

description: microRNA expression data from PBMCs from healthy subjects (controls)

hyb_protocol: The labeled targets were hybridized to the GeneChip miRNA 4.0 arrays per standard miRNA protocol, which includes 16 h (overnight) hybridization at 48◦C at 60 RPM in the Affymetrix GeneChip Hybridization oven 645. The arrays were then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Partek Genomics Suite Software. Normalization was done suing Robust Multi-array Average (RMA) , followed by log2 transformation of data and one-way ANOVA. Multi-testing correction was done using Benjamini-Hochberg Step-Up FDR-controlling procedure for all the expressed miRNAs (default FDR Alpha level 0.05).

source_name: Peripheral blood mononuclear cells from healthy subjects (controls)

label_protocol: 130 ng total RNA was assessed for quality using Bioanalyzer 2100 (Agilent), followed by Poly-A tailing and labeling with biotin using a Affymetrix FlashTag Biotin HSR RNA Labeling kit according to the manufacturer’s protocol.

extract_protocol:
PBMCs were derived from whole peripheral blood samples of IM patients or healthy controls.
Total RNA was extracted using TRIzol Reagent  and cleaned-up with RNeasy spin columns using a modified protocol as described in Supplementary Materials.

value: healthy control

tag: time

value: control


title: EB_P1D09_RNA-seq


title: PBMC_2month_Subject5

description: microRNA expression data from PBMCs at 2 months

source_name: Peripheral blood mononuclear cells at 2 months

value: IM

value: 2 months


title: PBMC_Control_Subject3


title: PBMC_2month_Subject3


title: EB_P1D10_RNA-seq


title: PBMC_7month_Subject3

description: microRNA expression data from PBMCs at 7 months

source_name: Peripheral blood mononuclear cells at 7 months

value: 7 months


title: PBMC_7month_Subject1


title: PBMC_Control_Subject1


title: EB_P1D02_RNA-seq


title: EB_P1D01_RNA-seq


title: PBMC_1month_Subject4

description: microRNA expression data from PBMCs at 1 month

source_name: Peripheral blood mononuclear cells at 1 month

value: 1 month


title: EB_P1D03_RNA-seq


title: EBcontrol_P2G12_RNA-seq

source_name: Embryoid body methylase control cell


title: EB_P1E01_RNA-seq


title: EBcontrol_P2E12_RNA-seq


title: PBMC_2month_Subject1


title: PBMC_1month_Subject3


title: PBMC_1month_Subject1


title: PBMC_IMDiagnosis_Subject5

description: microRNA expression data from PBMCs at IM Diagnosis

source_name: Peripheral blood mononuclear cells at diagnosis

value: at diagnosis


title: PBMC_1month_Subject5


title: EBcontrol_P1F12_RNA-seq


title: EBcontrol_P2B12_RNA-seq


title: EBcontrol_P2D12_RNA-seq


title: EB_P2G07_NOMe-seq


title: EBcontrol_P1D12_RNA-seq


title: PBMC_1month_Subject2


title: EB_P2F02_NOMe-seq


title: EB_P2G05_NOMe-seq


title: EB_P1H09_NOMe-seq


title: EBcontrol_P2F12_RNA-seq


title: EB_P1H06_NOMe-seq


title: EBcontrol_P1E12_RNA-seq


title: EBcontrol_P1G12_RNA-seq


title: EB_P1H07_NOMe-seq


title: PBMC_IMDiagnosis_Subject4


title: 355_1: Kras lung

source_name: lung


title: EB_P1D07_RNA-seq


title: CleftProband_138

city: Iowa City

first: J.

middle: Robert

last: Manak

state: Iowa

address: 455 Biology Building, 129 East Jefferson Street

department: Biology and Pediatrics

institute: The University of Iowa

hyb_protocol: 34 ug of each labeled DNA was co-hybridized to a Roche NimbleGen human whole genome tiling microarray (Human CGH 2.1M Whole-Genome Tiling v2.0D Array)

scan_protocol: Arrays were scanned on a Roche NimbleGen microarray scanner.

data_processing:
532.tif and 635.tif files were analyzed using DEVA software to generate a data_summary.txt file and segMNT.txt file. Data_summary.txt files were analyzed using Nexus 7 Software to generate NexusData.bed files and then compared to the segMNT.txt file using BEDTOOLS 50% reciprocal overlap function. Only calls which shared a reciprocal overlap of 50% or greater were retained for further analysis.
BioDiscovery’s FASST2 Segmentation Algorithm, a Hidden Markov Model (HMM) based approach, was the algorithm used to make copy number calls using Nexus 7 Software. The significance threshold for segmentation was set at 1.0E-6 also requiring a minimum of 3 probes per segment and a maximum probe spacing of 1000 between adjacent probes before breaking a segment. The log ratio thresholds for single copy gain and single copy loss were set at 0.3 and -0.3, respectively. A 3:1 sex chromosome gain threshold was set to 1.2 and a 4:1 sex chromosome gain threshold was set to 1.7. NimbleGen's DEVA segMNT algorithm, which minimizes squared error relative to the segment means, was used as a second algorithm for all copy number calls after data extraction, LOESS spatial correction and background correction. Default parameters were used with the exception of setting the minimum segment difference to 0.3 and requiring a minimum of 3 probes per segment.

source_name: case, whole blood

label_protocol: 1 ug of case DNA was labeled with Cy3-coupled nonamers and 1 ug of control DNA (from an unaffected Filipino male) was labeled with Cy5-coupled nonamers.

extract_protocol: DNA was extracted from whole blood samples using the Quickgene610L.

tag: Sex

tag: cleft type

value: cleft palate only

value: whole blood

source_name: control, whole blood

value: unaffected Filipino male


title: CleftProband_139

value: female


title: PBMC_IMDiagnosis_Subject3


title: PBMC_IMDiagnosis_Subject2


title: CleftProband_140

value: cleft lip and palate


title: EB_P1H02_NOMe-seq

value: E14 embyonic stem cell derived


title: CleftProband_136


title: EB_P1G09_NOMe-seq


title: CleftProband_137


title: EB_P1E03_RNA-seq


title: CleftProband_135


title: EB_P1G06_NOMe-seq


title: PBMC_2month_Subject4

value: Peripheral blood mononuclear cells


title: CleftProband_134


title: EB_P1G03_NOMe-seq


title: EB_P1G02_NOMe-seq


title: EB_P1G01_NOMe-seq


title: EB_P1G04_NOMe-seq


title: EB_P1F08_NOMe-seq


title: EB_P1F09_NOMe-seq


title: EB_P1F07_NOMe-seq


title: EB_P1H05_NOMe-seq


title: EB_P1F02_NOMe-seq


title: EB_P1F03_NOMe-seq


title: EB_P1F01_NOMe-seq


title: CleftProband_132


title: CleftProband_131


title: EB_P1E08_NOMe-seq


title: EB_P1F06_NOMe-seq


title: EB_P1E11_NOMe-seq


title: EB_P1G07_NOMe-seq


title: EB_P1E07_NOMe-seq


title: CleftProband_130


title: EB_P1E03_NOMe-seq


title: EB_P1E05_NOMe-seq


title: CleftProband_129


title: CleftProband_128


title: EB_P1E02_NOMe-seq


title: CleftProband_133


title: CleftProband_127


title: EB_P1D11_NOMe-seq


title: EB_P1E01_NOMe-seq


title: EB_P1D08_NOMe-seq


title: EB_P1D03_NOMe-seq


title: EB_P1D10_NOMe-seq


title: EB_P1D09_NOMe-seq


title: CleftProband_126


title: EB_P1D07_NOMe-seq


title: CleftProband_125


title: EB_P1D02_NOMe-seq


title: CleftProband_124


title: EBcontrol_P2F12_NOMe-seq


title: PBMC_IMDiagnosis_Subject1


title: CleftProband_122


title: EBcontrol_P2E12_NOMe-seq


title: EB_P1D01_NOMe-seq


title: CleftProband_123


title: EBcontrol_P2G12_NOMe-seq


title: CleftProband_121


title: EBcontrol_P1G12_NOMe-seq


title: EBcontrol_P2B12_NOMe-seq


title: EBcontrol_P1F12_NOMe-seq


title: EBcontrol_P1E12_NOMe-seq


title: CleftProband_120


title: CleftProband_119


title: EBcontrol_P1D12_NOMe-seq


title: CleftProband_118


title: EBcontrol_P2D12_NOMe-seq


title: CleftProband_114


title: CleftProband_115


title: CleftProband_111


title: CleftProband_113


title: E16.5_Six2+_ATAC_Seq_3

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

data_processing:
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed
Fastq files were aligned using Bowtie2
ATAC-Seq peaks were called using QuEST (Valouev et al., 2008)
peak files were generated by extracting the chromosome numbers coordinates and QuEST enrichment score from QuEST.out files
wig profiles were generated using QuEST; BigWig files were generated using Wig2BigWig published by UCSC genome browser
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing peak coordinates; BigWig files containing UCSC genome browser visualization tracks

source_name: developing kidneys

extract_protocol:
ATAC-Seq (Buenrostro et al, 2013)
ATAC-Seq (Buenrostro et al, 2013)

value: CFW

tag: developmental stage


title: E16.5_Six2+_ATAC_Seq_1


title: E16.5_Six2+_ATAC_Seq_2


title: E16.5_Six2-_ATAC_Seq_2


title: E16.5_Six2-_ATAC_Seq_1


title: CleftProband_110

value: male


title: E16.5_Six2-_ATAC_Seq_3


title: CleftProband_112


title: EB_P1G08_NOMe-seq


title: CleftProband_105


title: CleftProband_109


title: CleftProband_108


title: CleftProband_107


title: CleftProband_106


title: CleftProband_104


title: CleftProband_96


title: CleftProband_102


title: CleftProband_99


title: CleftProband_116


title: CleftProband_100


title: CleftProband_98


title: CleftProband_117


title: CleftProband_103


title: CleftProband_95


title: CleftProband_94


title: CleftProband_93


title: CleftProband_91


title: CleftProband_90


title: CleftProband_87


title: CleftProband_101


title: CleftProband_92


title: CleftProband_97


title: CleftProband_88


title: DR1 under 0.1mM hydrogen peroxide

city: seoul

first: BORA

last: SHIN

state: 성북구 안암로

country: South Korea

institute: Korea university

data_processing:
RNA sequencing was performed on an Illumina HiSeq 2500 platform using single end 50-bp sequencing
The reference genome sequence was retrieved from the NCBI database.
Quality-filtered reads were aligned to the reference genome sequence using Bowtie2.
The relative abundance of transcripts is presented as RPKM, defined as the total exon reads/(mapped reads in millions × exon length in kilobases).
Genome_build: Acinetobacter oleivorans DR1 chromosome, complete genome RefSeq (NC_014259.1)

organism: Acinetobacter oleivorans DR1

source_name: Bacteria cells

growth_protocol: A. oleivorans DR1, cells were grown to exponential phase (OD600 ~0.4) on nutrient broth (NB) media

extract_protocol:
Total RNA was extracted using an RNeasy Mini kit (Qiagen, USA) following the manufacturer's instructions.
Illumina sequencing library was constructed by the TruSeq Stranded mRNA Library Prep Lit (Illumina, San Diego, CA, USA) following the manufacturer's protocol

treatment_protocol: Exponential cells of A. oleivorans DR1 treated low and high level of hydrogen peroxide for 15min .

value: Mid-exponential phase (OD=0.5-0.6)


title: CleftProband_86


title: DR1 under 1mM hydrogen peroxide


title: CleftProband_85


title: CleftProband_83


title: CleftProband_82


title: CleftProband_84


title: TC1_Mouse_5

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Probes tha uniquely mapped to human chromosome 21 and those which mapped to mouse but not human 21 were kept for analysis.

label: Cy3, Cy5

source_name: Liver

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: age (wks)

value: liver


title: TC1_Mouse_4

tag: strain


title: CleftProband_89


title: TC1_Mouse_3


title: TC1_Mouse_6


title: Macaque_3

organism: Macaca mulatta

source_name: Blood

value: blood


title: Macaque_1


title: CleftProband_81


title: Macaque_4


title: CleftProband_80


title: Macaque_2


title: CleftProband_79


title: CleftProband_77


title: Macaque_6


title: CleftProband_78


title: Macaque_5


title: CleftProband_75


title: CleftProband_76


title: TC1_Mouse_1


title: CleftProband_74


title: TC1_Mouse_2


title: WT

city: Minato-ku, Tokyo

first: Sumiko

last: Watanabe

address: 4-6-1 Shirokane-dai

department: Institute of Medical Science

country: Japan

institute: University of Tokyo

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The Feature Extraction software (Agilent) was used to produce the processed signal values, and the values were normalized by 75percentile by using the GeneSpring software (Tomy Digital Biology).

source_name: control mouse

label_protocol: not provided

growth_protocol: mouse (mixed background)

extract_protocol: Lenses were removed, flash frozen on dry ice, and RNA was isolated using Trizol reagent. Microarray was done using SurePrint G3 Mouse GE microarray 8x60K (Agilent)

treatment_protocol: Foxp1-flox/flox; Pax6-L-Cre

value: lens

value: wild-type

value: C57BL/6 mixed background


title: CleftProband_73


title: CKO

source_name: Foxp1-lens specific KO mice

value: Foxp1 KO


title: WT 8 Gy rep4

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays 4X44K v2 (G4846A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k v.2 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.2 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 026655_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or not significantly above background were excluded.

source_name: whole blood 24h post irradiation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were housed under standard vivarium conditions, and all procedures were conducted under an approved IACUC protocol.

extract_protocol: RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment, followed by globin reduction using GLOBINclear-Mouse/Rat.

treatment_protocol: Blood was collected by cardiac puncture at the time of euthanasia at 24 hours post-irradiation. Each sample  was added to a 15 ml centrifuge tube that contained of PAXgene Blood RNA stabilization and lysis solution and mixed thoroughly

value: wild type

tag: x-ray dose (gy)


title: WT 0 Gy rep5

source_name: whole blood 24h post mock irradiation


title: WT 8 Gy rep5


title: Scid 0 Gy rep5

value: Scid


title: ATM-KO 4 Gy rep5

value: whole blood

value: ATM-/-


title: ATM-KO 4 Gy rep6


title: WT 0 Gy rep6


title: Scid 3 Gy rep5


title: Scid 3 Gy rep4


title: ATM-KO 4 Gy rep4


title: ATM-KO 0 Gy rep5


title: ATM-KO 4 Gy rep2


title: CleftProband_69

value: female

value: unaffected Filipino male


title: CleftProband_71

value: cleft lip and palate


title: negative_A01_NOMe-seq

organism: synthetic construct

source_name: Negative control well

value: Not applicable (synthetic construct)


title: CleftProband_66


title: Scid 0 Gy rep3


title: Scid 0 Gy rep4


title: ATM-KO 0 Gy rep4


title: ATM-KO 4 Gy rep3


title: WT 8 Gy rep2


title: Scid 3 Gy rep3


title: WT 0 Gy rep4


title: CleftProband_70


title: Scid 3 Gy rep2


title: WT 8 Gy rep1


title: Scid 3 Gy rep1


title: WT 0 Gy rep3


title: CleftProband_68


title: CleftProband_63


title: WT 8 Gy rep3


title: CleftProband_67


title: ATM-KO 0 Gy rep3


title: CleftProband_61

value: cleft palate only


title: CleftProband_64

value: male


title: ATM-KO 0 Gy rep2


title: CleftProband_59


title: CleftProband_72


title: WT 0 Gy rep2


title: c-Myc_myotube_ChIP-seq

first: Wen

last: Luo

address: Wushan

institute: South China Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Data were filtered using Trimmomatic (version 0.30)
Data quality evaluation were using FastQC (version 0.10.1)
ChIP-seq reads were aligned to the gga4 genome assembly using bowtie2 version 2.1.0.
peaks were called using HOMER v4.6 with the following setting: Estimated False Discovery Rate 0.1%
Genome_build: Galgal4
Supplementary_files_format_and_content: txt files were generated using HOMER v4.6. The processed data files including peaks information, such as peak score, peak location, p-value etc.

organism: Gallus gallus

source_name: chicken embryo myotube

growth_protocol: chicken primary myoblasts were growed in growth medium containing RPMI-1640, 15% FBS and 2% pen/srep

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed closely according to the standard illumina pair-end ChIP-seq procedure

treatment_protocol: chicken primary myoblasts were induced to differentiation by culturing in differentiation medium (RPMI-1640, 2% horse serum and 2% pen/strep)

value: chicken embryo skeletal muscle derived myotubes

value: differentiated myotube

tag: passages

tag: chip antibody

value: c-Myc (abcam, ab56)


title: IgG_myotube_ChIP-seq

value: IgG (bioss, bs-0310P)


title: CleftProband_60

tag: tissue


title: ATM-KO 0 Gy rep1


title: DM-3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to gga5 whole genome using HISAT with default parameters.
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using HTSeq.
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: chicken embryo myoblast

extract_protocol:
Total RNA of the proliferating myoblasts or differentiated myotubes were harvested using Trizol reagent according to the manufacturer’s direction.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: ATM-KO 4 Gy rep1


title: c-Myc_myoblast_ChIP-seq

value: chicken embryo skeletal muscle derived myoblasts

value: proliferating myoblast


title: Scid 0 Gy rep2


title: CleftProband_57


title: CleftProband_56


title: CleftProband_54


title: DM-2


title: CleftProband_58


title: CleftProband_53


title: WT 0 Gy rep1


title: CleftProband_52


title: IgG_myoblast_ChIP-seq


title: Scid 0 Gy rep1


title: GM-3


title: CleftProband_55


title: GM-2


title: CleftProband_50


title: CleftProband_48


title: CD34H_CD90L_Cad11H fibroblasts gated by flow cytometry from donor RA3

city: Charlestown

first: Kamil

last: Slowikowski

state: Massachusetts

address: Mailstop CNY 149-8, 149 13th Street

institute: Massachusetts General Brigham

description: gene expression

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: none provided by the submitter

source_name: fibroblasts gated by flow cytometry

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by the submitter

tag: disease

value: RA

value: Female

tag: joint

value: Knee


title: CD34H_CD90H_Cad11H fibroblasts gated by flow cytometry from donor RA3

description: gene expression

tag: age


title: CD34H_CD90H_Cad11L fibroblasts gated by flow cytometry from donor RA3

description: gene expression


title: negative_H12_RNA-seq

description: Single-cell RNA-seq


title: DM-1

tag: cell type


title: CD34L_CD90H_Cad11H fibroblasts gated by flow cytometry from donor RA3

description: gene expression


title: CD34L_CD90L_Cad11H fibroblasts gated by flow cytometry from donor RA3

description: gene expression


title: CleftProband_46

value: whole blood


title: CleftProband_62


title: CD34L_CD90L_Cad11L fibroblasts gated by flow cytometry from donor RA3

description: gene expression


title: negative_H01_RNA-seq

description: Single-cell RNA-seq


title: GM-1


title: CleftProband_49


title: CleftProband_51


title: CleftProband_45


title: negative_A12_RNA-seq

description: Single-cell RNA-seq


title: CleftProband_47


title: CD34H_CD90H_Cad11L fibroblasts gated by flow cytometry from donor RA2

description: gene expression


title: CD34H_CD90H_Cad11H fibroblasts gated by flow cytometry from donor RA2

description: gene expression


title: CD146H fibroblasts gated by flow cytometry from donor RA3

description: gene expression


title: CleftProband_44


title: CleftProband_43


title: negative_A01_RNA-seq

description: Single-cell RNA-seq


title: Yellow-green cotyledon replicate4 B

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

hyb_protocol: Hybridization was performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnight. Slides were washed and dried prior to scanning.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche_NimbleGen MS200. DEVA Software v1.2.1 was used to extract pair_data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using R language, version 2.5.1 (R Development Core Team, 2011) and LIMMA package (Smyth G.K., 2005) from the Bioconductor project. For the processing steps, data were normalized by the lowess method in LIMMA.

organism: Castanospermum australe

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse_transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine_3 (Cy3) or Cyanine_5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean_up column kits (Macherey_Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND_1000 (Nanodrop Technologies, DE, USA). Labelled samples (30 pmol) were combined and co_hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Castanospermum australe trees located in Pietermaritzburg (29°37'09.3S 30°23'58.1E), KwaZulu-Natal, South Africa, flower early in November and its seeds mature late in May. Based on physiological traits, six stages of seed development (DS) were identified and harvested from this area in 2013. These stages fall under two broad categories, soft and hard pods. Soft pods appear green, thus three of the six DS were based on changes in seed mass (1.51g – 2.5g, 3.51g – 4.5g and 5.51g – 7.5g). The latter three DS were based on changes in seed coat and pod colour (Green, Yellow Green and Brown)

extract_protocol: Total RNA was extracted from both cotyledon and embryos using the hot phenol method (Bove et al., 2005). RNA Concentration and purity was measured using a NanoDrop spectrophotometer ND - 1000 UV - VIS (NanoDrop Technologies) and its integrity was determined by electrophoresis, fractioning 1μg RNA on agarose gel [1.2% (w/v), 0.5xTBE buffer].

treatment_protocol: Immediately after harvesting, seeds were extracted from its pods followed by the removal of the seed coat. Cotyledonary tissue from all six stages and embryonic axis from the latter three stages only, were excised separately, snap frozen in liquid nitrogen, lyophilised and stored at -80°C for further processing.

tag: tissus

value: Seed Cotyledons

tag: genetic background

value: Wild-type

tag: genotype

value: unknown

tag: phenotype

tag: treatment

value: yellow-green

tag: harvest date


title: CD34H_CD90L_Cad11L fibroblasts gated by flow cytometry from donor RA2

description: gene expression

tag: Sex


title: CD34H_CD90L_Cad11H fibroblasts gated by flow cytometry from donor RA2

description: gene expression


title: CleftProband_42

tag: cleft type

value: cleft lip and palate

value: unaffected Filipino male


title: CD34L_CD90L_Cad11L fibroblasts gated by flow cytometry from donor RA2

description: gene expression


title: ChIP-seq for ZNF701 [SL116164]

city: Baltimore

first: Anand

last: Venkataraman

state: MD

address: 733 N Broadway, MRB 322

department: Neuroscience

institute: Johns Hopkins University

data_processing:
CHIP-seq reads were aligned to hg19-female using Bowtie2 with default parameters
Peaks were called using MACS2 with default parameters
Genome_build: hg19-female
Supplementary_files_format_and_content: Bam files were generated using Bowtie2 and bed files were generated using macs2

extract_protocol:
Exponentially growing cells from ENCODE Tier 1 and Tier 2 cell lines were crosslinked in 1% formaldehyde and harvested in batches of 20 million cells per replicate.  Prepared nuclei were resuspended in RIPA buffer and chromatin shearing was performed on a Bioruptor Twin instrument (Diagenode).   Antibody (5 µg/rxn) was coupled to M-280 Dynabeads (ThermoFisher Scientific; 11201) overnight prior to addition of sheared chromatin.  A small aliquot of the sheared chromatin was reserved as an input control.  Following incubation and wash steps, captured chromatin and input control were reverse crosslinked overnight at 65°C and recovered using the QIAquick PCR Purification System (Qiagen; 28104).
ChIP-seq libraries (illumina) were prepared and run on an Illumina HiSeq 2500 instrument.

tag: cell line

tag: antibody  (clone id#) used


title: Yellow-green cotyledon replicate3 B

tag: developmental stage


title: Brown cotyledon replicate2.2

value: brown


title: Brown cotyledon replicate3 B


title: H3K27me3_ChIPSeq 4HT-, rep3

city: Madsion

first: Duy

last: Nguyen

state: WI

address: 1300 University Ave

department: Statistics

institute: University of Wisconsin, Madison

data_processing:
ChIP-Seq reads were aligned to the human hg19 genome using bowtie version 0.12.7 with the following configurations “bowtie  -q -S -p 10 -v 2 -m 4 --best --strata ”
peaks were called using MOSAiCS version 2.9.9
Genome_build: hg19
Supplementary_files_format_and_content: peak_regions.bed

source_name: LCLs cells

extract_protocol:
EBNA3CHT LCLs were maintained in RPMI 1640 supplemented with 10% FBS, L-glutamine, streptomycin, and penicillin and with or without 400 nM 4HT for 3 weeks.  LCLs were cross-linked with 1% formaldehyde and immuneprecipitated with H3K27me3 antibody.  After extensive washing, Protein-DNA complexes were eluted and cross-linking was reversed. The purified DNA was sequenced using a HiSeq 2500.
Libraries were prepared according to Illumina's standard instructions

value: LCLs cells

tag: antibody

tag: agent


title: CleftProband_41

value: male

tag: tissue


title: CD34L_CD90H_Cad11H fibroblasts gated by flow cytometry from donor RA2

description: gene expression

tag: disease

tag: joint


title: H3K27me3_ChIPSeq 4HT-, rep4

tag: cell type


title: CD34L_CD90L_Cad11H fibroblasts gated by flow cytometry from donor RA2

description: gene expression

tag: age


title: Yellow-green cotyledon replicate1 B

tag: tissus

tag: genetic background


title: Brown cotyledon replicate4 B

tag: genotype

tag: phenotype


title: CleftProband_40


title: CD34H_CD90H_Cad11L fibroblasts gated by flow cytometry from donor RA1

description: gene expression

value: Male

value: MP


title: CD34L_CD90H_Cad11L fibroblasts gated by flow cytometry from donor RA2

description: gene expression


title: Brown cotyledon replicate2 B

tag: treatment

tag: harvest date


title: H3K27me3_ChIPSeq 4HT-, rep2


title: Green axis replicate4

value: Seed Axis

value: green


title: CleftProband_37

tag: Sex

tag: cleft type


title: CleftProband_38


title: H3K27me3_ChIPSeq 4HT+, rep4


title: Yellow-green cotyledon replicate2 B


title: CleftProband_39

value: female


title: H3K27me3_ChIPSeq 4HT+, rep3


title: H3K27me3_ChIPSeq 4HT+, rep2


title: CleftProband_65


title: H3K27me3_ChIPSeq 4HT-, rep1


title: CD34H_CD90H_Cad11H fibroblasts gated by flow cytometry from donor RA1

description: gene expression

value: RA


title: CleftProband_34


title: CleftProband_35


title: CleftProband_36


title: CD34L_CD90L_Cad11L fibroblasts gated by flow cytometry from donor RA1

description: gene expression


title: H3K27me3_ChIPSeq 4HT+, rep1


title: CleftProband_33


title: CD34H_CD90L_Cad11H fibroblasts gated by flow cytometry from donor OA3

description: gene expression

value: OA

value: Knee


title: CD34L_CD90H_Cad11L fibroblasts gated by flow cytometry from donor RA1

description: gene expression


title: Brown axis replicate3 B


title: CleftProband_30

value: whole blood


title: Brown axis replicate4 B

value: Wild-type


title: CD34H_CD90H_Cad11H fibroblasts gated by flow cytometry from donor OA3

description: gene expression


title: CleftProband_32


title: Green axis replicate2

value: unknown


title: CleftProband_31


title: CD34L_CD90H_Cad11H fibroblasts gated by flow cytometry from donor RA1

description: gene expression


title: Green axis replicate3


title: CD34L_CD90L_Cad11H fibroblasts gated by flow cytometry from donor RA1

description: gene expression


title: CD34L_CD90L_Cad11L fibroblasts gated by flow cytometry from donor OA3

description: gene expression


title: CD34L_CD90H_Cad11H fibroblasts gated by flow cytometry from donor OA3

description: gene expression


title: Brown axis replicate2 B


title: Brown axis replicate1 B


title: Yellow-green axis replicate3

value: yellow-green


title: CleftProband_29

value: cleft lip and palate


title: CD34H_CD90H_Cad11H fibroblasts gated by flow cytometry from donor OA2

description: gene expression

value: Female


title: Yellow-green axis replicate4


title: CleftProband_28

value: unaffected Filipino male


title: Brown axis replicate4 A

value: brown


title: Green axis replicate1


title: Brown axis replicate3 A


title: CleftProband_27

value: male


title: CleftProband_25


title: CleftProband_24


title: CleftProband_26


title: CleftProband_23


title: CleftProband_22


title: CD34H_CD90L_Cad11H fibroblasts gated by flow cytometry from donor OA2

description: gene expression


title: CD34L_CD90H_Cad11H fibroblasts gated by flow cytometry from donor OA2

description: gene expression


title: HFD 2 LKSneg

city: Pittsburgh

first: Lisa

middle: Ann

last: Borghesi

state: PA

address: 200 Lothrop ST

department: Immunology

institute: University of Pittsburgh

hyb_protocol: 100 ng of extracted RNA was used for hybridization to the probes at 65°C for 18 hours, following the manufacturer’s protocol.

scan_protocol: Hybridized probes were counted on nCounter Prep Station and Digital Analyzer

data_processing: The nCounter results were analyzed statistically using manufacturer's software nSolver 2.5.

label: labeled by manufacturer

source_name: bone marrow

label_protocol: Labeled probes are provided by the manufacturer.

extract_protocol: RNA extracted from cells was subjected to nCounter RNA sample preparation according to the manufacturer’s instructions.

tag: diet

value: high fat diet

value: bone marrow

tag: gender

value: BM LKSneg


title: Brown axis replicate2 A

value: Seed Axis

tag: developmental stage


title: CleftProband_21


title: CD34L_CD90L_Cad11H fibroblasts gated by flow cytometry from donor OA2

description: gene expression


title: Yellow-green axis replicate1


title: Brown axis replicate1 A


title: CD34L_CD90L_Cad11L fibroblasts gated by flow cytometry from donor OA2

description: gene expression


title: CD34L_CD90L_Cad11H fibroblasts gated by flow cytometry from donor OA3

description: gene expression

value: Male


title: CD34L_CD90L_Cad11L fibroblasts gated by flow cytometry from donor OA1

description: gene expression


title: CD34L_CD90H_Cad11H fibroblasts gated by flow cytometry from donor OA1

description: gene expression


title: Yellow-green axis replicate2


title: Brown cotyledon replicate4 A

value: Seed Cotyledons


title: CD34H_CD90H_Cad11H fibroblasts gated by flow cytometry from donor OA1

description: gene expression

value: OA


title: Brown cotyledon replicate3 A


title: CD34H_CD90L_Cad11H fibroblasts gated by flow cytometry from donor OA1

description: gene expression

value: Knee


title: HFD 1 LKSneg


title: NCD 2 LKSneg

value: normal chow


title: NCD 3 LKSneg


title: NCD 1 LKSneg


title: CleftProband_19

value: female

value: whole blood


title: CleftProband_20


title: Green cotyledon replicate4

value: Wild-type

value: unknown

value: green


title: CleftProband_18

value: cleft lip and palate

value: unaffected Filipino male


title: HFD 3 CLP

value: male

value: BM CLP


title: Six2DE_4C-Seq_Br

data_processing:
Library strategy: 4C-seq
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed
Fastq files were aligned using Bowtie2 following specific guiodance in R.4Cker pipeline (Raviram et al., 2016)
bam files were converted to bedGraph using bamToBed and bedGraphToBigWig apps published by UCSC genome browser
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph files which can be visualized on UCSC genome browser

source_name: nephron-genic zone cells from Br/+ kidneys

extract_protocol:
4C-Seq (van de Werken et al., 2012)
4C-Seq (van de Werken et al., 2012)

tag: strain

value: CFW

tag: developing stage

value: Br/+


title: Six2DE_4C-Seq_WT

source_name: nephron-genic zone cells from wildtype kidneys

value: wild-type


title: CleftProband_16

source_name: case, whole blood

tag: tissue

source_name: control, whole blood


title: HFD 1 CLP

value: high fat diet

value: bone marrow


title: CleftProband_14


title: NCD 1 CLP


title: CD34L_CD90L_Cad11H fibroblasts gated by flow cytometry from donor OA1

description: gene expression

tag: disease

value: OA

value: Female

tag: joint


title: Brown cotyledon replicate2 A

value: Seed Cotyledons

value: brown


title: Green cotyledon replicate2


title: Green cotyledon replicate3


title: HFD 2 CLP

tag: cell type


title: CleftProband_11

value: whole blood


title: CleftProband_17

value: female


title: Green cotyledon replicate1

tag: tissus

value: Wild-type

value: unknown


title: Brown cotyledon replicate1

tag: genetic background


title: 7.5g cotyledon replicate4

tag: genotype


title: Yellow-green cotyledon replicate3 A

tag: phenotype

value: yellow-green


title: NCD 3 CLP

value: normal chow


title: CleftProband_15

value: cleft palate only

value: male

value: unaffected Filipino male


title: CleftProband_10

value: cleft lip and palate


title: CleftProband_9


title: CleftProband_13


title: CleftProband_12


title: Yellow-green cotyledon replicate4 A

tag: treatment


title: CK2

city: Beijing

first: Xiayin

address: 17 Qing Hua East Road Hai Dian District

institute: China Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing  reads containing adapter, reads containing ploy-N and low quality reads from  raw data. At the same time, Q20, Q30 and GC content sequence of the clean  data were calculated. All the downstream analyses were based on the clean data  with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly (NZ_CP012148.1). Both building index of reference genome and aligning  clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S.  L. Salzberg, 2012)
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And  then FPKM of each gene was calculated based on the length of the gene and  reads count mapped to this gene.
(For DESeq with biological replicates) Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using  the DESeq R package (1.18.0). DESeq provide statistical routines for  determining differential expression in digital gene expression data using a  model based on the negative binomial distribution. The resulting P-values were  adjusted using the Benjamini and Hochberg’s approach for controlling the false  discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were  assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the GOseq R package, in which gene length bias was corrected.  GO terms with corrected Pvalue less than 0.05 were considered significantly  enriched by differential expressed genes.
Genome_build: NZ_CP012148.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Lacticaseibacillus paracasei

source_name: L. paracasei L9

growth_protocol: L. paracasei L9 was cultured in de Man-Rogosa-Sharpe (MRS) medium anaerobically at 37 oC with or without 0.13% oxgall

extract_protocol:
Total RNA isolation was carried out using TRIzol reagent (Invitrogen, Carlsbad, CA) as the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® Ultra™Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.

tag: medium

value: MRS

tag: period

value: mid-exponential phase， about 3-4×107 cfu/mL


title: NCD 2 CLP

value: bone marrow

value: BM CLP


title: CK3


title: CleftProband_8

tag: Sex

tag: cleft type


title: CK1


title: OG2

value: MRS with 0.13% oxgall


title: OG1


title: OG3


title: CleftProband_6


title: CleftProband_5


title: CleftProband_7


title: CleftProband_4


title: CleftProband_3


title: CleftProband_2


title: 7.5g cotyledon replicate3

value: Seed Cotyledons

tag: harvest date


title: Yellow-green cotyledon replicate2 A

tag: developmental stage


title: 7.5g cotyledon replicate2


title: 4.5g cotyledon replicate4


title: Yellow-green cotyledon replicate1 A


title: 7.5g cotyledon replicate1


title: CleftProband_1


title: CQ12_Mo_Gene_ST_2_12_SIRT6KD_T0_Un3

status: Public on Jan 16 2018

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were nomanized by RMA with Parteck Genomic Suit 6.6

growth_protocol: Mouse grow in NIDDK animal core facility.

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

treatment_protocol: Two types of mouse(Wt vs. SIRT6) were treated with Un-untreated vs Tr-treated of inhibitor under three time points.

tag: genotype/variation

tag: time point

value: untreated


title: CQ10_Mo_Gene_ST_2_10_SIRT6KD_T0_Un1


title: BV173 doxycycline 1

data_processing: Microarray data was analyzed by Expression Console, Transcriptom Analysis Console (Thermo Fisher Scientific) and GeneSpring Software (Agilent).

source_name: cell line BV173

extract_protocol: RNA was extracted from 4-5 millions of cells by using the RNeasy Plus Mini-Kit (Qiagen #74134)

tag: cell line


title: BV173 doxycycline 2


title: CQ4_Mo_Gene_ST_2_4_WT_T20_Tr1

value: wild type

value: treated of inhibitor


title: 2.5g cotyledon replicate4

value: Wild-type


title: 2.5g cotyledon replicate3

value: unknown


title: CQ13_Mo_Gene_ST_2_13_SIRT6KD_T20_Tr1


title: BV173 doxycycline 3


title: CQ11_Mo_Gene_ST_2_11_SIRT6KD_T0_Un2


title: CQ14_Mo_Gene_ST_2_14_SIRT6KD_T20_Tr2


title: CQ18_Mo_Gene_ST_2_18_SIRT6KD_T40_Tr3


title: CQ8_Mo_Gene_ST_2_8_WT_T40_Tr2


title: CQ7_Mo_Gene_ST_2_7_WT_T40_Tr1


title: 2.5g cotyledon replicate1


title: 2.5g cotyledon replicate2


title: CQ3_Mo_Gene_ST_2_3_WT_T0_Un3


title: CQ9_Mo_Gene_ST_2_9_WT_T40_Tr3


title: CQ16_Mo_Gene_ST_2_16_SIRT6KD_T40_Tr1


title: CQ15_Mo_Gene_ST_2_15_SIRT6KD_T20_Tr3


title: CQ17_Mo_Gene_ST_2_17_SIRT6KD_T40_Tr2


title: 4.5g cotyledon replicate2


title: 4.5g cotyledon replicate3


title: CQ2_Mo_Gene_ST_2_2_WT_T0_Un2


title: CQ6_Mo_Gene_ST_2_6_WT_T20_Tr3


title: BV173 untreated 1


title: BV173 untreated 2


title: Patient_F5

city: Aurora

first: Maranke

last: Koster

address: 12800 E19th Avenue

department: Dermatology

data_processing:
Illumina Real-Time Analysis (RTA) was used for base calling
Adapter sequences were trimmed using Trimmomatic and RNA-seq reads were mapped to the human genome (hg19) using STAR
DESeq2 was used to obtain differential expression
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files including basemean, log2FoldChange,IfCSE,stat, pvalue, padj were obtained for two patient samples in comparison to two gene corrected samples

source_name: Patient_iPSC-derived keratinocytes

extract_protocol:
RNA was harvested from IPS derived keratinocytes using Trizol reagent.
Sequencing libraries for RNA-Seq was prepared by Genomics and Microarray Core Facility at University of Colorado-Anschutz Medical Campus

tag: subject status

value: patient affected by ankyloblepharon ectodermal dysplasia and clefting (AEC)

tag: subject id

tag: tissue source

value: Skin biopsy

value: IPS derived keratinocytes

tag: gentoype/variation

value: with a disease-associated TP63 mutation


title: Gene corrected_E3

institute: University of Colorado-Anschutz Medical Campus

tag: cell type

value: without a disease-associated TP63 mutation


title: Gene corrected_F5


title: CQ5_Mo_Gene_ST_2_5_WT_T20_Tr2


title: 4.5g cotyledon replicate1

tag: tissus

tag: genetic background

tag: genotype


title: H5N1_mock_meth_18

city: Chapel Hill

first: Alexandra

last: Schaefer

state: NC

address: 3109 MHRC

institute: University of North Carolina at Chapel Hill

data_processing:
Analysis was performed by using the CLC Genomics Workbench 10.0; Bisulfite Sequencing plug-in
mapping bisulfite reads to reference genomes: stringent read matching (mismatch cost 2, insertion cost 3, deletion cost 3, no non-specific matching)
corresponding mock as control
calling of methylation levels: Fisher exact as statistical model with max p-value = 0.05, window length = 200, minimum number of samples =1, min high-confidence site coverage =1, min. high-confidence site count =1, max mean site coverage = 0.0
quality measeures for ChIP-seq dataset: high number of reads, relative strand correlation >0.8, normalized strand coefficient >1.05
bed files were used to generate qunativative distribution of differential methyaltion marks on chromosome 6; visualized by chromosome plots
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bed were generated by using CLC Genomics Workbench 10.0

source_name: Calu3 cells

growth_protocol: Calu3 cells were plated into 6 well plates

extract_protocol:
Lysates were pooled (3 samples) were clarified from sonicated nuclei and methylated DNA was enriched by using the MethylMiner Methylated DNA Enrichment Kit (Invitrogen, ME10025)
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: cells infected with MERS-CoV at an MOI=5 and with H5N1 at an MOI=3 for 18hpi, respectively

value: airway epithelial cell line

tag: passages


title: H5N1_meth_18


title: MERS_mock_meth_18


title: BV173 untreated 3

city: Philadelphia

first: Marco

last: De Dominici

institute: Thomas Jefferson University


title: HLCs_1

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: Replicate 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Illumina BeadStation 500 using the standard Illumina scanning protocol.

data_processing: The data were log2-transformed and normalised using quantile normalisation with R/Bioconductor package lumi.

source_name: hepatocyte-like cells from IPSCs

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.

growth_protocol: Human ES cell were maintained under sterile conditions in a humidified incubator in a 5% CO2-95% air atmosphere at 37 degree Celsius. In a routine culture cells were maintained on Matrigel in conditioned media.

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Qiagen), and DNase digestion (RNase-free DNase Set, Qiagen) has been applied on the columns during isolation.

treatment_protocol: The derivation of HLCs from the hESCs followed protocols described by Hay et al. and Agarwal et al. Differentiation was initiated when cells reached 50-60% confluence. RNA samples were extracted after each step of the differentiation protocol in order to ex-amine the activation of endoderm and hepatocyte-associated genes. On day 18 functional tests were performed.

value: hepatocyte-like cells


title: PHH_2

description: Replicate 2

source_name: primary hepatocytes

value: primary hepatocytes


title: Fetal_Liver_1

description: Replicate 1

source_name: fetal liver

tag: tissue

value: fetal liver


title: DE_3

description: Replicate 3

source_name: definite endoderm from IPSCs

value: definite endoderm


title: MERS_meth_18


title: HE_3

description: Replicate 3

source_name: hepatic endoderm from IPSCs

value: hepatic endoderm


title: CQ1_Mo_Gene_ST_2_1_WT_T0_Un1

tag: treatment


title: input_H3K27me3_ChIPSeq

data_processing:
Analysis was performed by using the CLC Genomics Workbench 10.0; Histone ChIP-Seq plug-in
mapping reads to reference genomes: stringent read matching (mismatch cost 2, insertion cost 3, deletion cost 3, no non-specific matching)
peak calling: max p-value = 0.05; corresponding mock as control
quality meassures for ChIP-seq dataset: high number of reads, relative strand correlation >0.8, normalized strand coefficient >1.05
bed files were used to generate qunativative distribution of enriched peaks on chromosome 6; visualized by chromosome plots
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bed were generated by using CLC Genomics Workbench 10.0

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

treatment_protocol: cells infected with MERS-CoV at an MOI=5 and with H5N1 at an MOI=3 for 12hpi, respectively

tag: chip antibody

value: H3K27me3 (Qiagen, GAH-8208)


title: Fetal_Liver_2

description: Replicate 2


title: HE_2

description: Replicate 2


title: DE_2

description: Replicate 2


title: HLCs_3

description: Replicate 3


title: NHBE_2.5%CSE_24h_rep2

city: Tokyo

first: Tadashi

last: Sato

address: 3-1-3 Hongo, Bunkyo-ku

department: Department of Respiratory Medicine

institute: Juntendo University Graduate School of Medicine

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes according to the manufacturer's instructions. On completion of the fragmentation reaction, 100 µl of fragmentation mixture were hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: lides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100%, XDR Lo 10%).

data_processing: Extract tif images using the Feature Extraction software FE9.5 by GE1-v5_95 protocols. Normalization was performed using global-normalization methods.

source_name: NHBE, 2.5%CSE, 24h, replicate2

label_protocol: RNA samples were labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: SAEC were cultured with Small Airway Epithelial Cell Growth Medium (Lonza) and NHBE were cultured with Bronchial Epithelial Cell Growth Medium (Lonza) following the supplier’s instructions.

extract_protocol: Total RNA was extracted using miRNeasy mini kits (Qiagen, Hilden, Germany) following the manufacturer’s instructions.

treatment_protocol: Cells were treated with or without 2.5% CSE for 24h.

value: Human Bronchial Epithelial Cell

tag: number of passage


title: NHBE_0%CSE_24h_rep2

source_name: NHBE, 0%CSE, 24h, replicate2


title: NHBE_0%CSE_24h_rep1

source_name: NHBE, 0%CSE, 24h, replicate1


title: SAEC_2.5%CSE_24h_rep2

source_name: SAEC, 2.5%CSE, 24h, replicate2

value: Human Small Airway Epithelial Cell


title: input_H3K4me3_ChIPSeq

value: H3K4me3 (Qiagen, GAH-8208)


title: mock_H3K27me3_ChIPSeq


title: HE_1

description: Replicate 1


title: HLCs_2

description: Replicate 2


title: SAEC_0%CSE_24h_rep1

source_name: SAEC, 0%CSE, 24h, replicate1


title: H5N1_H3K27me3_ChIPSeq

value: H3K27me3 (Qiagen, GAH-9205)


title: SAEC_2.5%CSE_24h_rep1

source_name: SAEC, 2.5%CSE, 24h, replicate1


title: MERS_H3K27me3_ChIPSeq


title: H5N1_H3K4me3_ChIPSeq


title: PHH_1

description: Replicate 1


title: SAEC_0%CSE_24h_rep2

source_name: SAEC, 0%CSE, 24h, replicate2


title: MERS_H3K4me3_ChIPSeq


title: NHBE_2.5%CSE_24h_rep1

source_name: NHBE, 2.5%CSE, 24h, replicate1


title: mock_H3K4me3_ChIPSeq


title: preadipocytes Pparg InVivo CE KnockOut1

city: Zuerich

first: Lennart

last: Opitz

address: Winterthurerstr. 190

country: Switzerland

institute: FGCZ Zuerich

description: preadipocytes Pparg InVivo CE KnockOut1

hyb_protocol: Labeled samples were hybridized overnight to the Agilent 4X44 Whole Mouse Genome Array.

scan_protocol: Arrays were washed and then scanned with the model G2505C Agilent DNA microarray Scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameter.

source_name: preadipocytes Pparg InVivo CE KnockOut

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) according to manufacturer's protocol

value: preadipocytes

tag: strain

tag: protocol

value: inVivo

value: Pparg KnockOut

value: ColdExposure


title: DE_1

description: Replicate 1


title: preadipocytes Pparg InVivo CE KnockOut3

description: preadipocytes Pparg InVivo CE KnockOut3

tag: genotype/variation


title: tRNA-GlyGCC in  Rescue D2 wild type

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

description: processed file contains calculated non-conversion rates (C-to-T) at every cytosine position in tRNAs in % as a quantative measure of (cytosine-5) methylation at this position

data_processing:
Illumina multiplex barcode sequences were extracted from the raw output as bam files
Bam files were imported into the Galaxy tool, version 0.0.2 (http://usegalaxy.org)
Bam files were converted to fastqcsanger files using the tool: SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq (Galaxy Version 2.7.1.0)
Individual reads matching particular tRNA isoacceptors were extracted from only READ1 using the CREP command
Reads were trimmed to include the custom 4-letter barcode surrounded by two random nucleotides on either side of this barcode at the 3' end (NN[XXXX]NN)
5'-(NNCCTTNN)-3' containing reads as well as 5'-(NNTTAANN)-3' were extracted (for barcode use: see attached readme.txt file)
Reads were aligned using BSMAP v2.87 (parameters : -s 12 -v 0.03 -g 0 -w 1000 -S 0 -p 1 -V 1 -I 1 -n 0 -r 2 -u -m 15 -x 1000 ; Xi and Li 2009) to a D. melanogaster reference of mature and non-spliced tRNAs (from all tRNA sequences in gtrnadb.ucsc.edu and flybase.org, dm6), summarized as described in (Legrand et al., 2017).
Uniquely aligned reads were further processed and filtered as in (Legrand et al., 2017) to produce non-conversion ratios. Briefly, resulting aligned reads were kept only if their length was 25 nt or more, if they aligned uniquely. Further, unconverted reads and correlated unconverted C - mismatch, if present, were discarded.
Heat maps for non-conversion of cytosine were generated using a custom bash script to convert aligned reads to a text-coded image, and using a custom R (v3.3.3) script for display, calculation of raw non-conversion ratios and image annotation.
Genome_build: dm6 (release 6.16 in flybase.org)
Supplementary_files_format_and_content:
bam file (not provided): BAM file (binary form of SAM-formatted files) containing aligned reads
unconvertion ratio tabular file: tab-delimited text files containing non-conversion ratio at each cytosine
fasta file (not provided): FASTA files containing reads to be aligned

organism: Drosophila melanogaster

source_name: Dnmt2 Null Mutant (#5.4); Rescue Dnmt2 wild type

growth_protocol: Flies were cultured on standard fly food in a humidified incubator (60% humidity) at a 12/12 hour day-night light cycle

extract_protocol:
Flies (10 females and 10 males) were mechanically homogenized in TriReagent (Sigma) using a pestle and total RNA was isolated. Bisulfite conversion was performed on 1 µg RNA after DNaseI treatment using the EZ RNA Methylation™ Kit (ZymoSearch).
Bisulfite-treated RNA was reverse transcribed with bisulfite-specific and tRNA-specific primers incorporating an internal 4-letter barcode preceded and succeeded by two randomized nucleotides (NNXXXXNN) to follow PCR biases using the SuperScript III First-Strand Synthesis System (Thermo Fisher Scientific). Amplicons for Illumina sequencing were generated by two sequential PCR and sequencing was performed on an Illumina miSeq platform.

tag: developmental stage

value: 3-5 days after hatching

value: mixed adult whole flies

tag: conditions

value: standard temperature

tag: trna 3' end

value: GGTTTGATTTTTGGTTGATG

tag: molecule subtype

value: tRNA-GlyGCC


title: tRNA-AspGUC in Rescue D2 cat mutant

source_name: Dnmt2 Null Mutant (#5.4); Rescue Dnmt2 cat dead

value: GGGTTTAATTTTTTGTTGGG

value: tRNA-AspGUC


title: tRNA-GlyGCC in  Rescue D2 cat mutant

value: Dnmt2 Null Mutant (#5.4); Rescue Dnmt2 cat dead


title: preadipocytes Pparg InVivo CE control1

description: preadipocytes Pparg InVivo CE control1

source_name: preadipocytes Pparg InVivo CE control

value: Pparg control


title: preadipocytes Pparg InVivo CE control2

description: preadipocytes Pparg InVivo CE control2


title: preadipocytes Pparg InVivo CE KnockOut2

description: preadipocytes Pparg InVivo CE KnockOut2


title: preadipocytes Pparg InVivo CE KnockOut4

description: preadipocytes Pparg InVivo CE KnockOut4


title: preadipocytes Pparg InVivo RT KnockOut2

description: preadipocytes Pparg RT KnockOut2

source_name: preadipocytes Pparg InVivo RT KnockOut

value: RoomTemperature


title: preadipocytes Pparg InVivo CE control4

description: preadipocytes Pparg InVivo CE control4


title: preadipocytes Pparg InVivo RT KnockOut3

description: preadipocytes Pparg RT KnockOut3


title: preadipocytes Pparg InVivo RT KnockOut4

description: preadipocytes Pparg RT KnockOut4


title: preadipocytes Pparg InVivo CE control3

description: preadipocytes Pparg InVivo CE control3


title: tRNA-GlyGCC in  Dnmt2 Null

source_name: Dnmt2 Null Mutant (#5.4)

value: Dnmt2 Null Mutant (#5.4)


title: preadipocytes Pparg InVivo RT KnockOut1

description: preadipocytes Pparg RT KnockOut1


title: preadipocytes Pparg InVivo RT control3

description: preadipocytes Pparg InVivo RT control3

source_name: preadipocytes Pparg InVivo RT control


title: tRNA-AspGUC in Dnmt2 Null


title: preadipocytes Pparg InVivo RT control4

description: preadipocytes Pparg InVivo RT control4


title: tRNA-Leu in NSun2 Null

source_name: NSun2 Null Mutant (#21.5)

value: NSun2 Null Mutant (#21.5)

value: TGAATTTTATTTTTGATA

value: tRNA-Leu


title: preadipocytes Pparg InVivo RT control1

description: preadipocytes Pparg InVivo RT control1

value: preadipocytes

value: inVivo


title: tRNA-AspGUC in Rescue D2 wild type

value: Dnmt2 Null Mutant (#5.4); Rescue Dnmt2 wild type


title: tRNA-iMetCAU in NSun2 Null

value: 3-5 days after hatching

value: TGAAATTTTGTTTTGTTA

value: tRNA-iMetCAU


title: tRNA-MetCAU in NSun2 Null

value: mixed adult whole flies

value: standard temperature

value: TGAGTTTTATTTGGGGTA

value: tRNA-MetCAU


title: tRNA-GlyGCC in NSun2 Null

value: GGTTTGATTTTTGGTTGATG

value: tRNA-GlyGCC


title: preadipocytes Pparg InVivo RT control2

description: preadipocytes Pparg InVivo RT control2

value: Pparg control

value: RoomTemperature


title: tRNA-AspGUC in NSun2 Null

value: NSun2 Null Mutant (#21.5)

value: GGGTTTAATTTTTTGTTGGG

value: tRNA-AspGUC


title: tRNA-Leu in control

source_name: wild type (w1118)

value: wild type (w1118)

value: TGAATTTTATTTTTGATA

value: tRNA-Leu


title: preadipocytes Gyk InVitro KnockDown2

description: preadipocytes Gyk InVitro KnockDown2

source_name: preadipocytes Gyk InVitro KnockDown

value: preadipocytes

value: inVitro

value: Gyk KnockDown


title: tRNA-iMetCAU in control

value: 3-5 days after hatching

value: mixed adult whole flies

value: TGAAATTTTGTTTTGTTA

value: tRNA-iMetCAU


title: preadipocytes Gyk InVitro KnockDown1

description: preadipocytes Gyk InVitro KnockDown1


title: preadipocytes Gyk inVitro control3

description: preadipocytes Gyk inVitro control3

source_name: preadipocytes Gyk inVitro control

value: Gyk control


title: preadipocytes Gyk InVitro KnockDown3

description: preadipocytes Gyk InVitro KnockDown3


title: tRNA-AspGUC in control

value: standard temperature


title: tRNA-MetCAU in control

value: TGAGTTTTATTTGGGGTA

value: tRNA-MetCAU


title: preadipocytes Gyk InVitro KnockDown4

description: preadipocytes Gyk InVitro KnockDown4

value: RoomTemperature


title: tRNA-GlyGCC in control

value: GGTTTGATTTTTGGTTGATG

value: tRNA-GlyGCC


title: preadipocytes Gyk inVitro control2

description: preadipocytes Gyk inVitro control2


title: preadipocytes Pparg inVitro KnockDown3

description: preadipocytes Pparg inVitro KnockDown3

source_name: preadipocytes Pparg inVitro KnockDown

value: Pparg KnockDown


title: whole blood taken from sample 2482

status: Public on Jan 15 2018

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

institute: University of Exeter

description: whole blood taken from sample 2482

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.
Average Beta or normalized (provide the normalization method) Average Beta

label: Cy5 and Cy3

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: Genomic DNA was extracted from frozen whole blood samples using a standard cell lysis, proteinase K digestion, phenol/chloroform, ethanol precipitation method.

tag: familyid

tag: twinid

tag: gender

value: M

tag: zygosity

value: MZ


title: preadipocytes Pparg inVitro control2

description: preadipocytes Pparg inVitro control2

source_name: preadipocytes Pparg inVitro control

tag: cell type

value: preadipocytes

value: Pparg control


title: whole blood taken from sample 2592

description: whole blood taken from sample 2592


title: whole blood taken from sample 2611

description: whole blood taken from sample 2611

value: F


title: preadipocytes Gyk inVitro control1

description: preadipocytes Gyk inVitro control1

value: inVitro


title: preadipocytes Pparg inVitro KnockDown1

description: preadipocytes Pparg inVitro KnockDown1


title: RSY252 – WT (Ura3-52 his4-619)

city: Tiruchirapalli

first: Vasanthi

last: Nachiappan

state: Tamil Nadu

address: School of Life Sciences

department: Biochemistry

country: India

institute: Bharathidasan University

hyb_protocol: The labeled cRNA samples were hybridized on to a Agilent Platform Custom Saccharomyces cerevisiae 8x15k designed by Genotypic Technology Private Limited (AMADID: 016333) 600ng of cy3 labeled samples were  fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (AgilentTechnologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift ( Gene based Analysis was performed)

organism: Saccharomyces cerevisiae

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Cells were grown at 30 ˚C in YPD (1%Yeast extract, 2% Peptone and 2% Glucose) medium for 48 hours at 180 rpm.

extract_protocol: RNA was extracted using the TRIzol (Invitrogen) method with glass beads (Sigma, 425-600um, Cat #G8772) for homogenization following the manufacturer's recommendations.

tag: growth phase

value: Stationary Phase cells


title: RSY27- sec59-1∆ (His4-593 ura3-52 suc2-432)


title: whole blood taken from sample 2481

description: whole blood taken from sample 2481


title: preadipocytes Gyk inVitro control4

description: preadipocytes Gyk inVitro control4


title: whole blood taken from sample 2402

description: whole blood taken from sample 2402


title: preadipocytes Pparg inVitro KnockDown2

description: preadipocytes Pparg inVitro KnockDown2


title: whole blood taken from sample 3252

description: whole blood taken from sample 3252


title: whole blood taken from sample 1992

description: whole blood taken from sample 1992


title: preadipocytes Pparg inVitro control3

description: preadipocytes Pparg inVitro control3


title: preadipocytes Pparg inVitro KnockDown4

description: preadipocytes Pparg inVitro KnockDown4


title: preadipocytes Pparg inVitro control1

description: preadipocytes Pparg inVitro control1


title: whole blood taken from sample 3251

description: whole blood taken from sample 3251


title: whole blood taken from sample 2612

description: whole blood taken from sample 2612


title: whole blood taken from sample 2591

description: whole blood taken from sample 2591


title: hippocampas_control

first: Takahito

last: Higashi

address: 7-3-1 Hongo Bunkyo-ku

department: Department of Cellular Neurobiology

institute: Graduate School of Medicine and Faculty of Medicine, The University of Tokyo

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: Dissociated hippocampal culture, DIV12

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Cultured hippocampal neurons were prepared from embryonic day 16.5 ICR  mouse embryos. Hippocampi were dissected, trypsinized, and dissociated. Cells were plated onto 35 mm-diameter culture dishes (BD Falcon) coated with poly-L-lysine (SIGMA Aldrich). Cells were cultured in Minimum Essential Medium with B18 supplement and 5.5% Fetal Bovine Serum (Equitech-Bio) at 37°C in 5% CO2-humidified incubator. At 2 days post-plating, 5 µM Ara-C was added to prevent glial cell proliferation.

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Neuronal cultures were treated with a sodium channel blocker TTX for 2 days before RNA extraction.

tag: tissue

value: Hippocampus

value: ICR

tag: div


title: hippocampas_TTX

source_name: Dissociated hippocampal culture, DIV12, 2mM TTX treatment for 2days


title: whole blood taken from sample 2401

description: whole blood taken from sample 2401


title: preadipocytes Pparg inVitro control4

description: preadipocytes Pparg inVitro control4

tag: treatment


title: whole blood taken from sample 1791

description: whole blood taken from sample 1791


title: whole blood taken from sample 1792

description: whole blood taken from sample 1792


title: whole blood taken from sample 4951

description: whole blood taken from sample 4951


title: whole blood taken from sample 1681

description: whole blood taken from sample 1681


title: whole blood taken from sample 2082

description: whole blood taken from sample 2082


title: whole blood taken from sample 951

description: whole blood taken from sample 951


title: whole blood taken from sample 1151

description: whole blood taken from sample 1151


title: whole blood taken from sample 952

description: whole blood taken from sample 952


title: whole blood taken from sample 2081

description: whole blood taken from sample 2081


title: whole blood taken from sample 1761

description: whole blood taken from sample 1761


title: whole blood taken from sample 1991

description: whole blood taken from sample 1991


title: whole blood taken from sample 741

description: whole blood taken from sample 741


title: whole blood taken from sample 1152

description: whole blood taken from sample 1152


title: whole blood taken from sample 1682

description: whole blood taken from sample 1682


title: whole blood taken from sample 422

description: whole blood taken from sample 422


title: whole blood taken from sample 892

description: whole blood taken from sample 892


title: whole blood taken from sample 742

description: whole blood taken from sample 742


title: whole blood taken from sample 591

description: whole blood taken from sample 591


title: whole blood taken from sample 361

description: whole blood taken from sample 361


title: whole blood taken from sample 891

description: whole blood taken from sample 891


title: whole blood taken from sample 9222

description: whole blood taken from sample 9222


title: whole blood taken from sample 1762

description: whole blood taken from sample 1762


title: whole blood taken from sample 421

description: whole blood taken from sample 421


title: whole blood taken from sample 8992

description: whole blood taken from sample 8992


title: whole blood taken from sample 8782

description: whole blood taken from sample 8782


title: whole blood taken from sample 732

description: whole blood taken from sample 732

value: DZ


title: whole blood taken from sample 8781

description: whole blood taken from sample 8781


title: whole blood taken from sample 731

description: whole blood taken from sample 731


title: whole blood taken from sample 8991

description: whole blood taken from sample 8991


title: whole blood taken from sample 592

description: whole blood taken from sample 592


title: Patient_E3

source_name: Patient_iPSC-derived keratinocytes

tag: subject status

value: patient affected by ankyloblepharon ectodermal dysplasia and clefting (AEC)

tag: subject id

tag: tissue source

value: Skin biopsy

value: IPS derived keratinocytes

tag: gentoype/variation

value: with a disease-associated TP63 mutation


title: whole blood taken from sample 8422

description: whole blood taken from sample 8422


title: whole blood taken from sample 7822

description: whole blood taken from sample 7822


title: whole blood taken from sample 8421

description: whole blood taken from sample 8421


title: whole blood taken from sample 8631

description: whole blood taken from sample 8631


title: whole blood taken from sample 8282

description: whole blood taken from sample 8282


title: whole blood taken from sample 8331

description: whole blood taken from sample 8331


title: whole blood taken from sample 8592

description: whole blood taken from sample 8592


title: whole blood taken from sample 7982

description: whole blood taken from sample 7982


title: whole blood taken from sample 8591

description: whole blood taken from sample 8591


title: whole blood taken from sample 9221

description: whole blood taken from sample 9221


title: whole blood taken from sample 8281

description: whole blood taken from sample 8281


title: whole blood taken from sample 8332

description: whole blood taken from sample 8332


title: whole blood taken from sample 7691

description: whole blood taken from sample 7691


title: whole blood taken from sample 7692

description: whole blood taken from sample 7692


title: whole blood taken from sample 7412

description: whole blood taken from sample 7412


title: whole blood taken from sample 362

description: whole blood taken from sample 362


title: whole blood taken from sample 7981

description: whole blood taken from sample 7981


title: whole blood taken from sample 7821

description: whole blood taken from sample 7821


title: whole blood taken from sample 8632

description: whole blood taken from sample 8632


title: whole blood taken from sample 7772

description: whole blood taken from sample 7772


title: whole blood taken from sample 7771

description: whole blood taken from sample 7771


title: whole blood taken from sample 6062

description: whole blood taken from sample 6062


title: whole blood taken from sample 6061

description: whole blood taken from sample 6061


title: whole blood taken from sample 6012

description: whole blood taken from sample 6012


title: whole blood taken from sample 7411

description: whole blood taken from sample 7411


title: whole blood taken from sample 4322

description: whole blood taken from sample 4322


title: whole blood taken from sample 6322

description: whole blood taken from sample 6322


title: whole blood taken from sample 4321

description: whole blood taken from sample 4321


title: whole blood taken from sample 3832

description: whole blood taken from sample 3832


title: whole blood taken from sample 6011

description: whole blood taken from sample 6011


title: whole blood taken from sample 3081

description: whole blood taken from sample 3081


title: whole blood taken from sample 3361

description: whole blood taken from sample 3361


title: whole blood taken from sample 2922

description: whole blood taken from sample 2922


title: whole blood taken from sample 4122

description: whole blood taken from sample 4122


title: whole blood taken from sample 6321

description: whole blood taken from sample 6321


title: whole blood taken from sample 3831

description: whole blood taken from sample 3831


title: whole blood taken from sample 2852

description: whole blood taken from sample 2852


title: whole blood taken from sample 3351

description: whole blood taken from sample 3351


title: whole blood taken from sample 2501

description: whole blood taken from sample 2501


title: whole blood taken from sample 2672

description: whole blood taken from sample 2672


title: whole blood taken from sample 2741

description: whole blood taken from sample 2741


title: whole blood taken from sample 2451

description: whole blood taken from sample 2451


title: whole blood taken from sample 2422

description: whole blood taken from sample 2422


title: whole blood taken from sample 2201

description: whole blood taken from sample 2201


title: whole blood taken from sample 2061

description: whole blood taken from sample 2061


title: whole blood taken from sample 2242

description: whole blood taken from sample 2242


title: whole blood taken from sample 1891

description: whole blood taken from sample 1891


title: whole blood taken from sample 2152

description: whole blood taken from sample 2152


title: whole blood taken from sample 2031

description: whole blood taken from sample 2031


title: whole blood taken from sample 2772

description: whole blood taken from sample 2772


title: whole blood taken from sample 4121

description: whole blood taken from sample 4121


title: whole blood taken from sample 1951

description: whole blood taken from sample 1951


title: whole blood taken from sample 1862

description: whole blood taken from sample 1862


title: whole blood taken from sample 1831

description: whole blood taken from sample 1831


title: whole blood taken from sample 2932

description: whole blood taken from sample 2932


title: whole blood taken from sample 1772

description: whole blood taken from sample 1772


title: whole blood taken from sample 1601

description: whole blood taken from sample 1601


title: whole blood taken from sample 1551

description: whole blood taken from sample 1551


title: whole blood taken from sample 1381

description: whole blood taken from sample 1381


title: whole blood taken from sample 1362

description: whole blood taken from sample 1362


title: whole blood taken from sample 1281

description: whole blood taken from sample 1281


title: whole blood taken from sample 2351

description: whole blood taken from sample 2351


title: whole blood taken from sample 1221

description: whole blood taken from sample 1221


title: whole blood taken from sample 1191

description: whole blood taken from sample 1191


title: whole blood taken from sample 1181

description: whole blood taken from sample 1181


title: whole blood taken from sample 972

description: whole blood taken from sample 972


title: whole blood taken from sample 871

description: whole blood taken from sample 871


title: whole blood taken from sample 1011

description: whole blood taken from sample 1011