title: NoEGF_UT_SiCT_3 (PXR)

value: liver

value: primary hepatocyte

tag: group

value: EGF-

value: SiCT


title: EGF_CITCO_SiCAR_5 (CAR)

status: Public on Apr 27 2018

type: RNA

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix® HG-U133+PM Array. StripChips were washed and stained on the fluidic station of the Affymetrix GeneAtlas system with HWS kit.

scan_protocol: GeneChips were washed stained and scanned using the Affymetrix GeneAtlas system.

data_processing: Raw data was RMA normalized using the limma package for R/Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: liver, CITCO, EGF+, SiCAR

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix GeneAtlas IVT PLUS protocol from 100 ng total RNA (GeneChip® 3'IVT PLUS Reagent Kit,P/N703210 Rev1 Affymetrix).

growth_protocol: Primary Human Hepatocytes were seeded in collagen-coated 24 well plates, maintained at confluence and cultured in a 5% CO2 humidified atmosphere at 37°C. Cells were maintained in Hepatocyte growth medium (HGM) (WME medium supplemented with 5µg/ml insulin, 0.1µM hydrocortisone, 10µg/ml transferrin, 250µg/ml ascorbic acid, 3.75mg/ml fatty acid free bovine serum albumin, penicillin, streptomycin, and glutamine). HGM was supplemented with EGF 10ng/ml in the +EGF condition

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

treatment_protocol: Primary Human Hepatocytes were transfected with targeting siRNA (si control (siCT) or siCAR) at D2 and D5 after plating. At D5, cells were treated with 1µM CITCO, 0.5mM PB or DMSO for 24h.

tag: donor id

tag: tissue

tag: cell type

value: CITCO

tag: medium

value: EGF+

tag: sirna

value: SiCAR


title: NoEGF_UT_SiCT_2 (PXR)

source_name: liver, none, EGF-, SiCT

treatment_protocol: Primary Human Hepatocytes were transfected with targeting siRNA (si control (siCT) or siPXR) at D2 and D5 after plating. At D5, cells were treated with 1µM CITCO, 0.5mM PB or DMSO for 24h.


title: microRNA-seq Hop2-/- #2

type: SRA

city: Bethesda

first: Galina

last: Petukhova

state: Maryland

address: 4301 Jones Bridge Rd

department: Biochemistry

country: USA

institute: USUHS

library_source: transcriptomic

data_processing:
Base-calls performed using CASAVA
microRNA seq Reads were mapping and quantified using MiRDeep2 v2.0.0.7. Significance testing for the differential expression analysis was performed using DESeq2.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: The file contains TPM for each sample.

organism: Mus musculus

source_name: Testis

extract_protocol: Small RNAs were isolated from whole testes using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific)

tag: strain

value: Testis

tag: antibody

tag: genotype

value: Hop2 KO


title: microRNA-seq Hop2-/- #1


title: EGF_CITCO_SiCAR_4 (CAR)


title: NoEGF_UT_SiCT_1 (PXR)


title: EGF_CITCO_SiCAR_2 (CAR)


title: EGF_CITCO_SiCAR_3 (CAR)


title: microRNA-seq Prdm9-/- #1

value: Prdm9 KO


title: microRNA-seq Prdm9-/- #2


title: mRNA-seq Hop2-/- #2

description:
mRNA-seq_TPM_genes.csv
mRNA-seq_TPM_transcripts.csv

data_processing:
Base-calls performed using CASAVA
mRNA seq Reads for each sample were quantified against mouse GRCm38 cDNA using kallisto0.43.0. Sleuth was used to perform the differential expression tests of genes and transcripts from kallisto quantifications.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: The file contains TPM for each sample.

extract_protocol: mRNA-eq libraries were prepared using mRNA-Seq Sample Preparation Kit (Illumina, RS-930-10)


title: EGF_CITCO_SiCAR_1 (CAR)


title: mRNA-seq Prdm9-/- #2


title: mRNA-seq Prdm9-/- #1


title: EGF_CITCO_SiCT_5 (CAR)

source_name: liver, CITCO, EGF+, SiCT


title: P22 ChIP-seq

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: processed data file: F2.DHR.DDT.csv.gz

library_source: genomic

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP and ChIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 (61) with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs and DHRs, the reference genome was broken into 100 bp windows. Genomic windows with less than 40 mapped reads summed across all samples were removed prior to further analysis. The MEDIPS R package (63) was then used to calculate differential coverage between control and exposure sample groups. The edgeR p-value (64) was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than 10-6 were considered DMRs or DHRs. The DMR/DHR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR/DHR.
CpG density and other information was then calculated for the DMR/DHR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Sperm

growth_protocol: Female and male rats of an outbred Hsd: Sprague Dawley SR®TM (Harlan) at about 70 and 100 days of age were fed ad lib with a standard rat diet and ad lib tap water for drinking. To obtain time-pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (day 0) rats were monitored for diestrus and body weight. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1. Non-littermate females and males aged 70-90 days from F1 generation of control, vinclozolin or DDT were bred to obtain F2 generation offspring. The F2 generation rats were similarly bred to obtain the F3 generation offspring. Individuals were maintained for 120 days and euthanized for sperm collection. The F1-F3 generation offspring were not themselves treated directly with vinclozolin or DDT. The control, vinclozolin and DDT lineage rats were housed in the same room with lighting, food and water as previously described

extract_protocol: The epididymis was dissected free of connective tissue, a small cut made to the cauda and tissue placed in 5 ml of 1xPBS for 10 minutes at 37°C and then kept at 4ºC to immobilize the sperm.  The epididymal tissue was minced and the released sperm centrifuged at 13, 000 x g and the pellet stored at -20ºC until processed further. The pellet was resuspended in NIM buffer and then one hundred μl of sperm suspension was combined with 820 μL DNA extraction buffer and 80 μl 0.1M DTT. The sample was incubated at 65°C for 15 minutes. Following this incubation 80 μl proteinase K (20 mg/ml) was added and the sample incubated at 55°C for at least 2 hours under constant rotation. Then 300 μl of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A) was added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 13,500 rpm for 20 minutes at 4°C. One ml of the supernatant was transferred to a 2 ml tube and 2 μl of glycoblue and 1 ml of cold 100 % isopropanol were added. The sample was mixed well by inverting the tube several times then left in -20°C freezer for at least one hour. After precipitation the sample was centrifuged at 13,500 rpm for 20 min at 4°C. The supernatant was taken off and discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol by adding 500μl of 70% ethanol to the pellet and returning the tube to the freezer for 20 minutes. After the incubation the tube was centrifuged for 10 min at 4°C at 13,500 rpm and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes). Pellet was then resuspended in 100 μl of nuclease free water. Equal amounts of DNA from several (3-6) individual sperm samples were used to produce three DNA pools per lineage and employed for methylated DNA immunoprecipitation (MeDIP). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: rat sperm DNA pools were generated using the appropriate amount of genomic DNA from each individual for 3 pools each of control and DDT lineage animals. Genomic DNA was sonicated using the Covaris M220 the following way: the pooled genomic DNA was diluted to 130 μl with TE into the appropriate Covaris tube. Covaris was set to 300 bp program and the program was run for each tube in the experiment. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube and the volume measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10min at 95˚C, then immediately cooled on ice for 10 min. Then 100μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4˚C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL) was added and the bead sample was resuspended. Tube was then placed into a magnetic rack for 1-2 minutes and the supernatant discarded. The tube was removed from the magnetic rack and the beads washed once. The washed beads were resuspended in the same volume of 1xIP buffer as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C. After the incubation the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into magnetic rack for 1-2 minutes and the supernatant discarded, then washed with 1xIP buffer 3 times. The washed bead-DNA solution is then resuspended in 250μl digestion buffer with 3.5μl Proteinase K (20mg/ml). The sample was then incubated for 2-3 hours on a rotator at 55˚ and then 250μl of buffered Phenol-Chloroform-Isoamylalcohol solution was added to the supe and the tube vortexed for 30 sec then centrifuged at 14,000rpm for 5min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250μl chloroform were added to the supernatant from the previous step, vortexed for 30sec and centrifuged at 14,000rpm for 5min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20˚C freezer for 1 hour to overnight. The precipitate was centrifuged at 14,000rpm for 20min at 4˚C and the supernatant removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20˚C freezer for 15 min. then centrifuged again at 14,000rpm for 5min at 4˚C and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212). Histone chromatin immunoprecipitation with genomic DNA was performed as follows: rat sperm pools were generated using a total of 8 million sperm for 3 pools of control and DDT lineage animals. The control pools contained 5-6 individuals for a total of n=17 rats, the DDT pools contained 4 individuals for a total of n=12 rats per exposure group. Sperm from each animal was sonicated 10 seconds using a Fisher Sonic Dismembrator Model 300 then counted individually on a Neubaeuer improved cell prior to pooling. The sperm pools were filled up to 1 ml with 1X PBS. To reduce disulfide bonds, 50 µl of 1M DTT was added to each pool and incubated for 2 hours at room temperature under constant rotation. To quench any residual DTT in the reaction, 120 µl of 1M of NEM (N-Ethylmaleimide, Thermo Scientific) was then added and incubated for 30 min at room temperature under constant rotation. The sperm cells were pelleted at 2,000g for 5 min at room temperature and the supernatant discarded. Pellets were resuspended in 1X PBS. The mixture was spinned again at 2,000g for 5 min at room temperature and the supernatant was discarded. The sperm cells were then resuspended in “complete buffer” in a ratio of 2 million sperm cells in 50 µl (as described by Hisano et al. 2013, (59)). “Complete buffer” was supplemented with tergitol 0.5% and DOC (sodium deoxycholate, Sigma Aldrich 30970). 50 µl of this mix was added to each aliquot. The tubes were homogenized and incubated for 20 min on ice. 10 Kuntz units of MNase (Roche, cat. no. 10107921001) were added and the samples incubated for 5 min at 37ºC. The reaction was stopped by the addition of 2 µl of EDTA 0.5 M. The sperm cells were aliquoted in ~ 4 µg of DNA. The genomic DNA was sonicated using the Covaris M220 the following way: ~ 4 µg of genomic DNA was resuspended in 130 µl of “complete buffer” supplemented with tergitol 0.5% and DOC 1%. Covaris was set to “Chromatin shearing” program for 10 min and the program was run for each tube in the experiment. Whether the samples were treated using the MNase or the Covaris, 10 µl of each sample was run on a 1.5% agarose gel to verify fragment size. The aliquots from the same sample were pooled back together and centrifuged at 12,500 rpm for 10 min at room temperature. The supernatant was transferred to a fresh microfuge tube. 65 µl of protease inhibitors were added in each sample. 3 µl of antibody (monoclonal r

treatment_protocol: On days 8 through 14 of gestation, the females were administered daily intraperitoneal injections of DDT (25 mg/kg BW/day) or dimethyl sulfoxide (DMSO) in oil (1 µl/kg BW/day vehicle). DDT (dichlorodiphenyltrichloroethane) was obtained from Chem Service Inc. (West Chester, PA). DDT was injected in DMSO vehicle. Treatment lineages are designated “control” or “DDT” lineages.

tag: gender

value: male

value: Sperm

tag: treatment

value: DDT exposed lineage

tag: generation


title: P23 ChIP-seq

description: processed data file: F2.DHR.DDT.csv.gz


title: mRNA-seq WT Adult

value: Wild type


title: P21 ChIP-seq

description: processed data file: F!.DHR.DDT.csv.gz


title: mRNA-seq Hop2-/- #1


title: EGF_CITCO_SiCT_3 (CAR)


title: P19 ChIP-seq

description: processed data file: F!.DHR.DDT.csv.gz


title: P20 ChIP-seq

description: processed data file: F!.DHR.DDT.csv.gz


title: P5 ChIP-seq

description: processed data file: F2.DHR.DDT.csv.gz

value: Control


title: CFT073 +pBAD rep 1

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

data_processing:
qC: We checked the quality of the raw reads data for each sample using FastQC (version 0.11.3) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.).
Alignment, Quantiatino and Normalization, Differential Expression : We used the SPARTA(version 1) software package for alignment, differential expression analysis, and post-analysis diagnostics. SPARTA is an RNA-Seq package specifically designed for bacterial studies. It uses the Bowtie(version 1.1.1) short read aligner, HTSeq(version 0.6.1) to count gene features, and edgeR for differential expression.
Annotation : The reference genome (Escherichia_coli_cft073.ASM744v1.dna.chromosome.Chromosome.fa) and annotations (Escherichia_coli_cft073.ASM744v1.32.gtf ) were downloaded from EnsemblBacteria
Genome_build: CFT073 E. coli
Supplementary_files_format_and_content: .xls,  spreadsheet of normalized read counts for each gene for each sample, differential expression data, and annotation

organism: Escherichia coli

source_name: Bacteria

growth_protocol: E. coli CFT073 carrying either pBAD or pBAD-tosR-his6 were cultured overnight in biological triplicates in LB medium containing ampicillin (100 µg/ml). Cultures were diluted 1:100 into fresh LB medium containing 10 mM L-arabinose and ampicillin and cultured at 37°C with aeration. A 400 µL sample was collected between OD600 0.46-0.96, and stabilized by the immediate addition of 800 µl of RNAprotect (Qiagen).

extract_protocol:
Cells were then lysed with 0.2 µM of lysozyme in TE (10 mM Tris-Cl, 1 mM EDTA, pH 8.0) for 5 min at room temperature, and total RNA was extracted using the RNeasy Mini Kit (Qiagen). DNA contamination was eliminated by treatment with TURBO DNase (Thermo Fisher). Depletion of ribosomal RNA was accomplished with the Ribominus Transcriptome Isolation Kit (Thermo Fisher) followed by ethanol precipitation.
Depletion of ribosomal RNA was accomplished with the Ribominus Transcriptome Isolation Kit (Thermo Fisher) followed by ethanol precipitation. A stranded library was prepared using a ScriptSeq kit (Illumina) using manufacturer’s recommended protocols.  Each sample was tagged with a six nucleotide barcode unique to each sample to allow multiplexing. The products are purified and enriched by PCR to create the final cDNA library. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (Kapa Biosystems) following the manufacturer's recommended protocols.  Six samples were sequenced per lane on a 50 cycle single end run on a HiSeq 2500 (Illumina) in high output mode using version 4 reagents.

tag: plasmid

value: pBAD


title: CFT073 +pBAD-tosR rep 3

value: pBAD-tosR


title: P4 ChIP-seq

description: processed data file: F2.DHR.DDT.csv.gz


title: CFT073 +pBAD rep 3


title: CFT073 +pBAD rep 2


title: EGF_PB_SiCAR_4 (CAR)

source_name: liver, Phenobarbital, EGF+, SiCAR

value: liver

value: Phenobarbital


title: EGF_PB_SiCAR_1 (CAR)

value: primary hepatocyte


title: EGF_CITCO_SiCT_1 (CAR)

value: SiCT


title: EGF_PB_SiCAR_3 (CAR)


title: EGF_CITCO_SiCT_2 (CAR)

value: CITCO


title: CFT073 +pBAD-tosR rep 2


title: EGF_PB_SiCAR_5 (CAR)

value: EGF+


title: P6 ChIP-seq

description: processed data file: F2.DHR.DDT.csv.gz


title: EGF_PB_SiCT_5 (CAR)

source_name: liver, Phenobarbital, EGF+, SiCT


title: EGF_PB_SiCAR_2 (CAR)

value: SiCAR


title: P2 ChIP-seq

description: processed data file: F!.DHR.DDT.csv.gz


title: CFT073 +pBAD-tosR rep 1


title: EGF_PB_SiCT_4 (CAR)


title: EGF_CITCO_SiCT_4 (CAR)


title: P3 ChIP-seq

description: processed data file: F!.DHR.DDT.csv.gz


title: DF3P27 MeDIP-seq

description: processed data file: F3.DMR.DDT.csv.gz


title: P1 ChIP-seq

description: processed data file: F!.DHR.DDT.csv.gz


title: EGF_PB_SiCT_2 (CAR)


title: EGF_PB_SiCT_1 (CAR)


title: EGF_UT_SiCAR_5 (CAR)

source_name: liver, none, EGF+, SiCAR


title: EGF_UT_SiCAR_4 (CAR)


title: DF3P26 MeDIP-seq

description: processed data file: F3.DMR.DDT.csv.gz


title: DF3P25 MeDIP-seq

description: processed data file: F3.DMR.DDT.csv.gz


title: human cervical cancer cell line HeLa

city: Shanghai

first: Hanbo

last: Ma

state: Shanghai

address: 389 Xin cun Road

department: Department of Obstetrics and Gynecology

country: China

institute: Tongji hospital

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 1 out of 8 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.

source_name: cervical cancer cell

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Total RNA was extracted using TRIZOL reagent (Invitrogen, NY, USA) in accordance with the manufacturer’s protocol. And then total RNA from each sample was quantified using the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA). The concentrations of the RNA samples were determined by OD260 using a NanoDrop instrument.  RNA integrity and gDNA contamination of each sample was assessed by denaturing agarose gel electrophoresis.

tag: cell line

value: HeLa

value: cervical cancer cell


title: CF3P8 MeDIP-seq

description: processed data file: F3.DMR.DDT.csv.gz


title: CF3P9 MeDIP-seq

description: processed data file: F3.DMR.DDT.csv.gz


title: human cervical cancer cell line CaSki

value: CaSki


title: human cervical cancer cell line SW756


title: human cervical cancer cell line SiHa

value: SiHa


title: human cervical cancer cell line C-33A


title: DF2P24 MeDIP-seq

description: processed data file: F2.DMR.DDT.csv.gz

value: male

value: Sperm


title: DF2P22 MeDIP-seq

description: processed data file: F2.DMR.DDT.csv.gz

value: DDT exposed lineage


title: CF2P6 MeDIP-seq

description: processed data file: F2.DMR.DDT.csv.gz

value: Control


title: CF3P7 MeDIP-seq

description: processed data file: F3.DMR.DDT.csv.gz


title: human normal cervical epithelial cell line HcerEpic

source_name: cervical epithelial cell

value: HcerEpic

value: normal cervical epithelial cell


title: EGF_UT_SiCT_2 (CAR)

source_name: liver, none, EGF+, SiCT

value: liver


title: EGF_UT_SiCAR_1 (CAR)


title: EGF_UT_SiCAR_2 (CAR)


title: CF2P5 MeDIP-seq

description: processed data file: F2.DMR.DDT.csv.gz


title: EGF_UT_SiCT_3 (CAR)


title: EGF_UT_SiCT_5 (CAR)


title: WT zebrafish embryo (6-somite)

first: Jeffrey

middle: Allen

last: Farrell

state: MD

address: 6 Center Drive (6A/1A06)

department: Division of Developmental Biology

institute: National Institute of Child Health and Human Development

data_processing:
Data was processed using Cell Ranger 2.0.2, following the pipeline posted on 10x Genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Command "cellranger mkfastq" was called to generate demultiplexed FASTQ files from the Illumina BCL output files.
Command "cellranger count" was used to align the reads to generate the bam files (provided as raw data).
Single-cell gene-barcode counts were calculated by "cellranger count", and were filtered to eliminate non-cellular barcodes (filtered gene-barcode counts are provided as processed data).
Genome_build: dr82
Supplementary_files_format_and_content: Compressed folder containing filtered gene-barcode matrices in Market Exchange Format (MEX), as outputted by "cellranger count".

molecule: polyA RNA

organism: Danio rerio

source_name: Wild-type TLAB Embryo

growth_protocol: Wild-type (Tupful longfin / AB) or MZoep (tz57) fish were incrossed, embryos were collected and grown at 28°C in chorions until they reached the desired stage (confirmed via visual morphological staging).

extract_protocol:
Embryos were dechorionated and deyolked manually, mechanically dissociated, washed and resuspended in PBS + 0.1% BSA + 20% Optiprep, filtered through a cell sieve, and encapsulated and lysed in droplets using the 10X Chromium controller.
Libraries were prepared using the 10X Chromium Single Cell 3' Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch.

tag: genotype/variation

value: wild type TLAB

tag: developmental stage

tag: hours post-fertilization


title: MZoep zebrafish embryo (6-somite)

source_name: Maternal Zygotic oep tz57 Mutant Embryo

value: MZoep mutant


title: EGF_UT_SiCT_4 (CAR)

value: primary hepatocyte

tag: group

value: SiCT


title: DF2P23 MeDIP-seq

description: processed data file: F2.DMR.DDT.csv.gz


title: EGF_UT_SiCT_1 (CAR)

tag: donor id

value: EGF+


title: CF2P4 MeDIP-seq

description: processed data file: F2.DMR.DDT.csv.gz

tag: tissue


title: DF1P20 MeDIP-seq

description: processed data file: F1.DMR.DDT.csv.gz


title: EGF_UT_SiCAR_3 (CAR)

tag: cell type

value: SiCAR


title: DF1P21 MeDIP-seq

description: processed data file: F1.DMR.DDT.csv.gz


title: NoEGF_CITCO_SiCAR_2 (CAR)

source_name: liver, CITCO, EGF-, SiCAR

value: CITCO

tag: medium

value: EGF-


title: NoEGF_CITCO_SiCAR_5 (CAR)

tag: sirna


title: NoEGF_CITCO_SiCAR_3 (CAR)


title: CF1P3 MeDIP-seq

description: processed data file: F1.DMR.DDT.csv.gz


title: NoEGF_CITCO_SiCAR_4 (CAR)


title: DF1P19 MeDIP-seq

description: processed data file: F1.DMR.DDT.csv.gz


title: EGF_PB_SiCT_3 (CAR)

value: Phenobarbital


title: CF1P2 MeDIP-seq

description: processed data file: F1.DMR.DDT.csv.gz


title: CF1P1 MeDIP-seq

description: processed data file: F1.DMR.DDT.csv.gz


title: P24 ChIP-seq

description: processed data file: F2.DHR.DDT.csv.gz


title: NoEGF_CITCO_SiCAR_1 (CAR)


title: NoEGF_CITCO_SiCT_4 (CAR)

source_name: liver, CITCO, EGF-, SiCT


title: NoEGF_CITCO_SiCT_3 (CAR)


title: NoEGF_CITCO_SiCT_2 (CAR)


title: NoEGF_CITCO_SiCT_1 (CAR)


title: NoEGF_PB_SiCAR_4 (CAR)

source_name: liver, Phenobarbital, EGF-, SiCAR


title: A549_shNORAD_TGFbeta

status: Public on Apr 26 2018

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: NORAD shRNA (5’ -> 3’): Forward: GATCCCCGCGGTTGGTCTTCATTCTACCACGTGTGCTGTCCGTGGTAGAATGAAGACCAACCGCTTTTTGGAAAT; Reverse: CTAGATTTCCAAAAAGCGGTTGGTCTTCATTCTACCACGGACAGCACACGTGGTAGAATGAAGACCAACCGCGGG

data_processing:
RNA-seq reads were trimmed down to 100 bases and processed by Tophat2 (version 2.0.13) and Bowtie2 (version 2.2.4) using hg19 version of index files. Parameters used are as follows: -a 6 --segment-length 25 --no-coverage-search --read-realign-edit-dist 0 -G.
FPKM calculation was performed by using Cuffdiff (cufflinks version 2.2.1, with option -u).
Genome_build: hg19
Supplementary_files_format_and_content: Expression data of the four samples were summarized into single processed file by Cuffdiff. Gene-level expressions are in genes.fpkm_tracking.txt.

source_name: RNA-seq, sh NORAD, TGF-beta treated

growth_protocol: A549 cells were from JCRB cell bank. Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM #11965; Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin G, and 100 µg/mL streptomycin.

extract_protocol:
Total RNAs were extracted as described previously (Mizutani et al., 2011, J Biol Chem).
Libraries were prepared using  Dynabeads mRNA DIRECT Purification Kit and Ion Total RNA-seq kit v2 (Thermo Fisher Scientific). Sequencing was performed as described (Sakurai et al., 2016, Oncogene).

treatment_protocol: A549 cells were infected with lentiviral vectors expressing shRNAs and stimulated with 1 ng/ml TGF-beta for 24 h or left untreated.

tag: histology

value: Invasive mucinous adenocarcinoma

tag: tgf-beta treatment

value: 1 ng/ml for 24 h


title: NoEGF_PB_SiCT_5 (CAR)

source_name: liver, Phenobarbital, EGF-, SiCT


title: A549_shNC_TGFbeta

description: Negative control shRNA (5’-> 3’): Forward: GATCCCCGCGCGCTTTGTAGGATTCGGTGTGCTGTCCCGAATCCTACAAAGCGCGCTTTTTGGAAAT;  Reverse: CTAGATTTCCAAAAAGCGCGCTTTGTAGGATTCGGGACAGCACACCGAATCCTACAAAGCGCGCGGG

source_name: RNA-seq, sh Negative control, TGF-beta treated


title: A549_shNORAD

description: NORAD shRNA (5' -> 3’): Forward: GATCCCCGCGGTTGGTCTTCATTCTACCACGTGTGCTGTCCGTGGTAGAATGAAGACCAACCGCTTTTTGGAAAT; Reverse: CTAGATTTCCAAAAAGCGGTTGGTCTTCATTCTACCACGGACAGCACACGTGGTAGAATGAAGACCAACCGCGGG

source_name: RNA-seq, sh NORAD, unstimulated


title: NoEGF_PB_SiCT_4 (CAR)


title: NoEGF_PB_SiCAR_2 (CAR)


title: A549_shNC

description: Negative control shRNA (5’ -> 3’): Forward: GATCCCCGCGCGCTTTGTAGGATTCGGTGTGCTGTCCCGAATCCTACAAAGCGCGCTTTTTGGAAAT;  Reverse: CTAGATTTCCAAAAAGCGCGCTTTGTAGGATTCGGGACAGCACACCGAATCCTACAAAGCGCGCGGG

source_name: RNA-seq, sh Negative control, unstimulated


title: NoEGF_UT_SiCAR_3 (CAR)

source_name: liver, none, EGF-, SiCAR


title: NoEGF_PB_SiCAR_5 (CAR)


title: NoEGF_UT_SiCAR_4 (CAR)


title: NoEGF_PB_SiCT_1 (CAR)


title: NoEGF_PB_SiCT_2 (CAR)


title: NoEGF_PB_SiCT_3 (CAR)


title: NoEGF_UT_SiCT_4 (CAR)

source_name: liver, none, EGF-, SiCT


title: NoEGF_UT_SiCT_3 (CAR)


title: NoEGF_UT_SiCAR_5 (CAR)


title: NoEGF_UT_SiCT_5 (CAR)


title: NoEGF_UT_SiCAR_2 (CAR)


title: NoEGF_PB_SiCAR_3 (CAR)


title: NKG2C+ VMAPQSLLL donor 81

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description: NK cells of HCMV-seronegative healthy individiuals were FACS-sorted for viable CD3- CD56dim cells. CD56dim NK cells were co-cultured for 7 days with RMA-S/HLA-E/LFA-3 target cells either pulsed with VMAPQSLLL in the presence of 10 ng/mL IL-15.

data_processing:
Sequence reads were mapped to human GRCh37/hg19 genome with TopHat2 in very-sensitive settings for Bowtie2 and GENCODE annotation release 19 (GRCh37.p13).
Gene expression was quantified by featureCounts and analyzed using DESeq2 1.18.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.

source_name: CD56dim NK cells isolated from PBMC

growth_protocol: CD56dim NK cells were isolated from PBMC by FACS-sorting for viable CD3- CD56dim cells

extract_protocol:
Total RNA was purified from FACS-sorted NKG2C+ NK cells with RNeasy Plus Micro kit (Qiagen) according to the manufacturer's instructions.
Illumina libraries were prepared using Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) and Nextera® XT DNA Sample Preparation Kit (Illumina), with max 10ng of purified cDNA, according to the manufacturer’s instructions and paired-end sequenced (2x75 bp) on an Illumina NextSeq500 device.

treatment_protocol: CD56dim NK cells were co-cultured for 7 days with RMA-S/HLA-E/LFA-3 target cells either pulsed with VMAPQSLLL or VMAPRTLFL peptide in the presence of 10 ng/mL IL-15. 10 ng/mL IL-12 and 100 IL-18 were either present or not during the initial 20 h of culture.

tag: cells

value: Viable NKG2C+ NK cells

tag: origin

value: HCMV-seronegative healthy donor

tag: organ

value: peripheral blood

value: in vitro VMAPQSLLL-pulsed target cells and IL-15


title: NoEGF_PB_SiCAR_1 (CAR)


title: NKG2C+ VMAPRTLFL IL-12/18 donor 81

description: NK cells of HCMV-seronegative healthy individiuals were FACS-sorted for viable CD3- CD56dim cells. CD56dim NK cells were co-cultured for 7 days with RMA-S/HLA-E/LFA-3 target cells either pulsed with VMAPRTLFL peptide in the presence of 10 ng/mL IL-15. 10 ng/mL IL-12 and 100 IL-18 were either present during the initial 20 h of culture.

tag: treatment

value: in vitro with VMAPRTLFL-pulsed target cells, IL-15, IL-12 and IL-18


title: NKG2C+ VMAPQSLLL donor 76


title: NoEGF_UT_SiCAR_1 (CAR)

value: liver


title: NKG2C+ VMAPRTLFL IL-12/18 donor 59


title: NKG2C+ VMAPRTLFL IL-12/18 donor 76


title: NKG2C+ VMAPRTLFL IL-12/18 donor 80


title: NKG2C+ VMAPRTLFL IL-12/18 donor 57


title: NoEGF_UT_SiCT_2 (CAR)


title: GFP(+) CD146(-) mesenchymal cells, sorted from small intestine, biological rep3

city: Glasgow

last: Cavanagh

address: 120 University Place

department: Immunology

country: United Kingdom

institute: University of Glasgow

description: Sorted from small intestine of Ackr4(+/GFP) mouse D

hyb_protocol: Fragmented samples were hybridised onto Mouse Transcriptome arrays in accordance with the NuGEN guidelines for hybridisation onto Affymetrix GeneChip® arrays

scan_protocol: Affymetrix Gene ChIP Scanner 3000

data_processing:
Data were processed using GeneSpringGX software. Following background correction, probe intensity data across chips were normalized by quantile normalization and summarization was performed using the ExonRMA 16 summarization algorithm.
meta-probeset file: MTA-1_0.na35.mm10.probeset.csv

source_name: Mesenchymal cells, small intestine, GFP(+) CD146(-)

label_protocol: Samples were enzymatically fragmented and biotinylated using an Encore Biotin module (NuGEN).

growth_protocol: Mice were bred in house and maintained in specific pathogen-free conditions until 8-10 weeks of age

extract_protocol: Small intestines from Ackr4(+/gfp) mice were enzymatically digested (1 mg/ml Collagenase VIII) and the resulting cell suspensions labelled using fluorescently-conjugated antibodies. Populations of iMC, identified as single, live, CD45(-)Ter119(-)EPCAM(-)GP38(+)CD31(-), were FACS sorted based on their expression of CD146 and Ackr4. Sorted cells were lysed in RLT Buffer (Qiagen), and RNA extracted using Qiagen RNeasy micro kit. Purified total RNA was converted to sense strand cDNA and amplified using Ovation Pico WTA System V2 kit  (NuGEN).

treatment_protocol: Not applicable, steady-state

tag: age

value: Small intestine

tag: genotype

tag: mouse

value: D


title: GFP(+) CD146(-) mesenchymal cells, sorted from small intestine, biological rep2

description: Sorted from small intestine of Ackr4(+/GFP) mouse C

value: C


title: GFP(+) CD146(-) mesenchymal cells, sorted from small intestine, biological rep1

description: Sorted from small intestine of Ackr4(+/GFP) mouse A

value: A


title: CD146(+) GFP(-) mesenchymal cells, sorted from small intestine, biological rep1

source_name: Mesenchymal cells, small intestine, CD146(+) GFP(-)


title: GFP(-) CD146(-) mesenchymal cells, sorted from small intestine, biological rep1

source_name: Mesenchymal cells, small intestine, GFP(-) CD146(-)


title: GFP(-) CD146(-) mesenchymal cells, sorted from small intestine, biological rep3


title: GFP(-) CD146(-) mesenchymal cells, sorted from small intestine, biological rep2

description: Sorted from small intestine of Ackr4(+/GFP) mouse B

value: B


title: NoEGF_UT_SiCT_1 (CAR)

value: primary hepatocyte

value: SiCT


title: PBMC_DARTseq_0

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: 301 Weill Hall

department: Meinig School of Biomedical Engineering

institute: Cornell University

description: Capture of messenger RNA and human B lymphocyte cell light and heavy chain constant regions (eight loci in total).

data_processing:
Paired-end fastq files were analylzed for quality (adpater dimers and k-mer representation).
Reads were de-duplicated using UMI (from read 1) and sequences were trimmed.
Reads were tagged with cell barcodes and aligned to host transcriptome usign STAR aligner. Exonic alignments were extracted.
Aligned reads underwent quality control for possible bead synthesis errors.
Digital expression was calculated across cells passing filter.
Genome_build: mm10 or hg19
Supplementary_files_format_and_content: tab-delimited text files indicating number of counted transcripts for detected genes in each cell

source_name: Commercial human peripheral blood mononuclear cells

growth_protocol: L929 cells were infected with recominant type 3 Dearing orthoreovirus at an MOI of 10 and incubated for 15 hours. PBMCs were purchased from Zen-Bio (SER-PBMC-F) and thawed when ready to perform experiment.

extract_protocol: The following steps are identical to those performed using standard Drop-seq protocol (Macasko, 2015). Briefly, droplets containing beads and lysed cells were broken and washed. Complementary DNA was created using Maxima Reverse Transcriptase (Thermo Fisher) and a transcript switch oligomer. cDNA was amplified using 15 cycles of PCR. Amplified cDNA libraried were tagmented and amplified using Nextera. Illumina sequencing was performed on the libaries using 20x130 paired-end sequencing.

treatment_protocol:
Cells were washed three times with PBS + 0.01% BSA. In the case of the L929 cells, 300,000 cells were resuspended in 1 mL of PBS-BSA. In the case of PBMCs, 150,000 cells were resuspended in 1 mL of PBS-BSA.
Cells were injected into a microfluidic device and coencapsulated with either Drop-seq or DART-seq beads which were resuspended in a lysis buffer.

value: PBMC

tag: capture

value: DART-seq bead


title: PBMC_Dropseq_0

description: Capture of messenger RNA only.

value: Drop-seq bead


title: HS1

city: Yangling

first: Chengyu

last: Yu

state: Shaanxi

address: 3 Taicheng Road

department: College of Agronomy

institute: Northwest A&F University

description: replicate of TBM  treatment

data_processing:
Illumina Casava1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  Brassica genome FPsc v1.3 (DOE-JGI, http://phytozome.jgi.doe.gov/) as reference using Bowtie V2-2.1.0.
The number of perfect reads matching to each unigene was normalized to Transcripts Per Kilobase of exon model per Million mapped reads (TPM).
Genome_build: Brassica rapa FPsc v1.3
Supplementary_files_format_and_content: tab-delimited text files include count number and Transcripts Per Kilobase of exon model per Million mapped reads (TPM) values for each Sample

organism: Brassica napus

source_name: young floral buds

growth_protocol: The seeds of cultivar SP2F was sown in field in September and the seedlings were transplanted into a greenhouse in early December after passing vernalization under field condition.

extract_protocol:
Young floral buds from TBM-treated (HS) and the control plants (CK) were dissected, put into RNAlater and stored at −80°C for later use. Total RNAs were extracted using the Trizol® Reagent (Invitrogen, USA) and purified using TRK1001 Kit (LC Science, Houston, TX). The total RNA quantity and purity were analyed by using of Bioanalyzer 2100 with RNA 6000 Nano LabChip Kit (Agilent, CA, USA). We used 10 µg total RNA from each sample to create normalized cDNAs. Two independent biological replicates were used for the TBM or control treatment.
RNA libraries were prepared for sequencing using Illumina’s Digital Gene Expression Tag Profiling Kit according to the manufacturer’s protocol

treatment_protocol: The bolting plants (fifteen days before flower open) were foliar-sprayed with 0.2 mg a.i./L TBM (75% water dispersible granule) solution, at a rate about 5 mL per plant. The solution was also added with 0.2 mL/L surfactant sodium alkylethersulfate. This treatment had three replicates, each containing of about 100 plants. Another group of 300 plants, served as the negative control, were sprayed with only water containing the surfactant.

value: young floral buds

tag: developmental stage

value: pollen mother cell


title: CK1

description: replicate of the control


title: HS2

description: replicate of TBM  treatment


title: CK2

description: replicate of the control


title: CD146(+) GFP(-) mesenchymal cells, sorted from small intestine, biological rep2


title: 8723R

city: San Francisco

first: Ruby

state: CA

address: 513 Parnassus Ave

institute: UCSF

data_processing:
sRNA reads that matched adapter or polyA sequences were removed using custom Python scripts.
Reads were aligned to the S. pombe genome using Novoalign: novoalign -d PombeGenome.index -f sample.fastq -l14 -t30 -r Random > sample.novoalign.txt
Alignment files were converted to an IGV-viewable format and normalized to reads per million using custom Python scripts.
Genome_build: S. pombe h- wildtype
Supplementary_files_format_and_content: IGV files are tab-delimited indicating normalized reads per million at each indicated nucleotide

organism: Schizosaccharomyces pombe

source_name: Haploid S. pombe cells

growth_protocol: Cells were grown in rich liquid media (YES) at 30C to a concentration of 2x10^7 cells/ml

extract_protocol:
Small RNAs were purified using the mirVana™ miRNA isolation kit (Ambion)
21-30nt small RNAs were size-selected on a 17.5% polyacrylamide/7M urea gel and ligated to a 3' adapter. Ligated species were size-selected on a 17.5% polyacrylamide/7M urea gel and ligated to a 5' adapter. RNA was reverse transcripted into cDNA and PCR-amplified in a two-step process. Amplified cDNA was gel-purified.

value: h? ura4? leu1-32 ade6-M210 meu10::kan-ade6 red clone n4


title: 6299

value: h- leu1-32, ura4-D18 nmt1+::ade6-hp+/Nat


title: 8720R

value: h? ura4? leu1-32 ade6-M210 meu10::kan-ade6 red clone


title: 8720W

value: h? ura4? leu1-32 ade6-M210 meu10::kan-ade6 white clone


title: 8706W

value: h? ura4? leu1-32 ade6-M210 efm3::kan-ade6 white clone


title: 84011

value: h+ otr1R(SphI)::ade6+ ura4-D18 leu1-32 leo1[delta]::kan ade6-OFF


title: 8403

value: h- leu1-32, ura4-D18 nmt1+::ade6-hp+/Nat leo1[delta]::kan ade6-OFF


title: 8683W

value: h? ura4? leu1-32 ade6-M210 mal1::kan-ade6


title: 8684R

value: h? ura4? leu1-32 ade6-M210 mal1::kan-ade6 off n2


title: RSA9a

value: h+ leu1-32 ura4-D18 ade6-OFF #9a


title: 8706R

value: h? ura4? leu1-32 ade6-M210 efm3::kan-ade6 red clone11


title: 8404


title: 6793

value: h- leu1-32 ade6-(barcodedWT)


title: 6551

value: h+ leu1-32 ade6-M216 mlo3[delta]::kanMX #1b


title: RSA40a

value: h- otr1R(SphI)::ade6+ leu1-32 ura4-D18 ade6-OFF #40a


title: RSA2

value: h+ leu1-32 ura4-D18 ade6-OFF #2


title: 4081

value: h+ otr1R(SphI)::ade6+ ura4-D18 leu1-32 #1


title: 6639W

value: h+ otr1R(SphI)::ade6+ ura4-D18 leu1-32 mlo3[delta]::kan white clone clone


title: RSA13

value: h+ otr1R(SphI)::ade6+ leu1-32 ura4-D18 ade6-OFF #13


title: 6639R

value: h+ otr1R(SphI)::ade6+ ura4-D18 leu1-32 mlo3[delta]::kan red clone #6


title: 84012


title: H3K9me3 8403

data_processing:
Raw reads were separated according to their barcodes and mapped to the S. pombe genome using Bowtie using default parameters.
Mapped reads were normalized to reads per million and converted to an IGV-viewable format.
For samples ending in .tdf, IGV files were converted to a more compact format for easier visualization on IGV using IGVtools "toTDF" command.
Genome_build: S. pombe h- wildtype
Supplementary_files_format_and_content: IGV files are tab-delimited indicating normalized reads per million at each indicated nucleotide (.gz indicates compression with gzip). Tdf files are binary files IGV files generated using IGVtools "toTDF" command.

extract_protocol:
Lysates were generated by bead beating and chromatin was sheared by sonication. Cleared lysate was incubated with antibody for 2 hours at 4C and immunoprecipitated genomic DNA was purified.
Libraries were prepared for Illumna sequencing using manufacturer's protocols, starting with ~5ng immune-precipitated DNA fragments. Each library was generated with custom-made adapters carrying unique barcode sequence at the ligating end. Barcoded libraries were mixed.

treatment_protocol: Cells were fixed with 1% formaldehyde for 15 min at room temeprature

tag: chip antibody

value: H3K9me3 (Diagnode C15500003)


title: H3K9me3 8404


title: H3K9me3 84011


title: H3K9me3 6299

value: h- leu1-32, ura4-D18 nmt1+::ade6-hp+/Nat


title: H3K9me3 4081


title: H3K9me3 9a


title: H3K9me3 86


title: H3K9me3 91


title: H3K9me3 90

value: h- otr1R(SphI)::ade6+ leu1-32 #90


title: H3K9me3 80

value: h- otr1R(SphI)::ade6+ leu1-32 #80


title: H3K9me3 4529

value: h+ otr1R(SphI)::ade6+ ura4-D18 leu1-32 mlo3[delta]::kan #6


title: H3K9me3 20

value: h- leu1-32 ura4-D18  ade6-OFF #20


title: H3K9me2 8403

value: h- leu1-32, ura4-D18 nmt1+::ade6-hp+/Nat leo1[delta]::kan ade6-OFF


title: NoEGF_CITCO_SiCT_5 (CAR)

tag: donor id

value: liver

value: primary hepatocyte

value: CITCO

tag: group

value: EGF-

value: SiCT


title: H3K9me3 16

value: h+ otr1R(SphI)::ade6+ leu1-32 ura4-D18 ade6-OFF #16


title: H3K9me3 40a

value: h- otr1R(SphI)::ade6+ leu1-32 ura4-D18 ade6-OFF #40a


title: H3K9me3 2

value: h+ leu1-32 ura4-D18 ade6-OFF #2


title: H3K9me2 4081

value: h+ otr1R(SphI)::ade6+ ura4-D18 leu1-32 #1


title: H3K9me2 84011

value: h+ otr1R(SphI)::ade6+ ura4-D18 leu1-32 leo1[delta]::kan ade6-OFF


title: H3K9me3 6639R

value: h+ otr1R(SphI)::ade6+ ura4-D18 leu1-32 mlo3[delta]::kan red clone #6

value: H3K9me3 (Diagnode C15500003)


title: H3K9me2 8404


title: H3K9me2 84012


title: H3K9me2 90

value: h- otr1R(SphI)::ade6+ leu1-32 #90


title: H3K9me2 91


title: H3K9me2 9a

value: h+ leu1-32 ura4-D18 ade6-OFF #9a


title: H3K9me3 84012


title: H3K9me3 13

value: h+ otr1R(SphI)::ade6+ leu1-32 ura4-D18 ade6-OFF #13


title: H3K9me2 6299

value: h- leu1-32, ura4-D18 nmt1+::ade6-hp+/Nat


title: H3K9me2 86


title: H3K9me2 4529

value: h+ otr1R(SphI)::ade6+ ura4-D18 leu1-32 mlo3[delta]::kan #6


title: H3K9me2 80

value: h- otr1R(SphI)::ade6+ leu1-32 #80


title: H3K9me2 6639R


title: H3K9me2 40a


title: H3K9me2 20

value: h- leu1-32 ura4-D18  ade6-OFF #20


title: H3K9me2 2


title: H3K9me2 16


title: H3K9me2 13


title: NKG2C+ VMAPQSLLL donor 80

value: Viable NKG2C+ NK cells

value: HCMV-seronegative healthy donor

value: peripheral blood

value: in vitro VMAPQSLLL-pulsed target cells and IL-15


title: Tumor_Tconv CD4+_Biological rep_2

city: Paris

first: Olivier

last: Lantz

address: 26 rue d'Ulm

country: France

institute: Curie Institute

description: Ex vivo isolated Tconv CD4+ cells from metastatic uveal melanoma patient

hyb_protocol: Following fragmentation, 2.25 ug of cDNA were hybridized for 17 hr at 48C on Affymetrix® Human Gene 2.1 ST Array Plate. GeneChips were washed and stained in the Affymetrix Genetitan Instrument.

scan_protocol: GeneChips were scanned using the Affymetrix Genetitan instrument scanner.

data_processing: Raw data were background corrected and normalized using the Robust Multichip Average (RMA) method with R/Bioconductor. Avereps() from the limma package in bioconductor to count only each gene once.

source_name: Peripheral blood

label_protocol: Biotinylated cDNA were prepared according to the standard kit wt expression Ambion from 100 ng total RNA

extract_protocol: Extraction of total RNA was performed with Qiagen RNeasy micro kit according to the manufacturer's instructions.

treatment_protocol: Conventional CD4+ T cells (Tconv cells=CD3+CD4+CD127+CD25±) and chronically activated CD4+ T cells (chCD4 T cells=CD3+CD4+CD127-CD25-) were sorted from the blood of healthy donor (n=2) or patients with metastatic uveal melanoma (n=3).

tag: disease

value: Metastatic Uveal Melanoma


title: FOXP3neg_Anergic Marilyn_3m_biological rep_1

description: Anergic Marilyn cells from mice bearing early tumors

hyb_protocol: Following fragmentation, 2.25 ug of cDNA were hybridized for 17 hr at 48C on Affymetrix® Mouse Gene 2.1 ST Array Plate. GeneChips were washed and stained in the Affymetrix Genetitan Instrument.

label: Biotin

source_name: tumor-draining lymph node (mediastinal lymph node)

label_protocol: Biotinylated cDNA were prepared according to the standard pico wt Affymetrix protocol from 100 pg total RNA (GeneChip® WT Pico Reagent Kit Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays).

treatment_protocol: Naive DBY-specific Marilyn CD4+ T (CD44lowCD62+FOXP3-GFP Neg) were transferred into mice bearing DBY expressing tumors . 3000 Tumor induced Marilyn  pTregs (FOXP3-GFPPos)  and anergic Marilyn cells  (FOXP3-GFP Neg )  were purified from the tumor-draining lymph node 7 days after transfer (3 pools of 5 mice per condition). Naive Marilyn cells, pTregs Marilyn cells (tumor- free mice receiving DBY peptide) and effector Marilyn cells (Tumor-free mice receiving DBY+CpG) were used as controls. Endogenous host Tregs (CD4+CD25hi) were also isolated from tumor-free and tumor-bearing mice.

tag: strain

tag: tumor stage

value: Early tumor stage

tag: time

value: 7 days post-transfer


title: HD_chCD4+_Biological rep_2

description: Ex vivo isolated chCD4+ T cells from healthy donor

value: Healthy donor


title: FOXP3neg_Anergic Marilyn_6m_biological rep_2

description: Anergic Marilyn cells from mice bearing advanced tumors

value: Advanced tumor stage


title: FOXP3pos_Marilyn pTregs_3m_biological rep_2

description: Marilyn pTregs generated in mice bearing early tumors


title: FOXP3pos_Marilyn pTregs_3m_biological rep_1


title: FOXP3pos_Marilyn pTregs_6m_biological rep_3

description: Marilyn pTregs generated in mice bearing advanced tumors


title: Tumor_chCD4+_Biological rep_1

description: Ex vivo isolated chCD4+ T cells from metastatic uveal melanoma patient


title: RPMI8226-AD-IgG-ChIPSeq

city: Houston

first: Jing

last: Yang

state: Texas

address: 7455 Fannin

institute: MD Anderson Cancer Center

data_processing:
Sequences were mapped to the GRCh37/hg19 using Bowtie (Galaxy Tool Version 1.1.2) and analyzed by MACS2 (Galaxy Version 2.1.0.20151222.0). Default parameters were used for peak calling with MACS2 with a p-value cut off of 1e-5 for all ChIP-Seq peak calling.
Between 1 million to 20 million reads were mapped with quality control by FastQC reported no sequence flagged as poor quality. The cut-off of P value of 1e-5 was used for all ChIP-seq peak calling. MFOLD high-confidence enrichment ratio of 10 was used against background for model building.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Sequences were mapped to the GRCh37/hg19 using Bowtie (Galaxy Tool Version 1.1.2) and analyzed by MACS2 (Galaxy Version 2.1.0.20151222.0). Default parameters were used for peak calling with MACS2 with a p-value cut off of 1e-5 for all ChIP-Seq peak calling.

source_name: adipocytes

growth_protocol: BM cells were flushed out from human fetal femoral bones (Advanced Bioscience Resources), and cultured in DMEM to generate MSCs. To generate mature adipocytes, MSCs were cultured in adipocyte medium for 2 weeks.

extract_protocol:
Cells were fixed in 4% formaldehyde and sonicated to prepare chromatin fragments. Chromatin samples were immunoprecipitated with antibodies against H3K27me3 and control immunoglobulin G (IgG) at 4°C for 3 h. Immunoprecipitates and total chromatin inputs were reverse cross-linked
Fifteen to 25 ng of ChIP DNA immunoprecipitated with anti-H3K27me3 antibodies or control IgG from parallel experiments was used for library preparation  and sequencing using a Solexa HiSeq 2000 (Illumina). The raw sequencing reads obtained on the Ion Torrent PGM platform were mapped to a human reference genome.

treatment_protocol: First, we seeded adipocytes onto the back of the Transwell insert and seeded myeloma cells in the insert. We chose the pore size of the insert membrane at 0.4 µm, which allows physical contact but at the same time the cells can’t penetrate through. Second, at the time of separation, we added collagenase to the intact insert, allowing the treated adipocytes to fall to the bottom of the culture well; then we removed the insert that contained myeloma cells from culture wells. Finally, we monitored for potential contamination by myeloma cells in the culture well after removal of the insert by assessing an aliquot of the adipocytes by flow cytometry using an antibody against CD138 (a myeloma cell marker); all tested cells were CD138 negative.

tag: cell type

value: MSC cells derived mature adipocytes

tag: passages

value: Normal Rabbit IgG  (Cell Signaling Technology, Catalog#2729)


title: RPMI8226-AD-H3K27me3-ChIPSeq

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (Cell Signaling Technology, Catalog#9733)


title: ARP-1-AD-H3K27me3-ChIPSeq


title: FOXP3pos_Marilyn pTregs_3m_biological rep_3


title: FOXP3neg_Anergic Marilyn_6m_biological rep_3


title: FOXP3neg_Anergic Marilyn_3m_biological rep_2


title: Tumor_chCD4+_Biological rep_2


title: HD_Tconv CD4+_Biological rep_1

description: Ex vivo isolated Tconv CD4+ cells from healthy donor


title: Tumor_Tconv CD4+_Biological rep_3


title: FOXP3pos_Marilyn pTregs_6m_biological rep_1


title: CD4CD25hi host Tregs_tumor_6m_biological rep_3

description: Host Tregs from mice bearing advanced tumors


title: FOXP3pos_Marilyn pTregs_6m_biological rep_2


title: FOXP3neg_Anergic Marilyn_6m_biological rep_1


title: FOXP3neg_Anergic Marilyn_3m_biological rep_3


title: HD_chCD4+_Biological rep_1


title: Tumor_chCD4+_Biological rep_3


title: Tumor_Tconv CD4+_Biological rep_1


title: CD4CD25hi host Tregs_tumor_6m_biological rep_1


title: CD4CD25hi host Tregs_tumor_3m_biological rep_3

description: Host Tregs from mice bearing early tumors


title: HD_Tconv CD4+_Biological rep_2


title: CD4CD25hi host Tregs_tumor_6m_biological rep_2


title: CD4CD25hi host Tregs_tumor_3m_biological rep_2


title: ARP-1-AD-IgG-ChIPSeq


title: AD-IgG-ChIPSeq


title: AD-H3K27me3-ChIPSeq


title: C16

city: Changsha

first: Yang

last: Wang

address: 87 Xiangya Road

department: Xiangya Hospital

institute: Central South University

data_processing:
Illumina NextSeq 500 raw sequencing read data that passed the Illumina chastity filter were used for the following analysis. Sequencing quality was examined by FastQC software.
After that, the sequencing reads were 5’, 3’-adaptor trimmed, filtered for more than 15 nt by Cutadapt software, and for exactly aligned to mature-tRNA and pre-tRNA sequences from GtRNAdb (http://gtrnadb.ucsc.edu/) using NovoAlign software (v2.07.11).
The tsRNA expression levels were measured and normalized as tag counts per million of total aligned tRNA reads (TPM). For each tRNA sequence-based profile, the number of tRNA sequence reads could be used to estimate expression level of each tsRNA.
Genome_build: hg19
Supplementary_files_format_and_content: excel files include tag count and TPM values for each Sample

growth_protocol: Sprague-Dawley rats (male, 180g-220g) were cared in accordance with the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health (NIH Publication No. 85-23, revised 1996). The Committee on the Use and Care of Animals of Central South University (CSU) (201403164) has approved animal protocols. Rats accessed to water and food freely under a room temperature at 25°C and a 12 h light-dark cycle.

extract_protocol:
After deeply anesthetized and saline perfused at days 21, brain tissue surrounding the hemorrhagic region (the right globus pallidus) was harvested for following detections. Total RNAs were extracted according to the manufacturer’s instruction (Qiagen, USA). The purity and concentration of total RNA samples were determined with NanoDrop ND-1000. Then we did the following treatments to remove some RNA modifications which might interfere with small RNA-sequencing library construction: 3’-aminoacyl (charged) deacylation to 3’-OH (hydroxyl group) for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH phosphorylation to 5’-P for 5’-adaptor ligation, N1-methyladenosine and N3-methylcytidine demethylation for efficient reverse transcription. All procedures were performed using rtStar tRF&tiRNA Pretreatment Kit (Arraystar) protocols.
Total RNA samples were sequentially ligated to 3’ and 5’ small RNA adapters using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, USA). cDNA was then synthesized and amplified using Illumina’s proprietary reverse transcription primers and amplification primers. Subsequently, 135-170 bp PCR amplified fragments (corresponding to 15-50 nt small RNA size range) were extracted and purified from the PAGE gel. The completed libraries were quantified by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amounts according to the quantification results and used for sequencing on the instrument. And then, the DNA fragments in well-mixed libraries were denatured to generate single-stranded DNA molecules and loaded onto the reagent cartridge. Finally, the sequencing run was performed on Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (Illumina) according to the manufacturer’s instructions. Sequencing was carried out by running 50 cycles.

treatment_protocol: Animals were randomly assigned into the sham operated group (sham), ICH group (ICH) and ICH+BYHWD-treated group (BYHWD). animals were anesthetized with pentobarbital (65 mg/kg). Afterward, the rats were pronely fixed on a stereotactic frame (Stoelting Co., Chicago, IL). After making a scalp incision, we drilled a small cranial burr near the right coronal suture (1.4 mm posterior and 3.2 mm lateral to bregma). Then collagenase type VII (0.5 U dissolved in 2.5 μl saline) was slowly injected into the right globus pallidus (5.6 mm deep) at an even speed in 2 minutes. The needle was kept in place for another 5 minutes then withdrawn to prevent backflow. Finally, the burr hole was filled with bone wax, and the scalp sutured closed. Sham rats underwent the same procedure but with 2.5 μl saline infusion instead. For BYHWD group, intragastrical administration of Buyang Huanwu Decoction (4.36 g/kg) was performed once a day for 21days.

tag: strain background

value: Sprague–Dawley

tag: Sex

value: male

value: post operation day 21

value: intracerebral hemorrhage (ICH)

tag: tissue

value: Brain tissue around the right globus pallidus

tag: molecule subtype

value: tress-induced tRNA fragments (tiRNA) and tRNA-derived fragments (tRF)


title: B11

tag: age

value: intracerebral hemorrhage (ICH) treated with Buyang Huanwu Decoction (BYHWD)


title: C13


title: B12


title: C15


title: A5

value: sham operated group (sham)


title: A3


title: ssrp1_RNA-Seq

city: Frederiksberg C

first: Maxim

last: Ivanov

address: Thorvaldsensvej 40

department: Dept. of Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

data_processing:
Illumina Casava v1.7 software was used for basecalling.
TSS-Seq: 1) Adapter trimming (Trim Galore v0.4.3; --adapter "ATCTCGTATGCCG"); 2) Trim UMI barcodes (8 nt; UMI-Tools extract); 3) Alignment (STAR v2.5.2b; --outSAMmultNmax 1 --alignEndsType Extend5pOfRead1); 4) Sort BAM files (Samtools v1.3.1); 5) Remove reads aligned to rRNA, tRNA, snRNA or snoRNA loci (BEDTools v2.17.0); 6) Remove reads with MAPQ < 10 (Samtools v1.3.1); 7) Deduplication (UMI-Tools dedup); 8) Make stranded bedGraph files from the 5' bases (BEDTools genomecov; -bg -5 -strand + / -); 9) Remove singletons (awk) and convert to Bigwig (kentUtils bedGraphToBigWig). See the full pipeline in https://github.com/Maxim-Ivanov/Nielsen_et_al_2018/01-Alignment_of_5Cap-Seq_data.sh
RNA-Seq: 1) Adapter trimming (Trim Galore v0.4.3; --paired --illumina); 2) Alignment (STAR v2.5.2b; --outSAMmultNmax 1 --alignEndsType Local); 3) Sort BAM file, remove reads with MAPQ < 10 (Samtools v1.3.1); 4) Make unstranded bedGraph files from the whole reads (BEDtools v2.17.0; -bg -split); 5) Convert to Bigwig (kentUtils bedGraphToBigWig).
Genome_build: TAIR10
Supplementary_files_format_and_content: Bigwig files show sequencing coverage with single base resolution (no signal smoothing or transformation were applied).

organism: Arabidopsis thaliana

source_name: Whole seedlings

growth_protocol: The Arabidopsis seedlings were grown on plates (1/2 Murashige and Skoog medium, 1% sucrose, 0.5% Microagar) with a 16h light/8h dark cycle at 22°C.

extract_protocol:
Total RNA was isolated from 14 day old seedlings using QIAgen Plant RNeasy Mini Kit following manufacturer’s instructions
TSS-Seq: libraries were prepared as described in Pelechano et al. Nat Protoc. 2016 Feb 11(2):359-76; PMID: 26820793. RNA-Seq: libraries were prepared using Illumina TruSeq Sample Prep Kit v2 following the manufacturer's protocol.

tag: ecotype

value: Columbia (Col-0)

value: Whole seedlings

tag: genotype

value: 14 day


title: CD4CD25hi host Tregs_tumor_3m_biological rep_1

value: Early tumor stage

value: 7 days post-transfer


title: FOXP3pos_Marilyn pTregs_DBY_biological rep_3

description: Marilyn pTregs generated in tumor-free mice receiving DBY peptide

source_name: lymph node draining the site of immunization (mediastinal lymph node)

value: Tumor free


title: FOXP3pos_Marilyn pTregs_DBY_biological rep_2


title: FOXP3pos_Marilyn pTregs_DBY_biological rep_1


title: A6


title: FOXP3neg_Effector Marilyn_DBY+CpG_biological rep_3

description: Effector antigen-specific Marilyn cells generated in tumor-free mice receiving DBY+CpG


title: CD4CD25hi host Tregs_Naive_B6_biological rep_2

description: Unmanipulated host Tregs

source_name: pool of lymph nodes

value: Freshly isolated


title: Col0_RNA-Seq

value: Wild type


title: arota_vildagliptin-treated_rep3

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

hyb_protocol: The sample preparation and hybridation of each cDNAs on Affymetrix GeneChip® Mouse Gene 2.0 ST arrays based on manufacturer's instruction.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 Affymetrix)

data_processing: All arrays were uploaded into Genespring v12.5 (Agilent Tchnologies, USA) for data normalization, quality control and first-pass analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for differentially regulated genes was a fold change>1.5 and a P value<0.05.

source_name: vildagliptin-treated rats, 17week

label_protocol: Affymetrix protocol

extract_protocol: Total tissue RNA was extracted using total RNA Isolation Kit (mirVanaTM, ABI).

value: arota

value: 17 week


title: CD4CD25hi host Tregs_Naive_B6_biological rep_1

description: Unmanipulated host Tregs


title: arota_vildagliptin-treated_rep2


title: FOXP3neg_Effector Marilyn_DBY+CpG_biological rep_2


title: ssrp1_TSS-Seq_rep2

data_processing:
Library strategy: TSS-Seq
Illumina Casava v1.7 software was used for basecalling.
TSS-Seq: 1) Adapter trimming (Trim Galore v0.4.3; --adapter "ATCTCGTATGCCG"); 2) Trim UMI barcodes (8 nt; UMI-Tools extract); 3) Alignment (STAR v2.5.2b; --outSAMmultNmax 1 --alignEndsType Extend5pOfRead1); 4) Sort BAM files (Samtools v1.3.1); 5) Remove reads aligned to rRNA, tRNA, snRNA or snoRNA loci (BEDTools v2.17.0); 6) Remove reads with MAPQ < 10 (Samtools v1.3.1); 7) Deduplication (UMI-Tools dedup); 8) Make stranded bedGraph files from the 5' bases (BEDTools genomecov; -bg -5 -strand + / -); 9) Remove singletons (awk) and convert to Bigwig (kentUtils bedGraphToBigWig). See the full pipeline in https://github.com/Maxim-Ivanov/Nielsen_et_al_2018/01-Alignment_of_5Cap-Seq_data.sh
RNA-Seq: 1) Adapter trimming (Trim Galore v0.4.3; --paired --illumina); 2) Alignment (STAR v2.5.2b; --outSAMmultNmax 1 --alignEndsType Local); 3) Sort BAM file, remove reads with MAPQ < 10 (Samtools v1.3.1); 4) Make unstranded bedGraph files from the whole reads (BEDtools v2.17.0; -bg -split); 5) Convert to Bigwig (kentUtils bedGraphToBigWig).
Genome_build: TAIR10
Supplementary_files_format_and_content: Bigwig files show sequencing coverage with single base resolution (no signal smoothing or transformation were applied).


title: arota_diabetic rats_rep3

source_name: diabetic rats, 17week


title: ssrp1_TSS-Seq_rep1


title: arota_vildagliptin-treated_rep1


title: arota_diabetic rats_rep2


title: spt16_TSS-Seq_rep2


title: FOXP3neg_Effector Marilyn_DBY+CpG_biological rep_1


title: spt16_TSS-Seq_rep1


title: arota_diabetic rats_rep1


title: CD4CD25hi host Tregs_Naive_B6_biological rep_3

description: Unmanipulated host Tregs


title: Naive_Marilyn_biological rep_3

description: Naive antigen-specific Marilyn cells


title: Wild Type TNF(nl) treated rep2_Experiment 2

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description: Sample 29

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.33; parameters:ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 AVGQUAL:20 TRAILING:20 MINLEN:33
Data were mapped to the mm10 reference genome with tophat2; version 2.1.0; parameters: --library-type fr-firststrand -p 3 -G mm10g.gtf –b2-sensitive
Multi-mapping reads were removed with samtools by filtering on the mapq field. command: samtools view -b -q 5
non-normalized read abundances were obtained with htseq-count using default setting, but with the stranded option set to reverse (-s reverse)
Differential expressed genes were obtained with DESeq2 wit standard analysis settings
Genome_build: mm10
Supplementary_files_format_and_content: processed files contain the output from htseq-count for each sample (raw abundance data).

source_name: Wild Type TNF(nl) treated

growth_protocol: Mice were kept in individually ventilated cages under a 12 hour dark/light cycle in a conventional and specific pathogen free (SPF) animal facility and received food and water ad libitum. All mice were used at 8-12 weeks of age.

extract_protocol:
Ileum was dissected, extensively flushed with PBS and incubated with lysis buffer (732 6802; Biorad) supplemented with 2-mercaptoethanol on ice for 5 minutes. Samples were then snapfrozen in liquid nitrogen
Illumina truseq RNA stranded library protocol (for single end sequencing)

treatment_protocol: In a first experiment (samples 1-24), wild type and GR dim mutant mice were treated with a lethal dose of TNF (see samples) or vehicle for eight hours. Pre-treatment with DEX or vehicle occured 30 min prior to TNF injection. In a second experiment (samples 25-30), Wild type mice were treated with a nonlethal (nl) dose of TNF or vehicle for eight hours.

value: FVB/N

value: Intestinal epithelial cells (IEC)

value: Wild Type

tag: treatment

value: vehicle/12.5 microgram TNF

tag: experiment


title: Wild Type Untreated rep3_Experiment 2

description: Sample 27

source_name: Wild Type Untreated

value: vehicle/vehicle


title: Wild Type TNF(nl) treated rep1_Experiment 2

description: Sample 28


title: Wild Type TNF(nl) treated rep3_Experiment 2

description: Sample 30


title: Naive_Marilyn_biological rep_2

description: Naive antigen-specific Marilyn cells


title: Naive_Marilyn_biological rep_1

description: Naive antigen-specific Marilyn cells


title: Col0_TSS-Seq_rep2


title: Col0_TSS-Seq_rep1


title: Wild Type Untreated rep1_Experiment 2

description: Sample 25


title: GRdim Mutant Dexamethasone + TNF treated rep3

description: Sample 24

value: GRdim Mutant

value: DEX/12.5 microgram TNF


title: Wild Type Untreated rep2_Experiment 2

description: Sample 26


title: GRdim Mutant Dexamethasone + TNF treated rep2

description: Sample 23


title: GRdim Mutant TNF treated rep3

description: Sample 21

source_name: GRdim Mutant TNF treated


title: GRdim Mutant Dexamethasone + TNF treated rep1

description: Sample 22


title: GRdim Mutant TNF treated rep2

description: Sample 20


title: GRdim Mutant Dexamethasone treated rep1

description: Sample 16

source_name: GRdim Mutant Dexamethasone treated

value: DEX/vehicle


title: GRdim Mutant Dexamethasone treated rep3

description: Sample 18


title: GRdim Mutant Untreated rep3

description: Sample 15

source_name: GRdim Mutant Untreated


title: GRdim Mutant Untreated rep2

description: Sample 14


title: Marilyn cells from tumor free mice receiving male splenocytes_biological rep_3

description: Antigen-specific Marilyn cells from tumor-free mice immunized with splenocytes expressing the model antigen

source_name: lymph node draining the site of immunization (popliteal lymph node)

label_protocol: Biotinylated cDNA were prepared according to the Nugen ovation WTA v2 amplification and encore biotin module protocol from 1ng total RNA.

treatment_protocol: Naïve tumor antigen-specific Marilyn CD4 T cells were transferred into mice bearing early or advanced tumors. 5x10^4 total Marilyn cells were purified 7 days after transfer from the lymph node draining the tumor site  (3 pools of 5 mice per condition). Naive Marilyn cells or Marilyn cells activated in tumor-free mice primed with a lentiviral vector encoding for the model tumor antigen or splenocytes expressing the model antigen were used as controls.

value: Tumor Free (Male splenocytes)


title: Marilyn cells from tumor free mice receiving male splenocytes_biological rep_2


title: Marilyn cells from tumor free mice receiving male splenocytes_biological rep_1


title: GRdim Mutant Untreated rep1

description: Sample 13


title: spt16_RNA-Seq

value: Columbia (Col-0)

value: Whole seedlings

value: 14 day


title: Naïve Marilyn cells biological rep_2

description: Antigen-specific naïve Marilyn cells

value: Tumor Free


title: Wild Type Dexamethasone + TNF treated rep3

description: Sample 12

source_name: Wild Type Dexamethasone + TNF treated

value: DEX/50 microgram TNF


title: Marilyn cells from mice bearing early tumors_biological rep_1

description: Tumor antigen-specific Marilyn cells from  mice bearing early tumors

value: Early tumor stage

value: 7 days post-transfer


title: GRdim Mutant TNF treated rep1

description: Sample 19


title: Marilyn cells from tumor free mice receiving lentivirus_biological rep_1

description: Antigen-specific Marilyn cells from tumor-free mice primed with a lentivirus encoding for the model antigen

value: Tumor Free (Lentivirus)


title: Marilyn cells from tumor free mice receiving lentivirus_biological rep_3


title: Marilyn cells from mice bearing early tumors_biological rep_2


title: Naïve Marilyn cells biological rep_1

description: Antigen-specific naïve Marilyn cells

value: Freshly isolated


title: GRdim Mutant Dexamethasone treated rep2

description: Sample 17

value: FVB/N

value: Intestinal epithelial cells (IEC)


title: Naïve Marilyn cells biological rep_3

description: Antigen-specific naïve Marilyn cells


title: Marilyn cells from mice bearing early tumors_biological rep_3


title: Marilyn cells from mice bearing advanced tumors_biological rep_3

description: Tumor antigen-specific Marilyn cells from mice bearing advanced tumors

value: Advanced tumor stage


title: Wild Type TNF treated rep2

description: Sample 8

source_name: Wild Type TNF treated

value: Wild Type

value: vehicle/50 microgram TNF


title: Wild Type Dexamethasone + TNF treated rep1

description: Sample 10


title: Wild Type TNF treated rep1

description: Sample 7


title: Marilyn cells from mice bearing advanced tumors_biological rep_2


title: Wild Type Dexamethasone treated rep3

description: Sample 6

source_name: Wild Type Dexamethasone treated


title: Marilyn cells from tumor free mice receiving lentivirus_biological rep_2


title: Wild Type Dexamethasone treated rep2

description: Sample 5


title: Marilyn cells from mice bearing advanced tumors_biological rep_1


title: Wild Type Dexamethasone + TNF treated rep2

description: Sample 11


title: Wild Type TNF treated rep3

description: Sample 9


title: Wild Type Untreated rep3

description: Sample 3

value: vehicle/vehicle


title: Wild Type Dexamethasone treated rep1

description: Sample 4

value: DEX/vehicle


title: Wild Type Untreated rep2

description: Sample 2


title: Wild Type Untreated rep1

description: Sample 1


title: RNA-seq of 30days post wounded skin biopsy from JunB deficient mice 2

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

institute: University of Ulm

data_processing:
Demultiplexing of raw reads were done using standard Illumina protocol
Demultiplexed fastq reads alignment using Hista2 with -dat cufflinks option
cufflinks based transcripts assembly
cuffdiff based differential gene expression
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: skin

extract_protocol:
Keratinocytes were isoldated from control (WT or Co) and JunB knock out (mutant or mut) using trysin based methods. Total RNA was isolated from the keratinocytes and rRNA was removed using ribozero gold (Illumina). The rRNA depleted RNA was used for library preparation using TruSeq Directional RNAseq kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

value: JunB -/-

value: 30days post wounded skin biopsy


title: RNA-seq of 4days post hair depilated skin biopsy from JunB deficient mice

source_name: keratinocyte

value: keratinocyte

value: 4days post hair depilated skin biopsy


title: RNA-seq of 4days post hair depilated skin biopsy from JunB wild type mice

value: JunB +/+


title: RNA-seq of 30days post wounded skin biopsy from JunB deficient mice


title: Liver_Sedentary_VitE_rep5

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description:
Sed_VitE_2417
Gene expression data from liver tissue from sedentary mice fed with vitamin E-enriched diet, biological replicate 5.

hyb_protocol: According to the Affymetrix expression protocol (HWS kit) including minor changes as suggested by the Encore Biotin protocol.

scan_protocol: According to the Affymetrix expression protocol (GeneChip Scanner 3000 7G).

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (build 1.4.1.46) including median polish and Sketch-Quantile normalisation.

source_name: Liver tissue from sedentary mice fed with vitamin E-enriched diet

label_protocol: Ovation Pico WTA System V2 and Encore Biotin Module (Nugen).

extract_protocol: RNeasy Fibrous Tissue Kit (Qiagen) including DNase digestion.

treatment_protocol: As described in the paper. Briefly, mice were assigned to either a diet supplemented with 100 mg/kg vitamin C and 2,000 IU/kg vitamin E (as α-tocopheryl acetate) or to control diet (0 mg/kg vitamin C, 149 IU/kg vitamin E) based on the purified diet C1000 (Altromin, Lage, Germany). After 4 weeks of feeding, at an age of 11-12 weeks, the animals were subjected to an acute bout of exercise (60 min at 13 m/min and 14° inclination) on a treadmill as described previously (Hoene et al., 2010). Mice remaining in their cages, but in close proximity to the treadmill, served as controls and were deprived of food for the last 60 min before they were killed, to align with the feeding state of the exercised group.

tag: strain/background

value: 11-12 weeks

tag: gender

value: Male

value: Liver

tag: diet

value: vitamin E enriched

tag: exercise

value: sedentary


title: Liver_Sedentary_VitE_rep8

description:
Sed_VitE_2714
Gene expression data from liver tissue from sedentary mice fed with vitamin E-enriched diet, biological replicate 8.


title: Liver_Sedentary_VitE_rep10

description:
Sed_VitE_2716
Gene expression data from liver tissue from sedentary mice fed with vitamin E-enriched diet, biological replicate 10.


title: Liver_Sedentary_VitE_rep6

description:
Sed_VitE_2712
Gene expression data from liver tissue from sedentary mice fed with vitamin E-enriched diet, biological replicate 6.


title: Liver_Sedentary_VitE_rep4

description:
Sed_VitE_2416
Gene expression data from liver tissue from sedentary mice fed with vitamin E-enriched diet, biological replicate 4.


title: Liver_Sedentary_VitE_rep9

description:
Sed_VitE_2715
Gene expression data from liver tissue from sedentary mice fed with vitamin E-enriched diet, biological replicate 9.


title: Liver_Sedentary_VitE_rep3

description:
Sed_VitE_2415
Gene expression data from liver tissue from sedentary mice fed with vitamin E-enriched diet, biological replicate 3.


title: Liver_Sedentary_VitE_rep7

description:
Sed_VitE_2713
Gene expression data from liver tissue from sedentary mice fed with vitamin E-enriched diet, biological replicate 7.


title: Liver_Sedentary_VitE_rep2

description:
Sed_VitE_2414
Gene expression data from liver tissue from sedentary mice fed with vitamin E-enriched diet, biological replicate 2.


title: RNA-seq of 30days post wounded skin biopsy from JunB wild type mice

tag: strain


title: RNA-seq of 30days post wounded skin biopsy from JunB wild type mice 2


title: Liver_Sedentary_VitE_rep1

description:
Sed_VitE_2413
Gene expression data from liver tissue from sedentary mice fed with vitamin E-enriched diet, biological replicate 1.


title: Hela_Ctrl_Input

city: Irvine

first: Jiejun

last: Shi

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie v1.1.0
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.4.2; Scores represent the ChIP-seq tag numbers

source_name: HeLa_control vector

growth_protocol: Hela cells were maintained in DMEM media [Dulbecco’s modified Eagle’s medium (DMEM, Cellgro) supplemented with 10% Fetal Bovine Serum (Sigma), 100 U/ml penicillin, 100 µg/ml streptomycin, 292 µg/ml L-glutamine]. Media was changed every other day.

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 1 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform.

treatment_protocol: For infections, Hela cells were incubated with viral supernatants in the presence of 8 µg/ml polybrene for 14 hr. After 48 hr, the infected cells were selected with blasticidin (5 µg/ml) for overexpression experiments.

tag: cell line

value: HeLa

tag: genotype/variation

value: stably expressing control vector (Ctrl)


title: Flag-H3.3 ChIP-seq in G34W

source_name: HeLa_G34W H3.3

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_22.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 1 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform.

value: stably expressing mutant (G34W)  H3.3

tag: chip antibody

tag: chip antibody vendor/cat.#

value: Sigma, F1804


title: RNA-seq of JunB deficient keratinocytes


title: Liver_Sedentary_Control_rep9

description:
Sed_Ctrl_2704
Gene expression data from liver tissue from sedentary mice fed with control diet, biological replicate 9.

source_name: Liver tissue from sedentary mice fed with control diet

value: control


title: Liver_Sedentary_Control_rep8

description:
Sed_Ctrl_2702
Gene expression data from liver tissue from sedentary mice fed with control diet, biological replicate 8.


title: Liver_Sedentary_Control_rep6

description:
Sed_Ctrl_2406
Gene expression data from liver tissue from sedentary mice fed with control diet, biological replicate 6.


title: RNA-seq of JunB wild type keratinocytes


title: Liver_Sedentary_Control_rep7

description:
Sed_Ctrl_2701
Gene expression data from liver tissue from sedentary mice fed with control diet, biological replicate 7.


title: H3K36me3 ChIP-seq in G34W

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_21.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 1 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform.

value: Abcam, Ab9050


title: H3K36me2 ChIP-seq in G34W

value: Abcam, Ab9049


title: Liver_Sedentary_Control_rep10

description:
Sed_Ctrl_2705
Gene expression data from liver tissue from sedentary mice fed with control diet, biological replicate 10.


title: pDCs and ARP1 in/out Transwell repeat 3

city: CLEVELAND

first: ENGUANG

last: BI

state: OH

address: 9500 EUCLID AVE

department: CANCER BIOLOGY

institute: CLEVELAND CLINIC LERNER RESEARCH INSTITUTE

description:
9269325019_D
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: pDCs were seeded into the Transwell polycarbonate membrane cell culture insert and ARP1 cells were out of the transwell insert with 1:1.5 ratio, and stimulated with CpG, then pDCs and ARP1 cells were harvested and mixed together for RNA extraction.

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

growth_protocol: Cells were cultured in RPMI1640 with 10% FCS.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: PDCs were treated with CpG (0.15 mM) for 12 hours with or without coculture with ARP1. Transwells were used in some cultures. In some condition, to avoid the two types of cells ARP1 and pDCs to contact directly, we cultured pDCs in transwell, a polycarbonate membrane cell culture inserts and ARP1 in the well. The soluble factors from ARP1 can still affect pDCs through the transwell membrane.

value: blood

tag: cell type

value: ARP1 and pDCs


title: pDCs and ARP1 in/out Transwell repeat 2

description:
9269325019_H
replicate 2

tag: tissue


title: pDCs and ARP1 Direct coculture repeat 1

description:
9269325017_G
replicate 1

source_name: pDCs and ARP1 cells were mixed with 1:1.5 ratio and stimulated with CpG and RNA was extracted.


title: pDCs and ARP1 in/out Transwell repeat 1

description:
9269325018_G
replicate 1


title: pDCs and ARP1 Direct coculture repeat 2

description:
9269325018_K
replicate 2


title: pDCs and ARP1 Direct coculture repeat 3

description:
9269325019_G
replicate 3


title: Liver_Sedentary_Control_rep5

description:
Sed_Ctrl_2405
Gene expression data from liver tissue from sedentary mice fed with control diet, biological replicate 5.


title: Lcell_T3Dneg_DARTseq_0

description: Capture of host messenger RNA in an uninfected cell. This sample serves as a negative control, as all ten segments of  the viral RNA genome were targeted at one loci each, but no virus was present in the cells.

source_name: Murine L929 cells

value: Lcell T3Dneg

tag: capture

value: DART-seq bead


title: Lcell_T3Dpos_DARTseq_1

description: Capture of host messenger RNA and viral messenger and positive-stranded genomic RNA. Reovirus genomic segment S2 (encoding mRNA for protein sigma-2) was targeted at seven loci.

value: Lcell T3Dpos


title: H3K27me3 ChIP-seq in G34W

value: Millipore, 07-449


title: Liver_Sedentary_Control_rep4

description:
Sed_Ctrl_2404
Gene expression data from liver tissue from sedentary mice fed with control diet, biological replicate 4.

tag: age

value: 11-12 weeks

value: Male


title: Liver_Sedentary_Control_rep3

description:
Sed_Ctrl_2403
Gene expression data from liver tissue from sedentary mice fed with control diet, biological replicate 3.

value: Liver


title: Lcell_T3Dpos_DARTseq_0

description: Capture of host messenger RNA and viral messenger and positive-stranded genomic RNA. Each of ten reovirus genomic segments was targeted at one locus.


title: pDCs and ARP1 mixture repeat 3

description:
9269325019_B
replicate 3

source_name: mixture pDCs and ARP1 cells were stimulated with CpG separately and then mixed with 1:1.5 ratio and RNA was extracted.


title: Liver_Sedentary_Control_rep1

description:
Sed_Ctrl_2401
Gene expression data from liver tissue from sedentary mice fed with control diet, biological replicate 1.

value: sedentary


title: pDCs and ARP1 mixture repeat 2

description:
9269325018_J
replicate 2


title: pDCs and ARP1 no culture repeat 3

description:
9269325019_F
replicate 3

source_name: Freshly isolated pDCs and no treated ARP1 cells were mixed with 1:1.5 ratio and RNA was extracted.


title: pDCs and ARP1 mixture repeat 1

description:
9269325018_H
replicate 1


title: Liver_Sedentary_Control_rep2

description:
Sed_Ctrl_2402
Gene expression data from liver tissue from sedentary mice fed with control diet, biological replicate 2.


title: Lcell_T3Dpos_Dropseq_0

description: Capture of host messenger RNA only.

value: Drop-seq bead


title: Liver_Exercise_VitE_rep12

description:
Run_VitE_2722
Gene expression data from liver tissue from mice after treadmill run fed with vitamin E-enriched diet, biological replicate 12.

source_name: Liver tissue from mice after treadmill run fed with vitamin E-enriched diet

value: vitamin E enriched

value: treadmill run


title: H3K27ac ChIP-seq in G34W

value: HeLa

value: stably expressing mutant (G34W)  H3.3

value: Abcam, Ab4729


title: Flag-H3.3 ChIP-seq in WT

source_name: HeLa_WT H3.3

value: stably expressing WT or mutant (G34L/G34W) H3.3

value: Sigma, F1804


title: H3.3 ChIP-seq in G34W

value: Millipore, 09-838


title: pDCs and ARP1 no culture repeat 2

description:
9269325018_L
replicate 2

value: blood

value: ARP1 and pDCs


title: H3K36me3 ChIP-seq in WT

value: Abcam, Ab9050


title: H3K27me3 ChIP-seq in WT

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_25.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 1 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform.

value: Millipore, 07-449


title: H3K36me2 ChIP-seq in WT

value: Abcam, Ab9049


title: H3.3 ChIP-seq in WT

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_26.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 1 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform.


title: Liver_Exercise_VitE_rep11

description:
Run_VitE_2721
Gene expression data from liver tissue from mice after treadmill run fed with vitamin E-enriched diet, biological replicate 11.

value: 11-12 weeks

value: Male


title: H3K36me3 ChIP-seq in K36M

source_name: HeLa_K36M H3.3


title: Liver_Exercise_VitE_rep7

description:
Run_VitE_2717
Gene expression data from liver tissue from mice after treadmill run fed with vitamin E-enriched diet, biological replicate 7.

value: Liver


title: Liver_Exercise_VitE_rep10

description:
Run_VitE_2720
Gene expression data from liver tissue from mice after treadmill run fed with vitamin E-enriched diet, biological replicate 10.


title: Liver_Exercise_VitE_rep8

description:
Run_VitE_2718
Gene expression data from liver tissue from mice after treadmill run fed with vitamin E-enriched diet, biological replicate 8.


title: pDCs - Transwell repeat 3

description:
9269325017_I
replicate 3

source_name: This sample includes only pDC cells from inside the transwell insert. ARP1 cells were outside transwell insert. Co-culture  was treated with CpG for 12 hours.

value: pDCs


title: Liver_Exercise_VitE_rep6

description:
Run_VitE_2424
Gene expression data from liver tissue from mice after treadmill run fed with vitamin E-enriched diet, biological replicate 6.

value: vitamin E enriched


title: H3K36me2 ChIP-seq in K36M


title: pDCs - Transwell repeat 2

description:
9269325017_H
replicate 2


title: pDCs and ARP1 no culture repeat 1

description:
9269325017_J
replicate 1


title: Flag-H3.3 ChIP-seq in G34L

source_name: HeLa_G34L H3.3

value: stably expressing mutant (G34L)  H3.3


title: pDCs - Transwell repeat 1

description:
9269325017_F
replicate 1