title: HFD-IMQ mouse, biological rep2

city: Lille

first: Denis

middle: A

last: Mogilenko

address: 1 Rue du Professeur Calmette, BP245

country: France

institute: INSERM

hyb_protocol: Following fragmentation, 5.5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: Microarray data were background-corrected and normalized using the robust multi-array average (RMA) algorithm by using affy R package

source_name: IMQ-treated abdominal skin from HFD-fed mouse

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: Animals were housed within the specific pathogen-free facility from the Institut Pasteur de Lille with ad libitum access to water and food.

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

treatment_protocol: Mice were treated with a daily topical dose (62.5 mg) of IMQ cream (Aldara 5%, Meda AB) or vehicle on the shaved abdominal skin for 5 days and sacrificed 24 h later.

tag: strain background

value: 9 weeks

tag: fed with

value: high fat diet (HFD)

tag: treated with

value: abdominal skin


title: VP_scRNA_seq_cell_53 dataset #3

status: Public on Jun 30 2019

type: SRA

city: Montréal

first: Claire

middle: Elizabeth

last: Nash

state: QC

address: 1001 Decarie Blvd

department: Urology

country: Canada

institute: Research Institute of McGill University Health Centre

description:
Rat_scRNAseq_Expr_Counts_VP1.txt
single-cell RNA sequencing Fluidigm C1

library_source: transcriptomic

data_processing:
ChIP-seq reads were aligned to the rnor6.0 genome assembly using Bowtie2 with default parameters
Duplicate ChIP-seq reads were removed using MarkDuplicates and uniquely mapped reads were determined using MAPQ score>=25 with Samtools
ChIP-seq peaks were called using MACS 2.0.10 cutoff of p-value = 1e-7
ChIP-seq peaks were called using HOMER with default settings
ChIP-seq shared peaks (called by both algorithms) were determined using HOMER mergePeaks
RNA-seq reads were aligned to the Ensembl Rnor6.0 genome assembly using Tophat 2.1.0
ChIP-seq and RNA-seq uniquely mapped reads were determined using MAPQ score>=25 with Samtools
RNA-seq read counts were quantified with featureCounts and TPM calculated
Single-cell RNA-seq raw paired-end reads were trimmed using Trimmomatic v0.33, to a minimum length of 30 nucleotides. Illumina Nextera XT adapters were removed in palindrome mode. A minimum Phred quality score of 30 was required for the 3’end. Single end reads as well as paired end reads failing previous minimum quality controls were discarded. Individual read groups were aligned, using TopHat first against the rat transcriptome as defined by the Ensembl gene models version 83, with default parameters and the remaining unmapped genes to the Ensembl Rnor_6.0 reference rat genome from Illumina iGenomes web site.  Trimming rates and insert length were controlled on each read group based on metrics reported by Trimmomatic, and Picard v1.128 respectively. Aligned reads from multiple read groups belonging to the same sample were indexed, sorted and merged using sambamba v0.5.1, a faster implementation of the Samtools algorithms. Amplification duplicates were removed using Picard v1.128. Various quality controls from the RNA-SeQC package were used, including the genes detected, mapping rates, duplication rates, and intronic rate, based on metrics collected for each sample used.
Single-cell RNA-seq read counts were quantified using HTSeq Count using Ensembl Rnor_6.0 and TPM calculated
Genome_build: Ensembl Rnor_6.0
Supplementary_files_format_and_content: bigwig files were generated by converting bedgraph to bigwig files using the bedGraphToBigWig UCSC converter. Scores represent treatment pileup
Supplementary_files_format_and_content: Shared peak files were determined using HOMER mergePeaks and then annoated relative to genes using HOMER AnnotatePeaks.
Supplementary_files_format_and_content: RNA-seq read counts were quantified with featureCounts and TPM calculated
Supplementary_files_format_and_content: Single-cell RNA-seq read counts were quantified using HTSeq Count using Ensembl Rnor_6.0 and TPM calculated

molecule: total RNA

organism: Rattus norvegicus

source_name: Male urogenital sinus

extract_protocol:
Tissues were disscociated with 2mg/mL Collagenase 1A (Sigma-Aldrich, Missouri, USA) for 60 minutes at 37 degrees C. Dispersed fibroblasts were separated by centrifugation and passing through a 0.7um cell strainer (Falcon, Corning, New York, USA). Cell suspensions were centrifuged for 10 minutes at 500g and resuspended in LIVE/DEAD Cell Viability/Cytotoxicity Assay for mammalian cells (ThermoFisher, L-3224).   After a 10 minute incubation at room temperature, cells were centrifuged and resuspended in Cell Wash Buffer (Fluidigm).  Cell concentration, size and viability were verified on hemocytometers (Incyto DHC-N01-5) through bright field, GFP and RFP on a EVOS FL Auto microscope (ThermoFisher).  Single cell RNA libraries were constructed according to the Fluidigm protocol using C1 to generate libraries for RNA sequencing (PN 100-7168).
Single cell RNA libraries were constructed according to the Fluidigm protocol using C1 to generate libraries for RNA sequencing (PN 100-7168).  Briefly, full length mRNA-Seq libraries were generated from single-cells captured on the Fluidigm C1 platform using SMARTer Ultra Low RNA Kit (P/N 634936 Clontech). ERCC RNA Spike-In mix (P/N 4456740 ThermoFisher) was added to the lysis mix for normalization and quality control purposes. Full length cDNAs were converted into sequence ready libraries using Nextera XT DNA Sample Preparation Kit (P/N FC-131-1096 Illumina), and sequenced on an Illumina HiSeq 2000 with paired-end 100bp read option. The Fluidigm C1 platform captured 52 and 70 single cells from VMP and SU respectively. The average full length cDNA yield/min/max were 6.06ng(+/-0.12)/2.25ng/14.81ng for VMP and 8.51ng(+/-0.21)/2.55ng/26.6ng for SU.  Libraries from 52 VMP and 63 SU single cells were sequenced.
Lysates were clarified from sonicated nuclei and AR-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end)

tag: tissue subset

value: Ventral prostate (VP)

tag: age

value: P0 (day of birth)

tag: strain

value: Wistar


title: Mouse forelimb D4 rep1

city: West Haven

first: Cong

last: Liang

address: 300 Heffernan Dr.

country: USA

institute: Yale University

description:
Mm_FL_D4_Rep1
processed data file:
mm_HTSeq_upload.txt

data_processing:
Basecalls performed using CASAVA
mRNA-seq reads were aligned to the alligator (allMis0.2), Anolis (AnoCar2.0), and mouse (GRCm38) cDNA builds using Tophat2
Number of reads overlapped with known features (gene counts) was counted using HTSeq
transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: alligator (allMis0.2), Anolis (AnoCar2.0), and mouse (GRCm38)
Supplementary_files_format_and_content: tab-delimited txt files include read counts for each sample.  Gene IDs for Anolis and Mouse are from Ensembl while alligator gene IDs are available at: http://crocgenome.hpc.msstate.edu

molecule: polyA RNA

organism: Mus musculus

source_name: forelimb digit4

extract_protocol:
Tissues were harvested and kept in RNAlater until extraction of RNA using Qiagen RNeasy extraction kit.
RNA libraries for alligator and mouse were prepared for sequencing using standard illumina protocols. Anolis RNA libraries were prepared using Clontech's Ultra Low V4 kit (Catalog # 634890).

tag: developmental stage

tag: tissue

value: forelimb digit4


title: HFD-IMQ mouse, biological rep3

type: RNA

label: biotin

value: daily topical dose (62.5 mg) of IMQ cream


title: HFD-IMQ mouse, biological rep5


title: HFD-IMQ mouse, biological rep4


title: HFD-IMQ mouse, biological rep1


title: VP_scRNA_seq_cell_50 dataset #3


title: Mouse forelimb D3 rep3

description:
Mm_FL_D3_Rep3
processed data file:
mm_HTSeq_upload.txt

source_name: forelimb digit3

value: forelimb digit3


title: Blood_U23_cocaine_crack

type: genomic

city: São Paulo

first: Caroline

middle: Perez

last: Camilo

state: São Paulo

address: Rua Doutor Ovídio Pires de Campos, 785

department: Institute of Psychiatry

country: Brazil

institute: University of São Paulo

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were scanned in the iScan Microarray Scanner (Illumina Inc., San Diego, California, USA)

data_processing: Data processing were performed using GenomeStudio software (version 1.8).

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: DNA blood, User 23, cocaine and crack dependent

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA from whole blood were extracted using salting-out method described by Miller and collaborators (Miller et al., Nucleic Acids Res., 1988;16(3):1215)

tag: gender

value: Male

value: Whole blood

tag: sample group

value: Drug user

tag: ethnicity

value: African

tag: education

value: Primary school or less

tag: smoke (use/abuse of other drugs)

value: Yes

tag: cannabbis (use/abuse of other drugs)

tag: solvents (use/abuse of other drugs)

value: No

tag: heroin (initial use/age ys)


title: VP_scRNA_seq_cell_49 dataset #3


title: Blood_U24_cocaine_crack

source_name: DNA blood, User 24, cocaine and crack dependent


title: Blood_C16_control

source_name: DNA blood, Control 16, healthy control

value: Healthy control


title: Blood_U21_cocaine_crack

source_name: DNA blood, User 21, cocaine and crack dependent

value: Caucasian

value: Secondary school


title: Blood_U20_cocaine_crack

source_name: DNA blood, User 20, cocaine and crack dependent


title: Blood_U22_cocaine_crack

source_name: DNA blood, User 22, cocaine and crack dependent


title: HFD-vehicle mouse, biological rep5

source_name: Vehicle-treated abdominal skin from HFD-fed mouse

value: 9 weeks

value: high fat diet (HFD)

value: vehicle

value: abdominal skin


title: Mouse forelimb D3 rep2

description:
Mm_FL_D3_Rep2
processed data file:
mm_HTSeq_upload.txt


title: HFD-vehicle mouse, biological rep3


title: Mouse forelimb D3 rep1

description:
Mm_FL_D3_Rep1
processed data file:
mm_HTSeq_upload.txt


title: Blood_U18_cocaine_crack

source_name: DNA blood, User 18, cocaine and crack dependent


title: VP_scRNA_seq_cell_46 dataset #3

value: Ventral prostate (VP)

value: P0 (day of birth)

value: Wistar


title: VP_scRNA_seq_cell_45 dataset #3


title: Blood_U19_cocaine_crack

source_name: DNA blood, User 19, cocaine and crack dependent

value: Male


title: Blood_C1_control

source_name: DNA blood, Control 1, healthy control

value: Whole blood


title: VP_scRNA_seq_cell_44 dataset #3


title: Mouse forelimb D2 rep3

description:
Mm_FL_D2_Rep3
processed data file:
mm_HTSeq_upload.txt

source_name: forelimb digit2

value: forelimb digit2


title: Mouse forelimb D2 rep1

description:
Mm_FL_D2_Rep1
processed data file:
mm_HTSeq_upload.txt


title: Mouse forelimb D2 rep2

description:
Mm_FL_D2_Rep2
processed data file:
mm_HTSeq_upload.txt


title: Mouse forelimb D1 rep3

description:
Mm_FL_D1_Rep3
processed data file:
mm_HTSeq_upload.txt

source_name: forelimb digit1

value: forelimb digit1


title: Mouse forelimb D5 rep2

description:
Mm_FL_D5_Rep2
processed data file:
mm_HTSeq_upload.txt

source_name: forelimb digit5

value: forelimb digit5


title: VP_scRNA_seq_cell_41 dataset #3


title: VP_scRNA_seq_cell_39 dataset #3


title: HFD-vehicle mouse, biological rep2


title: Blood_U15_cocaine_crack

source_name: DNA blood, User 15, cocaine and crack dependent

value: Drug user

value: Yes


title: VP_scRNA_seq_cell_38 dataset #3

source_name: Male urogenital sinus


title: CD-IMQ mouse, biological rep2

source_name: IMQ-treated abdominal skin from CD-fed mouse

value: control chow diet (CD)

value: daily topical dose (62.5 mg) of IMQ cream


title: HFD-vehicle mouse, biological rep4


title: CD-IMQ mouse, biological rep4


title: CD-IMQ mouse, biological rep3


title: Mouse forelimb D1 rep1

description:
Mm_FL_D1_Rep1
processed data file:
mm_HTSeq_upload.txt


title: VP_scRNA_seq_cell_37 dataset #3


title: HFD-vehicle mouse, biological rep1


title: VP_scRNA_seq_cell_36 dataset #3


title: Mouse forelimb D1 rep2

description:
Mm_FL_D1_Rep2
processed data file:
mm_HTSeq_upload.txt


title: CD-IMQ mouse, biological rep5


title: Blood_U13_cocaine_crack

source_name: DNA blood, User 13, cocaine and crack dependent

value: Caucasian

value: Secondary school

value: No


title: Blood_U12_cocaine_crack

source_name: DNA blood, User 12, cocaine and crack dependent

value: Primary school or less


title: Blood_U11_cocaine_crack

source_name: DNA blood, User 11, cocaine and crack dependent


title: CD-vehicle mouse, biological rep5

source_name: Vehicle-treated abdominal skin from CD-fed mouse

value: 9 weeks

value: vehicle

value: abdominal skin


title: VP_scRNA_seq_cell_35 dataset #3

value: Ventral prostate (VP)

value: P0 (day of birth)

value: Wistar


title: Blood_U14_cocaine_crack

source_name: DNA blood, User 14, cocaine and crack dependent

value: Male

value: Whole blood

value: African


title: Blood_U16_cocaine_crack

source_name: DNA blood, User 16, cocaine and crack dependent

value: Drug user


title: VP_scRNA_seq_cell_33 dataset #3


title: Blood_U10_cocaine_crack

source_name: DNA blood, User 10, cocaine and crack dependent

value: Yes


title: VP_scRNA_seq_cell_34 dataset #3


title: VP_scRNA_seq_cell_29 dataset #3


title: CD-vehicle mouse, biological rep4

value: control chow diet (CD)


title: VP_scRNA_seq_cell_26 dataset #3


title: VP_scRNA_seq_cell_25 dataset #3


title: CD-IMQ mouse, biological rep1

value: daily topical dose (62.5 mg) of IMQ cream


title: Col-0-GR(2017_Oct)

city: Jeongeup-si

first: Jin-Hong

last: Kim

state: Jeonbuk-do

address: 29 Geumgu-gil

country: South Korea

institute: Korea Atomic Energy Research Institute

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml 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 Arabidopsis Gene Expression Microarray (V4) (021169) 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 1x44k 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 9.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: whole seedling_24hr_200Gy_gamma-ray

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 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: Arabidopsis thaliana (ecotype Columbia-0) seeds were surface-sterilized for 1 min in 70% ethanol and for 5 min in 20% bleach solution, and then rinsed five times with sterile water. The seeds were cold-treated for three days at 4°C in the dark and grown on 1/2 MS medium (pH 5.7) with 1% sucrose and 0.65% phytoagar under long-day conditions of 16 h light and 8 h dark at about 23°C and 50% relative humidity.

extract_protocol: Total RNA was isolated from whole seedlings using the RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: Fourteen-day-old seedlings were exposed to 200 Gy of gamma radiation (dose rate 50 Gy/hr) using a Co-60 gamma irradiator (IR-222, MDS Nordion Inc.)

tag: ecotype

value: Whole seedling

tag: exposed to

value: 50 Gy/hour for 4 hours

tag: time point

value: 24 hours after the exposure


title: CD-vehicle mouse, biological rep3

tag: strain background

tag: fed with

tag: treated with


title: Col-0-CT(2017_Oct)

source_name: whole seedling_mock

value: mock


title: CD-vehicle mouse, biological rep1

tag: age

value: 9 weeks


title: VP_scRNA_seq_cell_24 dataset #3

tag: tissue subset

tag: strain


title: Col-0-GR(2017_Apr)

tag: developmental stage

tag: tissue


title: CD-vehicle mouse, biological rep2

value: vehicle


title: Blood_U8_cocaine_crack

source_name: DNA blood, User 8, cocaine and crack dependent

tag: gender

tag: sample group

tag: ethnicity

value: Caucasian

value: Secondary school

value: No


title: Blood_U7_cocaine_crack

source_name: DNA blood, User 7, cocaine and crack dependent

tag: education

value: Primary school or less

tag: smoke (use/abuse of other drugs)

tag: cannabbis (use/abuse of other drugs)


title: Col-0-CT(2017_Apr)

tag: ecotype


title: RNAseq_sh2_rep3

city: Shanghai

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

country: China

institute: Fudan University

description:
treatment_2
DESeq_results_sh2vsCtrl.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
We trimmed and mapped reads to the mouse mm9 reference assembly by the Tophat2 software.
We used default parameters expect that we reduced maximum insertion and deletion length to 2 bp, and kept only uniquely mapped, “no mixed” and “no discordant” reads.
For differential gene expression analysis, we analyzed raw read counts for GENCODE M1 gene models using HTSeq (Anders et al., 2015), and then calculated statistics of differential expression via DESeq2 version 1.8.2 (Love et al., 2014) with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include DESeq2 results

growth_protocol: The mouse hepatocyte cell line alpha mouse liver 12 (AML12)  cells were cultured in DMEM/F12 (HyClone) supplemented with 10% fetal bovine serum (FBS, Biowest), ITS Liquid Media Supplement (Sigma) and 0.1μM dexamethasone (Sigma) at 37 °C and 5% CO2.

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

treatment_protocol: For small hairpin RNA (shRNA)-based knockdown, AML12 cells were infected with  two different shRNAs targeting SRRM2-containing lentivirus 5d.

tag: shRNA

value: shRNA-containing lentivirus 5d


title: Blood_U9_cocaine_crack

source_name: DNA blood, User 9, cocaine and crack dependent

value: Male

value: Whole blood

tag: solvents (use/abuse of other drugs)

tag: heroin (initial use/age ys)


title: RNAseq_sh2_rep2

description:
treatment_2
DESeq_results_sh2vsCtrl.txt


title: Col-0-CT(2017_Mar)

tag: exposed to

tag: time point


title: VP_scRNA_seq_cell_23 dataset #3

value: Ventral prostate (VP)

tag: age

value: P0 (day of birth)

value: Wistar


title: VP_scRNA_seq_cell_22 dataset #3

tag: tissue subset


title: WT_IR(2015_Oct)


title: RNAseq_sh2_rep1

description:
treatment_2
DESeq_results_sh2vsCtrl.txt


title: Blood_U4_cocaine_crack

source_name: DNA blood, User 4, cocaine and crack dependent

value: Drug user

value: African

value: Yes


title: WT_con(2015_Oct)

value: Whole seedling

value: 24 hours after the exposure


title: Col-0-GR(2017_Mar)

value: 50 Gy/hour for 4 hours


title: RNAseq_sh1_rep3

description:
treatment_1
DESeq_results_sh1vsCtrl.txt


title: VP_scRNA_seq_cell_18 dataset #3

tag: strain


title: RNAseq_sh1_rep2

description:
treatment_1
DESeq_results_sh1vsCtrl.txt


title: VP_scRNA_seq_cell_17 dataset #3


title: RNAseq_sh1_rep1

description:
treatment_1
DESeq_results_sh1vsCtrl.txt


title: shCD133-3

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
RPKM_table.txt
Sample6

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
reads were aligned to mm10 genome assembly using Tophat2 with default settings
gene expression levels of Refseq genes were counted with Htseq-count
RPKM value was calculated by dividing the read count by total aligned reads and gene length
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file reports RPKM values

source_name: Pancreatic Progenitor Cells

growth_protocol: CD133/high CD71/low cells (which enrich for progenitor cells) were FACS sorted from dissociated pancreata of adult (2-4 month old) B6 mice and grown in 3D semi-solid media comprised of DMEM/F12, fetal calf serum, various growth factors (RSPO1, nicotinamide, exendin-4, activin B), conditioned media, methylcellulose and extracellular matrix protines (Matrigel).

extract_protocol:
Colonies were isolated from culture and placed into "RLT" buffer from Qiagen to preserve RNAs. Total RNAs were subsequently extraced using Qiagen RNAmini kit.
Kapa poly(A) stranded RNA-seq library Preperation following manufacture's recommendations

treatment_protocol: Freshly sorted CD133/high CD71/low cells were incubated overnight with lentiviral vectors containing pools of 5 independent shRNA clones against Glis3 or CD133, in the presence of polybrene, and plated into 3D cutlure in the presence of puromycin. A single non-mammalian shRNA control lentivirus was used as control. Colonies were collected 3 weeks post-culture.

tag: cell type

value: Pancreatic Progenitor Cells

tag: passage

value: Primary colonies

tag: genotype

value: CD133 knockdown


title: Blood_U3_cocaine_crack

source_name: DNA blood, User 3, cocaine and crack dependent

tag: gender

tag: tissue

tag: sample group

value: Caucasian

value: No


title: shCD133-1

description:
RPKM_table.txt
Sample5


title: VP_scRNA_seq_cell_16 dataset #3

source_name: Male urogenital sinus


title: RNAseq_Ctrl_rep2

description:
control
DESeq_results_sh1vsCtrl.txt, DESeq_results_sh3vsCtrl.txt

value: control


title: VP_scRNA_seq_cell_15 dataset #3


title: VP_scRNA_seq_cell_14 dataset #3


title: Blood_U6_cocaine_crack

source_name: DNA blood, User 6, cocaine and crack dependent

value: Male

tag: ethnicity

tag: education

value: Primary school or less

tag: smoke (use/abuse of other drugs)


title: Blood_U1_cocaine_crack

source_name: DNA blood, User 1, cocaine and crack dependent

value: Whole blood

tag: cannabbis (use/abuse of other drugs)


title: VP_scRNA_seq_cell_20 dataset #3

value: Ventral prostate (VP)

value: P0 (day of birth)


title: shGlis3-1

description:
RPKM_table.txt
Sample3

value: Glis3 knockdown


title: VP_scRNA_seq_cell_13 dataset #3

value: Wistar


title: RNAseq_Ctrl_rep3

description:
control
DESeq_results_sh1vsCtrl.txt, DESeq_results_sh4vsCtrl.txt

tag: shRNA


title: WT_IR(2015_Jun)

tag: ecotype

tag: developmental stage


title: WT_con(2015_Jun)

tag: exposed to

value: mock

tag: time point


title: HCT-8/V

city: Tianjin

first: Yan Liu

last: Rong

address: Tianjin

institute: Tianjin International Biomedical Research Institute

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Human colon cancer cell line resistant to vincristine

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: These cell lines were maintained in RPMI 1640 supplemented with 10% fetal bovine serum  in a humidified atmosphere of 5% CO2 at 37 °C

extract_protocol: RNA was extracted with GenElute™ Total RNA Purification Kit

treatment_protocol: Transfer into pcDNA3.1-Twist 48h

tag: cell line

value: HCT-8/V (resistant to vincristine)


title: VP_scRNA_seq_cell_12 dataset #3

tag: tissue subset

tag: age

tag: strain


title: HCT-8

description: replicate 1

source_name: Human colon cancer cell line


title: High dose_kidney_3

city: Hannover

first: Juergen

last: Borlak

state: Lower Saxony

address: Feodor-Lynen-Str. 35

department: Centre for Pharmacology and Toxicology

country: Germany

institute: Hannover Medical School

hyb_protocol: Microarray studies were performed with an initial amount of 250 ng total RNA. All steps of cDNA synthesis, biotin labeling, fragmentation, hybridization, staining, washing and scanning were performed according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA).

scan_protocol: The Affymetrix Canine Genome 2.0 GeneChip was used for microarray analysis and was scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: The microarray intensity files (.cel file) were analysed by GeneXpalin 3.0 software (http://genexplain-platform.com). Data normalization was performed using MAS 5.0. Differentially expressed genes were determined based on the filtering criteria >1.5 and <-1.5 fold change and P < 0.05.

label: Biotin

organism: Canis lupus familiaris

source_name: Kidney

extract_protocol: Liver and kidneys were surgically removed from diclofenac treated (1 and 3 mg/kg/day) and control groups and snap-frozen in liquid nitrogen. The liver and kidney samples were stored in a deep freezer until RNA extraction. Frozen liver samples were immediately added to buffer RLT with β mercaptoethanol and homogenized using a TissueLyser (Qiagen, Hilden, Germany) for microarray analysis. Total RNA from each tissue was isolated and purified using the RNase mini kit (Qiagen) according to the manufacturer’s protocol. Furthermore, the concentration of total RNA was measured using NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE) and RNA integrity was determined on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Fifteen male beagle dogs were purchased (n=3 for each group) and maintained under laboratory conditions. The diclofenac sodium was administrated orally at 1 mg/kg/day or 3 mg/kg/day for up to 28 days. The drug substance was loaded into gelatine capsules to achieve individual doses based on body weights and the vehicle control group received one empty capsule per day.

tag: breed

value: Beagle

value: Kidney


title: shControl-1

description:
RPKM_table.txt
Sample1

tag: cell type

value: Pancreatic Progenitor Cells

tag: passage

tag: genotype


title: VP_scRNA_seq_cell_11 dataset #3


title: VP_scRNA_seq_cell_09 dataset #3


title: RNAseq_Ctrl_rep1

description:
control
DESeq_results_sh1vsCtrl.txt, DESeq_results_sh2vsCtrl.txt


title: Oct4 CRIST-Seq

city: Palo Alto

first: Jifan

last: Hu

address: 3801 Miranda Ave, Bldg 100, Room E4-200

department: Palo Alto Veterans Institute for Research

institute: Stanford University Medical School

data_processing:
Library strategy: CRIST-Seq
Raw data were filtered with Seqtk
clean reads were mapped by mouse genome (mm10, GRCm38) with Hisat2 (version:2.0.4)
The mapped RNA reads were quantitated using Stringtie（version:1.3.0）. To define the specific binding of RNAs, the CRIST-Seq signal intensities were normalized over the controls with EdgeR using parameters of fold change difference ≥2 and p-value < 0.05, with false discovery rate (FDR) <0.1. The adjusted CIST-Seq data were used for mapping the Oct4 and Sox2 RNA interactions.
Genome_build: mm10, GRCm38

source_name: iPS cells (BC170039)

growth_protocol: Fibroblasts were reprogrammed by Oct4-Sox2-Klf4-c-Myc defined factors. After reprogramming, iPS cells were collected for the study.

extract_protocol:
Cells were treated with formaldehyde to fix the RNA-chromatin structure. RNAs were reverse transcribed in situ using biotin-dCTP. The cDNA-promoter chromatin complexes were immunoprecipitated with an anti Cas9-FLAG antibody and an anti IgG control antibody. cDNAs were then isolated with streptavidin beads. The purified lncDNAs were eluted for Illumina library sequencing. As the control, a Cas9 random gRNA was used in the CRIST assay in parallel with Oct4 and Sox2 promoter specific Cas9 gRNAs. In addition, an IgG control library was also constructed and sequenced as the assay control.
Sox2 and Oct4 promoter-interacting lncRNA libraries were prepared using Illumines Kit (Part# 0801-0303).

value: Induced pluripotent stem cells

tag: project

value: Reprogramming


title: CRIST Cas9 IgG control

source_name: iPS cells (BC160340)


title: VP_scRNA_seq_cell_05 dataset #3


title: shControl-3

description:
RPKM_table.txt
Sample2

value: Primary colonies


title: CRIST Cas9 random gRNA control


title: Blood_U5_cocaine_crack

source_name: DNA blood, User 5, cocaine and crack dependent

tag: gender

tag: tissue

tag: sample group

value: Drug user

tag: ethnicity

value: African

tag: education

value: Yes

tag: solvents (use/abuse of other drugs)

value: No

tag: heroin (initial use/age ys)


title: VP_scRNA_seq_cell_03 dataset #3


title: High dose_kidney_1

label_protocol: Microarray studies were performed with an initial amount of 250 ng total RNA. All steps of cDNA synthesis, biotin labeling, fragmentation, hybridization, staining, washing and scanning were performed according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA).


title: VP_scRNA_seq_cell_02 dataset #3


title: VP_scRNA_seq_cell_01 dataset #3


title: VP_scRNA_seq_cell_07 dataset #3


title: Blood_U17_cocaine_crack

source_name: DNA blood, User 17, cocaine and crack dependent

value: Male

value: Whole blood

value: Primary school or less

tag: smoke (use/abuse of other drugs)

tag: cannabbis (use/abuse of other drugs)


title: VMP_scRNA_seq_cell_94 dataset #3

description:
Rat_scRNAseq_Expr_Counts_VMP1.txt
single-cell RNA sequencing Fluidigm C1

source_name: Female urogenital sinus

tag: tissue subset

value: Ventral mesenchymal pad (VMP)

value: P0 (day of birth)


title: Low dose_kidney_2


title: Low dose_kidney_3


title: Low dose_kidney_1


title: Control_kidney_2


title: VMP_scRNA_seq_cell_93 dataset #3

tag: age

value: Wistar


title: VMP_scRNA_seq_cell_44 dataset #3

tag: strain


title: VMP_scRNA_seq_cell_89 dataset #3


title: VMP_scRNA_seq_cell_43 dataset #3


title: High dose_liver_3

source_name: Liver

tag: breed

value: Liver


title: High dose_liver_2

value: Beagle


title: High dose_liver_1


title: VMP_scRNA_seq_cell_86 dataset #3


title: Low dose_liver_3


title: Control_kidney_3

value: Kidney


title: Control_kidney_1


title: Control_liver_3


title: Low dose_liver_1


title: Control_liver_1


title: VMP_scRNA_seq_cell_91 dataset #3


title: VMP_scRNA_seq_cell_38 dataset #3


title: VMP_scRNA_seq_cell_37 dataset #3


title: VMP_scRNA_seq_cell_87 dataset #3


title: VMP_scRNA_seq_cell_34 dataset #3


title: VMP_scRNA_seq_cell_79 dataset #3


title: VMP_scRNA_seq_cell_81 dataset #3


title: VMP_scRNA_seq_cell_31 dataset #3


title: VMP_scRNA_seq_cell_33 dataset #3


title: VMP_scRNA_seq_cell_78 dataset #3


title: VMP_scRNA_seq_cell_77 dataset #3


title: VMP_scRNA_seq_cell_76 dataset #3


title: High dose_kidney_2


title: VMP_scRNA_seq_cell_28 dataset #3


title: Suspension, Scr (24 hrs), rep2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
Sus_scr_24hrs_R2
Gene expression of suspension cells stable for scr, rep2

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Agilent's human GXP_8X60k Array (AMADID: 039494) using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, 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 percentile shift normalization method .

source_name: MDA-MB-231_Suspension_Scr (24 hrs)

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 in DMEM containing 10% of FBS

extract_protocol: RNA extraction was performed by using Qiagen Rneasy mini kit with Dnase Treatment.

treatment_protocol: Cells were detached using trypsin and cultured on nobel agar coated dish for 24 hrs. However attached cells were cultured on tcps tissue culture dish

tag: cell line

tag: cell type

value: Breast cancer cell line


title: VMP_scRNA_seq_cell_73 dataset #3


title: VMP_scRNA_seq_cell_29 dataset #3


title: Attached, A76 (24 hrs), rep2

description:
Adh_scr_A7_24hrs_R2
Gene expression of attached cells treated with A76, rep2

source_name: MDA-MB-231_Attached_A76 (24 hrs)


title: Suspension, ShAMPK Alpha2 (24 hrs), rep1

description:
Sus_Alpha2sh_24hrs_R1
Gene expression of suspension cells stable for shAMPK alpha 2, rep1

source_name: MDA-MB-231_Suspension_ShAMPK Alpha2 (24 hrs)


title: Low dose_liver_2


title: VMP_scRNA_seq_cell_84 dataset #3


title: Attached, DMSO (24 hrs), rep2

description:
Adh_scr_dmso_24hrs_R2
Gene expression of attached cells treated with DMSO, rep2

source_name: MDA-MB-231_Attached_DMSO (24 hrs)


title: VMP_scRNA_seq_cell_26 dataset #3


title: Attached, A76 (24 hrs), rep1

description:
Adh_scr_A7_24hrs_R1
Gene expression of attached cells treated with A76, rep1


title: Attached, DMSO (24 hrs), rep1

description:
Adh_scr_dmso_24hrs_R1
Gene expression of attached cells treated with DMSO, rep1


title: VMP_scRNA_seq_cell_25 dataset #3


title: Suspension, ShAMPK Alpha2 (24 hrs), rep2

description:
Sus_Alpha2sh_24hrs_R2
Gene expression of suspension cells stable for shAMPK alpha 2, rep2


title: Suspension, Scr (24 hrs), rep1

description:
Sus_scr_24hrs_R1
Gene expression of suspension cells stable for scr, rep1


title: VMP_scRNA_seq_cell_23 dataset #3


title: VMP_scRNA_seq_cell_72 dataset #3


title: VMP_scRNA_seq_cell_24 dataset #3


title: VMP_scRNA_seq_cell_66 dataset #3


title: VMP_scRNA_seq_cell_21 dataset #3


title: VMP_scRNA_seq_cell_65 dataset #3


title: VMP_scRNA_seq_cell_64 dataset #3


title: VMP_scRNA_seq_cell_20 dataset #3


title: VMP_scRNA_seq_cell_16 dataset #3


title: VMP_scRNA_seq_cell_63 dataset #3


title: VMP_scRNA_seq_cell_27 dataset #3


title: VMP_scRNA_seq_cell_62 dataset #3


title: VMP_scRNA_seq_cell_13 dataset #3


title: VMP_scRNA_seq_cell_10 dataset #3


title: VMP_scRNA_seq_cell_15 dataset #3


title: VMP_scRNA_seq_cell_08 dataset #3


title: VMP_scRNA_seq_cell_56 dataset #3


title: VMP_scRNA_seq_cell_55 dataset #3


title: VMP_scRNA_seq_cell_09 dataset #3


title: VMP_scRNA_seq_cell_54 dataset #3


title: VMP_scRNA_seq_cell_53 dataset #3


title: triple negative and lymph node metastasis_2

city: guangzhou

first: xinhua

last: xie

state: guangdong

address: dongfeng east road

institute: Sun Yat-sen University Cancer Center

description: 23; breast cancer tumor tissues NO23

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: breast cancer tumor tissues NO23

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

growth_protocol: no growth

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: no treatment

tag: sample type

value: frozen tissue

value: female

value: breast cancer tumor tissue

tag: tissue type

tag: molecule subtype

value: microRNA


title: VMP_scRNA_seq_cell_05 dataset #3


title: VMP_scRNA_seq_cell_06 dataset #3


title: VMP_scRNA_seq_cell_50 dataset #3


title: triple negative and lymph node metastasis_1

description: 22; breast cancer tumor tissues NO22

source_name: breast cancer tumor tissues NO22

tag: gender

tag: tissue


title: triple negative and lymph node metastasis_3

description: 24; breast cancer tumor tissues NO24

source_name: breast cancer tumor tissues NO24


title: triple negative and lymph node non-metastasis_1

description: 19; breast cancer tumor tissues NO19

source_name: breast cancer tumor tissues NO19


title: VMP_scRNA_seq_cell_60 dataset #3


title: triple negative and lymph node non-metastasis_2

description: 20; breast cancer tumor tissues NO20

source_name: breast cancer tumor tissues NO20


title: leo1D T2W, Input, rep2

city: Huddinge

first: Eriko

last: Oya

address: Blickagången 16

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Samples were prepared and hybridized to GeneChip S.pombe Tiling 1.0FR Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing: The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1). Duplicate data were normalized with input using quantile normalization plus scaling and run with a bandwidth of 100. Data obtained from TAS were then directly loaded into Seqmonk, antibody background were next removed using ∆clr4 mutant and visualized using the following parameters (number of classes 30, Min probes count 30, Max probes count 100).

organism: Schizosaccharomyces pombe

source_name: leo1D T2W, Input, rep2

growth_protocol: Cells grown in PMG (OD600 ~0.25) at 30C, and were washed twice with PMG-N. Cells were resuspended in PMG-N and incubated at 30C.

extract_protocol: For immunoprecipitation, 30 µL whole cell extracts were incubated with 4 µl anti-H3K9me2 (abcam 1220) and 10 µL Dynabeads conjugated to protein-A (New England BioLabs) for 2 hours at 4°C with agitation. The supernatant was removed and the beads were washed twice with Lysis buffer, followed by two washes each with Wash Buffer 1 (50 mM HEPES (pH 7.5), 500 mM NaCl, 1 mM EDTA, 1% TritonX-100, and 0.1% Na-deoxycholate), Wash Buffer 2 (10 mM Tris (pH 8.0), 250 mM LiCl, 0.5% NP-40, and 0.5% Na-deoxycholate) and TE buffer (10 mM Tris (pH 8.0), 1 mM EDTA). Beads were resuspended in 100 μg/ml RNase A containing TE buffer incubated for 10 min at 37°C. Then, Proteinase K (0.5 mg/ml) was added and the mixture digested for 1 hour at 42°C. The crosslinks in samples were reversed by incubating for 4 hours at 65°C. After de-cross-linking, DNA was purified using a QIAquick PCR purificationkit (Qiagen).

treatment_protocol: 2x10^8 cells at each time point were cross-linked with 1% formaldehyde at 25C for 30min. Crosslinking was quenched with 0.125M glycine for 5min and the cells were washed 2 times with cold PBS. Cell pellets were resuspended in 400μl lysis buffer (50mM HEPES(pH 7.5), 140mM NaCl, 1mM EDTA, 1% Triton-X, 0.1% Na-Deoxycholate and ) containing a protease inhibitor cocktail (cOmplete EDTA-free, Merck) and lysed with glass beads. Whole cell extracts (WCEs) were sonicated for 10min (20 cycles of 30 sec on 30 sec off) using a Bioruptor Pico sonicator (diagenode) producing chromatin 100-500bps in size. The extract was then incubated for 10 minutes at 4°C, and centrifuged for 5 minutes, 4°C at 14,000 × g and the supernatants were used for immunoprecipitation.

tag: genotype

tag: antibody


title: clr4D T0, Input, rep2

source_name: clr4D T0, Input, rep2

label_protocol: Samples were prepared and hybridized to GeneChip S.pombe Tiling 1.0FR Array according to Affymetrix specifications.


title: clr4D T24, Input, rep2

source_name: clr4D T24, Input, rep2


title: leo1D T48, Input, rep2

source_name: leo1D T48, Input, rep2


title: Her2 amplification and lymph node metastasis_2

description: 17; breast cancer tumor tissues NO17

source_name: breast cancer tumor tissues NO17


title: Her2 amplification and lymph node non-metastasis_3

description: 15; breast cancer tumor tissues NO15

source_name: breast cancer tumor tissues NO15


title: triple negative and lymph node non-metastasis_3

description: 21; breast cancer tumor tissues NO21

source_name: breast cancer tumor tissues NO21


title: Her2 amplification and lymph node metastasis_3

description: 18; breast cancer tumor tissues NO18

source_name: breast cancer tumor tissues NO18


title: Her2 amplification and lymph node metastasis_1

description: 16; breast cancer tumor tissues NO16

source_name: breast cancer tumor tissues NO16


title: DP_Tissue_RNASeq dataset #3

description:
Rat_RNAseq_Expr_Counts.txt
RNA sequencing

source_name: Male urogenital sinus

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Lysates were clarified from sonicated nuclei and AR-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end)

value: Dorsal/Dorsolateral prostate (DP)

value: P0 (Day of birth)


title: leo1D T24, Input, rep2

source_name: leo1D T24, Input, rep2


title: Her2 amplification and lymph node non-metastasis_1

description: 13; breast cancer tumor tissues NO13

source_name: breast cancer tumor tissues NO13


title: luminal B and lymph node metastasis_3

description: 12; breast cancer tumor tissues NO12

source_name: breast cancer tumor tissues NO12

value: luminal B and lymph node metastasis


title: leo1D T8, Input, rep2

source_name: leo1D T8, Input, rep2


title: luminal B and lymph node metastasis_2

description: 11; breast cancer tumor tissues NO11

source_name: breast cancer tumor tissues NO11


title: luminal B and lymph node metastasis_1

description: 10; breast cancer tumor tissues NO10

source_name: breast cancer tumor tissues NO10


title: leo1D T0, Input, rep2

source_name: leo1D T0, Input, rep2


title: Her2 amplification and lymph node non-metastasis_2

description: 14; breast cancer tumor tissues NO14

source_name: breast cancer tumor tissues NO14


title: NormalBreastTissue-Normal-N54-sample3

city: Nanjing

first: Yan

last: Wang

state: Jiangsu

address: No. 121 Jiangjiayuan Rd

department: Department of Pathology

institute: The Second Affiliated Hospital of Nanjing Medical University

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation) following their standard operating protocol.

data_processing: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.

source_name: Normal

label_protocol: Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

extract_protocol: Total RNA was extracted with an RNeasy kit (Qiagen), followed by digested with DNase I and extracted with phenol/chloroform and precipitated with isopropanol. Total RNA sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: An extra portion of tissues unnecessary for histological diagnosis after surgery were taken from six patients with AR-positive and ER/PR-negative breast cancer for gene expression profiling study. Of which, 3 breast cancer samples (T39, T40 and T54) were HER2-positive, and other 3 breast cancer samples (B13, B29 and B32) were HER2-negative. Three normal breast tissue samples (N39, N40 and N54) were used for gene expression analysis as a reference group. The tissue materials were collected and snap-frozen in liquid nitrogen after surgery. The patients gave their informed consent to the study, and the experimental procedures were approved by the local Ethics Committee.

value: Female

value: Normal breast tissue


title: EV_rep3

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

description: SAMPLE 6

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 ml 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 platform GPL19764 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting.

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Data was thresholded to 1, log2 transformed and normalized to the 75th percentile in Genespring GX (Agilent).

organism: Nicotiana attenuata

source_name: EV peduncles collected at ZT0

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Empty vector (EV) and irZTL plants were grown in glasshouse conditions under a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

extract_protocol: Total RNA was extracted from floral peduncles using the Plant RNeasy kit (Qiagen) and its quality checked by spectrophotometry (NanoDrop). Genomic DNA was removed by DNAse treatment following commercial instructions (Ambion). RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: Peduncles were collected at ZT0 the day flowers start to move.

tag: genotype/variation

value: EV

value: peduncles


title: irZTL_rep3

description: SAMPLE 3

source_name: irZTL peduncles collected at ZT0

value: irZTL


title: SU_Tissue_RNASeq dataset #3

source_name: Female urogenital sinus

value: Smooth muscle, peri-urethral mesenchyme and urethral epithelium (SU)

value: Wistar


title: irZTL_rep2

description: SAMPLE 2


title: EV_rep2

description: SAMPLE 5


title: EV_rep1

description: SAMPLE 4


title: irZTL_rep1

description: SAMPLE 1


title: NormalBreastTissue-Normal-N39-sample1


title: wt T2W, Input, rep2

source_name: wt T2W, Input, rep2

value: wt


title: VMP_Tissue_RNASeq dataset #3

value: Ventral mesenchymal pad (VMP)


title: NormalBreastTissue-Normal-N40-sample2


title: luminal B and lymph node non-metastasis_3

description: 9; breast cancer tumor tissues NO9

source_name: breast cancer tumor tissues NO9

value: luminal B and lymph node non-metastasis


title: VP_Tissue_RNASeq dataset #3

value: Ventral prostate (VP)


title: shGlis3-3

description:
RPKM_table.txt
Sample4

source_name: Pancreatic Progenitor Cells

value: Pancreatic Progenitor Cells

tag: passage

value: Primary colonies

value: Glis3 knockdown


title: wt T48, Input, rep2

source_name: wt T48, Input, rep2


title: wt T24, Input, rep2

source_name: wt T24, Input, rep2


title: Female_Input_DNA dataset #3

library_source: genomic

extract_protocol:
Lysates were clarified from sonicated nuclei and AR-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end)


title: Male_Input_DNA dataset #3

source_name: Male urogenital sinus


title: BreastCancerTissue-HER2positive-T54-sample3

value: AR-positive, ER-/PR-negative, HER2-positive tumor


title: luminal B and lymph node non-metastasis_2

description: 8; breast cancer tumor tissues NO8

source_name: breast cancer tumor tissues NO8

value: frozen tissue

value: female

value: breast cancer tumor tissue

value: microRNA


title: wt T8, Input, rep2

source_name: wt T8, Input, rep2


title: wt T0, Input, rep2

source_name: wt T0, Input, rep2


title: DP_AR_ChIPSeq dataset #3

description:
DP_MACS2_peaks.bw
DP_HOMER_peaks.bw
DP_shared_peaks.txt

value: Dorsal/Dorsolateral prostate (DP)

value: P0 (Day of birth)

tag: chip antibody

value: AR (Santa Cruz, H280, sc-13062, Lot D0414)


title: VP_AR_ChIPSeq dataset #3

description:
VP_MACS2_peaks.bw
VP_HOMER_peaks.bw
VP_shared_peaks.txt


title: Sox2 CRIST-Seq

source_name: iPS cells (BC170039)

value: Induced pluripotent stem cells

tag: project

value: Reprogramming


title: clr4D T24, H3K9me2, rep2

source_name: clr4D T24, H3K9me2, rep2

value: anti-H3K9me2 (abcam 1220)


title: luminal A and lymph node metastasis_3

description: 6; breast cancer tumor tissues NO6

source_name: breast cancer tumor tissues NO6

value: luminal A and lymph node metastasis


title: clr4D T0, H3K9me2, rep2

source_name: clr4D T0, H3K9me2, rep2


title: SU_AR_ChIPSeq dataset #3

description:
SU_MACS2_peaks.bw
SU_HOMER_peaks.bw
SU_shared_peaks.txt

tag: tissue subset

value: Smooth muscle, peri-urethral mesenchyme and urethral epithelium (SU)

value: Wistar


title: leo1D T2W, H3K9me2, rep2

source_name: leo1D T2W, H3K9me2, rep2


title: luminal A and lymph node metastasis_2

description: 5; breast cancer tumor tissues NO5

source_name: breast cancer tumor tissues NO5

tag: age


title: VMP_AR_ChIPSeq dataset #3

description:
VMP_MACS2_peaks.bw
VMP_HOMER_peaks.bw
VMP_shared_peaks.txt

value: Ventral mesenchymal pad (VMP)

tag: strain


title: luminal B and lymph node non-metastasis_1

description: 7; breast cancer tumor tissues NO7

source_name: breast cancer tumor tissues NO7

value: luminal B and lymph node non-metastasis


title: leo1D_T48_rep2

description: rRNA-depleted RNA

data_processing:
Raw data from the Hiseq (fastq files) were aligned to ASM294v2 using Star with default parameters. The ASM294v2.24 annotation was downloaded from pombase.org.
The aligned data (bam files) were used to count reads in annotated genes using the featureCounts program.
Counts were then imported to R/Bioconductor and edgeR which was used for the gene expression analysis.
Prior to analysis, counts were filtered to remove unexpressed/low expressed genes and subsequently TMM normalized.
Differential expression was carried out by comparing the duplicate samples of the leo1 mutant to the wt at each time point.
Genome_build: S. pombe ASM294v2.22
Supplementary_files_format_and_content: excell file include log2FC values for each Sample

extract_protocol:
Cells were harvested at 3000 rpm at 25 °C. Then the cells were washed with phosphate buffered saline (PBS; pH 7.4) once. The pellet was re-suspended in 500 µl RNA extraction buffer (2% TritonX-100, 1% SDS, 100 mM NaCl, 10 mM Tris–HCl (pH 8.0), 1 mM EDTA (pH 8.0)) and 500 µl acid phenol (pH 5.2) and then 500 µl acid-washed glass beads were added into the tubes. The tubes were vortexed vigorously at 4°C to disrupt cells. The tubes were centrifuged at 13,000 rpm for 5 min at 4°C and the upper aqueous phase was collected into a gel phase tube with same volume chloroform. After mixing the tubes were centrifuged at 13,000 rpm for 5 min at 25°C and the upper aqueous phase was collected. Ammonium acetate (pH 5.2) was added to a final concentration of 2.5 M along with 2.5 volumes of ethanol. The tubes were kept at −20°C for overnight for RNA precipitation. The precipitated RNA was washed with 70% ethanol once and dissolved in RNase free water. DNase I treatment was performed using TURBO DNase (Thermo Fisher Sci.) following the manufacturer’s instructions.
To remove rRNA, 4µg of purified total RNA was treated with ScriptSeq Complete Gold Kit Yeast (Epicentre). 40ng rRNA-depleted stocks were used to generate sequencing libraries using the ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre).


title: leo1D_T2W_rep2

description: rRNA-depleted RNA


title: Nucl_Mnase_N-myc_kd_rep2

first: Weisheng

last: Zheng

address: Siping Road, No.1239

department: Department of Bioinformatics

institute: Tongji University

data_processing:
Basecalls performed using CASAVA version 1.9
MNase-seq reads were cleaned by using trim_galore (v.0.4.4) to remove adapter sequences and low quality sequences.
The clean reads were mapped to the hg19 assembly using bowtie2 (v.2.2.4) with parameters: -I 100 -X 300
The mapped reads were filtered by the following specifications: only the read pairs mapped properly and with a mapq > 10 were retained for further analysis.
The midpoints of proper pairs were used as input to predicted the nucleosome positions by Genetrack.
Genome_build: hg19
Supplementary_files_format_and_content: bed files of predicted nucleosome positions with read count and fuzziness values by Genetrack

source_name: Neuroblastoma cells

growth_protocol: Human neuroblastoma cell line BE(2)C cells were routinely cultured in DMEM(Life Technologies 11995065) supplemented with 10%FBS (foetal bovine serum) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Lysates  were clarified from nuclei by Mnase.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: ~4X105 cells were cultured in dish and incubated with siRNA（siRNA concentration=80nM） and Lipofectamine 2000 (Life Technologies 11668019) in Optimem (Life Technologies 51985034) at 37°C 6h. The next day, isolate the DNA, protein and the cells.

value: N-myc kd


title: luminal A and lymph node non-metastasis_3

description: 3; breast cancer tumor tissues NO3

source_name: breast cancer tumor tissues NO3

value: luminal A and lymph node non-metastasis


title: luminal A and lymph node non-metastasis_2

description: 2; breast cancer tumor tissues NO2

source_name: breast cancer tumor tissues NO2

value: frozen tissue


title: leo1D_T8_rep2

description: rRNA-depleted RNA


title: luminal A and lymph node non-metastasis_1

description: 1; breast cancer tumor tissues NO1

source_name: breast cancer tumor tissues NO1

value: female


title: BreastCancerTissue-HER2positive-T32-sample1

value: Female

value: AR-positive, ER-/PR-negative, HER2-positive tumor


title: Nucl_Mnase_ctrl_N-myc_kd_rep2

value: wild type


title: leo1D T24, H3K9me2, rep2

source_name: leo1D T24, H3K9me2, rep2


title: BreastCancerTissue-HER2negative-B32-sample3

value: AR-positive, ER-/PR-negative, HER2-negative breast tumor


title: BreastCancerTissue-HER2negative-B13-sample1


title: leo1D_T0_rep2

description: rRNA-depleted RNA


title: leo1D T48, H3K9me2, rep2

source_name: leo1D T48, H3K9me2, rep2


title: BreastCancerTissue-HER2positive-T40-sample2


title: BreastCancerTissue-HER2negative-B29-sample2


title: Suspension/GFP-HA-Akt-T308D S473D (24 hrs), rep2

description:
DDAKT_Sus_24hrs_2
Gene expression of suspension culture stable for GFP-HA-Akt-T308D S473D, 24 hrs, rep2

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Agilent's human GXP_8X60k Array (AMADID: 072363) designed by Genotypic Technology Private limited, bangalore using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

source_name: MDA-MB-231_Suspension/GFP-HA-Akt-T308D S473D (24 hrs)

treatment_protocol: Cells were detached using trypsin and cultured on nobel agar coated dish for 24 hrs.

value: Breast cancer cell line


title: IgG_MYCN_kd_rep2

data_processing:
Basecalls performed using CASAVA version 1.9
ChIP-seq reads were cleaned by using trim_galore (v.0.4.4) to remove adapter sequences and low quality sequences.
The clean reads were mapped to the hg19 assembly using bowtie2 (v.2.2.4) with parameters: -I 100 -X 500
The mapped reads were filtered by the following specifications: only the read pairs mapped properly and with a mapq≥10 were retained for further analysis.
Bigwig files were generated using Deeptools with parameters: -b 10 --smoothLength 30 --normalizeUsingRPKM
Genome_build: hg19

extract_protocol:
Lysates  were clarified from nuclei by MNase and histone-DNA complexes were isolated with antibody
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: ~4X105 cells were cultured in dish and incubated with siRNA（siRNA concentration=80nM） and Lipofectamine 2000 (Life Technologies 11668019) in Optimem (Life Technologies 51985034) at 37°C 6h. The next day, isolate the total DNA and protein and the cells.

tag: strain/cell line

value: cell signaling 2729


title: leo1D_T24_rep2

description: rRNA-depleted RNA


title: luminal A and lymph node metastasis_1

description: 4; breast cancer tumor tissues NO4

source_name: breast cancer tumor tissues NO4

value: breast cancer tumor tissue

value: microRNA


title: leo1D T8, H3K9me2, rep2

source_name: leo1D T8, H3K9me2, rep2

value: anti-H3K9me2 (abcam 1220)


title: leo1D T0, H3K9me2, rep2

source_name: leo1D T0, H3K9me2, rep2


title: IgG_ctrl_kd_rep2


title: Suspension/GFP-HA-Akt-T308D S473D (24 hrs), rep1

description:
DDAKT_Sus_24hrs_1
Gene expression of suspension culture stable for GFP-HA-Akt-T308D S473D, 24 hrs, rep1


title: wt T2W, H3K9me2, rep2

source_name: wt T2W, H3K9me2, rep2

value: wt


title: wt_T48_rep2

description: rRNA-depleted RNA


title: wt_T24_rep2

description: rRNA-depleted RNA


title: wt_T2W_rep2

description: rRNA-depleted RNA


title: Suspension/shPHLPP2+LY (24 hrs), rep2

description:
shPHLPP2_Sus+LY_24hrs_2
Gene expression of suspension culture stable for shPHLPP2 and treated with LY, 24 hrs, rep2


title: H3K9ac_MYCN_kd_rep2

value: abcam ab10812


title: Suspension/shPHLPP2+LY (24 hrs), rep1

description:
shPHLPP2_Sus+LY_24hrs_1
Gene expression of suspension culture stable for shPHLPP2 and treated with LY, 24 hrs, rep1


title: H3K9ac_ctrl_kd_rep2


title: Suspension/shPHLPP2 (24 hrs), rep2

description:
shPHLPP2_Sus_24hrs_2
Gene expression of suspension culture stable for shPHLPP2, 24 hrs, rep2

source_name: MDA-MB-231_Suspension/shPHLPP2 (24 hrs)


title: wt_T8_rep2

description: rRNA-depleted RNA


title: wt T48, H3K9me2, rep2

source_name: wt T48, H3K9me2, rep2


title: Suspension/shPHLPP2 (24 hrs), rep1

description:
shPHLPP2_Sus_24hrs_1
Gene expression of suspension culture stable for shPHLPP2, 24 hrs, rep1


title: H3K4me3_MYCN_kd_rep2

value: abcam ab8580


title: H3K4me3_ctrl_kd_rep2


title: wt T24, H3K9me2, rep2

source_name: wt T24, H3K9me2, rep2


title: Alligator late stage forelimb D5 rep3

description:
Am_FL_L_D5_Rep3
processed data file:
am_HTSeq_upload.txt

organism: Alligator mississippiensis

source_name: forelimb digit5

extract_protocol:
Tissues were harvested and kept in RNAlater until extraction of RNA using Qiagen RNeasy extraction kit.
RNA libraries for alligator and mouse were prepared for sequencing using standard illumina protocols. Anolis RNA libraries were prepared using Clontech's Ultra Low V4 kit (Catalog # 634890).

tag: developmental stage

value: forelimb digit5


title: wt T8, H3K9me2, rep2

source_name: wt T8, H3K9me2, rep2


title: leo1D_T2W_rep1

description: rRNA-depleted RNA


title: wt T0, H3K9me2, rep2

source_name: wt T0, H3K9me2, rep2


title: leo1D_T48_rep1

description: rRNA-depleted RNA


title: H3K4me1_ctrl_kd_rep2

source_name: Neuroblastoma cells

value: abcam ab8895


title: Suspension (24 hrs), rep1

description:
Sus_24hrs_1
Gene expression of suspension culture, 24 hrs, rep1

source_name: MDA-MB-231_Suspension (24 hrs)

tag: cell type


title: leo1D_T24_rep1

description: rRNA-depleted RNA


title: H3K4me1_MYCN_kd_rep2

value: N-myc kd


title: clr4D T24, Input, rep1

source_name: clr4D T24, Input, rep1


title: Suspension (24 hrs), rep2

description:
Sus_24hrs_2
Gene expression of suspension culture, 24 hrs, rep2


title: Alligator late stage forelimb D5 rep1

description:
Am_FL_L_D5_Rep1
processed data file:
am_HTSeq_upload.txt


title: clr4D T0, Input, rep1

source_name: clr4D T0, Input, rep1


title: leo1D_T8_rep1

description: rRNA-depleted RNA


title: Alligator late stage forelimb D4 rep3

description:
Am_FL_L_D4_Rep3
processed data file:
am_HTSeq_upload.txt

source_name: forelimb digit4

value: forelimb digit4


title: Alligator late stage forelimb D5 rep2

description:
Am_FL_L_D5_Rep2
processed data file:
am_HTSeq_upload.txt


title: H3K36me3_MYCN_kd_rep2

value: abcam ab9050


title: leo1D T2W, Input, rep1

source_name: leo1D T2W, Input, rep1


title: leo1D_T0_rep1

description: rRNA-depleted RNA


title: Alligator late stage forelimb D4 rep2

description:
Am_FL_L_D4_Rep2
processed data file:
am_HTSeq_upload.txt


title: H3K27me3_MYCN_kd_rep2

value: active motif 39155


title: wt_T2W_rep1

description: rRNA-depleted RNA


title: H3K36me3_ctrl_kd_rep2


title: leo1D T48, Input, rep1

source_name: leo1D T48, Input, rep1


title: wt_T0_rep2

description: rRNA-depleted RNA


title: Alligator late stage forelimb D4 rep1

description:
Am_FL_L_D4_Rep1
processed data file:
am_HTSeq_upload.txt


title: Alligator late stage forelimb D3 rep3

description:
Am_FL_L_D3_Rep3
processed data file:
am_HTSeq_upload.txt

source_name: forelimb digit3

value: forelimb digit3


title: wt_T48_rep1

description: rRNA-depleted RNA


title: H3K27ac_MYCN_kd_rep2

value: abcam ab4729


title: H3K27me3_ctrl_kd_rep2

value: wild type


title: wt_T24_rep1

description: rRNA-depleted RNA


title: Alligator late stage forelimb D3 rep2

description:
Am_FL_L_D3_Rep2
processed data file:
am_HTSeq_upload.txt


title: H3K27ac_ctrl_kd_rep2


title: wt_T8_rep1

description: rRNA-depleted RNA


title: Alligator late stage forelimb D3 rep1

description:
Am_FL_L_D3_Rep1
processed data file:
am_HTSeq_upload.txt


title: HI0628BECC_GAATTCGT-CAGGACGT

city: Belfast

first: Shi-qi

last: An

address: Lisburn Road

country: United Kingdom

institute: Queen's University Belfast

data_processing:
Quality checking and trimming using Qiagen Biomedical Genomics Workbench ready-to-use workflow "prepare raw data" with default paremeters
RNA-seq analysis is done using Qiagen Biomedical Genomics Workbench RNA-seq analysis module
Breify, 1) all annotated transcripts are extracted 2) the reads are mapped against all the transcripts plus to the whole genome 3) the reads are mapped against all the transcripts plus to the whole genome, and 4) from this mapping, the reads are categorized and assigned to the genes using the EM estimation algorithm , and expression values for each gene and each transcript are calculated
Genome_build: GCF_000027305.1_ASM2730v1_genomic
Supplementary_files_format_and_content: RPKM values for each Sample

organism: Haemophilus influenzae Rd KW20

source_name: Bacterial culture: HI0628+bec rep3

growth_protocol: H. influenzae Rd KW20 strains (including mutants) were inoculated at an OD600 of 0.1 in sBHI (with 50 µM beclomethasone dipropionate if used). Cultures were harvested during mid-log phase (OD600 = 0.7)

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Rd KW20

tag: growth stage

value: mid-log phase

value: HI0628 deletion mutant

tag: treatment

value: 50 µM beclomethasone dipropionate


title: Alligator late stage forelimb D2 rep3

description:
Am_FL_L_D2_Rep3
processed data file:
am_HTSeq_upload.txt

data_processing:
Basecalls performed using CASAVA
mRNA-seq reads were aligned to the alligator (allMis0.2), Anolis (AnoCar2.0), and mouse (GRCm38) cDNA builds using Tophat2
Number of reads overlapped with known features (gene counts) was counted using HTSeq
transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: alligator (allMis0.2), Anolis (AnoCar2.0), and mouse (GRCm38)
Supplementary_files_format_and_content: tab-delimited txt files include read counts for each sample.  Gene IDs for Anolis and Mouse are from Ensembl while alligator gene IDs are available at: http://crocgenome.hpc.msstate.edu

source_name: forelimb digit2

value: forelimb digit2


title: wt_T0_rep1

description: rRNA-depleted RNA

value: wt


title: HI0628BECB_GAATTCGT-TAATCTTA

source_name: Bacterial culture: HI0628+bec rep2


title: HI0628BECA_GAATTCGT-AGGCGAAG

source_name: Bacterial culture: HI0628+bec rep1


title: HI0628C_GAATTCGT-GGCTCTGA

source_name: Bacterial culture: HI0628 rep3

value: DMSO (control)


title: leo1D T8, Input, rep1

source_name: leo1D T8, Input, rep1


title: wt T24, Input, rep1

source_name: wt T24, Input, rep1


title: leo1D T0, Input, rep1

source_name: leo1D T0, Input, rep1


title: wt T2W, Input, rep1

source_name: wt T2W, Input, rep1


title: wt T8, Input, rep1

source_name: wt T8, Input, rep1


title: wt T48, Input, rep1

source_name: wt T48, Input, rep1


title: leo1D T24, Input, rep1

source_name: leo1D T24, Input, rep1


title: HI0628A_GAATTCGT-ATAGAGGC

source_name: Bacterial culture: HI0628 rep1


title: wt T0, Input, rep1

source_name: wt T0, Input, rep1


title: Alligator late stage forelimb D2 rep1

description:
Am_FL_L_D2_Rep1
processed data file:
am_HTSeq_upload.txt


title: Alligator late stage forelimb D1 rep3

description:
Am_FL_L_D1_Rep3
processed data file:
am_HTSeq_upload.txt

source_name: forelimb digit1

value: forelimb digit1


title: Alligator late stage forelimb D2 rep2

description:
Am_FL_L_D2_Rep2
processed data file:
am_HTSeq_upload.txt


title: FAPMuscle5

city: Stevenage

first: Paul

last: Wilson

state: Hertfordshire

address: GlaxoSmithKline Medicine Research Centre

department: Target Sciences

institute: GSK

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 the mm10 genome using Bowtie version  2.1.0.0 (Phred 33)
Count files generated using HTSeq: http://bioinformatics.oxfordjournals.org/content/31/2/166 and EdgeR: Empirical analysis of digital gene expression data in R, see http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

source_name: FAP Muscle

extract_protocol:
Total RNA extracted with Trizol Lysis Reagent (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy Micro kit (Qiagen) per manufacturer's instructions. The RNA integrity (RNA Integrity Score >= 7) and quantity determined on the Agilent 2100 Bioanalyzer (Agilent; Palo Alto, CA, USA) per manufacturer's recommendation and subjected to Illumina library prep for RNAseq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Muscle

value: FAP


title: MEF1

source_name: MEF

value: MEF


title: MEF4


title: HIBECC_CTGAAGCT-AGGCGAAG

source_name: Bacterial culture: WT+bec (beclomethoasome) rep3

value: Wild type


title: Alligator late stage forelimb D1 rep1

description:
Am_FL_L_D1_Rep1
processed data file:
am_HTSeq_upload.txt


title: FAPMuscle4


title: Alligator early stage forelimb D5 rep3

description:
Am_FL_E_D5_Rep3
processed data file:
am_HTSeq_upload.txt

source_name: forelimb digit5

value: forelimb digit5


title: FAPMuscle3


title: clr4D T24, H3K9me2, rep1

source_name: clr4D T24, H3K9me2, rep1

value: anti-H3K9me2 (abcam 1220)


title: MEF2


title: MEF3


title: leo1D T2W, H3K9me2, rep1

source_name: leo1D T2W, H3K9me2, rep1


title: HI0628B_GAATTCGT-CCTATCCT

source_name: Bacterial culture: HI0628 rep2


title: Alligator early stage forelimb D5 rep2

description:
Am_FL_E_D5_Rep2
processed data file:
am_HTSeq_upload.txt


title: Alligator late stage forelimb D1 rep2

description:
Am_FL_L_D1_Rep2
processed data file:
am_HTSeq_upload.txt


title: HIBECA_CTGAAGCT-CCTATCCT

source_name: Bacterial culture: WT+bec (beclomethoasome) rep1


title: FAPMuscle2


title: Alligator early stage forelimb D5 rep1

description:
Am_FL_E_D5_Rep1
processed data file:
am_HTSeq_upload.txt


title: Alligator early stage forelimb D4 rep3

description:
Am_FL_E_D4_Rep3
processed data file:
am_HTSeq_upload.txt

source_name: forelimb digit4

value: forelimb digit4


title: leo1D T24, H3K9me2, rep1

source_name: leo1D T24, H3K9me2, rep1


title: FAPLung5

source_name: FAP Lung

value: Lung


title: Alligator early stage forelimb D4 rep2

description:
Am_FL_E_D4_Rep2
processed data file:
am_HTSeq_upload.txt


title: HIWTB_CTGAAGCT-TATAGCCT

source_name: Bacterial culture: WT rep2


title: FAPLung4


title: clr4D T0, H3K9me2, rep1

source_name: clr4D T0, H3K9me2, rep1


title: leo1D T48, H3K9me2, rep1

source_name: leo1D T48, H3K9me2, rep1


title: leo1D T0, H3K9me2, rep1

source_name: leo1D T0, H3K9me2, rep1


title: FAPLung3


title: HIBECB_CTGAAGCT-GGCTCTGA

source_name: Bacterial culture: WT+bec (beclomethoasome) rep2


title: wt T2W, H3K9me2, rep1

source_name: wt T2W, H3K9me2, rep1


title: FAPLung2


title: Alligator early stage forelimb D4 rep1

description:
Am_FL_E_D4_Rep1
processed data file:
am_HTSeq_upload.txt


title: RW1 cultured with succinate replicate 3

city: East Lansing

first: Benli

last: Chai

state: Michigan

address: 567 Wilson Road Rm 2225 A

department: Center for Microbial Ecology

institute: Michigan State University

data_processing:
Illumina Casava v1.8 software was used for basecalling.
Sequenced reads were trimmed at Read Segment Quality Control Indicator to remove low quality 3' end, then mapped to Sphingomonas wittichii genome (including chromosome and two plastmids) using bowtie v1.0.0 with parameters -n 2 -e 70 -l 28 --best
Gene expression were measured as counts of reads matching any part of annotated gene features, which were tallied using Python scripts deposited at https://github.com/chaibenl/RW1
Reads Per Kilobase of gene per Megabase of mapped reads (RPKM) were calculated using count of reads (C), gene length (L) and total mapped reads (T) with the standard formula: RPKM = C/(L/10^3*T/10^6)
Genome_build: NC_009511.1,  NC_009508.1,  NC_009507.1
Supplementary_files_format_and_content: tab-delimited files for gene counts and RPKM

organism: Rhizorhabdus wittichii

source_name: Log phase cells in liquid culture

growth_protocol: RW1 was grown at 30 degree C using defined mineral DSMZ medium µM 457 (Brunner medium) (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, http://www.dsmz.de/).

extract_protocol:
Total RNA was isolated from early-to-mid log phase cultures (CFU of 1.0x109 to 1.5x109 cells/mL) using PureLink Mini Kit (Life Technologies, Carlsbad, CA) with lysis step modified as per the RiboPure Kit instructions (Life Technologies, Carlsbad, CA). To ensure complete removal of DNA, RNA samples underwent a two-step DNAse I treatment, first with DNAse I (amplification grade, Life Technologies) followed by TURBO DNAse I (Life Technologies). RNA concentration was measured using Qubit (Life Technologies) and its quality was validated using BioAnalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Carbon substrates were added as follows: succinate (SUC) was added to final 20 mM concentration, dibenzo-p-dioxin (DD) (365 µM) was added to sterile flasks from acetone stock and the flasks were left open in a sterile hood for 5 h to allow acetone to completely evaporate. Brunner medium was then added and flasks were sonicated for 10 sec to dislodge and break up substrate crystals. Cs-SAP and clay-sorbed-dioxin (DDSAP) were added to 1% (w/v) final concentration (1% DDSAP corresponded to 365 µM DD) in Brunner medium and sonicated to homogenize clay particles. For DD+SAP, dioxin was added from acetone stock followed by acetone evaporation followed by the addition of clay.

tag: sole carbon source

value: succinate


title: leo1D T8, H3K9me2, rep1

source_name: leo1D T8, H3K9me2, rep1


title: wt T48, H3K9me2, rep1

source_name: wt T48, H3K9me2, rep1


title: Control_liver_2

source_name: Liver

tag: breed

value: Beagle

value: Liver


title: FAPLung1

tag: tissue


title: Alligator early stage forelimb D3 rep2

first: Cong

last: Liang

address: 300 Heffernan Dr.

institute: Yale University

description:
Am_FL_E_D3_Rep2
processed data file:
am_HTSeq_upload.txt

source_name: forelimb digit3

value: forelimb digit3


title: Alligator early stage forelimb D3 rep1

description:
Am_FL_E_D3_Rep1
processed data file:
am_HTSeq_upload.txt


title: RW1 cultured with succinate replicate 1


title: HIWTC_CTGAAGCT-ATAGAGGC

source_name: Bacterial culture: WT rep3

value: Rd KW20

value: mid-log phase

tag: genotype


title: Alligator early stage forelimb D2 rep3

description:
Am_FL_E_D2_Rep3
processed data file:
am_HTSeq_upload.txt

source_name: forelimb digit2

value: forelimb digit2


title: Alligator early stage forelimb D2 rep2

description:
Am_FL_E_D2_Rep2
processed data file:
am_HTSeq_upload.txt


title: HIWTA_GAATTCGT-GTACTGAC

source_name: Bacterial culture: WT rep1

value: DMSO (control)


title: wt T0, H3K9me2, rep1

source_name: wt T0, H3K9me2, rep1

value: wt

tag: antibody


title: RW1 cultured with crystalline dioxin replicate 3

value: crystalline dioxin


title: wt T8, H3K9me2, rep1

source_name: wt T8, H3K9me2, rep1


title: RW1 cultured with crystalline dioxin replicate 2


title: Alligator early stage forelimb D2 rep1

description:
Am_FL_E_D2_Rep1
processed data file:
am_HTSeq_upload.txt


title: RW1 cultured with clay-sorbed dioxin replicate 3

value: clay-sorbed dioxin


title: Alligator early stage forelimb D1 rep2

description:
Am_FL_E_D1_Rep2
processed data file:
am_HTSeq_upload.txt

source_name: forelimb digit1

value: forelimb digit1


title: RW1 cultured with clay-sorbed dioxin replicate 2


title: Alligator early stage forelimb D1 rep1

description:
Am_FL_E_D1_Rep1
processed data file:
am_HTSeq_upload.txt


title: RW1 cultured with clay-sorbed dioxin replicate 1


title: RW1 cultured with crystalline dioxin replicate 1


title: RW1 cultured with succinate replicate 2


title: wt T24, H3K9me2, rep1

source_name: wt T24, H3K9me2, rep1


title: Alligator early stage forelimb D1 rep3

description:
Am_FL_E_D1_Rep3
processed data file:
am_HTSeq_upload.txt


title: NONLESIONAL.DAY1 [patient: 48]

status: Public on Jun 29 2019

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from skin biopsy

hyb_protocol: Affymetrix Human U133Plus 2.0 gene arrays were used. Total RNA (50 ng) was reverse transcribed and amplified with Ovation Whole Blood Solution from NuGen (San Carlos, CA). The labeled target was fragmented and hybridized to probe gene arrays, using Encore Biotin Module from NuGen (San Carlos, CA). The chips were washed, stained with streptavidin-phycoerythrin, and scanned (HP GeneArray Scanner; Hewlett-Packard Company, Palo Alto, CA). On each chip, the human housekeeping genes β-actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) served as controls. Suite 5.0 software normalized the expression level values using these controls.

scan_protocol: Hewlett-Packard GeneArray Scanner G2500A

data_processing: Quality control of Affymetrix chips was done using standard QC metrics and R packages. Expression measures were obtained using GC Robust Multi-array Average (GCRMA) algorithm. Batch effects corresponding to the hybridization date were detected by principal component analyses and adjusted using ComBat algorithm from R’s sva package. Probe sets with expression >3 in at least 15 samples were used for further analyses. Gene expression changes were modeled using mixed-effect models, with treatment, time and tissue type as a fixed interaction term, and a random effect for each patient. Fold changes (FCHs) for the comparisons of interest were estimated, and hypothesis testing was conducted with contrasts under the general framework of linear models in the R limma package. P-values were adjusted for multiple hypotheses using the Benjamini-Hochberg procedure, which controls the false discovery rate (FDR).

source_name: Skin biopsy

label_protocol: Ovation WB Reagent (Nugen)

extract_protocol: Skin biopsies were stored in RNAlater® (Invitrogen) until further processing. RNA was extracted (Covance Genomics Lab).

value: NONLESIONAL

tag: week


title: NONLESIONAL.DAY1 [patient: 50]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 51]

description: Gene expression data from skin biopsy

value: LESIONAL

value: Vehicle


title: Crisaborole.DAY15 [patient: 49]

description: Gene expression data from skin biopsy

value: Crisaborole


title: Crisaborole.DAY1 [patient: 50]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 48]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 51]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 49]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 51]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 48]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 48]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 50]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 50]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 51]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 50]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 49]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 51]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 49]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 47]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 49]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 51]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 48]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 51]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 49]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 47]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 48]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 48]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 47]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 47]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 47]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 47]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 45]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 45]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 45]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 43]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 47]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 45]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 44]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 43]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 42]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 44]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 41]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 42]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 44]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 45]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 42]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 43]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 42]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 44]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 43]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 41]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 43]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 41]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 45]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 42]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 42]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 41]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 41]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 45]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 44]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 42]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 40]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 41]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 37]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 40]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 40]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 37]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 37]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 40]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 39]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 39]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 40]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 41]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 40]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 36]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 39]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 35]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 34]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 37]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 37]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 36]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 39]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 34]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 40]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 35]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 36]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 36]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 35]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 36]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 35]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 35]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 34]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 34]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 34]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 33]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 34]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 33]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 33]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 34]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 31]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 32]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 31]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 33]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 30]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 33]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 32]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 32]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 29]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 30]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 30]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 30]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 32]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 30]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 29]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 32]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 32]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 32]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 31]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 31]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 31]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 29]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 29]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 28]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 29]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 28]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 29]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 27]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 27]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 28]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 23]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 23]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 23]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 23]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 25]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 22]

description: Gene expression data from skin biopsy


title: Vehicle.ET [patient: 27]

description: Gene expression data from skin biopsy

value: ET


title: Vehicle.DAY1 [patient: 23]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 27]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 28]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 25]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 25]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 25]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 22]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 25]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 28]

description: Gene expression data from skin biopsy


title: Crisaborole.ET [patient: 27]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 22]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 22]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 29]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 22]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 22]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 22]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 17]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 25]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 17]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 16]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 17]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 16]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 16]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 16]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 15]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 16]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 15]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 16]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 14]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 16]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 15]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 15]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 14]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 17]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 14]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 17]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 13]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 14]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 15]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 13]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 14]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 13]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 13]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 13]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 12]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 11]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 14]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 12]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 11]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 11]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 11]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 12]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 12]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 11]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 11]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 14]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 13]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 12]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 9]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 9]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 9]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 9]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 9]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 7]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 7]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 7]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 7]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 13]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 11]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 9]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 9]

description: Gene expression data from skin biopsy