title: Air_D21T_rep3 [Lung mRNA]

city: Morgatown

first: Nancy

middle: Lan

last: Guo

state: WV

address: 2816 Health Sciences Center

department: Occupational and Environmental Health Sciences

institute: West Virginia University

description: Gene expression from rat blood

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Rat Gene ST 2.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592)

data_processing: The oligo package of bioconductor was used to generate RMA expression values and linear models were fit using the limma package of bioconductor in R version 3.4

organism: Rattus norvegicus

source_name: lung, control, 21 days, implanted with radio telemetry system

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

growth_protocol: One hundred thirty-four healthy, male, 9 weeks old Sprague-Dawley rats, weighing an average of 300 grams were purchased from Taconic Farms Inc. (Hudson, NY). The rats were allowed to acclimatize for 1 week before the studies were initiated. Baseline data was collected for 1 week before the exposures occurred. The rats were maintained on a 12-hour light/dark cycle and food and water were provided ad libitum. Upon arrival, animals were randomly assigned a unique identification number, which determines the exposure group for the animal. There were two treatment groups: a) Control group: high efficiency particulate air (HEPA) filtered air, and b) PEPs Exposure group. All the animals were treated humanely in accordance with the guiding principles on the Use of Animals in Toxicology and the Animal Care and Use Committee of Harvard University (Ethical permit No.- 04623).

extract_protocol: Total RNA was isolated from rat blood using a mirVana miRNA Isolation Kit from Ambion per the manufacturer's protocol. Rat lungs were initially disrupted by transferring them to a 2 mL microcentrifuge tube containing 400 μL silica beads and 600 μL Lysis/Binding Solution.

treatment_protocol: The exposed group consisted of rats housed in individual cages and exposed via full body inhalation to PEPs and gaseous pollutants emitted by laser printer B1 using the Printer Exposure Generation System (PEGS) described in detail in a previous publication (Pirela et al, 2014). (Supplementary Material, Figure S1). In summary, printer B1 was used to generate PEPs emissions by printing a 5%-page coverage monochrome document using standardized settings (Pirela et al 2014). The laser printer B1 was selected based on exposure profiles reported in our previous studies (Pirela et al., 2014). In parallel, another group of rats was exposed to HEPA filtered air. The system was configured for twelve chambers (one animal per chamber), each equipped with a port for aerosol delivery and temperature and humidity measurement, a water bottle port, and a gas sampling port.   The whole exposure experiment was repeated twice, in 2016 and 2017. Animals were placed in their chambers for 1-5 hours for 5 days prior to the exposures to ensure they gradually acclimated to exposure chambers before the exposures occurred. The following week, animals were exposed to PEPs pollutants and the room HEPA-filtered air 5 hours/day for 21 consecutive days.

value: 9 weeks old

value: male

tag: strain

value: Sprague-Dawley

value: lung


title: PEP_D1_rep2 [Lung mRNA]

status: Public on Jan 13 2020

type: RNA

country: USA

description: Gene expression from rat blood

label: biotin

molecule: total RNA

source_name: lung, exposed, 1 day

tag: age

tag: Sex

tag: tissue


title: 2013 m6A-IP

type: SRA

city: CHICAGO

first: Zijie

last: Zhang

state: IL

department: Chemistry

institute: University of Chicago

description: m6A enriched RNA

library_source: transcriptomic

data_processing:
Seequencing reads were aligned to reference genome by Hisat2
Read count of connected bins was quantified by R package RADAR.
Differential methylation sites detection by RADAR
Genome_build: hg38
Supplementary_files_format_and_content: differential methylation sites in BED12 file. Bins in text files are consecutive bins of 50 bp size on the longest isoform of a gene, which is by concatenating the exons of a gene.

organism: Homo sapiens

source_name: ovary

extract_protocol:
TRIzol (Invitrogen)
Takara Pico-Input Strand-Specific Total RNA-seq for Illumina
MeRIP-seq

tag: group

value: normal Fallopian tube


title: Air_D21T_rep1 [Lung mRNA]

description: Gene expression from rat blood


title: 2064 m6A-IP

description: m6A enriched RNA


title: PEP_D21T_rep4 [Lung mRNA]

description: Gene expression from rat blood

source_name: lung, exposed, 21 days, implanted with radio telemetry system


title: 2186 m6A-IP

description: m6A enriched RNA

value: omental tumor


title: Air_D21T_rep2 [Lung mRNA]

description: Gene expression from rat blood


title: PEP_D1_rep4 [Lung mRNA]

description: Gene expression from rat blood


title: 2221 m6A-IP

description: m6A enriched RNA


title: PEP_D21T_rep3 [Lung mRNA]

description: Gene expression from rat blood


title: 2261 m6A-IP

description: m6A enriched RNA


title: PEP_D1_rep5 [Lung mRNA]

description: Gene expression from rat blood


title: PEP_D1_rep1 [Lung mRNA]

description: Gene expression from rat blood


title: PEP_D1_rep3 [Lung mRNA]

description: Gene expression from rat blood


title: Air_D21T_rep4 [Lung mRNA]

description: Gene expression from rat blood


title: Air_D1_rep4 [Lung mRNA]

description: Gene expression from rat blood

source_name: lung, control, 1 day


title: 2005 m6A-IP

description: m6A enriched RNA


title: PEP_D21T_rep1 [Lung mRNA]

description: Gene expression from rat blood


title: 2270 m6A-IP

description: m6A enriched RNA


title: Air_D1_rep3 [Lung mRNA]

description: Gene expression from rat blood


title: Air_D1_rep5 [Lung mRNA]

description: Gene expression from rat blood


title: 2072 input

description: total RNA


title: 2380 m6A-IP

description: m6A enriched RNA


title: Air_D5_rep3 [Lung mRNA]

description: Gene expression from rat blood

source_name: lung, control, 5 days


title: Air_D1_rep2 [Lung mRNA]

description: Gene expression from rat blood


title: 1917 input

description: total RNA


title: 2005 input

description: total RNA


title: 2013 input

description: total RNA


title: 2186 input

description: total RNA


title: 2053 input

description: total RNA


title: Air_D1_rep1 [Lung mRNA]

description: Gene expression from rat blood


title: 2221 input

description: total RNA


title: Air_D5_rep1 [Lung mRNA]

description: Gene expression from rat blood


title: Air_D5_rep4 [Lung mRNA]

description: Gene expression from rat blood


title: 2343 m6A-IP

description: m6A enriched RNA


title: 1850 input

description: total RNA


title: Air_D5_rep5 [Lung mRNA]

description: Gene expression from rat blood


title: 2270 input

description: total RNA


title: 2261 input

description: total RNA


title: 2064 input

description: total RNA


title: 2343 input

description: total RNA


title: PEP_D5_rep3 [Lung mRNA]

description: Gene expression from rat blood

source_name: lung, exposed, 5 days


title: PEP_D5_rep4 [Lung mRNA]

description: Gene expression from rat blood


title: 2380 input

description: total RNA


title: PEP_D5_rep2 [Lung mRNA]

description: Gene expression from rat blood


title: PEP_D5_rep1 [Lung mRNA]

description: Gene expression from rat blood


title: SCL SCDP1-resF3

city: Kyoto

first: Cantas

last: Alev

address: Medical Faculty Bldg. B, Yoshida-Konoe-cho, Sakyo-ku

department: Institute for the Advanced Study of Human Biology (ASHBi)

country: Japan

institute: Kyoto University

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
The low-quality bases at the 3' read ends and the adaptor sequences were trimmed by cutadapt-1.14.
The sequenced reads were mapped to the hg38 human reference genome plus the luciferase reporter sequence using HISAT2 (version 2.1.0) with the human GENCODE v25 annotation gtf file.
The uniquely mapped reads were counted using HTSeq (version 0.6.1) with the human GENCODE v25 annotation gtf file.
Genome_build: hg38
Supplementary_files_format_and_content: The tab-delimited text file include raw counts of sequenced reads for each sample obtained with HTSeq-count.

source_name: SCDP1-resF3 rescue iPSC

growth_protocol: Human iPSCs (patient, rescue and control lines) were maintained without feeder cells and cultured on iMatrix-511-silk (Nippi) coated dishes or plates with StemFit® AK02N (Ajinomoto) medium supplemented with 50 U penicillin and 50 mg/ml streptomycin (Gibco).

extract_protocol:
Total RNA was extracted with the RNeasy mini kit (Qiagen) following the manufacturer’s instructions.
RNA-seq libraries were generated from 200-300 ng total RNA with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.

treatment_protocol: Human iPSCs (patient, rescue and control lines) were seeded on iMatrix-511 silk-coated plates or dishes at appropriate densities as single cells (e.g. 1.3 × 104 cells/well into 6 well plate; 8.0 × 104 cells/dish into 10cm dish) 5 days before induction. All differentiation and induction steps were performed in chemically defined medium with insulin (CDMi). Human primitive streak (PS) cells were induced by treatment of iPSCs with bFGF (20 ng/ml), CHIR99021 (10 µM) and Activin A (50 ng/ml) for 24 hours. Presomitic mesoderm (PSM) cells were induced from PS cells by exposure to SB431542 (10 µM), CHIR99021 (3 µM), LDN193189 (250 nM) and bFGF (20 ng/ml) for 24 hours. Subsequently, somitic mesoderm (SM) cells were induced from PSM cells using PD173074 (100 nM) and XAV939 (1 µM) for 24 hours. Following initial step-wise somitic mesoderm (SM) induction, human sclerotome (SCL) cells were induced with combination of SAG (100 nM) and LDN193189 (600 nM) for 72 hours. Dermomyotome (DM) cells were induced from human somitic mesoderm, using a combination of CHIR99021 (3 µM), GDC0449 (150 nM) and BMP4 (50 ng/ml) for 48 hours.

tag: background line

value: SCDP1 rescue iPSC line (clone F3)

tag: Stage

value: SCL (sclerotome)

tag: original source

value: Coriell GM13539


title: PEP_D5_rep5 [Lung mRNA]

description: Gene expression from rat blood


title: SCL SCDP1-resF2

source_name: SCDP1-resF2 rescue iPSC

value: SCDP1 rescue iPSC line (clone F2)


title: PEP_D9_rep2 [Lung mRNA]

description: Gene expression from rat blood

source_name: lung, exposed, 9 days


title: PEP_D9_rep5 [Lung mRNA]

description: Gene expression from rat blood


title: PEP_D9_rep4 [Lung mRNA]

description: Gene expression from rat blood


title: PEP_D9_rep1 [Lung mRNA]

description: Gene expression from rat blood


title: Air_D9_rep5 [Lung mRNA]

description: Gene expression from rat blood

source_name: lung, control, 9 days


title: SCL SCDP1-resA1

source_name: SCDP1-resA1 rescue iPSC

value: SCDP1 rescue iPSC line (clone A1)


title: Air_D9_rep2 [Lung mRNA]

description: Gene expression from rat blood


title: SCL SCDP1-F

source_name: SCDP1-F patient iPSC

value: SCDP1 patient iPSC line (clone F)


title: Air_D9_rep4 [Lung mRNA]

description: Gene expression from rat blood


title: Air_D9_rep3 [Lung mRNA]

description: Gene expression from rat blood


title: PEP_D9_rep3 [Lung mRNA]

description: Gene expression from rat blood


title: Air_D9_rep1 [Lung mRNA]

description: Gene expression from rat blood


title: SCL SCDP1-A

source_name: SCDP1-A patient iPSC

value: SCDP1 patient iPSC line (clone A)


title: SCL (201B7) Ex3

source_name: iPSC (healthy control)


title: PEP_D21_rep6 [Lung mRNA]

description: Gene expression from rat blood

source_name: lung, exposed, 21 days


title: PEP_D21_rep5 [Lung mRNA]

description: Gene expression from rat blood


title: SCL (201B7) Ex2


title: SCL (201B7) Ex1


title: DM SCDP1-resF3

value: DM (dermomyotome)


title: DM SCDP1-resF2


title: DM SCDP1-A


title: DM (201B7) Ex3


title: DM SCDP1-resA1


title: DM SCDP1-F


title: DM (201B7) Ex2


title: SM SCDP1-resF3

value: SM (somitic mesoderm)


title: SM SCDP1-resF2


title: DM (201B7) Ex1


title: PEP_D21_rep1 [Lung mRNA]

description: Gene expression from rat blood


title: PEP_D21_rep2 [Lung mRNA]

description: Gene expression from rat blood


title: PEP_D21_rep3 [Lung mRNA]

description: Gene expression from rat blood


title: PEP_D21T_rep2 [Lung mRNA]

description: Gene expression from rat blood


title: PEP_D21_rep4 [Lung mRNA]

description: Gene expression from rat blood


title: Air_D21_rep4 [Lung mRNA]

description: Gene expression from rat blood

source_name: lung, control, 21 days


title: SM SCDP1-F


title: Air_D21_rep5 [Lung mRNA]

description: Gene expression from rat blood


title: Air_D21_rep3 [Lung mRNA]

description: Gene expression from rat blood


title: SM SCDP1-A


title: SM (201B7) Ex3


title: SM (201B7) Ex2


title: Air_D21_rep1 [Lung mRNA]

description: Gene expression from rat blood


title: SM (201B7) Ex1


title: SM SCDP1-resA1


title: PSM SCDP1-resF3

value: PSM (presomitic mesoderm)


title: Air_D21_rep2 [Lung mRNA]

description: Gene expression from rat blood


title: Air_D21_rep6 [Lung mRNA]

description: Gene expression from rat blood


title: Air_D21T_rep2 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, control, 21 days, implanted with radio telemetry system

value: blood


title: PEP_D21T_rep2 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 21 days, implanted with radio telemetry system

value: 9 weeks old


title: PEP_D21T_rep3 [Blood mRNA]

description: Gene expression from rat blood

value: male


title: PEP_D21T_rep1 [Blood mRNA]

description: Gene expression from rat blood

value: Sprague-Dawley


title: PEP_D21T_rep4 [Blood mRNA]

description: Gene expression from rat blood


title: PEP_D1_rep5 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 1 day


title: Air_D5_rep2 [Lung mRNA]

description: Gene expression from rat blood

value: lung


title: Air_D21T_rep3 [Blood mRNA]

description: Gene expression from rat blood


title: PSM SCDP1-A


title: PEP_D1_rep3 [Blood mRNA]

description: Gene expression from rat blood


title: Air_D21T_rep1 [Blood mRNA]

description: Gene expression from rat blood


title: PSM SCDP1-resF2


title: PSM (201B7) Ex3


title: PEP_D1_rep4 [Blood mRNA]

description: Gene expression from rat blood


title: PSM (201B7) Ex2


title: PSM (201B7) Ex1


title: PS SCDP1-resF3

value: PS (primitive streak)


title: Air_D21T_rep4 [Blood mRNA]

description: Gene expression from rat blood


title: PSM SCDP1-resA1


title: PS SCDP1-resF2


title: PS SCDP1-resA1


title: PS SCDP1-F


title: PS (201B7) Ex2


title: PS (201B7) Ex3


title: PS (201B7) Ex1


title: iPSC SCDP1-resF3

value: iPSC (induced pluripotent stem cell)


title: iPSC SCDP1-resF2


title: PEP_D1_rep2 [Blood mRNA]

description: Gene expression from rat blood


title: Air_D1_rep5 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, control, 1 day


title: iPSC SCDP1-resA1


title: Air_D1_rep4 [Blood mRNA]

description: Gene expression from rat blood


title: Air_D1_rep2 [Blood mRNA]

description: Gene expression from rat blood


title: iPSC SCDP1-F


title: Air_D1_rep3 [Blood mRNA]

description: Gene expression from rat blood


title: Air_D5_rep4 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, control, 5 days


title: PS SCDP1-A


title: PEP_D5_rep5 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 5 days


title: PEP_D5_rep4 [Blood mRNA]

description: Gene expression from rat blood


title: iPSC SCDP1-A


title: Air_D5_rep3 [Blood mRNA]

description: Gene expression from rat blood


title: iPSC (201B7) Ex3


title: PEP_D1_rep1 [Blood mRNA]

description: Gene expression from rat blood


title: Air_D5_rep2 [Blood mRNA]

description: Gene expression from rat blood


title: PEP_D5_rep2 [Blood mRNA]

description: Gene expression from rat blood


title: Air_D5_rep1 [Blood mRNA]

description: Gene expression from rat blood


title: Air_D5_rep5 [Blood mRNA]

description: Gene expression from rat blood


title: PEP_D9_rep5 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 9 days


title: iPSC (201B7) Ex2


title: PEP_D5_rep1 [Blood mRNA]

description: Gene expression from rat blood


title: iPSC (201B7) Ex1


title: PEP_D9_rep4 [Blood mRNA]

description: Gene expression from rat blood


title: PSM LFNG-KO 1 [KO]

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
The low-quality bases at the 3' read ends and the adaptor sequences were trimmed by cutadapt-1.14.
The sequenced reads were mapped to the hg38 human reference genome plus the luciferase reporter sequence using HISAT2 (version 2.1.0) with the human GENCODE v25 annotation gtf file.
The mapped reads with high mapping quality (MAPQ >= 2) were used for further analyses.
FPKM values were determined by Cuffdiff within Cufflinks version 2.2.1 package and the human GENCODE v25 annotation file (protein_coding genes).
Genome_build: hg38
Supplementary_files_format_and_content: The tab-delimited text file include FPKM values for each sample.

source_name: PSM LFNG-KO clone 2

growth_protocol: Human iPSCs (control and knock-out reporter lines of HES7, DLL3, LFNG, MESP2) were maintained without feeder cells and cultured on iMatrix-511-silk (Nippi) coated plates with StemFit® AK02N (Ajinomoto) medium supplemented with 50 U penicillin and 50 mg/ml streptomycin (Gibco).

treatment_protocol: Human iPSCs of healthy controls and knock-out reporter lines were seeded on iMatrix-511-silk coated plates at appropriate densities as single cells (1.3 × 10^4 cells/well into 6 well plate) 5 days before induction. All differentiation and induction steps were performed in chemically defined medium with insulin (CDMi). Initially human primitive streak (PS) cells were induced by treatment of iPSCs with bFGF (20 ng/ml), CHIR99021 (10 µM) and Activin A (50 ng/ml) for 24 hours. Presomitic mesoderm (PSM) cells were induced from PS cells by exposure to SB431542 (10 µM), CHIR99021 (3 µM), LDN193189 (250 nM) and bFGF (20 ng/ml) for 24 hours.

tag: line

value: knock-out iPSC line (201B7 reporter)

value: 201B7 (Hes7-luciferase reporter)


title: PEP_D9_rep3 [Blood mRNA]

description: Gene expression from rat blood


title: PSM DLL3-KO 2 [KO]

source_name: PSM DLL3-KO clone 6


title: PSM MESP2-KO 1 [KO]

source_name: PSM MESP2-KO clone 7


title: PEP_D9_rep1 [Blood mRNA]

description: Gene expression from rat blood


title: PEP_D5_rep3 [Blood mRNA]

description: Gene expression from rat blood


title: PSM MESP2-KO 2 [KO]

source_name: PSM MESP2-KO clone 11


title: PSM DLL3-KO 1 [KO]

source_name: PSM DLL3-KO clone 2


title: PSM HES7-KO 1 [KO]

source_name: PSM HES7-KO clone 1


title: Air_D9_rep5 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, control, 9 days


title: Air_D9_rep4 [Blood mRNA]

description: Gene expression from rat blood


title: Air_D1_rep1 [Blood mRNA]

description: Gene expression from rat blood


title: PSM HES7-KO 3 [KO]

source_name: PSM HES7-KO clone 8


title: Air_D9_rep3 [Blood mRNA]

description: Gene expression from rat blood


title: PSM WT Ex2 [KO]

source_name: PSM WT (201B7)

value: healthy/wild type iPSC line (201B7)


title: Air_D17_rep1 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, control, 17 days


title: iPSC MESP2-KO 1 [KO]

source_name: iPSC MESP2-KO clone 7


title: PSM HES7-KO 2 [KO]

source_name: PSM HES7-KO clone 7


title: Air_D17_rep3 [Blood mRNA]

description: Gene expression from rat blood


title: iPSC MESP2-KO 2 [KO]

source_name: iPSC MESP2-KO clone 11


title: Air_D9_rep1 [Blood mRNA]

description: Gene expression from rat blood


title: Air_D17_rep4 [Blood mRNA]

description: Gene expression from rat blood


title: Air_D17_rep2 [Blood mRNA]

description: Gene expression from rat blood


title: Air_D9_rep2 [Blood mRNA]

description: Gene expression from rat blood


title: PEP_D17_rep5 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 17 days


title: PEP_D17_rep1 [Blood mRNA]

description: Gene expression from rat blood


title: iPSC LFNG-KO 1 [KO]

source_name: iPSC LFNG-KO clone 2


title: PSM WT Ex3 [KO]


title: PSM LFNG-KO 2 [KO]

source_name: PSM LFNG-KO clone 12


title: iPSC DLL3-KO 1 [KO]

source_name: iPSC DLL3-KO clone 2


title: PSM WT Ex1 [KO]


title: PEP_D9_rep2 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 9 days


title: iPSC WT Ex3 [KO]

source_name: iPSC WT (201B7)


title: iPSC HES7-KO 3 [KO]

source_name: iPSC HES7-KO clone 8


title: PEP_D17_rep4 [Blood mRNA]

description: Gene expression from rat blood


title: PEP_D17_rep3 [Blood mRNA]

description: Gene expression from rat blood


title: PEP_D13_rep4 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 13 days


title: PEP_D13_rep2 [Blood mRNA]

description: Gene expression from rat blood


title: PEP_D13_rep3 [Blood mRNA]

description: Gene expression from rat blood


title: iPSC LFNG-KO 2 [KO]

source_name: iPSC LFNG-KO clone 12


title: iPSC DLL3-KO 2 [KO]

source_name: iPSC DLL3-KO clone 6


title: iPSC WT Ex1 [KO]


title: Oscillation Ex2 Time Point 16 [Hs]

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
The low-quality bases at the 3' read ends and the adaptor sequences were trimmed by cutadapt-1.14.
The sequenced reads were mapped to the hg38 human reference genome plus the luciferase reporter sequence using HISAT2 (version 2.1.0) with the human GENCODE v25 annotation gtf file.
The uniquely mapped reads (MAPQ>=2) were counted using HTSeq (version 0.6.1) with the human GENCODE v25 annotation gtf file (protein_coding genes).
Genome_build: hg38
Supplementary_files_format_and_content: The tab-delimited text file include raw counts of sequenced reads for each sample obtained with HTSeq-count.

source_name: Hes7-luciferase iPSC reporter derived human PSM Ex2

growth_protocol: Our standard step-wise PSM induction protocol was used with modifications. HES7-reporter cells were seeded on 35 mm dishes coated with Matrigel.

extract_protocol:
Total RNA was extracted with the RNeasy mini kit (Qiagen) following the manufacturer’s instructions.
RNA-seq libraries were generated from 120 ng total RNA using NeoPrep system (Illumina) following the manufacturer's instructions

treatment_protocol: Following initial induction of primitive streak (PS) cells from human iPSCs with bFGF (20 ng/ml), CHIR99021 (10 µM) and Activin A (50 ng/ml) for 24 hours, presomitic mesoderm (PSM) cells were induced by exposure to SB431542 (10 µM), CHIR99021 (3 µM), LDN193189 (250 nM) and bFGF (20 ng/ml). At 12 hours during the 2nd-step (PSM induction), the cells were split into multiple 35 mm dishes at 4.0 × 10^5 cells/dish and cultured in CDMi containing SB431542 (10 µM), LDN193189 (250 nM) and CHIR99021 (3 µM). After 12 hours culture the medium was changed into CDMi containing SB431542 (10 µM), LDN193189 (250 nM), CHIR99021 (1 µM) and bFGF (20 ng/ml). The luminescence was continuously monitored with Kronos Dio Luminometer with one sample, and the other samples were frozen at each time point.

value: 201B7 based Hes7-reporter

tag: time


title: PEP_D17_rep2 [Blood mRNA]

description: Gene expression from rat blood


title: iPSC HES7-KO 1 [KO]

source_name: iPSC HES7-KO clone 1


title: iPSC HES7-KO 2 [KO]

source_name: iPSC HES7-KO clone 7


title: iPSC WT Ex2 [KO]


title: Oscillation Ex2 Time Point 15 [Hs]

value: 990 min


title: Oscillation Ex2 Time Point 14 [Hs]

value: 945 min


title: Oscillation Ex2 Time Point 13 [Hs]

value: 895 min


title: Oscillation Ex2 Time Point 11 [Hs]

value: 815 min


title: Oscillation Ex2 Time Point 12 [Hs]

value: 855 min


title: PSM SCDP1-F

source_name: SCDP1-F patient iPSC

value: SCDP1 patient iPSC line (clone F)

value: PSM (presomitic mesoderm)

value: Coriell GM13539


title: Oscillation Ex2 Time Point 10 [Hs]

value: 775 min


title: Oscillation Ex2 Time Point 8 [Hs]

value: 690 min


title: Oscillation Ex2 Time Point 9 [Hs]

value: 735 min


title: Air_D13_rep5 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, control, 13 days

value: 9 weeks old

value: male

value: Sprague-Dawley

value: blood


title: Oscillation Ex2 Time Point 7 [Hs]

value: 640 min


title: Air_D13_rep4 [Blood mRNA]

description: Gene expression from rat blood


title: PEP_D13_rep5 [Blood mRNA]

description: Gene expression from rat blood


title: PEP_D13_rep1 [Blood mRNA]

description: Gene expression from rat blood


title: Oscillation Ex2 Time Point 6 [Hs]

value: 201B7 based Hes7-reporter

value: 590 min


title: Air_D13_rep1 [Blood mRNA]

description: Gene expression from rat blood


title: Air_D13_rep3 [Blood mRNA]

description: Gene expression from rat blood


title: PEP_D21_rep6 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 21 days


title: Oscillation Ex2 Time Point 4 [Hs]

value: 505 min


title: Air_D13_rep2 [Blood mRNA]

description: Gene expression from rat blood


title: Oscillation Ex2 Time Point 5 [Hs]

value: 545 min


title: PEP_D21_rep4 [Blood mRNA]

description: Gene expression from rat blood


title: Oscillation Ex2 Time Point 3 [Hs]

value: 463 min


title: Oscillation Ex2 Time Point 1 [Hs]

value: 380 min


title: Oscillation Ex1 Time Point 16 [Hs]

source_name: Hes7-luciferase iPSC reporter derived human PSM Ex1

value: 975 min


title: Oscillation Ex2 Time Point 2 [Hs]

value: PSM (presomitic mesoderm)

value: 423 min


title: PEP_D21_rep2 [Blood mRNA]

description: Gene expression from rat blood


title: Oscillation Ex1 Time Point 14 [Hs]

value: 885 min


title: PEP_D21_rep5 [Blood mRNA]

description: Gene expression from rat blood


title: Oscillation Ex1 Time Point 12 [Hs]

value: 798 min


title: Oscillation Ex1 Time Point 13 [Hs]

value: 840 min


title: PEP_D21_rep3 [Blood mRNA]

description: Gene expression from rat blood

value: 9 weeks old


title: PEP_D21_rep1 [Blood mRNA]

description: Gene expression from rat blood

value: male


title: Air_D21_rep4 [Blood mRNA]

description: Gene expression from rat blood

source_name: blood, control, 21 days

value: Sprague-Dawley


title: Air_D21_rep6 [Blood mRNA]

description: Gene expression from rat blood

value: blood


title: Oscillation Ex1 Time Point 11 [Hs]

value: 755 min


title: Air_D21_rep5 [Blood mRNA]

description: Gene expression from rat blood


title: Oscillation Ex1 Time Point 10 [Hs]

value: 201B7 based Hes7-reporter

value: 713 min


title: Oscillation Ex1 Time Point 9 [Hs]

value: 670 min


title: Oscillation Ex1 Time Point 8 [Hs]

value: 628 min


title: Air_D21_rep2 [Blood mRNA]

description: Gene expression from rat blood


title: Air_D21_rep3 [Blood mRNA]

description: Gene expression from rat blood


title: Oscillation Ex1 Time Point 7 [Hs]

value: 585 min


title: NaB_48h_R1_rep1

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

description: molecule: bru-labeled RNA

data_processing:
Illumina Casava v1.8.2 was used for basecalling.
Reads were aligned to the human ribosomal DNA complete repeating unit (U13369.1) and human mitochondrial genome (chrM from hg38) using Bowtie 2 v2.3.3.1 and options: -a -q --end-to-end --score-min L,-0.8,-0.8. Unaligned reads were then aligned to the human reference genome (hg38) using STAR and options: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --chimSegmentMin 20 --outFilterMatchNminOverLread 0.88 --outSAMmultNmax 1
A coverage determination was then made per base in the human reference genome such that a base covered by one read was given a coverage value of 1 / read length. These base coverages were used to obtain pseudo-read counts in regions of interest using bedtools 2 v2.28.0 (bedtools intersect with strand-specific option -s).
Reads Per Kilobase per Megabase of library size (RPKM) were calculated using a protocol adapted from from Chepelev et al., Nucleic Acids Research, 2009. In short, the exons from all isoforms of a gene were merged to create one meta-transcript with inter-exonic regions defined as introns. Thus genes were measured by counting reads (pseudo counts) falling within the exons and introns of these meta-transcripts and normalized by the size of the gene (effective length) and by the size of the library (uniquely mapped read count).
For EBV gene expression quantification: reads were aligned to the human reference genome (hg38) using Bowtie 2 v2.3.4.  Unmapped reads were aligned to the EBV reference genome (B95-8; NC_007605.1) using Bowtie 2 v2.3.4.  Read counts for EBV genes were obtained using featureCounts from the R package Subread v1.5.3.  Counts were normalized using the TMM method via the R package edgeR v2.34.3.  R version used was 3.5.1.
Genome_build: hg38
Supplementary_files_format_and_content: Hg38 gene expression files are tab-delimited text files where the first 6 columns conform to standard BED6 format.  Column definitions: (1) "chr" - chromosome; (2) "start"; (3) "end"; (4) "name" - gene symbol; (5) "score" (set to 0 as a placeholder); (6) "strand"; (7) "ensembl_gene" - Ensembl gene ID; (8) "effective_length" - sum of feature lengths, i.e. exons and introns; (10) "read_count" - pseudo read count; (11) "read_density" read_count/effective_length; (12) "RPKM" - read_count/(effective_length/1x10^3)/(mapped read count/1x10^6).  human_genes_counts.txt, human_genes_RPKM.txt, and EB_genes_TMM.txt are tab-delimited text files where each line represents a gene and columns are either gene annotations or expression values for samples indicated in the column headers.  For EBV_genes_TMM.txt, annotation columns (1-7) are obtained from the featureCounts output and contain semicolon-collapsed values where a gene has multiple isoforms.

growth_protocol: HH514-16 cells were cultured in RPMI1640 (Gibco) with 10% fetal bovine serum (Alphabioregen) and 1% penicillin-streptomycin (Gibco).

extract_protocol:
Following bromouridine labeling, cell were immediately collected by centrifugation and lysed in 1 mL TRIzol (Invitrogen).  RNA was extracted per TRIzol protocol. Goat anti-mouse IgG magnetic Dynabeads (110.33; Invitrogen) were prepared by washing 50 µL of beads with 200 μl 0.1% BSA in DEPC-PBS three times. Beads were resuspended in 200 μl 0.1% BSA in DEPC-PBS, followed by incubation with 2 μg anti-BrdU mouse monoclonal antibody (555627; BD Biosciences) and 20 U RNaseOUT (10777-019; Invitrogen) for 1 hour at room temperature. Beads were washed three times and resuspended in 200 μl 0.1% BSA in DEPC-PBS containing 20 U RNaseOUT. To isolate BrU labeled RNA, samples were heated at 80°C for 10 min, placed on ice, and 90% of the sample was added to prepared beads and incubated with rotation for 1 hour at room temperature. Nascent RNA bound beads were washed three times with 0.1% BSA in DEPC-PBS. For elution, beads were resuspended in 40 μl DEPC-water and incubated at 95 °C for 10 min, followed by magnetic capture. Supernatant containing purified nascent BrU-containing RNA was removed and quantified (Nanodrop; Thermo Scientific).
cDNA libraries were prepared using reagents in the Illumina TruSeq RNA Prep Kit. Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then synthesized, in the presence of Actinomycin D, to result in strand specific reads. After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, followed by cDNA end repair, adenylation, and adapter ligation (TruSeq RNA Prep Kit). The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then DNA fragments were enriched using the PCR reagents from the TruSeq RNA Prep Kit. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.
Bru-seq

treatment_protocol: HH514-16 cells (1x10^11) were treated (or not) with 3mM sodium butyrate (Sigma-Aldrich #303410) for 3, 24, and 48 hours.  Bromouridine (2mM; Sigma #850187) was then added to the condition media for 30 min.

tag: disease

value: Epstein-Barr virus-related Burkitt lymphoma

tag: cell type

value: Cancer cell line

tag: treatment

value: NaB

tag: concentration

tag: treatment time

value: 48 hours

tag: bru labeling time

value: 0.5 hours

tag: time between bru labeling and rna extraction

value: 0 hours

tag: labeling agent

value: Bromouridine (Bru)


title: Oscillation Ex1 Time Point 6 [Hs]

value: PSM (presomitic mesoderm)

value: 543 min


title: NaB_24h_R1_rep2

description: molecule: bru-labeled RNA

value: male

value: 24 hours


title: Air_D21_rep1 [Blood mRNA]

description: Gene expression from rat blood

tag: age

value: 9 weeks old

tag: strain

value: Sprague-Dawley

value: blood


title: U2OS_mock

type: genomic

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

institute: National Cancer Center Research Institute

description: cell line

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

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software (V2011.1 Methylation module 1.9.0) was used.  Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Osteosarcoma cell line 06_mock

label_protocol: Standard Illumina Protocol

growth_protocol: HOS, MNNG/HOS, 143B, MG63, U2OS, and A673 were maintained in DMEM, RE-ES and W-ES were in RPMI1640, SaOS2 and SK-ES-1 were in McCoy's 5A medium.

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol.

treatment_protocol: Two OS cells (MG63, U2OS2) were treated with 1 µM of 5-aza-dC, and methylation status compared with mock-treated cells were searched.

tag: gender


title: NaB_48h_R1_rep2

description: molecule: bru-labeled RNA

tag: Sex


title: F_05_28d_1500: Rv2663

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

description: Rats were gavaged daily with acetamide in water vehicle

data_processing:
Illumina NextSeq 500 control software v2.1.0 with BCL files uploaded to Illumina BaseSpace for FASTQ file generation
Sequences trimmed from both based on QC (TRIMMOMATIC, min. retained read length 50bp), and mapped to Illumina iGenomes UCSC Rn6 using BOWTIE2
SAM files to BAM, and gene counts extracted from BAM files with HTSeq
Genome_build: UCSC Rn6 (Illumina iGenomes)
Supplementary_files_format_and_content: Tab delimited text files of gene counts

source_name: Liver (left lobe)

extract_protocol:
Total RNA was isolated using the Maxwell RSC Simply RNA Tissue Kit (Promega, Cat No: AS1340).
Library preparation was accomplished using the TruSeq Stranded mRNA Library Preparation Kit (Illumina, CatNo: RS-122-2103)

treatment_protocol: Rat were gavaged daily with water vehicle or acetamide, and the left lobe of the liver collected (at 7 or 28 days) for RNA-seq analysis.

tag: tissue

value: Liver (left lobe)

value: Female

tag: age unit

value: weeks

value: Acetamide

tag: treatment cas

tag: dose

tag: dose unit

value: mg/kg/day

tag: treatment duration

tag: duration unit

value: days

tag: replicate

tag: exposure series

value: Exposure Experiment 2


title: MG63_DAC 1uM

description: cell line

source_name: Osteosarcoma cell line 04_DAC 1uM


title: NaB_24h_R1_rep1

description: molecule: bru-labeled RNA

tag: disease

value: Epstein-Barr virus-related Burkitt lymphoma

tag: cell type

value: Cancer cell line

tag: treatment

value: NaB

tag: concentration

tag: treatment time

value: 0.5 hours


title: F_04_28d_1500: Rv2662

tag: strain

tag: age


title: W-ES

description: cell line

source_name: Ewing sarcoma cell line 02

tag: gender


title: Oscillation Ex1 Time Point 4 [Hs]

tag: background line

value: 201B7 based Hes7-reporter

tag: Stage

value: PSM (presomitic mesoderm)

tag: time

value: 458 min


title: NaB_3h_R1_rep2

description: molecule: bru-labeled RNA

tag: Sex

value: male

value: 3 hours

tag: bru labeling time

tag: time between bru labeling and rna extraction

value: 0 hours

tag: labeling agent

value: Bromouridine (Bru)


title: Oscillation Ex1 Time Point 3 [Hs]

value: 415 min


title: U2OS_DAC 1uM

description: cell line

source_name: Osteosarcoma cell line 06_DAC 1uM


title: F_03_28d_1500: Rv2661

tag: tissue

value: Liver (left lobe)

value: Female

tag: age unit

value: weeks

tag: treatment cas

tag: dose

tag: dose unit

tag: treatment duration

tag: duration unit

tag: replicate


title: F_02_28d_1500: Rv2660

tag: strain

tag: age

tag: treatment

value: Acetamide

value: mg/kg/day

value: days

tag: exposure series


title: NaB_3h_R1_rep1

description: molecule: bru-labeled RNA

tag: disease

value: Epstein-Barr virus-related Burkitt lymphoma

tag: cell type

value: Cancer cell line

tag: concentration

tag: treatment time


title: RD-ES

description: cell line

source_name: Ewing sarcoma cell line 01

tag: gender


title: F_01_28d_1500: Rv2659

tag: tissue

tag: Sex

value: Exposure Experiment 2


title: MG63_mock

description: cell line

source_name: Osteosarcoma cell line 04_mock


title: SK-ES-1

description: cell line

source_name: Ewing sarcoma cell line 04


title: SaOS2

description: cell line

source_name: Osteosarcoma cell line 05


title: Oscillation Ex1 Time Point 1 [Hs]

tag: background line

value: 201B7 based Hes7-reporter

tag: Stage

tag: time

value: 330 min


title: UT_48h_R1_rep2

description: molecule: bru-labeled RNA

value: untreated

value: 48 hours

tag: bru labeling time

value: 0.5 hours

tag: time between bru labeling and rna extraction

tag: labeling agent


title: U2OS

description: cell line

source_name: Osteosarcoma cell line 06


title: HOS

description: cell line

source_name: Osteosarcoma cell line 03


title: M_05_28d_1500: Rv2657

tag: strain

value: Male

tag: age unit

tag: treatment cas

tag: dose

tag: dose unit

tag: treatment duration

tag: duration unit

tag: replicate


title: SCL (1231A3) Ex3 [Differentiation]

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
The low-quality bases at the 3' read ends and the adaptor sequences were trimmed by cutadapt-1.14.
The sequenced reads were mapped to the hg38 human reference genome plus the luciferase reporter sequence using HISAT2 (version 2.1.0) with the human GENCODE v25 annotation gtf file.
The mapped reads with high mapping quality (MAPQ >= 2) were used for further analyses.
FPKM values were determined by Cuffdiff within Cufflinks version 2.2.1 package and the human GENCODE v25 annotation file.
Genome_build: hg38
Supplementary_files_format_and_content: The tab-delimited text file include FPKM values for each sample.

source_name: iPSC (healthy control)

growth_protocol: Human iPSCs were maintained without feeder cells and cultured on iMatrix-511-silk (Nippi) coated dishes or plates with StemFit® AK02N (Ajinomoto) medium supplemented with 50 U penicillin and 50 mg/ml streptomycin (Gibco).

extract_protocol:
RNA was extracted with the RNeasy mini kit (Qiagen) following the manufacturer’s instructions.
RNA-seq libraries were generated from 200-300 ng total RNA with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.

treatment_protocol: Human iPSCs were seeded on iMatrix-51-silk (Nippi) coated plates at appropriate densities as single cells (1.3 × 10^4 cells/well into 6 well plate) 5 days before induction. All differentiation and induction steps were performed in chemically defined medium with insulin (CDMi). Human primitive streak (PS) cells were induced by treatment of iPSCs with human recombinant proteins bFGF (20 ng/ml) and Activin A (50 ng/ml) and small molecule CHIR99021 (10 µM)  for 24 hours. Presomitic mesoderm (PSM) cells were induced from PS cells by exposure to SB431542 (10 µM), CHIR99021 (3 µM), LDN193189 (250 nM) and bFGF (20 ng/ml) for 24 hours. Subsequently, somitic mesoderm (SM) cells were induced from PSM cells using PD173074 (100 nM) and XAV939 (1 µM) for 24 hours. Following initial step-wise somitic mesoderm (SM) induction, human sclerotome (SCL) cells were induced with combination of SAG (100 nM) and LDN193189 (600 nM) for 72 hours. Dermomyotome (DM) cells were induced from human somitic mesoderm, using a combination of CHIR99021 (3 µM), GDC0449 (150 nM) and BMP4 (50 ng/ml) for 48 hours.

value: SCL (sclerotome)


title: Oscillation Ex1 Time Point 5 [Hs]

value: PSM (presomitic mesoderm)

value: 500 min


title: UT_48h_R1_rep1

description: molecule: bru-labeled RNA

tag: disease

tag: cell type

value: male

tag: treatment

tag: treatment time

value: 0 hours

value: Bromouridine (Bru)


title: M_04_28d_1500: Rv2656

tag: tissue

value: Liver (left lobe)

tag: Sex

tag: age

value: weeks

value: Acetamide

value: mg/kg/day

tag: exposure series


title: Oscillation Ex1 Time Point 2 [Hs]

tag: background line

tag: Stage

tag: time

value: 373 min


title: SCL (1231A3) Ex2 [Differentiation]


title: Mus05

description: resection, normal muscle

source_name: Normal muscle 05

tag: gender


title: MG63

description: cell line

source_name: Osteosarcoma cell line 04


title: UT_24h_R1_rep2

description: molecule: bru-labeled RNA

value: Epstein-Barr virus-related Burkitt lymphoma

value: Cancer cell line

value: 24 hours

tag: bru labeling time

tag: time between bru labeling and rna extraction

tag: labeling agent


title: Mus03

description: resection, normal muscle

source_name: Normal muscle 03

value: Female


title: M_03_28d_1500: Rv2655

tag: strain

tag: age unit

tag: treatment cas

tag: dose

tag: dose unit

tag: treatment duration

tag: duration unit

value: days

value: Exposure Experiment 2


title: UT_24h_R1_rep1

description: molecule: bru-labeled RNA

tag: disease

tag: cell type

tag: Sex

tag: treatment

value: untreated

tag: treatment time

value: 0.5 hours


title: 143B

description: cell line

source_name: Osteosarcoma cell line 01

tag: age


title: UT_3h_R1_rep2

description: molecule: bru-labeled RNA

value: 3 hours


title: A673

description: cell line

source_name: Ewing sarcoma cell line 03

tag: gender


title: Lung1(OS21M_N)

description: resection, normal lung

source_name: Normal lung 02

value: Male


title: SCL (1231A3) Ex1 [Differentiation]

tag: background line

tag: Stage

value: SCL (sclerotome)


title: M_01_28d_1500: Rv2653

source_name: Liver (left lobe)

tag: tissue

tag: replicate

tag: exposure series


title: DM (1231A3) Ex3 [Differentiation]

value: DM (dermomyotome)


title: DM (1231A3) Ex2 [Differentiation]


title: empty +

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description: 11 days after infection with sgRNA (Linked to GFP) vector with no payload sgRNA (as non-PDXK inhibited control), sorted GFP +

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Genome_build: Reads were aligned to the mouse transcriptome (mm10, GRCm38) or human transcriptome (hg19, GRCh37)
Supplementary_files_format_and_content: Tab-delimited text file includes rpkm normalized table for each sample

source_name: MOLM13 human leukemia line

growth_protocol: Cells were cultured with RPMI medium supplemented with 10% FBS (Gibco)

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

tag: cell line

value: no drug treatment, sample with intact PDXK


title: F_05_28d_1000: Rv2652

value: Liver (left lobe)

tag: strain

tag: age unit

value: weeks

tag: treatment cas

tag: dose


title: DM (1231A3) Ex1 [Differentiation]


title: empty -

description: 11 days after infection with sgRNA (Linked to GFP) vector with no payload sgRNA (as non-PDXK inhibited control), sorted GFP -


title: MNNG

description: cell line

source_name: Osteosarcoma cell line 02


title: F_04_28d_1000: Rv2651

value: Acetamide

tag: dose unit

value: mg/kg/day

tag: treatment duration

tag: duration unit


title: SM (1231A3) Ex3 [Differentiation]

value: SM (somitic mesoderm)


title: SM (1231A3) Ex2 [Differentiation]


title: Rosa26 -

description: 11 days after infection with sgRNA (Linked to GFP) targeting mouse Rosa26 locus (as non-PDXK inhibited control), sorted GFP -

tag: treatment


title: F_02_28d_1000: Rv2648

tag: Sex


title: Oscillation Ex1 Time Point 15 [Hs]

source_name: Hes7-luciferase iPSC reporter derived human PSM Ex1

value: 201B7 based Hes7-reporter

value: PSM (presomitic mesoderm)

tag: time

value: 930 min


title: SM (1231A3) Ex1 [Differentiation]


title: Rosa26 +

description: 11 days after infection with sgRNA (Linked to GFP) targeting mouse Rosa26 locus (as non-PDXK inhibited control), sorted GFP +


title: hPDXK-aa230 +

description: 11 days after infection with sgRNA (Linked to GFP) targeting human PDXK, sorted GFP +

value: no drug treatment, sample with PDXK knock-out


title: Fat03

description: resection, normal fat

source_name: Normal fat 03

tag: gender

value: Female

tag: age


title: UT_3h_R1_rep1

description: molecule: bru-labeled RNA

tag: disease

value: Epstein-Barr virus-related Burkitt lymphoma

tag: cell type

value: Cancer cell line

value: male

value: untreated

tag: treatment time

tag: bru labeling time

tag: time between bru labeling and rna extraction

value: 0 hours

tag: labeling agent

value: Bromouridine (Bru)


title: F_03_28d_1000: Rv2649

tag: tissue

tag: strain

tag: age unit

value: days

tag: replicate

tag: exposure series

value: Exposure Experiment 2


title: F_01_28d_1000: Rv2647

value: Liver (left lobe)

value: weeks

tag: treatment cas

tag: dose

tag: dose unit

tag: treatment duration

tag: duration unit


title: M_05_28d_1000: Rv2646

tag: Sex

value: Male

tag: age

tag: treatment

value: Acetamide

value: mg/kg/day


title: PSM (1231A3) Ex2 [Differentiation]

tag: background line

tag: Stage

value: PSM (presomitic mesoderm)


title: M_04_28d_1000: Rv2645


title: PSM (1231A3) Ex1 [Differentiation]


title: hPDXK-aa105 +

tag: cell line


title: hPDXK-aa105 -

description: 11 days after infection with sgRNA (Linked to GFP) targeting human PDXK, sorted GFP -

value: no drug treatment, sample with intact PDXK


title: OS-8M

description: resection, fibula metastasis

source_name: Osteosarcoma metastatic tumor tissue 03 fibula

tag: gender


title: Bone05

description: resection, normal bone

source_name: Normal bone 05


title: PS (1231A3) Ex3 [Differentiation]

value: PS (primitive streak)


title: M_03_28d_1000: Rv2643

tag: tissue


title: M_02_28d_1500: Rv2654

tag: strain


title: OS-33M

description: resection, lung metastasis

source_name: Osteosarcoma metastatic tumor tissue 05 lung

value: Female


title: hPDXK-aa22 +

value: no drug treatment, sample with PDXK knock-out


title: M_02_28d_1000: Rv2642

tag: age unit


title: Bone03

description: resection, normal bone

source_name: Normal bone 03


title: PS (1231A3) Ex2 [Differentiation]


title: hPDXK-aa22 -


title: hPDXK-aa15 +


title: F_05_28d_750: Rv2639

tag: replicate


title: PS (1231A3) Ex1 [Differentiation]


title: M_01_28d_1000: Rv2641

tag: exposure series


title: OS-16M

description: resection, lung metastasis

source_name: Osteosarcoma metastatic tumor tissue 04 lung


title: hPDXK-aa230 -


title: Fat05

description: resection, normal fat

source_name: Normal fat 05


title: iPSC (1231A3) Ex3 [Differentiation]

source_name: iPSC (healthy control)

value: iPSC (induced pluripotent stem cell)


title: hPDXK-aa15 -


title: F_04_28d_750: Rv2638

tag: treatment cas


title: Cr8 +

description: 11 days after infection with sgRNA (Linked to GFP) targeting mouse chrom 8 locus (as non-PDXK inhibited control), sorted GFP +


title: F_02_28d_750: Rv2636

tag: dose


title: SCL (201B7) Ex3 [Differentiation]

value: SCL (sclerotome)


title: Cr8 -

description: 11 days after infection with sgRNA (Linked to GFP) targeting mouse chrom 8 locus (as non-PDXK inhibited control), sorted GFP -


title: EWS-11M

description: resection, lung metastasis

source_name: Ewing sarcoma matastatic tumor tissue 01 lung


title: WM278 shCDR1as_IGF2BP3_RIP_3

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

description:
processed data files:
RIPseq_shCDR1as_FPKM.xlsx
RIPseq_shCDR1as_DEG.xlsx

data_processing:
Read alignment: STAR aligner was used to map reads against the reference genome hg38. Only uniquely mapping reads were kept.
Read counting: STAR aligner integrated counting method (specific paramter --quantMode GeneCounts) was applied using gene level annotations downloaded from Genecode version 26.
Normalization: DESeq2 was used to normalize read counts per sample, using CDS length from Genecode V26 to calculate FPKM values.
DEG: DESeq2 was used to calculate differential expression between RIP and input samples in order to estimate significant enrichment of bound vs. unbound transcripts.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM and DEG as xlsx

source_name: human melanoma cell line

growth_protocol: WM278 shNTC and shCDR1as were cultured in TU2% (80% MCDB153 pH7.5/20% L15 supplemented with 2% Tet-free FBS, Insulin (5ug/mL), and 1.68mM CaCl2.

extract_protocol:
RIP assay was performed with control IgG or IGF2BP3-specific antibody (MBL International) using RIP Assay Kit (MBL International) following manufacturer supplied protocol, following the high-salt wash method. Cell suspensions were thawed briefly on ice prior to lysis and RIP assay. Input RNA samples and eluted IGF2BP3 RIP RNA samples were used in standard RNA-seq library preparations.
Total RNA was depleted of rRNA by Ribo-zero gold. Stranded libraries were prepared by Illumina ScriptSeq Complete Gold/TruSeq Stranded following manufacturer's recommendations.

treatment_protocol: WM278 shNTC and shCDR1as cells were treated with 1ug/mL Doxycycline for 72hrs prior to cell harvest in 4 x 15cm dishes per condition per replicate.  Cells were harvested for RNA extraction at ~80% confluence. Briefly, cells were washed 1X with PBS, detached from culture vessels by trypsinzation, quenched with growth media, then placed on ice. Cell suspensions were washed 1X with PBS, counted, and 10e7 cells pellets were snap-frozen prior to RIP.

tag: cell type

value: melanoma cell line

tag: sample type (input or igf2bp3 rip)

value: IGF2BP3 RIP

value: TetON pLKO shCDR1as + 1ug/mL Doxycycline


title: F_01_28d_750: Rv2635

tag: dose unit

tag: treatment duration

tag: duration unit

value: days


title: OS-31M

description: resection, lung metastasis

source_name: Osteosarcoma metastatic tumor tissue 31 lung

tag: age


title: OS-28T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 28 femur


title: OS-25T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 25 femur


title: OS-30T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 30 femur


title: SCL (201B7) Ex2 [Differentiation]

tag: background line


title: M_05_28d_750: Rv2633

source_name: Liver (left lobe)

tag: Sex

tag: treatment

value: Exposure Experiment 2


title: SCL (201B7) Ex1 [Differentiation]

tag: Stage


title: WM278 shCDR1as_IGF2BP3_RIP_2

tag: cell line


title: OS-24T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 24 femur

tag: gender


title: OS-26T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 26 femur


title: OS-21M

description: resection, lung metastasis

source_name: Osteosarcoma metastatic tumor tissue 06 lung


title: PSM (1231A3) Ex3 [Differentiation]


title: OS-22T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 22 tibia


title: DM (201B7) Ex3 [Differentiation]

value: DM (dermomyotome)


title: WM278 shNTC_IGF2BP3_RIP_3

description:
processed data files:
RIPseq_shNTC_FPKM.xlsx
RIPseq_shNTC_DEG.xlsx

value: TetON pLKO shNTC + 1ug/mL Doxycycline


title: M_03_28d_750: Rv2631

tag: tissue

value: Liver (left lobe)

tag: strain

value: Male

tag: age unit

value: weeks


title: iPSC (1231A3) Ex2 [Differentiation]


title: OS-32M

description: resection, lung metastasis

source_name: Osteosarcoma metastatic tumor tissue 02 lung


title: DM (201B7) Ex2 [Differentiation]


title: WM278 shNTC_IGF2BP3_RIP_2


title: OS-23T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 23 ilium


title: M_04_28d_750: Rv2632

value: Acetamide

tag: treatment cas

value: mg/kg/day

tag: replicate

tag: exposure series


title: OS-21T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 21 femur


title: M_02_28d_750: Rv2630

tag: dose


title: iPSC (1231A3) Ex1 [Differentiation]


title: F_03_28d_750: Rv2637

tag: dose unit


title: M_01_28d_750: Rv2629

tag: treatment duration


title: WM278 shCDR1as_Input_3

tag: cell type

tag: sample type (input or igf2bp3 rip)

value: Input


title: SM (201B7) Ex3 [Differentiation]

tag: background line

value: SM (somitic mesoderm)


title: F_05_28d_500: Rv2627

tag: Sex

value: Female

tag: age

tag: duration unit


title: WM278 shCDR1as_Input_2

tag: cell line

tag: treatment


title: DM (201B7) Ex1 [Differentiation]

tag: Stage


title: OS-18T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 18 femur

tag: gender


title: F_04_28d_500: Rv2626

tag: tissue

tag: strain

tag: age unit


title: F_03_28d_500: Rv2625

tag: treatment cas

tag: replicate

tag: exposure series


title: SM (201B7) Ex2 [Differentiation]


title: PSM (201B7) Ex3 [Differentiation]

value: PSM (presomitic mesoderm)


title: SM (201B7) Ex1 [Differentiation]


title: WM278 shCDR1as_Input_1


title: OS-14T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 14 femur


title: F_01_28d_500: Rv2623

tag: dose

tag: dose unit

tag: treatment duration


title: WM278 shNTC_Input_2

tag: cell type

tag: sample type (input or igf2bp3 rip)


title: WM278 shNTC_Input_3


title: OS-27T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 27 femur

tag: age


title: PSM (201B7) Ex1 [Differentiation]

source_name: iPSC (healthy control)

tag: background line


title: F_02_28d_500: Rv2624

tag: Sex

tag: duration unit


title: PSM (201B7) Ex2 [Differentiation]

tag: Stage


title: OS-16T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 16 femur

tag: gender


title: WM278 shNTC_Input_1

source_name: human melanoma cell line

tag: cell line

tag: treatment


title: OS-19T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 19 tibia


title: WM278 shCDR1as_IGF2BP3_RIP_1


title: PS (201B7) Ex3 [Differentiation]

value: PS (primitive streak)


title: M_05_28d_500: Rv2621

tag: tissue

tag: strain

tag: age unit


title: OS-20T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 20 femur


title: 4L_rep-002

description:
RNAseq_processed_FPKM.tsv
4L_rep2

data_processing:
Read alignment: STAR aligner version 2.5.0c was used to map reads against the reference genome hg38. Only uniquely mapping reads were kept (specific parameters: --trim5p=13, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.05)
Read counting: STAR aligner version 2.5.0c integrated counting method (specific paramter --quantMode GeneCounts) was applied using gene level annotations downloaded from Ensembl Genes V85.
Normalization: edgeR version 3.14.0 was used to normalize read counts per sample and genes were filtered for counts-per-million > 1. CDS length from Ensembl Genes V85 was used to calculate FPKM values for filtered genes (edgeR function 'rpkm').
Genome_build: hg38
Supplementary_files_format_and_content: FPKM table (tsv)

source_name: melanoma cell line

growth_protocol: Cultured melanocytes were grown in manufacturer supplied/recommended media. Media was changed every other day and cells were passaged/harvested for RNA extraction at ~80% confluence. Melanoma STCs were isolated as described in De Miera et al. PMID: 22404973 and cultured in DMEM supplemented with 10% FBS, Non-essential amino acids, and Pen-Strep. Established melanoma cell lines were cultured in DMEM supplemented with 10% FBS and Pen-Strep (501MEL, SK-MEL-147, SK-MEL-239, A375) or TU2% (80% MCDB153 pH7.5/20% L15 supplemented with 2% FBS, Insulin (5ug/mL), and 1.68mM CaCl2 (WM278 and WM1361a).

extract_protocol:
Total RNA extraction was performed using Qiagen miRNeasy mini kits following manufacturer's recommended protocol, including on-column DNAse treatment.
Total RNA was depleted of rRNA by Ribo-zero gold. Stranded libraries were prepared by Illumina ScriptSeq Complete Gold/TruSeq Stranded following manufacturer's recommendations.

treatment_protocol: All cells were harvested for RNA extraction between 60-80% confluence. Briefly, cells were washed 1X with PBS, detached from culture vessels by trypsinzation or cell dissociation buffer, quenched with growth media, then placed on ice. Cell suspensions were washed 1X with PBS, pelleted, and lysed in Qiazol. If indicated, cells were infected with lentiviral contstructs and selected with antibiotics. WM278 shNTC and shCDR1as cells were treated with 1ug/mL Doxycycline for 72hrs prior to cell harvest, RNA extraction, and RNA-seq.

tag: commercial or academic source

value: University of Toronto, Robert Kerbel

value: pLKO.1 shNTC


title: PS (201B7) Ex1 [Differentiation]


title: 4L_rep-003

description:
RNAseq_processed_FPKM.tsv
4L_rep3


title: M_03_28d_500: Rv2619

source_name: Liver (left lobe)

tag: treatment cas

tag: dose

tag: replicate

tag: exposure series


title: M_02_28d_500: Rv2618

tag: dose unit

tag: treatment duration


title: 4L_rep-001

description:
RNAseq_processed_FPKM.tsv
4L_rep1


title: M_04_28d_500: Rv2620

tag: age


title: SK-MEL-239_rep-002

description:
RNAseq_processed_FPKM.tsv
skmel239_rep2

value: Memorial Sloan Kettering, Alan Houghton


title: WM278 shNTC_IGF2BP3_RIP_1

tag: cell type

value: melanoma cell line

tag: sample type (input or igf2bp3 rip)

value: IGF2BP3 RIP


title: M_01_28d_500: Rv2617

tag: Sex

tag: duration unit

value: days

value: Exposure Experiment 2


title: OS-15T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 15 tibia

tag: gender


title: PS (201B7) Ex2 [Differentiation]

tag: background line

tag: Stage


title: SK-MEL-239_rep-001

description:
RNAseq_processed_FPKM.tsv
skmel239_rep1


title: iPSC (201B7) Ex2 [Differentiation]

value: iPSC (induced pluripotent stem cell)


title: F_05_28d_300: Rv2615

tag: tissue

value: Liver (left lobe)

tag: strain

tag: treatment


title: iPSC (201B7) Ex1 [Differentiation]


title: iPSC (201B7) Ex3 [Differentiation]


title: A375_rep-003

description:
RNAseq_processed_FPKM.tsv
A375_rep3

tag: commercial or academic source

value: ATCC


title: F_04_28d_300: Rv2614

tag: age unit

value: weeks

value: Acetamide

tag: treatment cas

tag: dose


title: A375_rep-002

description:
RNAseq_processed_FPKM.tsv
A375_rep2


title: OS-11T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 11 tibia

value: Male


title: A375_rep-001

description:
RNAseq_processed_FPKM.tsv
A375_rep1


title: OS-9T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 09 femur


title: F_03_28d_300: Rv2613

tag: dose unit

value: mg/kg/day

tag: replicate

tag: exposure series


title: OS-12T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 12 ilium

tag: age


title: F_02_28d_300: Rv2612

value: Female

tag: treatment duration


title: OS-17T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 17 tibia


title: WM1361a_rep-003

description:
RNAseq_processed_FPKM.tsv
wm1361a_rep3

value: Rockland, Inc.

value: pWPI Empty


title: F_01_28d_300: Rv2611

tag: Sex


title: WM1361a_rep-002

description:
RNAseq_processed_FPKM.tsv
wm1361a_rep2


title: M_05_28d_300: Rv2609

tag: duration unit


title: OS-10T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 10 femur

tag: gender


title: WM1361a_rep-001

description:
RNAseq_processed_FPKM.tsv
wm1361a_rep1


title: OS-7T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 07 fibula


title: M_04_28d_300: Rv2608


title: OS-5T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 05 femur


title: FIPV nsp1-3

city: Wuhan

first: Zhou

last: Shen

state: Hubei

address: 1 Shi-zi-shan Street

country: China

institute: Huazhong agriculture university

data_processing:
FastQC
Hisat2
Samtools
StringTie
Deseq2
Genome_build: hg19
Supplementary_files_format_and_content: Normalized read count matrix processed by Deseq2

source_name: HEK 293T_FIPV nsp1

extract_protocol:
Using TRIzol based method following manufactures instruction
Using VAZYME NR612 following manufactures instruction

tag: cell line

value: HEK 293T

tag: cell type

value: Human embryo kidney cell line

tag: genotype/variation

value: Transfection of FIPV oriented NSP3 contained PCAGGS


title: Melanoma_STC_primary_12-126

description:
RNAseq_processed_FPKM.tsv
primary_12_126

source_name: human melanoma short-term culture

value: NYU Langone Health

tag: primary/metastatic

value: primary


title: M_02_28d_300: Rv2606

tag: tissue

tag: strain

tag: treatment

value: days


title: FIPV nsp1-1

value: Transfection of FIPV oriented NSP1 contained PCAGGS


title: OS-8T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 08 femur


title: M_03_28d_300: Rv2607

tag: age unit

tag: treatment cas

value: Exposure Experiment 2


title: FIPV nsp1-2

value: Transfection of FIPV oriented NSP2 contained PCAGGS


title: Melanoma_STC_LN_12-215

description:
RNAseq_processed_FPKM.tsv
LN_12_215

tag: commercial or academic source

value: metastatic (lymph node)


title: SADS-CoV nsp1-1

source_name: HEK 293T_SADS-CoV nsp1

value: Transfection of SADS-CoV oriented NSP1 contained PCAGGS


title: Melanoma_STC_LN_12-019

description:
RNAseq_processed_FPKM.tsv
LN_12_019


title: F_04_28d_0: Rv2602

value: Liver (left lobe)

value: weeks

value: Acetamide

tag: dose

tag: dose unit

tag: replicate


title: PCAGGS-3

source_name: HEK 293T_PCAGGS

value: Transfection of empty backbone


title: OS-4T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 04 maxilla

value: Female

tag: age


title: Melanoma_STC_LN_10-040

description:
RNAseq_processed_FPKM.tsv
LN_10_040


title: OS-1T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 01 femur

value: Male


title: OS-3T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 03 ilium


title: SADS-CoV nsp1-3

value: HEK 293T

value: Transfection of SADS-CoV oriented NSP3 contained PCAGGS


title: M_01_28d_300: Rv2605

source_name: Liver (left lobe)

tag: Sex

value: mg/kg/day

tag: treatment duration

tag: exposure series


title: Melanoma_STC_primary_09-162

description:
RNAseq_processed_FPKM.tsv
primary_07_013

value: NYU Langone Health


title: F_05_28d_0: Rv2603

tag: duration unit


title: OS-13T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 13 tibia

tag: gender


title: OS-2T

description: biopsy, bone tumor

source_name: Osteosarcoma primary tumor tissue 02 femur


title: Melanoma_STC_Par_10-230

description:
RNAseq_processed_FPKM.tsv
Par_10_230

value: metastatic (parotid)


title: EWS-8T

description: biopsy, soft tussue tumor

source_name: Ewing sarcoma primary tumor tissue 08 neck


title: Melanoma_STC_primary_07-013

description:
RNAseq_processed_FPKM.tsv
primary_09_162

value: primary


title: EWS-7T

description: biopsy, bone tumor

source_name: Ewing sarcoma primary tumor tissue 07 ilium


title: PCAGGS-1

tag: cell line

tag: cell type

value: Human embryo kidney cell line

tag: genotype/variation


title: M_05_28d_0: Rv2597

tag: tissue

tag: strain

value: days

value: Exposure Experiment 1


title: Melanoma_STC_BM_11-161

description:
RNAseq_processed_FPKM.tsv
BM_11_161

tag: primary/metastatic

value: metastatic (brain)


title: SADS-CoV nsp1-2

value: Transfection of SADS-CoV oriented NSP2 contained PCAGGS


title: F_02_28d_0: Rv2600

value: Liver (left lobe)

tag: age unit

tag: treatment

tag: treatment cas

value: Exposure Experiment 2


title: F_01_28d_0: Rv2599

value: weeks

value: Acetamide

tag: dose

tag: dose unit


title: M_04_28d_0: Rv2596

tag: age

tag: replicate


title: set2IgGB1000_smRNA

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: microRNA of set2IgGB1000

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
Abundance measurements were otained using HTSeq for RNA-Seq and Flicker for smallRNA-Seq
Genome_build: UCSC hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene or miRNA

source_name: B cells

growth_protocol: Human IgD+ naïve B cells were purified by negative selection from healthy donor PBMCs using the EasySep Human Naïve B Cell Enrichment Kit (19254, STEMCELL Technologies).  Naïve B cells were then cultured in FCS-RPMI and stimulated with trimeric CD154 (10 U ml-1), IL-4 (20 ng ml-1, R&D Systems) and IL-21 (50 ng ml-1, R&D Systems) or CD154 (10 U ml-1), IL-21 (50 ng ml-1) and TGF-β (0.5 ng ml-1) in the presence of nil, butyrate ((1000 M)) for 60 hours.

extract_protocol:
Total RNA was extracted using Direct-zol RNA Miniprep Plus kit (Zymo Research) following manufacturer's instructions.
Libraries were prepared for sequencing using standard Illumina TruSeq protocol for mRNA and small RNA

treatment_protocol: PBS or sodium butyrate (1000 mM in PBS) were added into human B cells cultures.

value: Human IgD+ naive B cells

tag: presence

value: short-chain fatty acid butyrate


title: PCAGGS-2

value: HEK 293T

value: Transfection of empty backbone


title: Melanoma_STC_BM_12-273

description:
RNAseq_processed_FPKM.tsv
BM_12_273

tag: commercial or academic source


title: EWS-9T

description: biopsy, soft tussue tumor

source_name: Ewing sarcoma primary tumor tissue 09 head

value: Female


title: Melanoma_STC_BM_12-126

description:
RNAseq_processed_FPKM.tsv
BM_12_126

value: NYU Langone Health


title: Melanoma_STC_BM_11-103

description:
RNAseq_processed_FPKM.tsv
BM_11_103


title: EWS-5T

description: biopsy, bone tumor

source_name: Ewing sarcoma primary tumor tissue 05 tibia


title: set2IgGNil_mRNA

description: mRNA of set2IgGNil


title: set2IgGNil_smRNA

description: microRNA of set2IgGNil


title: M_02_28d_0: Rv2594

tag: Sex

value: Male

value: mg/kg/day

tag: treatment duration

tag: duration unit

tag: exposure series


title: set2IgGB1000_mRNA

description: mRNA of set2IgGB1000

tag: cell type


title: M_03_28d_0: Rv2595

tag: tissue


title: Melanoma_STC_BM_11-001

description:
RNAseq_processed_FPKM.tsv
BM_11_001


title: M_01_28d_0: Rv2593

tag: strain


title: EWS-10T

description: biopsy, soft tussue tumor

source_name: Ewing sarcoma primary tumor tissue 10 thigh

tag: gender


title: EWS-6T

description: biopsy, bone tumor

source_name: Ewing sarcoma primary tumor tissue 06 ilium


title: 14yo_rep2

city: Salt Lake City

first: Jingtao

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

description:
processed data file:
Pubertal_combined_UMI.txt.gz
column header naming format:
Y14-barcode_sequence-2

data_processing:
Samples were sequenced as paired end sequencing. Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v2.2.0). Fastq files were then run with count application (Cell Ranger v2.2.0) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: Testicular cells

extract_protocol:
Testicular tissues were firstly minced into small pieces mechanically, and subject to trypsin digestion for ~25 min at 37 C. Cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 26 X 100 cycle paired-end run via a Illumina 2500 instrument. Each sample was sequenced in one separate sequencing lane.

value: Testicle


title: G5A_HD_06: Ru5710

tag: age unit

value: days


title: 14yo_rep1

description:
processed data file:
Pubertal_combined_UMI.txt.gz
column header naming format:
Y14-barcode_sequence-1


title: 13yo_rep2

description:
processed data file:
Pubertal_combined_UMI.txt.gz
column header naming format:
Y13-barcode_sequence-2


title: G5A_HD_04: Ru5708

description: Rats were gavaged daily with acetamide in water vehicle

tag: treatment

value: Exposure Experiment 1


title: 13yo_rep1

description:
processed data file:
Pubertal_combined_UMI.txt.gz
column header naming format:
Y13-barcode_sequence-1


title: G5A_HD_03: Ru5707

tag: treatment cas


title: G5A_HD_05: Ru5709

tag: dose


title: 11yo_rep2

description:
processed data file:
Pubertal_combined_UMI.txt.gz
column header naming format:
Y11-barcode_sequence-2


title: G5A_HD_02: Ru5706

tag: dose unit


title: 11yo_rep1

description:
processed data file:
Pubertal_combined_UMI.txt.gz
column header naming format:
Y11-barcode_sequence-1

tag: age


title: G4A_ID_06: Ru5704

tag: replicate


title: EWS-3T

description: biopsy, bone tumor

source_name: Ewing sarcoma primary tumor tissue 03 rib


title: G4A_ID_05: Ru5703


title: EWS-2T

description: biopsy, bone tumor

source_name: Ewing sarcoma primary tumor tissue 02 fibula


title: F_03_28d_0: Rv2601


title: 7yo_rep2

description:
processed data file:
Pubertal_combined_UMI.txt.gz
column header naming format:
Y7-barcode_sequence-2


title: G4A_ID_04: Ru5702


title: EWS-4T

description: biopsy, bone tumor

source_name: Ewing sarcoma primary tumor tissue 04 fibula


title: G4A_ID_02: Ru5700


title: EWS-1T

description: biopsy, soft tussue tumor

source_name: Ewing sarcoma primary tumor tissue 01 thigh


title: GS1492_1acute_DHF_DP_100

city: Seattle

first: Yuan

last: Tian

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to GRCh38 reference genome and Gencode 27 annotations using TopHat v1.4.1 (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite v0.20.3 (Schmieder and Edwards, 2011) and low-complexity reads (DUST > 4) were removed from the BAM files. The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (Anders et al., 2015) using the “union” option. After removing absent features (zero counts in all samples), the raw counts were then imported to DESeq2 to identify differentially expressed genes between groups (Love et al., 2014).
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file containing DESeq2 counts with variance stabilizing transformation

molecule: polyA RNA

source_name: Cryopreserved PBMC

extract_protocol:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
For each condition, 100 cells were collected at 4 ˚C in 8 μL of lysis buffer composed by 0.2% Triton X-100, 2 U/ul of recombinant RNase inhibitor (Clontech/Takara), 5 mM dNTP mix (Life Technologies) in 0.2 ml PCR tube (Maxymum recovery, Axygen). Right after sort, tubes were vortexed at medium speed, spun for 5 minutes at >2000 g and stored at -80˚C until the completion of the whole set of samples. Purified total RNA (≈5 ng) was amplified following the Smart-seq2 protocol (Picelli et al., 2014; Rosales et al., 2018). Briefly, mRNA was captured using poly-dT oligos and directly reverse-transcribed into full-length cDNA using the described template-switching oligo (Picelli et al., 2014; Rosales et al., 2018). cDNA was amplified by PCR for 18 cycles and purified using AMPure XP magnetic bead (0.9:1 (vol:vol) ratio, Beckman Coulter).
For each sample, 1 ng of cDNA was used to prepare a standard NextEra XT sequencing library (NextEra XT DNA library prep kit and index kits; Illumina). Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). Both whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR preamplification cycles, and fragment library size. Samples that failed quality controls were eliminated from downstream steps. Library that passed strict quality controls were pooled at equimolar concentration, loaded and sequenced on the Illumina Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina) mapping uniquely to mRNA reference, generating a total of about 204.3 million mapped reads (median of about 8.6 million filtered mapped reads per sample).

treatment_protocol: Human PBMCs were rested overnight at 37 °C and subsequently stimulated with DENV CD4 T cell peptide pool (1 μg/ml for individual peptides) for 3 h at 37 °C. IFN-g- and IL-10-producing cells were labeled using IFN-γ Secretion Assay – Detection Kit (PE), human (catalog# 130-054-202, Miltenyi Biotech) and IL-10 Secretion Assay – Detection Kit (APC), human (catalog# 130-090-761, Miltenyi Biotech), respectively, according to the manufacturer’s instructions. Subsequently, PBMCs were stained with anti-human CD3, CD4, CD8, CD14, CD19, CD45RA, and CCR7. CD4 IL-10-IFN-g- DN, IL-10+IFN-g- IL-10 SP and IL-10-IFN-g+ IFN-g SP, and IL-10+IFN-g+ DP cells were sorted into 8 μL of lysis buffer consisting of Triton X-100 (Sigma-Aldrich), recombinant ribonuclease inhibitor (Takara), and dNTP mix (Thermo Fisher Scientific).

tag: disease group

value: DHF

tag: donor

value: PBMC

tag: cell subset

value: DP


title: G4A_ID_01: Ru5699

value: Liver (left lobe)

tag: Sex

tag: treatment duration


title: GS1465_1acute_DHF_DP_100


title: GS1492_1acute_DHF_IL10_pos_75


title: G3A_MD_06: Ru5698

value: weeks

tag: duration unit

tag: exposure series


title: GS1465_1acute_DHF_IL10_pos_100

tag: cell type


title: G3A_MD_05: Ru5697

tag: tissue

tag: strain

value: Acetamide


title: GS1465_1acute_DHF_IFNg_pos_100


title: GS1492_1acute_DHF_IFNg_pos_100


title: G3A_MD_03: Ru5695

tag: age unit


title: PEP_D21T_rep4 [Lung miRNA]

description: Gene expression from rat blood

hyb_protocol: Following Labeling procedure, .88 ug were hybridized at 45C on miRNA-4.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592)

data_processing: TAC 4.0 was used with annotation miRNA-4_1-st-v1.annotations.20160922.csv to generate RMA expression values. Linear models were fit using the limma package of bioconductor in R version 3.4

source_name: lung, exposed, 21 days, implanted with radio telemetry system

value: male

value: lung

value: Sprague-Dawley

value: 9 weeks


title: Air_D21T_rep2 [Lung miRNA]

description: Gene expression from rat blood

source_name: lung, control, 21 days, implanted with radio telemetry system

value: 9 weeks old


title: PEP_D21T_rep1 [Lung miRNA]

description: Gene expression from rat blood


title: Air_D21T_rep3 [Lung miRNA]

description: Gene expression from rat blood


title: PEP_D1_rep3 [Lung miRNA]

description: Gene expression from rat blood

source_name: lung, exposed, 1 day


title: PEP_D21T_rep3 [Lung miRNA]

description: Gene expression from rat blood


title: Air_D21T_rep4 [Lung miRNA]

description: Gene expression from rat blood


title: GS1492_1acute_DHF_DN_100

value: DN


title: G3A_MD_02: Ru5694

source_name: Liver (left lobe)

value: Male

tag: treatment


title: G2A_LD_05: Ru5691

tag: treatment cas

value: mg/kg/day


title: PEP_D1_rep5 [Lung miRNA]

description: Gene expression from rat blood


title: G2A_LD_04: Ru5690

tag: dose


title: Air_D21T_rep1 [Lung miRNA]

description: Gene expression from rat blood


title: GS1465_1acute_DHF_DN_100


title: 7yo_rep1

description:
processed data file:
Pubertal_combined_UMI.txt.gz
column header naming format:
Y7-barcode_sequence-1

value: Testicle


title: G3A_MD_04: Ru5696

tag: dose unit

value: days


title: PEP_D21T_rep2 [Lung miRNA]

description: Gene expression from rat blood

tag: age


title: PEP_D1_rep4 [Lung miRNA]

description: Gene expression from rat blood


title: PEP_D1_rep2 [Lung miRNA]

description: Gene expression from rat blood


title: GS1445_1acute_DHF_IL10_pos_100


title: G2A_LD_03: Ru5689

tag: replicate

value: Exposure Experiment 1


title: GS1445_1acute_DHF_DP_100

tag: disease group

value: DHF


title: PDAC-A inDrop2

first: Itai

last: Yanai

state: NY

address: 435 E. 30th Street, 8th Floor

institute: Institute for Computational Medicine, NYU Langone Health

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
Raw sequencing data obtained from the inDrop method were processed using a custom-built pipeline, available online (https://github.com/flo-compbio/singlecell). Briefly, the “W1” adapter sequence of the inDrop RT primer was located in the barcode read (the second read of each fragment), by comparing the 22-mer sequences starting at positions 9-12 of the read with the known W1 sequence (“GAGTGATTGCTTGTGACGCCTT”), allowing at most two mismatches. Reads for which the W1 sequence could not be located in this way were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read, which can range from 8-11 bp, as well as the start position of the second part of the inDrop cell barcode, which always consists of 8 bp. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read, allowing at most one mismatch. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally, the UMI sequence was extracted, and reads with low-confidence base calls for the six bases comprising the UMI sequence (minimum PHRED score less than 20) were discarded. The reads containing the mRNA sequence (the first read of each fragment) were mapped by STAR 2.5.1 with parameter “—outSAMmultNmax 1” and default settings otherwise36. Mapped reads were split according to their cell barcode and assigned to genes by testing for overlap with exons of protein-coding genes.
Raw sequencing data obtained from the Spatial Transcriptomics (ST) method were processed using a publicly available pipeline (https://github.com/jfnavarro/st_pipeline). Briefly, quality trimming is performed to remove low quality bases and reads with long nucleotide stretches (> 15). Read 2 (transcript sequence) is mapped with STAR 2.5.1 and Read 1 (spatial barcode) is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq-count; to get a final read count annotated reads are grouped by spatial barcode.
Genome_build: hg38
Supplementary_files_format_and_content: for inDrop data: tab-delimited files with genes as rows and cells as columns. For ST data: tab-delimited files with spots as rows (with first column is the coordinate of each spot along the array) and genes are columns.

source_name: pancreatic adenocarcinoma tissue

extract_protocol:
For single-cell RNA-seq (inDrop platform), cell suspension was generated by incubating minced pancreatic cancer tissue with trypsin for 15' at 37C prior to droplet encapsulation and individual barcoding of cells using the inDrop platform. Cell lysis was performed in droplets to release RNA, and reverse transcription and barcoding took place in droplets at 50C for 2h. For spatial transcriptomics of pancreatic cancer tissue, 10 µm cryosections were mounted onto spatially barcoded arrays where reverse transcription of cellular transcripts took place in situ after tissue permeabilisation.
For single-cell RNA-seq library construction, we followed the inDrop library construction protocol detailed by Klein et al,  Cell 2015, with minor changes. Briefly, RNA was reverse transcribed (RT) with SuperScript III (Invitrogen) in droplets. Droplet emulsions were broken, and post-RT material underwent second strand syntehsis and in vitro transcription using the T7 High Yield Enzyme mix (New England Biolabs). RNA was fragmented for 105 seconds with 1X fragmentation reagent (1CellBio) prior to RT with random hexamers, eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).   For spatial transcriptomics (ST) library construction, we followed the previously published ST protocol from Stahl et al. Science 2016, with minor changes. Briefly, after brightfield imaging of stained tissue, tissue was permeabilized with collagenase and 0.1% pepsin prior to an overnight RT step with SuperScript III on the ST slide. Tissue was digested away with proteinase K and 1% 2-mercaptoethanol prior to cleavage of probes from the slide surface with USER enzyme. Second strand synthesis was performed with DNA Pol I and RNase H (New england biolabs) followed by an in vitro transcription amplification step with the MEGAScript T7 kit (Thermofisher). Amplified RNA then underwent a second RT with random hexamers and SuperScript II (Invitrogen), eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).

value: pancreatic adenocarcinoma

tag: tissue preparation

value: single-cell suspension of tissue


title: Air_D1_rep5 [Lung miRNA]

description: Gene expression from rat blood

source_name: lung, control, 1 day


title: Air_D1_rep3 [Lung miRNA]

description: Gene expression from rat blood


title: PEP_D1_rep1 [Lung miRNA]

description: Gene expression from rat blood


title: PDAC-A inDrop1


title: Air_D1_rep2 [Lung miRNA]

description: Gene expression from rat blood


title: Air_D1_rep4 [Lung miRNA]

description: Gene expression from rat blood


title: Air_D1_rep1 [Lung miRNA]

description: Gene expression from rat blood


title: G2A_LD_02: Ru5688

value: Liver (left lobe)


title: GS1405_1acute_DHF_IFNg_pos_47

tag: donor

value: PBMC

tag: cell subset


title: GS1405_1acute_DHF_DN_100


title: Air_D5_rep4 [Lung miRNA]

description: Gene expression from rat blood

source_name: lung, control, 5 days

tag: Sex


title: GS1445_1acute_DHF_IFNg_pos_100


title: Melanoma_STC_LN_09-203

description:
RNAseq_processed_FPKM.tsv
LN_09_203

source_name: human melanoma short-term culture

tag: commercial or academic source

value: NYU Langone Health

tag: primary/metastatic

value: metastatic (lymph node)


title: G1A_VC_04: Ru5684

value: weeks

value: Acetamide

tag: treatment duration

tag: duration unit

tag: exposure series


title: Air_D5_rep5 [Lung miRNA]

description: Gene expression from rat blood

value: male

tag: strain

value: Sprague-Dawley

tag: tissue

value: lung


title: G2A_LD_01: Ru5687

value: Male

tag: age unit

tag: treatment

tag: treatment cas


title: G1A_VC_05: Ru5685

tag: age

tag: dose

tag: dose unit

value: mg/kg/day


title: GS1445_1acute_DHF_DN_100

tag: disease group

tag: cell type

value: DN


title: GS1594_1acute_DHF_DP_100

tag: donor

tag: cell subset

value: DP


title: GS1594_1acute_DHF_IL10_pos_100


title: G1A_VC_02: Ru5682

tag: Sex

value: days

tag: replicate

value: Exposure Experiment 1


title: GS1594_1acute_DHF_IFNg_pos_100

value: DHF


title: F_05_7d_1500: Rv2591

value: Female

tag: treatment duration

value: Exposure Experiment 2


title: GS1594_1acute_DHF_DN_100

value: PBMC


title: G1A_VC_03: Ru5683

value: Liver (left lobe)

tag: duration unit


title: Air_D5_rep2 [Lung miRNA]

description: Gene expression from rat blood

value: 9 weeks old


title: GS1442_1acute_DF_IL10_pos_43

value: DF


title: PEP_D5_rep4 [Lung miRNA]

description: Gene expression from rat blood

source_name: lung, exposed, 5 days


title: Treated_6

city: Pamplona

first: Jose

last: Hermida

address: Pio XII 55

country: Spain

institute: CIMA

description:
TC_6.CEL
Gene expression data from a mouse treated with CM-695

hyb_protocol: Labeled sense cDNA was hybridized to the GeneChip® Mouse Gene 2.0 ST Arrays, washed and stained on a GeneChip® Fluidics 450 workstation (Affymetrix) according to the manufacturer protocols.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000 7G

data_processing: Data were normalized with Bioconductor software using RMA algorithm.

organism: Mus musculus

source_name: Aortic vessel tissue_CM-695 administration

label_protocol: The sense cDNA was prepared from 450 ng of total RNA using the QIAgen® RNeasy Mini Kit. The sense strand cDNA was then fragmented and biotinylated according to the manufacturer's instructions.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions.

treatment_protocol: Two groups of 6 female CD-1 mice (Harlan Interfauna Iberica S.A., Barcelona, Spain) were intraperitoneally administered with CM-695 (80 mg/kg twice: two and one hour before sacrifice) or vehicle ((saline solution). CM-695 is a dual inhibitor of HDAC6 and phosphodiesterase 9. After sacrifice, mice were perfused with 10 mL phosphate buffered saline and aortic vessel was then extracted, snap frozen and stored at -80C until RNA extraction was performed.

tag: gender

value: female

tag: treated with

value: Aortic vessel tissue


title: GS1438_1acute_DF_IL10_pos_100


title: Treated_5

description:
TC_5.CEL
Gene expression data from a mouse treated with CM-695

tag: strain

tag: tissue


title: F_04_7d_1500: Rv2590

tag: age unit

value: weeks

tag: treatment

value: Acetamide

tag: exposure series


title: Air_D5_rep3 [Lung miRNA]

description: Gene expression from rat blood

extract_protocol: Total RNA was isolated from rat blood using a mirVana miRNA Isolation Kit from Ambion per the manufacturer's protocol. Rat lungs were initially disrupted by transferring them to a 2 mL microcentrifuge tube containing 400 μL silica beads and 600 μL Lysis/Binding Solution.

tag: age

value: male

value: Sprague-Dawley

value: lung


title: G1A_VC_01: Ru5681

value: Male

tag: treatment cas

tag: dose

tag: dose unit

value: mg/kg/day


title: Treated_4

description:
TC_4.CEL
Gene expression data from a mouse treated with CM-695


title: F_02_7d_1500: Rv2588

value: days


title: PEP_D5_rep5 [Lung miRNA]

description: Gene expression from rat blood


title: F_03_7d_1500: Rv2589


title: Control_6

description:
NT_6.CEL
Gene expression data from a mouse treated with saline solution

source_name: Aortic vessel tissue_vehicle administration

value: Saline (vehicle) solution


title: Treated_3

description:
TC_3.CEL
Gene expression data from a mouse treated with CM-695


title: Treated_2

description:
TC_2.CEL
Gene expression data from a mouse treated with CM-695


title: Air_D5_rep1 [Lung miRNA]

description: Gene expression from rat blood


title: F_01_7d_1500: Rv2587

value: Female


title: non-infect

description: 7 days after infection (mock infection with spinnning and polybrene but no vrus added)

source_name: MLLAF9-NrasG12D mouse leukemia

tag: cell line

value: no drug treatment, sample with intact pdxk


title: PEP_D5_rep2 [Lung miRNA]

description: Gene expression from rat blood


title: M_05_7d_1500: Rv2585

value: Exposure Experiment 2


title: PEP_D5_rep1 [Lung miRNA]

description: Gene expression from rat blood


title: Treated_1

description:
TC_1.CEL
Gene expression data from a mouse treated with CM-695


title: PEP_D5_rep3 [Lung miRNA]

description: Gene expression from rat blood


title: GS1442_1acute_DF_IFNg_pos_100

tag: disease group

tag: donor

tag: cell type

value: PBMC

tag: cell subset


title: Control_5

description:
NT_5.CEL
Gene expression data from a mouse treated with saline solution


title: GS1431_1acute_DF_DP_100

value: DP


title: GS1438_1acute_DF_DN_100

value: DF

value: DN


title: GS1442_1acute_DF_DN_100


title: Control_4

description:
NT_4.CEL
Gene expression data from a mouse treated with saline solution

value: female

value: Aortic vessel tissue


title: human-2 +

description: 7 days after infection with sgRNA (Linked to GFP) targeting human locus (as non-Pdxk inhibited control), sorted GFP +


title: human-2 -

description: 7 days after infection with sgRNA (Linked to GFP) targeting human locus (as non-Pdxk inhibited control), sorted GFP -


title: M_03_7d_1500: Rv2583

description: Rats were gavaged daily with acetamide in water vehicle

value: Liver (left lobe)

tag: Sex

value: weeks

value: Acetamide

tag: treatment duration

tag: duration unit

tag: replicate


title: human-1 +


title: M_02_7d_1500: Rv2582

tag: tissue

tag: strain


title: PEP_D9_rep5 [Lung miRNA]

description: Gene expression from rat blood

source_name: lung, exposed, 9 days

value: 9 weeks old

value: male

value: Sprague-Dawley

value: lung


title: GS1417_1acute_DF_DN_100


title: Control_2

description:
NT_2.CEL
Gene expression data from a mouse treated with saline solution

tag: gender

tag: treated with

value: Saline (vehicle) solution


title: Control_3

description:
NT_3.CEL
Gene expression data from a mouse treated with saline solution


title: PEP_D9_rep4 [Lung miRNA]

description: Gene expression from rat blood

tag: age


title: PEP_D9_rep3 [Lung miRNA]

description: Gene expression from rat blood


title: PEP_D9_rep2 [Lung miRNA]

description: Gene expression from rat blood


title: Control_1

description:
NT_1_2.CEL
Gene expression data from a mouse treated with saline solution


title: PEP_D9_rep1 [Lung miRNA]

description: Gene expression from rat blood


title: Pdxk-6 +

description: 7 days after infection with sgRNA (Linked to GFP) targeting mouse.Pdxk, sorted GFP +

tag: treatment

value: no drug treatment, sample with pdxk knock-out


title: M_04_7d_1500: Rv2584

value: Male

tag: age unit

tag: treatment cas

tag: dose

value: mg/kg/day

value: days

tag: exposure series


title: F_05_7d_1000: Rv2579

value: Female

tag: dose unit

value: Exposure Experiment 2


title: GS1431_1acute_DF_DN_100

tag: disease group

value: DF

tag: donor

tag: cell type

value: PBMC

value: DN


title: GS1449_1acute_DF_DP_100

tag: cell subset

value: DP


title: Pdxk-6 -

description: 7 days after infection with sgRNA (Linked to GFP) targeting mouse.Pdxk, sorted GFP -

tag: cell line

value: no drug treatment, sample with intact pdxk


title: GS1431_1acute_DF_IL10_pos_100


title: F_04_7d_1000: Rv2578

value: Liver (left lobe)

tag: Sex

value: weeks

value: Acetamide

tag: treatment duration

tag: duration unit

tag: replicate


title: human-1 -


title: F_03_7d_1000: Rv2577

tag: tissue

tag: strain


title: GS1449_1acute_DF_IL10_pos_100


title: Pdxk-5 +

tag: treatment


title: F_02_7d_1000: Rv2576

tag: age

tag: age unit


title: Pdxk-5 -


title: GS1449_1acute_DF_IFNg_pos_100


title: F_01_7d_1000: Rv2575

tag: treatment cas

tag: dose


title: M_01_7d_1500: Rv2581

tag: dose unit

tag: exposure series


title: Pdxk-4 +


title: GS1431_1acute_DF_IFNg_pos_100

tag: disease group

tag: donor


title: Air_D9_rep2 [Lung miRNA]

description: Gene expression from rat blood

source_name: lung, control, 9 days

value: 9 weeks old

value: male

value: Sprague-Dawley


title: Air_D9_rep3 [Lung miRNA]

description: Gene expression from rat blood

value: lung


title: Air_D9_rep4 [Lung miRNA]

description: Gene expression from rat blood


title: Air_D9_rep1 [Lung miRNA]

description: Gene expression from rat blood


title: Air_D9_rep5 [Lung miRNA]

description: Gene expression from rat blood


title: GS1458_1acute_DHF_DP_100

value: DHF

tag: cell type

tag: cell subset


title: M_03_7d_1000: Rv2571

tag: Sex

value: Male

value: mg/kg/day


title: M_04_7d_1000: Rv2572

tag: treatment duration

value: days


title: GS1404_1acute_DHF_DP_100


title: PEP_D21_rep4 [Lung miRNA]

description: Gene expression from rat blood

source_name: lung, exposed, 21 days


title: Pdxk-3 -

tag: cell line


title: Pdxk-4 -


title: GS1470_1acute_DHF_IL10_pos_100


title: GS1449_1acute_DF_DN_100


title: Pdxk-2 +

value: no drug treatment, sample with pdxk knock-out


title: GS1470_1acute_DHF_DP_100


title: M_02_7d_1000: Rv2570

tag: duration unit

tag: replicate

value: Exposure Experiment 2


title: M_01_7d_1000: Rv2569

tag: tissue

tag: strain


title: GS1458_1acute_DHF_IL10_pos_100

value: PBMC


title: GS1404_1acute_DHF_IL10_pos_100


title: M_05_7d_1000: Rv2573

tag: age

tag: treatment


title: Pdxk-2 -


title: Pdxk-1 +


title: F_05_7d_750: Rv2567

value: Female

tag: age unit

tag: treatment cas


title: Pdxk-3 +


title: PEP_D21_rep5 [Lung miRNA]

description: Gene expression from rat blood


title: GS1470_1acute_DHF_IFNg_pos_100


title: PEP_D21_rep6 [Lung miRNA]

description: Gene expression from rat blood


title: Pdxk-1 -


title: F_04_7d_750: Rv2566

tag: dose

tag: dose unit


title: PEP_D21_rep2 [Lung miRNA]

description: Gene expression from rat blood


title: PEP_D21_rep1 [Lung miRNA]

description: Gene expression from rat blood


title: Air_D21_rep6 [Lung miRNA]

description: Gene expression from rat blood

source_name: lung, control, 21 days


title: PEP_D21_rep3 [Lung miRNA]

description: Gene expression from rat blood


title: GS1458_1acute_DHF_IFNg_pos_100

source_name: Cryopreserved PBMC

tag: disease group


title: F_03_7d_750: Rv2565

tag: exposure series


title: Rosa26 + 2

description: 7 days after infection with sgRNA (Linked to GFP) targeting Rosa26 mouse locus (as non-Pdxk inhibited control), sorted GFP +


title: GS1404_1acute_DHF_IFNg_pos_100

tag: donor

tag: cell type


title: F_02_7d_750: Rv2564

tag: Sex


title: Rosa26 - 2

description: 7 days after infection with sgRNA (Linked to GFP) targeting Rosa26 mouse locus (as non-Pdxk inhibited control), sorted GFP -


title: Air_D21_rep4 [Lung miRNA]

description: Gene expression from rat blood


title: GS1470_1acute_DHF_DN_100

tag: cell subset

value: DN


title: F_01_7d_750: Rv2563

tag: treatment duration


title: Air_D21_rep5 [Lung miRNA]

description: Gene expression from rat blood


title: GS1458_1acute_DHF_DN_100


title: Rosa26 - 1

tag: cell line

value: no drug treatment, sample with intact pdxk


title: Rosa26 + 1


title: M_05_7d_750: Rv2561

value: Liver (left lobe)

tag: duration unit

tag: replicate


title: GS1436_1acute_DHF_DN_100


title: M_04_7d_750: Rv2560

tag: tissue

tag: strain

value: weeks


title: Air_D21_rep2 [Lung miRNA]

description: Gene expression from rat blood

tag: age


title: GS1404_1acute_DHF_DN_100


title: M_03_7d_750: Rv2559

tag: age unit

tag: treatment

value: Acetamide