title: H3K4me3_Meso48h_WT

data_processing:
Following quality controls (performed with FastQC v0.11.2), sequencing reads were aligned to mouse reference genome (mm10/GRCm38) using Bowtie v2.3.4.1 (options: -q --local). Duplicated alignments (identified by Picard MarkDuplicates, https://broadinstitute.github.io/picard) and low-quality alignments/multi-mapping reads were excluded using SAMtools (command: samtools view –F1804 –q 30). Coverage tracks were generated from filtered alignments using the deepTools bamCoverage utility. IP and corresponding control (Input DNA) datasets were treated identically. Peak calling was performed using MACS v2.1.1 (options: callpeak -t=<IP> -c=<Input> -g mm --nomodel –extsize=<ES> --broad –q 0.05 --broad-cutoff 0.05 --fe-cutoff 1). The read extension size (ES) was estimated by cross-correlation using the phantompeakqualtools package. Input-normalized ChIP-seq signals were obtained using the deepTools bamCompare utility (options: --extendReads=<ES> --scaleFactorsMethod readCount --binSize 10 --operation log2). These processing steps were applied to all sample groups.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: BigWig files containing ChIP-seq read densities for IP and Input DNA control (RPKM unit).

extract_protocol:
Approximately 2*10^7 cells were cross-linked by addition of formaldehyde to 1% for 10 min at RT, quenched with 0.125 M glycine for 5 min at RT, and then washed twice in cold PBS. The cells were resuspended in Lysis Buffer 1 (50 mM Hepes-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100 and protease inhibitor) to disrupt the cell membrane and in Lysis Buffer 2 (10 mM Tris-HCl pH8.0, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA and protease inhibitor) to isolate nuclei. The isolated nuclei were then resuspended in SDS ChIP Buffer (20 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS and protease inhibitors). Extracts were sonicated using the BioruptorH Twin (Diagenode) for 2 runs of 10 cycles [30 sec ‘‘ON’’, 30 sec ‘‘OFF’’] at high power setting. Cell lysate was centrifuged at 12,000 g for 10 min at 4°C. The supernatant was diluted with ChIP Dilution Buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton) before immunoprecipitation step. Streptavidin beads (Dynabeads®Protein G, Life Technologies) were saturated with PBS/1% BSA and the samples were incubated with 2 ug of antibody overnight at 4°C on a rotator.  Next day samples were incubated with saturated beads for two hours at 4°C on a rotator. Successively immunoprecipitated complexes were washed five times with RIPA buffer (50 mM Hepes-KOH pH7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0,7% Na-Deoxycholate) at 4°C for 5 minutes each on a rotator. Elution Buffer was added and incubated at 65°C for 15 minutes. The decrosslinking was performed at 65°C overnight. De-crosslinked DNA was purified using QIAQuick PCR Purification Kit (QIAGEN) according to the manufacturer’s instruction.
Starting from 10 ng of ChIP eluted sample, the library was produced for the genome wide analysis following the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® (E 6240L NEB) manufacturer’s instructions. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75 bp reads).

value: Wild type (WT)

value: EpiSC derived ME progenitors

value: ME T48h

tag: antibody


title: BAS cells - biological sample 1

status: Public on Jan 23 2023

type: RNA

city: London

first: Ernesto

last: Yague

address: Du Cane Road

department: Division of Cancer

country: United Kingdom

institute: Imperial College London

description: Total RNA isolated from cells in culture

hyb_protocol: Following fragmentation and labeling, ss-cDNA were hybridized for 16 hr at 45°C to Clariom S Human Arrays. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix, P/N 00-0079).

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

data_processing: The raw CEL files were normalized using RMA background correction with quantile normalization, log2 transformation and mean probe-set summarization with adjustment for GC content. Differentially expressed genes were considered significant if p-value with FDR ≤ 0.05 and fold-change of >2 or < -2.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: BAS cells

label_protocol: Affymetrix GeneChipTM WT PLUS Reagent Kit

growth_protocol: HS578T cells were grown in low-glucose DMEM containing 10% fetal calf serum, glutamine and insulin. BAS cells were grown in keratynocyte serum-free medium supplemented with human recombinant epidermal growth factor and bovine pituitary extract

extract_protocol: Qiagen Rneasy total RNA extraction

tag: tissue

value: breast cancer

tag: cell line

value: BAS

tag: resistance

value: parental naive


title: 291 PRE

city: Bari

first: Simona

last: De Summa

state: (Click to Select US State)

address: Via Orazio Flacco, 65

country: Italy

institute: IRCCS-Istituto Tumori "Giovanni Paolo II"

hyb_protocol: Firstly, poly (A) tailing was carried out at 37°C for 15 min in a volume of 15 ml reaction mix that  contained 1 ml Reaction Buffer, 1.5 ml MgCl2 (25 mM), 1 ml ATP Mix diluted 1:500 and 1 ml PAP enzyme. Subsequently, Flash Tag Ligation was performed at room temperature for 30 min by adding 4 ml of 5 Flash Tag Ligation Mix Biotin and 2 ml T4 DNA Ligase into 15 ml of reaction mix. Next, 2.5 ml of Stop Solution was added to stop the reaction. Each sample was hybridized on the array, washed, stained with the Affymetrix Fluidics Station 450

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using the Command Console software (Affymetrix).

data_processing: Raw data were normalized with the Robust Multiarray Average (RMA) method to remove systematic variations.

label: biotin

source_name: plasma

label_protocol: For each sample, 500 ng of total RNA was labelled using the 3 DNA Array Detection Flash Tag RNA Labelling Kit (http://www.genisphere.com), according to the manufacturer’s instructions.

extract_protocol: Total RNA was isolated from plasma using mirVana™ miRNA Isolation Kit (Ambion, Austin, TX, USA), according to the manufacturer’s recommendations.

treatment_protocol: Eight milliliters of peripheral blood were collected into Cell-Free DNA BCT (Streck Corporate, La Vista, NE) at each time-point and was centrifuged at 3000 rpm at 4 °C for 15. The obtained plasma samples were further centrifuged at 16 000 g at 4 °C for 10 min to remove cell debris. The separated plasma was stored at 80 °C until nucleic acid extraction.

value: plasma

tag: diet yes/no

value: no


title: 251 POST


title: BAS cells - biological sample 2


title: 252 POST


title: HS578T cells - paclitaxel resistant - biological sample 3

source_name: HS578T cells - paclitaxel resistant

value: paclitaxel-resistant


title: MdMYB68-1

type: SRA

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

library_source: transcriptomic

data_processing:
FASTQ files were imported in pairs in CLC genomics workbench v11.0.1 discarding poor-quality reads (<Q30). For each library, reads were trimmed and filtered using the following criteria: sequence quality <0.01, no ambiguous nucleotides, minimum read length >35 nucleotides, trimming against the Illumina adaptor sequence, and finally a hard trim of 14 nucleotides at the 5’ end and 3 nucleotides at the 3’ end. The filtered reads were mapped to the N. benthamiana transcriptome v5-primary transcript (Nakasugi et al., 2014) obtained from the N. benthamiana genome and transcriptome website (http://benthgenome.qut.edu.au/) with the following criteria: a mismatch, gap and insertion cost set at 2,3 and 3 respectively (3=stringent mapping), reads should have 80% identity and 80% coverage with the reference transcriptome.
Assembly: N. benthamiana transcriptome v5-primary and alternate transcript (Nakasuki et al. 2014)
Supplementary files format and content: tab-delimited text files include, unique and toal hit reads, RPKM values for each Sample fold change for each contig.

organism: Nicotiana benthamiana

source_name: Leaves

growth_protocol: A. tumefaciens GV3101-pMP90 strains (p103::MD08G1076200, p103-empty and pBIN61-p19) were grown in 50 mL of LB liquid medium supplemented with gentamycin (30 mg/L), rifampicin (10 mg/L), kanamycin (50 mg/L), and acetosyringone (30 mg/L). As A. tumefaciens is not sensitive to the CcdB protein, we used the p103-empty vector as control in the present work (Traore and Zhao, 2011). Cultures in 100 mL Erlenmeyer flasks were agitated at 130 rpm/30°C for 48 h. After centrifugation (1000 g/10 min), cultures were re-suspended in infiltration buffer (20 mM MES, 20 mM MgSO4, 150 mg/L acetosyringone). After 3 hours, p103::MD08G1076200, p103-empty and pBIN61-p19 A. tumefaciens cultures were mixed and adjusted to OD600=0.8, 0.8 and 1, respectively. For the RNA-Seq, qPCR validation, cell wall analysis and lipid analysis, independent transient expression experiments have been performed using p103:: MD08G1076200/pBIN61-p19 and p103-empty vector/pBIN61-P19 A. tumefaciens mixtures using four biological replicates (n=4). Each biological replicate is constituted by three plants and four leaves per plants.

extract_protocol:
total RNA were extracted from two groups (p103:: MD08G1076200 /pBIN61-p19 (overexpression) and P103 (empty vector)/pBIN61-p19 (control)) of agroinfiltrated leaves. Four biological replicates were used for RNA-Seq. Each biological replicate was comprised of a pool of 3 plants with 4 agroinfiltrated leaves per plant. Total RNA extracts were obtained using the RNeasy plant mini kit (QIAGEN, Leusden, The Netherlands) coupled with on-column DNase I treatment, following the manufacturer’s guidelines.  Total RNA integrity (RIN>8) and purity were assessed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and a Nanodrop ND1000 spectrophotometer (Thermo scientific, Villebon-sur-Yvette, France), respectively. Total RNA was quantified using a Qubit RNA assay kit (Life technologies, Carlsbad, CA, USA).
cDNA libraries were prepared from 3 µg total RNA of each replicate according to the KAPA HyperPrep Kit manufacturer’s guidelines (Roche, Basel, Switzerland). All libraries were analyzed and quantified as described in Legay et al. (2016). The pooled libraries were sequenced on an Illumina NextSeq500 (NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles)) to generate 75 base-pairs paired-end reads.

value: Leaves

tag: age

value: 4-week old

tag: treatment


title: H3K4me1_Meso48h_WT

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

institute: University of Turin

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse Meso-Endodermal Progenitors

growth_protocol: E14 mouse WT and mutant (Dnmt3a -/-   and Dnmt3b -/-) ESCs were cultured in high-glucose DMEM (Euroclone) supplemented with 15% FBS (Millipore Corp., Billerica, MA, USA), 0.1 mmol/l nonessential amino acids (Invitrogen), 1 mmol/l sodium pyruvate (Invitrogen), 0.1 mmol/l β-mercaptoethanol, 1500 U/ml Leukemia Inhibitory Factor (LIF; Millipore), 25 U/ml penicillin, and 25 μg/ml streptomycin. For EpiSC induction, a single-cell suspension was seeded onto Geltrex (A1413202 GIBCO)-coated plates at a density of 10,000 cells cm-2 in N2B27 medium supplemented with 20ng/ml ActivinA (PHC9564 GIBCO) and 12 ng/ml bFGF (PHG0026 GIBCO). The cells were passaged 1:3 as small clumps using Collagenase IV (17104019 GIBCO). EpiSCs were collected for DNA and RNA analyses after 14 days of induction followed by daily medium changes. N2B27 medium is composed by 50% advanced DMEM/F12 (12634028 GIBCO) and 50% Neurobasal medium (21103049 GIBCO), supplemented with 0.5% N2 Supplement (17502048 GIBCO), 1% B27 Supplement (17504044 GIBCO), 0.033% BSA solution (A9647 SIGMA), 50 uM β-mercaptoethanol (M3148 Sigma), 2mM Glutamax (35050038 GIBCO), 100U/ml penicillin and 100 ug/ml streptomycin (DE17-602E LONZA). For Meso-endoderm directed lineage specific differentiation, EpiSCs were plated as small clumps onto Geltrex-coated plates in EpiSCs medium for 24 hours. The day after, medium was replaced with N2NB27 medium consisted of 50% advanced DMEM/F12 (12634028 GIBCO) and 50% Neurobasal medium (21103049 GIBCO), supplemented with 0.5% N2 Supplement (17502048 GIBCO), 1% B27 supplement minus Vitamin A (12587010 GIBCO) and 3 uM iGSK3β (CHIR99021 SIGMA). Cells were fed daily until the end of differentiation.

tag: strain background

tag: genotype

tag: cell type

tag: Stage


title: Input_Meso48h_WT_Rep1

value: Input


title: HS578T cells - paclitaxel resistant - biological sample 2


title: 251 PRE


title: HS578T cells - paclitaxel resistant - biological sample 1


title: MdMYB68-2


title: HS578T cells - doxorubicin resistant - biological sample 3

source_name: HS578T cells - doxorubicin resistant

value: doxorubicin-resistant


title: HPV16 infected keratinocytes

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

country: USA

institute: Cincinnati Children's Hospital Research Foundation

data_processing:
Raw sequencing data was processed through 10X Genomics CellRanger v3.0.2 using default parameters to obtain the gene expression matrices
Genome_build: Modified hg19 including annotated HPV16 genome
Supplementary_files_format_and_content: CellRanger output files (barcodes, genes, matrix)

source_name: cell culture

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: immortalized keratinocytes

tag: infection


title: HS578T cells - doxorubicin resistant - biological sample 2


title: Input_EpiSC_WT_Rep2

source_name: Mouse Epiblast Stem Cells

value: ES-E14 derived EpiSC

value: EpiSC


title: MdMYB68-4


title: 238 POST


title: MdMYB68-3


title: HS578T cells - doxorubicin resistant - biological sample 1


title: Input_Meso48h_WT_Rep2


title: 238 PRE


title: 252 PRE


title: Empty vector-3

value: Infiltration with EmptyVector/pBIN(p19)


title: Empty vector-2


title: Empty vector-4


title: H3K27ac_Meso48h_WT

value: Wild type (WT)


title: HS578T cells - biological sample 4

source_name: HS578T cells


title: Empty vector-1


title: p-dC_muscularis_externa_in_naive_porcine_6

status: Public on Jan 22 2023

city: Los Angeles

first: Tao

last: Li

state: California

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

data_processing:
For bulk RNA-seq data processing, the libraries derived from total RNA of ganglia in porcine were sequenced on an Illumina HiSeq 3000 sequencer as 50 base pair single-end reads. Sus_scrofa genome files (.fa) and annotation file (.gtf) were downloaded at https://uswest.ensembl.org/Sus_scrofa/Info/Index, which were used to create the sus_scrofa genome index using STAR v2.7.1a. Human reads were aligned to Ensembl release 97 human with STAR. The fastq files were then aligned against the genome assembly using STAR, followed by assessment for the total number of aligned reads and total number of uniquely aligned reads to evaluate sequencing performance, with parameters --runMode alignReads --outSAMtype BAM SortedByCoordinate Unsorted --outFilterMultimapNmax 1 --quantMode GeneCounts --twopassMode Basic --sjdbOverhang 50.
For single-cell RNA-seq data processing, Cell Ranger 3.1.0 count function was used to align and quantify the reads against sus_scrofa genome assembly with parameters --localcores=32 --expect-cells=10000 --localmem=200, created using the Cell Ranger 3.1.0 mkref function based on the downloaded Sus_scrofa genome files (.fa) and annotation file (.gtf).
Genome_build: hg38, susScr11
Supplementary_files_format_and_content: Bulk RNA-seq processed data files contain matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Single-cell RNA-seq processed data files contain only detected cell-associated barcodes in MEX format. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).

organism: Sus scrofa

source_name: Muscularis externa from descending colon

extract_protocol:
For bulk RNA-seq, a range of 25-40 ganglia/subject were harvested from ISG and MG respectively of p-pC and p-dC and from MG of h-aC and h-dC using LMD-6000 Laser Micro-dissection System. Total RNA was extracted using QIAgen RNAeasy Micro Kit. SMART-Seq® Stranded Kit was used with around 190 pg of total RNA for the construction of sequencing libraries. For preparation of cell suspensions, full thickness colon tissue samples were collected from each p-pC and p-dC of 4 naïve porcine. The tissue samples were washed in ice-cold, carbogen (95% O2 and 5% CO2)-bubbled PBS. The muscularis externa containing myenteric ganglia were peeled off from the underlying tissue using forceps, followed by incubation in enteric neuron media, containing Neurobasal A media with B-27, 2 mM L-glutamine, 1% fetal bovine serum (FBS), 10 ng/ml Glial Derived Neurotrophic Factor and 1× Antibiotic/Antimycotic, in the presence of 45 µM Actinomycin D (ActD) for 15 min on ice. The samples were then cut into small pieces < 1 mm and transferred to the enteric neuron media containing 1mg/ml collagenase B and dispase II and 45 µM ActD for 1 hour at 37°C. After the addition of 1 mg/ml deoxyribonuclease I and 10% FBS, the tissue pieces were dissociated using fire polished Pasteur pipettes. Following manual trituration, the cells were filtered through 70 µm Nitex mesh filter and pelleted at 375 g for 10 min, and resuspended in the ice-cold, carbogen-bubbled rinse medium containing F12 media with 10% FBS and 1× antibiotic/antimycotic. Importantly, the solutions used in all steps were equilibrated in the carbogen gas. Estimation of viable cell number was done by Trypan Blue dye exclusion method. After cell staining with DAPI, the viable cells were collected via fluorescence-activated cell sorting (FACS). ~10,000 single cells per cell suspension were loaded on the 10x Genomics Chromium platform accompanying Chromium™ Single Cell 3’ Library Construction and sequenced on an Illumina NextSeq 500 Sequencer.
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: A detailed experimental protocol for VNS in porcine is available at https://www.protocols.io/view/tache‐mulugeta‐ot2od024899‐colon‐tissue‐electrical‐3rmgm.

tag: strain

value: Yucatan minipigs

value: colon

value: ~7 months old

value: Muscularis externa

value: untreated


title: 237 PRE

value: plasma


title: H3K4me1_EpiSC_WT


title: p-pC_muscularis_externa_in_naive_porcine_6

source_name: Muscularis externa from proximal colon


title: NSH

city: Madison

first: Paul

last: Marker

state: WI

address: 777 Highland Ave

department: School of Pharmacy

institute: University of Wisconsin-Madison

description: UGS NH H

data_processing:
Illumina 1.9 software used for base calling
Reads were alligned to the mm9 genome using the splice-junction aware read aligner STAR
RSEM was used for normalization
EdgeR was used to perform differential gene expression analysis
Used fastqc in R to analyze
Genome_build: mm9
Supplementary_files_format_and_content: text files

source_name: Urogenital Sinus

extract_protocol:
RNA was extraced from tissues and cultured UGS using Machery-Nagel Nucleospin RNA kit (REF 740955.50)
RNA libraries were prepared for sequencing following Illumina protocols

treatment_protocol: Testosterone (25mg) and oestrogen (2.5mg) were implanted subcutaneously into male C57/BL6 mice (T+E2 Treated). After two weeks, mice were euthanized and the prostatic urethra, AP, and DLP lobes of the prostate were extracted.Tissues were flash frozen immediately. Control mice received no hormone treatment. UGS were dissected from male embryonic mice at E16.5 and cultured in testosterone for six days time.

value: Control


title: HS578T cells - biological sample 3

value: breast cancer

value: parental naive


title: H3K27ac_EpiSC_WT


title: Input_EpiSC_WT_Rep1


title: p-pC_muscularis_externa_in_naive_porcine_3


title: p-pC_muscularis_externa_in_naive_porcine_2


title: H3K4me3_EpiSC_WT


title: 237 POST

value: no


title: NSD

description: UGS NH D


title: 35-5

city: La Tronche

first: Alexandre

last: Bougdour

state: Isère

address: Domaine de la Merci, Campus santé

department: Prevention and Therapy of Chronic diseases

country: France

institute: Centre de Recherche Inserm U1209 / CNRS UMR5309 / UGA

data_processing:
The RNA-Seq reads (FASTQ) were processed and analyzed using the Lasergene Genomics Suite version 15 (DNASTAR, Madison, WI, USA) using default parameters.
The paired-end reads were uploaded onto the SeqMan NGen (version 15, DNASTAR. Madison, WI, USA) platform for reference-based assembly using the Toxoplasma Type I GT1 strain (ToxoDB-46, GT1 genome) as reference template.
The ArrayStar module (version 15, DNASTAR. Madison, WI, USA) was used for normalization, variant detection and statistical analysis of uniquely mapped paired-end reads using the default parameters.
Variant calls were filtered to select variants present in coding regions with the following criteria: variant depth ≥ 10, SNP% ≥ 90%, and absent in the parental wild-type strain. SNVs, insertions and deletions present in regulatory or intergenic regions were filtered out as they are unlikely to contribute to drug resistance.
The expression data quantification and normalization were calculated using the RPKM (Reads Per Kilobase of transcript per Million mapped reads) normalization method.
Assembly: Toxoplasma GT1 strain (ToxoDB-46, GT1 genome).
Supplementary files format and content: xlsx format. The matrix table includes RNA-Seq report, RPKM values of T. gondii transcripts for each sample. Variants detected in each strain when compared to the GT1 reference genome are also provided.

molecule: polyA RNA

organism:
Homo sapiens
Toxoplasma gondii RH

source_name: Human fibroblasts infected by T. gondii RH strain

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% heat-inactivated FBS (Invitrogen), 10 mM HEPES buffer, pH 7.2, 2 mM L-glutamine, and 50 μg/ml penicillin and streptomycin (Thermo Fisher Scientific). Cells were incubated at 37°C in 5% CO2.

extract_protocol:
18 hours post-infection, cells were harvested and total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen). RNA quantity and quality were measured by NanoDrop 2000 (Thermo Scientific). RNA integrity was assessed by standard non-denaturing 1.2% TBE agarose gel electrophoresis. The ribosomal large subunits from Toxoplasma and the host cells was used to verify that the ratio between Toxoplasma RNA versus host RNA was equivalent between the different biological samples, thus indicating that the samples had equivalent infection rates.
RNA libraries were prepared using polyA selected RNAs for sequencing using standard Illumina protocols (Illumina TruSEQ RNA library prep).

tag: host cell_line

value: HFF

tag: host cell_type

value: Human fibroblasts

tag: infection status

value: infected by T. gondii RH strain

tag: parasite genotype

value: mutagenized, drug-resistant parasites


title: 35-4


title: +TH

description: UGS T H

value: Cultured in testosterone


title: 35-6


title: NSA

description: UGS NH A


title: 35-3


title: p-pC_muscularis_externa_in_naive_porcine_1


title: p-dC_muscularis_externa_in_naive_porcine_1


title: +TB

description: UGS T B


title: +TC

description: UGS T C


title: NSC

description: UGS NH C


title: 35-1


title: p-pC_MG_in_porcine_with_VNS_3

description: Read_counts_in_male_porcine_without_and_with_vagal_nerve_stimulation.csv

source_name: Myenteric ganglia from proximal colon

value: Myenteric ganglia

value: Electrical stimulation of the celiac branch of the abdominal vagus nerve


title: 35-2


title: +TG

description: UGS T G


title: HS578T cells - biological sample 2


title: p-dC_muscularis_externa_in_naive_porcine_3

value: Yucatan minipigs


title: p-dC_muscularis_externa_in_naive_porcine_2

value: colon


title: p-pC_MG_in_porcine_with_VNS_1

value: ~7 months old


title: p-pC_MG_in_porcine_with_VNS_2


title: HS578T cells - biological sample 1


title: 18D

description: DLP treated 18D

source_name: Dorsal Lateral Prostate

value: T+E2 treated for 2 weeks


title: p-pC_MG_in_naive_porcine_5

description: Read_counts_in_naive_porcine_both_sex.csv

value: untreated


title: 2D

description: DLP treated 2D


title: 10D

description: DLP control 10D


title: 9D

description: DLP control 9D


title: 8U

description: urethra control 8U

source_name: Urethra


title: 8D

description: DLP control 8D


title: 7U

description: urehtra control 7U


title: p-pC_MG_in_naive_porcine_2


title: 6U

description: urethra control 6U


title: KURAMOCHI, 10uM indisulam, 24h, rep 3

first: Anke

last: Nijhuis

state: London

address: Du Cane road, IRDB building 2nd floor

data_processing:
cutadapt (trimming and quality control)
STAR (alignment) v2.7.10a
Assembly: Genome Reference Consortium Human Build 38 patch release 107
Supplementary files format and content: Counts and processed RNA splicing analysis

source_name: KURAMOCHI

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol: RNA extraction using qiazol and RNAeasy kit (qiagen)

treatment_protocol: HGSOC KURAMOCHI cells were exposed to 0.1% DMSO (Vehicle control) or 10uM indisulam for 24h before RNA extraction and RNAseq

value: KURAMOCHI

value: Human ovarian high grade serous carcinoma


title: 3U

description: urethra treated 3U


title: 1U

description: urethra treated 1U


title: KURAMOCHI, 10uM indisulam, 24h, rep 2


title: p-pC_ISG_in_porcine_with_VNS_3

source_name: Inner submucosal ganglia from proximal colon

value: Inner submucosal ganglia


title: DMS273_HiChIP_H3K27ac

city: Bethesda

first: Lorinc

middle: Sandor

last: Pongor

state: Maryland

address: 37 Convent drive

department: NCI

institute: NIH

data_processing:
Sequenced reads were processed using the HicPro pipeline (v3.1.0), aligning the data to the hg19 genome version and MboI motif for the analysis.
The resulting valid read pairs were converted to a contact matrix “.hic” format with the hicpro2juicebox.sh tool from the Juicebox suite.
Bigwig files were generated using the BAMscale tool on the sorted genome alignment BAM files.
Assembly: hg19
Supplementary files format and content: hic: contact file
Supplementary files format and content: bw: normalized sequencing depth
Library strategy: HiChIP

source_name: Lung

growth_protocol: Cells were maintained in RPMI media  supplemented with 5% heat deactivated fetal bovine serum without antibiotics at 37 °C in a humidified atmosphere containing 5% CO2 and 95% air.

extract_protocol:
Briefly, cells grown at 70% confluency were detached, cross-linked with formaldehyde for 10mins and quenched with 125mM Glycine.
Cells were lysed in preparation for in-situ contact generation. Isolated nuclei were permeabilized, restriction digestion was carried out for 2hrs at 37C with MboI (New England Biolabs). Restriction sites filed with dNTP’s using Biotin-14-dATP (Jena Biosciences) for 1hr at 37C. The filled ends were then ligated together using a T4 ligase at room temperature for 4 hr with before nuclei were lysed, sonicated (using Covaris) and then H3k27ac (Abcam, ab4729) immunoprecipitation was carried out overnight using antibodies. The morning after, 30ul of beads were added to collect the chromatin-antibody complex; then the ChIP DNA was collected, washed and crosslinks reversed overnight using Proteinase K. ChIP DNA was eluted and samples purified using the DNA Clean up kit. The DNA was quantified using a Qubit before biotin ligation junction capture using Streptavidin C-1 beads. Samples were washed and taken forward for Tn5 Tagmentation. Tagmentation and PCR amplification was performed as described8.
Libraries were size selected to 200–700 bp and sequenced on the NovaSeq 600 using paired-end sequencing.

value: Lung


title: p-pC_MG_in_naive_porcine_6


title: p-pC_ISG_in_porcine_with_VNS_2


title: 24D

description: DLP treated 24D


title: 9A

description: AP control 9A

source_name: Anterior prostate

value: Control


title: 8A

description: AP control 8A


title: KURAMOCHI, Vehicle, 24h, rep 2


title: KURAMOCHI, 10uM indisulam, 24h, rep 1


title: p-pC_MG_in_naive_porcine_4_1


title: 7A

description: AP control 7A


title: p-pC_ISG_in_naive_porcine_6


title: 18A

description: AP treated 18A


title: p-pC_MG_in_naive_porcine_4_2


title: 3A

description: AP treated 3A


title: 2U

description: urethra treated 2U


title: 17A

description: AP treated 17A


title: 7D

description: DLP control 7D


title: 1D

description: DLP treated 1D


title: p-pC_ISG_in_naive_porcine_5


title: StRG47-Reg-hCD45-5 (scRNA-seq)

city: Tarrytown

first: Gabrielle

last: Choonoo

state: NY

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals, Inc

library_source: transcriptomic single cell

data_processing:
The cell suspensions were loaded on a Chromium Connect Single Cell Liquid Handler (10X Genomics) and RNA-seq and V(D)J libraries were prepared using Chromium Next GEM Automated Single Cell 5’ Kit, v2 (10X Genomics)
Assembly: Human.B37.3-Mouse.mm10
Supplementary files format and content: Seurat R data object includes CD4 cell counts and clustering across all samples
Supplementary files format and content: Seurat R data object includes CD8 cell counts and clustering across all samples
Supplementary files format and content: Seurat R data object includes all cell counts and clustering across all samples
Supplementary files format and content: R data object includes CD4 TCR data across all samples
Supplementary files format and content: R data object includes CD8 TCR data across all samples

organism:
Homo sapiens
Mus musculus

source_name: colorectal tumor

extract_protocol:
Single cell suspensions of StRG colorectal tumors were sorted for CD45+ and collected into tubes containing PBS with 0.04% BSA.
The cell suspensions were loaded on a Chromium Connect Single Cell Liquid Handler (10X Genomics) and RNA-seq and V(D)J libraries were prepared using Chromium Next GEM Automated Single Cell 5’ Kit, v2 (10X Genomics)

value: colorectal tumor

value: StRG

tag: tumor class

value: StRG47 HIS regressor


title: StRG47-Reg-hCD45-4 (scRNA-seq)

tag: tissue


title: 10U

description: urethra control 10U


title: KURAMOCHI, Vehicle, 24h, rep 3

tag: cell line


title: p-pC_MG_in_naive_porcine_3


title: p-pC_ISG_in_naive_porcine_4_1


title: p-pC_ISG_in_naive_porcine_3


title: p-pC_ISG_in_porcine_with_VNS_1


title: Human_h-dC_MG_2

source_name: Myenteric ganglia from descending colon

value: median age 47 years old


title: p-pC_ISG_in_naive_porcine_2


title: 4U

description: urethra treated 4U


title: p-pC_ISG_in_naive_porcine_1


title: 2A

description: AP treated 2A


title: 6A

description: AP control 6A


title: p-pC_MG_in_naive_porcine_1


title: p-pC_ISG_in_naive_porcine_4_2


title: KURAMOCHI, Vehicle, 24h, rep 1


title: Human_h-aC_MG_4

source_name: Myenteric ganglia from ascending colon


title: StRG47-Prog-hCD45-6 (scRNA-seq)

value: StRG47 HIS progressor


title: StRG47-Reg-hCD45-2 (scRNA-seq)


title: WT control, endothelial cells

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

data_processing:
Sequencing data was aligned to Mus Musculus Reference Genome (version GRCm38).
For analysis, gene-level counts were normalized using the DESeq2 package, filtered to remove those with a median expression less than 32, and converted to log2.
Assembly: GRCm38
Supplementary files format and content: Comma-delimited format. Contains gene counts per sample

extract_protocol:
Lungs were collected and digested as described above and processed into a single cell suspension and stained with a panel of fluorophore conjugated antibodies. Immune cells (CD45+), epithelial cells (CD45-EpCAM+CD31-), and endothelial cells (CD45-EpCAM-CD31+),  were purified using the Aria II fluorescence activated cell sorter (BD Bioscience) and lysed in 350μL of Buffer RLT with β-ME (Qiagen). RNA was extracted using the RNeasy Mini kit (Qiagen) with on-column DNase digestion.
RNAseq libraries were prepared using 6ng of RNA and the Kapa library preparation kit (Roch) and sequenced at 2x75bp on Illumina instrument.

value: Endothelial cells

value: CD11c-Cre-/- Adar1fl/fl R26YFP

value: B.1.351 strain of SARS-CoV-2 virus


title: WT control, epithelial cells

value: Epithelial cells


title: Human_h-dC_MG_3

value: colon

value: Myenteric ganglia


title: p-dC_MG_in_porcine_with_VNS_3

value: Yucatan minipigs

value: ~7 months old

value: Electrical stimulation of the celiac branch of the abdominal vagus nerve


title: StRG47-Reg-hCD45-3 (scRNA-seq)


title: ADAR1 KO, immune cells

value: Immune cells

value: CD11c-Cre+/- Adar1fl/fl R26YFP


title: StRG47-Prog-hCD45-5 (scRNA-seq)


title: ADAR1 KO, epithelial cells

value: Lung


title: WT control, immune cells


title: ADAR1 KO, endothelial cells


title: p-dC_MG_in_porcine_with_VNS_2


title: Human_h-dC_MG_4


title: StRG47-Reg-hCD45-1 (scRNA-seq)

value: colorectal tumor


title: Human_h-dC_MG_1


title: Tobacco leaf tissue - K326×JCP_rep1

city: Guiyang

first: kai

last: pi

state: Guizhou

department: Key Laboratory for Tobacco Quality Research Guizhou Province

country: China

institute: Guizhou University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome） with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) .
RSEM （http://deweylab.github.io/RSEM/）establishes the maximum likelihood abundance estimation model based on the maximum expectation algorithm, and considers the paid end reads, the length of reads, the length distribution of fragments, and the quality value to distinguish which transcripts are different subtypes of the same gene. The results of expression quantification are expressed in TPM/FPKM. The homogenization process of TPM/FPKM makes the total expression amount in different samples consistent.
Assembly: Tobacco K326 Reference Genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome）
Supplementary files format and content: all_ express.txt includes 15 transcriptome sequencing materials and 69500 gene expressions. The file can be opened in Excel for viewing.

organism: Nicotiana tabacum

source_name: hybrid K326×JCP

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) andquantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. After quantified by TBS380, paired-end RNA-seq   sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 ×   150bp read length)

tag: developmental stage

value: seedling stage

value: Young root


title: Tobacco leaf tissue - K326×JCP_rep2


title: StRG47-Prog-hCD45-3 (scRNA-seq)

value: StRG


title: Human_h-aC_MG_3

value: median age 47 years old


title: Tobacco leaf tissue - K326×JCP_rep3


title: Human_h-aC_MG_2


title: StRG47-Prog-hCD45-1 (scRNA-seq)

value: StRG47 HIS progressor


title: StRG47-Reg-hCD45-5 (TCR-seq)

value: StRG47 HIS regressor


title: p-dC_MG_in_porcine_with_VNS_1


title: StRG47-Prog-hCD45-2 (scRNA-seq)


title: p-dC_MG_in_naive_porcine_4

value: untreated


title: p-dC_MG_in_naive_porcine_6


title: StRG47-Reg-hCD45-4 (TCR-seq)


title: StRG47-Prog-hCD45-4 (scRNA-seq)


title: Human_h-aC_MG_1


title: StRG47-Reg-hCD45-2 (TCR-seq)


title: StRG47-Reg-hCD45-3 (TCR-seq)


title: p-dC_MG_in_naive_porcine_2


title: Tobacco leaf tissue - G70×JCP_rep3

source_name: hybrid G70×JCP


title: StRG47-Reg-hCD45-1 (TCR-seq)


title: p-dC_MG_in_naive_porcine_1


title: shFF2_24hr_plusTam_2

city: Houston

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

institute: Baylor College of Medicine

description: Control 24hr 4-OHT replicate 3

data_processing:
After demultiplexing, reads were processed using SAMtools (v1.4) and aligned using Hisat2 (v2.0.4) with default parameters.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: mammary

growth_protocol: MYC-ER HMEC mammary epithelial cells were cultured in MEGM media (Lonza) and treated with 60 nM 4-hydroxytamoxifen (4-OHT) to induce MYC-hyperactivation in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA (1µg/sample) was used as input for the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB)
After rRNA depletion, libraries were made using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®, and quantified using KAPA Library Quantification Kit.
Libraries were pooled and sequenced on the NextSeq 500/550.

treatment_protocol: 4-OHT (60nM) was addedd to induce MYC. Control cells were treated with EtOH.

value: mammary

value: HMEC

value: epithelial cells

value: control


title: shFF2_24hr_plusTam_0

description: Control 24hr 4-OHT replicate 1


title: Tobacco leaf tissue - G70×JCP_rep2


title: Tobacco leaf tissue - G70×JCP_rep1


title: shFF2_24hr_plusTam_1

description: Control 24hr 4-OHT replicate 2


title: StRG47-Prog-hCD45-6 (TCR-seq)


title: Tobacco leaf tissue - K326_rep1

source_name: Female parent K326 of hybrid K326×JCP


title: p-dC_MG_in_naive_porcine_3

value: Yucatan minipigs

value: colon

value: ~7 months old

value: Myenteric ganglia


title: p-dC_MG_in_naive_porcine_5


title: p-dC_ISG_in_porcine_with_VNS_3

source_name: Inner submucosal ganglia from descending colon

value: Inner submucosal ganglia

value: Electrical stimulation of the celiac branch of the abdominal vagus nerve


title: StRG47-Prog-hCD45-5 (TCR-seq)

value: colorectal tumor


title: StRG47-Prog-hCD45-4 (TCR-seq)


title: shFF2_24hr_minusTam_2

description: Control 24hr EtOH replicate 3

value: EtOH


title: Tobacco leaf tissue - K326_rep3

value: seedling stage

value: Young root


title: shFF2_24hr_minusTam_1

description: Control 24hr EtOH replicate 2


title: p-dC_ISG_in_porcine_with_VNS_2


title: p-dC_ISG_in_naive_porcine_6


title: Tobacco leaf tissue - JCP_rep2

source_name: male parent JCP of hybrid G70×JCP

value: JCP


title: Tobacco leaf tissue - K326_rep2


title: shDIS3L_24hr_plusTam_2

description: shDIS3L 24hr 4-OHT replicate 3

value: DIS3L knockdown


title: shFF2_24hr_minusTam_0

description: Control 24hr EtOH replicate 1


title: StRG47-Prog-hCD45-2 (TCR-seq)

value: StRG

value: StRG47 HIS progressor


title: shDIS3L_24hr_plusTam_1

description: shDIS3L 24hr 4-OHT replicate 2

value: mammary

value: HMEC


title: Tobacco leaf tissue - JCP_rep3


title: p-dC_ISG_in_naive_porcine_4

value: untreated


title: shDIS3L_24hr_minusTam_2

description: shDIS3L 24hr EtOH replicate 3

value: epithelial cells


title: p-dC_ISG_in_naive_porcine_3

value: Yucatan minipigs

value: colon


title: Tobacco leaf tissue - G70_rep3

source_name: Female parent G70 of hybrid G70×JCP


title: WT

source_name: Human fibroblasts infected by T. gondii RH strain

value: HFF

value: Human fibroblasts

value: infected by T. gondii RH strain

value: wild-type parasites


title: StRG47-Prog-hCD45-3 (TCR-seq)

value: colorectal tumor


title: p-dC_ISG_in_naive_porcine_2

value: ~7 months old

value: Inner submucosal ganglia


title: Tobacco leaf tissue - JCP_rep1

value: seedling stage

value: Young root

value: JCP


title: p-dC_ISG_in_naive_porcine_1


title: Spleen - control

data_processing:
Single cell RNA-seq data on Lung (LU) and spleen (SP) were analyzed separately using Seurat (Stuart et al., 2019). Cells containing number of feature RNA less than 200 were removed. Filtered RNA counts were normalized using LogNormalize method implemented in Seurat with a scale factor of 10,000. FindIntegrationAnchors and IntegrateData function in Seurat were used to integrate all the samples.
Assembly: mm10
Supplementary files format and content: Barcodes - tab delimited, gzipped
Supplementary files format and content: Gene lists - tab delimited, gzipped
Supplementary files format and content: Count matrices - tab delimited, gzipped

source_name: Spleen

extract_protocol:
10x Genomics standard extraction protocol
Chromium single cell standard protocol

value: Spleen

value: Sorted T cells, alveolar macrophages (AMs), and CD11c+SiglecF- cells, and other immune cells

value: WT


title: p-dC_ISG_in_porcine_with_VNS_1

value: Electrical stimulation of the celiac branch of the abdominal vagus nerve


title: Tobacco leaf tissue - G70_rep2


title: HUVEC_rep3_promoter

status: Public on Jan 21 2023

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

description: DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

data_processing:
Library strategy: NG Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie 2
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Genome_build: hg19
Supplementary_files_format_and_content: custom format (chr start stop interactions viewpoint)

source_name: HUVEC (PromoCell)

growth_protocol: Fresh blood was sourced either as 100 ml whole blood collected from three healthy donors (two males, one female) using EDTA Vacuettes (Becton Dickson) or 5 ml leukocyte cones (NHS Blood & Transport). Whole cell counts were performed on a Pentra ES60 (Horiba) for donor blood to ensure clinically healthy red blood cell counts. Blood was diluted with PBS and overlaid onto Histopaque-1077 (Sigma) and centrifuged for 30 min at 630 rcf (no brake). Peripheral Blood Mononuclear Cells (PBMCs) were washed in PBS and MACS buffer (PBS, 2 µM EDTA, 0.5% BSA) and stained with Human CD34 Microbead kit (Miltenyi Biotec) following the manufacturer’s instruction for 30 minutes (4 ºC) before being passed successively through two LS Columns (Miltenyi Biotec) with three MACs buffer washes. Counting of cells was performed on a Luna FL (Logos) after staining with acridine orange (AO) and propidium iodide (PI). CD34+ cells were either stored in freezing buffer (90% FBS, 10% DMSO) or resuspended in Phase I mediumfor a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 0.5-2.5x105 cells were resuspended on day 0 in Phase I media at 10^5 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 10^5 cells ml-1. On day 7, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase II media at 3x10^5 cells ml-1. Cells were counted on day 9 and diluted to 3x105 cells ml-1 Phase II media. On day 11, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase III media at 106 cells ml-1. Cells were counted on days 13 and 15 and diluted to 10^6 cells ml-1 in Phase III media. Reproducibility between differentiations was confirmed morphologically with cytospins and immunologically with six FACS cell surface markers (CD34, CD36/Fatty acid translocase, CD71/Transferrin receptor, CD235a/Glycophorin A, CD49d/α-Integrin, CD233/Band). Human ESC line H1 (H1-hESC; WiCell) was grown on Matrigel (Corning) coated plates in mTeSR1 medium (StemCell technologies). Cells were harvested as a single cell suspension using Accutase (EDM Millipore); Fixation were carried out in mTeSR1 medium. Primary neonatal Human Umbilical Vein Endothelial Cells (HUVEC) were sourced from three suppliers to provide genetic diversity (Lonza, Gibco, PromoCell). HUVECs were expanded in endothelial cell growth medium (Sigma) up to five passages following the manufacturer’s protocol. Briefly, HUVECs were grown to 60% confluence, washed with HBSS at room temperature and sub-cultured following light trypsination using Trypsin-EDTA (Sigma) at room temperature and terminating the reaction with trypsin inhibitor (Sigma) upon rounding of the cells and gentle release from the flask. HUVECs were fixed in RPMI supplemented with 10 % FBS.

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies)
5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads)

value: HUVEC

tag: day of differentiation

tag: Sex


title: Huh7-NT 1

city: Newcastle upon Tyne

first: Ruchi

last: Shukla

address: Ellison A Building

department: Applied Biosciences

institute: Northumbria University

data_processing:
RNAseq alignment tool (V1.1.1)
Differential expression using DEseq2
Genome_build: UCSC hg19
Supplementary_files_format_and_content: counts

source_name: liver

growth_protocol: Cell lines were maintained in Dulbecco’s modiﬁed Eagle’s medium supplemented with 10% fetal calf serum and antibiotics and incubated at 37°C with 5% CO2.followed by puromycin selection

extract_protocol:
Total RNA was isolated using RNeasy kit (Qiagen)
Illumina Tru-seq stranded mRNA library

treatment_protocol: For stable L1-knockdown, cells were transduced with  lentiviruses encoding L1-targeting or control shRNA hence derived Huh7-L1-KD and Huh7-NT cell lines.

value: liver

value: control


title: shDIS3L_24hr_plusTam_0

description: shDIS3L 24hr 4-OHT replicate 1

value: mammary

value: HMEC

value: epithelial cells

value: DIS3L knockdown

tag: treatment


title: Huh7-NT 3


title: HUVEC_rep2_promoter

source_name: HUVEC (Gibco)


title: shDIS3L_24hr_minusTam_1

description: shDIS3L 24hr EtOH replicate 2

value: EtOH


title: Lungs - control

source_name: Lung

value: Lung


title: HUVEC_rep3_enhancer


title: Spleen - ADAR1 conditional knockout


title: Huh7-L1-KD 2


title: StRG47-Prog-hCD45-1 (TCR-seq)

value: colorectal tumor

value: StRG

value: StRG47 HIS progressor


title: p-dC_ISG_in_naive_porcine_5

value: Yucatan minipigs

value: colon

tag: age

value: ~7 months old

value: Inner submucosal ganglia

value: untreated


title: Huh7-L1-KD 3

tag: genotype


title: Tobacco leaf tissue - G70_rep1

value: seedling stage

value: Young root


title: Lungs - ADAR1 conditional knockout

tag: cell type

value: Sorted T cells, alveolar macrophages (AMs), and CD11c+SiglecF- cells, and other immune cells


title: Huh7-L1-KD 1

value: liver


title: hESC_rep1_promoter

source_name: H1 hESC (WiCell)

value: H1 hESC

value: Male


title: hESC_rep2_promoter


title: shDIS3L_24hr_minusTam_0

description: shDIS3L 24hr EtOH replicate 1

value: mammary

value: HMEC

value: epithelial cells

value: DIS3L knockdown


title: HUVEC_rep2_enhancer

value: HUVEC


title: Ery_Don001_promoter

source_name: CD34 Culture

value: Erythroid

value: Day 10

value: Female

tag: donor id


title: Huh7-NT 2

value: control


title: ChIP_NCO9_d10jf_Input

description: Genome-wide library of Immunoprecipitated fragments

data_processing:
Mapping : bowtie -m 2 --maxIns 350, hg9
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig : (DEEPtools) bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

growth_protocol: Fresh blood was sourced either as 100 ml whole blood collected from three healthy donors (two males, one female) using EDTA Vacuettes (Becton Dickson) or 5 ml leukocyte cones (NHS Blood & Transport). Whole cell counts were performed on a Pentra ES60 (Horiba) for donor blood to ensure clinically healthy red blood cell counts. Blood was diluted with PBS and overlaid onto Histopaque-1077 (Sigma) and centrifuged for 30 min at 630 rcf (no brake). Peripheral Blood Mononuclear Cells (PBMCs) were washed in PBS and MACS buffer (PBS, 2 µM EDTA, 0.5% BSA) and stained with Human CD34 Microbead kit (Miltenyi Biotec) following the manufacturer’s instruction for 30 minutes (4 ºC) before being passed successively through two LS Columns (Miltenyi Biotec) with three MACs buffer washes. Counting of cells was performed on a Luna FL (Logos) after staining with acridine orange (AO) and propidium iodide (PI). CD34+ cells were either stored in freezing buffer (90% FBS, 10% DMSO) or resuspended in Phase I mediumfor a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 0.5-2.5x105 cells were resuspended on day 0 in Phase I media at 105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase II media at 3x105 cells ml-1. Cells were counted on day 9 and diluted to 3x105 cells ml-1 Phase II media. On day 11, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase III media at 106 cells ml-1. Cells were counted on days 13 and 15 and diluted to 106 cells ml-1 in Phase III media. Reproducibility between differentiations was confirmed morphologically with cytospins and immunologically with six FACS cell surface markers (CD34, CD36/Fatty acid translocase, CD71/Transferrin receptor, CD235a/Glycophorin A, CD49d/α-Integrin, CD233/Band).

extract_protocol:
isolation protocol: For ChIP-seq, chromatin was crosslinked with 1 % formaldehyde (Sigma) by the addition of 1 ml 10x crosslinking buffer (50 mM HEPES, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 10 % formaldehyde) to 10^7 cells in 9 ml of media and incubation at room temperature for 10 minutes. Crosslinking was quenched with 130 mM glycine, and cells were washed with cold PBS before snap freezing pelleted cells. Fixed material was stored at -80 ºC for less than 12 months. Chromatin immunoprecipitation was performed using Agarose ChIP Assay Kit (Merck Millipore). Briefly, 10^7 cells were lysed by incubation on ice with 130 µl lysis buffer for 15 minutes. Lysed cells were transferred to Covaris microtubes and sonicated on the Covaris S220 (Duty cycle: 2 %, Intensity: 3, Cycles per burst: 200, Power mode: Frequency sweeping, Duration: 480 sec, Temp.: 6 ºC) to generate 200-400 bp fragments. Insoluble material was removed by centrifugation (15,000 rcf, 15 min, 4 ºC) and soluble material was diluted to 4 ml with dilution buffer. Immunoprecipitation was performed by incubation of 2 ml diluted chromatin (equivalent to 5x106 input cells) with antibodies for H3K4me1 (3 µg ab195391, lot: GR304893-2; AbCam), H3K4me3 (1 µl 07-473, lot: 2664283; Millipore), H3K27ac (0.3 µg ab4729, lot: GR3205523-1; AbCam), or CTCF (10 µl 07-729, lot: 2836929; Millipore) overnight. Chromatin binding to Protein A/agarose slurry, washes and elution were performed according to the manufacturer’s instructions.
DNA was purified by phenol-chloroform extraction with PhaseLock tubes (5Prime) and ethanol precipitation with NaOAc, and 2 µl GlycoBlue (Invitrogen). ChIP enrichment was determined by RT-qPCR
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

tag: antibody

tag: differentiation day


title: Ery_Don002_promoter


title: Ery_Don002_enhancer


title: Ery_Don003_enhancer


title: ChIP_NCO9_d10jf_H3K27ac


title: hESC_rep1_enhancer


title: hESC_rep2_enhancer


title: Ery_Don001_enhancer


title: ChIP_NCO18_d10jf_H3K4me3


title: hESC_rep3_enhancer


title: ChIP_NCO20_d10jf_H3K4me3


title: ChIP_NCO20_d10jf_Input


title: ChIP_NCO20_d10jf_H3K27ac


title: ChIP_NCO9_d10jf_H3K4me1


title: HUVEC_rep1_promoter

source_name: HUVEC (Lonza)


title: ChIP_NCO9_d10jf_H3K4me3


title: hESC_rep3_promoter


title: ChIP_NCO18_d10jf_Input


title: ChIP_NCO20_d10jf_CTCF


title: ChIP_NCO9_d10jf_CTCF


title: Ery_Don003_promoter


title: ChIP_NCO18_d10jf_H3K4me1


title: ChIP_NCO20_d10jf_H3K4me1


title: HUVEC_rep1_enhancer


title: ChIP_NCO18_d10jf_H3K27ac


title: RNAseq_WT_rep3_d0

data_processing:
Mapping: STAR --runThreadN 4 --outFilterMultimapNmax 1
Duplicate removal: samtools rmdup
Genome_build: hg19
Supplementary_files_format_and_content: bigwig: forward reads (deeptools) - bamCoverage -p4 --binSize 1 --normalizeUsingRPKM --filterRNAstrand forward
Supplementary_files_format_and_content: bigwig: reverse reads (deeptools) - bamCoverage -p4 --binSize 1 --normalizeUsingRPKM --filterRNAstrand reverse

growth_protocol:
Human Umbilical Derived Erythroid Progenitor line 2 cells (HUDEP-2; Kurita, PLoS One 2013) were maintained at 0.7-1.5x106 cells ml-1 in HUDEP expansion media and changed into fresh media containing 2x doxycycline (DOX) every two days. For differentiation we used a modified version of the CD34 BEL-A differentiation protocol (Trakarnsanga, Nat. Comm 2017). 2-3x106 cells were resuspended at 0.3-05x106 cells ml-1 in HUDEP Phase I media with 1x DOX on day 0. On days 1 and 3 cells were counted, pelleted (5 min, 250 rcf, RT) and resuspended to 0.3-0.5x106 cells ml-1 in fresh HUDEP Phase I media supplemented with 2x DOX. On day 5, cells were counted, pelleted and resuspended to 0.5x106 cells ml-1 in HUDEP Phase II media without DOX. On days 7 and 9 cells were counted, pelleted and resuspended to 0.5x106 cells ml-1 in fresh HUDEP Phase II media.
1-5x106 cells were fixed in 1 ml TRI-reagent (Sigma), snap frozen and stored at -80ºC for less than one year.

extract_protocol:
RNA was extracted by addition of 0.1 ml 1-bromo-3-chloropropane, pipette mixing and separation in a Phase Lock gel Heavy tube (5Prime) and then precipitation with 1 µl of GlycoBlue and an equal volume (~500 µl) isopropanol and centrifugation (10 min, 12,000 rcf, 4 ºC). The RNA pellet was washed with 75 % ethanol, resuspended in DEPC-treated water, and stored at -80 ºC for less than one year.
For RNA-seq total RNA was treated with Turbo DNAse (Invitrogen) at 25 ºC for 60 min, then RNA was separated using phenol-chloroform isoamylalcohol and a PhaseLock Light-gel tube (5Prime).  Treated RNA was precipitated at -80 ºC overnight with sodium acetate, glycoblue, and 75 % ethanol, before centrifugation (12,000 rcf, 4 ºC), 75 % ethanol wash and resuspension in DEPC-treated water. Globin and rRNA sequences were depleted from up to 5 µg of treated RNA using Globin-Zero Gold (Illumina), before PolyA selection with NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs), and indexing with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturers’ instructions.

value: expansion


title: RNAseq_WT_rep1_d0


title: RNAseq_WT_rep1_d7

value: Day 7


title: RNAseq_rs10758656_G_d7_clone1E4

value: CRISPR/Cas9 Edited


title: RNAseq_rs10758656_G_d10_clone3A6


title: RNAseq_rs10758656_A_d7_clone12C6


title: RNAseq_rs10758656_A_d10_clone13D7


title: RNAseq_WT_rep2_d0


title: RNAseq_rs10758656_A_d10_clone15E8


title: RNAseq_rs10758656_G_d0_clone1A2


title: ChIP_NCO18_d10jf_CTCF


title: RNAseq_WT_rep2_d7


title: RNAseq_rs10758656_A_d7_clone15E8


title: RNAseq_rs10758656_A_d0_clone13D7


title: RNAseq_rs10758656_G_d0_clone3A6


title: Input_WT_exp_rep2

description: Genome-wide library of sonicated fragments

growth_protocol:
Human Umbilical Derived Erythroid Progenitor line 2 cells (HUDEP-2; Kurita, PLoS One 2013) were maintained at 0.7-1.5x106 cells ml-1 in HUDEP expansion media and changed into fresh media containing 2x doxycycline (DOX) every two days. For differentiation we used a modified version of the CD34 BEL-A differentiation protocol (Trakarnsanga, Nat. Comm 2017). 2-3x106 cells were resuspended at 0.3-05x106 cells ml-1 in HUDEP Phase I media with 1x DOX on day 0. On days 1 and 3 cells were counted, pelleted (5 min, 250 rcf, RT) and resuspended to 0.3-0.5x106 cells ml-1 in fresh HUDEP Phase I media supplemented with 2x DOX. On day 5, cells were counted, pelleted and resuspended to 0.5x106 cells ml-1 in HUDEP Phase II media without DOX. On days 7 and 9 cells were counted, pelleted and resuspended to 0.5x106 cells ml-1 in fresh HUDEP Phase II media.
For ChIP-seq, chromatin was crosslinked with 1 % formaldehyde (Sigma) by the addition of 1 ml 10x crosslinking buffer (50 mM HEPES, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 10 % formaldehyde) to 107 cells in 9 ml of media and incubation at room temperature for 10 minutes. Crosslinking was quenched with 130 mM glycine, and cells were washed with cold PBS before snap freezing pelleted cells. Fixed material was stored at -80 ºC for less than 12 months. Chromatin immunoprecipitation was performed using Agarose ChIP Assay Kit (Merck Millipore). Briefly, 107 cells were lysed by incubation on ice with 130 µl lysis buffer for 15 minutes. Lysed cells were transferred to Covaris microtubes and sonicated on the Covaris S220 (Duty cycle: 2 %, Intensity: 3, Cycles per burst: 200, Power mode: Frequency sweeping, Duration: 480 sec, Temp.: 6 ºC) to generate 200-400 bp fragments. Insoluble material was removed by centrifugation (15,000 rcf, 15 min, 4 ºC) and soluble material was diluted to 4 ml with dilution buffer. Immunoprecipitation was performed by incubation of 2 ml diluted chromatin (equivalent to 5x106 input cells) with antibodies for H3K27ac (0.3 µg ab4729, lot: GR3205523-1; AbCam) or Gata-1 (~7.2 µg ab11852, lots: GR290167-7, GR239235-8; AbCam) overnight. Chromatin binding to Protein A/agarose slurry, washes and elution were performed according to the manufacturer’s instructions.

extract_protocol:
DNA was purified by phenol-chloroform extraction with PhaseLock tubes (5Prime) and ethanol precipitation with NaOAc, and 2 µl GlycoBlue (Invitrogen). ChIP enrichment was determined by RT-qPCR
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).


title: RNAseq_WT_rep3_d7


title: RNAseq_rs10758656_A_d10_clone12C6


title: RNAseq_rs10758656_G_d10_clone1A2


title: RNAseq_rs10758656_G_d0_clone1E4


title: RNAseq_rs10758656_G_d7_clone3A6


title: Escherichia coli K-12 tetracycline treated culture replicate 3 (VCE non-enriched 5’ end of primary transcripts)

city: Orenburg

first: Alexander

middle: S

last: Balkin

address: 11 Pionerskaya st.

country: Russia

institute: Institute for Cellular and Intracellular Symbiosis

description:
total RNA
Cappable-Seq library of Escherichia coli K-12 tetracycline treated culture (VCE non-enriched 5’ end of primary transcripts)

data_processing:
Demultiplexed reads were trimmed against adapters and ribosomal RNA with bbduk.
Clean reads were mapped against the Escherichia coli K-12 full genome (GCA_000005845.2) with Bowtie2 in local mode (L-16).
The reads per transcript coverage of Ultra directional libraries were evaluated with Salmon (Patro et al., 2017).
The reads per tss were evaluated with perl script as previously described (https://github.com/Ettwiller/TSS).
Assembly: GCA_000005845.2
Supplementary files format and content: Tabular file include operon coverage values for each sample .

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: Escherichia coli K-12 was grown on Luria broth at 37°C without antibiotics up to the logarithmic phase.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Thermo Fisher Scientific, Waltham, MA USA). The RNA samples were treated with a TURBO DNA-free™ kit (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions. The RNA content was determined in a Qubit fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity, purity, and concentration were assessed with a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
The Cappable-Seq procedure was performed as previously described [Ettwiller et al., 2016]. The Ultra directional libraries was prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA)
library strategy: Cappable-Seq/Ultra directional

treatment_protocol: Logarithmic culture of E. coli on rich medium was treated with tetracycline (20 mg / L, 30 min.), rifampicin (50 mg / L, 30 min.), and novobiocin (100 mg / L, 20 min.).

tag: strain

tag: condition

value: tetracycline treated


title: RNAseq_rs10758656_A_d0_clone12C6


title: Input_rs10758656_G_exp_clone1A2


title: Input_rs10758656_G_d7_clone3A6


title: Input_rs10758656_G_exp_clone3A6


title: Escherichia coli K-12 tetracycline treated culture replicate 3 (VCE enriched 5’ end of primary transcripts)

description:
total RNA enriched for primary transcripts
Cappable-Seq library of Escherichia coli K-12 tetracycline treated culture (VCE enriched 5’ end of primary transcripts)


title: Input_rs10758656_A_d7_clone13D7


title: Input_rs10758656_G_d7_clone1A2


title: RNAseq_rs10758656_G_d7_clone1A2


title: Escherichia coli K-12 tetracycline treated culture replicate 2 (VCE non-enriched 5’ end of primary transcripts)


title: RNAseq_rs10758656_A_d7_clone13D7


title: RNAseq_rs10758656_A_d0_clone15E8


title: H3K27ac_rs10758656_G_d7_clone1E4


title: H3K27ac_rs10758656_G_d7_clone3A6


title: Input_rs10758656_G_d7_clone1E4


title: Escherichia coli K-12 tetracycline treated culture replicate 3 (Ultra directional library preparation)

description:
total RNA
Ultra directional library of Escherichia coli K-12 tetracycline treated culture total RNA non treated with antibiotic


title: RNAseq_rs10758656_G_d10_clone1E4


title: Input_WT_exp_rep1


title: Input_WT_exp_rep3


title: Gata1_WT_exp_rep3


title: Gata1_WT_exp_rep2


title: Input_rs10758656_G_exp_clone1E4


title: Escherichia coli K-12 tetracycline treated culture replicate 1 (VCE non-enriched 5’ end of primary transcripts)


title: Input_rs10758656_A_d7_clone12C6


title: Escherichia coli K-12 rifampicin treated culture replicate 3 (VCE non-enriched 5’ end of primary transcripts)

description:
total RNA
Cappable-Seq library of Escherichia coli K-12 rifampicin treated culture (VCE non-enriched 5’ end of primary transcripts)

value: rifampicin treated


title: Gata1_rs10758656_G_exp_clone1E4


title: Gata1_rs10758656_G_exp_clone3A6


title: Escherichia coli K-12 tetracycline treated culture replicate 2 (VCE enriched 5’ end of primary transcripts)


title: Gata1_rs10758656_G_d7_clone3A6


title: Escherichia coli K-12 tetracycline treated culture replicate 1 (Ultra directional library preparation)


title: Escherichia coli K-12 rifampicin treated culture replicate 3 (VCE enriched 5’ end of primary transcripts)

description:
total RNA enriched for primary transcripts
Cappable-Seq library of Escherichia coli K-12 rifampicin treated culture (VCE enriched 5’ end of primary transcripts)


title: H3K27ac_rs10758656_A_d7_clone13D7


title: Gata1_WT_exp_rep1


title: Escherichia coli K-12 tetracycline treated culture replicate 2 (Ultra directional library preparation)


title: Escherichia coli K-12 rifampicin treated culture replicate 2 (VCE enriched 5’ end of primary transcripts)


title: Escherichia coli K-12 rifampicin treated culture replicate 2 (VCE non-enriched 5’ end of primary transcripts)


title: Gata1_rs10758656_A_d7_clone13D7


title: Escherichia coli K-12 novobiocin treated culture replicate 3 (VCE enriched 5’ end of primary transcripts)

description:
total RNA enriched for primary transcripts
Cappable-Seq library of Escherichia coli K-12 novobiocin treated culture (VCE enriched 5’ end of primary transcripts)

value: novobiocin treated


title: Input_rs10758656_A_d7_clone15E8


title: Gata1_rs10758656_G_exp_clone1A2


title: Escherichia coli K-12 novobiocin treated culture replicate 3 (Ultra directional library preparation)

description:
total RNA
Ultra directional library of Escherichia coli K-12 novobiocin treated culture total RNA non treated with antibiotic


title: ATACseq_rs9349205_G_d0_cloneG4_rep1

description: Genome-wide library of tagmented fragments

data_processing:
Library Strategy: ATAC-seq
Mapping : bowtie -m 2 --maxIns 350, hg9
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig : (DEEPtools) bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

growth_protocol: Human Umbilical Derived Erythroid Progenitor line 2 cells (HUDEP-2; Kurita, PLoS One 2013) were maintained at 0.7-1.5x106 cells ml-1 in HUDEP expansion media and changed into fresh media containing 2x doxycycline (DOX) every two days. For differentiation we used a modified version of the CD34 BEL-A differentiation protocol (Trakarnsanga, Nat. Comm 2017). 2-3x106 cells were resuspended at 0.3-05x106 cells ml-1 in HUDEP Phase I media with 1x DOX on day 0. On days 1 and 3 cells were counted, pelleted (5 min, 250 rcf, RT) and resuspended to 0.3-0.5x106 cells ml-1 in fresh HUDEP Phase I media supplemented with 2x DOX. On day 5, cells were counted, pelleted and resuspended to 0.5x106 cells ml-1 in HUDEP Phase II media without DOX. On days 7 and 9 cells were counted, pelleted and resuspended to 0.5x106 cells ml-1 in fresh HUDEP Phase II media.

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).


title: ATACseq_rs9349205_G_d0_cloneG4_rep2


title: Escherichia coli K-12 novobiocin treated culture replicate 2 (Ultra directional library preparation)


title: Escherichia coli K-12 rifampicin treated culture replicate 3 (Ultra directional library preparation)

description:
total RNA
Ultra directional library of Escherichia coli K-12 rifampicin treated culture total RNA non treated with antibiotic


title: Escherichia coli K-12 rifampicin treated culture replicate 2 (Ultra directional library preparation)


title: ATACseq_rs9349205_G_d0_cloneD7_rep1


title: Escherichia coli K-12 novobiocin treated culture replicate 3 (VCE non-enriched 5’ end of primary transcripts)

description:
total RNA
Cappable-Seq library of Escherichia coli K-12 novobiocin treated culture (VCE non-enriched 5’ end of primary transcripts)


title: Escherichia coli K-12 novobiocin treated culture replicate 1 (VCE non-enriched 5’ end of primary transcripts)


title: Escherichia coli K-12 tetracycline treated culture replicate 1 (VCE enriched 5’ end of primary transcripts)


title: Escherichia coli K-12 rifampicin treated culture replicate 1 (VCE enriched 5’ end of primary transcripts)


title: Escherichia coli K-12 rifampicin treated culture replicate 1 (Ultra directional library preparation)


title: Escherichia coli K-12 novobiocin treated culture replicate 1 (VCE enriched 5’ end of primary transcripts)


title: ATACseq_rs9349205_G_d0_cloneA3_rep2


title: Escherichia coli K-12 rifampicin treated culture replicate 1 (VCE non-enriched 5’ end of primary transcripts)


title: Gata1_rs10758656_A_d7_clone15E8


title: ATACseq_rs9349205_G_d0_cloneD5_rep1


title: Gata1_rs10758656_G_d7_clone1E4


title: Escherichia coli K-12 control culture replicate 3 (VCE enriched 5’ end of primary transcripts)

description:
total RNA enriched for primary transcripts
Cappable-Seq library of Escherichia coli K-12 control culture (VCE enriched 5’ end of primary transcripts)

source_name: Escherichia coli K-12 control culture


title: Escherichia coli K-12 novobiocin treated culture replicate 2 (VCE non-enriched 5’ end of primary transcripts)


title: ATACseq_rs4508712_G_d0_cloneD10_rep1


title: Gata1_rs10758656_A_d7_clone12C6


title: ATACseq_rs9349205_G_d0_cloneA3_rep1


title: Escherichia coli K-12 control culture replicate 3 (Ultra directional library preparation)

description:
total RNA
Ultra directional library of Escherichia coli K-12 control culture total RNA non treated with antibiotic


title: Escherichia coli K-12 control culture replicate 1 (Ultra directional library preparation)


title: Gata1_rs10758656_G_d7_clone1A2


title: differentiation of hIPSC line WTSIi004-A to dopaminergic neurons day 7 NICD condition

city: Saint-Petersburg

first: Nataliia

middle: Victorovna

last: Katolikova

address: Universitetskaya emb. 7-9-11

department: Institute of Translational Biomedicine

institute: Saint-Petersburg State University

data_processing:
The Fastq sequences were checked for quality using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Fastq sequences were trimmed using Cutadapt v4.1 with default parameters for single-strand reads
Quantify transcript expression, pre-processed reads were aligned to the reference genome with STAR
Gene expression was calculated with featureCounts from Subread package
Gene expression was performed using the DeSeq2 R package
Transcript variants were annotated with AnnotationDbi R package
Assembly: GENCODE v36
Supplementary files format and content: tab-delimited text files

extract_protocol:
Cells were washed by PBS and isolated using ExtractRNA reagent (cat. # BC032, Eurogen) All procedures were performed according manufacture’s recommendations.
Quality of RNA was checked with fluorimetric analysis by Quantus and capillary electrophoresis by QIAxel. PolyA RNA was purified with Dynabeads mRNA Purification Kit (Ambion). Libraries were made from polyA RNA with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manual. Single-read sequencing was performed on Illumina HiSeq2500 with 140 bp read length, with at least 30 million reads generated for each sample.

value: differentiated human induced pluripotent stem cells day 7

value: NICD overexpression


title: ATACseq_rs9349205_G_d0_cloneD5_rep2


title: ATACseq_rs10758656_G_d10_clone3A6_rep1


title: Escherichia coli K-12 control culture replicate 3 (VCE non-enriched 5’ end of primary transcripts)

description:
total RNA
Cappable-Seq library of Escherichia coli K-12 control culture (VCE non-enriched 5’ end of primary transcripts)


title: differentiation of hIPSC line WTSIi004-A to dopaminergic neurons day 7 DAPT condition

value: DAPT


title: ATACseq_rs10758656_G_d7_clone3A6_rep1


title: Escherichia coli K-12 novobiocin treated culture replicate 2 (VCE enriched 5’ end of primary transcripts)


title: ATACseq_rs10758656_G_d0_clone3A6_rep1


title: ATACseq_rs4508712_G_d0_cloneD10_rep2


title: Escherichia coli K-12 novobiocin treated culture replicate 1 (Ultra directional library preparation)


title: Escherichia coli K-12 control culture replicate 2 (Ultra directional library preparation)


title: ATACseq_rs9349205_G_d0_cloneD7_rep2


title: ATACseq_rs10758656_G_d7_clone1E4_rep1


title: differentiation of hIPSC line AD3 to dopaminergic neurons day 7 contr condition


title: ATACseq_rs10758656_G_d0_clone1E4_rep2


title: Escherichia coli K-12 control culture replicate 2 (VCE enriched 5’ end of primary transcripts)


title: Escherichia coli K-12 control culture replicate 2 (VCE non-enriched 5’ end of primary transcripts)


title: ATACseq_rs4508712_G_d0_cloneB1_rep2


title: ATACseq_rs4508712_G_d0_cloneC1_rep2


title: ATACseq_rs4508712_G_d0_cloneC1_rep1


title: ATACseq_rs10758656_G_d10_clone1E4_rep1


title: ATACseq_rs4508712_G_d0_cloneB3_rep1


title: ATACseq_rs4508712_G_d0_cloneB1_rep1


title: ATACseq_rs10758656_G_d7_clone1A2_rep2


title: Escherichia coli K-12 control culture replicate 1 (VCE enriched 5’ end of primary transcripts)


title: ATACseq_rs10758656_G_d7_clone3A6_rep2


title: ATACseq_rs10758656_G_d10_clone3A6_rep2


title: ATACseq_rs10758656_G_d0_clone3A6_rep2


title: ATACseq_rs10758656_G_d7_clone1A2_rep1


title: differentiation of hIPSC line AD3 to dopaminergic neurons day 7 DAPT condition


title: differentiation of hIPSC line AD3 to dopaminergic neurons day 7 NICD condition


title: human induced pluripotent stem cells line WTSIi004-A

value: human induced pluripotent stem cells


title: Escherichia coli K-12 control culture replicate 1 (VCE non-enriched 5’ end of primary transcripts)


title: differentiation of hIPSC line WTSIi046-A to dopaminergic neurons day 7 SH condition

value: shRNA to RBPJ


title: differentiation of hIPSC line WTSIi046-A to dopaminergic neurons day 7 DAPT condition


title: ATACseq_rs4508712_G_d0_cloneB3_rep2


title: differentiation of hIPSC line WTSIi046-A to dopaminergic neurons day 7 NICD condition


title: ATACseq_rs10758656_G_d0_clone1A2_rep2


title: differentiation of hIPSC line AD3 to dopaminergic neurons day 7 SH condition


title: differentiation of hIPSC line WTSIi004-A to dopaminergic neurons day 7 contr condition


title: ATACseq_rs10758656_G_d7_clone1E4_rep2


title: Para-carcinoma tissue P5

city: 上海市

first: Shiyi

last: Yang

state: 上海

address: 中国上海市徐汇区华山路1954号

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: Colorectum

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colorectum

tag: tissue pair

value: tissue pair:para-carcinoma tissue P5


title: Para-carcinoma tissue P9

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P9


title: Para-carcinoma tissue P7

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P7


title: Para-carcinoma tissue P6

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P6


title: differentiation of hIPSC line WTSIi004-A to dopaminergic neurons day 7 SH condition


title: ATACseq_rs10758656_A_d10_clone15E8_rep2

value: Day 10


title: ATACseq_rs10758656_G_d0_clone1E4_rep1

value: expansion


title: ATACseq_rs10758656_G_d10_clone1E4_rep2


title: ATACseq_rs10758656_A_d10_clone15E8_rep1


title: ATACseq_rs10758656_A_d0_clone15E8_rep2


title: Para-carcinoma tissue P25

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P25


title: differentiation of hIPSC line WTSIi046-A to dopaminergic neurons day 7 contr condition


title: Para-carcinoma tissue P23

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P23


title: Para-carcinoma tissue P22

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P22


title: Para-carcinoma tissue P18

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P18


title: ATACseq_rs10758656_A_d7_clone13D7_rep1

value: CRISPR/Cas9 Edited

value: Day 7


title: ATACseq_rs10758656_G_d10_clone1A2_rep1


title: human induced pluripotent stem cells line WTSIi046-A


title: ATACseq_rs10758656_G_d10_clone1A2_rep2


title: ATACseq_rs10758656_A_d10_clone13D7_rep1


title: Para-carcinoma tissue P15

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P15


title: ATACseq_rs10758656_G_d0_clone1A2_rep1


title: Mouse forebrain, IgG

city: Yokohama

first: Sefan

last: Asamitsu

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
Torrent Suite Software v. 5.2.2 was used to remove adapter sequences and low-quality ends.
Cufflinks software package was used to analyze BG4-enriched mRNAs compared with IgG-treated samples.
Assembly: mm10
Supplementary files format and content: Excel files include FPKM values for each sample and Fold Change values (BG4 vs IgG) obtained from the Cufflinks.

source_name: forebrain

extract_protocol:
BG4- or IgG-bound RNA fraction was purified using the RNeasy Mini Kit (Qiagen)
Library preparation was performed with the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific).

value: forebrain

value: IgG


title: Para-carcinoma tissue P24

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P24


title: HCT116: Andrographis-1

city: Monrovia

first: Ajay

last: Goel

address: 1218 S. Fifth Avenue

department: Molecular Diagnostics and Experimental Therapeutics

institute: Beckman Research Institute of City of Hope

data_processing:
Base calling was performed with the Illumina Real-Time Analysis software (RTA3, v3.4.4) and the FASTQ files were generated with bcl2fastq (version 2.20.0.422).
Partek Flow v10.0.22.0121 used to process bulk RNA-sequencing data.
Multiplexed sequencing raw reads were trimmed to remove low-quality reads from both ends based on Phred quality scores lower than 35 before alignment.
Sequence reads mapped to the human genome GRCh38 by STAR 2.7.8a (Dobin et al., 2013) with default parameters.
After alignment the final BAM files were quantified using Partek E/M (Xing et al., 2016) algorithm and annotated using Ensembl Transcripts release 102 to generate gene counts.
The gene counts were normalized and differential gene analyzed by DESeq2 (Love et al., 2014) between 5FUR resistant and parental CRC cells.
Genome_build: GRCh38
Assembly: mm10
Supplementary files format and content: excel data sheets include RPKM values for each Sample

growth_protocol: Human CRC cell lines (HCT116 and SW480) were obtained from the American Type Culture Collection (ATCC, Manassas, VA). Both cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Carlsbad, CA) supplemented with 10% fetal bovine serum (Gibco, Waltham, MA) and 1% penicillin-streptomycin. All cells were maintained in a 37°C incubator with a 5% humidified CO2 atmosphere, and the cell culture media was replenished every two days.

extract_protocol:
MiRNeasy Mini kit (Qiagen, Hilden, Germany)
the library was constructed using TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) with 1 μg purified RNA input.

treatment_protocol: For these experiments, 2.5 × 105 cells from SW480 and HCT116 lines were treated with each compound for 16 hours before undertaking total RNA extraction.

value: CRC cells

value: Andrographis


title: HCT116: Andrographis-2


title: ATACseq_rs10758656_A_d0_clone13D7_rep1


title: human induced pluripotent stem cells line AD3

value: human induced pluripotent stem cells


title: HCT116: non-treated control-2 (for Andrographis)

value: non-treated control


title: ATACseq_rs10758656_A_d0_clone15E8_rep1


title: Para-carcinoma tissue P13

address: 中国上海市徐汇区华山路1954号

value: Colorectum

value: tissue pair:para-carcinoma tissue P13


title: Para-carcinoma tissue P3

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P3


title: ATACseq_rs10758656_A_d7_clone12C6_rep2


title: ATACseq_rs10758656_A_d7_clone15E8_rep2


title: Para-carcinoma tissue P4

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P4


title: ATACseq_rs10758656_A_d7_clone15E8_rep1


title: Para-carcinoma tissue P12

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P12


title: exo_12hr_hypoxic_rep1

city: shanghai

first: Li

last: Xu

address: 1239，Siping Road

institute: Tongji University

description:
Gene expression after 12hr in hypoxic induced A549 cell supernatant exosomes
lnc RNA and circRNA

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human V6 (4*180K) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: exosome, 12hr, hypoxic

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Pulmonary adenocarcinoma cell lines A549 was grown in Dulbecco's Modified Eagle Medium supplemented with 10% exosome-depleted bovine fetal serum (Life Technologies, USA) in a humidified 5% CO2 environment. The cells were grown under circumstances of 20% O2 (normoxic) or 1% O2 (hypoxic), in a 3-gas incubator (Binder) balanced with N2. Then the supernatant was collected for extracting exosomes

value: Pulmonary adenocarcinoma cell line A549

tag: sample type

value: cell line exosomes

tag: stress

value: hypoxic

tag: time


title: Sporangia 48hrs biological rep 1

city: Riverside

first: Jason

last: Stajich

address: 900 University Ave

department: Microbiology and Plant Pathology

institute: University of California-Riverside

data_processing:
Mosquito transcripts were removed from the transcriptome data using BBMap against a mosquito (Accession: GBTE00000000) reference transcriptome.
To create a Coelomomyces lattivatus reference, we used CD-HIT-EST to cluster transcripts at 90% sequence identity from three C. lattivatus draft annotations (Accessions: JADGJU010000000, JADGJV010000000 and JADHYY010000000).
We then used kallisto v. 0.48.0 to quantify read counts against this combined reference.
data were loaded into R with tximport and hypothesis testing applied with DEseq2
Assembly: JADGJU010000000, JADGJV010000000 and JADHYY010000000
Supplementary files format and content: kallisto.counts.csv - comma delimited file containg raw counts from kallisto
Supplementary files format and content: kallisto.TPM.csv - comma delimited file with normalized expression, Transcripts Per Million (TPM) compted by kallisto

organism: Coelomomyces lativittatus

source_name: fungal sporangia

growth_protocol: Developmental stages of the mosquito larvae were monitored and tissues selected at appropriate timepoint

extract_protocol:
Trizol extraction of RNA from tissue was performed on each tissue sample
Library was constructed with NEBNext Ultra Directional RNA Library Prep Kit

tag: tissue

value: fungal sporangia


title: SW480: Andrographis-2

tag: cell line


title: Para-carcinoma tissue P8

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P8


title: Mouse forebrain, BG4

value: forebrain


title: Para-carcinoma tissue P11

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P11


title: Sporangia 24hrs biological rep 2


title: ATACseq_rs10758656_A_d7_clone13D7_rep2

value: CRISPR/Cas9 Edited

value: Day 7


title: ATACseq_rs10758656_A_d10_clone13D7_rep2

value: Day 10


title: Para-carcinoma tissue P1

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P1


title: Sporangia 24hrs biological rep 1


title: SW480: non-treated control-2 (for Andrographis)

value: CRC cells

value: non-treated control


title: ATACseq_rs10758656_A_d0_clone12C6_rep2

value: expansion


title: Colorectal carcinoma tissue C9

address: 中国上海市徐汇区华山路1954号

value: Colorectum

value: tissue pair:colorectal carcinoma tissue C9


title: SW480: Andrographis-1

value: Andrographis


title: HCT116: Curcumin-2

value: Curcumin


title: Sporangia 48hrs biological rep 2


title: Colorectal carcinoma tissue C8

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C8


title: ATACseq_rs10758656_A_d0_clone13D7_rep2


title: exo_24hr_normoxic_rep1

description:
Gene expression after 24hr in normoxic induced A549 cell supernatant exosomes
lnc RNA and circRNA

source_name: exosome, 24hr, normoxic

value: Pulmonary adenocarcinoma cell line A549

value: cell line exosomes

value: normoxic


title: Para-carcinoma tissue P20

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P20


title: Para-carcinoma tissue P14

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P14


title: HCT116: Curcumin-1


title: Hep3B-TET-empty rep2

data_processing:
Post-trimming quality control was performed with FastQC (version: 1.0.0). The resulting FastQ files were mapped on to human reference genome using RNAseq alignment tool (V2.0.2) in Illumina BaseSpace software.
Differential expression gene (DEG) list was obtained using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: .csv file containing tpm values for all the genes in all the samples

source_name: Liver cancer cell

growth_protocol: Cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum, L-Glutamine and Penicillin-Streptomycin and were incubated at 37°C with 5% CO2.

extract_protocol:
Qiagen RNeasy Kit
Standard library preparation using Illumina Truseq stranded mRNA kit

treatment_protocol: For conditional overexpression of L1orf1p, L1orf1 was cloned under a TET-ON promoter in a piggybac vector containing puromycin resistance cassette. Hep3B cells were co-transfected with PB-TET-empty or PB-TET-L1orf1 along with plasmid expressing Transposase using Trans-LT1 transfection reagent (Mirus Bio, 6003) as per manufacturer’s instructions. Cells with stable integration were selected by puromycin selection (1 µg/ml). The cells were then induced with doxycycline (1µM, Sigma, D9891) for further experimentation.

value: TET-On-empty

value: Hep3B liver cancer cells

value: doxycycline (1ug/ml)  treatment for 72 hrs


title: Sporangia 36hrs biological rep 2

value: fungal sporangia


title: ATACseq_rs10758656_A_d10_clone12C6_rep2

value: CRISPR/Cas9 Edited

value: Day 10


title: Para-carcinoma tissue P10

address: 中国上海市徐汇区华山路1954号

value: tissue pair:para-carcinoma tissue P10


title: ATACseq_rs10758656_A_d7_clone12C6_rep1

value: Day 7


title: Colorectal carcinoma tissue C6

address: 中国上海市徐汇区华山路1954号

value: Colorectum

value: tissue pair:colorectal carcinoma tissue C6


title: ATACseq_rs10758656_A_d10_clone12C6_rep1


title: Hep3B-TET-empty rep1


title: Colorectal carcinoma tissue C5

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C5


title: Sporangia 36hrs biological rep 1


title: SW480: non-treated control-1 (for Andrographis)

value: CRC cells

value: non-treated control


title: HCT116: non-treated control-1 (for Andrographis)


title: exo_24hr_hypoxic_rep1

description:
Gene expression after 24hr in hypoxic induced A549 cell supernatant exosomes
lnc RNA and circRNA

source_name: exosome, 24hr, hypoxic

value: Pulmonary adenocarcinoma cell line A549

value: cell line exosomes

value: hypoxic


title: Sporangia 0hrs biological rep 1


title: exo_12hr_normoxic_rep1

description:
Gene expression after 12hr in normoxic induced A549 cell supernatant exosomes
lnc RNA and circRNA

source_name: exosome, 12hr, normoxic

value: normoxic


title: Hep3B-TET-L1orf1 rep3


title: ATACseq_rs10758656_A_d0_clone12C6_rep1

value: expansion


title: Sporangia 0hrs biological rep 2


title: Colorectal carcinoma tissue C4

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C4


title: SW480: Curcumin-1

value: Curcumin


title: Middle Infection biological rep 2

description: MiddleInf.rB

source_name: excised fungus from infected mosquito

value: excised fungus from infected mosquito


title: Late Infection biological rep 2

description: LateInf.rB


title: HCT116: non-treated control-1 (for Curcumin)


title: Middle Infection biological rep 1

description: MiddleInf.rA


title: HCT116: non-treated control-2 (for Curcumin)


title: SW480: Curcumin-2


title: Hep3B-TET-empty rep3

value: TET-On-empty

value: Hep3B liver cancer cells

value: doxycycline (1ug/ml)  treatment for 72 hrs


title: Early Infection biological rep 2

description: EarlyInf.rB


title: Colorectal carcinoma tissue C7

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C7


title: Hep3B-TET-L1orf1 rep2


title: Colorectal carcinoma tissue C25

address: 中国上海市徐汇区华山路1954号

value: Colorectum

value: tissue pair:colorectal carcinoma tissue C25


title: Hep3B-TET-L1orf1 rep1


title: Colorectal carcinoma tissue C3

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C3


title: SW480: non-treated control-1 (for Curcumin)

value: CRC cells


title: TgR: Hippocampus 3

city: Jerusalem

first: Hermona

last: Soreq

state: Israel

address: The Edmond J. Safra Campus, Givat Ram

department: Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Base calling, QC and fastq file generation by the illumina Basespace platform
Quality control was performed using FastQC
Short RNA was aligned to the miRBase version 21 using miRExpress 2.0 with default parameters.
Normalization and Differencial expression using Deseq2
Genome_build: mirBase v.21
Supplementary_files_format_and_content: .fq.txt File per sample with alligned miR counts

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from murine brain tissues using the miRNeasy Mini Kit (Qiagen, 217004). Four TgR and three FVB/N mice were used for the prefrontal cortex (PFC), and three TgR and three FVB/N mice were used for the hippocampus. RNA quality and quantity were measured using a Nanodrop 2000 (PeqLab/Thermo Scientific). RNA integrity was tested using the 2100 Bioanalyzer (Agilent Technologies) RNA 6000 Nano LabChip Kits (Agilent Technologies) which revealed RIN values range of 8.6-9.3.
300ng of RNA were subjected to small-RNA sequencing. Libraries were generated using an RNA Library prep kit (NEBNext Multiplex Small RNA Library Prep Set for Illumina, E7300) following manufacturer’s instructions.

value: FVB/N

value: hACHE-R overexpression

value: Hippocampus


title: Colorectal carcinoma tissue C22

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C22


title: SW480: non-treated control-2 (for Curcumin)

value: non-treated control


title: HCT116 cells, Cystine deprovation, 48hours-3

address: 中国上海市徐汇区华山路1954号

description:
Cys_dep48_3
rsem_tpm.xls

growth_protocol: HCT116 human colorectal caricinoma cells were maintained in full DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 1.The following day, cystine deprivation cells were washed and fed with warm DMEM supplemented with 10% fetal bovine serun (FBS), antibiotics and 0 mM cystine for 24 or 48 hours.   2.Control cells were still maintained in full DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics for 24 or 48 hours.

value: Human Colorectal Carcinoma Cells

value: WT

value: Amino acid deprivation


title: Colorectal carcinoma tissue C24

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C24


title: Colorectal carcinoma tissue C23

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C23


title: Late Infection biological rep 1

description: LateInf.rA

value: excised fungus from infected mosquito


title: TgR: Hippocampus 2


title: Early Infection biological rep 1

description: EarlyInf.rA


title: HCT116 cells, Cystine deprivation, 24hours-3

address: 中国上海市徐汇区华山路1954号

description:
Cys_dep24_3
rsem_tpm.xls


title: TgR: Hippocampus 1


title: HCT116 cells, Cystine deprovation, 48hours-1

address: 中国上海市徐汇区华山路1954号

description:
Cys_dep48_1
rsem_tpm.xls


title: FVB/N: Hippocampus 1