title: 12_RAW 264.7 + Inulin + TsSP (+LPS)

city: Frederiksberg

first: Laura

middle: J

last: Myhill

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description:
Inulin+TsSP 3
Gene expression data from cultured RAW 264.7 macrophages.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Standard Affymetrix normalization.

label: biotin

source_name: Murine RAW 264.7 macrophage cultured with Inulin + TsSP (+LPS)

label_protocol: Standard Affymetrix protocol.

growth_protocol: Murine RAW 264.7 macrophages cultured for 6 hours at 37°C, 5% CO2.

extract_protocol: RAW 264.7 macrophages were lysed and RNA extracted using RNeasy mini kit (Qiagen).

treatment_protocol: Macrophages were cultured with either inulin @ 500 µg/mL or TsSP @ 50 µg/mL, or in combination, plus LPS @ 500 ng/mL.

value: macrophage

value: Inulin + TsSP (+LPS)


title: 11_RAW 264.7 + Inulin + TsSP (+LPS)

status: Public on Apr 01 2020

type: RNA

description:
Inulin+TsSP 2
Gene expression data from cultured RAW 264.7 macrophages.

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: treatment


title: RNAseq_A2780cis_CRISPRa_R#2

type: SRA

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

country: USA

institute: UCSD

library_source: transcriptomic

data_processing:
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Cells  were cultured in RPMI-1640-Glutamax I (#61870-036, Life Technologies) and 10% fetal bovine serum (FBS, #FB-11, Omega Scientific) at 5% CO2 37ºC, and sub-cultured at 1:5 to 1:6 dilutions after dissociation with 0.25% trypsin. Media was changed every other day, or daily when cells reached >50-60% confluency.

extract_protocol:
GRO-seq analysis was perfromed as prevkiously reported (PMID: 21572438, Wang et al., 2011); RNA-seq and ribosome profiling was performed using the ARTseq Ribosome Profiling kit  following the manufacture’s protocol (Epicentre).
RNA quality was calculated on TapeStation (Agilent Technologies). PolyA+ RNA-seq libraries were generated using the Illumina TruSeq Stranded RNA LT kit and following manufacturer’s detailed instructions.

treatment_protocol: The treatment administrated to A2780cis cells was described in the Sigma-Aldrich website as chronic exposure of the parent A27890 line to increasing concentrations of cisplatin Sigma-Aldrich (#93112517-19). Acute treatments (IC50) were administrated for 3 days, adding fresh media with drug at day 0 and after 2 days again.


title: 10_RAW 264.7 + Inulin + TsSP (+LPS)

description:
Inulin+TsSP 1
Gene expression data from cultured RAW 264.7 macrophages.


title: 9_RAW 264.7 + Inulin (+LPS)

description:
Inulin 3
Gene expression data from cultured RAW 264.7 macrophages.

source_name: Murine RAW 264.7 macrophage cultured with Inulin (+LPS)

value: Inulin (+LPS)


title: Pt-msx1_st6_rep2_d14

city: Takatsuki

first: Hiroki

last: Oda

state: Osaka

address: 1-1 Murasaki-cho

country: Japan

institute: JT Biohistory Research Hall

description:
HTseq_count_per_gene_aug3.txt
HTseq_count_per_gene_aug3_RPKM.txt
DEG_msx_st6.txt

data_processing:
Base call and quality scoring were performed by the Real Time Analysis software application during Illumina's sequencing runs.
Sequence reads were trimmed for adaptor and primer sequences and low-quality sequences using the CLC Genomics Workbench 7.0.4 (Qiagen) with the following parameter settings for the quality trim: trim using quality scores, limit=0.05; trim ambiguous nucleotides, maximum number of ambiguities=2; filter on length, discard reads below length=50. Trimmed reads were then aligned to Ptep_1.0 genome assembly using the BLAT algorithm version 34 in the DDBJ Read Annotation Pipeline with default settings.
The output alignments were filtered based on quality, coverage, and uniqueness using a perl script filterPSL.pl available from the AUGUSTUS 3.0.1 scripts folder. The parameter settings were as follows: minimum coverage, 60%; minimum percent identity, 90%; unique threshold, 0.96. The filtered alignments were converted into sam and psl files with a custom perl script.
Using the sam files, abundance of mRNAs against AUGUSTUS gene models (Schwager et al., 2017, BMC Biol. 15, 62) was calculated with htseq-count v. 0.5.4p5 in -s reverse, -m union settings and was normalized in Reads Per Kilobase of exon per Million reads (RPKM).
Based on the abundance of mRNAs against AUGUSTUS gene models, differentially expressed genes (DEGs) were estimated using EdgeR.
The alignments in the psl format were converted into wig files using a script aln2wig available from the AUGUSTUS 3.0.1 scripts folder, and the wig files were converted into bigWig files using the program wigToBigWig available from the ucsc directory.
Genome_build: Ptep_1.0
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for gene models and the features of the gene models.
Supplementary_files_format_and_content: tab-delimited text file includes logFC and FDR values for the identified DEGs.
Supplementary_files_format_and_content: wig files ; Scores represent normalized read coverage (per 10 million reads).
Supplementary_files_format_and_content: bigWig files ; Scores represent normalized read coverage (per 10 million reads).

organism: Parasteatoda tepidariorum

growth_protocol: Embryos were incubated at 25˚C until they reached the appropriate stages.

extract_protocol:
Poly(A) mRNA was extracted using a QuickPrep Micro mRNA purification kit (GE Healthcare) and a Dynabeads mRNA DIRECT Kit (Ambion) from 50-120 embryos.
mRNA was fragmented using the NEBNext RNase III RNA Fragmentation Module (New England BioLabs). Sequencing libraries were constructed from fragmented RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, New England BioLabs).

treatment_protocol: Mated adult females were injected with approximately 1-2 µl of Pt-hh, Pt-ptc, or Pt-msx1 dsRNA solution (2µg/µl) four times at 2-3 days intervals. Embryos derived from egg sacs produced by the injected females 13-24 days after the first injection of the dsRNA were used for RNA extraction. Embryos from the same females 1-3 days before the dsRNA injection were used as untreated samples.

tag: isolate

value: Osaka

tag: tissue

value: whole embryo

value: Pt-msx1 pRNAi

tag: developmental stage

value: early stage 6


title: miR-21-/- RNA-seq rep2

city: Shenzhen

first: Zhijun

last: Han

state: Guangdong

address: No 1088,xueyuan Rd., Nanshan District

country: China

institute: Southern University of Science and Technology

data_processing:
Basecalls performed using CASAVA version 1.4
ATAC-seq reads were trimmed using trim_galore 0.4.4_dev with default settings and then aligned to mm10 using bowtie2 with --end-to-end  -X 2000. Reads with MAPQ < 10 were removed using samtools. Singletons are removed using in house Perl script.  Duplicated reads were removed using samtools.
Filtered reads were sampled to the same reads number for comparing between samples using samtools. Differential chromatin accessible regions were identified using rgt-THOR version 0.1 with parameters --pvalue 0.05 --binsize 100 --step 50. Then significant differential peaks were further filtered according to the switch point from rank plot. Peaks were annotated to refGene annotation downloaded from UCSC Genome Browser using in house Perl script. Motifs were scanned using HOMER findMotifsGenome.pl from the top 1000 differential accessible peaks extended from the peak summit to +/- 100bp.
RNA-seq reads were mapped to mm10 with refGene annotation downloaded from UCSC Genome Browser using TopHat2 v2.1.0. Gene expression level were counted by htseq-count 0.11.0. Differential expressed genes were called by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: BigWiig files were generated by rgt-THOR, scores representing the normalized ATAC-seq reads coverage. TAB-delimited text file included the raw reads count for each gene from RNA-seq sample.

source_name: TH17(23) cells

growth_protocol: Naïve CD4+ T cells were isolated from lymph nodes or spleen of mice using a CD4+ CD62L+ T cell isolation kit II (Miltenyi Biotec) according to the manufacturer’s instruction. Naïve CD4+ T cells were stimulated with plate-bound anti-CD3ε mAb (5 µg/ml) in the presence of anti-CD28 mAb (2 µg/ml) in a 48-well plate under neutral conditions (10 µg/ml anti–IL-4 mAb and 10 µg/ml anti–IFN-γ mAb), IL-6 conditions (10 ng/ml IL-6, 10 µg/ml anti–IL-4 mAb, and 10 µg/ml anti–IFN-γ mAb), TH17 (β) conditions (2 ng/ml TGF-β1, 20 ng/ml IL-6, 10 µg/ml anti–IL-4 mAb, and 10 µg/ml anti–IFN-γ mAb), TH17 (23) conditions (20 ng/ml IL-6, 20 ng/ml IL-1β, 20 ng/ml IL-23, 10 µg/ml anti–IL-4 mAb, and 10 µg/ml anti–IFN-γ mAb).

extract_protocol:
Naive CD4+ T cells from control and miR-21-/- mice were differentiated under pathogenic TH17 (23) differentiation condition. Total RNA was prepared from these cells using Trizol reagent (Invitrogen). RNA-seq libraries were prepared using a TruSeq Stranded Total RNA Library Prep Kit (Illumina). For GFP+ TH17 cells sorted from in vivo suspensions, 50,000 cells were resuspended in 700 ul Trizol reagent, total RNA was prepared by miRNeasy Micro Kit (Qiagen), RNA-seq libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (clontech). Sequencing was performed on an Illumina HiSeq X Ten System in a 150 bp/150 bp Paired end mode. ATAC-seq library preparations were performed as described(Buenrostro et al., 2013). In brief, 50,000 cells were washed in cold PBS and lysed. Transposition was performed at 37 °C for 30 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), DNA was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5× ratio. Libraries were sequenced on a HiSeq X Ten System in a 150 bp/150 bp Paired end mode.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: TH17(23) cells


title: RNAseq_A2780cis_CRISPRa_R#1


title: Pt-msx1_st6_rep3_d-3

value: untreated


title: miR-21-/- RNA-seq rep1


title: Pt-msx1_st6_rep2_d-3


title: RNAseq_A2780cis_CRISPRcontrol


title: 6_RAW 264.7 + TsSP (+LPS)

description:
TsSP 3
Gene expression data from cultured RAW 264.7 macrophages.

source_name: Murine RAW 264.7 macrophage cultured with TsSP (+LPS)

value: TsSP (+LPS)


title: RNAseq_A2780_CRISPRi_R#2


title: RNAseq on DMSO treated siMCRS1 replicate A

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

description:
DMSO_MCRS1_A
processed data file:
drug_norm_counts.csv

data_processing:
Kallisto was used to quantitate transcript expression levels using GRCh38 reference with the following paramters --single -l 200 -s 50 -b 50
tximport was used to aggregate count data per gene using Kallisto output.
DESeq2 was used for differential expression analysis with an FDR of 0.5 and no explicit fold change cut off
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files of count data for each sample

source_name: HepG2_DMSO treated siMCRS1

growth_protocol: Cells were grown in DMEM + 10% FBS + P +S and maintained for less than 10 passages.

extract_protocol:
RNA was extracted using trizol and Direct-zol kit (Zymo Research) per manufacturers instructions
Libraries were constructed using Kapa stranded mRNA sequencing kit

treatment_protocol: siRNA experiments were conducted by adding 50nM siRNA in optimem using RNAimax transfection reagent per manufacturers instructions. Cells were harvested at 72 hours post transfection for processing. For drug treatment experiments. 1uM EPZ-6438 or 1uM DMSO were added 3 days prior to transfections with siRNA as previously described.

value: liver cancer cell line

tag: sirna

value: MCRS1 (s20435 Life Tech)

tag: treated with

value: 1uM DMSO


title: 8_RAW 264.7 + Inulin (+LPS)

description:
Inulin 2
Gene expression data from cultured RAW 264.7 macrophages.


title: Ad-c-Rel RNA-seq rep2

source_name: TH17(β) cells

value: TH17(β) cells


title: 5_RAW 264.7 + TsSP (+LPS)

description:
TsSP 2
Gene expression data from cultured RAW 264.7 macrophages.


title: RNAseq_A2780_CRISPRi_R#1


title: Pt-msx1_st5_rep2_d-3

description:
HTseq_count_per_gene_aug3.txt
HTseq_count_per_gene_aug3_RPKM.txt
DEG_msx_st5.txt

value: late stage 5


title: 4_RAW 264.7 + TsSP (+LPS)

description:
TsSP 1
Gene expression data from cultured RAW 264.7 macrophages.


title: Pt-msx1_st5_rep2_d14


title: Pt-msx1_st6_rep1_d18


title: 3_RAW 264.7 + LPS

description:
Control 3
Gene expression data from cultured RAW 264.7 macrophages.

source_name: Murine RAW 264.7 macrophage cultured with LPS

value: LPS


title: Ad-c-Rel RNA-seq rep1


title: RNAseq_A2780_CRISPRcontrol


title: Donor-4 CD8 Tcell  coculture with pDC cells without antigen

city: Nijmegen

first: Jessie

middle: van

last: Buggenum

address: Heyendaalseweg 135

country: Netherlands

institute: Radboud University

description:
CD8 Tcell  coculture with pDC cells without antigen
Three donors were used for each treatment

data_processing:
After quality control, high quality reads were mapped to GRCh38 using HISTAT2
Differential expression analysis was performed using DESeq2 R package version 1.22.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file with gene counts per sample

source_name: Blood

extract_protocol:
RNA was extracted using Trizol
Library contruction and sequencing was performed by BGI Tech Solutions (Hong Kong) paired-end at 150 bp on Illumina NovaSeq platform

value: purified CD8+ T-cells

tag: donor


title: Ad-control RNA-seq rep1


title: Donor-3 CD8 Tcell  coculture with pDC cells without antigen


title: GROseq_A2780_cisplatin_R#2

data_processing:
library strategy: GRO-seq
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig


title: Pt-msx1_st6_rep1_d-3


title: Pt-msx1_st5_rep1_d18


title: 1_RAW 264.7 + LPS

description:
Control 1
Gene expression data from cultured RAW 264.7 macrophages.

value: macrophage


title: Ileum TH17 RNA-seq rep2

source_name: Ileum TH17 cells

value: Ileum TH17 cells


title: GROseq_A2780_vehicle_R#2


title: Donor-2 CD8 Tcell  coculture with pDC cells without antigen


title: Pt-msx1_st5_rep1_d-3


title: Donor-4 CD8 Tcell  coculture with pDC cells with antigen

description:
CD8 Tcell  coculture with pDC cells with antigen
Three donors were used for each treatment


title: Ileum TH17 RNA-seq rep1


title: Donor-3 CD8 Tcell  coculture with pDC cells with antigen


title: Ribosome_profiling_A2780cis_vehicle

data_processing:
library strategy: Ribosome-profiling
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig


title: Ad-control RNA-seq rep2


title: Donor-2 CD8 Tcell  coculture with pDC cells with antigen


title: CNS TH17 RNA-seq rep1

source_name: CNS-infiltrated TH17 cells

value: CNS-infiltrated TH17 cells


title: Pt-ptc_st5_rep3_d14

description:
HTseq_count_per_gene_aug3.txt
HTseq_count_per_gene_aug3_RPKM.txt
DEG_ptc_st5.txt

value: Osaka

value: Pt-ptc pRNAi


title: Pt-ptc_st5_rep3_d-1

value: whole embryo


title: TH17(β) ATAC-seq rep2

library_source: genomic

molecule: genomic DNA

source_name: Nonpathogenic TH17 cells

value: Nonpathogenic TH17 cells


title: Donor-4 CD8 Tcell  coculture with CD1c 'and pDC cells without antigen

description:
CD8 Tcell  coculture with CD1c 'and pDC cells without antigen
Three donors were used for each treatment


title: Ribosome_profiling_A2780_vehicle


title: 2_RAW 264.7 + LPS

description:
Control 2
Gene expression data from cultured RAW 264.7 macrophages.


title: RNAseq_A2780cis_cisplatin


title: RNAseq_A2780cis_vehicle


title: Donor-3 CD8 Tcell  coculture with CD1c 'and pDC cells without antigen


title: Donor-2 CD8 Tcell  coculture with CD1c 'and pDC cells without antigen


title: Ribosome_profiling_A2780_cisplatin


title: Ribosome_profiling_A2780cis_cisplatin


title: CNS TH17 RNA-seq rep2


title: Pt-ptc_st3_rep3_d14

description:
HTseq_count_per_gene_aug3.txt
HTseq_count_per_gene_aug3_RPKM.txt
DEG_ptc_st3.txt

value: early stage 3


title: Pt-ptc_st3_rep3_d-1

value: untreated


title: Pt-ptc_st5_rep3_d19


title: Donor-4 CD8 Tcell  coculture with CD1c 'and pDC cells with antigen

description:
CD8 Tcell  coculture with CD1c 'and pDC cells with antigen
Three donors were used for each treatment


title: TH17(23) ATAC-seq rep1

source_name: Pathogenic TH17 cells

value: Pathogenic TH17 cells


title: Donor-3 CD8 Tcell  coculture with CD1c 'and pDC cells with antigen


title: Ileum TH17 ATAC-seq rep2


title: RNAseq_A2780_vehicle


title: Pt-ptc_st5_rep2_d19


title: Pt-ptc_st3_rep3_d19


title: Donor-2 CD8 Tcell  coculture with CD1c 'and pDC cells with antigen


title: TH17(β) ATAC-seq rep1


title: Ileum TH17 ATAC-seq rep1


title: Pt-ptc_st5_rep2_d14


title: Pt-ptc_st5_rep2_d-1


title: CNS TH17 ATAC-seq rep2


title: GROseq_A2780cis_vehicle


title: Pt-ptc_st3_rep2_d19


title: TH17(23) ATAC-seq rep2


title: Donor-3 CD8 Tcell  coculture with CD1c+ cells without antigen

description:
CD8 Tcell  coculture with CD1c+ cells without antigen
Three donors were used for each treatment


title: GROseq_A2780_cisplatin


title: Pt-ptc_st3_rep2_d14


title: Donor-2 CD8 Tcell  coculture with CD1c+ cells without antigen


title: WT (lys2) replicate 4

city: Madrid

first: Teresa

last: Laguna

address: Ctra. Cantoblanco, 8

department: Precision Nutrition and Personalized Medicine

country: Spain

institute: IMDEA Food Institute

data_processing:
Mapping was performed using STAR (v.2.5.1b)
Counts per gene were derived using htseq count (v.1.4.6-p2)
Differential expression analysis between each mutant type and wt species was done using DESeq2 (v.1.10.1)
Genome_build: R64-1-1.84
Supplementary_files_format_and_content: read counts in tab-delimited txt format

organism: Saccharomyces cerevisiae

growth_protocol: all strains were cultivated in synthetic minimal media (YNB, supplemented with Lys(0)) and harvested at OD600=1.0 after 10 cell divisions.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Germany) following the instructions of the manufacturer
NGS library prep was performed with Illumina’s TruSeq stranded mRNA LT Sample Prep Kit following Illumina’s standard protocol (Part # 15031047 Rev. E). Libraries were prepared by using only ¼ of the reagents with a starting amount of 250ng and they were amplified in 11 PCR cycles.

tag: genotype

value: WT (lys2)


title: RNAseq_A2780_cisplatin


title: GROseq_A2780_vehicle


title: NETs_Rep3

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

data_processing:
RNA-seq FASTQ files were aligned using Bowtie to human refernce genome GRCh37.
Normalized gene expressions were generated using Cufflinks.
Gene counts were obtained using Bioconductor’s GenomicAlignment.
DeSeq was used to analyze the raw gene counts and calculate differentially expressed genes
(21) Genes were deemed differentially expressed that had a fold change >2.5x, an nbinomTest p-value <.01 and RPKMs >2 for 50% of the samples in at least one condition.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw counts

source_name: Primary human bronchial epithelial cells

growth_protocol: HBEs were differentiated and grown at an air liquid interface (ALI) on TranswellÒ inserts

extract_protocol:
QIAGEN RNeasy #74134
RNA sequencing was performed by CCHMC’s Gene Expression Core utilizing the Illumina HiSeq2500

treatment_protocol: HBEs were exposed to NETs 5μg/ml + anakinra 100ng/ml or anakinra alone 100ng/ml for 18 hours.


title: WT (lys2) replicate 3


title: Pt-ptc_st5_rep1_d18


title: Pt-ptc_st3_rep2_d-1


title: Donor-3 CD8 Tcell  coculture with CD1c+ cells with antigen

description:
CD8 Tcell  coculture with CD1c+ cells with antigen
Three donors were used for each treatment


title: Donor-4 CD8 Tcell  coculture with CD1c+ cells with antigen


title: WT (lys2) replicate 2


title: NETs_Rep1

value: Primary human bronchial epithelial cells


title: WT (lys2) replicate 1


title: Donor-4 CD8 Tcell  coculture with CD1c+ cells without antigen


title: Donor-2 CD8 Tcell  coculture with CD1c+ cells with antigen


title: PBS_Rep3


title: TU (urm1 tcd1 lys2) replicate 4

value: TU (urm1 tcd1 lys2)


title: Pt-ptc_st5_rep1_d14


title: TC-797_Triptolide_replicate2 (HiC)

city: Houston

first: Kyle

last: Eagen

state: TX

address: 1 Baylor Plaza

department: Department of Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Reads were aligned to concatenated hg38/Genome Reference Consortium Human Reference 38 Patch 15 (GRCh38.p15) and dm6/BDGP Release 6 + ISO1 MT assemblies of the human and Drosophila melanogaster genomes, respectively, using BWA-MEM v0.7.15-r1140.
Reads were then assigned to MboI restriction fragments, duplicates removed, reads with a MAPQ ≥ 30 were retained, and intra restriction fragment reads removed.
The genome was divided into equally spaced, non-overlapping bins and the number of reads counted in each pair of bins gave the number of contacts, generating a Hi-C contact map.
Hi-C contact maps were normalized by matrix balancing using the KR normalization algorithm (Durand et al., 2016; Knight and Ruiz, 2012; Rao et al., 2014) using Juicer Tools v1.8.9.
Biological replicates were combined after filtering and the combined contact map KR normalized.  All subsequent analysis was performed on the combined, KR normalized contact map.
TADs were identified using the previously described Arrowhead algorithm (Durand et al., 2016; Rao et al., 2014) using Juicer Tools v1.8.9.
Loops were identified using the previously described HiCCUPs algorithm (Durand et al., 2016; Rao et al., 2014) using Juicer Tools v1.8.9.
All of the above steps were performed using the previously described Juicer pipeline (Durand et al., 2016; Rao et al., 2014) and Juicebox visualization interface (Durand et al., 2016).
Megadomain-megadomain interactions were identified using a model that accounted for enrichment relative to local background based on Poisson statistics.
Genome_build: GRCh38.p15 concatenated with dm6/BDGP Release 6 + ISO1 MT
Supplementary_files_format_and_content: *.hic file of Hi-C contacts in compressed format.  Readable by open-source Juicebox software (http://aidenlab.org/juicebox/).
Supplementary_files_format_and_content: *_TADs.bedpe file of TAD coordinates in Juicebox format.
Supplementary_files_format_and_content: *_loops.bedpe file of loop coordinates in Juicebox format.
Supplementary_files_format_and_content: *_mega-mega.bedpe file of megadomain-megadomain interactions in Juicebox format.
Supplementary_files_format_and_content: *bw

source_name: TC-797 cultured cells

growth_protocol: 293TRex-Flag-BRD4-NUT-HA cells were a kind gift from Christopher A. French (Brigham and Women’s Hospital, Boston, MA). Cells were grown in DMEM with 4.5 g/L glucose and sodium pyruvate without L-glutamine (Corning #15013CV) + 10% Fetal Bovine Serum (Atlanta Biologicals #S10350) + 1% GlutaMAX (Gibco #35050061) + 1% Penicillin-Streptomycin (Gibco #15140122) + 15 µg/mL blasticidin (Gibco #A1113903) + 100 µg/mL hygromycin (Corning #30240CR) at 37° C with 5% CO2. TC-797 cells were a kind gift from Jeffrey A. Toretsky (Georgetown University, Washington, DC). Cells were grown in DMEM with 4.5 g/L glucose and sodium pyruvate without L-glutamine (Corning #15013CV) + 10% Fetal Bovine Serum (Atlanta Biologicals #S10350) + 1% GlutaMAX (Gibco #35050061) + 1% Penicillin-Streptomycin (Gibco #15140122) at 37° C with 5% CO2. Kc167 cells were obtained from the Drosophila Genomics Resource Center (#1; Bloomington, IN). Cells were grown in CCM3 Media (HyClone #SH30062.02) at 25° C.

extract_protocol:
Human cells were mixed with Drosophila cells at a 2:1 ratio and then cells were cross-linked with 1% EM-grade paraformaldehyde.  Intact nuclei were crudely isolated using detergent lysis.  DNA was digested with MboI (prior to digestion an aliquot was saved as an input control), DNA ends filled in with biotin-14-dATP, and free DNA ends ligated together in situ. DNA-protein cross-links were reversed and the DNA then purified.
DNA sheared to a size of approximately 500 bp.  DNA was end-repaired and adaptor-ligated by following “NEBNext End Prep” and “Adaptor Ligation” in the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).  The biotinylated DNA was pulled down with streptavidin beads and PCR amplified by following "PCR Amplification" in the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Tetracycline hydrochloride (Sigma-Aldrich #T7660) was solubilized in water. 293TRex-Flag-BRD4-NUT-HA were induced to express BRD4-NUT with 1 µg/mL tetracycline for 8 hours. MZ1 (Cayman Chemical #21622) was solubilized in DMSO. Triptolide (TPL; Cayman Chemical #11973) was solubilized in DMSO. TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) or 500 nM triptolide (0.01% final DMSO) for 4 hours. For washout experiments, TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours, washed three times with PBS, and then returned to normal culture media (as described above) for 24 hours.

value: NUT carcinoma

tag: spike-in

value: Drosophila melanogaster Kc167 cells


title: CNS TH17 ATAC-seq rep1


title: GROseq_A2780cis_cisplatin


title: TU (urm1 tcd1 lys2) replicate 3


title: PBS_Rep2


title: Pt-ptc_st3_rep1_d14


title: TU (urm1 tcd1 lys2) replicate 2


title: PBS_Rep1


title: Pt-ptc_st3_rep1_d-3


title: TU (urm1 tcd1 lys2) replicate 1


title: RNAseq on siINO80#2 replicate C

description:
siINO80_2_C
processed data file:
siINO80_norm_counts.csv

value: liver cancer cell line

value: siINO80#2 (29255 Life Tech)


title: TC-797_replicate6 (HiC)


title: Pt-ptc_st5_rep1_d-3

value: late stage 5


title: TC-797_replicate5 (HiC)


title: NETs_Rep2


title: Pt-ptc_st3_rep1_d18


title: ET (elp3 tcd1 lys2) replicate 3

value: ET (elp3 tcd1 lys2)


title: ET (elp3 tcd1 lys2) replicate 4


title: RNAseq on siINO80#1 replicate C

description:
siINO80_1_C
processed data file:
siINO80_norm_counts.csv

value: siINO80#1 (s224308 Life Tech)


title: TC-797_replicate3 (HiC)


title: RNAseq on siINO80#2 replicate B

description:
siINO80_2_B
processed data file:
siINO80_norm_counts.csv


title: Pt-hh_st5_rep2_d-2

description:
HTseq_count_per_gene_aug3.txt
HTseq_count_per_gene_aug3_RPKM.txt
DEG_hh_st5.txt

value: Osaka


title: TC-797_replicate4 (HiC)


title: Pt-hh_st5_rep2_d22

value: Pt-hh pRNAi


title: RNAseq on siINO80#1 replicate B

description:
siINO80_1_B
processed data file:
siINO80_norm_counts.csv


title: ET (elp3 tcd1 lys2) replicate 2


title: RNAseq on NTG replicate C

description:
NTG_C
processed data file:
siINO80_norm_counts.csv

value: NTG (AM4611 Life Tech.)


title: Pt-hh_st3_rep2_d18

description:
HTseq_count_per_gene_aug3.txt
HTseq_count_per_gene_aug3_RPKM.txt
DEG_hh_st3.txt

value: whole embryo


title: Pt-hh_st3_rep2_d22

value: early stage 3


title: ED (elp3 deg1 lys2) replicate 4

value: ED (elp3 deg1 lys2)


title: ET (elp3 tcd1 lys2) replicate 1


title: RNAseq on NTG replicate B

description:
NTG_B
processed data file:
siINO80_norm_counts.csv


title: RNAseq on siINO80#2 replicate A

description:
siINO80_2_A
processed data file:
siINO80_norm_counts.csv


title: Pt-hh_st5_rep1_d20


title: RNAseq on siINO80#1 replicate A

description:
siINO80_1_A
processed data file:
siINO80_norm_counts.csv


title: TC-797_Triptolide_replicate1 (HiC)


title: ED (elp3 deg1 lys2) replicate 2


title: Pt-hh_st5_rep2_d18


title: Pt-hh_st5_rep1_d16


title: RNAseq on NTG replicate A

description:
NTG_A
processed data file:
siINO80_norm_counts.csv


title: Pt-hh_st5_rep1_d-2

value: untreated


title: YY1_Huh7_B

description:
processed data file:
YY1_Huh7_peaks.narrowPeak.filtered.fixed.txt

data_processing:
Align bowtie2 --sensitive
samtools rmdup
samtools merge
bamCoverage --binSize 10 --extendReads 150 --normalizeUsingRPKM --centerReads (For drug treated samples additionally --scaleFactor was used with the normalization factor derived as 1/#of tags mapped against reference drosophila genome in millions - file dtags_agg.csv
macs2 callpeak -q 0.001 --keep-dup all --shift 37 --nomodel --extsize 147 -g hs
peaks were filtered against blacklist (ENCODE) using bedtools and recursviely merged with other peaks within 500bp to yield final peak calls
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files = Reads per million (no treatment samples) or reference normalized reads per million (DMSO/EPZ64-38 treated) signal tracks
Supplementary_files_format_and_content: bed files = peaks called from merged replicates of bam files for INO80 subunits in Huh7 and HepG2
Supplementary_files_format_and_content: raw files ending in rmdup.dtags.bam  were aligned against dm3 to count the total number of non-duplicate uniquely mapping drosohpila reads in each IP sample and used for normalization - count values are in dtags_agg.csv

growth_protocol: Cells were grown in DMEM + 10% FBS + penicillin + streptomycin at 37 degrees in 5% C02. Experiments were performed on cells less than 10 passages.

extract_protocol:
Cells were fixed in 0.3% formaldehyde for 30 minutes at 4 degrees prior to processing for ChIP using protocol from Raab et al 2015.
Kapa Hyperprep kit using Illumina Truseq barcoded adapters

treatment_protocol: In experiments with drug treamtne (EPZ-6438 or DMSO at 1.0uM ) was added to cells for 120 hours prior to fixing for ChIP.

tag: chip antibody

tag: chip antibody vendor

value: santa cruz

tag: chip antibody cat. #

tag: lot


title: YY1_Huh7_A


title: DU (urm1 deg1 lys2) replicate 2

value: DU (urm1 deg1 lys2)


title: RUVBL2_Huh7_B

description:
processed data file:
RUVBL2_Huh7_peaks.narrowPeak.filtered.fixed.txt

value: bethyl


title: DU (urm1 deg1 lys2) replicate 3


title: Pt-hh_st3_rep1_d20


title: DU (urm1 deg1 lys2) replicate 1


title: RUVBL2_Huh7_A


title: gfp_st6_rep5_d20

description:
HTseq_count_per_gene_aug3.txt
HTseq_count_per_gene_aug3_RPKM.txt

value: gfp pRNAi

value: early stage 6


title: Pt-hh_st3_rep1_d16


title: ED (elp3 deg1 lys2) replicate 3


title: Pt-hh_st3_rep2_d-2


title: RUVBL2_HepG2_B

description:
processed data file:
RUVBL2_HepG2_peaks.narrowPeak.filtered.fixed.txt

value: liver cancer cell line


title: RUVBL2_HepG2_A


title: gfp_st5_rep5_d20


title: gfp_st6_rep5_d-2


title: 292CON

city: Boston

first: Annie

last: Kathuria

state: MA

address: 185 cambridge street

institute: Mass Gen Hospital

data_processing:
Analysis was performed by DNA Link USA, Inc.
Sequence quality was assessed using FASTQC
Sequences were trimmed using cutadapt v 1.18, paired-end reads mode -u 7 -u -3 -U 7 -U -3
Trimmed reads were aligned to the reference genome using TopHat v2.1.1 (--no-coverage-search, -G refseqhg38p9.gtf)
Bam files were merged using samptools v 1.9 for samples with techincal replicates.
FPKM calulcation done using cufflinks v2.2.1 using annotation from RefSeq assembly hg38 p9 which was modified according UCSC-style-name
Pairwise differential expression analysis was performed using cuffdiff v2.2.1
Genome_build: Homo sapience hg38 (UCSC tophat version as downloaded May 2017)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: tracking_id, gene_id, gene_short_name, locus, FPKM for each sample

source_name: cerebral organoids

extract_protocol:
Tissue was dissolved in Trizol and RNA was extracted using qiagen rneasy kit
RNA libraries were prepared for sequencing using Truseq Stranded Total RNA H/M/R

tag: diagnosis

value: healthy control

value: Human iPSC derived cerebral organoids

tag: state

value: 6 months of differention


title: RUVBL1_HepG2_B

description:
processed data file:
RUVBL1_HepG2_peaks.narrowPeak.filtered.fixed.txt

tag: cell line

tag: cell type


title: 56CON


title: DU (urm1 deg1 lys2) replicate 4


title: RUVBL1_HepG2_A


title: 22CON.2


title: gfp_st5_rep5_d-2

tag: isolate

tag: treatment

value: late stage 5


title: Pt-hh_st3_rep1_d-2

value: Osaka

tag: tissue

tag: developmental stage


title: MCRS1_Huh7_B

description:
processed data file:
MCRS1_Huh7_peaks.narrowPeak.filtered.fixed.txt

value: protein-tech


title: gfp_st6_rep4_d-3


title: 22CON.1


title: MCRS1_Huh7_A


title: 27CON


title: Control-1

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human V2 GE 8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: DMSO treatment

label_protocol: 0.2 μg of total RNA was amplified by a Agilent Low Input Quick-Amp WT Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: Human A549 lung carcinoma cells were purchased from the American Type Culture Collection. Briefly, cells were maintained in Dulbecco’s Modiﬁed Eagle’s Medium conditioned with 10% (v/v) fetal bovine serum in humidified air at 37°C with 5% carbon dioxide and routinely passaged when 85% to 90% conﬂuent.

extract_protocol: To isolate total RNA from three independent exponential growth phase A549 cells and extracted using the Direct-zol ™ RNA MiniPrep kit (zymo research) according to the manufacturer's protocol. The samples were quantified and assessed for quality with a Nanodrop ND-1000 ultraviolet spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), respectively.

treatment_protocol: Citreoviridin (Santa Cruz Biotechnology, CA, USA) solution was solubilized in DMSO (AppliChem, Darmstadt, Germany) at 40 mmol/L. 1×105 A549 cells were seeded in 6-well plate and allowed to attach for 24 hours. The cells were refreshed with medium containing 5.76 μmol/L citreoviridin or 0.1% DMSO as control for 48 hours. All the procedures including drug preparation and treatment were carried out in the dark.

value: DMSO


title: 135CON.2


title: Control-2


title: gfp_st5_rep4_d19

value: whole embryo


title: fLP3_loop_RNA1_IPTG

city: Los Angeles

first: Guillaume

last: Urtecho

state: CA

address: 607 Charles E. Young Drive

department: Molecular Biology

institute: University of California, Los Angeles

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the essQ-cspB intergenic region. This is the 1st biological replicate.
fLP3.loop_MOPS_glu_expression.txt.gz

data_processing:
Counts for each unique barcode in the census files were complete in Unix as follows: Raw sequences were extracted from each fastq file and the first 20 bp (corresponding to the barcode) was extracted. This sequence was reverse complemented and the entire file was sorted before counting the number of counts of each barcode. Counts were normalized as a proportion of total reads per sample and all samples aggregated together in R.
Barcode mapping was completed as follows: Demultiplexed reads were paired using Paired-End reAd mergeR (PEAR v0.9.1, default settings). Custom python code was used to identify reads corresponding to perfectly synthesized promoters and their respective barcodes. Briefly, this code searched the first 150 bp of each read for perfect matches to library variants. For reads with perfect matches, the last 20 bp of each read (the barcode) was extracted and a list was compiled mapping each barcode to the most frequently associated library variant. A single barcode appears many times in the sequencing data, and we took steps to ensure a barcode consistently mapped to the same variant. We required that all variants mapped to a single barcode be within an edit distance (Levenshtein distance) of 5 from one another (five single bp changes between the two sequences). We determined this number by bootstrapping a distribution of the edit distance between any two random sequences in our variant library, and setting the threshold to the first percentile (1%) of this bootstrapped distribution. Additionally, each barcode had to appear at least three times in order to be considered for downstream analysis. This step hopefully eliminates barcodes which contained sequencing errors.
Promoter variant expression was calculated in R by assigning barcodes to their mapped promoter and, for each promoter, dividing the sum of all RNA counts for all of its barcodes by the sum of all DNA counts for all of its barcodes.

organism: Escherichia coli

source_name: Escherichia coli

extract_protocol: All libraries are constructed using two-step PCR of extraced molecule (Genomic DNA, cDNA, or Plasmid DNA). Initial PCR adds custom sequencing primers and the second PCR adds flow cell adapters for Illumina systems.

tag: strain

tag: growth medium

value: MOPS EZ-Rich + .2% Glucose + 1 mM IPTG

tag: extraction protocol

value: Qiagen RNeasy Midi Kit

tag: molecule

value: Total RNA


title: fLP3_loop_RNA2_IPTG

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the essQ-cspB intergenic region. This is the 2nd biological replicate.
fLP3.loop_MOPS_glu_expression.txt.gz


title: MCRS1_HepG2_B

description:
processed data file:
MCRS1_HepG2_peaks.narrowPeak.filtered.fixed.txt


title: ED (elp3 deg1 lys2) replicate 1

tag: genotype

value: ED (elp3 deg1 lys2)


title: Treatment-3

source_name: Citreoviridin treatment

value: Citreoviridin (Santa Cruz Biotechnology, CA, USA)


title: 135CON.1


title: gfp_st5_rep3_d21


title: fLP3_loop_RNA2

value: MOPS EZ-Rich + .2% Glucose


title: fLP3_loop_RNA1


title: 7_RAW 264.7 + Inulin (+LPS)

description:
Inulin 1
Gene expression data from cultured RAW 264.7 macrophages.

source_name: Murine RAW 264.7 macrophage cultured with Inulin (+LPS)

value: macrophage

value: Inulin (+LPS)


title: 51CON


title: Input_Huh7_B

value: liver cancer cell line

tag: chip antibody

value: none (input)


title: MCRS1_HepG2_A

tag: chip antibody vendor


title: Input_Huh7_A


title: gfp_st6_rep4_d19

value: gfp pRNAi

value: early stage 6


title: Treatment-1


title: 300CON.2

value: healthy control

value: Human iPSC derived cerebral organoids

value: 6 months of differention


title: Treatment-2


title: Control-3

value: DMSO


title: fLP3_loop_DNA1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the essQ-cspB intergenic region. This is the 1st biological replicate.
fLP3.loop_MOPS_glu_expression.txt.gz

value: Qiagen Puregene Yeast/Bact. Kit 2

value: Genomic DNA


title: gfp_st3_rep3_d21

value: Osaka

value: whole embryo

value: early stage 3


title: gfp_st3_rep3_d-1

value: untreated


title: gfp_st5_rep4_d-3

value: late stage 5


title: 300CON.1


title: TC-797_washout_replicate2 (HiC)

data_processing:
Reads were aligned to concatenated hg38/Genome Reference Consortium Human Reference 38 Patch 15 (GRCh38.p15) and dm6/BDGP Release 6 + ISO1 MT assemblies of the human and Drosophila melanogaster genomes, respectively, using BWA-MEM v0.7.15-r1140.
Reads were then assigned to MboI restriction fragments, duplicates removed, reads with a MAPQ ≥ 30 were retained, and intra restriction fragment reads removed.
The genome was divided into equally spaced, non-overlapping bins and the number of reads counted in each pair of bins gave the number of contacts, generating a Hi-C contact map.
Hi-C contact maps were normalized by matrix balancing using the KR normalization algorithm (Durand et al., 2016; Knight and Ruiz, 2012; Rao et al., 2014) using Juicer Tools v1.8.9.
Biological replicates were combined after filtering and the combined contact map KR normalized.  All subsequent analysis was performed on the combined, KR normalized contact map.
TADs were identified using the previously described Arrowhead algorithm (Durand et al., 2016; Rao et al., 2014) using Juicer Tools v1.8.9.
Loops were identified using the previously described HiCCUPs algorithm (Durand et al., 2016; Rao et al., 2014) using Juicer Tools v1.8.9.
All of the above steps were performed using the previously described Juicer pipeline (Durand et al., 2016; Rao et al., 2014) and Juicebox visualization interface (Durand et al., 2016).
Megadomain-megadomain interactions were identified using a model that accounted for enrichment relative to local background based on Poisson statistics.
Genome_build: GRCh38.p15 concatenated with dm6/BDGP Release 6 + ISO1 MT
Supplementary_files_format_and_content: *.hic file of Hi-C contacts in compressed format.  Readable by open-source Juicebox software (http://aidenlab.org/juicebox/).
Supplementary_files_format_and_content: *_TADs.bedpe file of TAD coordinates in Juicebox format.
Supplementary_files_format_and_content: *_loops.bedpe file of loop coordinates in Juicebox format.
Supplementary_files_format_and_content: *_mega-mega.bedpe file of megadomain-megadomain interactions in Juicebox format.

treatment_protocol: Tetracycline hydrochloride (Sigma-Aldrich #T7660) was solubilized in water. 293TRex-Flag-BRD4-NUT-HA were induced to express BRD4-NUT with 1 µg/mL tetracycline for 8 hours. MZ1 (Cayman Chemical #21622) was solubilized in DMSO.  TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours. For washout experiments, TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours, washed three times with PBS, and then returned to normal culture media (as described above) for 24 hours.

value: NUT carcinoma

tag: spike-in

value: Drosophila melanogaster Kc167 cells


title: gfp_st5_rep3_d-1


title: 15CON


title: Input_HepG2_A

value: liver cancer cell line


title: INO80_Huh7_B

description:
processed data file:
INO80_Huh7_peaks.narrowPeak.filtered.fixed.txt

value: abcam

tag: chip antibody cat. #

tag: lot


title: ZK819_star-B2_S22_R1_001

city: Bengaluru

first: Aswin

middle: Sai Narain

last: Seshasayee

state: Karnataka

address: GKVK campus Bellary road

country: India

institute: National Centre for Biological Sciences

data_processing:
Illumina HiSeq-2500 for sequencing
BWA (0.6.2-r126) was used for indexing the reference genome and aligning the reads (q >= 20)
SAMTOOLS (1.3; using htslib 1.3) o filter out multiply mapped reads
BEDTOOLS(v2.25.0) was used to calculate the read counts per gene
Normalisation and differential gene expression analysis was done using EdgeR (genes with atleast 5 reads were selected for each comparative analysis) using method proposed by Smyth et al (F1000, 2016)
Genome_build: Reference genome used : Escherichia coli str K12 substr W3110, accession number : NC_007779.1
Supplementary_files_format_and_content: tab delimited .txt files containing raw reads count (raw_coverage.txt) and normalised count data (Normalised_CPM_allstr.txt)and parison of genes’ expression for sample pairs
Supplementary_files_format_and_content: Normalised_CPM_allstr.txt tab delimited .txt files containing raw reads count
Supplementary_files_format_and_content: Diffreg_delrpoSmut_delrpoS.txt tab delimited .txt files containing differential gene expression comparison between rpoC(A494V) mutant(Samples 3,4) and rpoCWT strains (samples 1,2) in rpoS knocked out background of E.coli ZK819
Supplementary_files_format_and_content: Diffreg_LCVmut_LCV.txt tab delimited .txt files containing differential gene expression comparison between rpoC(A494V) mutant(Samples 7,8) and rpoCWT strains (samples 5, 6) in LCV background
Supplementary_files_format_and_content: Diffreg_SCV_scv_plus.txt tab delimited .txt files containing differential gene expression comparison between rpoC(A494V) mutant(Samples 9,10) and rpoCWT strains (samples 11, 12) in SCV background
Supplementary_files_format_and_content: Diffreg_ZK126mut_ZK126.txt tab delimited .txt files containing differential gene expression comparison between rpoC(A494V) mutant(Samples 15, 16) and rpoCWT strains (samples 13, 14) in ZK126 background
Supplementary_files_format_and_content: Diffreg_ZK819mut_ZK819.txt tab delimited .txt files containing differential gene expression comparison between rpoC(A494V) mutant(Samples 19, 20) and rpoCWT strains (samples 17, 18) in ZK819 background

source_name: bacteria grown overnight in LB

growth_protocol: RpoCWt and rpoC(A494V) mutant strains in different genetic backgrounds of E.coli was grown in rich media (LB) till stationary phase at 37 degrees Celcius at 180 rpm.

extract_protocol:
Total RNA was extracted from bacteria with TRIZOL extraction protocol and subjected to purification and removal of genomic DNA contamination.  MRNA enrichment was performed with the MicrobeExpress kit(AMBION) to obtain enriched mRNA pool for library preparation.
Fragmentation and random priming of samples was done for 10 nanograms of mRNA for each sample. First and second strand cDNA synthesis was carried out using TruSeq strand specific RNA library prep kit ( Illumina) according to manufacturer’s protocol. Equimolar quantities of all libraries were pooled and sequenced in a highthroughput run on the Illumina HiSeq 2500 sequencer using 1X50 bp single-end reads.

tag: genotype/variation

value: Evolutionary ancestor of SCV, Escherichia coli ZK819, isolated on 10 day in rpolonged stationary phase, natively carrying rpoS819 allele alongwith rpoCA494V mutation


title: ZK819_star-B1_S21_R1_001


title: gfp_st7_rep2_d15

value: gfp pRNAi

value: late stage 7


title: TC-797_MZ1_replicate2 (HiC)

tag: cell line


title: gfp_st7_rep2_d20


title: gfp_st7_rep2_d-1


title: INO80_Huh7_A

tag: cell type


title: ZK819-B2_S20_R1_001

value: Evolutionary ancestor of SCV, Escherichia coli ZK819, isolated on 10 day in rpolonged stationary phase, natively carrying rpoS819 allele


title: TC-797_DMSO_replicate2 (HiC)


title: gfp_st5_rep2_d20

tag: isolate


title: ZK819-B1_S19_R1_001


title: Input_HepG2_B

value: none (input)


title: INO80_HepG2_B

description:
processed data file:
INO80_HepG2_peaks.narrowPeak.filtered.fixed.txt


title: fLP3_loop_DNA2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the essQ-cspB intergenic region. This is the 2nd biological replicate.
fLP3.loop_MOPS_glu_expression.txt.gz

value: MOPS EZ-Rich + .2% Glucose + 1 mM IPTG


title: INO80_HepG2_C


title: ZK126_star-B2_S18_R1_001

value: Parent strain of ZK819, E.coli ZK126 carrying wild type rpoS allele and rpoCA494V mutation


title: gDNA_control

city: London

first: Kathrin

last: Witmer

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description:
processed data:
featurecounts_ABS_FG_MG_OOK_sense_antisense.xlsx

data_processing:
for ChIP: RTA v2 software for base calling and bcl2fastq v2.16.0.10 conversion software for fastq conversion
for ChIP: Data were mapped with BWA samse (Version: 0.7.12-r1039) against the PbANKA_v3
for ChIP:Sam files were converted to bam files and mapped reads were filtered to mapping quality ≥15 (SAM tools v1.2). Only uniquely mapped reads were used for further analysis.
bigwig files were created as follows: bam filed containing mapped reads from each ChIP was normalised against its input using bamcompare in DeepTools2 (v2.5.0) (Ramirez et al., 2016). For PbHP1, the default settings were used with the following changes: 100bp bin size, 0.01 pseudocount and 1000bp smoothing. For H3K9ac, default settings were using with the following changes: bin size 50bp, 0.01 pseudocount, 100bp smoothing.
For RNAseq reads were aligned separately for each lane to PbANKA genome v3 using HiSat2 with default settings (v 2.0.5.2; --max intron size 5000; --fr) (Kim et al., 2015). Each replicate was split over four lanes, and mapped reads were pooled into one bam file per condition and replicate.
Featurecounts was performed  counting fragments instead of reads (-p) (Galaxy Version 1.4.6.p5) with strand-specific read counting and the following settings: only allow fragments with both reads aligned (TRUE); orientation of the two reads from same pair (fr); exclude chimeric fragments (TRUE); allow read to contribute to multiple features (FALSE); minimum mapping quality per read (12); minimum overlap (1); only count primary alignments (FALSE); ignore reads marked as dulicate (TRUE); ingore unspliced alignments (FALSE).
Deseq2 was performed (Galaxy Version 2.11.39) using default settings. Count data from featurecount was used as input. Only mRNA producing genes located on chromosomes 1- 14 were included.
Genome_build: PbANKA_v3
Supplementary_files_format_and_content: bigwig log2 ratio files show the coverage as log2 ratio of ChIP over Input using bam files. For PbHP1, the default settings were used with the following changes: 100bp bin size, 0.01 pseudocount and 1000bp smoothing.

organism: Plasmodium berghei

source_name: gDNA

extract_protocol:
Parasite/RBC pellet was lysed with 10ml RBC-lysis buffer (150mM NH4Cl, 10mM KHCO3, 1mM EDTA) for 20min on ice. Parasite-pellets were washed once in ice-cold PBS and lysed in buffer A (500mM NaAc, 100mM NaCl, 1mM EDTA, pH5.2) and 3% SDS. DNA was extracted using Phenol:chloroform and sheared to 150bp fragments.
Stranded sequencing libraries were prepared using the RNA HyperPrep Kit (KAPA) following manufacturer’s protocol with the exception of the amplification step set to 60⁰C. The RNA library was sequenced in 43bp paired-end reads on a NextSeq sequencer and each sample was split over four non-independent lanes.

value: asexual blood stage

tag: strain/isolate


title: INO80_HepG2_A


title: ZK126_star-B1_S17_R1_001


title: gfp_st5_rep2_d-1

value: Osaka

tag: tissue

tag: treatment


title: 507_RNA_rep3

description:
processed data:
Deseq2_FG_over_OOK.xlsx
featurecounts_ABS_FG_MG_OOK_sense_antisense.xlsx

source_name: OOK

extract_protocol:
Ookinete were cultured in vitro as described (Rodríguez et al., 2002). Briefly, mice were pretreated by intra peritoneal injection of 0.2 ml phenylhydrazine (6 mg/ml in PBS) to stimulate reticulocyte formation two days prior to infection with parasites. Gametocytes-enriched blood was harvested via heart puncture and blood was immediately resuspended in 30ml of ookinete medium (RPMI-HEPES complemented with 100uM xanthurenic acid, 200 uM hypoxanthine and 10% BSA, pH7.4) and incubated at 21⁰C for 24 hours. After 24 hours, ookinetes were magnet-purified using 1ul monoclonal anti-P28 antibody 13.1 (Winger et al., 1988) coupled to 10ul magnetic beads (Dynabeads™ M-280 Sheep Anti-Mouse IgG).
RNA was extracted using the Direct-zol™ RNA MiniPrep kit (Zymo). Residual gDNA was digested with the TurboDNA-free kit (Ambion). Stranded RNA sequencing libraries were prepared using the RNA HyperPrep Kit (KAPA) following manufacturer’s protocol with the exception of the amplification step set to 60⁰C. The RNA library was sequenced in 43bp paired-end reads on a NextSeq sequencer and each sample was split over four non-independent lanes.

tag: developmental stage

value: ookinete


title: 507_RNA_rep2


title: 507_RNA_rep1


title: ZK126-B2_S16_R1_001

value: Parent strain of ZK819, E.coli ZK126 carrying wild type rpoS allele


title: gfp_st3_rep2_d15

value: whole embryo

value: early stage 3


title: ATACseq on NTG replicate C

description:
processed data file:
NTG_peaks.filtered.narrowPeak
NTG_C

data_processing:
trim-galore (0.4.1) --nextera --paired
bowtie2 -X 2000
sed '/chrM/d'
samtools view -u -q 20
macs/2.1.0 macs2 callpeak --keep-dup all -g hs --call-summits
deeptools/2.2.4 bamCoverage --binSize 1 --normalizeUsingRPKM --Mnase --minFragmentLength 50 --maxFragmentLength 200
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files genreated using Deeptools (.bw) peak calls using Macs2 (.narrowPeak)

growth_protocol: Cells were grown in DMEM + 10% FBS + penicillin + streptomycin at 37 degrees in 5% C02

extract_protocol:
ATAC-seq was carried out as described (Buenrostro et al 2013)
ATAC-seq libraries were created using protocol from Buenrostro et al 2013, and processed using Nextera adapter sequences for Illumina sequencing

treatment_protocol: Cells were treated with indicated siRNA at 50nM for 72 hours using RNAimax transfection reagent as per manufacturers instructions

tag: sirna

value: NTG (AM4611 Life Tech.)


title: ATACseq on siINO80#2 replicate B

description:
processed data file:
INO80_2_peaks.filtered.narrowPeak
siINO80_2_B

value: siINO80#2 (29255 Life Tech)


title: SCV_rpoCWT-B2_S4_R1_001

value: Small colony variant(SCV) isolated from deep stationary phase natively carrying extended rpoS+92 allele and wild type rpoC allele


title: ATACseq on siINO80#1 replicate C

description:
processed data file:
INO80_1_peaks.filtered.narrowPeak
siINO80_1_C

value: liver cancer cell line

value: siINO80#1 (s224308 Life Tech)


title: gfp_st3_rep2_d20

description:
HTseq_count_per_gene_aug3.txt
HTseq_count_per_gene_aug3_RPKM.txt

data_processing:
Base call and quality scoring were performed by the Real Time Analysis software application during Illumina's sequencing runs.
Sequence reads were trimmed for adaptor and primer sequences and low-quality sequences using the CLC Genomics Workbench 7.0.4 (Qiagen) with the following parameter settings for the quality trim: trim using quality scores, limit=0.05; trim ambiguous nucleotides, maximum number of ambiguities=2; filter on length, discard reads below length=50. Trimmed reads were then aligned to Ptep_1.0 genome assembly using the BLAT algorithm version 34 in the DDBJ Read Annotation Pipeline with default settings.
The output alignments were filtered based on quality, coverage, and uniqueness using a perl script filterPSL.pl available from the AUGUSTUS 3.0.1 scripts folder. The parameter settings were as follows: minimum coverage, 60%; minimum percent identity, 90%; unique threshold, 0.96. The filtered alignments were converted into sam and psl files with a custom perl script.
Using the sam files, abundance of mRNAs against AUGUSTUS gene models (Schwager et al., 2017, BMC Biol. 15, 62) was calculated with htseq-count v. 0.5.4p5 in -s reverse, -m union settings and was normalized in Reads Per Kilobase of exon per Million reads (RPKM).
Based on the abundance of mRNAs against AUGUSTUS gene models, differentially expressed genes (DEGs) were estimated using EdgeR.
The alignments in the psl format were converted into wig files using a script aln2wig available from the AUGUSTUS 3.0.1 scripts folder, and the wig files were converted into bigWig files using the program wigToBigWig available from the ucsc directory.
Genome_build: Ptep_1.0
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for gene models and the features of the gene models.
Supplementary_files_format_and_content: tab-delimited text file includes logFC and FDR values for the identified DEGs.
Supplementary_files_format_and_content: wig files ; Scores represent normalized read coverage (per 10 million reads).
Supplementary_files_format_and_content: bigWig files ; Scores represent normalized read coverage (per 10 million reads).

value: gfp pRNAi


title: GFP_RNA_rep3

description:
processed data:
Deseq2_FG_over_MG.xlsx
featurecounts_ABS_FG_MG_OOK_sense_antisense.xlsx

source_name: MG

extract_protocol:
The method for the purification of gametocytes was modified from (Beetsma et al., 1998). Briefly, mice were pretreated by intra peritoneal injection of 0.2 ml phenylhydrazine (6 mg/ml in PBS) to stimulate reticulocyte formation two days prior to infection with parasites. Gametocytes were harvested via heart puncture and blood was immediate resuspended in 4⁰C coelenterazine loading buffer (CLB) (1x PBS, 20 mM HEPES, 20 mM glucose, 4 mM sodium bicarbonate, 1 mM EDTA, 0.1% BSA in PBS, pH 7.24–7.31) and magnet-purified using D Columns on a SuperMACS™ II Separator (Miltenyi Biotec). Magnet-purified parasites were resuspended in FACS buffer (PBS with 2mM HEPES, 2mM glucose, 0.4mM NaHCO3, 0.01% BSA, 2.5mM EDTA). Male and female gametocytes were sorted according to color (GFP for males and RFP for females) on a FACSAria III with a 100uM nozzle at 4⁰C. Purified gametocyte pellets were lysed in 500ul TRIzol (Invitrogen) and stored at -80⁰C. Parasites were then pooled and lysed in 500ul TRIzol (Invitrogen) and stored at -80⁰C.
RNA was extracted using the Direct-zol™ RNA MiniPrep kit (Zymo). Residual gDNA was digested with the TurboDNA-free kit (Ambion). Stranded RNA sequencing libraries were prepared using the RNA HyperPrep Kit (KAPA) following manufacturer’s protocol with the exception of the amplification step set to 60⁰C. The RNA library was sequenced in 43bp paired-end reads on a NextSeq sequencer and each sample was split over four non-independent lanes.

value: male gametocyte

value: 820cl1m1cl1 (Ponzi et al., 2009)


title: GFP_RNA_rep2


title: ZK126-B1_S15_R1_001


title: gfp_st3_rep2_d-1

value: untreated


title: SCV_rpoCWT-B1_S3_R1_001


title: gfp_st7_rep1_d22

value: late stage 7


title: GFP_RNA_rep1


title: ATACseq on NTG replicate B

description:
processed data file:
NTG_peaks.filtered.narrowPeak
NTG_B


title: gfp_st7_rep1_d17


title: RFP_RNA_rep3

description:
processed data:
Deseq2_FG_over_ABS.xlsx
Deseq2_FG_over_MG.xlsx
Deseq2_FG_over_OOK.xlsx
featurecounts_ABS_FG_MG_OOK_sense_antisense.xlsx

source_name: FG

value: female gametocyte


title: gfp_st5_rep2_d15

value: late stage 5


title: SCV_B2_S6_R1_001

value: Small colony variant(SCV) isolated from deep stationary phase natively carrying extended rpoS+92 allele and rpoCA494V mutation


title: ATACseq on siINO80#1 replicate B

description:
processed data file:
INO80_1_peaks.filtered.narrowPeak
siINO80_1_B


title: gfp_st7_rep1_d13

value: Osaka


title: ATACseq on siINO80#2 replicate A

description:
processed data file:
INO80_2_peaks.filtered.narrowPeak
siINO80_2_A


title: ATACseq on siINO80#2 replicate C

description:
processed data file:
INO80_2_peaks.filtered.narrowPeak
siINO80_2_C


title: RFP_RNA_rep2


title: LCV_star_B2_S24_R1_001

value: Evolutionary co-exisitng strain (LCV), carrying wild type rpoS allele and rpoCA494V mutation


title: SCV_B1_S5_R1_001


title: gfp_st7_rep1_d-2

value: whole embryo


title: ATACseq on siINO80#1 replicate A

description:
processed data file:
INO80_1_peaks.filtered.narrowPeak
siINO80_1_A


title: RFP_RNA_rep1


title: 233_RNA_rep3

description:
processed data:
Deseq2_FG_over_ABS.xlsx
featurecounts_ABS_FG_MG_OOK_sense_antisense.xlsx

source_name: ABS

extract_protocol:
Asexual blood stage parasites were harvested via heart puncture and resuspended in 15ml RPMI-HEPES and passed through a Plasmodipur filter (Europroxima) to remove white blood cells. Parasite/RBC pellet was lysed with 10ml RBC-lysis buffer (150mM NH4Cl, 10mM KHCO3, 1mM EDTA) for 20min on ice. Parasite-pellets were washed once in ice-cold PBS and lysed in 500ul TRIzol (Invitrogen) and stored at -80⁰C.
RNA was extracted using the Direct-zol™ RNA MiniPrep kit (Zymo). Residual gDNA was digested with the TurboDNA-free kit (Ambion). Stranded RNA sequencing libraries were prepared using the RNA HyperPrep Kit (KAPA) following manufacturer’s protocol with the exception of the amplification step set to 60⁰C. The RNA library was sequenced in 43bp paired-end reads on a NextSeq sequencer and each sample was split over four non-independent lanes.

value: asexual blood stage


title: LCV-B2_S2_R1_001

value: Evolutionary co-exisitng strain (LCV), carrying wild type rpoS allele


title: ATACseq on NTG replicate A

description:
processed data file:
NTG_peaks.filtered.narrowPeak
NTG_A

value: NTG (AM4611 Life Tech.)


title: LCV_star_B1_S23_R1_001


title: gfp_st5_rep1_d17

extract_protocol:
Poly(A) mRNA was extracted using a QuickPrep Micro mRNA purification kit (GE Healthcare) and a Dynabeads mRNA DIRECT Kit (Ambion) from 50-120 embryos.
mRNA was fragmented using the NEBNext RNase III RNA Fragmentation Module (New England BioLabs). Sequencing libraries were constructed from fragmented RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, New England BioLabs).


title: gfp_st5_rep1_d13


title: gfp_st5_rep1_d22


title: gfp_st5_rep1_d-2


title: 233_RNA_rep1


title: LCV-B1_S1_R1_001


title: 507_H3K9ac

description:
processed data:
507_H3K9ac.bigwig

extract_protocol:
Ookinete were cultured in vitro as described (Rodríguez et al., 2002). Briefly, mice were pretreated by intra peritoneal injection of 0.2 ml phenylhydrazine (6 mg/ml in PBS) to stimulate reticulocyte formation two days prior to infection with parasites. Gametocytes-enriched blood was harvested via heart puncture and blood was immediately resuspended in 30ml of ookinete medium (RPMI-HEPES complemented with 100uM xanthurenic acid, 200 uM hypoxanthine and 10% BSA, pH7.4) and incubated at 21⁰C for 24 hours. After 24 hours, ookinetes were magnet-purified using 1ul monoclonal anti-P28 antibody 13.1 (Winger et al., 1988) coupled to 10ul magnetic beads (Dynabeads™ M-280 Sheep Anti-Mouse IgG). Purified ookinetes were crosslinked in 1% formaldehyde for 10 minutes at 37˚C, quenched with Glycine to an end concentration of 0.125M. Purified ookinetes pellets were lysed in 150ul sonication buffer and chromatin was prepared as above.
For each sequencing library up to 10 ng of ChIP or input DNA were end-repaired, extended with 30 A-overhangs and ligated to barcoded NextFlex adapters (Bio Scientific) as described previously (Hoeijmakers et al., 2011). Libraries were amplified (98⁰C for 2 min; four cycles 98⁰C for 20 sec, 62⁰C for 3 min; 62⁰C for 5 min) using KAPA HiFi HotStart ready mix (KAPA Biosystems) and NextFlex primer mix (Bio Scientific) as described (Kensche et al., 2016). 225-325 bp fragments (including the 125 bp NextFlex adapter) were size- selected using a 2% E-Gel Size Select agarose gel (Thermo Fisher Scientific) and amplified by PCR for ten (asexual blood stages and ookinetes) or eleven (female and male gametocytes) cycles under the same condition as described above. Library purification and removal of adapter dimers was performed with Agencourt AMPure XP beads in a 1:1 library:beads ratio (Beckman Coulter). ChIP-seq libraries were sequenced for 75 bp single-end reads using the NextSeq 500/550 High Output v2 kit (Illumina) on the Illumina NextSeq 500 system.

value: ookinete

value: α-H3K9ac (Diagenode pAb-004-050)


title: 507_HP1

description:
processed data:
507_HP1_bin100_smooth1000.bigwig

value: α-PbHP1 (Fraschka et al, 2018)


title: delrpos-rpoc_star_B2_S9_R1_001

value: E.coli ZK819 carrying rpoCA494V mutation and lacking rpoS gene grown overnight in LB


title: delrpos-rpoc_star_B1_S8_R1_001


title: gfp_st3_rep1_d22

value: gfp pRNAi

value: early stage 3


title: 2018-1651_30

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

data_processing:
Adaptor removing and quality trimming was conducted using the TrimGalore 0.4.2 wrapper tool and default parameters. Library quality was investigated using fastQC imbedded in the TrimGalore wrapper (https://github.com/FelixKrueger/TrimGalore)
Mapping was counducted using HiSat2 software.
Read counts were generated using FeatureCounts
Read counst were filtered and normalized using the DESeq2 software.
Genome_build: Labrus_bergylta.BallGen_V1.95, 11/25/2018
Supplementary_files_format_and_content: Normalized read counts (FPKM) from all samples

organism: Labrus bergylta

source_name: Intestinal samples from the anterior bulbus

growth_protocol: Eviscerated intestines (5 – 9 cm length) were immediately immersed in Ringer’s solution according to Rønnestad et al. (2000) with some modifications (in mM: NaCl, 129; KCl, 2.5; MgCl2, 0.47; CaCl2, 1.5; NaHCO3, 20.2; and NaH2PO4, 0.42). The prepared intestines were rapidly mounted in individual glass tubes containing 25 mL of Ringer’s solution at 14oC, aerated with 95% O2 and 5% CO2. The fed intestines were carefully stretched out longitudinally with the oral opening closed and the anus open inside the tube and incubated for one hour.

extract_protocol:
Total RNA was extracted and treated BioRobot® EZ1 and RNA Tissue Mini Kit (Qiagen, Hilden, Germany) as previously described (Le et al. 2019) . RNA quality and integrity were validated using a NanoDrop ND-1000 UV–vis Spectrophotometer (NanoDrop Technologies, Wilmington, USA) and Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, USA) respectively. All samples had 260/230 and 260/280 ratios above 2.0 and 2.2 respectively. The average RNA integrity number (RIN) of all samples was 7.9 ± 0.7
DNA libraries were prepared as using 90 ng total RNA input to the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturers instrucitons. For multiplexing, standard Illumina adaptors were used.
One library was made for each individual RNA sample. The libraries were sequenced using the NextSeq Illumina platform according to manufacturer instructions, generating single end 75bp read libraries with an average library size of 25 ± 6 million reads.

treatment_protocol: The intestines were inserted with a bolus of one of the five diets (IL, HL, IP, HP, and CL were described in 2.1 Nutrient bolus) or one plastic bead (2 – 3 mm diameter and 20 – 30 mg weight) to mimic a meal of 0.1 % body weight

tag: Sex

value: Female

value: Empty


title: delrpoS-B2_S7_R1_001

value: E.coli ZK819 lacking rpoS gene grown overnight in LB


title: 2018-1651_31

value: Intestinal samples from the anterior bulbus

value: Cellulos


title: 2018-1651_32

value: Proteins


title: gfp_st3_rep1_d17

value: Osaka


title: 507_input

description:
processed data:
507_HP1_bin100_smooth1000.bigwig
507_H3K9ac.bigwig

value: none/input


title: gfp_st3_rep1_d13

value: whole embryo


title: 2018-1651_29

value: Lipids


title: 2018-1651_28


title: GFP_H3K9ac

description:
processed data:
gamsGFP_H3K9ac.bigwig

extract_protocol:
The method for the purification of gametocytes was modified from (Beetsma et al., 1998). Briefly, mice were pretreated by intra peritoneal injection of 0.2 ml phenylhydrazine (6 mg/ml in PBS) to stimulate reticulocyte formation two days prior to infection with parasites. Gametocytes were harvested via heart puncture and blood was immediate resuspended in 4⁰C coelenterazine loading buffer (CLB) (1x PBS, 20 mM HEPES, 20 mM glucose, 4 mM sodium bicarbonate, 1 mM EDTA, 0.1% BSA in PBS, pH 7.24–7.31) and magnet-purified using D Columns on a SuperMACS™ II Separator (Miltenyi Biotec). Magnet-purified parasites were crosslinked in 1% formaldehyde for 10 minutes at 37˚C, quenched with Glycine to an end concentration of 0.125M and resuspended in FACS buffer (PBS with 2mM HEPES, 2mM glucose, 0.4mM NaHCO3, 0.01% BSA, 2.5mM EDTA). Male and female gametocytes were sorted according to color (GFP for males and RFP for females) on a FACSAria III with a 70uM nozzle at 4⁰C. Purified gametocyte pellets were lysed in 150ul sonication buffer and chromatin prepared as above.
For each sequencing library up to 10 ng of ChIP or input DNA were end-repaired, extended with 30 A-overhangs and ligated to barcoded NextFlex adapters (Bio Scientific) as described previously (Hoeijmakers et al., 2011). Libraries were amplified (98⁰C for 2 min; four cycles 98⁰C for 20 sec, 62⁰C for 3 min; 62⁰C for 5 min) using KAPA HiFi HotStart ready mix (KAPA Biosystems) and NextFlex primer mix (Bio Scientific) as described (Kensche et al., 2016). 225-325 bp fragments (including the 125 bp NextFlex adapter) were size- selected using a 2% E-Gel Size Select agarose gel (Thermo Fisher Scientific) and amplified by PCR for ten (asexual blood stages and ookinetes) or eleven (female and male gametocytes) cycles under the same condition as described above. Library purification and removal of adapter dimers was performed with Agencourt AMPure XP beads in a 1:1 library:beads ratio (Beckman Coulter). ChIP-seq libraries were sequenced for 75 bp single-end reads using the NextSeq 500/550 High Output v2 kit (Illumina) on the Illumina NextSeq 500 system.

value: male gametocyte

value: 820cl1m1cl1 (Ponzi et al., 2009)


title: 2018-1651_33


title: gfp_st3_rep1_d-2

value: untreated


title: 233_RNA_rep2

value: asexual blood stage


title: 2018-1651_27


title: delrpoS-B1_S6_R1_001


title: FACS sorted CD14+ NP+ Woodchuck Liver Cells

city: Toronto

first: Jeff

last: Liu

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

country: Canada

institute: University Health Network

data_processing:
Raw sequencing data (bcl files) were converted to fastq files with Illumina bcl2fastq
fastq files aligned to Ensemble Marmota genome (Marmota_marmota_marmota.marMar2.1.dna.toplevel.fa)  using STAR 2.6
featureCount from SUBREAD package was used to determine gene expression into raw counts
Data normalization by trimmed mean  of the median (TMM) at counts-per-million = 2 and differentiating gene expression calculated by edgeR R package
Pathway analysis performed using GSEA with mouse homologous genes and mouse gene sets, results visualized by Enrichment map in Cytoscape
Genome_build: marMar2.1
Supplementary_files_format_and_content: Raw Counts from bam files

organism: Marmota monax

source_name: WHV-positive tumor bearing woodchuck

growth_protocol: primary woodchuck cells

extract_protocol:
Briefly, the samples underwent first-strand synthesis via random priming oligos on the 3’-end. A template switching oligo mix (TSO) was then incorporated to allow the RT reaction to continue replicating the 5’-end of the RNA strand. Following this, the samples were PCR amplified to incorporate full-length Illumina adapters and sample barcodes by binding to either the TSO stretch on the 5’-end, or the random priming oligo sequence on the 3’-end.
The amplified cDNA is treated with ZapR which specifically targets ribosomal RNA in the presence of mammalian-specific R-Probes. This process leaves non-ribosomal RNA untouched, while ribosomal RNA are cleaved, leaving them unamplifiable. A final PCR reaction is done to enrich the uncut strands of cDNA to generate the final RNA library. Final RNA library sizing was verified on the Agilent high sensitivity DNA kit (Agilent Technologies) using the Agilent Bioanalyzer while library concentration was quantified by qPCR using the KAPA SYBR FAST qPCR kit (Kapa Biosystems). Libraries were normalized to 10 nM, diluted to 2 nM, denatured using 0.2 N NaOH, and diluted to a final concentration of 2.2 pM before loading onto the NextSeq 500 system. The samples were sequenced as a pair-end 150 cycle sequencing run to achieve a minimum of ~40 M reads per sample.

treatment_protocol: primary woodchuck liver cells directly ex vivo.

value: Liver

tag: cell population

tag: sampletype

value: FACS sorted cells


title: GFP_HP1

description:
processed data:
gamsGFP_HP1_bin100_smooth1000.bigwig

tag: chip antibody

value: α-PbHP1 (Fraschka et al, 2018)


title: FACS sorted CD14- NP+ Woodchuck Liver Cells


title: GFP_input

description:
processed data:
gamsGFP_HP1_bin100_smooth1000.bigwig
gamsGFP_H3K9ac.bigwig


title: RDES_shSOX6(3), dox+, 1 biological Rep, 96h [exon]

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Affymetrix Clariom D Array.

scan_protocol: Affymetrix Clariom D Array.

data_processing:
Samples were normalised (log2) with Affymetrix Expression Console Software (v1.4) using SST-RMA algorithm and annotated on exon/gene level with the library for Clariom D Array (human).
Probe group file: Clariom_D_Human.r1.pgf
Meta-probeset file: Clariom_D_Human.r1.mps

source_name: shRNA against SOX6(3)

label_protocol: Affymetrix WT PLUS Labeling Kit.

growth_protocol: 120,000 cells/6-well were cultured for 96h.

extract_protocol: Cells were harvested with trypsin and RNA was isolated.

treatment_protocol: Cells were treated with 0.1 µg doxycycline pro ml medium for 96h to induce knockdown to 20-30%.

value: RDES

value: Ewing sarcoma cell line

tag: doxycycline

value: dox+


title: 2018-1651_26

value: Female

value: Intestinal samples from the anterior bulbus

value: Empty


title: RDES_shSOX6(3), dox-, 1 biological Rep, 96h [exon]

value: dox-


title: FACS sorted CD14- NP- Woodchuck Liver Cells


title: RFP_H3K9ac

description:
processed data:
gamsRFP_H3K9ac.bigwig

value: female gametocyte

value: α-H3K9ac (Diagenode pAb-004-050)


title: 2018-1651_25

value: Cellulos


title: RDES_shSOX6(2), dox+, 1 biological Rep, 96h [exon]

source_name: shRNA against SOX6(2)


title: 2018-1651_24


title: RDES_shControl_dox+, 1 biological Rep, 96h [exon]

source_name: shControl construct

value: non-coding


title: RDES_shSOX6(2), dox-, 1 biological Rep, 96h [exon]


title: RFP_HP1

description:
processed data:
gamsRFP_HP1_bin100_smooth1000.bigwig

value: 820cl1m1cl1 (Ponzi et al., 2009)


title: RFP_input

description:
processed data:
gamsRFP_HP1_bin100_smooth1000.bigwig
gamsRFP_H3K9ac.bigwig

value: none/input


title: 233_H3K9ac

description:
processed data:
233_H3K9ac.bigwig

extract_protocol:
Asexual blood stage parasites were harvested via heart puncture and passed through a Plasmodipur filter (Europroxima), resuspended in RPMI-1640 medium (Sigma-Aldrich) and crosslinked with 1% Formaldehyde in PBS for 10min at 37⁰C. Crosslinking was quenched adding glycine to an end concentration of 0.125M. RBC were then lysed with 0.15% saponin (in PBS) for 5-10 minutes on ice. To obtain nuclei the resulting parasite pellet was lysed with cell lysis buffer (20 mM Hepes, 10mM KCl,1mM EDTA, 1mM EGTA, 0.65% NP-40, 1mM DTT, 1x protease inhibitor (Roche)). The pellet was resuspended in sonication buffer (1% SDS, 50mM Tris pH8, 10 mM EDTA, 1x protease inhibitor (cOmplete™, Mini, EDTA-free, Roche) and sheared for 25 minutes (30sec ON, 30 sec OFF; settings HIGH) using a Bioruptor® Plus sonication device (Diagenode) to obtain DNA fragments of around 100-300bp.
For each sequencing library up to 10 ng of ChIP or input DNA were end-repaired, extended with 30 A-overhangs and ligated to barcoded NextFlex adapters (Bio Scientific) as described previously (Hoeijmakers et al., 2011). Libraries were amplified (98⁰C for 2 min; four cycles 98⁰C for 20 sec, 62⁰C for 3 min; 62⁰C for 5 min) using KAPA HiFi HotStart ready mix (KAPA Biosystems) and NextFlex primer mix (Bio Scientific) as described (Kensche et al., 2016). 225-325 bp fragments (including the 125 bp NextFlex adapter) were size- selected using a 2% E-Gel Size Select agarose gel (Thermo Fisher Scientific) and amplified by PCR for ten (asexual blood stages and ookinetes) or eleven (female and male gametocytes) cycles under the same condition as described above. Library purification and removal of adapter dimers was performed with Agencourt AMPure XP beads in a 1:1 library:beads ratio (Beckman Coulter). ChIP-seq libraries were sequenced for 75 bp single-end reads using the NextSeq 500/550 High Output v2 kit (Illumina) on the Illumina NextSeq 500 system.

value: asexual blood stage


title: RDES_shControl_dox-, 1 biological Rep, 96h [exon]


title: furA triple mutant rep 2

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

data_processing:
Using FASTX-Toolkit, raw data derived from RNA-seq was filtered to a minimum phred quality score of 28.
The BWA-MEM algorithm was employed to align the filtered reads into the reference genome.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by Bam2readcount.
Counted values were nomalised in the RPKM method.
Genome_build: Mycobacterium smegmatis MC2 155 ASM1500v1
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample

organism: Mycolicibacterium smegmatis

source_name: in vitro aerobic culture of the furA triple mutant strain

growth_protocol: The M. smegmatis strains were grown aerobically in Middlebrook 7H9 medium supplemented with 0.2% glucose and 0.02% Tween 80 (vol/vol) on a gyratory shaker (200 rpm) at 37°C.

extract_protocol:
The stains were grown until an optical density at 600 nm reached 0.45 to 0.5. Cells were harvested by centrifugation at 4°C with 3500×g for 3 min. The cell pellets were resuspended with 1 ml TRIzol (Invitrogen). Procedures of total RNA extract from the cell pellets were performed using TRIZol purchased from Invitrogen and followed the instructions provided to users.
Six ibraries for RNA-seq were prepared using the Illumina TruSeqTM RNA sample prep kit with the standard low-throughput protocol. Sequencing was performed on an Illumina HiSeq2000 instrument.

tag: strain background

tag: conditions

value: in vitro


title: furA triple mutant rep 3


title: FACS sorted CD14+ NP- Woodchuck Liver Cells

value: Liver

value: FACS sorted cells


title: 2018-1651_22

value: Proteins


title: furA triple mutant rep 1


title: TC-32_shSOX6(3), dox+, 1 biological Rep, 96h [exon]

value: Ewing sarcoma cell line


title: 2018-1651_21

value: Lipids


title: 233_HP1

description:
processed data:
233_HP1_bin100_smooth1000.bigwig

value: α-PbHP1 (Fraschka et al, 2018)


title: 2018-1651_20

value: Female

value: Intestinal samples from the anterior bulbus


title: Wild type rep 3

source_name: in vitro aerobic culture of the wild type strain

value: wild type


title: 233_input

description:
processed data:
233_HP1_bin100_smooth1000.bigwig
233_H3K9ac.bigwig


title: TC-32_shSOX6(3), dox-, 1 biological Rep, 96h [exon]

value: dox-


title: 2018-1651_23


title: TC-32_shSOX6(2), dox+, 1 biological Rep, 96h [exon]

value: dox+


title: 2018-1651_18


title: TC-32_shSOX6(2),dox-, 1 biological Rep, 96h [exon]


title: Wild type rep 1


title: Wild type rep 2


title: 2018-1651_17

value: Cellulos


title: 2018-1651_19

value: Empty


title: P2_RitterIsland

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: results.f1.csv, results.sm.csv, results.ly.csv, results.wa.csv

data_processing:
Basic read quality was verified using summaries produced by FastQC. Raw reads were trimmed and filtered by quality characteristics using Trimmomatic.
The reads for each sample were mapped to a concatonated Potamopyrgus antipodarum transcriptome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 100 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than 1e-5 were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
Genome_build: Transcriptome contigs obtained from http://bioweb.biology.uiowa.edu/neiman/download.php were used as the reference genome.
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values. Four comparisons were made between the samples collected for this study and previously collected samples from GSE99912, GSE99911, and GSE93836

organism: Potamopyrgus antipodarum

source_name: Foot tissue

growth_protocol: River snails were collected from tributary spring stream of the Snake River at Ritter Island (42.7439°N, 114.8420°W). Samples were obtained by searching the substrate and scraping snails off the underside of rocks and woody debris.

extract_protocol:
Genomic DNA from snail foot tissue was prepared as follows. Snail tissue was suspended in 100 μl of 1 x Phosphate Buffered Saline (PBS), then 820 μl DNA extraction buffer (50mM Tris pH8, 10mM EDTA pH8, 0.5% SDS) and 80 μl Proteinase K (20 mg/ml) was added and the sample incubated on a rotator at 55 C for 2-3 hours. After incubation, 300 μl of protein precipitation solution (Promega, A795A) was added, the sample mixed and incubated on ice for 15 minutes, then spun at 4 C at 13,000 rpm for 20 minutes. The supernatant was transferred to a fresh tube, then precipitated over night with the same volume 100% isopropanol and 2 μl glycoblue at -20 C. The sample was then centrifuged and the pellet washed with 75% ethanol, then air-dried and resuspended in 100 μl H2O. Genomic DNA from ten individuals was pooled into a single sample. Three pooled samples were processed for each sampling location.   Methylated DNA Immunoprecipitation (MeDIP) from genomic DNA was performed as follows. For the snail samples approximately 6 μg of each genomic DNA pool was diluted to 130 μl with TE buffer into the appropriate Covaris tube. Covaris was set to 300 bp program. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube and the volume measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10min at 95˚C, then immediately cooled on ice for 5min. Then 100μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4˚C.   The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube The same volume of Washing Buffer (at least 1 mL) was added and the bead sample was resuspended. Tube was then placed into a magnetic rack for 1-2 minutes and the supernatant discarded. The tube was removed from the magnetic rack and the washed beads were resuspended in the same volume of 1xIP buffer as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C.  After the incubation the beads were washed three times with 1X IP buffer as follows: The tube was placed into magnetic rack for 1-2 minutes and the supernatant discarded, then washed with 1xIP buffer 3 times. The washed beads were then resuspended in 250μl digestion buffer (50 mM Tris-HCI pH8, 10mM EDTA pH8, 0.5% SDS) with 3.5μl Proteinase K (20mg/ml). The sample was then incubated for 2-3 hours on a rotator at 55˚C. After incubation the tube was put again into the magnetic rack for 3 minutes and the supernatant removed to a new microfuge tube. The beads were discarded. 250μl of buffered Phenol-Chloroform-Isoamylalcohol solution were added to the supe and the tube vortexed for 30 sec then centrifuged at 14,000rpm for 5min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250μl chloroform were added to the supernatant from the previous step, vortexed for 30sec and centrifuged at 14,000rpm for 5min at room temperature.  The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in  -20˚C freezer for 1 hour to overnight.   The precipitate was centrifuged at 14,000rpm for 20min at 4˚C and the supernatant removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20˚C freezer for 15 min. then centrifuged again at 14,000rpm for 5min at 4˚C and the supernatant discarded. The tube was spun again briefly to collect residual ethanol at bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes) then resuspended in 25μl H2O or TE. DNA concentration was measured in Qubit with ssDNA kit.
For library preparation we used the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each pool received a separate index primer. Next generation sequencing (NGS) was performed at the WSU Spokane Genomic Core laboratory using the Illumina® HiSeq 2500 with a PE50 application, with a read size of approximately 50bp.

treatment_protocol: For the transgenerational observations of shell shape, 5 iso-female lines were initiated. Snails were isolated in plastic cups to start iso-female lines. All lab snails were maintained at a temperature of 14°C and a salinity of 2-4 ppt on 12:12 light-dark cycles. Water was changed and snails were fed 2-3 times a week.  Offspring of the 5 females were isolated into smaller plastic cups where they were raised until they were approximately 1 mm in length. When they reached this size they were then transferred to larger cups. After the first generation reproduced, snails were photographed under a dissecting microscope and their tissue was harvested for analysis of DNA methylation.

tag: generation


title: TC-32_shControl_dox+, 1 biological Rep,96h [exon]

value: non-coding


title: P1_RitterIsland


title: TC-32_shControl_dox-, 1 biological Rep, 96h [exon]


title: 2018-1651_16


title: 2018-1651_15


title: CDEB_2

city: Tochigi

first: shota

last: Nakagawa

address: 2606, Akabane, Ichikai-Machi, Haga-Gun

institute: Kao Corporation

description:
Gene expression after 24hr exposure of CDEB (300 µM)
sample name:
SAMPLE 17

hyb_protocol: The labeled samples were hybridized to the SurePrint G3 GE 8×60K Ver 2.0 Microarray (Agilent Technologies, Palo Alto, CA, USA) with rotation at 10 rpm for 17 h at 65°C.

scan_protocol: After hybridization, the microarray chips were washed with the Gene Expression Wash Pack (Agilent Technologies, Palo Alto, CA, USA) and scanned with a DNA microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

data_processing:
All microarray data were processed using Genespring GX 14.5 (Agilent Technologies, Palo Alto, CA, USA). These data were normalized and modified using quality control flags.
processed data matrices include normalized signal intensity

organism: Rattus norvegicus

source_name: hepatocytes, 24h, CDEB, 300 µM

label_protocol: RNA was converted to cDNA and then the labeled cRNA were produced from the cDNA using the Low Input Quick Amp Labeling kit (Agilent Technologies, Palo Alto, CA, USA).

growth_protocol: Cryopreserved male Sprague Dawley primary rat hepatocytes (KaLy-Cell, Plobsheim, France) were used for in vitro assay. The cells were cultured at 37°C with 5% CO2 in the supplied medium (Kurabo, Osaka, Japan).

extract_protocol: After the 24 hours exposure with each chemical, total RNAs were extracted from rat primary hepatocytes using the mRNAeasy kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions. For elucidating the gene expression profile, 100 ng of RNA in total were used for microarray analysis.

treatment_protocol: After 24 h pre-culture, the cells were exposed to each compound at 300 µM for 24 h.

value: primary hepatocytes

tag: strain

value: SD

tag: gender

value: Male


title: CDEB_3

description:
Gene expression after 24hr exposure of CDEB (300 µM)
sample name:
SAMPLE 18

tag: cell type


title: 2018-1651_14


title: CDMB_3

description:
Gene expression after 24hr exposure of CDMB (300 µM)
sample name:
SAMPLE 15

source_name: hepatocytes, 24h, CDMB, 300 µM


title: 2018-1651_13


title: CDEB_1

description:
Gene expression after 24hr exposure of CDEB (300 µM)
sample name:
SAMPLE 16


title: P3_RitterIsland


title: RDES_shSOX6(3), dox+, 1 biological Rep, 96h [gene]

tag: cell line

value: RDES


title: 2018-1651_12


title: CDMB_2

description:
Gene expression after 24hr exposure of CDMB (300 µM)
sample name:
SAMPLE 14


title: 2018-1651_11


title: 2018-1651_10


title: 2018-1651_9


title: DDEB_2

description:
Gene expression after 24hr exposure of DDEB (300 µM)
sample name:
SAMPLE 11

source_name: hepatocytes, 24h, DDEB, 300 µM


title: DDEB_1

description:
Gene expression after 24hr exposure of DDEB (300 µM)
sample name:
SAMPLE 10


title: DDMB_3

description:
Gene expression after 24hr exposure of DDMB (300 µM)
sample name:
SAMPLE 9

source_name: hepatocytes, 24h, DDMB, 300 µM


title: Celery_Neg_Ctrl2

city: Laurel

first: Christine

middle: Fang

last: Yu

state: MD

address: 8301 Muirkirk Rd.

department: Center for Food Safety and Applied Nutrition

institute: US Food and Drug Administration

description: ultracentrifugation: viral RNA

hyb_protocol: Samples were prepared and hybridized to FDA-EVIR GeneChip Tiling Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip scanner with a scanning resolution of 1.56 µm pixelsize according to manufacturer's instruction.

data_processing: The probe intensities were extracted with Affymetrix PowerTools software (APT 2.10.2.2), and then exported to Excel for further processing.

organism: Apium graveolens

source_name: non-spiked celery RNA

growth_protocol: Confluent culture of FRhK-4 cells in 75 cm2 flasks (5 x 106 cells) were infected with 5-10 pfu/cell of HAV/18f in 1.5 ml of MEM containing 1% heat inactivated FBS.  After 1 hr of adsorption, 13.5 ml of the same medium was added to each flask and Incubation continued for 5-6 days.

extract_protocol: HAV/18f was spiked onto tomatoes, and the samples were shaked in TGBE buffer and homogenized.  The eluate was collected and clarified by centrifugation to remove food particulates.  The supernatant was recovered, and RNA was precipitated with 70% ice cold isopropanol.  The RNA pellet was collected by centrifugation and re-suspended in the lysis buffer following the instructions of RNAqueous Kit.  Potassium acetate was added to precipitate any remaining polysaccharides.  The extracted RNA samples were further treated with DNase and Dynabeads mRNA Purification Kit.   For virus-spiked green onions and celery, material was eluted using either Glycine Buffer or TGBE buffer supplemented with pectinase, respectively, then virus particles were concentrated by ultracentrifugation and RNA was extracted with commercial kits.

treatment_protocol: HAV/18f culture supernatant was collected and used for inoculation.  NoV GII.4 Minerva stool sample was suspended in 10% phosphate-buffered saline (PBS), centrifuged at 9000 ×g for 3 min, and the supernatant was collected and used for inoculation.

tag: treatment(s)

value: no virus spiked celery

tag: infection

tag: virus strain

tag: virus genotype


title: CDMB_1

description:
Gene expression after 24hr exposure of CDMB (300 µM)
sample name:
SAMPLE 13


title: RDES_shSOX6(2), dox-, 1 biological Rep, 96h [gene]

tag: treatment


title: Celery_NoV_HAV

description: ultracentrifugation: viral RNA

source_name: NoV/HAV-spiked celery

label_protocol: Samples were prepared and hybridized to FDA-EVIR GeneChip Tiling Array according to Affymetrix specifications.

value: celery + NoV + HAV

value: human norovirus, hepatitis A virus

value: Minerva, HM175/18f  (ATCC VR1402)

value: GII.4, IB


title: Celery_NoV

description: ultracentrifugation: viral RNA

source_name: NoV-spiked celery

value: celery + NoV

value: human norovirus

value: Minerva


title: RDES_shControl_dox+, 1 biological Rep, 96h [gene]

value: Ewing sarcoma cell line


title: RDES_shSOX6(3), dox-, 1 biological Rep, 96h [gene]

value: dox-


title: RDES_shControl_dox-, 1 biological Rep, 96h [gene]


title: DDEB_3

description:
Gene expression after 24hr exposure of DDEB (300 µM)
sample name:
SAMPLE 12


title: Celery_HAV

description: ultracentrifugation: viral RNA

source_name: HAV-spiked celery

value: celery + HAV

value: hepatitis A virus

value: IB


title: RDES_shSOX6(2), dox+, 1 biological Rep, 96h [gene]

value: dox+


title: Celery_NoV_P

description: ultracentrifugation: viral RNA

source_name: NoV-spiked celery, PowerPlant kit extraction

value: Celery + NoV + PowerPlant kit


title: TC-32_shSOX6(2), dox+, 1 biological Rep, 96h [gene]


title: TC-32_shSOX6(3), dox-, 1 biological Rep, 96h [gene]


title: TC-32_shSOX6(3), dox+, 1 biological Rep, 96h [gene]


title: DDMB_1

description:
Gene expression after 24hr exposure of DDMB (300 µM)
sample name:
SAMPLE 7

value: primary hepatocytes

value: SD

value: Male


title: VC_2_3

description:
Gene expression after 24hr exposure of control (DMSO)
sample name:
SAMPLE 6

source_name: hepatocytes, 24h, DMSO


title: VC_2_1

description:
Gene expression after 24hr exposure of control (DMSO)
sample name:
SAMPLE 4


title: Celery_NoV_V

description: ultracentrifugation: viral RNA

source_name: NoV-spiked celery, QIAamp viral kit extraction

value: Celery + NoV + QIAamp viral kit


title: Hep-VDR-E3

city: Valencia

first: RAMIRO

last: JOVER

address: Avenida Fernando Abril Martorell, 106.

department: Experimental Hepatology Unit

institute: IIS Hospital La Fe

description: 48 h transfection + 4 h treatment (Veh=DMSO)

hyb_protocol: The hybridization cocktail was heated at 99° for 5 minutes followed by 45° for 5 minutes and then centrifuged at max speed for 1 minute. 80µL were transferred to each array. Genechip array was incubated overnight at 45°C while rotating in a Hybridization Oven 645 (Affymetrix). After 16h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip Fluidics Station 450, according to the FS450_0007 protocol.

scan_protocol: The distribution of fluorescent signals on the array was obtained using GeneChip Scanner 3000 7G (Affymetrix). GeneChip Operating Software (Affymetrix) was used to generate the CEL files.

data_processing: The data were normalized using the RMA method, and probes were summarized using the revised entrez-based probe annotation. A probe-filtering step excluding those probes that show a lower coefficient of variation, low intensity levels in all observations or that are non-informative (not annotated) was employed. Differential expression analysis was assessed using linear models for microarray data based on empirical Bayes moderated t-statistics for all filtered probe sets. To correct for multiple testing, the false discovery rate was estimated from p-values derived from the moderated t-statistics using the method of Benjamini and Hochberg. The data were also analyzed with Transcriptome Analysis Console version 4.0.2 (TAC 4.0.2) using Affymetrix default analysis settings.

label_protocol: The fragmented biotinylated cRNA, using WT Terminal Labeling Kit (Affymetrix), derived from 300 ng of total RNA

growth_protocol: HepG2 cells were cultured in Ham’s F-12/Leibovitz L-15 (1:1, v/v) medium supplemented with 7% newborn calf serum, 2 mmol/L L-glutamine, 50 U/mL penicillin, and 50 mg/mL streptomycin

extract_protocol: Total cellular RNA was extracted with the RNeasy Plus minikit (Qiagen), which removes contaminating genomic DNA. RNA concentration was measured by absorbance at 260 nm with a capillary spectrophotometer (GeneQuant Pro, GE Healthcare Biosciences). Purity was examined by OD260/230 and OD260/280 ratios. RNA integrity was assessed with a 2100 Bioanalyzer with Eukaryote total RNA Nano Assay (Agilent Technologies). RNA Integrity Numbers were all above 9.3.

treatment_protocol: HepG2 cells were infected with adenoviral vectors (Ad-VDR, encoding human VDR, or Ad-C, an insertless adenovirus) and 48 h latter cells were shifted to adenovirus-free medium and cultured for 4 h in the presence of 10 nM VitD (1a,25-dihydroxyvitamin D3 / calcitriol)

value: Ad-VDR + Vehicle

value: hepatocellular carcinoma


title: Hep-VDR/VitD-E3

description: 48 h transfection + 4 h VitD in DMSO

value: Ad-VDR + 10nMVitD


title: TC-32_shControl_dox-, 1 biological Rep, 96h [gene]

value: non-coding


title: TC-32_shControl_dox+, 1 biological Rep,96h [gene]


title: VC_1_3

description:
Gene expression after 24hr exposure of control (DMSO)
sample name:
SAMPLE 3


title: Celery_NoV_Vt

description: ultracentrifugation: viral RNA

source_name: NoV-spiked celery, QIAamp viral kit with tRNA extraction

value: Celery + NoV + QIAamp viral kit + tRNA

value: human norovirus


title: TC-32_shSOX6(2),dox-, 1 biological Rep, 96h [gene]

source_name: shRNA against SOX6(2)

value: Ewing sarcoma cell line


title: VC_1_2

description:
Gene expression after 24hr exposure of control (DMSO)
sample name:
SAMPLE 2