title: W+S D14_rep1

description: Mus musculus + Homo sapiens

data_processing:
Paired-end sequencing was performed on the Illumina HiSeq2500 platform
We applied FastQC for a standard quality control of our 100-bp length, paired-end RNA-seq data generated by Illumina HiSeq2500, tested both the raw sequence data, and trimmed sequence data.
Trimmomatic was used to trim the adaptor, and discarded low quality reads and the reads with length less then 36 bp. After trimming, we reserved the paired reads and abandoned unpaired reads for next step analysis. Then cleaned reads (paired reads) were submitted to the tuxedo pipeline.
Tophat2 internally called bowtie2 to map raw reads against the human genome hg38 and mouse genome mm10 with 2 mismatches allowed
Cufflinks were applied to generate the Fragments Per Kilobase Million (FPKM) value for each gene, based on the hg38 or mm10 gene annotation GTF file of University of California Santa Cruz. Human and mouse genome sequences, annotation files, and genome indexes were downloaded from iGenome
Genome_build: human genome hg38 and mouse genome mm10
The RNA-seq data was statically analyzed with R. One-way ANOVA test and fold change were used to identify DEG. We downloaded all the gene sets used for function/pathway enrichment from Gene Set Enrichment Analysis of the Broad Institute, and elucidated the hypergeometric distribution to determine P values of each enriched pathway. The R package “gplots” and “ggpubr” were used to prepare all figures.
Supplementary_files_format_and_content: FPKM

organism:
Homo sapiens
Mus musculus

source_name: D14 Wounded skin with EMSCSp treatment_replicate1

extract_protocol:
Mice were sacrificed at designated time points, skin samples including the wound and 2 mm of the surrounding skin were harvested using an 8-mm biopsy punch, and three wounds were pooled per group. The tissues were sliced into small pieces and homogenized with a pestle. Skin fragments were added into a lysis buffer provided by QIAGEN RNeasy kit to isolate total RNA according to the manufacturer’s instructions.
The integrity and quality of samples were verified using the Nano RNA Bioanalyzer Assay (Agilent Technologies). Samples with RNA integrity number larger than 9 were used for Next Generation Sequencing library preparation using the NEB Ultra Directional RNA Library Preparation Kit.

tag: strain

value: NOD/SCID

tag: cell type

value: human ES derived MSC


title: W+S D14_rep2

status: Public on May 29 2020

type: SRA

city: Macao

first: Renhe

last: Xu

address: Avenida de Universidade  Taipa

department: Faculty of Health Sciences

country: China

institute: University of Macao

description: Mus musculus + Homo sapiens

library_source: transcriptomic

molecule: total RNA

source_name: D14 Wounded skin with EMSCSp treatment_replicate2

growth_protocol: EMSC were generated by inducing hESC to differentiate into MSC using the method we reported previously. EMSC were cultured in high-glucose Dulebcco’s modified Eagle’s medium supplemented with 20% fetal bovine serum at 37.0℃ in 5% CO2 incubator, and passaged every 5-7 days. MSC between passages 6-10 were used for all experiments. For spheroid formation, MSC were split and seeded on adhesion substrates by using handing drop method at a density of 2.5×104 cells/drop as we recently reported 15, and the MSC in the handing drop formed spheroids within 2-day culture. Either MSC spheroids or cells dissociated from MSC in monolayer were harvested for transplantation.

treatment_protocol: The excisional wound splinting model was generated as reported. For the EMSCSp group, around 40 spheres equivalent of 1×106 EMSC were directly dropped onto the surface of each wound right after the wounding. For the EMSCDiss group, EMSCDiss at 0.7×106 cells in 100 l PBS (70% of the total cell dose) per wound were evenly injected into the dermis in four spots around the wound, and 0.3×106 EMSCDiss (30% of the total cell dose) mixed with 30-l Matrigel were dropped onto the surface of the wound. For the vehicle control group, 100-l PBS alone per wound was evenly injected around the wound, and 30-l Matrigel was dropped onto the surface of the wound as above.


title: PD7_B

type: genomic

city: Honolulu

first: Maarit

middle: I

last: Tiirikainen

state: HI

address: 701 Ilalo St, Genomics Shared Resource

country: USA

institute: UHCC

hyb_protocol: Illumina Infinium HD Methylation Assay

scan_protocol: Illumina Infinium HD Methylation Assay

data_processing: Illumina Genome Studio

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: Illumina Infinium HD Methylation Assay

extract_protocol: AllPrep DNA/RNA Mini kit (Qiagen)

tag: tissue

value: blood

tag: age draw/autopsy

tag: time to autopsy (for t_brain)

tag: plant exp code (3=10+, 0=0 yrs)

tag: disease state

value: Parkinsons Disease


title: PD6_B


title: Plasma_after surgery_148BA

type: RNA

city: Nicosia

first: Areti

last: Moushi

address: Iroon Avenue 6, Agios Dometios

country: Cyprus

institute: Cyprus Insitute of Neurology and Genetics

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

data_processing: Relative log expression normalization was conducted with R  DEseq2 and in house scripts

source_name: Thoracic Aortic Aneurysm

extract_protocol: Total RNA was extracted from samples

treatment_protocol: Affected Individuals

tag: individual

value: patient 148

value: Plasma collected after aneurysm surgery


title: PD5_T

source_name: Brain

value: brain


title: W+S D7_rep1

description: Mus musculus + Homo sapiens

source_name: D7 Wounded skin with EMSCSp treatment_replicate1


title: SC_CWS_5

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

hyb_protocol: Samples were hybridised to the Clariom S GeneChip microarray (Thermofisher UK) as per directions for the GeneChip WT Plus Reagent kit (Thermofisher UK). Overnight hybridisation to the Clariom S GeneChip took place at 45oC for 16 hours.

scan_protocol: After washing and staining as per directions for the  GeneChip WT Plus Reagent kit (Thermofisher UK) images were captured and cel files generated using the GeneChip Scanner 3000 and raw data converted to .CEL files using the Affymetrix GCOS Software (Thermofisher UK).

data_processing: The .CEL data were analysed using R/Bioconductor using an updated chip definition file (CDF) from the Brainarray resource based on Ensembl gene definitions (ENSG version 22.0.0). Raw microarray data were normalised using the SCAN method (Piccolo et al, 2012 DOI:10.1016/j.ygeno.2012.08.003). Normalised data were filtered using the UPC method (see Piccolo et al) with expression intensity and UPC filters were set at 0 and 0.5 respectively. Changes in differential expression were examined using empirical Bayes and a moderated t statistic implemented in the limma package with subject identifier as a blocking factor in linear modelling to account for the repeated measures structure (see section Additive Models and Blocking in the limma manual). Category enrichment analysis was carried out using the camera algorithm and the Broad Institute curated Hallmark Genesets collection. A FDR <5% was taken to indicate significant enrichment of a category.

source_name: Subcutaneous adipose tissue from weight stable cancer patient

label_protocol: Sense strand cDNA was generated, fragmented and labelled using the GeneChip WT Plus Reagent kit (Thermofisher UK) as per directions.

extract_protocol: Aliquots of adipose tissue were homogenised in Qiazol reagent (Qiagen, UK) using the BeadBeater instrument with 1.5mm ceramic beads (Qiagen, UK). Tissue aliquots were shaken at 5000Hz for 30s with 30s cooling on ice. This process was repeated 3 times or until no gross debris was visible. Samples were then spun at 5xg for 15mins at 4oC and the supernatant collected into fresh Eppendorf tubes.  RNA was isolated from adipose tissue samples using the Qiagen RNeasy lipid tissue kit (Qiagen UK) following the manufacturers directions.

treatment_protocol: Following surgical skin incision under general anaesthesia, biopsies of subcutaneous fat were taken from all patients at the start of the operation. Visceral fat was sampled from the greater omentum in cancer patients and perinephric fat from the transplant donors after the kidney had been excised. All samples were snap frozen in liquid nitrogen and stored at -80oC until analysis.

value: SubCut

tag: group

value: CWS

tag: Sex

value: Male

tag: age

tag: tumour

value: Oesophageal adenocarcinoma

tag: height(cm)

tag: weight(kg)

tag: weight loss %

tag: sk muscle area (cm2)

tag: visceral adipose area (cm2)

tag: subcutaneous adipose area (cm2)

tag: skeletal muscle density (hu)

tag: visceral adipose density (hu)

tag: subcutaneous adipose density (hu)

tag: skeletal muscle index


title: Plasma_before surgery_224BB

scan_protocol: Refer to the NanoString nCounter Assay System Manual

value: patient 224

tag: tissue

value: Plasma collected before aneurysm surgery


title: SC_CWL_1

source_name: Subcutaneous adipose tissue from weight losing cancer patient

value: CWL

value: Female

value: Gastric adenocarcinoma


title: W+S D3_rep2

description: Mus musculus + Homo sapiens

source_name: D3 Wounded skin with EMSCSp treatment_replicate2

tag: strain

tag: cell type


title: PD7_T

tag: age draw/autopsy

tag: time to autopsy (for t_brain)

tag: plant exp code (3=10+, 0=0 yrs)

tag: disease state


title: PD4_T


title: PD5_B


title: Plasma_before surgery_206BB

label_protocol: Refer to the NanoString nCounter Assay System Manual

tag: individual

value: patient 206


title: W+S D3_rep1

description: Mus musculus + Homo sapiens

source_name: D3 Wounded skin with EMSCSp treatment_replicate1

value: NOD/SCID


title: Plasma_before surgery_162BB

value: patient 162


title: VIS_CWS_2

source_name: Visceral adipose tissue from weight stable cancer patient

value: Visceral

tag: group

tag: Sex

tag: age

tag: tumour

tag: height(cm)

tag: weight(kg)


title: PD3_T

value: Parkinsons Disease


title: PD4_B

value: blood


title: Plasma_before surgery_148BB

value: patient 148


title: W+S D7_rep2

description: Mus musculus + Homo sapiens

source_name: D7 Wounded skin with EMSCSp treatment_replicate2

value: human ES derived MSC


title: SC_CTRL_1

source_name: Subcutaneous adipose tissue from healthy control

value: SubCut

value: CONTROL

tag: weight loss %

tag: sk muscle area (cm2)

tag: visceral adipose area (cm2)

tag: subcutaneous adipose area (cm2)

tag: skeletal muscle density (hu)

tag: visceral adipose density (hu)


title: PD6_T

tag: tissue

value: brain

tag: age draw/autopsy


title: DGM-11779_M6_sm (BMP4 study)

status: Public on May 28 2020

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite software, version 6.6 using default analysis settings and robust multi-array (RMA) normalization method.

source_name: small airway epithelium cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: COPD smoker

tag: cell type

value: small airway epithelium cells

tag: time of serial bronchoscopy (month)


title: DGM-11779_M3_sm (BMP4 study)


title: VIS_CWS_1

tag: group

value: CWS

value: Male

value: Oesophageal adenocarcinoma

tag: subcutaneous adipose density (hu)

tag: skeletal muscle index


title: DGM-10794_M3_sm (BMP4 study)


title: DGM-11779_M12_sm (BMP4 study)


title: DGM-11465_M6_sm (BMP4 study)


title: DGM-10794_M0_sm (BMP4 study)


title: PD2_B

tag: time to autopsy (for t_brain)

tag: plant exp code (3=10+, 0=0 yrs)

tag: disease state


title: VIS_CWS_3

tag: Sex

value: Female

tag: age

tag: tumour

value: Oesophageal SCC

tag: height(cm)

tag: weight(kg)

tag: weight loss %


title: DGM-01961_M6_sm (BMP4 study)


title: DGM-10794_M12_sm (BMP4 study)


title: DGM-11779_M0_sm (BMP4 study)


title: DGM-11298_M12_sm (BMP4 study)


title: DGM-10794_M6_sm (BMP4 study)


title: DGM-11465_M12_sm (BMP4 study)


title: DGM-11465_M0_sm (BMP4 study)


title: DGM-11465_M3_sm (BMP4 study)


title: DGM-01961_M0_sm (BMP4 study)


title: DGM-11298_M3_sm (BMP4 study)


title: DGM-01961_M12_sm (BMP4 study)


title: DGM-11298_M0_sm (BMP4 study)


title: DGM-01961_M3_sm (BMP4 study)


title: PD1_B

tag: tissue


title: DGM-02164_M3_sm (BMP4 study)


title: DGM-11298_M6_sm (BMP4 study)


title: DGM-02164_M6_sm (BMP4 study)


title: PD8_B

tag: age draw/autopsy


title: 48hr INCB059872 A H3K4me1

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave.

institute: Vanderbilt University

library_source: genomic

data_processing:
Trimmomatic-0.32: trim adapter sequences
Bowtie2: read alignment to hg19+dm3
samtools: filter out low quality alignments and remove duplicate reads
samtools: divide hg19 reads and dm3 reads into separate files
MACS2: call peaks (q-value 0.001)
Genome_build: combined genome: hg19 + dm3
Supplementary_files_format_and_content: Processed data files are in bedgraph format with input signal subtracted from ChIP signal.

source_name: THP-1 cell line

extract_protocol:
Cells were lysed by resuspending in cell lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.5% NP-40) and sitting on ice for 10 min. Samples were centrifuged, and nuclei were resuspended in nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 0.5% SDS) and kept on ice for 10 min before sonication using a Bioruptor (Diagenode) on high setting for 15 cycles (30 sec on, 30 sec off). After removing an aliquot to serve as input, chromatin from each sample was divided between two tubes and diluted 1:4 with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 1.2 mM EDTA pH 8.0, 167 mM NaCl, 1.1% Triton X-100, 0.01% SDS). 3μg anti-H3K4me2 or anti-H3K4me1 was added to each tube. Samples were rotated at 4°C for 2 hours before adding 15μl Protein A Dynabeads and 15μl Protein G Dynabeads. Samples were rotated at 4°C for 1 hour before washing beads 7 times: (twice with low salt buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS), twice with high salt buffer (500 mM NaCl, otherwise same as low salt buffer), once with LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 1% NP-40, 1% Na-deoxycholate), and twice with TE. Samples were eluted twice by resuspending beads in elution buffer (10% SDS, 1 M NaHCO3) and rotating for 15 min at room temperature.
Libraries were prepared by taking 100 ng DNA from each input and IP sample for polishing, A-tailing, and ligation of adapters. Agencourt AMPure XP Beads were used at 1.8X volume according to manufacturer’s instructions for size selection, and eluted material was PCR amplified with Q5 Hot Start DNA Polymerase for 21 cycles.
Immediately prior to crosslinking, drosophila S2 cells were added to treated THP-1 cells to serve as spike-in control (~1:27 ratio of drosophila:human cells). Cells were crosslinked with 1% formaldehyde, quenched with glycine, and washed with cold PBS. See "ChIP protocol" column above for experiment-specific protocols.

tag: chip antibody

value: anti-H3K4me1 (Abcam, ab8895)


title: PD3_B


title: 48hr INCB059872 B H3K4me1


title: DGM-11269_M6_sm (BMP4 study)

tag: smoking status

tag: cell type


title: 48hr DMSO A H3K4me1


title: DGM-11269_M3_sm (BMP4 study)

tag: time of serial bronchoscopy (month)


title: 48hr DMSO B H3K4me1


title: DGM-02164_M12_sm (BMP4 study)


title: 48hr DMSO B H3K4me2

value: anti-H3K4me2 (Abcam, ab7766)


title: DGM-11269_M12_sm (BMP4 study)


title: DGM-02164_M0_sm (BMP4 study)


title: 48hr INCB059872 B H3K4me2


title: 48hr DMSO A H3K4me2


title: 48hr INCB059872 A H3K4me2


title: 48hr INCB059872 B input


title: 48hr INCB059872 A input


title: DGM-11269_M0_sm (BMP4 study)


title: 48hr DMSO B input


title: PD10_T


title: DGM-11261_M3_sm (BMP4 study)


title: DGM-11261_M12_sm (BMP4 study)


title: 48hr DMSO A input


title: DGM-11270_M0_sm (BMP4 study)


title: DGM-11192_M6_sm (BMP4 study)


title: DGM-11270_M3_sm (BMP4 study)


title: DGM-11261_M6_sm (BMP4 study)


title: DGM-11261_M0_sm (BMP4 study)


title: DGM-11270_M6_sm (BMP4 study)


title: DGM-11270_M12_sm (BMP4 study)


title: THP-1 cells, 6hr INCB059872 A

data_processing:
Library strategy: PRO-seq
Trimmomatic-0.32: trim adapter sequences
fastx_reverse_complement: generate reverse complemented reads
Bowtie2: read alignment to hg19
samtools: filter out low quality alignments
NRSA: pause_PROseq.pl and eRNA.pl
Genome_build: hg19
Supplementary_files_format_and_content: Two bedgraph files, separated by plus or minus strand, are provided for each sample.

extract_protocol:
Nuclear run-on assays were performed with ATP, UTP, GTP, and biotin-11-CTP. Nuclei were lyzed with TRIzol, nuclear RNA was extracted and fragmented, and biotinylated RNA was purified with strepavidin magnetic beads.
Library construction included 3' adaptor ligation, 5' repair, 5' adaptor ligation, reverse transcription, and PCR full-scale amplification.

tag: cell line

tag: treatment

tag: time


title: THP-1 cells, 24hr INCB059872 B


title: THP-1 cells, 12hr INCB059872 B


title: THP-1 cells, 6hr INCB059872 B


title: THP-1 cells, 12hr INCB059872 A


title: DGM-11192_M12_sm (BMP4 study)


title: DGM-11192_M0_sm (BMP4 study)


title: THP-1 cells, control B

value: control


title: THP-1 cells, 24hr INCB059872 A


title: PD2_T

tag: time to autopsy (for t_brain)

tag: plant exp code (3=10+, 0=0 yrs)

value: Parkinsons Disease


title: DGM-11163_M6_sm (BMP4 study)


title: PD1_T

tag: disease state


title: wild-type HCT116, control, Replicate 2

city: Boulder

first: Dylan

middle: J

last: Taatjes

state: CO

address: Campus Box 596

department: Biochemistry

institute: University of Colorado Boulder

description:
nascent RNA
nascent RNA (PRO-seq) from HCT116 cells
counts_hct116.txt

data_processing:
processing of all sequencing data was performed using the NascentFlow Pipeline (doi: 10.17605/OSF.IO/NDHJ2)
Genome_build: GRCh38 for HCT116 cells, DM6 for S2 cells

source_name: wild type HCT116 cells

growth_protocol: HCT116 cells were grown in McCoy's media (Gibco, 16600082) with Gibco 100x Antibiotic-Antimycotic (Fisher Sci, 15240062) penicillin-streptomycin and 10% fetal bovine serum (FBS) supplementation. Drosophila cell culture and RNAi. D. melanogaster Schneider line 2 (S2) cells were maintained at 25°C in Schneider‘s medium containing 10% (vol/vol) Fetalplex (Gemini), 100 units/mL penicillin, and 0.1 mg/mL streptomycin. RNAi was performed as described [Clemens, 2000] using 20-40 µg dsRNA. Cells were incubated with dsRNA for 2.5 d.

extract_protocol: Nuclear run-on experiments were performed as described previously (Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., et al. (2016). Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nature Protocols, 11(8), 1455–1476. http://doi.org/10.1093/bioinformatics/btq033) with the following modification. The final concentration of non-biotinylated CTP was raised from 0.25uM to 25uM, and the final library clean up and size selection was accomplished using 1X AMPure XP (Beckman).

treatment_protocol: The method used was adapted from [Clift/Schuh Cell 2017]. HCT116 cells cultured in McCoy’s 5A medium were grown to approximately 70% confluency. Media was aspirated off, and the cells were washed with PBS. 2ml of trypsin per plate were used to harvest adherent cells, after which an equal volume of Opti-MEM was added to each plate to neutralize the trypsin. Cells were combined in a 50ml centrifuge tube and spun down at 2,000xg for 5 minutes, then washed in PBS and spun down again at 2,000xg for 5 minutes. Cells were counted using a hemocytometer and diluted to 25 million cells/mL. 100 µl reactions were prepared, and cells were re-suspended in Buffer R and anti-TAF1 C413 antibody. A pulse only control was prepared, which consisted of cells suspended only in Buffer R. Transfections were performed using the Neon Transfection Kit (1530V, 1ms width, 1 pulse). Transfected cells were then pipetted into 1 mL of Opti-MEM in a 35mm dish and incubated at 37˚C for 1 hour. The Opti-Mem media (containing some suspended cells) was then pipetted off and saved. 500 µl of PBS was added to the cells on the plates, which were then harvested and centrifuged at 6,000xg for 5 minutes. Supernatant was aspirated off, and cell nuclei were subsequently isolated. For D. melanogaster Schneider line 2 (S2) cells RNAi was performed as described [Clemens, 2000] using 20-40 µg dsRNA. Cells were incubated with dsRNA for 2.5 d.

value: wild type HCT116 cells

value: Colon cancer cells

value: electroporation pulse only


title: wild-type HCT116, control, Replicate 1


title: wild-type HCT116, TAF1 Trim-Away, Replicate 2

value: TAF1 Trim-Away


title: wild-type HCT116, TAF1 Trim-Away, Replicate 1


title: THP-1 cells, control A


title: P1_HC_GFP_rep1_ChIP_H3K27ac

city: Los Angeles

first: Neil

last: Segil

state: CA

address: 1425 san pablo st, BCC 503K

department: BCC

institute: University of Southern California

description:
CHIP_P1_HC_H3k27ac_rep1
processed data file: combination99ATAC999K27.bed_combinations_P1HC.bed.gz

data_processing:
Sequenced reads trimmed with Cutadapt (v1.18) -m 5 -e 0.1, then mapped to Gencode Mm10v11 genome using STAR (v2.5.4b) with parameters end-to-end and alignIntronMax=1.
Multi-mapped reads and duplicates were removed with SAMtools (v1.9) and Picard's MarkDuplicates, respectively. Blacklist regions for the mm10 genome from ENCODE and non-autosomal chromosomes were removed using bedtools intersect -v (v2.25.0).
Peak calling and differential analysis was performed with Chromstar (parameters: binsize=500bp, stepsize = 250bp, mode = full). A posterior probability cutoff of 0.001 was applied to each bin to yield a stringent set of peaks. Peaks with <= 2 RPKM were removed. Differential scores <= 1E-6 were considered non-differential and peak with > 0.999999 differential score were consider differential.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bed files generated from Chromstar; regions represent accessible and H3K27ac chromatin state calls.

organism: Mus musculus

source_name: Cochlea

growth_protocol: Cochleae were dissected from P1 mice and enzymatically dissociated with 0.25% trypsin. Cells were pelleted and resuspended in DMEM/F12 and then FACS purified to collect the Atoh1-GFP positive cells.

extract_protocol:
Cells were collected by FACS purification into cold PBS, and centrifuged 500 xg for 15 min. Cell pellet were resuspended with 50 ul transposition buffer consisting of 10mM Tris-HCL pH8.0, 5 mM MgCl2, 10% DMF, 0.2% NP40, and home-made transposase Tn5. Transposition was performed at 37 degree for 20 min. DNA was collected immediately after transposition using Qiagen Mini-elute kit.
Histone ChIP-seq protocol was developed by us based on μChIP-PCR protocol published previously (Stojanova et al., 2015) with additional Tn5 tagmentation step. Briefly, chromatin was cross-linked with 1% formaldehyde (Thermo Fisher) for 8 min, quenched with 125mM Glycine (Sigma) for 5 min at room temperature, sonicated using the microtip of a High Intensity Ultrasonic Processor (Sonics & Materials, Newtown, CT; amplitude 50, power 50) for 8 x 30 sec with 30 sec pause, tagmentated with Tn5 transposase for 30 min at 37°C, incubated with antibody complexed with Dynabeads Protein A (Thermo Fisher) overnight at 4°C, precipitated and washed three times on magnetic rack, and finally PCR amplified with primers matching Tn5 adapters.

tag: genotype/variation

tag: developmental stage

value: postnatal day 1

value: Cochlea


title: P1_HC_GFP_rep2_ChIP_H3K27ac

description:
CHIP_P1_HC_H3k27ac_rep2
processed data file: combination99ATAC999K27.bed_combinations_P1HC.bed.gz


title: GLUCOSE 2D

city: Southampton

first: Jeremy

middle: Paul

last: Blaydes

state: Hampshire

address: Southampton General Hospital, Tremona Road

department: Faculty of Medicine

institute: University of Southampton

data_processing:
basecalling - bcl2fastq
filtering, alignment - STAR aligner (v2.5.0a)
digital gene expression - Drop_Seq_tools_v1.0
Genome_build: hg19
Supplementary_files_format_and_content: Digital gene expression matrix format. (A row for each gene, and a column for each cell barcode and a UMI count matrix)

growth_protocol: MCF-7 cells were adapted to culture in 2D in DMEM containing either 25 mM glucose or 10 mM fructose, for 30 days.

extract_protocol:
Trypsin/ EDTA disaggregated cells
PCR on bead then Nextera XT

treatment_protocol: Adapted cell cultures were plated on standard cell culture plate and grown to c. 70% confluency. Media was replaced 24 hours prior to assay.

tag: protocol

value: 2D cultured

tag: sugar source

value: 25 mM glucose


title: DGM-11163_M3_sm (BMP4 study)

value: COPD smoker

value: small airway epithelium cells


title: DGM-00342_M6_sm (BMP4 study)

value: Nonsmoker


title: DGM-00342_M0_sm (BMP4 study)


title: DGM-11163_M12_sm (BMP4 study)


title: DGM-01774_M6_sm (BMP4 study)


title: DGM-00342_M12_sm (BMP4 study)


title: DGM-11163_M0_sm (BMP4 study)


title: DGM-01774_M0_sm (BMP4 study)


title: DGM-11007_M3_sm (BMP4 study)


title: DGM-01774_M12_sm (BMP4 study)


title: D14_BAGS_rep1_ATAC

description:
ATAC_D14_iHC_rep1
processed data file: combination99Custp.bed_combinations_iHC.bed.

data_processing:
Sequenced reads trimmed with Cutadapt (v1.18) -m 5 -e 0.1, then mapped to mm10 genome using bowtie2 (v2.2.6) -X2000 --mm --local.
Multi-mapped reads and duplicates were removed with SAMtools (v1.9) and Picard's MarkDuplicates, respectively. Blacklist regions for the mm10 genome from ENCODE and non-autosomal chromosomes were removed using bedtools intersect -v (v2.25.0).
Peak calling and differential analysis was performed with Chromstar (parameters: binsize=500bp, stepsize = 250bp, mode = full). A posterior probability cutoff of 0.01 was applied to each bin to yield a stringent set of peaks. Peaks with <= 2 RPKM were removed. Differential scores <= 1E-6 were considered non-differential and peak with > 0.999999 differential score were consider differential.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bed files generated from Chromstar; regions represent accessible chromatin state calls.

source_name: Fibroblast

growth_protocol: MEFs were infected with retroviral overexpression constructs for Six1, Atoh1, Pou4f3 and Gfi1. The cells were reprogrammed for 14 days and then FACS purified to collect the Atoh1-GFP positive cells.

extract_protocol:
Cells were collected by FACS purification into cold PBS, and centrifuged 500 xg for 15 min. Cell pellet were resuspended with 50 ul transposition buffer consisting of 10mM Tris-HCL pH8.0, 5 mM MgCl2, 10% DMF, 0.2% NP40, and home-made transposase Tn5. Transposition was performed at 37 degree for 20 min. DNA was collected immediately after transposition using Qiagen Mini-elute kit.
Library was prepared using primers from Illumina Nextera DNA Library Preparation Kit.

value: embryonic day 14

value: Fibroblast


title: D14_BAGS_rep2_ATAC

description:
ATAC_D14_iHC_rep2
processed data file: combination99Custp.bed_combinations_iHC.bed.


title: DGM-11007_M6_sm (BMP4 study)


title: D14_MEF_rep1_ATAC

description:
ATAC_D14_MEF_rep1
processed data file: combination99Custp.bed_combinations_MEF.bed

growth_protocol: MEFs were infected with a retroviral overexpression constructs for dsRed. The cells were cultured for 14 days to mimic the iHC culturing protocol and then FACS purified to collect the dsRed positive cells.


title: FRUCTOSE 2D

value: 10 mM fructose


title: DGM-11007_M0_sm (BMP4 study)


title: DGM-10800_M6_sm (BMP4 study)


title: P1_HC_GFP_rep1_ATAC

description:
ATAC_P1_HC_rep1
processed data file: combination99Custp.bed_combinations_P1HC.bed


title: P1_HC_GFP_rep2_ATAC

description:
ATAC_P1_HC_rep2
processed data file: combination99Custp.bed_combinations_P1HC.bed


title: DGM-01774_M3_sm (BMP4 study)


title: D14_MEF_rep2_ATAC

description:
ATAC_D14_MEF_rep2
processed data file: combination99Custp.bed_combinations_MEF.bed


title: P1_MC_rep2_RNA

data_processing:
Sequenced reads were mapped to Gencode Mm10v11 genome using STAR (v2.5.4b).
Transcript quantification was performed with RSEM.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.isoforms.results.tsv: Tab-delimited text files of transcript quantification were generated with RSEM.

molecule: polyA RNA

source_name: Skin

growth_protocol: Skin was dissected from P1 mice, epidermis was separated from dermis and enzymatically dissociated using Accutase. Cells were pelleted and resuspended in DMEM/F12 and then FACS purified to collect the Atoh1-GFP positive cells.

extract_protocol:
Cells were FACS purified and collected in RNA lysis buffer. Total RNA was extracted with Quick-RNA Microprep kit (Zymo Research).
Libraries were prepared using QIAseq FX Single Cell RNA Library Kit (Qiagen).

tag: genotype

value: post natal day 1

value: Skin


title: P1_MC_rep1_RNA

tag: tissue


title: P1_MC_rep3_RNA


title: DGM-10800_M3_sm (BMP4 study)


title: DGM-11007_M12_sm (BMP4 study)


title: P1_NonHC_rep1_RNA

growth_protocol: Cochleae were dissected from P1 mice and enzymatically dissociated with 0.25% trypsin. Cells were pelleted and resuspended in DMEM/F12 and then FACS purified to collect the Atoh1-GFP negative cells.


title: P1_NonHC_rep3_RNA


title: DGM-10800_M0_sm (BMP4 study)


title: DGM-11192_M3_sm (BMP4 study)


title: DGM-10800_M12_sm (BMP4 study)


title: DGM-11122_M6_sm (BMP4 study)


title: P1_HC_GFP_rep3_RNA


title: P1_HC_GFP_rep1_RNA


title: P1_NonHC_rep2_RNA


title: DGM-11122_M12_sm (BMP4 study)


title: CAD KO RiboFoot RFP C

city: Aurora

first: Matthew

last: Taliaferro

address: 12801 E 17th Ave, RC1 South Room 10403D

department: Biology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Adapters were trimmed from the 3' end of reads using cutadapt
Transcript abundances were calculated using salmon or kallisto against the mm10 or hg38 genomes
Gene abundances were calculated from transcript abundances using tximport
Reads were mapped to mouse genome (mm10 or hg38) using STAR
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: transcript abundances in txt format

source_name: CAD cell line

extract_protocol:
RNA extraction was performed with Qiagen or Zymo Microprep Kits
Illumina TruSeq

tag: cell compartment

value: whole cell

value: KO


title: CAD KO RiboFoot RFP B


title: DGM-10984_M0_sm (BMP4 study)

value: COPD Smoker (GOLD III)


title: CAD KO RiboFoot RFP A


title: DGM-11122_M0_sm (BMP4 study)


title: DGM-10984_M3_sm (BMP4 study)


title: DGM-11077_M6_sm (BMP4 study)


title: DGM-11122_M3_sm (BMP4 study)


title: CAD KO RiboFoot RNA B


title: CAD KO RiboFoot RNA C


title: P1_HC_GFP_rep2_RNA


title: CAD WT RiboFoot RFP C

value: WT


title: DGM-00342_M3_sm (BMP4 study)


title: CAD WT RiboFoot RFP B


title: CAD KO RiboFoot RNA A


title: CAD WT RiboFoot RFP A


title: CAD WT RiboFoot RNA C


title: CAD WT RiboFoot RNA B


title: DGM-11061_M3_sm (BMP4 study)


title: DGM-11077_M12_sm (BMP4 study)


title: DGM-11077_M0_sm (BMP4 study)


title: DGM-11077_M3_sm (BMP4 study)


title: DGM-10984_M12_sm (BMP4 study)


title: DGM-11061_M6_sm (BMP4 study)


title: DGM-10984_M6_sm (BMP4 study)


title: CAD KO Neurite A

value: neurite

value: FMR1 KO


title: DGM-01753_M3_sm (BMP4 study)


title: DGM-01753_M6_sm (BMP4 study)


title: DGM-01753_M12_sm (BMP4 study)


title: DGM-11061_M12_sm (BMP4 study)


title: CAD KO Soma B

value: soma


title: CAD KO Soma A


title: CAD KO Neurite B


title: DGM-01753_M0_sm (BMP4 study)


title: DGM-11061_M0_sm (BMP4 study)


title: CAD KO Neurite C


title: CAD WT Neurite C


title: DGM-10475_M6_sm (BMP4 study)


title: DGM-10475_M3_sm (BMP4 study)


title: CAD WT Neurite B


title: DGM-01275_M6_sm (BMP4 study)


title: DGM-10475_M0_sm (BMP4 study)


title: CAD WT RiboFoot RNA A


title: CAD WT Neurite A


title: DGM-10475_M12_sm (BMP4 study)


title: CAD WT Soma C


title: CAD WT Soma A


title: GM59A_LPS

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

hyb_protocol: For transcriptional profiling using the Affymetrix GeneChip Human Transcriptome 2.0 Arrays, 1 ng of total RNA was processed using the WT Pico Kit. Fragmentation, hybridization, and scanning were all performed according to Affymetrix manufacturer’s instructions.

scan_protocol: According to Affymetrix manufacturer’s instructions

data_processing: libaffy-2.1.5/bin/iron --norm-quantile --median-polish using GPL17586 annotation HTA-2_0.na36.hg19

source_name: Tracheal aspirate cells

growth_protocol: Tracheal aspirate cells were collected from intubated preterm infants as detailed below. After instillation of 0.5 ml of normal saline into the endotracheal tube, a suction catheter was introduced into the endotracheal tube and tracheal secretions were aspirated into a sterile mucus trap. The suction catheter was subsequently rinsed with an additional 1.5 ml of sterile saline to clear any remaining aspirate from the catheter into the mucus trap. Cells were collected by centrifugation and resuspended in DMEM with 10% fetal bovine serum, penicillin, and streptomycin. Equal aliquots of resuspended cells were divided between two separate tissue culture treated plates and incubated at 37 ˚C in a humidified environment of 95% air and 5% CO2 to allow macrophage attachment. After 30 min, nonadherent cells were removed by gentle washing and fresh cell culture media was applied.

treatment_protocol: Lipopolysaccharide from E. coli (strain 055:B5, gel purified, Sigma-Aldrich L2637; 250 ng/ml) was added to one of the plates and both were incubated for 4 h at 37 ˚C.

tag: title

tag: nicu

value: UCSD

tag: collection place

value: GM

value: LPS

tag: bpd

value: Yes

tag: severity

value: Moderate

tag: gender

value: Male

tag: delivery type

value: Cesarean


title: GM50A_CTRL

label_protocol: According to Affymetrix manufacturer’s instructions

tag: treatment

value: CTRL

value: Severe

value: Female


title: GM75A_CTRL

extract_protocol: According to Affymetrix manufacturer’s instructions


title: DGM-10503_M6_sm (BMP4 study)

tag: smoking status

value: Nonsmoker

tag: cell type

value: small airway epithelium cells

tag: time of serial bronchoscopy (month)


title: DGM-10503_M3_sm (BMP4 study)


title: DGM-01275_M12_sm (BMP4 study)

value: COPD smoker


title: DGM-10503_M12_sm (BMP4 study)


title: DGM-01275_M0_sm (BMP4 study)


title: GM41C_LPS

value: Mild


title: DGM-10503_M0_sm (BMP4 study)


title: DGM-10500_M6_sm (BMP4 study)


title: DGM-01275_M3_sm (BMP4 study)


title: DGM-10500_M3_sm (BMP4 study)


title: CAD WT Soma B

value: WT


title: GM75C_LPS


title: GM78F_LPS


title: GM83C_LPS

value: Vaginal


title: GMR09D_CTRL

value: RADY

value: GMR


title: GM78F_CTRL

value: UCSD

value: GM


title: GM62C_LPS

value: LPS

value: Yes


title: DGM-10500_M12_sm (BMP4 study)


title: DGM-10500_M0_sm (BMP4 study)


title: DGM-10727_M6_sm (BMP4 study)


title: DGM-10727_M3_sm (BMP4 study)


title: GM08G_LPS

value: Male


title: DGM-10565_M3_sm (BMP4 study)


title: GM65A_LPS

value: No


title: DGM-10565_M12_sm (BMP4 study)


title: M14-CTRL

value: CTRL


title: GM83E_LPS

value: Severe


title: DGM-10727_M0_sm (BMP4 study)


title: GM80A_LPS

value: Female

value: Cesarean


title: GM59A_CTRL

value: Moderate


title: GM17A_LPS


title: GM42A_CTRL


title: GM42C_CTRL


title: DGM-10401_M6_sm (BMP4 study)

value: COPD smoker

value: small airway epithelium cells


title: 2722_CTRL

value: VANDERBILT

value: VAND


title: GM30A_LPS

value: Mild


title: GM62B_CTRL


title: DGM-10401_M12_sm (BMP4 study)


title: DGM-10565_M6_sm (BMP4 study)

value: Nonsmoker


title: DGM-10401_M3_sm (BMP4 study)


title: GM74A_CTRL

value: UCSD


title: M10_CTRL


title: DGM-10565_M0_sm (BMP4 study)


title: DGM-10568_M3_sm (BMP4 study)


title: DGM-10727_M12_sm (BMP4 study)


title: DGM-10568_M0_sm (BMP4 study)


title: DGM-10568_M12_sm (BMP4 study)


title: DGM-10447_M3_sm (BMP4 study)


title: DGM-10447_M0_sm (BMP4 study)


title: DGM-10447_M12_sm (BMP4 study)


title: DGM-10447_M6_sm (BMP4 study)


title: DGM-10401_M0_sm (BMP4 study)


title: GM30A_CTRL

value: GM


title: GM30B_LPS

value: LPS


title: GM78C_LPS

value: Yes


title: DGM-10549_M0_sm (BMP4 study)


title: GM39A_CTRL

value: Male


title: DGM-10549_M3_sm (BMP4 study)


title: DGM-10549_M12_sm (BMP4 study)


title: DGM-10568_M6_sm (BMP4 study)


title: GMR02C_LPS

value: RADY

value: GMR


title: M18_CTRL

value: CTRL


title: CAD KO Soma C

value: soma

value: FMR1 KO


title: DGM-10549_M6_sm (BMP4 study)


title: GMR02G_CTRL

value: Severe

value: Cesarean


title: GM22A_LPS


title: GM14C_CTRL

value: Female


title: GMR02I_LPS


title: GM93A_LPS


title: GM55A_LPS


title: M07_CTRL


title: GM70C_CTRL

value: Moderate


title: DGM-10194_M6_sm (BMP4 study)

value: small airway epithelium cells


title: 2722_LPS

value: VANDERBILT

value: VAND

value: Vaginal


title: 2721_LPS


title: DGM-10194_M12_sm (BMP4 study)

value: Nonsmoker


title: DGM-10194_M3_sm (BMP4 study)


title: GM19B_CTRL

value: UCSD

value: GM

value: No


title: GM90G_LPS

value: LPS

value: Yes


title: DGM-10340_M6_sm (BMP4 study)

value: COPD smoker


title: DGM-10340_M12_sm (BMP4 study)


title: GM89F_LPS


title: DGM-10286_M3_sm (BMP4 study)


title: GM94A_LPS


title: GM88A_CTRL

value: CTRL


title: DGM-10194_M0_sm (BMP4 study)


title: DGM-10286_M6_sm (BMP4 study)


title: GM90G_CTRL


title: DGM-10286_M0_sm (BMP4 study)


title: DGM-10286_M12_sm (BMP4 study)


title: 2721_CTRL

value: Male


title: DGM-10340_M3_sm (BMP4 study)


title: DGM-10270_M6_sm (BMP4 study)


title: DGM-10270_M0_sm (BMP4 study)


title: DGM-10270_M12_sm (BMP4 study)


title: GM83F_CTRL

value: Severe


title: DGM-10406_M12_sm (BMP4 study)


title: DGM-10406_M6_sm (BMP4 study)


title: DGM-10406_M3_sm (BMP4 study)


title: DGM-10406_M0_sm (BMP4 study)


title: GM80B_LPS

value: Cesarean


title: GMR09C_LPS

value: RADY

value: GMR

value: Mild


title: DGM-10340_M0_sm (BMP4 study)

value: small airway epithelium cells


title: DGM-10322_M6_sm (BMP4 study)


title: DGM-10270_M3_sm (BMP4 study)


title: VU03_CTRL

value: VANDERBILT

value: VAND


title: GM80C_LPS

value: Female


title: DGM-10322_M3_sm (BMP4 study)

value: Nonsmoker


title: DGM-10322_M12_sm (BMP4 study)


title: GM42B_CTRL

value: UCSD

value: GM

value: Vaginal


title: M18_LPS

value: LPS

value: Yes

value: Moderate


title: DGM-10343_M6_sm (BMP4 study)


title: DGM-10322_M0_sm (BMP4 study)


title: GMR02A_CTRL

value: CTRL

value: Male


title: GM93B_CTRL

value: Severe

value: Cesarean


title: DGM-10343_M12_sm (BMP4 study)


title: DGM-10343_M3_sm (BMP4 study)


title: DGM-10343_M0_sm (BMP4 study)


title: GM08G_CTRL


title: DGM-10380_M6_sm (BMP4 study)


title: GM22J_LPS


title: GM58B_CTRL


title: GMR09B_LPS

value: RADY

value: GMR


title: GM90E_LPS


title: GM84B_LPS


title: GM16B_CTRL


title: GM80B_CTRL


title: DGM-10380_M0_sm (BMP4 study)

value: small airway epithelium cells


title: DGM-10380_M12_sm (BMP4 study)


title: GM62B_LPS


title: GM41D_CTRL

value: Mild


title: GM94A_CTRL


title: GM30D_LPS


title: GMR02I_CTRL


title: GM70F_CTRL


title: GM80A_CTRL


title: DGM-10383_M6_sm (BMP4 study)


title: DGM-10383_M12_sm (BMP4 study)


title: GM03B_CTRL


title: GM70C_LPS


title: DGM-10383_M0_sm (BMP4 study)


title: DGM-10383_M3_sm (BMP4 study)


title: GM26A_CTRL


title: DGM-10284_M3_sm (BMP4 study)


title: DGM-10284_M0_sm (BMP4 study)


title: DGM-10380_M3_sm (BMP4 study)


title: DGM-10284_M12_sm (BMP4 study)


title: DGM-10284_M6_sm (BMP4 study)


title: GMR02B_LPS


title: DGM-10335_M6_sm (BMP4 study)

value: COPD smoker


title: DGM-10335_M3_sm (BMP4 study)


title: DGM-10335_M0_sm (BMP4 study)


title: VU02_CTRL

value: VANDERBILT

value: VAND


title: GM70E_CTRL

value: UCSD


title: M01_CTRL


title: GMR06A_CTRL

value: No

value: Female


title: GM63A_LPS

value: GM

value: LPS

value: Vaginal


title: DGM-10335_M12_sm (BMP4 study)


title: GM08B_CTRL

value: CTRL

value: Yes


title: GM63A_CTRL


title: GM02I_CTRL

value: Male


title: GM08D_LPS

value: Severe

value: Cesarean


title: DGM-10288_M6_sm (BMP4 study)

value: Nonsmoker


title: DGM-00061_M12_sm (BMP4 study)

value: small airway epithelium cells


title: DGM-00061_M3_sm (BMP4 study)


title: GM32K_CTRL


title: GM26A_LPS

value: Mild


title: DGM-00061_M0_sm (BMP4 study)

value: COPD smoker


title: DGM-10288_M12_sm (BMP4 study)


title: DGM-10288_M0_sm (BMP4 study)


title: DGM-10288_M3_sm (BMP4 study)


title: DGM-10283_M6_sm (BMP4 study)


title: DGM-10283_M3_sm (BMP4 study)


title: DGM-10283_M12_sm (BMP4 study)


title: DGM-10261_M3_sm (BMP4 study)


title: M01_LPS


title: GM85A_CTRL


title: DGM-10283_M0_sm (BMP4 study)


title: DGM-10261_M12_sm (BMP4 study)


title: M10_LPS


title: Day3_3

city: Serdang

first: Boo

last: Sook Yee

state: Selangor

address: Universiti Putra Malaysia

department: Institute of Bioscience

country: Malaysia

institute: Universiti Putra Malaysia

data_processing:
Fastq files were generated from BCL files using the bcl2fastq software
the fastq files were loaded inside the CLC Genomics Workbench for quality and adapter trimming
the filtered fastq files were proceeded for alignment to chicken genome using CLC Genomics Workbench
The differential expression analysis was conducted to find out the DE genes
Genome_build: Galgal4_ensembl
Supplementary_files_format_and_content: Read counts and expression value

organism: Gallus gallus

source_name: Day3_CD3-, 28.4+ IEL-NK cells isolated from duodenum

growth_protocol: specific-pathogen-free (SPF) embryonated chicken eggs were obtained from Veterinary Research Institute, Ipoh, Perak and hatched in our laboratory under sterile conditions. The chicken was transferred to the Biosafety level-2 facility at our animal house where they were fed with pelleted feed and supplied with water ad libitum.

extract_protocol:
Total RNA was extracted from enriched IEL-NK cells using the trizol reagent. The mRNA was captured from total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module kit
The mRNA sample was proceeded to the library prep using the ScriptSeq V2 RNA-Seq library prep kit

treatment_protocol: infected by vvIBDV (UPM0081) at a dosage of 103 EID50/0.1ml

tag: sample group

value: chicken infected by vvIBDV for 3 days

tag: virus strain

value: Duodenum

value: CD3-, 28.4+ IEL-NK cells


title: DGM-10261_M0_sm (BMP4 study)


title: GM22J_CTRL

value: UCSD


title: Day3_2


title: Control_3

source_name: control_CD3-, 28.4+ IEL-NK cells isolated from duodenum

value: uninfected chicken


title: Day1_3

source_name: Day1_CD3-, 28.4+ IEL-NK cells isolated from duodenum

value: chicken infected by vvIBDV for 1 day


title: Day3_1


title: DGM-10161_M6_sm (BMP4 study)


title: Day1_1


title: GM83D_LPS

value: GM

value: LPS


title: GM36A_LPS

value: No

value: Female


title: DGM-10161_M3_sm (BMP4 study)


title: Control_2


title: GMR10B_LPS

value: RADY

value: GMR

value: Yes

value: Vaginal


title: DGM-10254_M6_sm (BMP4 study)

value: Nonsmoker

value: small airway epithelium cells


title: M14_LPS

value: Severe

value: Male


title: Control_1

value: Duodenum


title: DGM-10261_M6_sm (BMP4 study)


title: DGM-10161_M0_sm (BMP4 study)


title: GM93A_CTRL

value: CTRL

value: Cesarean


title: Day1_2

value: CD3-, 28.4+ IEL-NK cells


title: DGM-10254_M3_sm (BMP4 study)


title: DGM-10254_M12_sm (BMP4 study)


title: DGM-10161_M12_sm (BMP4 study)


title: GM78C_CTRL

value: UCSD


title: GM19G_CTRL

value: GM


title: DGM-10254_M0_sm (BMP4 study)


title: Patient A13 week 2-3

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Affymetrix Human Gene 2.0 ST Array (Cat No. 902112); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip® fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software AGCC 4.0.0)

data_processing:
Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Genomics Suite, v.6.6): RMA (background correction, quantile normalization across all chips in the experiment, log2  transformation, median polish summarization)

label: Biotin

source_name: Patient A13 week 2-3

label_protocol: 500ng for Affymetrix WT PLUS Reagent Kit P/N 703147 Rev5, (Cat No. 902280)

extract_protocol: miRNeasy Mini Kit inclusive DNase digest (Qiagen; Hilden, Germany; Cat No. 217004)

treatment_protocol: Topical application of dithranol in increasing concentrations (Clinical Trials.gov no. NCT02752672)

tag: time point

value: psoriasis lesion at end of treatment


title: GM08I_CTRL


title: GM76C_LPS

value: LPS


title: GM41C_CTRL

value: Mild

value: Female


title: GM08I_LPS


title: DGM-10131_M0_sm (BMP4 study)

value: COPD smoker


title: GM90C_LPS

value: Yes


title: GM46D_LPS

value: Vaginal


title: DGM-10131_M3_sm (BMP4 study)


title: Patient A12 week 2-3

source_name: Patient A12 week 2-3


title: Patient A13 non-lesional

source_name: Patient A13 non-lesional

value: non-lesional skin at baseline


title: Patient A13 day 6

source_name: Patient A13 day 6

value: psoriasis lesion after 6 days of dithranol treatment


title: DGM-10159_M6_sm (BMP4 study)

value: Nonsmoker

value: small airway epithelium cells


title: DGM-10131_M12_sm (BMP4 study)


title: DGM-10131_M6_sm (BMP4 study)


title: Patient A12 day 6

source_name: Patient A12 day 6


title: DGM-10159_M12_sm (BMP4 study)


title: Patient A13 baseline

source_name: Patient A13 baseline

value: psoriasis lesion at baseline


title: M13_CTRL

value: CTRL

value: Severe


title: Patient A12 baseline

source_name: Patient A12 baseline


title: DGM-10159_M3_sm (BMP4 study)

source_name: small airway epithelium cells


title: GM46D_CTRL


title: Patient A12 non-lesional

source_name: Patient A12 non-lesional


title: GM21B_LPS


title: Patient A10 week 2-3

source_name: Patient A10 week 2-3


title: DGM-10159_M0_sm (BMP4 study)


title: DGM-00061_M6_sm (BMP4 study)


title: Patient A10 day 6

source_name: Patient A10 day 6


title: Ps68

city: MADRID

first: María

middle: C

last: Ovejero-Benito

state: MADRID

address: C DIEGO DE LEÓN 62

country: Spain

institute: Instituto de Investigación Sanitaria la Princesa (IIS-IP)

description: psoriasis peripheral blood sample

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

scan_protocol: Arrays were imaged using Illumina iScanSQ platform

data_processing:
GenomeStudio Methylation Software Module (v 1.9.0, Illumina).
Unmethylated and methylated signal intensities in supplementary file

label: Cy5 and Cy3

source_name: Psoriasis 68

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from peripheral blood samples using the MagNa Pure® System (Roche Applied Science)

value: Male

value: peripheral blood

tag: disease state

value: psoriasis

tag: response

value: ER

tag: age

tag: age at initiation

tag: biological drug

value: Adalimumab


title: Ps69

description: psoriasis peripheral blood sample

source_name: Psoriasis 69

tag: tissue


title: DGM-10123_M6_sm (BMP4 study)


title: GMR11A_CTRL

source_name: Tracheal aspirate cells

tag: title

tag: nicu

value: RADY

tag: collection place

value: GMR

tag: bpd

value: Mild

value: Cesarean


title: GM54B_LPS

value: UCSD

value: GM

tag: treatment

value: LPS

value: Yes

tag: severity

tag: gender

tag: delivery type


title: Ps70

description: psoriasis peripheral blood sample

source_name: Psoriasis 70


title: DGM-10123_M0_sm (BMP4 study)

tag: smoking status

value: Nonsmoker

tag: cell type

value: small airway epithelium cells

tag: time of serial bronchoscopy (month)


title: Patient A10 baseline

source_name: Patient A10 baseline

tag: time point

value: psoriasis lesion at baseline


title: Patient A9 week 2-3

source_name: Patient A9 week 2-3

value: psoriasis lesion at end of treatment


title: DGM-10123_M3_sm (BMP4 study)


title: DGM-10123_M12_sm (BMP4 study)


title: GM81A_LPS

value: Severe

value: Male


title: Ps65

description: psoriasis peripheral blood sample

source_name: Psoriasis 65

value: Female

value: peripheral blood

tag: disease state

value: psoriasis

tag: response


title: Ps67

description: psoriasis peripheral blood sample

source_name: Psoriasis 67

value: ER

tag: age

tag: age at initiation

value: Adalimumab


title: Ps64

description: psoriasis peripheral blood sample

source_name: Psoriasis 64

tag: tissue

value: PR

tag: biological drug

value: Etanercept


title: GM84A_CTRL

tag: title

tag: nicu

value: UCSD

value: CTRL

value: Cesarean


title: Patient A9 day 6

source_name: Patient A9 day 6

value: psoriasis lesion after 6 days of dithranol treatment


title: GM55A_CTRL

tag: collection place

value: GM

tag: bpd

value: Yes


title: GM82C_CTRL

tag: treatment

tag: severity


title: Ps66

description: psoriasis peripheral blood sample

source_name: Psoriasis 66

tag: gender


title: DGM-10157_M3_sm (BMP4 study)

tag: smoking status

value: COPD smoker

value: small airway epithelium cells


title: Patient A7 week 2-3

source_name: Patient A7 week 2-3

value: psoriasis lesion at end of treatment


title: Patient A7 non-lesional

source_name: Patient A7 non-lesional

value: non-lesional skin at baseline


title: Ps62

description: psoriasis peripheral blood sample

source_name: Psoriasis 62

value: Male

value: Infliximab


title: Ps61

description: psoriasis peripheral blood sample

source_name: Psoriasis 61

value: peripheral blood

value: psoriasis


title: DGM-10157_M12_sm (BMP4 study)

source_name: small airway epithelium cells

tag: cell type


title: Ps63

description: psoriasis peripheral blood sample

source_name: Psoriasis 63

value: Female

value: ER


title: GM78D_LPS

value: LPS

value: Severe

tag: delivery type


title: Patient A7 day 6

source_name: Patient A7 day 6

tag: time point


title: Patient A7 baseline

source_name: Patient A7 baseline

value: psoriasis lesion at baseline


title: DGM-10157_M0_sm (BMP4 study)

tag: time of serial bronchoscopy (month)


title: DGM-10157_M6_sm (BMP4 study)


title: Ps59

description: psoriasis peripheral blood sample

source_name: Psoriasis 59

tag: disease state

tag: response

value: PR

value: Etanercept


title: Patient A9 baseline

source_name: Patient A9 baseline


title: GM22B_LPS

source_name: Tracheal aspirate cells

value: UCSD

value: GM

value: Cesarean


title: GM02I_LPS

value: Yes

value: Mild


title: Ps57

description: psoriasis peripheral blood sample

source_name: Psoriasis 57

tag: age

tag: age at initiation


title: Ps60

description: psoriasis peripheral blood sample

source_name: Psoriasis 60

tag: tissue

tag: biological drug

value: Adalimumab


title: Ps58

description: psoriasis peripheral blood sample

source_name: Psoriasis 58


title: DGM-10132_M12_sm (BMP4 study)

value: COPD smoker

value: small airway epithelium cells


title: M07_LPS

tag: title

tag: nicu

value: Male


title: DGM-10132_M3_sm (BMP4 study)


title: DGM-10132_M0_sm (BMP4 study)


title: Ps55

description: psoriasis peripheral blood sample

source_name: Psoriasis 55

value: peripheral blood

value: psoriasis


title: Ps56

description: psoriasis peripheral blood sample

source_name: Psoriasis 56

value: Female


title: Patient A6 week 2-3

source_name: Patient A6 week 2-3

value: psoriasis lesion at end of treatment


title: 786-O-sh-YB1 rep2

city: wuhan

first: Hailong

last: Ruan

state: hubei

address: 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, China

institute: wuhan union hospital

description: processed data file: fpkm_anno.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads. Clean reads for each sample were retained for subsequent analyses.
The clean reads were mapped to the human genome (GRCh38) using HISAT2. FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count.
Differential expression analysis was performed using the DESeq (2012) R package. P value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression.
Hierarchical cluster analysis of differentially expressed genes (DEGs) was performed to demonstrate the expression pattern of genes in different groups and samples. GO enrichment and KEGG pathway enrichment analysis of DEGs were performed respectively using R based on the hypergeometric distribution.
Genome_build: GRCh38 p7
Supplementary_files_format_and_content: fpkm_anno.txt: Tab-delimited text file includes FPKM values for each Sample.

extract_protocol:
Cell lysates were used to extract RNA using Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: ccRCC-derived renal cancer cells

tag: passages

tag: shRNA


title: 786-O-sh-YB1 rep3

description: processed data file: fpkm_anno.txt


title: GM90C_CTRL

tag: collection place

tag: treatment

value: CTRL

tag: bpd

tag: severity

value: Severe

tag: gender


title: Patient A6 baseline

source_name: Patient A6 baseline

tag: time point

value: psoriasis lesion at baseline


title: Patient A4 week 2-3

source_name: Patient A4 week 2-3


title: GM83A_CTRL

value: UCSD

tag: delivery type

value: Vaginal


title: Ps53

description: psoriasis peripheral blood sample

source_name: Psoriasis 53

tag: disease state

tag: response

value: ER

value: Etanercept


title: 786-O-sh-vector rep2

description: processed data file: fpkm_anno.txt

tag: cell type

value: scrambled


title: 786-O-sh-vector rep3

description: processed data file: fpkm_anno.txt


title: 786-O-sh-YB1 rep1

description: processed data file: fpkm_anno.txt


title: GM14B_CTRL

value: GM

value: Yes

value: Mild

value: Cesarean


title: GM80C_CTRL


title: GM81C_LPS

value: LPS

value: Male


title: Ps54

description: psoriasis peripheral blood sample

source_name: Psoriasis 54

value: Female

tag: tissue

value: peripheral blood

value: psoriasis

tag: age

tag: age at initiation

value: Adalimumab


title: 786-O-sh-vector rep1

description: processed data file: fpkm_anno.txt

value: ccRCC-derived renal cancer cells


title: GM31A_LPS

tag: title

tag: nicu

value: No


title: Patient A6 day 6

source_name: Patient A6 day 6

value: psoriasis lesion after 6 days of dithranol treatment


title: MEC1_Idel_10uM_48h_192

city: Québec

first: Chantal

last: Guillemette

state: Québec

address: 2705 blvd Laurier

department: Faculty of Pharmacy

country: Canada

institute: Laval University

description: rRNA-depleted RNA

data_processing:
Quality trimming with trimmomatic min quality = 30; min length = 32
Alignment with HISAT2 v2.1 to the hg38 human genome
Assembly and generation of count matrices with StringTie v1.3.4
Between-sample normalization and differential expression analysis with  edgeR v3.22.5
Genome_build: hg38
Supplementary_files_format_and_content: Raw read counts matrices for all samples.

source_name: Lymphoid

extract_protocol:
RNA was extracted from 5 million cells from each sample using QIAGEN RNeasy Mini Kit with DNAse I. 1 ug total RNA from each sample was used to prepare sequencing librairies with Illumina HiSeq RNA Sample Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were treated with 50uM fludarabine, 5uM ibrutinib, 10uM idelalslib or DMSO control, in triplicate, prior to extraction.

tag: cell line


title: Patient A4 baseline

source_name: Patient A4 baseline

value: psoriasis lesion at baseline


title: Patient A4 day 6

source_name: Patient A4 day 6


title: MEC1_Idel_10uM_48h_191

description: rRNA-depleted RNA


title: Patient A4 non-lesional

source_name: Patient A4 non-lesional

value: non-lesional skin at baseline


title: Patient A3 week 2-3

source_name: Patient A3 week 2-3

value: psoriasis lesion at end of treatment


title: DGM-10132_M6_sm (BMP4 study)

source_name: small airway epithelium cells

tag: smoking status

value: COPD smoker

value: small airway epithelium cells

tag: time of serial bronchoscopy (month)


title: GM19B_LPS

source_name: Tracheal aspirate cells

value: UCSD

tag: collection place

value: GM

tag: treatment


title: GM32H_CTRL

value: CTRL

tag: bpd

value: Yes

tag: severity

value: Severe

value: Cesarean


title: Patient A3 day 6

source_name: Patient A3 day 6

tag: time point


title: MEC1_Idel_10uM_48h_190

description: rRNA-depleted RNA


title: Ps49

description: psoriasis peripheral blood sample

source_name: Psoriasis 49

tag: gender

value: Male

value: peripheral blood

value: PR

tag: biological drug

value: Etanercept


title: GM 81A_CTRL

description: GM 81A_CTRL

value: GM 81A_CTRL

tag: delivery type


title: Ps50

description: psoriasis peripheral blood sample

source_name: Psoriasis 50

tag: disease state

value: psoriasis

tag: response

value: ER

value: Infliximab


title: MEC1_Ibru_5uM_48h_186

description: rRNA-depleted RNA


title: Ps52

description: psoriasis peripheral blood sample

source_name: Psoriasis 52

value: Female

tag: tissue

tag: age

value: Adalimumab


title: MEC1_Ibru_5uM_48h_185

description: rRNA-depleted RNA


title: Ps51

description: psoriasis peripheral blood sample

source_name: Psoriasis 51

tag: age at initiation


title: MEC1_Ibru_5uM_48h_184

description: rRNA-depleted RNA


title: MEC1_Flud_50uM_48h_48

description: rRNA-depleted RNA


title: GM83B_CTRL

tag: title

tag: nicu

value: Vaginal


title: Patient A3 non-lesional

source_name: Patient A3 non-lesional

value: non-lesional skin at baseline


title: GM30B_CTRL

value: UCSD

value: GM

value: Mild


title: Patient A2 day 6

source_name: Patient A2 day 6

value: psoriasis lesion after 6 days of dithranol treatment


title: GM78B_LPS

value: LPS

value: Yes

value: Severe

value: Cesarean


title: Patient A2 baseline

source_name: Patient A2 baseline

value: psoriasis lesion at baseline


title: Ps47

description: psoriasis peripheral blood sample

source_name: Psoriasis 47

value: Male

value: peripheral blood


title: Ps46

description: psoriasis peripheral blood sample

source_name: Psoriasis 46

value: psoriasis

value: ER


title: Patient A2 non-lesional

source_name: Patient A2 non-lesional


title: GM90E_CTRL

value: CTRL

value: Female


title: MEC1_Flud_50uM_48h_47

description: rRNA-depleted RNA

source_name: Lymphoid

tag: cell line


title: GM78E_LPS


title: MEC1_Flud_50uM_48h_46

description: rRNA-depleted RNA


title: Patient A2 week 2-3

source_name: Patient A2 week 2-3

value: psoriasis lesion at end of treatment


title: Patient A1 week 2-3

source_name: Patient A1 week 2-3


title: Ps44

description: psoriasis peripheral blood sample

source_name: Psoriasis 44

value: Etanercept


title: MEC1_DMSO_CTRL_48h_39

description: rRNA-depleted RNA

value: DMSO


title: Ps43

description: psoriasis peripheral blood sample

source_name: Psoriasis 43

value: PR

value: Infliximab


title: MEC1_DMSO_CTRL_48h_38

description: rRNA-depleted RNA


title: F3-8

city: London

first: Kelly

middle: Joan

last: Baines

state: Ontario

address: 1151 Richmond St

department: Anatomy and Cell Biology

institute: The University of Western Ontario

data_processing:
Base calling was done using bcl2fastq v2.17
Using CLC Genomics Workbench v10.1.2, reads were mapped to Rnor 6.0.91.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench v10.1.2.
Genome_build: Rn6 NCBI: Rnor_6.0 GenBank Assembly Accession: GCA_000001895.4
Supplementary_files_format_and_content: counts, RPKM, TPM, CPM

organism: Rattus norvegicus

source_name: Pregnant Uterus Tissue

extract_protocol:
Whole implantation sites (including uterus, placenta, and developing embryo) were homogenized and RNA was extracted from tissues using a Trizol-Rneasy hybrid protocol.
RNA libraries were prepared using the Epicentre ScriptSeq v2 RNA-seq library prep kit.

treatment_protocol: Pregnant female SD rats were injected intraperitoneally with PolyI:C or saline at GD 8.5 and sacrificed 6 h later.

tag: agent

tag: strain

value: Sprague-Dawley

value: Implantation Site

tag: developmental stage

value: Gestational Day 8.5


title: F3-7


title: GM42A_LPS

source_name: Tracheal aspirate cells

value: UCSD

tag: collection place

value: GM

tag: treatment

value: LPS

tag: bpd

value: Yes

value: Severe

value: Vaginal


title: Patient A1 day 6

source_name: Patient A1 day 6

tag: time point

value: psoriasis lesion after 6 days of dithranol treatment


title: Ps45

description: psoriasis peripheral blood sample

source_name: Psoriasis 45

tag: gender

value: peripheral blood

value: psoriasis

value: ER

tag: biological drug

value: Adalimumab


title: GM42B_LPS

tag: severity

value: Male

tag: delivery type


title: F3-5

tag: tissue


title: JVM2_Idel_10uM_240

description: rRNA-depleted RNA


title: GM41D_LPS

value: Mild

value: Female

value: Cesarean


title: Ps42

description: psoriasis peripheral blood sample

source_name: Psoriasis 42

tag: disease state

tag: response

tag: age

value: Etanercept


title: GM78A_CTRL

tag: title

tag: nicu

value: CTRL


title: Patient A1 baseline

source_name: Patient A1 baseline

value: psoriasis lesion at baseline


title: JVM2_Idel_10uM_239

description: rRNA-depleted RNA

tag: cell line


title: Ps37

description: psoriasis peripheral blood sample

source_name: Psoriasis 37

value: PR

tag: age at initiation


title: Ps40

description: psoriasis peripheral blood sample

source_name: Psoriasis 40


title: JVM2_Idel_10uM_238

description: rRNA-depleted RNA


title: GMR08A_CTRL

value: RADY

value: GMR


title: F2-16

tag: agent

value: saline

tag: strain

value: Sprague-Dawley

value: Implantation Site

tag: developmental stage

value: Gestational Day 8.5


title: Ps48

description: psoriasis peripheral blood sample

source_name: Psoriasis 48

value: peripheral blood

value: psoriasis

value: infliximab


title: F3-2


title: GM32K_LPS

value: UCSD

tag: collection place

value: GM

tag: treatment

value: LPS

tag: bpd

value: Yes

value: Severe

value: Male


title: Ps36

description: psoriasis peripheral blood sample

source_name: Psoriasis 36

tag: gender

tag: biological drug

value: Infliximab


title: Ps34

description: psoriasis peripheral blood sample

source_name: Psoriasis 34

value: ER

value: Adalimumab


title: GM22A_CTRL

value: CTRL

tag: severity

tag: delivery type

value: Cesarean


title: JVM2_Ibru_5uM_233

description: rRNA-depleted RNA


title: GM87A_CTRL

value: No


title: JVM2_Ibru_5uM_232

description: rRNA-depleted RNA


title: JVM2_Ibru_5uM_234

description: rRNA-depleted RNA


title: F3-10

value: saline

value: Sprague-Dawley

tag: tissue

value: Implantation Site


title: JVM2_Flud_50uM_96

description: rRNA-depleted RNA


title: GM76B_LPS

value: Female

value: Vaginal


title: Ps33

description: psoriasis peripheral blood sample

source_name: Psoriasis 33

value: peripheral blood

tag: disease state

value: psoriasis

tag: response

value: PR


title: GM75C_CTRL

tag: title

value: UCSD

value: GM

value: Yes


title: GM78A_LPS

tag: nicu

value: LPS

value: Severe

value: Male


title: JVM2_Flud_50uM_95

description: rRNA-depleted RNA

source_name: Lymphoid

tag: cell line


title: normal 2

city: Wuhan

first: Xiao

last: He

state: Hu Bei

address: Donghu Road 169

department: Zhongnan Hospital

institute: Wuhan University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: normal prostate

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

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

value: normal


title: JVM2_Flud_50uM_94

description: rRNA-depleted RNA


title: normal 3


title: Ps41

description: psoriasis peripheral blood sample

source_name: Psoriasis 41

value: ER

tag: age

tag: age at initiation

value: Infliximab


title: GM93B_LPS

value: Cesarean


title: normal 1


title: Ps39

description: psoriasis peripheral blood sample

source_name: Psoriasis 39

value: Adalimumab


title: Ps31

description: psoriasis peripheral blood sample

source_name: Psoriasis 31

value: Etanercept


title: Ps30

description: psoriasis peripheral blood sample

source_name: Psoriasis 30


title: JVM2_CTRL_DMSO_87

description: rRNA-depleted RNA

value: DMSO


title: benign prostatic hyperplasia 5

source_name: hyperplasia prostate

value: BPH


title: JVM2_CTRL_DMSO_86

description: rRNA-depleted RNA


title: benign prostatic hyperplasia 4


title: GM16B_LPS

source_name: Tracheal aspirate cells

value: Female


title: GM88A_LPS

value: No


title: Ps32

description: psoriasis peripheral blood sample

source_name: Psoriasis 32

value: peripheral blood

value: psoriasis

value: PR


title: MEC1_DMSO_CTRL_48h_37

description: rRNA-depleted RNA


title: Ps29

description: psoriasis peripheral blood sample

source_name: Psoriasis 29


title: EHEB_Idel_10uM_288

description: rRNA-depleted RNA

value: EHEB


title: Ps38

description: psoriasis peripheral blood sample

source_name: Psoriasis 38


title: GM89F_CTRL

value: UCSD

value: GM

value: CTRL

value: Yes


title: Ps28

description: psoriasis peripheral blood sample

source_name: Psoriasis 28

value: ER


title: benign prostatic hyperplasia 2


title: EHEB_Idel_10uM_287

description: rRNA-depleted RNA


title: GM75A_LPS

value: LPS

value: Severe


title: M13_LPS

value: Vaginal


title: benign prostatic hyperplasia 1


title: EHEB_Idel_10uM_286

description: rRNA-depleted RNA


title: benign prostatic hyperplasia 3


title: Patient A3 baseline

source_name: Patient A3 baseline

tag: time point

value: psoriasis lesion at baseline


title: GMR06A_LPS

value: RADY

value: GMR

value: Cesarean


title: Ps25

description: psoriasis peripheral blood sample

source_name: Psoriasis 25

value: Male

value: Adalimumab


title: Ps35

description: psoriasis peripheral blood sample

source_name: Psoriasis 35

value: peripheral blood

value: psoriasis

value: Etanercept


title: EHEB_Ibru_5uM_282

description: rRNA-depleted RNA

value: EHEB


title: Ps27

description: psoriasis peripheral blood sample

source_name: Psoriasis 27

value: Infliximab


title: Ps24

description: psoriasis peripheral blood sample

source_name: Psoriasis 24

value: Female


title: GM14B_LPS

value: UCSD

value: GM

value: Yes

value: Mild


title: GMR08A_LPS

value: LPS

value: Severe


title: Ps22

description: psoriasis peripheral blood sample

source_name: Psoriasis 22

value: ER


title: Ps23

description: psoriasis peripheral blood sample

source_name: Psoriasis 23

value: PR


title: EHEB_Ibru_5uM_280

description: rRNA-depleted RNA

source_name: Lymphoid


title: GM08B_LPS

value: Cesarean


title: Participant16 dAMJaTP2

city: Belgrade

first: Aleksandra

last: Stankovic

address: Mike Petrovica Alasa 12

department: Department of Health and Environment

country: Serbia

institute: VINCA Institute of Nuclear Sciences, University of Belgrade

hyb_protocol: Illumina® Direct Hybridization Assay protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background subtracted and normalised using quantile normalisation with GenomeStudio software 2011.1 (Illumina)

label_protocol: TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip® (Epicentre)

extract_protocol: Lymphocyte Separation Medium (GE Healthcare) protocol for isolation of the PBMC from whole blood samples, followed by TRI Reagent® Solution (Ambion) protocol for extraction of the total RNA from PBMC

tag: subject id

tag: age (years)

value: male

tag: polyphenol dose

value: Aronia melanocarpa juice-based beverage (dAMJ)

tag: intervention point

value: After treatment period 2 (aTP2)


title: JVM2_CTRL_DMSO_85

description: rRNA-depleted RNA

tag: treatment

value: DMSO


title: Ps21

description: psoriasis peripheral blood sample

source_name: Psoriasis 21

tag: gender

value: peripheral blood

value: psoriasis

tag: biological drug

value: Adalimumab


title: Ps19

description: psoriasis peripheral blood sample

source_name: Psoriasis 19

value: Male


title: Participant16 dAMJbTP2

value: Before treatment period 2 (bTP2)


title: Ps26

description: psoriasis peripheral blood sample

source_name: Psoriasis 26

value: Etanercept


title: Participant17 dAMJbTP2


title: EHEB_Flud_50uM_143

description: rRNA-depleted RNA

value: EHEB


title: Participant11 AMJaTP3

value: female

value: Aronia melanocarpa juice (AMJ)

value: After treatment period 3 (aTP3)


title: Participant11 dAMJaTP2


title: EHEB_Flud_50uM_142

description: rRNA-depleted RNA


title: EHEB_Ibru_5uM_281

description: rRNA-depleted RNA


title: EHEB_CTRL_DMSO_135

description: rRNA-depleted RNA


title: GM76B_CTRL

value: UCSD

tag: collection place

value: GM

value: CTRL

tag: bpd

tag: severity

value: Female

tag: delivery type

value: Vaginal


title: GMR09B_CTRL

tag: title

value: RADY

value: GMR

value: Yes

value: Mild


title: EHEB_Flud_50uM_144

description: rRNA-depleted RNA


title: EHEB_CTRL_DMSO_134

description: rRNA-depleted RNA

value: DMSO


title: VU03_LPS

tag: nicu

value: VANDERBILT

value: VAND

value: LPS

value: Severe

value: Male

value: Cesarean


title: Participant17 dAMJaTP2

value: male

value: Aronia melanocarpa juice-based beverage (dAMJ)

value: After treatment period 2 (aTP2)


title: Participant7 AMJaTP3

value: female

value: Aronia melanocarpa juice (AMJ)

value: After treatment period 3 (aTP3)


title: GM83F_LPS

value: UCSD

value: GM

value: Vaginal


title: Participant7 dAMJbTP2

value: Before treatment period 2 (bTP2)


title: EHEB_CTRL_DMSO_133

description: rRNA-depleted RNA

tag: cell line

value: EHEB

value: DMSO


title: Participant7 dAMJaTP2


title: Participant11 dAMJbTP2


title: Participant18 dAMJaTP2


title: Ps17

description: psoriasis peripheral blood sample

source_name: Psoriasis 17

tag: tissue

value: peripheral blood

tag: disease state

value: psoriasis

tag: response

value: ER

tag: age

value: Etanercept


title: Ps16

description: psoriasis peripheral blood sample

source_name: Psoriasis 16

value: Female

tag: age at initiation


title: GM31A_CTRL

source_name: Tracheal aspirate cells

value: CTRL

value: No

value: Cesarean


title: Ps18

description: psoriasis peripheral blood sample

source_name: Psoriasis 18

value: Male

value: Adalimumab


title: Patient Day 123 Rep2

city: Bethesda

first: Koray Dogan

last: Kaya

state: MD

address: 6 CENTER DR

department: NEI

institute: NIH

data_processing:
Raw reads passing chastity filter were trimmed for Illumina adapters with Trimmomatic (v0.36) (Bolger et al., 2014).
Trimmed reads were quantified at the transcript level using kallisto (v0.45.0). Then they were summarized to gene level using R package tximport (v1.8) using the option “countFromAbundance=lengthScaledTPM”.
The tximport summarized gene level count values were normalized with TMM and converted to count per million (CPM) using edgeR (v3.20.9)
Differential expression analysis was performed using limma (v3.34.9).
Genome_build: GRCh38.p7 ENSEMBL v82
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample ...
Supplementary_files_format_and_content: controlde.xlsx: xlsx file containing full de table of time-wise comparison of control samples
Supplementary_files_format_and_content: patientde.xlsx: xlsx file containing full de table of time-wise comparison of patient samples
Supplementary_files_format_and_content: clusterde.xlsx: xlsx file containing cluster membership of de genes with largest FC comparison
Supplementary_files_format_and_content: SummarizedGeneLevelCounts.txt: tab-delimited text file including Gene Level Counts Summarized by txtimport
Supplementary_files_format_and_content: NormalizedCpms.txt: tab-delimited text file including CPM values

source_name: Retinal Organoid differentiated from iPCS

extract_protocol:
Trizol
Illumina Stranded mRNA-Seq

tag: individual

value: Patient

tag: d.e. group name

tag: time point

value: Day 123


title: Ps20

description: psoriasis peripheral blood sample

source_name: Psoriasis 20

tag: gender

value: Infliximab


title: Participant13 dAMJaTP2

tag: subject id

tag: age (years)

value: female

tag: polyphenol dose

value: Aronia melanocarpa juice-based beverage (dAMJ)

tag: intervention point

value: After treatment period 2 (aTP2)


title: Ps14

description: psoriasis peripheral blood sample

source_name: Psoriasis 14

tag: biological drug


title: GMR02C_CTRL

tag: title

value: RADY

tag: collection place

value: GMR

tag: treatment

tag: bpd

value: Yes

tag: severity

value: Severe

tag: delivery type


title: GM03B_LPS

tag: nicu

value: UCSD

value: GM

value: LPS


title: Participant19 dAMJaTP3

value: male

value: After treatment period 3 (aTP3)


title: GM50A_LPS

value: Female

value: Cesarean


title: Participant8 dAMJaTP2


title: Ps15

description: psoriasis peripheral blood sample

source_name: Psoriasis 15

tag: tissue

value: peripheral blood

tag: disease state

value: psoriasis

tag: response

value: ER

tag: age

tag: age at initiation

value: Etanercept


title: Patient Day 123 Rep1

tag: individual

value: Patient

tag: d.e. group name

tag: time point

value: Day 123


title: VU02_LPS

value: VANDERBILT

value: VAND

tag: gender

value: Male

value: Vaginal


title: Participant9 dAMJaTP2

tag: subject id

tag: age (years)

value: female

tag: polyphenol dose

value: Aronia melanocarpa juice-based beverage (dAMJ)

tag: intervention point

value: After treatment period 2 (aTP2)


title: Participant18 AMJaTP3

value: male

value: Aronia melanocarpa juice (AMJ)


title: Patient Day 123 Rep3


title: Patient Day 88 Rep3

value: Day 88


title: Ps12

description: psoriasis peripheral blood sample

source_name: Psoriasis 12

tag: biological drug

value: Adalimumab


title: Ps11

description: psoriasis peripheral blood sample

source_name: Psoriasis 11

value: Female

value: peripheral blood

value: PR

value: Infliximab


title: GMR02B_CTRL

tag: title

value: RADY

tag: collection place

value: GMR

tag: treatment

value: CTRL

tag: bpd

value: Yes

tag: severity

value: Severe

value: Cesarean


title: Patient Day 60 Rep2

value: Patient

value: Day 60


title: Patient Day 88 Rep2


title: Patient Day 88 Rep1


title: Patient Day 60 Rep1


title: GM82C_LPS

tag: nicu

value: UCSD

value: GM

value: LPS

value: Male

tag: delivery type


title: Ps7

description: psoriasis peripheral blood sample

source_name: Psoriasis 7

tag: tissue

tag: disease state

value: psoriasis

tag: response

value: ER

tag: age

tag: age at initiation

value: Adalimumab


title: Participant13 dAMJbTP2

tag: subject id

tag: gender

value: female

value: Aronia melanocarpa juice-based beverage (dAMJ)

value: Before treatment period 2 (bTP2)


title: Participant13 AMJaTP3

tag: age (years)

tag: polyphenol dose

value: Aronia melanocarpa juice (AMJ)

value: After treatment period 3 (aTP3)


title: VU01_LPS

value: VANDERBILT

value: VAND

value: Yes

value: Female

value: Vaginal


title: Participant18 dAMJbTP2

value: male

tag: intervention point


title: GM08D_CTRL

tag: title

value: UCSD

value: GM

value: CTRL

value: Severe

value: Cesarean


title: GM14C_LPS

tag: collection place

value: LPS

value: Mild


title: Patient Day 25 Rep4

tag: individual

value: Patient

tag: d.e. group name

tag: time point

value: Day 25


title: Patient Day 25 Rep3


title: Patient Day 25 Rep2


title: Participant9 AMJaTP3

value: female

value: Aronia melanocarpa juice (AMJ)


title: 2273 2016: 327DP

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

description: Mammary gland cells Ductal progenitors

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: Microarrays were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: Mus musculus HT-MG430-PM strip arrays were processed with Bioconductor, using RMA background correction, quantile normalization and RMA summarization. Differentially expressed probesets were determined with limma, using thresholds of |FC|>2 and pvalue < 0.01.

source_name: Ductal progenitors

label_protocol: 15 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Freshly sorted mammary epithelial cells

extract_protocol: Trizol extraction

treatment_protocol: No specific treatment was used.

value: Mammary gland

tag: mouseid

tag: color

value: black

tag: Sex

tag: age (weeks(days))

tag: line

value: DMI

tag: genotype

value: Sox2-Cre +/+ ; Cpeb2 +/+

tag: strain

tag: fatherid

tag: motherid


title: 2275 2016: 327Myo

description: Mammary gland cells Myoepithelial

source_name: Myoepithelial

tag: tissue

value: Female


title: 2274 2016: 327AP

description: Mammary gland cells Alveolar progenitors

source_name: Alveolar progenitors


title: GM36A_CTRL

tag: nicu

tag: treatment

tag: bpd

value: No

tag: severity

tag: gender

tag: delivery type


title: GMR07A_LPS

tag: title

value: RADY

tag: collection place

value: GMR

value: Yes

value: Moderate


title: Ps8

description: psoriasis peripheral blood sample

source_name: Psoriasis 8

value: Male

value: peripheral blood

tag: disease state

value: psoriasis

tag: response

value: ER

tag: age

tag: age at initiation

tag: biological drug

value: Infliximab


title: Ps10

description: psoriasis peripheral blood sample

source_name: Psoriasis 10

value: PR

value: Adalimumab


title: GM89H_CTRL

value: UCSD

value: GM

value: CTRL

value: Severe

value: Cesarean


title: Control Day 123 Rep5

tag: individual

tag: d.e. group name

tag: time point

value: Day 123


title: Ps3

description: psoriasis peripheral blood sample

source_name: Psoriasis 3

value: Female

tag: tissue

value: Etanercept


title: GMR09A_LPS

tag: nicu

value: RADY

value: GMR

value: LPS

value: Yes

value: Mild

value: Vaginal


title: Patient Day 25 Rep1

value: Patient

value: Day 25


title: Control Day 123 Rep4


title: Participant18 AMJbTP3

tag: subject id

tag: age (years)

value: male

tag: polyphenol dose

value: Aronia melanocarpa juice (AMJ)

tag: intervention point

value: Before treatment period 3 (bTP3)


title: 2271 2016: 326Myo

description: Mammary gland cells Myoepithelial

value: Mammary gland

tag: mouseid

tag: color

value: black

tag: Sex

tag: age (weeks(days))

tag: line

value: DMI

tag: genotype

value: Sox2-Cre +/+ ; Cpeb2 -/-

tag: strain

tag: fatherid

tag: motherid


title: Participant7 AMJbTP3

tag: gender

value: female


title: Ps5

description: psoriasis peripheral blood sample

source_name: Psoriasis 5

value: Male

value: peripheral blood

tag: disease state

value: psoriasis

tag: response

value: ER

tag: age

tag: age at initiation

tag: biological drug

value: Etanercept


title: 2269 2016: 326DP

description: Mammary gland cells Ductal progenitors

tag: tissue

value: Female


title: GMR11A_LPS

tag: title

tag: nicu

value: RADY

tag: collection place

value: GMR

tag: treatment

value: LPS

tag: bpd

value: Yes

tag: severity

value: Mild

tag: delivery type

value: Cesarean


title: Ps6

description: psoriasis peripheral blood sample

source_name: Psoriasis 6

value: Infliximab


title: Ps1

description: psoriasis peripheral blood sample

source_name: Psoriasis 1

value: Adalimumab


title: 2270 2016: 326AP

value: Mammary gland

tag: mouseid

tag: color

value: black

tag: Sex

tag: age (weeks(days))

tag: line

value: DMI

tag: genotype

tag: strain


title: Participant11 AMJbTP3

tag: subject id

tag: age (years)

tag: gender

value: female

tag: polyphenol dose

value: Aronia melanocarpa juice (AMJ)

tag: intervention point

value: Before treatment period 3 (bTP3)


title: Ps2

description: psoriasis peripheral blood sample

source_name: Psoriasis 2

tag: tissue

value: peripheral blood

tag: disease state

value: psoriasis

tag: response

value: ER

tag: age

tag: age at initiation

tag: biological drug


title: GM21B_CTRL

source_name: Tracheal aspirate cells

tag: title

tag: nicu

value: UCSD

tag: collection place

value: GM

tag: treatment

value: CTRL

tag: bpd

tag: severity

value: Severe

value: Female

tag: delivery type

value: Vaginal


title: Participant9 dAMJbTP2

tag: subject id

tag: age (years)

value: Aronia melanocarpa juice-based beverage (dAMJ)

value: Before treatment period 2 (bTP2)


title: Control Day 123 Rep3

source_name: Retinal Organoid differentiated from iPCS

tag: individual

tag: d.e. group name

tag: time point

value: Day 123


title: Control Day 123 Rep2


title: GM65A_CTRL

value: No

tag: gender


title: Participant9 AMJbTP3

tag: polyphenol dose

tag: intervention point


title: Control Day 123 Rep1


title: Ps9

description: psoriasis peripheral blood sample

source_name: Psoriasis 9

tag: tissue

tag: disease state

tag: response

tag: age

tag: age at initiation

value: Adalimumab


title: GM78E_CTRL

tag: title

tag: nicu

tag: collection place

tag: treatment

value: Yes

value: Male

value: Cesarean


title: GM54B_CTRL

tag: bpd

tag: severity

tag: delivery type


title: Participant13 AMJbTP3

tag: subject id

tag: age (years)

value: female

value: Aronia melanocarpa juice (AMJ)

value: Before treatment period 3 (bTP3)


title: GM19G_LPS

value: UCSD

value: LPS

tag: gender


title: Control Day 88 Rep2

tag: individual

tag: d.e. group name

tag: time point

value: Day 88


title: Control Day 88 Rep3


title: M11_CTRL

value: CTRL

value: Severe


title: Ps4

description: psoriasis peripheral blood sample

source_name: Psoriasis 4

tag: tissue

value: peripheral blood

tag: disease state

value: psoriasis

value: PR

tag: biological drug


title: 2268 2016: 326NCL

description: Mammary gland cells Non-clonogenic Luminal

source_name: Non-clonogenic Luminal

value: Mammary gland

tag: mouseid

tag: color

value: black

tag: Sex

value: Female

tag: age (weeks(days))

tag: line

value: DMI

tag: genotype

value: Sox2-Cre +/+ ; Cpeb2 -/-

tag: strain

tag: fatherid

tag: motherid


title: GM32W_LPS

tag: title

tag: nicu

tag: collection place

value: GM

tag: treatment

tag: bpd

value: Yes

tag: severity

value: Male

tag: delivery type

value: Cesarean


title: Control Day 88 Rep1

tag: individual

tag: d.e. group name

tag: time point


title: 2267 2016: 319Myo

description: Mammary gland cells Myoepithelial

tag: tissue

tag: mouseid

tag: color

tag: Sex

value: Sox2-Cre +/+ ; Cpeb2 +/+


title: GM87A_LPS

value: UCSD

value: LPS

value: No

tag: gender


title: Control Day 60 Rep3

value: Day 60


title: 2266 2016: 319AP

tag: age (weeks(days))

tag: line

tag: genotype

tag: strain

tag: fatherid


title: 2265 2016: 319DP

description: Mammary gland cells Ductal progenitors

tag: motherid


title: Participant8 AMJbTP3

tag: subject id

tag: age (years)

value: male

tag: polyphenol dose

value: Aronia melanocarpa juice (AMJ)

tag: intervention point

value: Before treatment period 3 (bTP3)


title: 2264 2016: 319NCL

value: Mammary gland


title: 2262 2016: 318AP

value: black


title: 2263 2016: 318Myo

description: Mammary gland cells Myoepithelial

value: Female


title: Participant1 dAMJbTP3

value: female

value: Aronia melanocarpa juice-based beverage (dAMJ)


title: GM17A_CTRL

tag: title

tag: nicu

tag: collection place

value: GM

tag: treatment

value: CTRL

tag: bpd

tag: severity

value: Moderate

tag: delivery type


title: Participant6 dAMJbTP3

tag: gender


title: Participant14 dAMJaTP3

value: After treatment period 3 (aTP3)


title: GM76C_CTRL

value: Vaginal


title: 2261 2016: 318DP

description: Mammary gland cells Ductal progenitors

tag: tissue

tag: mouseid

tag: color

tag: Sex

tag: age (weeks(days))

tag: line

value: DMI

value: Sox2-Cre +/+ ; Cpeb2 -/-


title: Control Day 60 Rep1

tag: individual

tag: d.e. group name

tag: time point


title: Participant19 dAMJbTP3

tag: subject id

tag: age (years)

tag: polyphenol dose

tag: intervention point


title: Participant14 AMJbTP2

value: Before treatment period 2 (bTP2)


title: Control Day 60 Rep2

value: Day 60


title: Participant14 dAMJbTP3


title: GM78B_CTRL

tag: title

tag: nicu

value: UCSD

tag: collection place

tag: treatment

tag: bpd

value: Yes

value: Severe

value: Male

value: Cesarean


title: Control Day 25 Rep5

value: Day 25


title: Control Day 25 Rep7


title: Control Day 25 Rep3


title: 33_HSCs-TGFb3

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
Reads aligned using Tophat v2.1.0
FeatureCounts used for calculating gene counts
edgeR used for differential expression
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: gene counts

source_name: HSCs-TGFb

growth_protocol: Company derived human hepatic stellate cells grown in complete DMEM supplemented with 1% P/S and 10% FBS

extract_protocol:
RNA was extracted according to manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 48 hours of recombinent human TGFβ treatment after overnight serum starvation

tag: cell type

value: Hepatic Stellate Cells

value: recombinent human TGFβ for 48hrs


title: 25_HSCs-Ctrl1

source_name: HSCs-Ctrl

value: Control


title: 2272 2016: 327NCL

tag: tissue

value: Mammary gland

tag: mouseid

tag: color

value: black

value: Female

tag: genotype

value: Sox2-Cre +/+ ; Cpeb2 +/+

tag: strain

tag: fatherid

tag: motherid


title: 26_HSCs-Ctrl2


title: 2260 2016: 318NCL

tag: Sex

tag: age (weeks(days))

tag: line

value: DMI


title: Control Day 25 Rep2

tag: individual

tag: d.e. group name

tag: time point


title: 31_HSCs-TGFb1


title: Participant10 AMJbTP2

tag: subject id

tag: age (years)

tag: gender

value: male

tag: polyphenol dose

value: Aronia melanocarpa juice (AMJ)

tag: intervention point


title: Participant10 dAMJaTP3

value: Aronia melanocarpa juice-based beverage (dAMJ)

value: After treatment period 3 (aTP3)


title: Participant6 dAMJaTP3


title: Participant6 AMJbTP2

value: Before treatment period 2 (bTP2)


title: Participant1 dAMJaTP3

value: female


title: 18_HSC_GIPC_shRNA_TGF

description: 18_HSC_GIPC_shRNA_TGF.FCC7Y6VACXX_L3_IGGCTAC

data_processing:
TopHat v2.0.12 for alignment
FeatureCounts to quantify expression
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: gene counts

treatment_protocol: Cells were treated with 2 hours of recombinent human TGFβ treatment after overnight serum starvation

tag: cell type

tag: lentivirus

value: GIPC shRNA


title: Control Day 25 Rep1


title: Participant1 AMJbTP2


title: 27_HSCs-Ctrl3

tag: treatment


title: 32_HSCs-TGFb2


title: Participant5 AMJaTP2

value: After treatment period 2 (aTP2)


title: Control Day 25 Rep4

value: Day 25


title: 15_HSC_GIPC_shRNA_TGF

description: 15_HSC_GIPC_shRNA_TGF.FCC7Y6VACXX_L3_IACTTGA

value: Hepatic Stellate Cells


title: GMR10C_CTRL

tag: title

tag: nicu

value: RADY

tag: collection place

value: GMR

value: CTRL

tag: bpd

value: Yes

tag: severity

value: Mild

tag: delivery type

value: Vaginal


title: VU01_CTRL

value: VANDERBILT

value: VAND

value: Severe

value: Female


title: DGM-00692_LA-BC (BMP4 study)

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

institute: Weill Cornell Medical College

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using the human reference genome build GRCh37/hg19, STAR (2.3.1z13_r470) for aligning reads, RefSeq gene definitions (2014-06-02) and Cufflinks (v2.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM).
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent STAR results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged STAR output to produce a file with FPKM values for each sample
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM text files include the RefSeq unique ID with gene ID and location, gene ID  and the FPKM values for all samples

source_name: large airway basal cells

growth_protocol: Pure populations of nonsmoker, smoker and COPD smoker large airway samples and nonsmoker, smoker and COPD smoker derived large airway basal cells (BC) were obtained and characterized using detailed protocols as previously described (PMID:1572528). Primary BC were maintained in Bronchial Epithelial Growth Media (BEGM, Lonza, Walkersville, MD) and passaged by seeding at a cell density of 3000 cells/cm2 in BEGM with fresh media changed every 2 days (PMID:24298994). RNA sequencing of primary (Passage 0) BC was performed on cells once they had reached 70-80% confluence as well as large airway samples.

extract_protocol:
Total RNA from nonsmoker, smoker and COPD smoker epithelium and  harvested basal cells was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIA-quick PCR purification kit (Qiagen, Valencia, CA)
Samples were loaded onto an Illumina flowcell for paired-end 125 x 2 sequencing reactions using the Illumina HiSeq 2500. HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images.

tag: smoking status

value: COPD smoker

value: basal cells cultured from airway epithelial cells


title: 12_HSC_GIPC_shRNA_TGF

description: 12_HSC_GIPC_shRNA_TGF.FCC7Y6VACXX_L2_IATTCCT


title: GM32X_CTRL

value: UCSD

value: GM

value: Male

value: Cesarean


title: 9_HSC_Control_shRNA_TGF

description: 9_HSC_Control_shRNA_TGF.FCC7Y6VACXX_L2_ICGTACG

value: Hepatic Stellate Cells

value: Control shRNA


title: GMR08B_CTRL

value: RADY

value: GMR


title: DGM-01774_090416_LA-BC (BMP4 study)

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using the human reference genome build GRCh37/hg19, STAR (2.3.1z13_r470) for aligning reads, RefSeq gene definitions (2014-06-02) and Cufflinks (v2.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM).
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent STAR results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged STAR output to produce a file with FPKM values for each sample
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM text files include UniqueID with gene ID and location, GeneID, and the FPKM values for all samples

extract_protocol:
Total RNA from nonsmoker, smoker and COPD smoker epithelium and harvested basal cells was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIA-quick PCR purification kit (Qiagen, Valencia, CA)
Samples were loaded onto an Illumina flowcell for paired-end 125 x 2 sequencing reactions using the Illumina HiSeq 2500. HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images.

value: nonsmoker


title: 6_HSC_Control_shRNA_TGF

description: 6_HSC_Control_shRNA_TGF.FCC7Y6VACXX_L1_IGGCTAC


title: GM58B_LPS

value: LPS

value: Yes


title: GM83D_CTRL

value: CTRL

value: Vaginal


title: DGM-11111_M6_lg (BMP4 study)

source_name: large airway epithelium cells

value: smoker

value: large airway epithelial cells

tag: time of serial bronchoscopy (month)


title: 3_HSC_Control_shRNA_TGF

description: 3_HSC_Control_shRNA_TGF.FCC7Y6VACXX_L1_IACTTGA


title: DGM-11066_M0_lg (BMP4 study)


title: THP-1 24hr 25nM INCB059872 B

city: Nashville

first: Scott

last: Hiebert

address: 2220 Pierce Ave.

institute: Vanderbilt University

data_processing:
Read alignment performed with TopHat
Differential gene expression determined by Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: plain text documents containing averaged RPKM values and calculated differential expression between treatment samples and corresponding control samples

extract_protocol:
RNA was harvested using TRIzol reagent.
Libraries were prepared from polyA-enriched RNA by standard Illumina protocols.

tag: cell line

value: acute myeloid leukemia (AML) cell line

value: 25nM INCB059872 for 24hrs


title: M11_LPS

value: UCSD

value: Severe


title: GM81C_CTRL

value: GM

value: Male


title: Participant5 AMJbTP2

tag: subject id

value: male

value: Aronia melanocarpa juice (AMJ)

value: Before treatment period 2 (bTP2)


title: DGM-12825_LA-BC (BMP4 study)

value: basal cells cultured from airway epithelial cells


title: THP-1 24hr 25nM INCB059872 A


title: GM83E_CTRL


title: Participant15 PLBaTP1

tag: age (years)

value: placebo beverage (PLB)

value: After treatment period 1 (aTP1)


title: Participant4 AMJaTP2

tag: gender

value: After treatment period 2 (aTP2)


title: Participant15 PLBbTP1

tag: polyphenol dose

value: Before treatment period 1 (bTP1)


title: THP-1 24hr DMSO B

source_name: THP-1 24hr DMSO

value: DMSO for 24hrs


title: Participant12 PLBaTP1

tag: intervention point


title: DGM-11008_M0_lg (BMP4 study)

value: smoker

tag: cell type


title: Participant4 AMJbTP2


title: DGM-10922_M0_lg (BMP4 study)

value: large airway epithelial cells


title: Participant12 PLBbTP1


title: THP-1 24hr DMSO A

value: acute myeloid leukemia (AML) cell line


title: GM83B_LPS

value: LPS

value: Yes

value: Vaginal


title: GMR09D_LPS

value: RADY

value: GMR

value: Mild


title: DGM-11016_M0_lg (BMP4 study)


title: DGM-10907_M0_lg (BMP4 study)


title: Ps13

description: psoriasis peripheral blood sample

source_name: Psoriasis 13

value: Female

tag: tissue

value: peripheral blood

tag: disease state

value: psoriasis

tag: response

value: ER

tag: age

tag: age at initiation

tag: biological drug

value: Etanercept


title: THP-1 3hr 25nM INCB059872 B

source_name: THP-1 3hr 25nM INCB059872

tag: treatment

value: 25nM INCB059872 for 3hrs


title: DGM-10906_M12_lg (BMP4 study)


title: THP-1 3hr 25nM INCB059872 A


title: GM74A_LPS

tag: title

tag: nicu

value: UCSD

tag: collection place

value: GM

tag: bpd

value: No

tag: severity

value: Male

tag: delivery type

value: Cesarean


title: GM70E_LPS

value: LPS

value: Moderate

tag: gender


title: THP-1 3hr DMSO B

source_name: THP-1 3hr DMSO

tag: cell line

value: acute myeloid leukemia (AML) cell line

value: DMSO for 3hrs


title: GMR10B_CTRL

value: RADY

value: GMR

value: CTRL

value: Yes

value: Vaginal


title: THP-1 3hr DMSO A


title: DGM-10869_M0_lg (BMP4 study)

tag: smoking status

value: smoker

value: large airway epithelial cells

tag: time of serial bronchoscopy (month)


title: GM84B_CTRL

value: Female


title: DGM-10522_M0_lg (BMP4 study)

tag: cell type


title: Participant5 PLBaTP1

tag: subject id

tag: age (years)

value: male

tag: polyphenol dose

value: placebo beverage (PLB)

tag: intervention point

value: After treatment period 1 (aTP1)


title: DGM-11613_M3_lg (BMP4 study)

value: COPD smoker


title: MV-4-11 24hr 100nM INCB059872 A

value: 100nM INCB059872 for 24hrs


title: GM62C_CTRL

value: UCSD

value: GM

value: Severe

value: Cesarean


title: GM78D_CTRL

value: Male


title: DGM-10170_M0_lg (BMP4 study)


title: Participant5 PLBbTP1

value: Before treatment period 1 (bTP1)


title: Participant8 AMJaTP3

value: Aronia melanocarpa juice (AMJ)

value: After treatment period 3 (aTP3)


title: Participant4 PLBaTP1


title: MV-4-11 3hr 100nM INCB059872 B

value: acute myeloid leukemia (AML) cell line

value: 100nM INCB059872 for 3hrs


title: Participant8 dAMJbTP2

value: Aronia melanocarpa juice-based beverage (dAMJ)

value: Before treatment period 2 (bTP2)


title: Participant19 AMJaTP2

value: male

value: After treatment period 2 (aTP2)


title: GM22B_CTRL

value: CTRL

value: Yes