title: SNF002_D0_batch2

value: PBMC

value: Day 0

tag: subject id

tag: age (years)

value: Female

value: Chinese


title: Brain telencephalon rep3

status: Public on Nov 14 2018

type: SRA

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

country: USA

institute: UNIVERSITY OF FLORIDA

library_source: transcriptomic

data_processing:
Illumina basespace  used for basecalling.
Reads acquired from the illumina HiSeq 4000 sequencing platform were cleaned up with the Cutadapt program to trim off sequencing adaptors and low quality bases with a quality phred-like score<20.  Reads <40 bases were excluded from RNA-seq analysis.
ICBR scripts along with SAMtools and the DESeq, EdgeR, and Bayseq (DEB) computational applications were applied to generate the gene expression data, including fold changes and p-values, to remove duplicates or artifacts from PCR, and choose uniquely mapped reads for gene expression analysis. Digital gene expression was assessed by counting the number of transcripts that mapped to a gene sequence
Genome_build: FHM_All_PTA_Assem.fasta
Supplementary_files_format_and_content: tab-delimited text files include the mapped read counts for each Sample

molecule: total RNA

organism: Pimephales promelas

source_name: tissue

extract_protocol:
Tissue extractions followed procedures previously described (Garcia-Reyero et al., 2009; Bisesi et al., 2017).  Briefly, tissues were homogenized in RNA Stat-60 (TelTest) using a handheld rotary homogenizer followed by organic separation with chloroform.
RNA was then subjected to a second round of RNA Stat-60/Chloroform extraction, followed by precipitation in isopropanol overnight at -20°C.  RNA was washed twice with 75% ethanol, dried, and reconstituted in RNAsecure (ThermoFisher Scientific). Reconstituted RNA was DNase-treated to remove possible genomic DNA contamination using Turbo DNase (ThermoFisher Scientific). The quality of the RNA was assessed using an Agilent Bioanalyzer 2100.  Only samples with RNA integrity numbers (RINs) exceeding 8 were used for sequencing.  Samples were then quantified using a ThermoFisher Scientific Qubit 3.0 fluorimeter.

treatment_protocol: Fish were sacrificed at different times for three different experiments by submersion in buffered 250 mg/L MS-222 (Western Chemical).

tag: tissue

value: telencephalon

tag: location

value: the Aquatic Toxicology Core Laboratory at the University of Florida

tag: age

value: Adult male


title: SNF002_D2_batch2

type: RNA

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

hyb_protocol: Labelled cRNAs were hybridized to Illumina human HT-12 V4.0 chips for 16 hours at 58°C in batches of 96 samples. The arrays were then washed and stained base on Illumina Wash Protocol.

scan_protocol: The human chips were scanned using BeadArray Scanner 500GX and the images were analyzed using Illumina GenomeStudio Gene Expression v 2011.1.

data_processing: Illumina Genome Studio was used to export the data in raw format. Raw expression data was loaded into R/Bioconductor and normalized using log2 quantile normalization method of the lumi R package.

label: Biotin

organism: Homo sapiens

source_name: PBMC Day 2 post-vaccination

label_protocol: Biotinylated cRNA was prepared according to the Illumina® Ambion TotalPrep™ 96 RNA Amplification kit (Thermo Fisher Scientific, San Jose, CA, USA) using 300ng of RNA.

growth_protocol: No growth protocol was used. PBMCs isolated from whole blood were directly processed for RNA isolation.

extract_protocol: PBMCs were isolated from whole blood. 1 million PBMCs were washed with 1 mL of PBS and centrifuged. The supernatant was removed. The cell pellet was loosened and lysed in mirVana Lysis/Binding buffer and stored in -80degC before extraction. Total RNA was isolated from PBMCs using mirVana™ miRNA isolation kit (Thermo Fisher Scientific, San Jose, CA, USA). Total RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: No treatment of PBMCs was performed.

tag: cell type

tag: treatment

value: Vaxigrip influenza vaccine

tag: time point

value: Day 2

tag: gender

tag: ethnicity

tag: microarray batch


title: Nilotinib resistant cells

city: C

first: E

last: F

state: D

address: B

institute: A

description: K562 Nilotinib resistant cells

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

label: biotin

source_name: CML K562 cell line

label_protocol: Standard Illumina label protocol

growth_protocol: Culture Collection and grown in RPMI1640 supplemented with 10% fetal bovine serum (FBS) at 37°C under 5% CO2.

extract_protocol: The total RNA was isolated using miRNeasy Kit (QIAGEN)

treatment_protocol: K562 cells were passaged with low concentrations of nilotinib (0.1 µM) and sequentially cultured in increasing concentrations of these TKIs (0.3, 1 µM) for 3 months. Cells cultured in parallel without drugs were served as parental negative controls. Cells were considered resistant when they could routinely grow in medium containing 1 µM nilotinib.

tag: cell line

value: CML K562

tag: sample type

value: nilotinib resistance


title: Parental cells

description: K562 parental cells

value: parental


title: NoGVHD_TSP_1

city: Paris

first: Emmanuel

last: Clave

state: Paris

address: INSERM

country: France

institute: UMRS 1160

hyb_protocol: Hybridation on GeneChip Human U133 plus 2.0 Arrays (Affymetrix) with 10 ng of labeled cRNA following manufacturer's protocols. Staining and washing has been realised on fluidics (FS 450, Affymetrix)

scan_protocol: Arrays scanning  has been realised using the GeneChip Scanner 3000 7G (Affymetrix) with AGCC software

data_processing: Probe set summarization and data  normalisation are realised from.CEL files  using algorithm Maximum Rank Sum (MAXRS) and normalized with global normalization (MAS 5) methods

label_protocol: Total RNA were amplified using the ExpressArt mRNA amplification Pico kit (AmpTec GmbH, Hambourg, Germany) and labeled with the BioArray HighYield RNA transcript labeling kit (Enzo Life Sciences, Villeurbanne, France),

growth_protocol: No

extract_protocol: micro Rneasy kit (Qiagen) with DNAase

treatment_protocol: After ficoll gradient separation mononuclear cell were sorted using a FACS ARIA III, 500 cells for each population were directly collected into Qiagen RLT buffer

tag: individual

value: allo-HSCT patient (BOUC)

tag: disease state

value: GVHD grade 0

tag: cell population

value: TSP


title: NoGVHD_CD10_2

value: allo-HSCT patient (AUGD)

value: GVHD grade 1


title: NoGVHD_CD10_1


title: Brain telencephalon rep1


title: Control_5hpi_rep2

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
Cells were infected with HCMV for 5 hours.
I8_5hpi_rep2
processed data file: 5hpi.txt

data_processing:
Prior to alignment, polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded. Then, reads that were not aligned to the genome were aligned to the transcriptome.
Genome_build: hg19 + NCBI EF999921.1
Supplementary_files_format_and_content: *.txt: Tab-separated text files with numbers of aligned reads for each gene.

organism:
Homo sapiens
Human betaherpesvirus 5

source_name: Primary fibroblasts

extract_protocol:
Total RNA was extracted using TRI reagent.
mRNA was isolated using polyA selection kit (Ambion) and then fragmented. Fragments were then dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circularized and PCR amplified. m6A-immunoprecipitation was done as previously described (Schwartz et al., Cell Reports, 2014).

value: Primary fibroblasts

tag: infection

value: HCMV for 5 hr


title: SGR-0-2

city: Ardmore

first: Kiran

last: Mysore

state: Oklahoma

address: 2510 Sam Noble Parkway

institute: Noble Research Institute

data_processing:
The raw reads were first cleaned to remove low quality reads by using a software, Sickle (Joshi and Fass, 2011). For Sickle analysis, following parameters were used: minimum length >= 30 bp and quality score >=30.
All trimmed reads from the same species were de novo assembled to reference transcriptome contigs by using Trinity (Grabherr et al., 2011, Haas et al., 2013).
The trimmed reads were aligned to reference transcriptome contigs by using Tophat2 (Langmead et al., 2009, Trapnell et al., 2009, Kim and Salzberg, 2011, Kim et al., 2013).
The normalized expression values (FPKM) were measured by using Cufflink (Trapnell et al., 2010).
The differentially expressed (DE) contigs were then identified by using Cuffdiff 2 (Trapnell et al., 2013)
Genome_build: de novo Transcriptome assembly was performed. The FASTA files of assembled transcripts are available on the series record. UG_ASR_Trininity.fasta =  Phakopsora pachyrhizi; UG_SGR_Trininity.fasta = Puccinia emaculata.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Puccinia emaculata

source_name: Germinating urediniospore_0mM Phi

growth_protocol: Urediniospores of Pe and Pp were dusted on 1× germination solution [500× stock: 0.0036% nonanol (v/v), 0.025% Tween 20 (v/v), 50% ethanol (v/v), in autoclaved distilled water] supplemented with 10 or 100 mM Phi on a Petri plate. Urediniospores were allowed to germinate for 24 h in the dark. After 24 h, germinated urediniospores were collected by skimming them from the surface of the solution with the help of a cover slip.

extract_protocol:
total RNA from Phi‐treated Pe and Pp was isolated using an RNeasy plant mini kit (Qiagen). Two biological replicates were used for each treatment. Illumina TruSeq sequencing‐by‐synthesis chemistry was used on a HiSeq 2000 platform (Illumina, https://www.illumina.com/) to generate paired‐end reads (2 × 100 bp).
As per Illumina library preparation guide

treatment_protocol: Treatments: 0 mM Phi, 10 mM Phi, and 100 mM Phi

value: Germinating urediniospore


title: Liver rep3

value: tissue


title: SO-4014-Repl4-LTBM015FU2_S17(12_Month_Treatment Replicate1)

city: Bangalore

first: Nagasuma

last: Chandra

state: Karnataka

address: C V Raman Road

department: Biochemistry

country: India

institute: IISC

data_processing:
Trimming and adapter removal using trimmomatic
differential expression analysis using the TUXEDO protocol
Tophat2 (v2.0.9)→cufflinks(v2.2.1)-→cuffdiff (v2.2.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab separated fpkm_tracking files

source_name: whole Blood sample

extract_protocol:
RNA isolation kit (Applied Biosystems)
NEXTflexRapid Directional RNA-Seqlibrary; NEXTflex™ RNA-Seq Barcode Adapters were added

treatment_protocol: Tuberculosis DOTS treatment

value: whole blood

tag: Sex

value: Male

tag: patient diagnosis

value: Tuberculosis

tag: disease status

value: 12 months after treatment


title: METTL3_22uv_rep2

description:
Cells were infected with UV-inactivated HCMV for 22 hours.
M3_22uv_rep2
processed data file: 22uv.txt

value: UV-inactivated HCMV for 22 hr


title: SGR-0-1

tag: tissue


title: Liver rep1

tag: location

value: the Aquatic Toxicology Core Laboratory at the University of Florida

tag: age

value: Adult male


title: SO-4014-Repl4-LTBM016FU2_S15(12_Month_Treatment Replicate1)


title: Brain hypothalamus rep3

value: hypothalamus


title: SGR-10-1

source_name: Germinating urediniospore_10mM Phi


title: Liver rep2


title: Control_22uv_rep2

description:
Cells were infected with UV-inactivated HCMV for 22 hours.
I8_22uv_rep2
processed data file: 22uv.txt

tag: cell type


title: SO-4014-Repl4-LTBM016BL_S13(Active TB Replicate3)

value: Active TB


title: ASR-100-2

organism: Phakopsora pachyrhizi

source_name: Germinating urediniospore_100mM Phi


title: ASR-100-1


title: Control_5hpi_rep1

description:
Cells were infected with HCMV for 5 hours.
I8_5hpi_rep1
processed data file: 5hpi.txt


title: SO-4014-Repl4-LTBM015BL_S16(Active TB Replicate4)


title: Brain hypothalamus rep2


title: SO-4014-Repl4-LTBM016FU1_S14(6_Month_Treatment Replicate3)

value: 6 months after treatment


title: ASR-10-2


title: Control_22uv_rep1

description:
Cells were infected with UV-inactivated HCMV for 22 hours.
I8_22uv_rep1
processed data file: 22uv.txt


title: METTL3_22uv_rep1

description:
Cells were infected with UV-inactivated HCMV for 22 hours.
M3_22uv_rep1
processed data file: 22uv.txt


title: ASR-10-1


title: METTL3_26hpi_4hrActD_rep2

description:
Cells were infected with HCMV for 26 hours. At 22 hours post infection, cells were treated with Actinomycin D (Sigma) at concentration of 5uM.
M3_26hpi_ActD4h_rep2
processed data file: 26hpi_4hrActD.txt

value: HCMV for 26 hr

tag: treatment

value: Actinomycin D 5uM at 22 hr post infection


title: Brain hypothalamus rep1


title: SO-4014-Repl4-LTBM036FU1_S11(6_Month_Treatment Replicate2)


title: Gut rep3


title: ASR-0-2


title: Gut rep2


title: METTL3_26hpi_4hrActD_rep1

description:
Cells were infected with HCMV for 26 hours. At 22 hours post infection, cells were treated with Actinomycin D (Sigma) at concentration of 5uM.
M3_26hpi_ActD4h_rep1
processed data file: 26hpi_4hrActD.txt


title: SO-4014-Repl4-LTBM036BL_S10(Active TB Replicate2)


title: Control_26hpi_4hrActD_rep2

description:
Cells were infected with HCMV for 26 hours. At 22 hours post infection, cells were treated with Actinomycin D (Sigma) at concentration of 5uM.
I8_26hpi_ActD4h_rep2
processed data file: 26hpi_4hrActD.txt


title: ASR-0-1


title: Gut rep1


title: SO-4014-LTBM021FU2_S9(12_Month_Treatment Replicate1)


title: Control_26hpi_4hrActD_rep1

description:
Cells were infected with HCMV for 26 hours. At 22 hours post infection, cells were treated with Actinomycin D (Sigma) at concentration of 5uM.
I8_26hpi_ActD4h_rep1
processed data file: 26hpi_4hrActD.txt


title: SO-4014-LTBM021BL_S7(Active TB Replicate1)


title: ta2-1 endosperm

city: Beijing

first: Jinxin

last: Liu

address: No.20 Nanxincun, Xiangshan

country: China

institute: Institute of Botany, CAS

library_source: genomic

data_processing:
Base-calling were performed with Illumina CASAVA pipeline.
We use FastQC (fastqc_v0.11.5) to perform basic statisticson the quality of the raw reads.Then, those reads sequences produced by the Illumina pipleline in FASTQ format were pre-processed through Trimmomatic (Trimmomatic-0.36) software use the parameter (SLIDINGWINDOW: 4:15; LEADING:3, TRAILING:3;ILLUMINACLIP: adapter.fa: 2: 30: 10; MINLEN:36).The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use FastQC to perform basic statistics on the quality of the cleandata reads.
Bismark software (version 0.16.3; Krueger F, 2011) was used to perform alignments of bisulfite-treated reads to a reference genome. The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2 (Langmead B, 2012).Sequence reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before they are aligned to similarly converted versions of the genome in a directional manner. Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. The same reads that aligned to the same regions of genome were regarded as duplicated ones. The sequencing depth and coverage were summarized using deduplicated reads.
The results of methylation extractor (bismark_methylation_extractor,-- no_overlap) were transformed into bigWig format for visualization using IGV browser. The sodium bisulfite non-coversion rate was calculated as the percentage of cytosine sequenced at cytosine reference positions in the lambda genome.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: bedGraph files were generated.

molecule: genomic DNA

organism: Oryza sativa

source_name: Endosperm

growth_protocol: Rice (Oryza sativa L. ssp. Geng, cultivar Zhonghua 11, ZH11) plants were cultivated in an experimental field at the Institute of Botany, Chinese Academy of Sciences, Beijing.

extract_protocol:
For whole-genome bisulfite sequencing, genomic DNA was isolated from endosperms and embryos using a QIAamp DNA Mini Kit (Qiagen).
The volumes of the combined gDNA sample and unmethylated lambda DNA control were adjusted to a total volume of 80 μL using 1x TE buffer, and fragmented to 300 bp. Subsequently, fragmented DNA was end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon) and a gDNA library was constructed according to the manufacturer's instructions (Illumina). Bisulfite conversion was performed using an EZ DNA Methylation-Gold Kit. The bisulfiate-converted library was amplified using KAPA HiFi HotStart DNA Polymerase (Kapa Biosystems).

tag: ecotype

value: Zhonghua 11

tag: genotype

value: Endosperm at 9 days after pollination


title: METTL3_24hpi_2hrActD_rep2

description:
Cells were infected with HCMV for 24 hours. At 22 hours post infection, cells were treated with Actinomycin D (Sigma) at concentration of 5uM.
M3_24hpi_ActD2h_rep2
processed data file: 24hpi_2hrActD.txt

value: Primary fibroblasts

value: HCMV for 24 hr


title: SO-4014-LTBM021FU1_S8(6_Month_Treatment Replicate1)


title: ZH11 endosperm

value: Wild-type


title: WT day45 rep3

city: Shanghai

first: Xiaofen

last: Wu

address: 345 Lingling Rd

department: Shanghai Institute of Organic Chemistry

institute: Chinese Academy of Sciences

description: head_aging_DESeq normalized_CountSet.txt

data_processing:
Sequencing reads were mapped to UCSC dm6(for sample 1-6) or flybase dm6_r6.05(for sample 7-18) with STAR by default parameter.
Read counts for each gene were calculated by HTSeq-count.
Count files were used as input to DESeq for normalization and differential expression analysis.
Genome_build: dm6
Supplementary_files_format_and_content: For sample1-6, differential expression between foxoc431/c431/WT was called using DESeq. For sample 7-18, sequencing depth was normalized to the same using DESeq.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: fly head

growth_protocol: Flies were cultured in standard media at 25ºC with 60% humidity unless otherwise specified. The control (WT) line used was 5905 (FlyBase ID FBst0005905, w1118). The given genotype flies were collected at the day of eclosion and transferred to new vials every other day during aging process.

extract_protocol:
Heads were removed at the given age, RNA was harvested using Trizol reagent, and polyA tail RNAs were selected.
NEBNext Ultra RNA library Prep Kit for Illumina (NEB, E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

value: post eclosion day 45

value: male


title: SO-4014-Repl4-LTBM036FU2_S12(12_Month_Treatment Replicate1)

value: whole blood

value: Male

value: Tuberculosis


title: ZH11 embryo

source_name: Embryo

value: Embryo at 9 days after pollination


title: Control_24hpi_2hrActD_rep2

description:
Cells were infected with HCMV for 24 hours. At 22 hours post infection, cells were treated with Actinomycin D (Sigma) at concentration of 5uM.
I8_24hpi_ActD2h_rep2
processed data file: 24hpi_2hrActD.txt


title: Control_24hpi_2hrActD_rep1

description:
Cells were infected with HCMV for 24 hours. At 22 hours post infection, cells were treated with Actinomycin D (Sigma) at concentration of 5uM.
I8_24hpi_ActD2h_rep1
processed data file: 24hpi_2hrActD.txt


title: WT day45 rep1


title: PJ16_MRS: MRS broth

city: BARI

first: pasquale

last: filannino

address: Via Amendola, 165/A

department: Dipartimento di Scienze del Suolo

country: Italy

institute: Università degli Studi di Bari “Aldo Moro”

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using GFOLD software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Lactiplantibacillus plantarum

source_name: MRS broth

growth_protocol: L. plantarum strains were cultivated on nine model media (bee and D. melanogaster intestine extracts [BE, DE], fecal omnivore and vegan extracts [FE_O, FE_V], olive extract [OE], tomato and pineapple juices [TJ, PJ], wheat flour hydrolysate [WFH], and cheese broth [CB])

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: isolation source

value: MRS broth


title: METTL3_22hpi_rep2

description:
Cells were infected with HCMV for 22 hours.
M3_22hpi_rep2
processed data file: 22hpi.txt

value: HCMV for 22 hr


title: BEE1ST_MRS: MRS broth


title: WT day30 rep3

value: post eclosion day 30


title: WFH19_MRS: MRS broth


title: METTL3_24hpi_2hrActD_rep1

description:
Cells were infected with HCMV for 24 hours. At 22 hours post infection, cells were treated with Actinomycin D (Sigma) at concentration of 5uM.
M3_24hpi_ActD2h_rep1
processed data file: 24hpi_2hrActD.txt


title: Control_22hpi_rep2

description:
Cells were infected with HCMV for 22 hours.
I8_22hpi_rep2
processed data file: 22hpi.txt


title: Untreated-control-24h-replicate-2

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

description: Resistant Dusa untreated control plants vs reference sample pool, replicate 2

hyb_protocol: Hybridization was carried out according to the two-colour microarray-based gene expression analysis protocol (Agilent)

scan_protocol: Microarray slides were scanned using the Axon GenePix 4000B scanner (Molecular Devices)

data_processing: Axon GenePix 6.0 software was used for image analysis. Normalization and statistical analysis was carried out in the R environment using limma

organism: Persea americana

source_name: Root samples of untreated control resistant plants

label_protocol: 4-6ug of RNA was transcribed into single stranded cDNA priming with random nonamer and oligo(dT) primers, using the Superscript III Reverse transcriptase. Samples and reference pools labelled with Cy3 and Cy5 (CyDye Post-Labelling Reactive Dye Pack, GE Healthcare Life Sciences)

growth_protocol: One-year-old Phytophthora cinnamomi-resistant clonal Dusa plants were provided by Westfalia Technological Services (WTS) (Tzaneen, South Africa).

extract_protocol: Total RNA extracted using the CTAB extraction method

treatment_protocol: Plants treated with SA received 70 ml of a 5 mM NaSA solution (Sigma-Aldrich, Missouri, USA) and the MeJA treated plants received 70 ml of a 5 mM MeJA solution (Sigma-Aldrich). Inoculation was carried out by applying 20 ml of a Pc zoospore suspension (3x10^5 spores/ml) and 70 ml Pc mycelial suspension to the soil at the base of each plant.

value: Dusa

value: Root

source_name: Pooled reference sample


title: METTL3_22hpi_rep1

description:
Cells were infected with HCMV for 22 hours.
M3_22hpi_rep1
processed data file: 22hpi.txt


title: WT day30 rep2


title: METTL3_IP_rep2

description:
Cells were infected with HCMV for 72 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
M3_IP_rep2
processed data file: 72hpi_m6A_IP.txt

value: HCMV for 72 hr

tag: ip antibody

value: anti-m6A antibody (Synaptic Systems)


title: OE1_MRS: MRS broth


title: Untreated-control-24h-replicate-1

description: Resistant Dusa untreated control plants vs reference sample pool, replicate 1


title: JA-treatment-24hpt-replicate-3

description: Resistant Dusa plants 24hr following treatment with jasmonic acid vs reference sample pool, replicate 3

source_name: Root samples of resistant plants treated with jasmonic acid, 24hr post-treatment


title: WT day30 rep1


title: Control_22hpi_rep1

description:
Cells were infected with HCMV for 22 hours.
I8_22hpi_rep1
processed data file: 22hpi.txt


title: WT day15 rep3

value: post eclosion day 15


title: JA-treatment-24hpt-replicate-2

description: Resistant Dusa plants 24hr following treatment with jasmonic acid vs reference sample pool, replicate 2


title: WT day45 rep2


title: Untreated-control-24h-replicate-3

description: Resistant Dusa untreated control plants vs reference sample pool, replicate 3


title: CB5_MRS: MRS broth


title: JA-treatment-24hpt-replicate-1

description: Resistant Dusa plants 24hr following treatment with jasmonic acid vs reference sample pool, replicate 1


title: Pc-infection-24hpi-replicate-3

description: Resistant Dusa plants 24hr following infection with Phytophthora cinnamomi vs reference sample pool, replicate 3

source_name: Root samples of resistant plants infected with Phytophthora cinnamomi, 24hr post-infection


title: WT day15 rep2


title: TJ22_MRS: MRS broth


title: Pc-infection-24hpi-replicate-2

description: Resistant Dusa plants 24hr following infection with Phytophthora cinnamomi vs reference sample pool, replicate 2


title: Pc-infection-24hpi-replicate-1

description: Resistant Dusa plants 24hr following infection with Phytophthora cinnamomi vs reference sample pool, replicate 1


title: DE12_MRS: MRS broth


title: METTL3_plus_ruxo_28hpi_rep1

description:
Cells were infected with HCMV for 28 hours. At 1 hour post infection, cells were treated with Ruxolitinib (InvivoGen) at concentration of 2uM.
M3_plus_ruxo_rep1
processed data file: 28hpi_minus_plus_ruxo.txt

value: Primary fibroblasts

value: HCMV for 28 hr

value: Ruxolitinib 2uM at 1 hr post infection


title: FEO3_MRS: MRS broth


title: WT day15 rep1

description: head_aging_DESeq normalized_CountSet.txt


title: JA-untreated-control-18h-replicate-2


title: WT day3 rep3

value: post eclosion day 3


title: JA-untreated-control-18h-replicate-3


title: FEV11_MRS: MRS broth


title: METTL3_no_ruxo_28hpi_rep2

description:
Cells were infected with HCMV for 28 hours.
M3_minus_ruxo_rep2
processed data file: 28hpi_minus_plus_ruxo.txt


title: Control_plus_ruxo_28hpi_rep2

description:
Cells were infected with HCMV for 28 hours. At 1 hour post infection, cells were treated with Ruxolitinib (InvivoGen) at concentration of 2uM.
I8_plus_ruxo_rep2
processed data file: 28hpi_minus_plus_ruxo.txt


title: METTL3_no_ruxo_28hpi_rep1

description:
Cells were infected with HCMV for 28 hours.
M3_minus_ruxo_rep1
processed data file: 28hpi_minus_plus_ruxo.txt


title: SNF005_D0_batch6F

source_name: PBMC Day 0 pre-vaccination

value: PBMC

tag: time point

value: Day 0

tag: subject id

tag: age (years)

tag: gender

tag: ethnicity

value: Chinese

tag: microarray batch


title: WCFS1_MRS: MRS broth


title: Control_plus_ruxo_28hpi_rep1

description:
Cells were infected with HCMV for 28 hours. At 1 hour post infection, cells were treated with Ruxolitinib (InvivoGen) at concentration of 2uM.
I8_plus_ruxo_rep1
processed data file: 28hpi_minus_plus_ruxo.txt

tag: infection


title: PJ1: Pineapple juice

source_name: Pineapple juice

value: Pineapple juice


title: JA-untreated-control-18h-replicate-1

tag: tissue


title: Input_ChIPSeq

city: Tallahassee

first: Brian

middle: P

last: Chadwick

address: 319 Stadium Drive, King 3076

department: Biological Science

institute: Florida State University

description: reads produced on combination of Illumina HiSeq 1500/2500 instruments.

data_processing:
All ChIP-Seq processing and mapping to human genome build hg19 were performed through the full service of Zymo Research.
RNA-Seq analysis for generation of bigwig files was achieved by first using cutadapt to remove the TruSeq 3’ adapter sequence. Strand-specific alignment to the hg38 used hisat2 with rna-strandness command. Sam files were converted to bam files using samtools. Bam files were converted to bedgraph using bedtools before conversion to bigwig using bedgraphtobigwig.
Genome_build: hg19 for ChIP-Seq and hg38 for RNA-Seq
Supplementary_files_format_and_content: Processed data files are all bigwig format.

source_name: hTERT-Immortalized Retinal Pigment Epithelial Cells

extract_protocol:
For ChIP-Seq, 3 replicate pellet were prepared for each sample. Pellets consisted of at least 5 million cells, cross linked with 1% formaldehyde in phosphate buffered saline for 7 minutes before quenching with 125mM glycine for 5 minutes. Cells were pelleted before flash freezing and storing at -80C. Pellets were then shipped on dry ice to Zymo Research for ChIP preparation. For RNA-Seq, total RNA was extracted from three replicate cultures of each sample using the Machery Nagel Nucleospin RNA Plus kit according to the manufacturers recommendations. RNA samples were shipped on dry ice to Novogene Corporation for quality control analysis followed by rRNA depleted total RNA-Seq.
Libraries for ChIP-Seq and RNA-Seq were prepared using the services provided by Zymo Research and Novogene Corporation respectively.

value: Input

tag: chip antibody

value: none (input)


title: METTL3_plus_ruxo_28hpi_rep2

description:
Cells were infected with HCMV for 28 hours. At 1 hour post infection, cells were treated with Ruxolitinib (InvivoGen) at concentration of 2uM.
M3_plus_ruxo_rep2
processed data file: 28hpi_minus_plus_ruxo.txt


title: S40_H3K27Ac_ChIPSeq

value: hTERT-Immortalized Retinal Pigment Epithelial Cells

value: SETDB1 Knock-out

value: anti-H3K27ac (Abcam ab4729; lot #GR232896-1)


title: Control_no_ruxo_28hpi_rep2

description:
Cells were infected with HCMV for 28 hours.
I8_minus_ruxo_rep2
processed data file: 28hpi_minus_plus_ruxo.txt


title: Untreated-control-18h-replicate-2

description: Resistant Dusa untreated control plants vs reference sample pool, replicate 2

value: Dusa

value: Root


title: PJ20: Pineapple juice


title: Untreated-control-18h-replicate-1

description: Resistant Dusa untreated control plants vs reference sample pool, replicate 1


title: JA-treatment-18hpt-replicate-3

description: Resistant Dusa plants 18hr following treatment with jasmonic acid vs reference sample pool, replicate 3

source_name: Root samples of resistant plants treated with jasmonic acid, 18hr post-treatment


title: Control_no_ruxo_28hpi_rep1

description:
Cells were infected with HCMV for 28 hours.
I8_minus_ruxo_rep1
processed data file: 28hpi_minus_plus_ruxo.txt

source_name: Primary fibroblasts


title: WT day3 rep2

tag: age

tag: Sex

value: male


title: LB16_MRS: MRS broth

value: MRS broth


title: WT day3 rep1


title: CB5: Cheese broth

source_name: Cheese broth

value: Cheese broth


title: JA-treatment-18hpt-replicate-2

description: Resistant Dusa plants 18hr following treatment with jasmonic acid vs reference sample pool, replicate 2


title: S40_H3K4me2_ChIPSeq

tag: cell type

value: anti-H3K4me2 (Abcam ab7766; lot #GR160184-2)


title: RPE1_H3K27Ac_ChIPSeq

value: Wild type


title: Untreated-control-18h-replicate-3

description: Resistant Dusa untreated control plants vs reference sample pool, replicate 3


title: Strain U07 rep 1

city: Riverside

first: Jason

last: Stajich

state: CA

address: 900 University Ave

department: Microbiology and Plant Pathology

institute: University of California-Riverside

description: Fluconazole sensitive

data_processing:
Raw reads were aligned to genome (ATCC 42720) with gsnap (2018-02-05) spliced alignment
sam to bam conversion with picardtools (2.14.1)
bam to read counts using "featureCounts" from subread (1.6.0)
Genome_build: Broad v1

organism: Clavispora lusitaniae

source_name: Exponential phase yeast cultures, YNBG10

growth_protocol: Overnight cultures grown in YPD were diluted into YNBG10 and grown at 30 C with shaking to mid-exponential phase, diluted into prewarmed medium then grown to mid-exponential phase before harvesting RNA.

extract_protocol:
RNA was harvested from snap-frozen pellets (using liquid nitrogen) using the MasterPure Yeast RNA Purification Kit (Epicentre)
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (NeoPrep) following standar Illumina protocols


title: Strain U04 rep 2

description: Fluconazole resistant


title: WFH20: Wheat flour hydrolyzate

source_name: Wheat flour hydrolyzate

value: Wheat flour hydrolyzate


title: RPE1_H3K9me3_ChIPSeq

value: anti-H3K9me3 (Abcam ab8898; lot #GR153112-1)


title: SA-treatment-18hpt-replicate-3

description: Resistant Dusa plants 18hr following treatment with salicylic acid vs reference sample pool, replicate 3

source_name: Root samples of resistant plants treated with salicylic acid, 18hr post-treatment


title: Strain U04 rep 1

description: Fluconazole resistant


title: JA-treatment-18hpt-replicate-1

description: Resistant Dusa plants 18hr following treatment with jasmonic acid vs reference sample pool, replicate 1


title: RPE1_H3K4me2_ChIPSeq


title: WFH19: Wheat flour hydrolyzate


title: S40_H3K9me3_ChIPSeq


title: Strain U05 rep 2

description: Fluconazole sensitive


title: SA-treatment-18hpt-replicate-2

description: Resistant Dusa plants 18hr following treatment with salicylic acid vs reference sample pool, replicate 2


title: PJ16: Pineapple juice


title: OE3: Olive extract

source_name: Olive extract

value: Olive extract


title: Strain U07 rep 2

description: Fluconazole sensitive


title: WFH1W: Wheat flour hydrolyzate


title: SA-treatment-18hpt-replicate-1

description: Resistant Dusa plants 18hr following treatment with salicylic acid vs reference sample pool, replicate 1


title: OE2: Olive extract


title: Strain U05 rep 1

description: Fluconazole sensitive


title: Strain L10 rep 2

description: Fluconazole resistant


title: OE1: Olive extract


title: Strain L10 rep 1

description: Fluconazole resistant


title: TJ22: Tomato juice

source_name: Tomato juice

value: Tomato juice


title: Strain L17 rep 2

description: Fluconazole resistant


title: TJ20: Tomato juice


title: TJ19: Tomato juice


title: FEV21: Faecal extract

source_name: Faecal extract

value: Faecal extract


title: Strain L17 rep 1

description: Fluconazole resistant


title: pum1_V8_24h_2

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

institute: the institute of microbiology chinese academy of sciences

description:
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 24h
PUM1oe_24h.2

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to JEC21α whole genome using Hisat2 v2.1.0 with parameters  hisat -p -x  -S --rna-strandness RF (for strand-specific RNA-seq)
Framents Per Kilobase of exon per Megabase of library size (TPM) were calculated using Stingtie v1.3.3 with parameters stringtie -p -e -G -o -A-C
The differential expression of genes (DEGs) was assessed using DEseq2 v1.16.1 of R package
Please note that the C. neoformans xl280 genome (unpublished) was used for mapping, but the mapping results are presented with the JEC21 homolog.
Genome_build: JEC21α
Supplementary_files_format_and_content: TPM values for each Sample

organism: Cryptococcus deneoformans XL280

growth_protocol: 50 ODs of cells from overnight YPD cultures were washed twice in water and resuspended in water at a final concentration of 1 DO600, dropped onto V8 (pH7) plates, and incubated for 12 hours at 25℃ in dark.

extract_protocol:
Frozen pellets were ground in liquid nitrogen and total RNA was purified using the Ultrapure RNA Kit (Kangweishiji, CW0581S) according to the manufacturer's instructions, and then reverse-transcribed with the Fastquant RT Kit (Tiangen KR106-02, with gDNase).
Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) as described by the manufacture. Samples were clustered using VAHRS RNA adapters set1/set2 and then sequenced using Illunima Hiseq 4000 platform in a 2x150 pair-ended manner.

treatment_protocol: Total RNA was purified using the Ultrapure RNA Kit. Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit.

value: Cryptococcus neoformans var. neoformans serotype D XL280 MATalpha

tag: time


title: FEV11: Faecal extract


title: WT_V8_72h_2

description:
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 72h
72h.2

source_name: wild type

tag: genotype

value: wild type


title: pum1_V8_24h_1

description:
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 24h
PUM1oe_24h.1

tag: strain


title: Om congestion3

city: Sendai

first: Satoshi

last: Shimada

address: 2-1, Seiryo-machi

country: Japan

institute: Tohoku University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing:
program-name = Expression Console
program-version = 1.4.1.46
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0

organism: Rattus norvegicus

source_name: Om congestion3

label_protocol: Affymetrix protocol

growth_protocol: Male Sprague-Dawley rats (7- to 9-weeks old, 250-350 g) were housed in environmentally controlled rooms under a 12-h light/dark cycle with free access to a standard diet and water.

extract_protocol: Total RNA from the renal cortex and medulla were extracted using ISOGEN and purificated by column chromatography

treatment_protocol: The IVC between the renal veins was totally ligated by silk suture 3-0 under anesthesia. Three days after surgery, the renal tissues were removed and  divided into the cortex and medulla under anesthesia.

tag: group

value: congestion

value: outer medulla

value: Sprague-Dawley

value: kidney


title: Pc-infection-18hpi-replicate-2

description: Resistant Dusa plants 18hr following infection with Phytophthora cinnamomi vs reference sample pool, replicate 2

source_name: Root samples of resistant plants infected with Phytophthora cinnamomi, 18hr post-infection

value: Dusa

value: Root

source_name: Pooled reference sample


title: Om congrol3

source_name: Om congrol3

value: control

value: male


title: Om congestion2

source_name: Om congestion2


title: WT_V8_72h_1

description:
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 72h
72h.1


title: FEO13: Faecal extract

tag: isolation source


title: FEO17: Faecal extract


title: Pc-infection-18hpi-replicate-3

description: Resistant Dusa plants 18hr following infection with Phytophthora cinnamomi vs reference sample pool, replicate 3


title: WT_V8_48h_2

description:
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 48h
48h.2


title: Untreated-control-6h-replicate-3

source_name: Root samples of untreated control resistant plants


title: FEO3: Faecal extract


title: WT_V8_48h_1

description:
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 48h
48h.1


title: Om control2

source_name: Om control2


title: WT_V8_24h_2

description:
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 24h
24h.2


title: Untreated-control-6h-replicate-2

description: Resistant Dusa untreated control plants vs reference sample pool, replicate 2


title: JA-treatment-6hpt-replicate-3

description: Resistant Dusa plants 6hr following treatment with jasmonic acid vs reference sample pool, replicate 3

source_name: Root samples of resistant plants treated with jasmonic acid, 6hr post-treatment


title: DE24: Drosophila sp. Extract

source_name: Drosophila sp. Extract

value: Drosophila sp. Extract


title: Untreated-control-6h-replicate-1

description: Resistant Dusa untreated control plants vs reference sample pool, replicate 1


title: JA-treatment-6hpt-replicate-1

description: Resistant Dusa plants 6hr following treatment with jasmonic acid vs reference sample pool, replicate 1


title: Om congestion1

source_name: Om congestion1


title: JA-untreated-control-6h-replicate-2


title: Cx congestion3

source_name: Cx congestion2

value: Cortex


title: JA-untreated-control-6h-replicate-3

description: Resistant Dusa untreated control plants vs reference sample pool, replicate 3


title: WT_V8_24h_1

description:
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 24h
24h.1


title: DE12II: Drosophila sp. Extract


title: JA-treatment-6hpt-replicate-2

description: Resistant Dusa plants 6hr following treatment with jasmonic acid vs reference sample pool, replicate 2


title: Cx congestion2


title: JA-untreated-control-6h-replicate-1


title: LSRR_2

city: BeiJing

first: Xiong

last: Yao

address: No. 17, Tsinghua East Road, Haidian District

institute: China Agriculture University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing  reads containing adapter, reads containing ploy-N and low quality reads from  raw data. At the same time, Q20, Q30 and GC content sequence of the clean  data were calculated. All the downstream analyses were based on the clean data  with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly (NZ_CP012148.1). Both building index of reference genome and aligning  clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S.  L. Salzberg, 2012)
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And  then FPKM of each gene was calculated based on the length of the gene and  reads count mapped to this gene.
(For DESeq with biological replicates) Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using  the DESeq R package (1.18.0). DESeq provide statistical routines for  determining differential expression in digital gene expression data using a  model based on the negative binomial distribution. The resulting P-values were  adjusted using the Benjamini and Hochberg’s approach for controlling the false  discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were  assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the GOseq R package, in which gene length bias was corrected.  GO terms with corrected Pvalue less than 0.05 were considered significantly  enriched by differential expressed genes.
Genome_build: NZ_CP011403.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Ligilactobacillus salivarius str. Ren

source_name: Lactobacillus salivarius Ren

growth_protocol: Lactobacillus salivarius Ren was cultured in de Man-Rogosa-Sharpe (MRS) medium at 37 oC with glucose and raffinose

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

tag: medium

value: MRS with raffinose

tag: period

value: pro-exponential phase


title: Cx control2

source_name: Cx control2


title: Cx control3


title: Cx control1

source_name: Cx control1


title: Om control1

source_name: Om control1


title: Cx congestion1

source_name: Cx congestion1


title: LSRR_3


title: FEV3: Faecal extract

source_name: Faecal extract


title: LSRR_1


title: DE12: Drosophila sp. Extract


title: WT_V8_12h_2

description:
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 12h
12h.2

source_name: wild type


title: SA-treatment-6hpt-replicate-1

description: Resistant Dusa plants 18hr following treatment with salicylic acid vs reference sample pool, replicate 1

source_name: Root samples of resistant plants treated with salicylic acid, 6hr post-treatment


title: SA-treatment-6hpt-replicate-2

description: Resistant Dusa plants 6hr following treatment with salicylic acid vs reference sample pool, replicate 2

source_name: Pooled reference sample


title: LSRG_3

value: MRS with glucose


title: WT_V8_12h_1

description:
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 12h
12h.1


title: WT_V8_6h_2

description:
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 6h
6h.2


title: LSRG_2


title: BEE3ST: Bee extract

source_name: Bee extract

value: Bee extract


title: LSRG_1


title: WT_V8_6h_1

description:
V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 6h
6h.1


title: BEE1ST: Bee extract


title: Pc-infection-6hpi-replicate-3

description: Resistant Dusa plants 6hr following infection with Phytophthora cinnamomi vs reference sample pool, replicate 3

source_name: Root samples of resistant plants infected with Phytophthora cinnamomi, 6hr post-infection


title: Pc-infection-6hpi-replicate-2

description: Resistant Dusa plants 6hr following infection with Phytophthora cinnamomi vs reference sample pool, replicate 2


title: Pc-infection-18hpi-replicate-1

description: Resistant Dusa plants 18hr following infection with Phytophthora cinnamomi vs reference sample pool, replicate 1

source_name: Root samples of resistant plants infected with Phytophthora cinnamomi, 18hr post-infection


title: SA-treatment-6hpt-replicate-3

description: Resistant Dusa plants 6hr following treatment with salicylic acid vs reference sample pool, replicate 3


title: BEE2ST: Bee extract


title: PROB_WT_5

status: Public on Nov 13 2018

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Wild-type littermates, Biological replicate 2

data_processing:
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: mm9
Supplementary_files_format_and_content: PROB_all_fpkm_exprs_raw.txt: Tab-delimited text file matix containing raw FPKM values for each transcript; PROB_all_fpkm_exprs_norm.txt:  Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript

organism: Mus musculus

source_name: proB

growth_protocol: primary mouse proB_Ts1Rhr cells expanded in culture

extract_protocol:
Exactly one million cells were pelleted and total RNA was isolated using Trizol reagent. For per cell normalization, 1 μl of Mix #1 ERCC exogenous spike-in RNA (diluted 1:1000) was added to each RNA sample. Special attention was paid to equal and consistent volume transfers.
TruSeq RNA Library Prep Kit

treatment_protocol: Whole bone marrow was harvested from 6-8-week-old mice and red blood cells were lysed. Cells were plated in B cell methylcelluose media containing interleukin-7. Colonies were collected by pooling the cultures after 7 days of growth.

tag: genotype/strain

value: Wild-type littermates


title: PROB_WT_6

description: Wild-type littermates, Biological replicate 3

value: primary mouse proB_Ts1Rhr cells expanded in culture


title: PROB_WT_4

description: Wild-type littermates, Biological replicate 1


title: PROB_TRI_6

description: Ts1Rhr, FVB × C57BL/6 F1 background, Biological replicate 3

value: Ts1Rhr, FVB x C57BL/6 F1 background


title: PROB_TRI_5

description: Ts1Rhr, FVB × C57BL/6 F1 background, Biological replicate 2


title: PROB_HMGN1_6

description: Hmgn1-overexpressing, C57BL/6, Biological replicate 3

value: Hmgn1-overexpressing, C57BL/6


title: w;tim-GAL4(UAS)/UAS-miR-210, biological replicate 2 (miR-210_over_ZT12-2)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

institute: University of Padova

description: Gene expression of miR-210 overexpressing flies (miR-210-ZT0_over_2).

hyb_protocol: 600 ng of labeled cRNA were used in each reaction and the hybridization was carried out at 65°C for 17 hours in an hybridization oven rotator (Agilent Technologies, Palo Alto, CA). The arrays were washed by Agilent Gene expression washing buffers and Stabilization and Drying Solution as suggest by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) and Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Inter-array normalization of expression levels was performed with quantile method to correct for possible experimental distortions. A normalization function was applied to the expression data of all the experiments and the values of within-arrays replicate spots were then averaged. Feature Extraction Software, which provided spot quality measures, was used to evaluate the quality and reliability of the hybridization. In particular, the flag glsPosAndSignif (set to 1 if the spot had an intensity value significantly different from the local background and to 0 when otherwise) was used to filter out unreliable probes: the flag equal to 0 was noted as null. Probes with a high proportion of null values were removed from the dataset in order to carry out a more solid, unbiased, statistical analysis. Fifty percent of null was used as the threshold in the filtering process, and a total of 23,665 Drosophila transcripts were obtained.

source_name: brains of adult flies

label_protocol: 50 ng of total RNA were labeled with “Low Input Quick Amp Labeling Kit, one color” according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labeled with Cy3-dCTP. Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurements (Nanodrop, Wilmington, DE).

extract_protocol: Total RNA was extracted from approximately 25 flies brains for each genotype using ZR RNA MicroPrepTM (ZYMO RESEARCH) according to the manufacter's instructions. All RNA samples were checked for quality by capillary electrophoresis (RNA 6000 Nano LabChip, Agilent Bioanalyzer 2100, Agilent Technologies).

tag: genotype/variation


title: w;tim-GAL4(UAS)/UAS-miR-210, biological replicate 3 (miR-210_over_ZT12-3)

description: Gene expression of miR-210 overexpressing flies (miR-210-ZT0_over_3).


title: w;tim-GAL4(UAS)/UAS-miR-210, biological replicate 3 (miR-210-ZT0_over_3)

data_processing: Inter-array normalization of expression levels was performed with quantile method to correct for possible experimental distortions. A normalization function was applied to the expression data of all the experiments and the values of within-arrays replicate spots were then averaged. Feature Extraction Software, which provided spot quality measures, was used to evaluate the quality and reliability of the hybridization. In particular, the flag glsPosAndSignif (set to 1 if the spot had an intensity value significantly different from the local background and to 0 when otherwise) was used to filter out unreliable probes: the flag equal to 0 was noted as null. Probes with a high proportion of null values were removed from the dataset in order to carry out a more solid, unbiased, statistical analysis. Fifty percent of null was used as the threshold in the filtering process, and a total of 23,717 Drosophila transcripts were obtained.

tag: developmental stage

value: adult flies

tag: time point

value: brain


title: w;tim-GAL4 (UAS)/+ control, biological replicate 2 (CTRL-2)

description: Gene expression of control flies (CTRL-2).

value: w;tim-GAL4 (UAS)/+)


title: w;tim-GAL4(UAS)/UAS-miR-210, biological replicate 4 (miR-210_over_ZT12-4)

description: Gene expression of miR-210 overexpressing flies (miR-210-ZT0_over_7).


title: Pc-infection-6hpi-replicate-1

description: Resistant Dusa plants 6hr following infection with Phytophthora cinnamomi vs reference sample pool, replicate 1

value: Dusa


title: w;tim-GAL4(UAS)/UAS-miR-210, biological replicate 1 (miR-210_over_ZT12-1)

description: Gene expression of miR-210 overexpressing flies (miR-210-ZT0_over_1).


title: w;tim-GAL4 (UAS)/+ control, biological replicate 1 (CTRL-1)

description: Gene expression of control flies (CTRL-1).


title: PROB_HMGN1_5

description: Hmgn1-overexpressing, C57BL/6, Biological replicate 2


title: w;tim-GAL4(UAS)/UAS-miR-210, biological replicate 2 (miR-210-ZT0_over_2)


title: w;tim-GAL4 (UAS)/+ control, biological replicate 1 (CTR1)

source_name: control_adult flies_brain

value: w;tim-GAL4 (UAS)/+


title: w;tim-GAL4 (UAS)/+ control, biological replicate 4 (CTRL-4)

description: Gene expression of control flies (CTRL-4).


title: w;tim-GAL4(UAS)/UAS-miR-210, biological replicate 1 (miR-210-ZT0_over_1)


title: PROB_HMGN1_4

description: Hmgn1-overexpressing, C57BL/6, Biological replicate 1


title: w;tim-GAL4 (UAS)/+ control, biological replicate 3 (CTRL-3)

description: Gene expression of control flies (CTRL-3).


title: w;tim-GAL4 (UAS)/+ control, biological replicate 2 (CTR2)


title: PROB_TRI_4

description: Ts1Rhr, FVB × C57BL/6 F1 background, Biological replicate 1


title: w;tim-GAL4 (UAS)/+ control, biological replicate 4 (CTR7)

description: Gene expression of control flies (CTRL-7).


title: GSS1403_173_F_NA

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

description: Gene expression data from LCM-separated epidermis from human forearm

hyb_protocol: Biotinylated cRNA was fragmented by limited alkaline hydrolysis and then hybridized overnight to Affymetrix GeneTitan U219 microarray plates using the Affymetrix GeneTitan instrument

scan_protocol: ArrayPlates were scanned using the Affymetrix GeneTitan Instrument utilizing AGCC GeneTitan Instrument Control software version 4.2.0.1566

data_processing: The RMA algorithm was used as the processing protocol to normalize the data for subsequent analysis.

source_name: batch_subjectID_gender_sampling time

label_protocol: Biotinylated cRNA were prepared  using the Affymetrix HT 3’ IVT Express kit (Cat. #901253) on a Beckman Biomek FXp Laboratory Automation Workstation (Beckman Cat. #A31842).

extract_protocol: Total RNA from LCM samples was isolated utilizing the Pico Pure RNA Isolation Kit (Life Technologies, Grand Island, NY) according to manufacturer's recommendations

treatment_protocol: Punch biopsy samples were frozen in OCT media. Laser capture microdissection (LCM) was performed to isolate the epidermal compartments for gene expression profiling.

value: Female

value: LCM-separated epidermis

tag: ancestry

value: European

tag: collection time


title: iWAT WT vehicle treated rep2

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description:
iWAT WT vehicle treated rep2
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
SubQ_VW_rep2

data_processing:
Basecalls were performed using CASAVA (v. 1.8.2).
Reads were aligned to mm10 genome assembly and transcript assembly was performed using tophat (v.2.0.12).
FPKM calculation and differential expression analysis was performed using cufflinks (v.2.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample; genes that have FPKM of >=1 in any sample in a given treatment were listed.

source_name: iWAT

growth_protocol: Mice were fed regular chow for the first 10 weeks followed by a high fat diet (60% cal) for the next 19 weeks.

extract_protocol:
RNA was extracted using RNeasy lipid tissue mini kits. On-column DNase treatment was done during the purification according to the manufacturer's protocol.
4 ug of total RNA, Illumina's TruSeq Stranded mRNA library prep kit following the manufacterer's protocol. libraries were geerated for 75 nt single end sequencing on the Illumina NextSeq 500 using V2 reagents.

treatment_protocol: 1% methylcellulose (vehicle) or rosiglitazone in vehicle (10 mg/kg body weight) was administered by oral gavage for one week.

tag: tissue

value: iWAT

tag: tissue phenotype

value: No significant characteristics observed

tag: histology phenotype

tag: sample type

value: Primary tissue

value: WT WT homogygote


title: iWAT K107R vehicle treated rep2

description:
iWAT K107R vehicle treated rep2
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
SubQ_VK_rep2

value: K107R K107R homozygote


title: iWAT WT vehicle treated rep1

description:
iWAT WT vehicle treated rep1
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
SubQ_VW_rep1


title: GSS1403_107_F_NA

tag: Sex


title: iWAT K107R vehicle treated rep1

description:
iWAT K107R vehicle treated rep1
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
SubQ_VK_rep1

tag: genotype


title: iWAT WT rosiglitazone treated rep2

description:
iWAT WT rosiglitazone treated rep2
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
SubQ_RW_rep2


title: iWAT WT rosiglitazone treated rep1

description:
iWAT WT rosiglitazone treated rep1
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
SubQ_RW_rep1


title: iWAT K107R rosiglitazone treated rep2

description:
iWAT K107R rosiglitazone treated rep2
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
SubQ_RK_rep2


title: iWAT K107R rosiglitazone treated rep1

description:
iWAT K107R rosiglitazone treated rep1
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
SubQ_RK_rep1


title: w;tim-GAL4(UAS)/UAS-miR-210, biological replicate 4 (miR-210-ZT0_over_7)

description: Gene expression of miR-210 overexpressing flies (miR-210-ZT0_over_7).


title: eWAT K107R vehicle treated rep2

description:
eWAT K107R vehicle treated rep2
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
epi_VK_rep2

source_name: eWAT

value: eWAT


title: eWAT WT vehicle treated rep1

description:
eWAT WT vehicle treated rep1
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
epi_VW_rep1


title: w;tim-GAL4 (UAS)/+ control, biological replicate 3 (CTR3)


title: eWAT K107R vehicle treated rep1

description:
eWAT K107R vehicle treated rep1
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
epi_VK_rep1


title: GSS1403_124_F_NA


title: GSS1403_152_F_NA


title: GSS1403_155_F_NA


title: GSS1403_300_F_NA


title: GSS1403_200_F_NA


title: GSS1403_248_F_NA


title: GSS1403_185_F_NA


title: GSS1403_281_F_NA


title: GSS1403_290_F_NA


title: eWAT K107R rosiglitazone treated rep2

description:
eWAT K107R rosiglitazone treated rep2
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
epi_RK_rep2


title: eWAT WT rosiglitazone treated rep1

description:
eWAT WT rosiglitazone treated rep1
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
epi_RW_rep1


title: eWAT WT vehicle treated rep2

description:
eWAT WT vehicle treated rep2
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
epi_VW_rep2


title: FC1245_GFP_48H_DOX

city: Cold Spring Harbor

first: Tim

middle: D D

last: Somerville

state: NY

address: 1 Bungtown Road

department: CSHL

institute: Cold Spring Harbor Laboratory

description: processed data file: TP63dN_vs_GFP_DOX_FC1245.txt

data_processing:
Single-end 50bp sequencing reads were mapped into hg19 genome using hisat2 with default settings
Structural RNAs were masked
Differentially expressed genes were identified using Cuffdiff, normalized to total mapped reads
Genome_build: hg19
Supplementary_files_format_and_content: txt files generated from Cuffdiff

growth_protocol: Human PDA cells were cultured in RPMI with 10%FBS and P/S.

extract_protocol:
RNA was extracted using TRIzol following manufacture’s protocol. 2ug total RNA was used for constructing RNA-seq library
RNA-seq libraries were constructed using the Illumina TruSeq sample prep kit v2 following manufacture’s protocol. Briefly, RNA was polyA selected and enzymatically fragmented. cDNA was synthesized using Super Script II master mix, followed by end repair, A-tailing and PCR amplification.

value: transduced with dox inducible vector to express GFP

tag: cell type

tag: mouse strain

value: KPC C56BL/6

tag: treatment time

value: 48 hours post dox


title: FC1242_TP63dN_48H_DOX

description: processed data file: TP63dN_vs_GFP_DOX_FC1242.txt

value: transduced with dox inducible vector to express TP63dN


title: FC1245_TP63dN_48H_DOX


title: FC1242_GFP_48H_DOX


title: eWAT WT rosiglitazone treated rep2

description:
eWAT WT rosiglitazone treated rep2
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
epi_RW_rep2


title: FC1199_TP63dN_48H_DOX

description: processed data file: TP63dN_vs_GFP_DOX_FC1199.txt


title: eWAT K107R rosiglitazone treated rep1

description:
eWAT K107R rosiglitazone treated rep1
epi_subq_K_W_R_V_fpkm_matrix_whole_genome_fpkm_1.txt
epi_RK_rep1


title: GSS1403_242_F_NA

description: Gene expression data from LCM-separated epidermis from human forearm


title: FC1199_GFP_48H_DOX


title: GSS1403_166_F_NA


title: GSS1403_144_F_NA


title: GSS1403_249_F_NA


title: EMB-Ex-CD31+CD45+c-Kit+CD41-

city: Memphis

first: Shannon

last: McKinney-Freeman

state: Tennessee

address: MS 341, Room D3007E, 262 Danny Thomas Place Memphis, TN

institute: st jude children's research hospital

data_processing:
bcl2fastq v2.19.1.403 is used to do base-calling
cellranger (2.0.1) is used to do demultiplexing, reads mapping and reads counting
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with each row represents a gene and each column represents a cell

source_name: CD31+CD45+c-Kit+CD41- cells were sorted from cultured E8.5 intraembryonyc tissues

growth_protocol: Embryo and YS-explants were cultured at the air-liquid interface on 0.65m DV Durapore Membrane Filters (Merck Millipore, Cork, Ireland) in Iscove’s Modified Dulbecco’s Medium-Glutamax (IMDM-Glutamax, Thermo Fisher Scientific, Waltham, MA), 20% FCS (Omega Scientific, Tarzana, CA), 0.1mM 2-Mercaptoethanol (Thermo Fisher Scientific, Waltham, MA), and 100 units/ml of Penicillin/Streptomycin (Thermo Fisher Scientific, Waltham, MA) supplemented with recombinant murine SCF, recombinant murine IL-3, and recombinant murine FLT3 Ligand (Peprotech, Rocky Hill, NJ, all at 100ng/ml) (or with other cytokine combinations indicated along the text) for 9-10 days to allow engraftment from E8.5 tissues.

extract_protocol:
Sorted YS-Ex-CD31+CD45+c-Kit+CD41- and Em-Ex-CD31+CD45+c-Kit+CD41- were resuspended in PBS containing 0.04%BSA at a concentration of 500-600 cells/ul. In total, 8600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 3000-3500 cells per sample. The captured cells then underwent lysis, reverse transcription, cDNA amplification, and library preparation with indexing per the manufacturer’s protocol (10X Genomics).
The libraries were sequenced together on an Illumina Nextseq500 using a high output 150 cycle kit with read lengths recommended by 10X Genomics.

treatment_protocol: Explants were then dissociated with collagenase (0.0012 g/ml, Sigma-Aldrich, St. Louis, MO) in Phosphate-Buffered Saline (PBS, Thermo Fisher Scientific, Waltham, MA) supplemented with 10% FCS (Omega Scientific, Tarzana, CA).

tag: strain

value: Theiler stage 12 (5-7 somite pairs; E8.5)

value: Intraembryonic tissues


title: GSS1403_167_F_NA


title: GSS1403_127_F_NA


title: GSS1403_213_F_NA


title: YS-Ex-CD31+CD45+c-Kit+CD41-

source_name: CD31+CD45+c-Kit+CD41- cells were sorted from cultured E8.5 Yolk sacs

value: yolk sack


title: GSS1403_214_F_NA


title: ATAC_B6_Sm_GF_rep1

city: Gainesville

first: Liang

last: Zhou

department: Department of Infectious Diseases and Immunology

institute: University of Florida

data_processing:
[RNA-seq]  De-multiplexed raw data files from the sequencing core were analyzed for quality control using FastQC (Babraham Bioinformatics). Reads were mapped (with TopHat2 fast splice junction mapper for RNA-Seq) to the mm10 assembly of the Mus musculus genome (National Center for Biotechnology Information) and filtered for uniquely mapped reads (Kim et al., 2013). Genome visualization tracks (bedgraph files) were uploaded to the University of California Santa Cruz (UCSC) Genome Browser for visual comparison of expression levels (Meyer et al., 2013; Patel and Jain, 2012). Quantitated relative mRNA expression levels (FPKM) were calculated based on exon regions using Cufflinks and the mm10 reference genome annotations (Trapnell et al., 2010). Significantly changed genes were identified by Cuffdiff (Trapnell et al., 2010).
[ATAC-seq] ATAC-Seq reads were mapped to the mouse genome (mm9) with bowtie2 (Langmead and Salzberg, 2012). The mapped reads were filtered using samtools (Li et al., 2009), keeping only the uniquely aligned reads, and bedgraph files (scaled to 10 million reads) were made with bedtools (Quinlan and Hall, 2010).  ATAC-seq peak locations were identified using Homer (Heinz et al., 2010). Differentially-expressed ATAC-seq peaks were identified by first quantifying peak signal using HTSeq-count, and then using DESeq2 for differential analysis (Anders et al., 2015; Love et al., 2014).
Genome_build: [RNA-seq]  mm10,  [ATAC-seq] mm9
Supplementary_files_format_and_content: [RNA-seq] (1) Tab-delimited text file includes FPKM values for each sample. (2) bedgraph files for each sample.  [ATAC-seq] (1) Tab-delimited text file includes count values for each sample.  (2) bedgraph files for each sample.

source_name: Sm. Int. Lamina Propria ILC2

extract_protocol:
[RNA-seq] Lamina propria cells were isolated and sorted by flow cytometry.  Sorted ILC2s (Lin–KLRG1+CD90+)  were lysed in Trizol (Invitrogen), and RNA was subsequently extracted with RNAeasy Mini Kit (Qiagen).  [ATAC-seq]  Lamina propria cells were isolated and ILC2s (Lin–KLRG1+CD90+) were sorted by flow cytometry.
[RNA-seq] Total RNA was treated with Ribo-zero kit and RNA-seq libraries were generated using kits from Illumina. Barcoded samples were pooled and sequenced over 2 lanes on an Illumina HiSeq 2500 instrument to produce 50 bp single-end reads. [ATAC-seq] Large intestinal CD4+TCRβ+YFP+ ILC2s were sorted and subjected to ATAC-Seq according to a published protocol (Buenrostro et al., 2013) with a modification in the library purification step. Briefly, 5x10^4 sorted ILC2s were washed once with 50 ul PBS, and then lysed in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) on ice. Pelleted nuclei were resuspended in transposition reaction mix with Tn5 transposase (Illumina) and incubated at 37℃ for 30 min with gentle shaking. The DNA was purified with MinElute PCR Purification Kit (Qiagen) and was used as a template of PCR with 10 cycles of amplification. The library was cleaned up with 1.2x SPRIselect beads (Beckman Coulter), to exclude the small fragments, before sequencing with Illumia HiSeq 2500.

value: Small Intestine

value: Ahr+/+


title: ATAC_B6_Sm_SPF_rep2


title: GSS1403_227_F_NA

value: Female

value: LCM-separated epidermis


title: ATAC_B6_Sm_GF_rep2


title: GSS1403_159_F_NA

value: European


title: GSS1403_150_F_NA


title: GSS1403_122_F_NA


title: ATAC_B6_Lg_SPF_rep2

source_name: Lg. Int. Lamina Propria ILC2

value: Large Intestine


title: GSS1403_260_F_NA


title: GSS1403_243_F_NA


title: ATAC_B6_Sm_SPF_rep1


title: GSS1403_269_F_NA


title: GSS1403_314_F_NA


title: GSS1403_238_F_NA


title: ATAC_B6_Lg_SPF_rep1


title: GSS1403_262_F_NA


title: GSS1403_186_F_NA


title: GSS1403_112_F_NA


title: ATAC_B6_Sm_Ahr_WT_rep2


title: ATAC_B6_Lg_GF_rep2


title: ATAC_B6_Sm_Ahr_WT_rep1


title: ATAC_B6_Lg_Ahr_KO_rep2

value: Ahr-/-


title: ATAC_B6_Sm_Ahr_KO_rep1


title: ATAC_B6_Lg_GF_rep1


title: ATAC_B6_Sm_Ahr_KO_rep2


title: ATAC_B6_Lg_Ahr_KO_rep1


title: ATAC_B6_Lg_Ahr_WT_rep1


title: ATAC_B6_Lg_Ahr_WT_rep2


title: GSS1403_171_F_NA


title: GSS1403_219_F_NA


title: GSS1403_125_F_NA


title: GSS1403_139_F_NA


title: GSS1403_183_F_NA


title: ATAC_RagKO_Sm_Ahr_KO_rep1


title: ATAC_RagKO_Sm_Ahr_WT_rep2


title: GSS1403_177_F_NA


title: ATAC_RagKO_Sm_Ahr_WT_rep1


title: GSS1403_103_F_NA


title: GSS1403_320_F_NA


title: GSS1403_286_F_NA


title: GSS1403_226_F_NA


title: GSS1403_271_F_NA


title: ATAC_RagKO_Lg_Ahr_KO_rep2


title: ATAC_RagKO_Lg_Ahr_WT_rep2


title: GSS1403_128_F_NA


title: ATAC_RagKO_Lg_Ahr_KO_rep1


title: GSS1403_134_F_NA


title: ATAC_RagKO_Lg_Ahr_WT_rep1


title: RNA_Sm_Ahr_KO_rep2


title: GSS1403_189_F_NA


title: RNA_Sm_Ahr_WT_rep2


title: RNA_Sm_Ahr_KO_rep1


title: RNA_Sm_Ahr_WT_rep1


title: GSS1403_135_F_NA


title: RNA_Lg_Ahr_KO_rep2


title: RNA_Lg_Ahr_WT_rep2


title: GSS1403_162_F_NA


title: RNA_Lg_Ahr_KO_rep1


title: RNA_Lg_Ahr_WT_rep1


title: GSS1403_207_F_NA


title: GSS1403_294_F_NA


title: GSS1403_140_F_NA


title: GSS1403_111_F_NA


title: GSS1403_138_F_NA


title: GSS1403_108_F_NA


title: GSS1403_233_F_NA


title: GSS1403_133_F_NA


title: GSS1403_121_F_NA


title: GSS1403_230_F_NA


title: GSS1403_142_F_NA


title: GSS1403_123_F_NA


title: GSS1403_114_F_NA


title: GSS1403_118_F_NA


title: GSS1403_158_F_NA


title: GSS1403_141_F_NA


title: GSS1403_188_F_NA


title: GSS1403_168_F_NA


title: GSS1403_198_F_NA


title: GSS1403_224_F_NA


title: GSS1403_179_F_NA


title: GSS1403_268_F_NA


title: GSS1403_131_F_NA


title: GSS1403_307_F_NA


title: GSS1403_222_F_NA


title: GSS1403_109_F_NA


title: GSS1403_221_F_NA


title: GSS1403_310_F_NA


title: GSS1403_129_F_NA


title: GSS1403_115_F_NA


title: GSS1403_212_F_NA


title: NALM6_HMGN_WT_DOX_C

description:
4SU labeled RNA
Wild-type HMGN1, biological replicate C

data_processing:
Forward and reverse reads from fastq files were merged and SlamDunk v0.2.4 (https://github.com/t-neumann/slamdunk) was run using “slamdunk all” with default parameters (trimming 12bp from the 5’ end, reporting up to 100 alignments for multi-mappers and activating the multi-mapper retention strategy, filtering for variants with a variant fraction of 0.2, and filtering for base-quality cutoff of ≥27). Whole gene and 3’ UTR annotations were obtained in BED format from the UCSC table browser (https://genome.ucsc.edu/cgi-bin/hgTables, GRCh37/hg19, RefSeq Curated). Reads were filtered for having ≥2 T>C conversions.
Genome_build: hg19
Supplementary_files_format_and_content: NALM6_HMGN_RAW.txt - For each gene (rows) across samples (columns) the C to T conversion rate and total counts per million (CPM) are provided
Supplementary_files_format_and_content: NALM6_HMGN_WHOLE_CONVERTED_ALL_unprocessed_fpkm.txt - For each gene (rows) across samples (columns) the FPKM (fragments per kilobase of pre-mRNA) of converted (C to T) reads aligning to unprocessed regions (introns, exon/intron boundaries) of mRNAs is provided

source_name: B-ALL

growth_protocol: RPMI + 10% FBS + 1% Penn/Strep/Glutamine at 37 degrees Celsius in 5% CO2

extract_protocol:
Exactly one million cells were pelleted and total RNA was isolated using Trizol reagent. RNA processing and thiol modification using 4 µg input RNA were performed as previously described (Herzog et al., 2017).
Illumina's TruSeq Stranded mRNA kit
Sequencing was performed on a Next-Seq 500 using a NextSeq 500/550 Mid Output v2 kit (150 cycles).

treatment_protocol: HMGN1 expression induced by adding doxycycline (100ng/ml) or vehicle for six hours. During the last 5 hours of induction, 4-thiouridine (100uM) was added to the culture medium at 100 µM final concentration.

tag: cell line

tag: input

tag: treatment

value: DOX

tag: barcode

value: GAATTCGT

value: Wild-type HMGN1


title: NALM6_HMGN_WT_DOX_B

description:
4SU labeled RNA
Wild-type HMGN1, biological replicate B

value: ATTCAGAA


title: GSS1403_137_F_NA


title: GSS1403_190_F_NA


title: GSS1403_194_F_NA


title: GSS1403_277_F_NA


title: GSS1403_237_F_NA


title: GSS1403_218_F_NA


title: GSS1403_160_F_NA


title: NALM6_HMGN_WT_CTL_C

value: Vehicle

value: CGCTCATT


title: GSS1403_130_F_NA


title: GSS1403_273_F_NA


title: GSS1403_288_F_NA


title: GSS1403_223_F_NA


title: NALM6_HMGN_WT_CTL_B

value: TCCGGAGA


title: GSS1403_206_F_NA


title: NALM6_HMGN_WT_CTL_A

description:
4SU labeled RNA
Wild-type HMGN1, biological replicate A

value: ATTACTCG


title: NALM6_HMGN_WT_DOX_A

value: GAGATTCC


title: NALM6_HMGN_MUT_DOX_B

description:
4SU labeled RNA
Nucleosome binding-deficient HMGN1 S20,24E mutant, biological replicate B

value: TCCGCGAA


title: Nalm6_Hmgn1_WT_HA_B2

description: Wild-type HMGN1, biological replicate B

data_processing:
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: hg19
Supplementary_files_format_and_content: NALM6_all_fpkm_exprs_raw.txt: Tab-delimited text file matix containing raw FPKM values for each transcript; NALM6_all_fpkm_exprs_norm.txt:  Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript

extract_protocol:
Exactly one million cells were pelleted and total RNA was isolated using Trizol reagent. For per cell normalization, 1 μl of Mix #1 ERCC exogenous spike-in RNA (diluted 1:1000) was added to each RNA sample. Special attention was paid to equal and consistent volume transfers.
TruSeq RNA Library Preparation Kit v2, Set A

treatment_protocol: HMGN1 expression induced by adding doxycycline (100ng/ml) or vehicle for six hours.

value: B-ALL cell line


title: GSS1403_154_F_NA


title: Nalm6_Hmgn1_WT_HA_B1

description: Wild-type HMGN1, biological replicate B


title: GSS1403_170_F_NA


title: NALM6_HMGN_MUT_DOX_A

description:
4SU labeled RNA
Nucleosome binding-deficient HMGN1 S20,24E mutant, biological replicate A

value: CGGCTATG


title: Nalm6_Hmgn1_WT_HA_A2

description: Wild-type HMGN1, biological replicate A


title: Nalm6_Hmgn1_SE_HA_B2

description: Nucleosome binding-deficient HMGN1 S20,24E mutant, biological replicate B


title: GSS1403_113_F_NA

value: Female


title: GSS1403_203_F_NA

value: LCM-separated epidermis


title: Nalm6_Hmgn1_WT_HA_A1

description: Wild-type HMGN1, biological replicate A


title: Nalm6_Hmgn1_SE_HA_B1

value: Nucleosome binding-deficient HMGN1 S20,24E mutant


title: Nalm6_Hmgn1_SE_HA_A2

description: Nucleosome binding-deficient HMGN1 S20,24E mutant, biological replicate A


title: Nalm6_Hmgn1_SE_HA_A1


title: NALM6_H3_DOX

description: Spike in normalized ChIP-Seq for H3 in NALM6 after DOX treatment

data_processing:
Sequenced reads were aligned to a custom reference bowtie2 index combinging the HG19 and MM9 genome builds
ChIP_RX scaling factors were determined as in Orlando et al., 2014, "Quantitative ChIP-Seq normalization reveals global modulation of the epigenome", PMID 25437568
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: hg19:mm9
Supplementary_files_format_and_content: Processed ChIP-Rx datasets are provided in a cell count normalized scaled bedgraph format.

growth_protocol: RPMI + 10% FBS + 1% Penn/Strep/Glutamine

extract_protocol:
Exactly ten million cells were pelleted and fixed with formaldehyde. Nuclei were harvested upon cell lysis, at which time drosophila S2 cell nuclei were spiked into cells in lysis buffer at one S2 cell nucleus per five experimental cells. Probe sonication (micro tip, 30 amplitude, 30” on, 8 cycles) was optimized for Nalm6 cells. Special attention was paid to equal and consistent volume transfers.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody

value: H3 (CST 4620, Cell Signaling)


title: NALM6_H3K4ME3_DOX

description: Spike in normalized ChIP-Seq for H3K4me3in NALM6 after DOX treatment

value: H3K4me3 (ab8580, Abcam)


title: GSS1403_181_F_NA

tag: ancestry

value: European


title: GSS1403_148_F_NA

tag: collection time


title: GSS1403_196_F_NA

tag: tissue


title: NALM6_H3K4ME3

description: Spike in normalized ChIP-Seq for H3K4me3 in NALM6


title: GSS1403_284_F_NA


title: GSS1403_318_F_NA


title: NALM6_H3K27ME3_DOX

description: Spike in normalized ChIP-Seq for H3K27me3 in NALM6 after DOX treatment

value: H3K27me3 (CST 9733s, Cell Signaling)

value: DOX


title: GSS1403_255_F_NA


title: NALM6_H3K27AC_DOX

description: Spike in normalized ChIP-Seq for H3K27ac in NALM6 after DOX treatment

value: H3K27ac (ab4729, Abcam)


title: NALM6_H3K27ME3

description: Spike in normalized ChIP-Seq for H3K27me3 in NALM6

value: Vehicle


title: GSS1403_251_F_NA


title: GSS1403_161_F_NA


title: GSS1403_274_F_NA


title: GSS1403_176_F_NA


title: ATAC_RagKO_Sm_Ahr_KO_rep2

value: Small Intestine


title: NALM6_H3

description: Spike in normalized ChIP-Seq for H3 in NALM6


title: GSS1403_259_F_NA


title: GSS1403_311_F_NA


title: GSS1403_295_F_NA


title: GSS1403_174_F_NA


title: GSS1403_151_F_NA


title: GSS1403_184_F_NA


title: GSS1403_231_F_NA


title: shTP63#4_BxPC3

description: processed data file: shTP63_VS shNEG_BxPC3.txt

tag: genotype/variation

value: transduced with shTP63#4

value: day 5 post-infection


title: shTP63#3_BxPC3

value: transduced with shTP63#3


title: shTP63#4_hF3

description: processed data file: shTP63_VS shNEG_hF3.txt

source_name: hF3 organoids

value: day 8 post-infection


title: NALM6_H3K27AC

description: Spike in normalized ChIP-Seq for H3K27ac in NALM6

value: B-ALL cell line


title: CFPAC1_TP63dN_48H_DOX

description: processed data file: TP63dN_vs_GFP_DOX_CFPAC1.txt

value: transduced with dox inducible vector to express TP63dN

value: 48 hours post dox


title: shTP63#3_hF3


title: shNEG_hF3

value: transduced with shNEG


title: ulp2pULP2500G

city: New Haven

first: Hong-Yeoul

last: Ryu

state: CT

address: 266 Whitney Ave

department: MB&B

institute: Yale

data_processing:
Library strategy: WGS-Seq
Whole genome sequencing was then performed by the Yale Center for Genome Analysis, using 2x 100 bp sequencing on Illumina HiSeq 2500 instruments, to an average depth of 500x per sample.
The reads were aligned to the S. cerevisiae genome using BWA MEM v0.7.15, and a joint calling of variants was performed using freebayes v0.9.14 with options (-P 0.5 -E 0 -q 10 -C 5).
Supplementary_files_format_and_content: Tab separate file where the columns are chromosome, position, reference, alternative sequence, allele frequency for each of the samples, and read-depth for each of the samples.

organism: Saccharomyces cerevisiae

source_name: ulp2Δ + pULP2_500 generation

growth_protocol: For laboratory evolution experiments, cells were grown to stationary phase in YPD and then diluted 1:120 into fresh YPD medium. This process was repeated daily (6.9 generations per day).

extract_protocol:
Genomic DNA was extracted from 1 OD600 equivalent of cells using a standard phenol/chloroform extraction method.
Standard YCGA protocol

tag: strain bacground

value: ulp2{delta} + pULP2

tag: passage

value: 500 generations


title: WT500G

source_name: WT_500 generation

value: WT


title: ulp2500G

source_name: ulp2Δ _500 generation


title: CFPAC1_GFP_48H_DOX

value: transduced with dox inducible vector to express GFP


title: Ulp2_500G_2

data_processing:
The libraries underwent 76-bp paired-end sequencing using an Illumina HiSeq 2500 according to Illumina protocols, generating an average of 14 million paired-end reads per library.
For each read, we trimmed the first 6 nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 using in-house scripts.
If, after trimming, the read was shorter than 45 bp, the entire read was discarded. Trimmed reads were mapped to the S. cerevisiae genome (Ensembl R64-1-1) with Tophat v2.1.1 using the very-sensitive preset, first-strand library type, and providing the corresponding gene model annotation.
Only the reads that mapped to a single unique location within the genome, with a maximum of two mismatches in the anchor region of the spliced alignment, were reported in these results.
We used the default settings for all other Tophat options. Tophat alignments were then processed by Cuffdiff (Cufflinks v2.2.1) to obtain differential gene expression using first-strand library type, providing gene model annotation, and the genome sequence file for detection and correction of sequence-specific bias that random hexamer can cause during library preparation.
Supplementary_files_format_and_content: FPKM table

source_name: ulp2Δ _500 generations

extract_protocol:
One OD600 equivalent of cells grown to mid-exponential phase was used for RNA isolation using the RNeasy kit (Qiagen). The Ambion DNA-free DNA removal kit was used to remove DNA contaminants.
Twelve strand-specific sequencing libraries, 3 replicates per condition, were produced from the purified total RNA samples by the Illumina TruSeq stranded protocol.

tag: stran background


title: PATU8988S_TP63dN_48H_DOX

description: processed data file: TP63dN_vs_GFP_DOX_PATU8988S.txt


title: PATU8988S_GFP_48H_DOX


title: Ulp2_500G_1

tag: genotype


title: HPAFII_TP63dN_48H_DOX

description: processed data file: TP63dN_vs_GFP_DOX_HPAFII.txt

source_name: HPAFII

tag: cell type

value: HPAFII


title: HPAFII_GFP_48H_DOX


title: Ulp2_500G_0


title: shNEG_BxPC3


title: GSS1403_272_F_NA

description: Gene expression data from LCM-separated epidermis from human forearm

tag: Sex

value: Female

value: LCM-separated epidermis

value: European


title: AsPC1_TP63dN_48H_DOX

description: processed data file: TP63dN_vs_GFP_DOX_AsPC1.txt

tag: treatment time


title: SUIT2_TP63dN_48H_DOX_rep2

description: processed data file: TP63dN_vs_GFP_DOX_SUIT2.txt


title: SUIT2_GFP_48H_DOX_rep1


title: SUIT2_GFP_48H_DOX_rep2


title: Ulp2_50G_1

source_name: ulp2Δ _50 generations

value: 50 generations


title: SUIT2_TP63dN_48H_DOX_rep1


title: Ulp2_50G_2


title: GSS1403_117_F_NA


title: GSS1403_132_F_NA


title: GSS1403_216_F_NA


title: GSS1403_211_F_NA


title: GSS1403_265_F_NA


title: GSS1403_169_F_NA


title: GSS1403_172_F_NA


title: Ulp2_50G_0


title: GSS1403_153_F_NA


title: WT_500G_1

source_name: WT_500 generations


title: Input_for_MIAPaca2_H3K27ac_ChIP

description: processed data file: MIAPaca2_H3K27ac_ChIP.bigwig

data_processing:
50bp single end sequencing reads were mapped to hg19 genome using Bowtie2 using default settings
PCR duplicates were removed from sequencing reads using SAM Tools rmdup.
MACS 1.4.2 was used to call peaks with input genomic DNA as control with other default parameters: 1e-05 Pvalue cutoff for peak detection, 10-30 within MFOLD range
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files converted from wiggle file generated from MACS peaks calling

extract_protocol:
After cross-link, cells were incubated with cell lysis buffer (10mM Tris pH8.0, 10mM NaCl, 0.2% NP-40) and then resuspended and sonicated in nuclei lysis buffer (50mM Tris pH8.0, 10mM EDTA, 1%SDS) for 15mins, followed by ChIP
Library was constructed using Illumina TruSeq ChIP Sample Prep kit following manufacture’s protocol. Briefly, ChIP DNA was end repaired, followed by A tailing and size selection (250-500 bp) by gel electrophoresis. 15 PCR cycles were used for final library amplification and the library was analyzed on Bioanalyzer using high sensitivity DNA chip (Agilent) on Bio-analyzer.

treatment_protocol: Cell cultures were collected and cross-likned with formaldehyde at room temperature for 15 mins.

value: wt cells

tag: chip antibodies


title: AsPC1_GFP_48H_DOX


title: PATU8988S_TP63dN_H3K27ac_DOX_ChIP

description: processed data file: PATU_TP63_H3K27ac_DOX_ChIP.bigwig

value: dox inducible vector to express TP63dN

value: ab4729, abcam


title: GSS1403_252_F_NA


title: GSS1403_308_F_NA


title: GSS1403_210_F_NA


title: HPAFII_TP63dN_H3K27ac_DOX_ChIP

description: processed data file: HPAFII_TP63_H3K27ac_DOX_ChIP.bigwig


title: Input_for_PATU8988S_TP63dN_DOX_ChIP


title: Input_for_HPAFII_TP63dN_DOX_ChIP


title: MIAPaca2_H3K27ac_ChIP


title: GSS1403_228_F_NA


title: GSS1403_302_F_NA


title: AsPC1_TP63dN_H3K27ac_DOX_ChIP

description: processed data file: AsPC1_TP63_H3K27ac_DOX_ChIP.bigwig


title: Input_for_AsPC1_TP63dN_DOX_ChIP


title: WT_500G_0


title: WT_50G_2

source_name: WT_50 generations


title: SUIT2_TP63dN_H3K27ac_DOX_ChIP

description: processed data file: SUIT2_TP63_H3K27ac_DOX_ChIP.bigwig


title: WT_500G_2


title: PATU8988S_GFP_H3K27ac_DOX_ChIP

description: processed data file: PATU_GFP_H3K27ac_DOX_ChIP.bigwig

value: dox inducible vector to express GFP


title: Input_for_SUIT2_TP63dN_DOX_ChIP


title: Input_for_PATU8988S_GFP_DOX_ChIP


title: GSS1403_116_F_NA

source_name: batch_subjectID_gender_sampling time


title: WT_50G_1


title: WT_50G_0


title: HPAFII_GFP_H3K27ac_DOX_ChIP

description: processed data file: HPAFII_GFP_H3K27ac_DOX_ChIP.bigwig


title: Input_for_HPAFII_GFP_DOX_ChIP


title: AsPC1_GFP_H3K27ac_DOX_ChIP

description: processed data file: AsPC1_GFP_H3K27ac_DOX_ChIP.bigwig


title: GSS1403_136_F_NA


title: GSS1403_106_F_NA


title: GSS1403_175_F_NA


title: Input_for_AsPC1_GFP_DOX_ChIP


title: SUIT2_GFP_H3K27ac_DOX_ChIP

description: processed data file: SUIT2_GFP_H3K27ac_DOX_ChIP.bigwig


title: GSS1403_215_F_NA


title: Input_for_SUIT2_GFP_DOX_ChIP


title: TP63dN_PATU8988S_rep1

description: processed data file: TP63dN_VS MTV_PATU8988S.txt

value: transduced with TP63dN cDNA in LentiVpuro vector

value: day 7 post-infection


title: MTV_PATU8988S_rep2

value: transduced with empty LentiVpuro vector


title: MTV_PATU8988S_rep1


title: Surgery+Maresin1, biological rep2

city: Stockholm

first: Souren

last: Mkrtchian

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from the hippocampusof the mouse treated by Maresin 1 prior to orthopedic surgery

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MoGene-1_1-st-v1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with the Affymetrix Expression Console. Method = plier (med-norm, target=0, doavg=false, calctarget=true, lowprecision=false,pm-gcbg)

source_name: Hippocampus from the mouse treated by Maresin 1 prior to orthopedic surgery

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

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

treatment_protocol: Mice in the first experimental group (Surgery) were subjected to orthopedic surgery (tibia fracture). Mice from the second experimental group (Surgery+M) were administered Maresin 1 prior to the surgery.

tag: strain

value: Brain hippocampus

tag: age

value: 12-14 weeks old mouse


title: TP63dN_SUIT2_rep2

description: processed data file: TP63dN_VS MTV_SUIT2.txt


title: TP63dN_SUIT2_rep1


title: MTV_SUIT2


title: sgTP63#4_BxPC3

description: processed data file: sgTP63_VS sgNEG_BxPC3.txt

value: transduced with Cas9 cDNA in LentiVpuro vector and sgTP63#4

value: day 5 post-infection


title: Surgery+Maresin1, biological rep3


title: GSS1403_321_F_NA


title: sgTP63#2_BxPC3

value: transduced with Cas9 cDNA in LentiVpuro vector and sgTP63#2


title: GSS1403_317_F_NA


title: sgNEG_BxPC3

value: transduced with Cas9 cDNA in LentiVpuro vector and sgNEG


title: Surgery+Maresin1, biological rep1


title: TP63dN_PATU8988S_rep2


title: Surgery, biological rep2

description: Gene expression data from the hippocampus of the mouse subjected to orthopedic surgery

source_name: Hippocampus from the mouse subjected to orthopedic surgery


title: SUIT2_FLAG-TP63dN_ChIP

value: FLAG-TP63dN cDNA in LentiVpuro vector

value: F1804, Sigma/Aldrich


title: GSS1403_283_F_NA

description: Gene expression data from LCM-separated epidermis from human forearm

value: Female

value: LCM-separated epidermis

value: European


title: GSS1403_195_F_NA


title: Surgery, biological rep1


title: GSS1403_208_F_NA


title: GSS1403_143_F_NA


title: Input_for_SUIT2_FLAG-TP63dN_ChIP


title: BxPC3_TP63_ChIP

value: wildtype


title: Input_for_SUIT2_TP63dN_H3K27ac_ChIP

value: TP63dN cDNA in Lenti-blast vector


title: Input_for_SUIT2_MTV_H3K27ac_ChIP

value: empty Lenti-blast vector


title: Patient 153-EGFR.4449

city: Tokyo

first: Sophia

last: Subat

address: 3-8-31 Ariake, Koto-ward,

institute: Japanese Foundation for Cancer Research

description: One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

hyb_protocol: The cDNA was hybridized to the SurePrint G3 Human Gene Expression 8×60K Microarray (Design ID 028004, Agilent Technologies).

scan_protocol: After the hybridization, scanning of the arrays was carried out with the Agilent Micro Scanner System (G2565CA, Agilent Technologies)..

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.

source_name: lung adenocarcinoma

label_protocol: Total RNA was reverse transcribed into cDNA and labeled using the Low Input Quick Amp Labeling Kit (5190-2305, Agilent Technologies) following the manufacturer’s instructions.

extract_protocol: Total RNAs were extracted using miRNeasy Mini Kit and RNase-free (Qiagen, Hilden, Germany) according to the manufacturer’s instructions

value: lung adenocarcinoma

tag: egfr status

value: EGFR mutation


title: Surgery, biological rep3


title: Patient 154-EGFR.4480


title: Patient 155-EGFR.5785


title: Patient 152-EGFR.4412


title: GSS1403_258_F_NA


title: Input_for_BxPC3_sgTP63#2_H3K27ac_ChIP

value: Cas9 cDNA in LentiVpuro vector and sgTP63#2


title: BxPC3_sgTP63#2_H3K27ac_ChIP

value: ab4729, abcam


title: Control mouse, biological rep2

description: Gene expression data from the control mouse hippocampus

source_name: Control mouse hippocampus

value: Brain hippocampus

value: 12-14 weeks old mouse


title: GSS1403_250_F_NA


title: Patient 151-EGFR.4384


title: GSS1403_192_F_NA


title: Control mouse, biological rep1


title: Input_for_BxPC3_sgTP63#4_H3K27ac_ChIP

value: Cas9 cDNA in LentiVpuro vector and sgTP63#4


title: SUIT2_TP63dN_H3K27ac_ChIP


title: Input_for_BxPC3_TP63_ChIP


title: Input_for_BxPC3_sgNEG_H3K27ac_ChIP

value: Cas9 cDNA in LentiVpuro vector and sgNEG


title: BxPC3_sgTP63#4_H3K27ac_ChIP


title: BxPC3_sgNEG_H3K27ac_ChIP


title: Control mouse, biological rep3


title: GSS1403_199_F_NA


title: GSS1403_147_F_NA


title: Patient 150-EGFR.4364


title: GSS1403_110_F_NA


title: GSS1403_201_F_NA


title: SUIT2_MTV_H3K27ac_ChIP


title: GSS1403_119_F_NA


title: GSS1403_157_F_NA


title: GSS1403_282_F_NA


title: Patient 149-EGFR.4317


title: Input_for_hN35_H3K27ac_ChIP

growth_protocol: Matrigel dome with Human complete Feeding Medium (hCPLT): advanced DMEM/F12, HEPES 10mM, Glutamax 1X, A83-01 500nM, hEGF 50ng/mL, mNoggin 100ng/mL, hFGF10 100ng/mL, hGastrin I 0.01μM, N-acetylcysteine 1.25mM, Nicotinamide 10mM, PGE2 1μM, B27 supplement 1X final, R-spondin1 conditioned media 10% final, Afamin/Wnt3A conditioned media 50% final.

value: hN35 human organoid


title: hN34_H3K27ac_ChIP

value: hN34 human organoid


title: hN35_H3K27ac_ChIP


title: Input_for_hN34_H3K27ac_ChIP


title: Input_for_hT85_H3K27ac_ChIP

value: hT85 human organoid


title: Patient 148-EGFR.4286


title: Patient 146-EGFR.4244


title: Patient 147-EGFR.4276


title: hF3_H3K27ac_ChIP

value: hF3 human organoid


title: BxPC3_H3K27ac_ChIP


title: Input_for_BxPC3_H3K27ac_ChIP


title: SUIT2_H3K27ac_ChIP


title: hT85_H3K27ac_ChIP


title: Patient 144-EGFR.3896


title: Input_for_SUIT2_H3K27ac_ChIP


title: Input_for_hF3_H3K27ac_ChIP


title: Patient 145-EGFR.4164


title: AsPC1_H3K27ac_ChIP


title: Input_for_AsPC1_H3K27ac_ChIP


title: Input_for_HPAFII_H3K27ac_ChIP

value: HPAFII


title: PATU8988S_H3K27ac_ChIP


title: Input_for_PATU8988S_H3K27ac_ChIP


title: Patient 141-EGFR.3836


title: GSS1403_220_F_NA

value: Female

value: LCM-separated epidermis

value: European


title: Patient 142-EGFR.3863


title: GSS1403_187_F_NA


title: GSS1403_191_F_NA


title: Patient 140-EGFR.3707


title: 69_PD1-intermediate_RNA-Seq

city: Daejeon

first: Su-Hyung

last: Park

address: 291 Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Reads were trimmed based on sequencing quality using Sickle.
Poly-A tails and adaptor contents were removed using Cutadapt.
Trimmed reads were aligned on a human reference sequence (hg19) using Tophat2.
The number of mapped reads on the 3’ end of each gene was calculated using Bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: Raw read count

source_name: hepatocellular carcinoma tissue

extract_protocol:
Cells were cryopreserved in Trizol reagent and RNA extracted according to the manufacturer’s instructions.
Total RNA quality was assessed with the Agilent 2100 Bioanalyzer System. Extracted RNA samples were processed using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Vienna) and sequenced on an Illumina NextSeq 500. A median 2.0x107 (range 1.7x107 to 2.4x107) single-end reads with 75 bp were generated.

value: CD8 T cells

tag: pd1 level

value: intermediate

value: hepatocellular carcinoma


title: 69_PD1-high_RNA-Seq

value: high


title: 64_PD1-negative_RNA-Seq

value: negative


title: Patient 139-EGFR.3272

value: lung adenocarcinoma

value: EGFR mutation


title: HPAFII_H3K27ac_ChIP

value: wildtype

value: ab4729, abcam


title: GSS1403_101_F_NA


title: 64_PD1-high_RNA-Seq


title: GSS0392_109_M_600

value: Male


title: GSS1403_105_F_NA


title: 64_PD1-intermediate_RNA-Seq


title: GSS1403_289_F_NA


title: Patient 138-EGFR.3138


title: 52_PD1-negative_RNA-Seq


title: GSS0392_109_M_1200


title: Patient 137-EGFR.3067


title: 69_PD1-negative_RNA-Seq


title: 52_PD1-intermediate_RNA-Seq


title: 52_PD1-high_RNA-Seq


title: GSS0392_109_M_1800


title: GSS0392_106_M_1800


title: Patient 136-EGFR.3042


title: Patient 135-EGFR.2964


title: 48_PD1-high_RNA-Seq


title: 48_PD1-intermediate_RNA-Seq


title: GSS0392_106_M_0


title: 41_PD1-negative_RNA-Seq


title: GSS0392_106_M_1200


title: GSS0392_109_M_0


title: 41_PD1-intermediate_RNA-Seq


title: 41_PD1-high_RNA-Seq


title: 31_PD1-negative_RNA-Seq


title: Patient 134-EGFR.2914


title: 31_PD1-high_RNA-Seq


title: 31_PD1-intermediate_RNA-Seq


title: GSS0392_112_M_600


title: Patient 133-EGFR.2888


title: Patient 132-EGFR.2803


title: Patient 131-EGFR.2787


title: BxPC3-Cas9

description: processed data file: Human_PDA_cell_lines.txt

value: transduced with Cas9 cDNA in LentiVpuro vector


title: MIAPaca2-Cas9


title: 48_PD1-negative_RNA-Seq


title: PANC1-Cas9


title: Patient 130-EGFR.2780


title: CFPAC1-Cas9


title: GSS0392_106_M_600


title: SUIT2-Cas9


title: Patient 129-EGFR.2773


title: GSS0392_112_M_1800


title: AsPC1-Cas9


title: PATU8988S-Cas9


title: HPAFII-Cas9


title: Patient 128-EGFR.2706


title: GSS0392_101_M_0


title: Patient 126-EGFR.2362


title: DNase-seq, iWAT adipocytes

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
DNase-seq data sets were mapped to the mm9 genome with STAR (Dobin et al., 2013) set to not map across splice junctions, and tag directory generation, peak calling/annotations and motif analyses were performed with HOMER (Heinz et al., 2010).
DNA hypersensitive sites were called using ”-style factor” setting with all other parameters set at default in eWAT-derived, iWAT-derived and BAT-derived adipocytes.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph, peaks

source_name: iWAT-derived primary adipocytes

growth_protocol: Brown adipose tissue (pooled interscapular, cervical, and axillary depots) as well as the epididymal (eWAT) and inguinal (iWAT) adipose tissue were optained from 4-5wk old male NMRI mice.  Adipose tissues were carefully minced and treated with collagenase (type II; Sigma) to separate the SVF from mature adipocytes.

extract_protocol:
DNase I digestion was performed in eWAT, iWAT and BAT-derived adipocytes on ~10,000,000 million nuclei, essentially as previously described (Siersbæk et al., 2011, EMBO J, 30(8):1459-72), except that the mature adipocytes were harvested directly in Buffer A (15 mM Tris–HCl pH=8, 15 mM NaCl, 60 mM KCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine) and 120 U/ml DNase I (Roche, cat# 11 284 932 001) was used for digestion.
DNase-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: The isolated SVF cells were cultured under differentiation-inducing conditions in a medium consisting of DMEM (Sigma), 10% newborn calf serum (NCS) (HyClone), 30 nM insulin, 25 μg/ml sodium ascorbate, 10 mM HEPES, pH 7.4, at 37°C, 4 mM l-glutamine (Invitrogen), 100 μg/ml streptomycin, 62.5 μg/ml penicillin, and 1 μM rosiglitazone (Novo Nordisk). The cultures were harvested 8 days after plating and for comparison between the in vitro differentiated adipocytes, only cultures with a >50% degree of differentiation were used.

value: NMRI

value: male

value: 4-5 weeks

value: inguinal white adipose tissus

value: Primary in vitro differentiated SVF cells