title: Mono-Mac infect 24h low MOI (M6676)

city: Hannover

first: Anna

last: Rafiei Hashtchin

state: Niedersachsen

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Medical School Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’, except that 2500ng of labeled cRNA were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing:
Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’.   Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)   Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.
Normalized processed signal intensity values (non-log), averaged across on-chip replicates / quintuplicate measurements. Measurements of control features were removed.

source_name: Mono-Mac infect 24h low MOI-29.03.19

label_protocol: 150ng of total RNA were used as input. Synthesis of Cy3-labeled cRNA was performed in ¾ reaction volumes with the ‘Low Input Quick Amp Labeling Kit One-Color’ (#5190-2305, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: Cells were maintained in RPMI medium+10%FCS+50ng/ml hM-CSF.

extract_protocol: RNA isolation was performed based on RNAeasy Micro Kit (#74004, Qiagen) instruction.

treatment_protocol: Cells were infected with an MOI 5 of S. aureus  Newman strain 2 hours and 24 hours before RNA isolation.

value: PBMC-Macrophages

tag: infection

value: S. aureus Newman infection 24h


title: wt_male_E12.5 rep1

status: Public on Sep 17 2021

type: SRA

city: tianjin

first: nannan

last: zhao

state: --- Select a state ---

address: nankai

country: China

institute: nankai university

library_source: transcriptomic

data_processing:
The quality control with the software FastQC v0.11.9
Clean reads were aligned to the mouse mm10 genome with the STAR 2.5.3a software
The normalized FPKM were calculated with the software cufflinks-2.2.1.Linux_x86_64

molecule: total RNA

organism: Mus musculus

source_name: primordial germ cells

extract_protocol:
1000 cells per sample were resuspended in PBS with 0.1% BSA and transferred to the bottom of a PCR tube consisting of 3 μl lysis buffer, and cDNA was synthesized in the tube containing mRNA,and then the libraries were prepared by using TruePrep DNA Library Prep Kit V2
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: primordial germ cells

tag: phenotype

value: wt


title: Hfq65_Total_Rep1

city: Bethesda

first: Kumaran

last: Ramamurthi

state: MD

address: 37 Convent Drive

country: USA

institute: National Cancer Institute

data_processing:
Illumina Hiseq 2500 System was used for sequencing.
The Illumina reads in FASTQ format were first trimmed by Trimmomtaic version 0.36 to remove the adaptor sequences and low quality reads.
The RNAseq pipeline READemption version 0.4.5. was then used to process those trimmed reads. Those longer than 12 nt were aligned to the Escherichia coli str. K-12 substr. MG1665 reference sequence (NC_000913.3) download from the NCBI ftp website by using segemehl version 0.2.0.
To find differentially expressed genes, the “deseq” subcommand in READemption executing   DESeq2 version 1.20.0 was used with the fold-change of 2.0 or higher and the adjusted p-value below 0.1.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab-delimited text files include rawcount for each Sample.

organism: Escherichia coli K-12

source_name: E.coli K12 MG1655

growth_protocol: All strains used in this study were grown at 37 oC under aerobic conditions in LB. Wherever required, the liquid and solid media was supplemented with Ampicillin (100 mg/ml). The bacteria used for the RNA Seq experiment were grown to OD600 =1 in LB.

extract_protocol:
Polyclonal antibodies to Hfq were generated previously by immunizing rabbits with purified Hfq protein (Covance). RNAs that co-IP with Hfq were isolated as described previously(Zhang, A., et al., Mol Cell, 9, 11-22) with the following modifications. Overnight cultures of strains KK2440 (WT) and KK2448 (Hfq65) cells were grown to OD600 ~ 1.0 in LB medium. Cells corresponding to the  equivalent of 40 OD600 were collected, and 2 ml cell lysates were prepared by vortexing with 212-300 μm glass beads (Sigma) in a final volume of 2 ml lysis buffer (20 mM Tris-HCl/pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT). Co-IPs were carried out either using 200 μl of α-Hfq, 240 mg of protein A-Sepharose CL-4B (GE Healthcare), and 1.9 ml of cell lysate. Co-IP RNA was isolated from protein A-Sepharose beads by extraction with phenol: chloroform:isoamyl alcohol (25:24:1), followed by ethanol precipitation. Total RNA was isolated from 100 μl of cell lysate by Trizol (Thermo Fisher Scientific) extraction followed by chloroform extraction and isopropanol precipitation. Total and co-IP RNA samples were resuspended in 30 μl and 50 μl of DEPC H2O.  The integrity of RNA was checked on 1% agarose gel. The RNA were treated with DNAase I(100 μl) followed by phenol: Chloroform: IAA based purification and ethanol precipitation. The gDNA contamination was checked by PCR amplification.  The DNA free RNA samples were then subjected to rRNA depletion using Ribo-zero kit and purified by using (2.5X)RNAClean XP Beads and isopropanol (1.5X). isopropanol ratio(1.5X) is critical to keeping short RNAs (>70 nt) om the RMA [pp;. The isopropanol and RNAClean XP bead ratios were both optimized in orger to remove nonligated adaptors while saving short RNA fragments.
The RNAs (400 ng) were used for cDNA library preparation.  Library construction was carried out based on the RNAtag-Seq methodology (Shishkin, et al. 2015, Nat Methods, 12, 323-325), which was adapted to capture (optimized amount of isopropanol and RNAClean XP for short sRNA) bacterial sRNA (Melamed, S et al.,  2018, Nat Protoc, 13, 1-33).   To enrich the libraries, 12 cycles of PCR were carried out at the end step of enrichment. Bead purification was performed twice at the last step to ensure high purity of the library from the adaptor dimer.

tag: genotype

value: Hfq65 mutant

tag: anti-hfq antibody


title: RG034-T0

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
Illumina NovaSeq 6000 RTA3: v3.4.4 and basecalling with bcl2fastq: v2.20.
Skewer was used to remove poor quality bases from the 3’ end of reads with a minimum phred threshold of 10.
Reads were mapped to the human gencode v33 transcriptome using Kallisto version 0.46.1
Transcript quantifications were aggregated to gene level counts for analysis with DESeq2
Genome_build: gencode v33 transcriptome
Supplementary_files_format_and_content: matrix.tsv is a matrix of gene expression read counts in tab delimited format.

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
RNA was extracted from 500 µL of PBMC suspended in TRIzol (Thermo Fisher Scientific, USA) according to manufacturer’s protocols
For each sample, 120 ng of RNA (in a volume of 50 µL) was used to prepare the library using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA) according to the manufacturer's protocol.

tag: crp highest level

tag: crp group

value: Low

tag: age

tag: Sex

value: female

tag: timepoint

value: preoperative


title: WT_IP_Rep1

description: RNA co-IP with Hfq

value: Wild Type

value: co-IP with anti-Hfq polyclonal antibodies


title: RG034-POD

value: postoperative


title: RG033-T0

value: High


title: wt_male_E12.5 rep2


title: Hfq65_IP_Rep2

description: RNA co-IP with Hfq


title: TRIM33_32D

city: Fontenay aux roses

first: federica

last: ferri

address: 18 route du panorama

country: France

institute: cea

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie v0.12.7 with the following parameters -m 1 --strata --best.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

molecule: genomic DNA

growth_protocol: Bone marrow cells were cultured in IMDM supplemented with 10% FCS (Invitrogen) 10μM thioglycerol (Sigma) and 25ng/ml mouse CSF1 (Milteny Biotech).

extract_protocol: ChIP-seq libraries were prepared using ChIP-Seq Sample Prep Kit (#IP-102-1001, Illumina) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C) and then purified using Agencourt AMPure XP beads (#A63881, Beckman). DNA library size selection was performed by excising the 250-350 bp fragments from a 2% agarose gel followed by purification using a QIAquick Gel Extraction Kit (#28906, Qiagen).

treatment_protocol: On day 7, macrophages were treated for 4h, 12h and 24h  with 100ng/ml LPS (Sigma) in IMDM supplemented with 2.5% FCS. Cells were cross-linked with 1% formaldehyde for 10 min at 37°C, lysed in SDS lysis buffer [50 mM Tris pH8, 10 mM EDTA, 1% SDS, protease inhibitor cocktail (Roche)] and sonicated (cycle conditions: 15sec ON/30sec OFF, 15 min; Bioruptor, Diagenode) to obtain DNA fragments with an average length of 200-600 bp. Supernatant was diluted 10 times in IP dilution buffer [16.7 mM Tris pH8, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X100, 0.01% SDS, protease inhibitor cocktail (Roche)] and immunoprecipitations were performed using 5μg of specific antibodies. Immunoprecipitated chromatin was collected using protein A agarose/Salmon Sperm DNA beads (Millipore) and, after washing and elution, reverse cross- linking was carried out with 0.2M NaCl at 65°C overnight. The chromatin was then digested by 20 μg of Proteinase K (Invitrogen) for 1h at 45°C and isolated by phenol- chloroform extraction.

tag: cell type

value: immature myeloid cell line

value: BALB/c

value: wild type

tag: chip antibody


title: TRIM33_MEL_I

source_name: MEL

value: erythroid cell line


title: TRIM33_MEL_NI


title: HUVEC infected with P. gingivalis [S_3_cell]

city: CHENGDU

first: CHENGCHENG

last: LIU

state: SICHUAN

address: No. 14, Section 3, Renminnan Road

institute: Sichuan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: raw gene count

source_name: HUVEC infected with P. gingivalis

extract_protocol:
Total RNA was isolated from the samples using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocols. Further, genomic DNA was removed using the commercially available DNase I system (Qiagen, Germantown, PA, USA), and RNA concentration was realized by determining the A260/A280 ratio using a Nanodrop 2000 system (ThermoFisher, Waltham, MA, USA). RNA integrity was verified via 1.5% agarose gel electrophoresis, and qualified RNAs were quantified using a Qubit 3.0 fluorometer with a QubitTM RNA Broad Range Assay Kit (ThermoFisher, Waltham, MA). Furthermore, the RNA samples were analyzed at the Huayin Genome Research Facility (Huayin Health Medical Group Co, Wuhan, China) to determine ribosomal RNA (rRNA) depletion and subsequent RNA sequencing, and rRNA was removed using a Ribo-off rRNA Depletion Kit (Vazyme Biotech Co., Nanjing, China) for humans (Catalog No. N406) and/or bacteria (catalog NO. N407). Additionally, cDNA libraries for Illumina® sequencing were generated using the KC-DigitalTM Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA). The library products corresponding to 200–250 bps were then enriched, quantified, and sequenced using a Nova-seq 6000 sequencer (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human umbilical vein endothelial cells (HUVECs) (EA. hy926)

value: EA. hy926

tag: treatment

value: infection


title: RG031-T0

value: male


title: HUVEC infected with P. gingivalis [S_2_cell]


title: RG033-POD


title: G1+E2-13-3

city: Changchun city

first: Tingdi

last: Zhang

state: Jilin Province

address: 2519 Jiefang Road

department: college of new energy and environment

institute: Jilin University

description: 17 beta-estradiol induction 13 hours 3

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: genome.fa; genome.gtf
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

organism: Comamonas testosteroni

source_name: C. testosteroni JLU460ET

growth_protocol: C. testosteroni JLU460ET was incubated with testosterone/17beta-estradiol or no substrates in LB broth at 28 celsius degrees

extract_protocol:
RNA was extracted from bacteria for detecting by Agilent 2100 bioanalyzer
The mRNA is obtained by removing ribosomal RNA (rRNA) from total RNA. Then, fragment buffer was added to randomly break the obtained mRNA into short fragments for construction of library.
The library was built according to the chain specific library (parkhomchuk D. 2009)

treatment_protocol: Samples were pipetted into centrifuge tube for collecting bacteria containing RNA protect-Bacteria-Reagent after 3 hours or 13 hours induction,respectively.

value: 17 beta-estradiol induction


title: Hfq65_IP_Rep1

description: RNA co-IP with Hfq

value: Hfq65 mutant


title: iPSC-Mac infect 24h low MOI (M6675)

type: RNA

country: Germany

source_name: iPSC-Mac infect 24h low MOI-29.03.19

value: iPSC-Macrophages

value: S. aureus Newman infection 24h


title: G1+E2-13-2

description: 17 beta-estradiol induction 13 hours 2


title: Mono-Mac Infected 24h (M6541)

source_name: Mono-Mac Infected 24h-13.10.18

value: PBMC-Macrophages


title: Mono-Mac Control 2h (M6673)

source_name: Mono-Mac Control 2h- 29.03.19

value: Non-infected cells


title: iPSC-Mac Control 2h  (M6671)

source_name: iPSC-Mac Control 2h- 29.03.19


title: HUVEC infected with P. gingivalis [S_1_cell]


title: Mono-Mac infect 2h low MOI (M6674)

source_name: Mono-Mac infect 2h low MOI-29.03.19

value: S. aureus Newman infection 2h


title: iPSC-Mac infect 2h low MOI (M6672)

source_name: iPSC-Mac infect 2h low MOI-29.03.19


title: Mono-Mac Control 2h (M6540)

source_name: Mono-Mac Control 2h-13.10.18


title: iPSC-Mac Infected 2h (M6537)

source_name: iPSC-Mac Infected 2h-13.10.18


title: Mono-Mac Infected 2 (M6539)

source_name: Mono-Mac Infected 2h-13.10.18


title: WT_IP_Rep2

description: RNA co-IP with Hfq

value: Wild Type

value: co-IP with anti-Hfq polyclonal antibodies


title: G1+E2-13-1

description: 17 beta-estradiol induction 13 hours 1


title: non-infected HUVEC [D_3]

source_name: non-infected HUVEC

value: untreated


title: RG030-T0

value: Low

value: female

value: preoperative


title: G1+T-13-3

description: testosterone induction 13 hours 3

value: testosterone induction


title: non-infected HUVEC [D_2]

value: Human umbilical vein endothelial cells (HUVECs) (EA. hy926)

value: EA. hy926


title: G1+T-13-2

description: testosterone induction 13 hours 2


title: RG030-POD

value: postoperative


title: RG026-T0


title: 01_WT_HDM_LN

city: San Francisco

first: Carlos

middle: Andres

last: Castellanos

state: CA

address: 513 Parnassus Ave, HSE-201

department: Microbiology & Immunology

institute: University of California, San Francisco

data_processing:
Sequencing and base-calling by Illumina NovaSeq 6000
Raw data was processed with 10X Cell Ranger package and further analyzed using Seurat
Cells were filtered to only keep those that had less than 7% mitochondrial genes usign Seurat
Downstream processing and visualization carried out with Seurat
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: hierarchical data format (HDF). Single cell matrices generated from 10x Cell Ranger

source_name: mediastinal LN WT HDM+ DCs

growth_protocol: N/A (primary DCs from mixed BM chimera mice).

extract_protocol:
DCs were first enriched by begative selection (by depleting B220+ TCRb+ and Ly6G+ cells) using an EasySep magnet and then sorted with a FACS Aria for CD11c+ MHCII+ HDM+ live single cells.
10X Chromium Single Cell 3′ Reagent Kit (v3 Chemistry)

treatment_protocol: Mice were treated with AF647 HDM 1 day before collecting the mediastinal LN.

value: lymphoid (mediastinal LN)

value: dendritic cell (DC)

value: mice treated with HDM AF647 (1 day before collection)


title: 02_KO_HDM_LN

source_name: mediastinal LN MARCH1 KO HDM+ DCs


title: RG031-POD

value: High

value: male


title: G1+T-13-1

description: testosterone induction 13 hours 1


title: RG026-POD


title: Prog_P004_b

city: Beijing

first: Yuanyuan

state: Beijing

address: Yiheyuan Road

department: BIOPIC

institute: Peking Univerisity

description: 10X Genomics

data_processing:
For 10X data, Cell Ranger 3.0.0 was used to quantify gene expression level, identify TCR sequences and quantify ATAC-seq peaks .
Genome_build: GRCh38 for RNA expression,TCR data and ATAC peaks.

molecule: polyA RNA

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated with HISTOPAQUE-1077 (Sigma-Aldrich) solution. In brief, 3 ml fresh peripheral blood was collected at baseline, 4 weeks after treatment initiation and disease progression in EDTA anticoagulant tubes and subsequently layered onto HISTOPAQUE-1077. Tumor biopsy samples were first stored in RNAlater RNA stabilization reagent (QIAGEN) after collection and kept on ice to avoid RNA degradation. Samples were then collected in the RPMI-1640 medium (Gibco) with 10% FBS (Gibco), and enzymatically digested with gentle MACS Tumor Dissociation Kit (Miltenyi Biotec) for 60 min on a rotor at 37 °C according to the manufacturer’s protocol. The dissociated cells were next passed through a 40-µm cell-strainer (BD) in the RPMI-1640 medium (Invitrogen) with 10% FBS until uniform cell suspensions were obtained. Subsequently, the suspended cells were passed through cell strainers and centrifuged at 400 g for 10 min. Red blood cells were removed via the same procedure described above. After washing twice with 1x PBS (Invitrogen), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/ul. Cells were loaded between 7,000 and 15,000 cells/chip position using the 10x Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V3 barcoding chemistry) according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina Hiseq X Ten sequencer with 150-bp paired-end reads.

treatment_protocol: Half of 22 TNBC patients were treated with paclitaxel monotherapy and the other half were treated with paclitaxel plus atezolizumab as first-line treatment

value: blood

tag: disease state

value: TNBC patient

tag: group

value: Progression


title: iPSC-Mac Control 2h (M6536)

source_name: iPSC-Mac Control 2h-13.10.18

value: iPSC-Macrophages

value: Non-infected cells


title: G1-13-3

description: without induction 13 hours culture3

value: without induction


title: RG023-T0

source_name: Peripheral blood

value: Low

value: female


title: iPSC-Mac Infected 24h (M6538)

source_name: iPSC-Mac Infected 24h-13.10.18

value: S. aureus Newman infection 24h


title: Post_P004_b

description: 10X Genomics

value: Post-treatment


title: Pre_P004_t

description: 10X Genomics

value: Pre-treatment


title: RG023-POD

value: postoperative


title: Pre_P004_b

description: 10X Genomics


title: G1-13-2

description: without induction 13 hours culture2


title: G1-13-1

description: without induction 13 hours culture1


title: RG019-T0

value: preoperative


title: RG019-POD


title: G1+E2-3-3

description: 17 beta-estradiol induction 3 hours 3

value: 17 beta-estradiol induction


title: G1+E2-3-2

description: 17 beta-estradiol induction 3 hours 2


title: RG013-T0


title: MTB-IGFIRba429C

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

country: Canada

institute: University of Guelph

data_processing:
reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming
preprocessed reads are aligned by STAR aligner
aligned reads are summarized to gene-level counts by the featureCounts tool
Genome_build: GRCh38_ens92_ercc_sirv

source_name: mammary tissue from 55 day old MTB-IGFIRba429 transgenic FVB mouse

extract_protocol:
RNA extracted using mirVana miRNA Isolation Kit following the manufacturer's protocol
KAPA stranded Illumina kits for the RNA-seq library preparation, which include procedures of RNA fragmentation, random hexamer primed first strand cDNA synthesis, dUTP based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation and library PCR amplification. Library prep performed by Arraystar Inc (Rockville, MD)

treatment_protocol: mice were placed on rodent chow containing 2g of doxycycline/kg chow beginning at 21 days of age. The doxycycline induces the expression of the IGF-IR and miR-200b/200a/429 transgenes

value: overexpresses both the IGF-IR transgene and the miR-200b/200a/429 cluster in mammary epithelial cells in a doxycycline inducible manner


title: Sim1td-Cont pooled

city: Toronto

first: Chi-chung

last: Hui

state: ON

address: 686 Bay street

institute: The Hospital for Sick Children

data_processing:
Base-calling performed with Illumina's bcl2fastq follwed by Picard FastqToSam. Read1 contains cellular and molecular barcodes (20 bp), Read2 contains cDNA sequence (50 bp).
Read2 was aligned with STAR v2.6.0b and tagged with its respective cellular and molecular barcode.
Aligned exonic reads were tagged with the name of the respective gene.
Digital gene expression (DGE) matrix was extracted from the aligned library, with a row for each gene and a column for each cell. The "knee" of the cummulative distribution plot of reads was used to estimate the number of cells being sequenced.
Cells from samples were merged into a single DGE matrix for analysis using Seurat v3, where cells expressing less than 200 genes and genes expressed in less than 3 cells were filtered out.
Dead/dying cells (determined by mitochonrial gene percentage >10%) and cell doublets (gene expressed > 4500) were removed.
Gene measurements in each cell were normalized by the total expression, multiplied by 10,000 and log-transformed.
Following identification of highly-variable genes and data scaling, the dimensionality of the dataset was heuristically dertermined by ElbowPlot (a ranking principle components based on the percentage of variance explained by each one).
Pituitary cluster (Cga+, Gh+) was removed.
Cell were clustered using the graph-based clustering approach applied in Seurat, followed by vizualization through UMAP plots.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include DGE matrices for each sample, with a row for each gene and a column for each cell. Cell number was determined by plotting the cummulative distribution plot of reads. Rds file containing Seurat object.

source_name: Sim1-Cre;tdTomato+ Hypothalamus cells

extract_protocol:
For Sim1-Cre;Ai14 tdTomato cell sorting, pups (P1-P4) were dissected, then hypothalami were rapidly extracted. Pooled hypothalamus samples from 5-6 mice were digested by papain solution (Worthington Biochemical) with DNase in Hibernate A media for 30 minutes at 37 °C with gentle agitation. Digestion was stopped by dilution with Hibernate A containing B27 (Thermo), Glutamax (Thermo) and 0.5% Trehalose (Sigma-Aldrich), then gently triturated using a series of three Pasteur pipettes with tips fire-polished to incrementally smaller openings. Cell suspension was centrifuged at 300g for 5 min, resuspended in Hank’s balanced salt solution (HBSS) with 0.5% BSA and 0.5% Trehalose. Sytox blue (Thermo, 1:1000) was added to the cell suspension, and cells were filtered a second time through a 70-m cell strainer. Viable (Sytox blue-negative) tdTomato+ cells were subsequently sorted using a MoFlo Astrios (Beckman Coulter) cell sorter. Following cell sorting, cells were pelleted at 400g for 5 min, re-suspended in PBS with 0.01% BSA, and counted with a hemocytometer. Cells were adjusted to a final concentration of 140,000 cells/mL. Drop-seq was then carried out at the Princess Margaret Genomics Facility.
The beads were washed and resuspended in a reverse transcriptase mix, followed by a treatment with exonuclease I to remove unextended primers. The beads were then counted and PCR amplified. The amplified cDNA was fragmented and amplified for sequencing with the Nextera XT DNA sample prep kit (Illumina) using custom primers that enabled the specific amplification of only the 3' ends (described in Macosko et al. Cell 2015).

value: tdTomato+ FACS sorted cells of hypothalamus

value: Postnatal day 1-4

tag: number of aminals pooled


title: MTB-IGFIRba429B


title: Sim1td_Sim1Het pooled


title: G1+E2-3-1

description: 17 beta-estradiol induction 3 hours 1

source_name: C. testosteroni JLU460ET


title: RRBS_iNSC 3, rep 1, Gibco protocol

city: London

first: Silvia

last: Marino

address: 4, Newark St

country: United Kingdom

institute: Queen Mary University of London

data_processing:
RRBS-Seq quality and alignment: Quality was assessed via FastQC. Trimming of low quality reads and adapters was performed via TrimGalore v. 0.4.5-1 with “--rrbs” mode enabled. Subsequently, Bismark v. 0.22.1 was used for the alignment of reads, calling the subroutines “nucleotide-coverage” and “methylation-extractor”. Default settings were used, including the usage of Bowtie2 as background aligner.
RRBS-Seq post-processing: The coverage files were post-processed via edgeR. CpG sites with a total coverage – i.e. the sum of methylated (Me) and unmethylated (Un) reads – greater than 10 across all samples were retained as well as only those in chromosomes 1-19 and X. M-values were calculated as log2(Me+2)-log2(Un+2).
RNA-Seq quality and alignment: Quality was assessed via FastQC and trimming of low quality reads and adapters was performed via TrimGalore v. 0.4.5-1 with default parameters. The pseudoalignment package Salmon v. 0.13.1 was used to obtain transcript per million (TPM) expression levels, normalized for library size and transcript length.
RNA-Seq post-processing: Transcript to gene quantification was performed via biomaRt in R.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: RRBS-Seq: coverage files (cov.gz); RNA-Seq: TPM count table (csv)

source_name: Dura mater

growth_protocol: Primary endogenous NSC (eNSC) were isolated from the sub ventricular zone (SVZ) of 3 months old C57Black6/J mice following established protocols. Briefly, SVZ were dissected from the cerebral hemispheres and digested using Papain dissociation kit (PDS, Worthington #0031150 and #003153), plated at a density of 4x104 mL-1 and grown as Neurospheres (NS) for 4 days in DMEM/F12 (Invitrogen #31330), mouse recombinant EGF and human recombinant FGF (20ng/ml, Peprotech #31509 and #100-18B), 2% B27 (Invitrogen #12587) and Pen/Strep 1X (Invitrogen #15140), then media was changed every 4 days. After the first passage, cells were plated in adherent condition in geltrex (Gibco # A1413302) coated 6 well plates (corning # 3516) at a density of 0,5x10^6 cells. Dissociation between passages was performed enzymatically with accutase (Millipore #SCR005). After 2 passages, media was changed to neural expansion media (Gibco Advanced DMEM/F 12 0,5X #12634, Neurobasal medium 0,5X # 21103, 1% Pen-Strep and 2% neural induction supplement #A1647801). Dura mater was collected from C57Black6/J mice before dissection of the hemispheres for eNSC isolation.

extract_protocol:
RNA and DNA were extracted from cell pellets using the RNA/DNA/Protein Purification Plus kit (NORGEN, #47700), following the manufactured protocol.
RNA samples were sequenced on HiSeq4000, at 75 bp PE after polyA selection. For the RRBS library preparation, DNA samples were digested overnight with restriction enzyme Mssp1 (Agilent), then prepared following the manufactured protocol of NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (Biolab, E7645). Finally, bisulfite conversion following Zimo kit (Qiagen, D5001) run on NextSeq 500 Mid Output Run 150 cycles.

treatment_protocol: Fibroblasts cultures were established from small strips of dura mater, collected at surgery. Tissue was minced with a scalpel then spun down and resuspended in trypsin for 5 minutes at 37 degrees. To stop the reaction fresh fibroblast media (DMEM, Glutamax, 10% Foetal calf serum, 2% L-Glutamin and 1% penicillin-streptomycin) was added. Samples were centrifuged and resuspended in fresh media, then plated in 6 well plates (Corning #BC010). Media was topped up frequently during the first week then changed every other day.  Fibroblasts reprogramming was performed following a previously described protocol. Briefly, fibroblasts were electroporated with reprogramming vectors expressing Oct4, c-Myc, Klf4, Sox2 (OCKS 4F, 5µg) and Rarg, Lfh1 (RL 2F, 5.0 µg) using Amaxa Nucleofector (Lonza, Germany) then plated on SNL feeders with M15 media (Knockout DMEM Invitrogen, 15% Fetal Bovine Serum Hyclone, 1X Glutatamin-Penicillin-Streptomycin Invitrogen, 1X non-essential amino acids Invitrogen). Upon the appearance of colonies, media was replaced with EPSCM (DMEM/F12 Invitrogen, 20% Knockout Serum Replacement Invitrogen, 1X Glutamin-Penicillin-Streptomycin, 1X non-essential amino acids Invitrogen, 0.1 mM β Mercapto-ethanol Sigma, 106 U/ml hLIF Millipore supplemented with the following inhibitors: CHI99021 Tocris 1µM, JNK Inhibitor VIII Tocris 4 µM, SB203580 Tocris 10µM, A-419259 Santa Cruz 1µM and XAV939 Stratech 1µM). Colonies were picked and plated in 24 well SNL feeders’ plates for expansion and characterization. For embryoid bodies (EB) generation, EPSC lines were harvested and feeders removal was performed in T25 flasks for 30 minutes at 37 degrees to allow feeders to attach to the bottom and floating EPSC harvested were transferred in ultra-low attachment 96 well plates at different densities (60K, 45K, 35K and 20K) in EB media (DMEM/Knockout Invitrogen #10829-018, Fetal Bovine serum Gibco #16141061, non-essential amino acid Invitrogen #11140, glut-pen-strep Invitrogen #10378 and β mercapto-ethanol) changed every other days. After 7 days, they were transferred in 24 well plates on gelatine coated glass coverslips and after 10 to 14 days, cells were fixed with PFA 4%, 30 minutes at room temperature and immunocytochemistry was performed. EPSC were induced into iNSC following two protocols. The Gibco protocol (iNSCGibco) previously described and a bespoke protocol. For the latter, feeders were removed and EPSC colonies dissociated with accutase and plated in geltrex coated 6 well plates in EPSCM and rock inhibitor 10μM at density from 0.25 to 0.5x106 cells/well, media was changed the next day with N2B27 induction media (Neurobasal medium Gibco #12348017, DMEM/F21 Gibco #11330032, N2 supplement #17502048, B27 supplement 12587010, EGF and bFGF 10ng/ml peprotech and Pen-Strep-Glut Sigma) and afterwards every 4 days for a week. Cells were passaged with accutase and plated at density of 0.5x106 cells/well in geltrex coated 6 well plates and media was replaced by N2 expansion medium (DMEM/F21 Gibco #11330032, N2 supplement #17502048, EGF, bFDF and Pen-Strep-Glut) and changed every 2 days, passages were performed by enzymatic cells dissociation with accutase 2 to 3 times to establish iNSC N2B27 lines (iNSCN2B27). eNSC, iNSCGibco and iNSCN2B27 were frozen in synth-a-Freeze cryopreservation medium (Gibco #A12542).

value: Dura mater


title: RG013-POD

value: High


title: MTB-IGFIRba429A


title: G1+T-3-3

description: testosterone induction 3 hours 3

value: testosterone induction


title: MTB-IGFIR3

source_name: mammary tissue from 55 day old MTB-IGFIR transgenic FVB mouse

value: overexpresses the IGF-IR transgene in mammary epithelial cells in a doxycycline inducible manner


title: RG012-POD


title: G1+T-3-2

description: testosterone induction 3 hours 2


title: MTB-IGFIR2


title: RRBS_iNSC 1, rep 1, Gibco protocol


title: RRBS_eNSC 3, rep 1

source_name: Sub ventricular zone

value: Sub ventricular zone


title: G1+T-3-1

description: testosterone induction 3 hours 1


title: non-infected HUVEC [D_1]

value: Human umbilical vein endothelial cells (HUVECs) (EA. hy926)

value: EA. hy926

value: untreated


title: MTB-IGFIR4


title: G1-3-2

description: without induction 3 hours culture2

value: without induction


title: MTB-200ba429D

source_name: mammary tissue from 55 day old MTB-200ba429 transgenic FVB mouse

value: overexpresses the miR-200b/200a/429 cluster in mammary epithelial cells in a doxycycline inducible manner


title: RG012-T0

value: male


title: RRBS_eNSC 2, rep 1


title: RG003-T0

value: Low

value: female


title: RRBS_iNSC 2, rep 1, Gibco protocol


title: MTB-200ba429B


title: MTB-IGFIR1


title: MTB-200ba429C


title: Control4

source_name: mammary tissue from 55 day old FVB mouse

value: control


title: UUO kidney_day_10_rep1

city: Aachen

first: Zhijian

last: Li

state: North Rhine-Westphal

address: Pauwelsstr. 19

institute: RWTH Aachen University

data_processing:
The Cell Ranger ATAC Software Suite (version 1.1.0) was used for processing sequencing information and single cell barcodes
Genome_build: mm10
Supplementary_files_format_and_content: barcodes: barcodes present in input data
Supplementary_files_format_and_content: fragments: a BED-like tabular file, where each line represents a unique ATAC-seq fragment captured by the assay and positions are 0-based. The columns are defined as following: chrom, chromStart, chromEnd, barcode and duplicateCount.
Supplementary_files_format_and_content: matrix: a count matrix with Market Exchange Format (MEX). The first line contains the type code and the second line includes format and cell-ranger versions. Number of peaks, barcodes, and non-zero entries can be found in the third line.  The rest of the lines represent  nonzero entries with the first two numbers corresponding to peak and barcode indices and the last one corresponding to  the number of cut sites.
Supplementary_files_format_and_content: peaks: a bed file contains the output of the peak calling algorithm. Each peak is an interval on the genome that has a local enrichment of transposase cut-sites.

source_name: Mouse Kidney of Unilateral Ureter Obstruction

extract_protocol: All protocols to generate scATAC-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-atac.

value: Kidney

tag: Stage

value: Unilateral Ureter Obstruction (UUO)

value: Day 10


title: RG002-T0

value: preoperative


title: RG003-POD

value: postoperative


title: Control2


title: PANC-1 cell _3

city: Wenzhou

first: hewei

last: zhang

state: Zhejiang

address: The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang, Ouhai

description: PANC-1 cells

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam). The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: Homo sapiens, Ensembl v96
Supplementary_files_format_and_content: FPKM values for each Sample.

source_name: PANC-1 cell lines

growth_protocol: PANC-1 cells were maintained in Dulbecco’s Modified Eagle Medium (Gibco, Grand Island, NY, USA), supplemented with 10% fetal bovine serum (Gibco, Grand Island, NY, USA), 100 µg/ml streptomycin, and 100 IU/ml penicillin (Invitrogen) at 37 ℃ in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: PANC-1 cells were treated with 40  μM Maslinic acid

tag: cell line


title: PANC-1 cell _1

institute: The First Affiliated Hospital of Wenzhou Medical University

description: PANC-1 cells


title: RG002-POD


title: G1-3-3

description: without induction 3 hours culture3

tag: strain


title: G1-3-1

description: without induction 3 hours culture1


title: PANC-1 cell _2

description: PANC-1 cells


title: IFNT rep1

city: Yangling

first: Haokun

last: Liu

address: Xinong Road 22

institute: Northwest A&F University

data_processing:
Raw reads were aligned to the goat genome using HISA T2 (v2.0.4) software.
Transcriptome assembly was performed using StringTie (v1.3.1) software in a reference-based approach.
Gene expression abundance was assessed by calculating the FPKMs of genes in each sample using Cufflinks (v2.1.1) software.
Genome_build: Capra hircus (goat); ID: 10731
Supplementary_files_format_and_content: .xls file include FPKM values for each Sample

organism: Capra hircus

source_name: Goat endometrial epithelial cells

extract_protocol:
Total RNA of gEECs was isolated using RNAiso Plus (Takara, Japan), and genomic DNA was removed using the Evo M-MLV RT Kit (Accurate Biology, China) according to the manufacturer’s protocols.
RNA libraries were prepared for sequencing using standard lllumina protocols.

value: Goat endometrial epithelial cells

value: 20 ng/mL of IFNT treatment for 6h


title: MTB-200ba429A


title: IFNT rep2


title: UUO kidney_day_0_rep1

tag: tissue

value: Day 0


title: Con rep1


title: Control3


title: Control1


title: RRBS_eNSC 1, rep 1

value: Sub ventricular zone


title: UUO kidney_day_2_rep1

value: Day 2


title: IFNT rep3


title: UUO kidney_day_10_rep2


title: UUO kidney_day_0_rep2


title: Con rep2


title: oxidised_1_rep1

status: Public on Sep 16 2021

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

description:
small RNA
SmallRNAcounts.methods.txt
C1-ox

data_processing:
Raw small RNA sequencing reads were quality-trimmed using cutadapt 1.9.1 using the parameters recommended in the NEXTflex Small RNA instructions to trim 3’ adapter (-a TGGAATTCTCGGGTGCCAAGG --minimum-length 10), and to trim 4 bases from either side of each read (-u 4 -u -4 ). Read quality was assessed using FastQC v0.11.4. Clean reads were aligned to a ribosomal RNA library made using SILVA database sequences for R. irregularis, and the Daucus_carota_388.v2.0 host genome using Bowtie-1.2.2 with the following parameters -q -a -v 0. All reads perfectly matching either rRNA or the carrot genome were filtered out. Remaining reads were aligned to the unmasked R. irregularis DAOM-181602 genome using Bowtie-1.2.2 and the following parameters: -q -k 500  -m 50 -v 1.
PolyA RNA-sequencing reads were filtered by Novogene to remove low-quality reads (reads containing Qscore <=5 in over 50% of bases, reads containing N > 10%). Reads were also trimmed by Novogene prior to our analysis. We assessed read quality was assessed using FastQC v0.11.4, all samples showed a Phred score higher than 30. Clean reads were aligned to the unmasked R. irregularis DAOM-181062 genome using STAR 2.5.4. For TE subfamily expression analyses, reads were aligned using the options --outFilterMultimapNmax 100 and --winAnchorMultimapNmax 100 and the counts were generated using the TEtranscripts package with the gene annotation and a curated version of TE annotation files produced in this study (options --mode multi and --stranded no). Our TE annotation was curated to exclude simple repeats, unclassified repeats, low complexity repeats, satellites, rRNAs, snRNAs and tRNAs. TE subfamilies with at least 100 normalised counts were considered expressed. The output count file was used to perform differential expression analysis of TEs with at least 1 normalised count using DESeq2, with 0h untreated samples as a control. TE subfamilies with a P adjusted value below 0.05 and an absolute log2 fold change higher than 0.5 were considered significantly differentially expressed. For locus-level TE expression, counts were generated with featureCounts (subread package 2.0.1, --fraction parameter used) and only TEs of a length > 100bp and at least 1RPKM in at least 6 samples were considered. For gene expression analysis, reads were mapped using STAR with the option --outFilterMultimapNmax 20 and counts were generated with featureCounts without the fraction option. Genes with at least 2 normalised counts in at least 2 samples were considered expressed.
Genomic CpG methylation data was produced from Nanopore sequencing data with DeepSignal (0.1.8), called against model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+ using default parameters. From the DeepSignal output, data for symmetrical CG sites was merged, and overlapped with TE or gene loci using bedtools map -median. Plots were generated using ggplot2.
Genome_build: Long read PacBio assembly http://nekko.nibb.ac.jp/ of the R. irregularis DAOM197198 genome was used.
Supplementary_files_format_and_content: spore_polyARNA_GENE_cntTable.txt: Gene polyA RNA counts
spore_polyARNA_TE.cntTable.txt: TE polyA RNA counts
SmallRNAcounts.methods.txt: Small RNA counts
20201007_1629_MN32650_single_fast5_result_frequency.gff.txt: Basecalled methylation

organism: Rhizophagus irregularis

source_name: Spore

growth_protocol: For a total of 20 RNA-seq samples, 5mL (50,000 spores/sample) of the spore solution was aliquoted to individual 16.8mL tissue culture wells, and the samples were incubated for seven days at 30°C and 2% CO2.

extract_protocol:
Prior to freezing, all spore samples were drained using 40μM cell strainers. For use in downstream processing, liquid-nitrogen frozen R. irregularis spore samples were homogenised using a mixer mill MM 400 and 25ml grinding jars (Retsch), shaking at 25 shakes/second for 20 seconds. High-molecular weight DNA was extracted using the protocol from Schwessinger & McDonald (doi: 10.1534/genetics.116.186734). RNA extraction was performed using an RNeasy Plant Kit (Quiagen, Germany)
Paired-end polyA+ RNA-libraries were produced and sequenced by Novogene UK Co. Ltd. with read lengths of 150 bp. Small RNA libraries were produced using the NEXTFLEX® Small RNA-Seq Kit v3 following the gel-based protocol. Small RNA libraries were sequenced on an Illumina Illumina HiSeq 1500 with read lengths of 50 bp. Genomic DNA sequencing libraries were prepared using the Oxford Nanopore Rapid DNA sequencing kit SQK-RAD004 and sequenced on MinION flow cells FLO-MIN106D following the accompanying protocol.

treatment_protocol: Following incubation, spore samples were either immediately frozen in liquid nitrogen for a 0h time point or were re-incubated at 30°C and 2% CO2 with either half-strength Hoagland’s solution or with sterilised rice exudates, for 24h or 48h hours. Four spore samples were produced per treatment.

value: NaIO4 oxidation


title: MA_PANC_1 cell _1

description: PANC-1 cells treated with  MA (40 uM) for 24 hours

value: treated with  MA (40 uM) for 24 hours


title: untreated_1_rep3

description:
small RNA
SmallRNAcounts.methods.txt
C3-un

value: Untreated


title: MA_PANC_1 cell _2


title: untreated_1_rep2

description:
small RNA
SmallRNAcounts.methods.txt
C2-un


title: Con rep3


title: untreated_1_rep1

description:
small RNA
SmallRNAcounts.methods.txt
C1-un


title: column_2_rep3

description:
small RNA
SmallRNAcounts.methods.txt
col-3

value: TRaPR column


title: 48h_exudate_rep3

description:
polyA
spore_polyARNA_GENE_cntTable.txt
spore_polyARNA_TE.cntTable.txt

value: Treated

tag: time point


title: column_2_rep1

description:
small RNA
SmallRNAcounts.methods.txt
col-1


title: 48h_exudate_rep2


title: untreated_2_rep2

description:
small RNA
SmallRNAcounts.methods.txt
input-2


title: 48h_exudate_rep1


title: untreated_2_rep3

description:
small RNA
SmallRNAcounts.methods.txt
input-3


title: UUO kidney_day_2_rep2


title: MA_PANC_1 cell _3


title: untreated_1_rep4

description:
small RNA
SmallRNAcounts.methods.txt
C4-un


title: oxidised_1_rep2

description:
small RNA
SmallRNAcounts.methods.txt
C2-ox


title: untreated_2_rep1

description:
small RNA
SmallRNAcounts.methods.txt
input-1


title: untreated_gDNA_ONT

description:
ONT
20201007_1629_MN32650_single_fast5_result_frequency.gff.txt

data_processing:
Library strategy: Basecalled methylation
Raw small RNA sequencing reads were quality-trimmed using cutadapt 1.9.1 using the parameters recommended in the NEXTflex Small RNA instructions to trim 3’ adapter (-a TGGAATTCTCGGGTGCCAAGG --minimum-length 10), and to trim 4 bases from either side of each read (-u 4 -u -4 ). Read quality was assessed using FastQC v0.11.4. Clean reads were aligned to a ribosomal RNA library made using SILVA database sequences for R. irregularis, and the Daucus_carota_388.v2.0 host genome using Bowtie-1.2.2 with the following parameters -q -a -v 0. All reads perfectly matching either rRNA or the carrot genome were filtered out. Remaining reads were aligned to the unmasked R. irregularis DAOM-181602 genome using Bowtie-1.2.2 and the following parameters: -q -k 500  -m 50 -v 1.
PolyA RNA-sequencing reads were filtered by Novogene to remove low-quality reads (reads containing Qscore <=5 in over 50% of bases, reads containing N > 10%). Reads were also trimmed by Novogene prior to our analysis. We assessed read quality was assessed using FastQC v0.11.4, all samples showed a Phred score higher than 30. Clean reads were aligned to the unmasked R. irregularis DAOM-181062 genome using STAR 2.5.4. For TE subfamily expression analyses, reads were aligned using the options --outFilterMultimapNmax 100 and --winAnchorMultimapNmax 100 and the counts were generated using the TEtranscripts package with the gene annotation and a curated version of TE annotation files produced in this study (options --mode multi and --stranded no). Our TE annotation was curated to exclude simple repeats, unclassified repeats, low complexity repeats, satellites, rRNAs, snRNAs and tRNAs. TE subfamilies with at least 100 normalised counts were considered expressed. The output count file was used to perform differential expression analysis of TEs with at least 1 normalised count using DESeq2, with 0h untreated samples as a control. TE subfamilies with a P adjusted value below 0.05 and an absolute log2 fold change higher than 0.5 were considered significantly differentially expressed. For locus-level TE expression, counts were generated with featureCounts (subread package 2.0.1, --fraction parameter used) and only TEs of a length > 100bp and at least 1RPKM in at least 6 samples were considered. For gene expression analysis, reads were mapped using STAR with the option --outFilterMultimapNmax 20 and counts were generated with featureCounts without the fraction option. Genes with at least 2 normalised counts in at least 2 samples were considered expressed.
Genomic CpG methylation data was produced from Nanopore sequencing data with DeepSignal (0.1.8), called against model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+ using default parameters. From the DeepSignal output, data for symmetrical CG sites was merged, and overlapped with TE or gene loci using bedtools map -median. Plots were generated using ggplot2.
Genome_build: Long read PacBio assembly http://nekko.nibb.ac.jp/ of the R. irregularis DAOM197198 genome was used.
Supplementary_files_format_and_content: spore_polyARNA_GENE_cntTable.txt: Gene polyA RNA counts
spore_polyARNA_TE.cntTable.txt: TE polyA RNA counts
SmallRNAcounts.methods.txt: Small RNA counts
20201007_1629_MN32650_single_fast5_result_frequency.gff.txt: Basecalled methylation


title: oxidised_1_rep4

description:
small RNA
SmallRNAcounts.methods.txt
C4-ox


title: 48h_untreated_rep1


title: 24h_exudate_rep4


title: 48h_untreated_rep4


title: 48h_exudate_rep4


title: 24h_exudate_rep3


title: 48h_untreated_rep2


title: 24h_untreated_rep3


title: 24h_untreated_rep4


title: 24h_untreated_rep1


title: 24h_untreated_rep2


title: 24h_exudate_rep1


title: oxidised_1_rep3

description:
small RNA
SmallRNAcounts.methods.txt
C3-ox


title: column_2_rep2

description:
small RNA
SmallRNAcounts.methods.txt
col-2


title: 48h_untreated_rep3


title: BglG_GFP_doxauxin_RNAseq_rep3

city: heidelberg

first: samuel

last: collombet

address: Meyerholfstrasse

institute: EMBL

data_processing:
All data were mapped to the mouse genome mm10, using the BL6-EiJ / CAST SNPs from the mouse genome project (v5 SNP142)
Reads were trimmed using Trimgalore (v.0.4.4), mapped using STAR (2.5.3a, parameters:–outFilterMultimapNmax 1–outFilterMismatchNmax 999–outFilterMismatchNoverLmax 0.06–alignIntronMax 500000–alignMatesGapMax 500000–alignEndsType EndToEnd–outSAMattributes NH HI NM MD), and removed when mapping to the mitochondrial genome. Remaining reads were split by allele using SNPsplit (v.0.3.2). Allele-specific and the unassigned bam files were sorted, duplicates removed using picard (v.2.18.2, parameters: REMOVE_DUPLICATES = true ASSUME_SORTED = true) and pooled as the total reads. Quantification of expression was performed using featureCount (parameters: -p -t exon -g gene_id, -s 1 for stranded RNA-seq of in vitro cell, -s 0 for non-stranded RNA-seq of single embryo). Data were then analysed in R using DESeq2 (v.1.18.1), calculating the sizeFactor on the count of total reads and applying it to the allele-specific counts
Genome_build: mm10
Supplementary_files_format_and_content:  processedData_countTable.tsv

growth_protocol: ES cells (TX1072) were seeded in 0.1% gelatin-coated 6-well plates (0.25*10^6 cells/well). Cells were grown in 2i + LIF serum-containing ES cell medium - DMEM (Sigma), 15% FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Chemicon), CHIR99021 (3uM), PD0325901 (1uM) in 8% CO2 37°C incubators.

extract_protocol:
RNA was extracted according to the manufacturer’s recommendations using RNeasy Mini Kit (Qiagen) with on-column DNAse digestion (Qiagen).
Only samples showing a RIN score above 9 were used to prepare RNAseq libraries (TruSeq). Libraries were sequenced using HiSeq2500 at PE100 settings.

treatment_protocol: 24 hours later, cells were exposed to doxycycline (1ug/mL). Cells were then collected 24 hours later.

value: mESC

value: BL/6J x CAST-EiJ


title: 0h_untreated_rep1


title: 0h_untreated_rep2


title: BglG_GFP_doxauxin_RNAseq_rep4


title: BglG_GFP_doxauxin_RNAseq_rep2


title: BglG_GFP_doxauxin_RNAseq_rep1


title: 0h_untreated_rep3


title: 24h_exudate_rep2


title: BglG_GFP_dox_RNAseq_rep2


title: BglG_GFP_dox_RNAseq_rep4


title: BglG_GFP_dox_RNAseq_rep1


title: BglG_GFP_dox_RNAseq_rep3


title: BglG_GFP_control_RNAseq_rep3


title: BglG_GFP_control_RNAseq_rep2


title: BglG_GFP_control_RNAseq_rep1


title: BglG_GFP_SPOC_doxauxin_RNAseq_rep2


title: BglG_GFP_SPOC_doxauxin_RNAseq_rep5


title: BglG_GFP_SPOC_doxauxin_RNAseq_rep4


title: BglG_GFP_SPOC_doxauxin_RNAseq_rep3


title: BglG_GFP_SPOC_doxauxin_RNAseq_rep1


title: BglG_GFP_SPOC_dox_RNAseq_rep5


title: BglG_GFP_SPOC_dox_RNAseq_rep4


title: BglG_GFP_SPOC_dox_RNAseq_rep1


title: BglG_GFP_SPOC_dox_RNAseq_rep2


title: BglG_GFP_SPOC_dox_RNAseq_rep3


title: BglG_GFP_SPOC_control_RNAseq_rep4


title: BglG_GFP_SPOC_control_RNAseq_rep5


title: BglG_GFP_SPOC_control_RNAseq_rep3


title: BglG_GFP_SPOC_control_RNAseq_rep2


title: BglG_GFP_SPOC_control_RNAseq_rep1


title: Tumour cell line 67NR sample 2

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

description: Cell line 67NR 2

data_processing:
Libraries were sequenced on an Illumina NextSeq 500.
Reads were aligned to the mouse genome mm10 by Rsubread version 1.22.3.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq gene annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: Tumour cell line

extract_protocol:
Total RNA was extracted.
Illumina's TruSeq RNA v2 sample preparation protocol was used.


title: BglG_GFP_control_RNAseq_rep4


title: Tumour cell line 66c14 sample 2

description: Cell line 66c14 2


title: Tumour cell line 66c14 sample 1

description: Cell line 66c14 1


title: Tumour cell line 4T1 sample 1

description: Cell line 4T1 1


title: Tumour cell line 4T1.2 sample 2

description: Cell line 4T1.2 2


title: Non-metastatic EMCNhiCD31hi sample 6

data_processing:
Libraries were sequenced on an Illumina NextSeq 500.
Reads were aligned to the mouse genome mm10 by Rsubread version 1.22.3
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: Bone marrow

extract_protocol:
Total RNA was extracted to generate libraries for whole transcriptome analysis.
Clontech SMART-Seq v4 Ultra Low Input RNA kit.

value: BALB/c

tag: mouse pool

tag: population

value: Non-metastatic

value: EMCNhi CD31hi endothelial cells


title: Non-metastatic EMCNhiCD31hi sample 5


title: Tumour cell line 4T1.2 sample 1

description: Cell line 4T1.2 1


title: Tumour cell line 4T1 sample 2

description: Cell line 4T1 2


title: Tumour cell line 67NR sample 1

description: Cell line 67NR 1


title: Metastatic EMCNhiCD31hi sample 2

value: Metastatic


title: Metastatic EMCNhiCD31hi sample 3


title: Non-metastatic EMCNhiCD31hi sample 2


title: Non-metastatic EMCNhiCD31hi sample 1


title: Control EMCNhiCD31hi sample 2

value: Control


title: Non-metastatic EMCNhiCD31hi sample 3


title: Non-metastatic EMCNhiCD31hi sample 4


title: Metastatic EMCNhiCD31hi sample 1


title: Control EMCNhiCD31hi sample 1


title: Day12-SEN-MSC-R2

city: Clayton

first: David

middle: Richard

last: Powell

address: Wellington Road

department: Bioinformatics Platform

institute: Monash University

data_processing:
The RNAsik pipeline (https://github.com/MonashBioinformaticsPlatform/RNAsik-pipe) was run on the raw fastq files. It uses STAR (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/) for aligning to the ensembl mouse genome (ver GRCm38.87) (ftp://ftp.ensembl.org/pub/release-87/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz).
FeatureCounts (http://bioinformatics.oxfordjournals.org/content/30/7/923.long) was then used to assign to annotated features (ftp://ftp.ensembl.org/pub/release-87/gtf/mus_musculus /Mus_musculus.GRCm38.87.gtf.gz) in the genome.
To check for human contamination, the RNAsik pipeline was also run while mapping to the ensembl human genome (GRCm38) (ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens /dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz).
Genome_build: ver GRCm38.87
Supplementary_files_format_and_content: gene counts in tsv format

source_name: Day12-SEN-MSC_alveolar macrophages

extract_protocol:
RNA was isolated from sorted AMs using the Ambion RNAqueous-Micro Kit (ThermoFisher Scientific/Ambion) as per manufacturer’s instructions
Library construction was carried out using the Illumina TruSeq mRNA Library Construction Kit.

value: female

value: 7-8 weeks old

value: bronchoalveolar lavage fluid

value: alveolar macrophages

tag: ova sensitisation

value: yes

tag: msc treatment

tag: day after ova sensitisation

value: day 12


title: Day12-UNS-MSC-R1

source_name: Day12-UNS-MSC_alveolar macrophages

tag: Sex

tag: age

value: no


title: Day12-UNS-MSC-R2

tag: cell type


title: Day12-UNS-R1

source_name: Day12-UNS_alveolar macrophages


title: Day8-SEN-MSC-R2

source_name: Day8-SEN-MSC_alveolar macrophages

value: day 8


title: Day12-UNS-R2


title: Day12-SEN-R2

source_name: Day12-SEN_alveolar macrophages


title: Day12-SEN-R1


title: Day8-UNS-MSC-R1

source_name: Day8-UNS-MSC_alveolar macrophages


title: 0h_untreated_rep4

tag: treatment

value: Untreated


title: Day12-SEN-MSC-R1


title: Day8-UNS-R2

source_name: Day8-UNS_alveolar macrophages


title: Day8-SEN-MSC-R1


title: Day8-SEN-R2

source_name: Day8-SEN_alveolar macrophages


title: Day8-SEN-R1


title: vasadrop_mm_hs_NextSeq

city: Leiden

first: Anna

last: Alemany

email: annalemany@gmail.com, a.alemany@lumc.nl

state: South Holland

address: ALBINUSDREEF 2

department: Anatomy and Embryology

country: Netherlands

institute: LUMC

data_processing:
Sequencing libraries were mapped with STAR-2.5.3a with default parameters to the ensembl version 93 of the mouse genome, and only reads mapping to gene bodies (exons or introns) were used for downstream analysis. Reads mapping simultaneously to an exon and to an intron were assigned to the exon.
Genome_build: Ensembl version 99 for both mouse and human genomes
Supplementary_files_format_and_content: Tabular-separated file indicating number of UFIs per cell. In "total.UFICounts.tsv.gz" spliced and unspliced transcripts are reported together, and multi-annotations are indicated as "geneA_geneB". In "uniaggGenes_spliced.UFICounts.tsv.gz" and "uniaggGenes_unspliced.UFICounts.tsv.gz", count tables for spliced and unspliced transcripts are provided separatedy, and multi-annotations are aggregated.

organism:
Homo sapiens
Mus musculus

extract_protocol:
vasaplate: Single cells were sorted by FACS into 384-well plates containing RT-primers and oil. Reagents were dispensed with a robot and plates incubated in a thermocycles after each dispensing. Briefly; 1) Lysis/fragmentation mix, 2) Poly(A)-tailing/end repair mix, 3) Reverse transcription mix, 4) Second strand synthesis mix. After second strand synthesis, wells were pooled and material was amplified with IVT. Amplified material was depleted of rRNA, second adapter was ligated and aRNA converted to cDNA. Full Illumina handles were added by PCR, and samples were sequenced.
vasadrop: Single-cells were co-encapsulated with barcoded inDrop v3 beads with with a lysis and RNA fragmentation buffer. The droplets were then incubated and further injected with a RNA repair and poly(A) tailing mix using a pico-injector. After incubation, the droplets were the injected with a reverse transcription mix and incubated. The. Droplets were then de-emulsified and processed similarly to the VASA-plate workflow.
cell dissociation: HEK293T were cultured in DMEM, dissociated with Trypsin-EDTA and washed with ice-cold PBS. Mouse ES cells were cultured in 2i/LIF conditions, dissociated with Accutase and washed with ice-cold PBS. Mouse embryos from E8.5 and E9.5 were cut into pieces under the microscope before collection in a tube, embryos from stage E6.5 and E7.5 were not cut. TrypLE Express was used for cell dissociation and washed with PBS supplemented with 0.4% BSA.
Illumina TruSeq adapaters

tag: protocol/barcodes

value: VASA-seq

tag: read format

value: Read 1 starts with a 6-nucleotide long UFI, followed by an 16 nucleotide long cell-specific barcode

tag: plate format

tag: sample type

value: mixed human HEK293T and mouse embryonic stem cells


title: vasaplate-HEK293T-mESC

value: Read 1 starts with a 6-nucleotide long UFI, followed by an 8 nucleotide long cell-specific barcode

value: human cells sorted inwells 1,3,5, etc(i.e. A1, A3, A5, etc.) and mouse cells sorted in 2,4,6, etc (A2, A4, A6, etc)


title: HUB-DB-012

city: Jena

first: Dennis

middle: de

last: de Bakker

address: Beutenbergstraße 11

institute: FLI

description:
Sample 4
prrx1b-/- plate 2

data_processing:
Paired-end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. (2014) Cell.
(Sample 1,2) Mapped reads were assigned to cells based on barcodes according to the CEL-seq2 protocol (Hashimshony et al., 2016)) In brief, read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier (UMI) and followed by a 24 nt PolyA stretch and a number (<40) of transcript derived bases. Cell specific barcodes are specified in the file "cel-seq2_barcodes.csv", well numbers refer to the 384-well plate in the following order: A1 to A24 - B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2, containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded.
(Sample 3,4) Mapped reads were assigned to cells based on barcodes according to the CEL-seq2 protocol (Hashimshony et al., 2016)) In brief, read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier (UMI) and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel-seq2_barcodes.csv". Read 1 was not used for quantification. Read 2, containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded.
Genome_build: zv9 (with improved 3' annotation, see Junker et al. (2014) Cell)
Supplementary_files_format_and_content: *.TranscriptCounts.tsv: Tab-delimited read count matrices in which rows correspond to genes and columns to single cells.
Supplementary_files_format_and_content: cel-seq2_barcodes.csv: Comma-separated values

organism: Danio rerio

source_name: Epicardial cells of the Zebrafish heart ventricle

extract_protocol:
Live cells were sorted into 384-well plates with Vapor-Lock oil containing a droplet with barcoded primers, spike-in RNA and dNTPs, followed by heat-induced cell lysis and cDNA syntheses using a robotic liquid handler. After cell lysis for 5 minutes at 65C, RT and second strand mixes were distributed with the Nanodrop II liquid handling platform.
Primers consisted of a 24bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific 8bp barcode, the 5' Illumina TruSeq small RNA kit adapter and a T7 promoter. After all cells were pooled in one library, the CEL-seq2 protocol was used for library prep (Hashimony et al., 2016).

treatment_protocol: Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tg(tcf21:mCherry) cells were subsequently FACS sorted based on mCherry expression in 384 well plates, each well containing 1 cell.

tag: line

tag: genotype/variation

value: Cryoinjured heart

tag: Stage

value: Epicardial cells of adult heart ventricle


title: HUB-DB-011

description:
Sample 3
prrx1b-/- plate 1


title: HUB-DB-009

description:
Sample 1
WT plate 1

value: WT


title: Day8-UNS-R1

tag: strain

value: BALB/c

value: female

tag: tissue


title: Healthy control sample 66

city: Nashville

first: Hung-Hsin

last: Chen

state: TN

address: 2525 West End Ave., Suite 700

department: Vanderbilt Genetics Institute

institute: Vanderbilt University Medical Center

data_processing:
All raw sequencing read libraries were checked with FastQC to ensure their sequencing quality
All RNA sequencing reads were aligned to the human reference genome (hg19) by Spliced Transcripts Alignment to a Reference (STAR v2.5.0a)
Genes without mapped reads in over 10% of samples or with median absolute deviation equal to 0 were excluded from further analysis
DEseq2 v1.30.1 was used to normalize the gene expression matrix, any normalized expression with value less than 1 were adjusted to 1
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: control subject 33, follow-up

extract_protocol:
The fasting peripheral blood specimens were collected using PaxGene tubes for each participant at both baseline and follow-up
RNA sequencing was performed with Illumina HiSeq 2000 at the Baylor Sequencing Center following standard protocols

tag: disease state

value: control

tag: individual

value: control subject 33

tag: timepoint

value: follow-up

value: peripheral blood

value: Control follow-up transcriptome


title: Healthy control sample 65

source_name: control subject 32, follow-up

value: control subject 32


title: pEXO_macrophage_02

city: Hong Kong

first: Jianlin

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Low-quality reads were removed by fastp with default parameters
Remaining clean reads were align to the Human genome 38 (hg38) by Hisat2 with default parameters
Raw gene counts were generated by featurecount and then normalized by DEseq2
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: human monocyte-derived macrophage

growth_protocol: Primary monocytes were isolated by Ficoll-Paque density gradient centrifugation. Monocyte isolated by positive immunomagnetic separation. Culture in RPMI1640 + 10% FBS

extract_protocol:
Total RNA was extracted by RNA spin column
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

treatment_protocol: Macrophages were prepared by treating monocytes with 50 ng/ml MCSF for7 days and at Day 8 treated in the presence or absence ofpEXO (20 μg/ml)

tag: source

value: buffy coat

tag: treatment with pexo

value: treated with pEXO

tag: induction

value: M-CSF


title: pEXO_macrophage_01


title: Healthy control sample 64

source_name: control subject 30, follow-up

value: control subject 30

tag: Sex

tag: age


title: Day8-UNS-MSC-R2

value: 7-8 weeks old

value: bronchoalveolar lavage fluid

tag: cell type

value: alveolar macrophages

tag: ova sensitisation

value: no

tag: msc treatment

value: yes

tag: day after ova sensitisation

value: day 8


title: Contorl_macrophage_02

value: untreated


title: Contorl_macrophage_01


title: Healthy control sample 56

source_name: control subject 22, follow-up

value: control

value: control subject 22

value: female

tag: sample type


title: Healthy control sample 60

source_name: control subject 26, follow-up

value: control subject 26

value: follow-up

value: peripheral blood


title: Healthy control sample 63

source_name: control subject 29, follow-up

value: control subject 29

value: Control follow-up transcriptome


title: Healthy control sample 59

source_name: control subject 25, follow-up

value: control subject 25


title: Healthy control sample 58

source_name: control subject 24, follow-up

value: control subject 24


title: Healthy control sample 54

source_name: control subject 20, follow-up

value: control subject 20

value: male


title: Healthy control sample 53

source_name: control subject 19, follow-up

value: control subject 19


title: HUB-DB-010

description:
Sample 2
WT plate 2

tag: line

tag: genotype/variation

value: WT

tag: treatment

value: Cryoinjured heart

value: Epicardial cells of adult heart ventricle


title: Healthy control sample 48

source_name: control subject 14, follow-up

value: control subject 14

tag: tissue


title: Healthy control sample 52

source_name: control subject 18, follow-up

tag: disease state

value: control

value: control subject 18


title: Healthy control sample 47

source_name: control subject 13, follow-up

tag: individual

value: control subject 13

value: female


title: Healthy control sample 61

source_name: control subject 27, follow-up

value: control subject 27

tag: timepoint

value: follow-up


title: Healthy control sample 51

source_name: control subject 17, follow-up

value: control subject 17

value: peripheral blood


title: Healthy control sample 55

source_name: control subject 21, follow-up

value: control subject 21

value: Control follow-up transcriptome


title: Healthy control sample 49

source_name: control subject 15, follow-up

value: control subject 15


title: Healthy control sample 43

source_name: control subject 9, follow-up

value: control subject 9


title: Healthy control sample 46

source_name: control subject 12, follow-up

value: control subject 12

value: male


title: Healthy control sample 45

source_name: control subject 11, follow-up

value: control subject 11


title: Healthy control sample 50

source_name: control subject 16, follow-up

value: control subject 16


title: Healthy control sample 44

source_name: control subject 10, follow-up

value: control subject 10


title: Healthy control sample 42

source_name: control subject 8, follow-up

value: control

value: control subject 8


title: Healthy control sample 40

source_name: control subject 6, follow-up

value: control subject 6


title: Healthy control sample 39

source_name: control subject 5, follow-up

value: control subject 5

value: female


title: Healthy control sample 37

source_name: control subject 3, follow-up

value: control subject 3

value: follow-up


title: Healthy control sample 62

source_name: control subject 28, follow-up

value: control subject 28

value: peripheral blood


title: Healthy control sample 57

source_name: control subject 23, follow-up

value: control subject 23

value: Control follow-up transcriptome


title: Healthy control sample 36

source_name: control subject 1, follow-up

value: control subject 1


title: Healthy control sample 41

source_name: control subject 7, follow-up

value: control subject 7


title: Healthy control sample 35

source_name: control subject 31, follow-up

value: control subject 31


title: Healthy control sample 29

source_name: control subject 28, baseline

value: baseline

value: Control baseline transcriptome


title: Healthy control sample 30

source_name: control subject 29, baseline

value: control subject 29


title: Healthy control sample 27

source_name: control subject 26, baseline

value: control

value: control subject 26


title: Healthy control sample 33

source_name: control subject 33, baseline

value: control subject 33


title: Healthy control sample 28

source_name: control subject 27, baseline

value: control subject 27


title: Healthy control sample 26

source_name: control subject 25, baseline

value: control subject 25

value: female


title: Healthy control sample 31

source_name: control subject 30, baseline

value: control subject 30


title: Healthy control sample 25

source_name: control subject 24, baseline

value: control subject 24


title: Healthy control sample 21

source_name: control subject 20, baseline

value: control subject 20

value: male

value: peripheral blood


title: Healthy control sample 24

source_name: control subject 23, baseline

value: control subject 23


title: Healthy control sample 20

source_name: control subject 19, baseline

value: control subject 19


title: Healthy control sample 23

source_name: control subject 22, baseline

value: control subject 22


title: Healthy control sample 22

source_name: control subject 21, baseline

value: control subject 21

value: baseline


title: Healthy control sample 17

source_name: control subject 16, baseline

value: control subject 16

value: Control baseline transcriptome


title: Healthy control sample 15

source_name: control subject 14, baseline

value: control

value: control subject 14


title: Healthy control sample 19

source_name: control subject 18, baseline

value: control subject 18


title: Healthy control sample 38

source_name: control subject 4, follow-up

value: control subject 4

value: follow-up

value: Control follow-up transcriptome


title: Healthy control sample 14

source_name: control subject 13, baseline

value: control subject 13

value: female


title: Healthy control sample 12

source_name: control subject 11, baseline

value: control subject 11


title: Healthy control sample 34

source_name: control subject 2, follow-up

value: control subject 2

value: peripheral blood


title: Healthy control sample 10

source_name: control subject 9, baseline

value: control subject 9


title: Healthy control sample 11

source_name: control subject 10, baseline

value: control subject 10


title: Healthy control sample 9

source_name: control subject 8, baseline

value: control subject 8


title: Healthy control sample 7

source_name: control subject 6, baseline

value: control subject 6

value: baseline


title: Healthy control sample 6

source_name: control subject 5, baseline

value: control subject 5

value: Control baseline transcriptome


title: Healthy control sample 32

source_name: control subject 32, baseline

value: control

value: control subject 32


title: Healthy control sample 13

source_name: control subject 12, baseline

value: control subject 12

value: male


title: Healthy control sample 5

source_name: control subject 4, baseline

value: control subject 4


title: Healthy control sample 3

source_name: control subject 1, baseline

value: control subject 1


title: Healthy control sample 4

source_name: control subject 3, baseline

value: control subject 3

value: female


title: Healthy control sample 16

source_name: control subject 15, baseline

value: control subject 15


title: T2D case sample 50

source_name: case subject 25, follow-up

value: T2D case

value: case subject 25

value: follow-up

value: peripheral blood

value: T2D follow-up transcriptome


title: Healthy control sample 18

source_name: control subject 17, baseline

value: control subject 17

value: baseline


title: T2D case sample 45

source_name: case subject 20, follow-up

value: case subject 20


title: Healthy control sample 2

source_name: control subject 31, baseline

value: control

value: control subject 31

value: Control baseline transcriptome


title: Healthy control sample 1

source_name: control subject 2, baseline

value: control subject 2


title: T2D case sample 46

source_name: case subject 21, follow-up

value: case subject 21


title: T2D case sample 47

source_name: case subject 22, follow-up

value: case subject 22


title: T2D case sample 40

source_name: case subject 15, follow-up

value: case subject 15


title: T2D case sample 43

source_name: case subject 18, follow-up

value: case subject 18

value: female


title: T2D case sample 42

source_name: case subject 17, follow-up

value: T2D case

value: case subject 17

value: male


title: T2D case sample 44

source_name: case subject 19, follow-up

value: case subject 19

value: follow-up

value: peripheral blood


title: T2D case sample 41

source_name: case subject 16, follow-up

value: case subject 16

value: T2D follow-up transcriptome


title: T2D case sample 39

source_name: case subject 14, follow-up

value: case subject 14


title: T2D case sample 38

source_name: case subject 13, follow-up

value: case subject 13


title: Healthy control sample 8

source_name: control subject 7, baseline

value: control

value: control subject 7

value: baseline

value: Control baseline transcriptome


title: T2D case sample 36

source_name: case subject 11, follow-up

value: case subject 11


title: T2D case sample 34

source_name: case subject 9, follow-up

value: case subject 9


title: T2D case sample 35

source_name: case subject 10, follow-up

value: case subject 10

value: female


title: T2D case sample 33

source_name: case subject 8, follow-up

value: T2D case

value: case subject 8


title: T2D case sample 30

source_name: case subject 5, follow-up

value: case subject 5


title: T2D case sample 31

source_name: case subject 6, follow-up

value: case subject 6

value: follow-up


title: T2D case sample 32

source_name: case subject 7, follow-up

value: case subject 7

value: male

value: peripheral blood


title: T2D case sample 27

source_name: case subject 2, follow-up

value: case subject 2

value: T2D follow-up transcriptome


title: T2D case sample 49

source_name: case subject 24, follow-up

value: case subject 24


title: T2D case sample 26

source_name: case subject 1, follow-up

value: case subject 1


title: T2D case sample 48

source_name: case subject 23, follow-up

value: case subject 23


title: T2D case sample 28

source_name: case subject 3, follow-up

value: case subject 3


title: T2D case sample 25

source_name: case subject 25, baseline

value: case subject 25

value: baseline

value: T2D baseline transcriptome


title: T2D case sample 24

source_name: case subject 24, baseline

value: T2D case

value: female


title: T2D case sample 20

source_name: case subject 20, baseline

value: case subject 20


title: T2D case sample 22

source_name: case subject 22, baseline

value: case subject 22


title: T2D case sample 18

source_name: case subject 18, baseline

value: case subject 18


title: T2D case sample 19

source_name: case subject 19, baseline

value: case subject 19


title: T2D case sample 23

source_name: case subject 23, baseline


title: T2D case sample 15

source_name: case subject 15, baseline

value: case subject 15


title: T2D case sample 13

source_name: case subject 13, baseline

value: case subject 13

value: peripheral blood


title: T2D case sample 12

source_name: case subject 12, baseline

value: case subject 12

value: male


title: T2D case sample 37

source_name: case subject 12, follow-up

value: follow-up

value: T2D follow-up transcriptome


title: T2D case sample 10

source_name: case subject 10, baseline

value: case subject 10


title: T2D case sample 11

source_name: case subject 11, baseline

value: case subject 11


title: T2D case sample 7

source_name: case subject 7, baseline

value: case subject 7

value: baseline


title: T2D case sample 29

source_name: case subject 4, follow-up

value: T2D case

value: case subject 4


title: T2D case sample 8

source_name: case subject 8, baseline

value: case subject 8

value: female

value: T2D baseline transcriptome


title: T2D case sample 9

source_name: case subject 9, baseline

value: case subject 9


title: T2D case sample 5

source_name: case subject 5, baseline

value: case subject 5


title: T2D case sample 6

source_name: case subject 6, baseline

value: case subject 6


title: T2D case sample 4

source_name: case subject 4, baseline

value: peripheral blood


title: T2D case sample 3

source_name: case subject 3, baseline

value: case subject 3


title: T2D case sample 1

source_name: case subject 1, baseline

value: case subject 1


title: T2D case sample 2

source_name: case subject 2, baseline

value: case subject 2


title: T2D case sample 14

source_name: case subject 14, baseline

value: case subject 14


title: T2D case sample 16

source_name: case subject 16, baseline

value: case subject 16


title: T2D case sample 21

source_name: case subject 21, baseline

value: case subject 21


title: T2D case sample 17

source_name: case subject 17, baseline

value: case subject 17

value: male


title: Pso2B_R1

city: Buffalo

first: Omer

last: Gokcumen

state: NY

address: 639 Cooke Hall

department: Biological Sciences

institute: University at Buffalo

description: RNAseq

data_processing:
RNA sequencing was performed via Illumina HiSeq, 2x150bp configuration.
Quality control of paired reads was performed using FastQC and MultiQC.
Illumina adaptor sequences and short or low quality sequences were further filtered using Trim Galore!. Reads were aligned to the human reference genome (Hg38) using Kallisto.
ligned data were then comparatively analyzed using the DESeq2 pipeline (Benjamini and Hochberg FDR corrected adjusted p-value, p<0.05), where psoriatic plaques were compared to non-psoriatic tissue as a control without inputting information of the sample of origin.
Supplementary_files_format_and_content: Tab1: Normalized gene expression (as output from DeSeq2). Tab2: Comparision of lesional and nonlesional
Genome_build: Hg38
Supplementary_files_format_and_content: Normalized gene expression (as output from DeSeq2)
Supplementary_files_format_and_content: Comparaitve analysis between lesional and nonlesional skin

source_name: Skin biopsy

extract_protocol: none provided by the submitter

tag: phenotype

value: nonlesional

tag: ethnicity

value: European

tag: pasi score

tag: biopsy site

value: lower back


title: Pso3A_R1

description: RNAseq

value: lesional

tag: Sex

value: female

tag: age

value: upper arm


title: Pso5A_R1

description: RNAseq

value: elbow


title: Pso5B_R1

description: RNAseq


title: Pso2A_R1

description: RNAseq


title: Pso3B_R1

description: RNAseq


title: PRE-R-054 [18R428_008]

city: Seoul

first: Tae Won

last: Kim

address: 88 Olympic-ro 43-gil

country: South Korea

institute: Asan Medical Center

data_processing:
All fastq format reads were assessed for quality control using FASTQC software (v0.11.8).
The Illumina sequencing platform-specific adaptors and poor quality read bases were trimmed using Trim Galore (v0.4.5).
The trimmed reads were mapped to the reference genome  with STAR aligner (v2.6.0) and the output sam/bam files were obtained.
Gene expression was quantified using RSEM (v1.2.23)
normalized through DESeq2 BiocManager package (v1.20.0)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: comma-delimited text files include raw counts and FPKM values for each Sample

source_name: colorectal cancer

extract_protocol:
macrodisssection of an unstained FFPE tissue section, followed by total RNA extraction using TRIzol reagent.
A cDNA library was constructed using TruSeq RNA Access Library Prep Kit (Illumina, Inc., San Diego, CA, USA) and paired-end sequencing was conducted using an HiSeq 2500 platform (Illumina Inc).

value: primary tumor (colorectum)

tag: time point

value: pre-treatment

tag: treatment response

value: pre-Tx


title: PAIR-R-021 [18R656_018]


title: POST-R-016 [18R465_006]

value: post-treatment

value: post-tx PD


title: PRE-R-055 [18R705_013]


title: PRE-R-052 [18R477_019]


title: POST-R-015 [18R673_05]

value: post-Tx non-PD


title: PRE-10 [18R507_004]


title: PRE-R-051 [18R454_027]


title: POST-R-014 [18R702_010]


title: PAIR-R-021 [18R657_019]


title: PRE-R-050 [18R480_022]


title: PRE-R-047 [18R701_09]


title: PAIR-R-020 [18R640_001]


title: PRE-R-046 [18R476_018]


title: PRE-R-049 [18R479_021]


title: PAIR-R-020 [18R641_002]

value: liver metastases


title: PRE-R-048 [18R478_020]


title: PRE-R-044 [18R474_015]


title: Case no 35, tumor biopsy, mediastinum

type: genomic

city: Leuven

first: Nicolas

last: Dierckxsens

address: ON I Herestraat 49

department: Human Genetics

country: Belgium

institute: KULeuven

hyb_protocol: According to the manufacturer's instructions.

scan_protocol: Cytoscan (Illumina, San Diego, CA, USA)

data_processing: GenomeStudio  (Illumina, San Diego, CA, USA)

label: C-Bio and A-DNP

source_name: tumor biopsy, mediastinum

value: tumor biopsy, mediastinum

tag: diagnosis

value: primary mediastinal B cell lymphoma

tag: gender

tag: stage (ann arbor)

value: II


title: PRE-R-043 [18R471_012]


title: PRE-R-045 [18R475_016]


title: PRE-R-042 [18R470_011]


title: PRE-R-041 [18R469_010]


title: PRE-R-040 [18R468_009]


title: Case no 29, tumor biopsy, mediastinum

label_protocol: According to the manufacturer's instructions.


title: Case no 28, tumor biopsy, small intestine

source_name: tumor biopsy, small intestine

extract_protocol: According to the manufacturer's instructions.

value: tumor biopsy, small intestine

value: primary mediastinal B cell lymphoma, non mediastinal

value: IV


title: Case no 33, tumor biopsy, mediastinum


title: Case no 30, tumor biopsy, mediastinum


title: Case no 27, tumor biopsy, mediastinum


title: Case no 34, tumor biopsy, mediastinum

value: male


title: Case no 24, tumor biopsy, mediastinum

value: female


title: Case no 23, tumor biopsy, mediastinum

value: I


title: Case no 21, tumor biopsy, mediastinum


title: PRE-R-039 [18R467_008]

value: other site metastases


title: PRE-R-038 [18R464_005]

value: primary tumor (colorectum)


title: Case no 18, tumor biopsy, mediastinum


title: PRE-R-037 [18R462_003]

value: pre-treatment


title: Case no 16, tumor biopsy, mediastinum


title: Case no 25, tumor biopsy, mediastinum


title: Case no 14, tumor biopsy, mediastinum


title: Case no 31, tumor biopsy, mediastinum


title: Case no 12, tumor biopsy, mediastinum


title: Case no 13, tumor biopsy, mediastinum


title: Case no 22, tumor biopsy, mediastinum


title: Case no 17, tumor biopsy, mediastinum

value: not available


title: Case no 26, tumor biopsy, mediastinum


title: Case no 32, tumor biopsy, mediastinum


title: Case no 19, tumor biopsy, mediastinum


title: PRE-R-031 [18R440_020]

value: pre-Tx


title: Case no 9, tumor biopsy, mediastinum


title: PRE-R-035 [18R459_027]


title: Case no 7, tumor biopsy, mediastinum


title: PRE-R-029 [18R449_023]


title: Case no 10, tumor biopsy, mediastinum


title: Case no 5, tumor biopsy, mediastinum


title: mNPC_WAPLAID_ChIP_CTCF_0h

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: Gene Regulation

institute: Netherlands Cancer Institute

description: CTCF ChIP-seq in E14TG2a mNPCs (with OsTir1; WAPL-AID-eGFP), after 0h of IAA

data_processing:
DamID: The full protocol is described in the corresponding manuscript. The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts. Remaining sequences were mapped to the mouse genome (mm10) using bwa mem 0.7.17. Reads overlapping GATC fragments were counted in 10kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts. LADs were called using hidden Markov modeling (https://github.com/ gui11aume/HMMt). Additionally, individual replicates were averaged for create a combined data track and LAD model.
ChIP-seq: The full protocol is described in the corresponding manuscript. Reads were mapped to a concatenated reference genome (mm10 and hg19) using bowtie2 2.3.4.1. Reads were filtered for a mapping quality of at least 15 and optical PCR duplicates were removed with SAMtools 1.9. Deeptools 3.0 was used to create a normalized coverage track, scaled to 1 million HEK293T reads. Peak calling was performed with MACS2 2.1.1.20160309 at a q-value cutoff of 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: DamID: BigWig files of log2-normalized LaminB1 pADamID scores for 10kb genomic bins, bed file with LAD coordinates; ChIP-seq: BigWig file of coverage, bed file with peak coordinates.

growth_protocol: Mouse neural precursor cells (mNPCs) were cultured in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%; Gibco), recombinant mouse EGF (10 ng/ml; PeproTech) and recombinant human FGF-basic (10 ng/ml; PeproTech) on 0.1% gelatin-coated plates. Cells were passaged every 3-4 days.

extract_protocol:
DamID: Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit. The DNA concentration was estimated with a Nanodrop; ChIP-seq: ChIP experiments were performed in the presence of 10% human HEK293T cells as internal reference. Cells were crosslinked (1% FA, 10 minutes) and quenced with glycine (2.0M). Chromatin was fragmented to ~300 bp fragments with a Bioruptor Plus sonication device (Diagenode). CTCF antibody (07-729, Merck Millipore; 5 μL per ChIP) was coupled with Protein G beads (Thermo Fisher Scientific) and incubated with fragmented chromatin overnight at 4 °C. Released DNA fragments were purified with the MinElute PCR Purification kit (Qiagen).
DamID: The full protocol is described in Leemans, 2019. 500 ng of genomic DNA was digested with DpnI at Dam-methylated GATC sequences, and ligated to adapters. Subsequent DpnII digestion destroyed DNA fragments containing unmethylated GATC sequences. DNA fragments were then amplified with 15-22 PCR cycles. Amplified fragments were further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters; ChIP-seq: The purified DNA fragments were prepared with the KAPA HTP Library Preparation kit (Roche).

treatment_protocol: DamID: Cells were transduced with lentiviral particles containing either Dam-control or Dam-LaminB1 constructs and cultured for an additional 3 days; ChIP-seq: Protein depletion was induced by addition of auxin (IAA) with a final concentration of 500 μM (I5148-10G, Sigma-Aldrich).

tag: cell type

value: Neural precursor cell

tag: protocl

value: ChIP-seq

tag: genetic modification

value: OsTir1; WAPL-AID-eGFP


title: PRE-R-028 [18R437_018]

tag: tissue


title: Case no 20, tumor biopsy, mediastinum

value: tumor biopsy, mediastinum


title: PRE-R-036 [18R461_002]


title: mNPC_DamID_Dam_r1

description: Dam-control DamID-seq in F121-9-CASTx129 mNPCs, replicate 1

data_processing:
Library strategy: DamID-seq
DamID: The full protocol is described in the corresponding manuscript. The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts. Remaining sequences were mapped to the mouse genome (mm10) using bwa mem 0.7.17. Reads overlapping GATC fragments were counted in 10kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts. LADs were called using hidden Markov modeling (https://github.com/ gui11aume/HMMt). Additionally, individual replicates were averaged for create a combined data track and LAD model.
ChIP-seq: The full protocol is described in the corresponding manuscript. Reads were mapped to a concatenated reference genome (mm10 and hg19) using bowtie2 2.3.4.1. Reads were filtered for a mapping quality of at least 15 and optical PCR duplicates were removed with SAMtools 1.9. Deeptools 3.0 was used to create a normalized coverage track, scaled to 1 million HEK293T reads. Peak calling was performed with MACS2 2.1.1.20160309 at a q-value cutoff of 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: DamID: BigWig files of log2-normalized LaminB1 pADamID scores for 10kb genomic bins, bed file with LAD coordinates; ChIP-seq: BigWig file of coverage, bed file with peak coordinates.

value: DamID-seq


title: Case no 8, tumor biopsy, mediastinum

value: primary mediastinal B cell lymphoma