title: CIS5HG3

description:
1
Gill-093

value: 5 hpe


title: IR24HG7

status: Public on Sep 21 2022

type: RNA

city: Frederiksberg

first: Per

middle: Walter

last: Kania

address: Stigbojlen 7

department: Department of Veterinary and Animal Sciences

country: Denmark

institute: University of Copenhagen

description:
2
Gill-037

data_processing:
All q-PCR assays exhibited efficiencies within 100% ± 5% so the simplified 2^-ΔΔCq method was used for analysing data (Livak and Schmittgen, 2001). For normalization and as internal calibrator the average of three genes (ARP, ELF1α and β-actin) was chosen by using NormFinder (Andersen et al., 2004). For gene expression analyses, all challenged groups were compared to non-exposed time point controls using Student’s t-test. We considered differences to be significant when regulations were at least two-fold and p < 0.05.
Target gene signals were normalized using the average of 3 housekeeping genes (ARP, b-actin and ELF 1a) as2^-ΔCt, where -ΔCt = -(Ct_Target − Ct_ average of 3 HKGs). Folds were calculated as  2^-ΔΔCt, where -ΔΔCt = -[ΔCt_infected -ΔCt_control].  First case of folds describes infected groups relative to the uninfected groups at the timepoints.  Second case  of folds describes non-QTL groups relative to the QTL groups at the timepoints.  Third case of folds (only relevant at day 20) describes 1x infected groups relative to the 2x infected groups  in both cases of non-QTL and QTL.

label: FAM

molecule: total RNA

organism: Oncorhynchus mykiss

label_protocol: cDNA synthesis was performed in T100 thermocycler, Biorad, Denmark, using Oligo d(T)16 primer and TaqMan® Reverse Transcription Reagents (cat.no. N8080234, Thermo Fischer Scientific, Denmark). Finally, cDNA was stored at −20°C until further use. Quantitative PCR assays were performed using an AriaMx Real-Time PCR machine (cat.no.G8830A-04R-010, AH diagnostics AS, Denmark). The cycling conditions were one cycle of predenaturation at 95°C for 3 min. This was followed by 40 cycles of denaturation at 94°C for 5 sec with a combined annealing/elongation process at 60°C for 15 sec with endpoint measurement. Primers and Taq-Man probes targeting immune-relevant rainbow trout genes were synthesized at TAG Copenhagen AS, Denmark. Reaction volumes were 12.5 μl (2.5 μl cDNA, 6.25 μl Brilliant III Ultra-Fast QPCR Master Mix (600881, AH Diagnostics AS, Denmark), 1.0 μl primer-probe mixture (forward primer, 10 μM and reverse primer, 10 μM), Taq-Man probe (5 μM), and 2.75 μl RNase-free water. Reverse transcriptase minus and negative controls were used for every plate setup. . NormFinder (Andersen et al., 2004) was applied to evaluate all combinations of three reference genes (Elongation factor (ELF) 1-α, β-actin and acidic ribosomal phosphoprotein P0 (ARP)) as endogenous control; the average of the three genes was chosen and stability values were 0.002, 0.005 and 0.002 for liver, spleen and gills, respectively. In order to quantify the bacterial load in different organs at the different time points we measured the gene expression level of the bacterial gene recA, which was described as a household gene in V.anguillarum  (GenBank ass.no. LC370212) by Crisafi et al. (2014).  Bacterial transcript level was estimated as 2^-ΔCq . It should be noted that dead or inactive bacteria may not be detected by this method.

growth_protocol: Fish were maintained in plastic tanks with low density. Water was recycled (20 L/min) by internal biofilters (EHEIM, Germany) applying 30% water replenishment daily. Water quality was monitored and kept constant at pH 7.6, nitrite < 0.01 mg/l, nitrate < 50 mg/l (TetraTest 6in1, cat.no. T704154, Eldorado A/S, Denmark) and ammonia < 0.5 mg/l (API Ammonia Test Strips, VioVet Ltd, UK). During the 14 days acclimation and 14 days experimental infection period, fish received commercial pelleted feed (1.5% biomass per day, INICIO 917, BioMar A/S, Denmark). After the pathogen exposure fish with clinical signs were euthanized with overdose (300 mg/L) of ethyl-3-aminobenzoate methanesulfonate (MS222) (cat.no. A5040, Sigma-Aldrich, Denmark)

extract_protocol: RNAlater fixed samples from fish (gills, liver and spleen) were homogenized (Tissue-lyser II, Qiagen, Denmark) using a homogenization buffer with 2-mercaptoethanol (Sigma-Aldrich). RNA was extracted using the GenEluteTM mammalian RNA kit (RTN350, Sigma-Aldrich, Denmark). Liver samples were pre-treated by Proteinase K (cat.no.P4850, Sigma-Aldrich, Denmark). DNase I (AMPD1, Sigma-Aldrich, Denmark) treatment was applied to remove genomic DNA. The concentration of RNA was determined in a NanoDrop 2000 spectrophotometer (Saveen & Werner, Denmark). Quality of RNA was evaluated by agarose (cat.no. 16500100, ThermoFisher Scientific, Denmark) gel electrophoresis. RNA was kept at −80°C until cDNA synthesis.

treatment_protocol: Tissue  spleen, gills) samples were fixed in RNAlater (cat.no R0901, Sigma-Aldrich, Denmark), placed at 4°C for 24 h and subsequently stored at -20°C until further processing.

tag: organ

value: Spleen

tag: genotype omy16

value: K

tag: genotype omy17

value: G

tag: status

value: non-QTL

tag: timepoint

value: Day 4

tag: no. of exposures

value: 1x infected


title: IR24HG4

description:
1
Gill-034

value: T


title: IR24HG5

description:
1
Gill-035


title: IR24HG3

description:
1
Gill-033


title: Mycth_90344_A4h_2

type: SRA

city: Tianjin

first: Liu

last: Qian

address: Xi 7 Dao No.32 Airport Economic Area

country: China

institute: TIB CAS

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Myceliophthora thermophila ATCC 42464 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
Assembly: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary files format and content: tab-delimited text files including RPKM for each sample.

organism: Thermothelomyces thermophilus

growth_protocol: M. thermophila strains were inoculated into 1×Vogel’s salt with 2% glucose and cultivated at 45 °C for 16h. Mycelia were collected and washed three times with 1×Vogel’s salt, and then transferred into the medium with 2% Avicel or 2% starch as the carbon source for an additional 4 h or 6 h of cultivation.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: source

tag: cell type

value: mycelia cells


title: IR24HG6

description:
2
Gill-036

value: R

value: Excluded


title: W.MP351N

type: genomic

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

country: USA

institute: Michigan State University

description: Bisulfite treated

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Raw IDAT files were processed using R package SeSAMe with noob background correction, non-linear dye bias correction, and non-detection masking.
Methylation beta values were called as quantitative percentage of methylated signals over both unmethylated and methylated signals ranging from 0 to 1, with “0” indicating full lack of methylation and “1” full methylation. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies and implemented in SeSAMe.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: uterus

label_protocol: Standard Illumina Protocol

extract_protocol: DNeasy Blood and Tissue kit (QIAGEN)

tag: race

value: White

tag: tissue type

value: Myometrium


title: Mycth_90344_A4h_1


title: IR24HG1

description:
1
Gill-031


title: IR24HG2

description:
1
Gill-032


title: Dnmt3aVillin724, RNA

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

country: Germany

institute: Institute of Clinical Molecular Biology

description: 2 X 50 bp

data_processing:
Fastq files were mapped and aligned using nf-core ((https://github.com/nf-core/rnaseq)) rnaseq pipeline.
Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore (version 0.4.4), which is a wrapper tool for Cutadapt and FastQC. Reads that were shorter than 35 bp after trimming were discarded.
The filtered reads were mapped to the human genome (GRCh38, gencode version 25) or mouse genome (GRCm38) using STAR aligner (version 2.5.2b).
featureCounts (version 1.5.2) was used to estimate the expression counts of the genes.
Assembly: GRCh38 (gencode version 25) and GRCm38
Supplementary files format and content: tab-delimited text files include feature counts

organism: Mus musculus

source_name: intestinal epithelial cells

growth_protocol: Caco-2 cells were maintained in MEM medium containing 20% (vol/vol) FCS at 37 °C with 5 % CO2.

extract_protocol:
RNA was isolated from Caco-2 cells and purified IECs using RNeasy kit (Qiagen) according to manufacturer´s instructions.
RNA samples from Caco-2 cells were sequenced on HiSeq3000 (Illumina, San Diego, United States) (2 X 75 bp) while that from mice IECs were sequenced NovaSeq 6000 (2 X 50 bp) using Illumina total RNA stranded TruSeq protocol.

treatment_protocol: Mice were provided with food and water ad libitum and maintained in conformity to national and international laws and policies and with appropriate permissions,

tag: disease state

value: Steady state

value: intestinal epithelial cells

tag: genotype

value: Dnmt3a {delta}IEC


title: CIR24HG10

description:
2
Gill-030

value: Uninfected


title: W.MP346N

description: Bisulfite treated


title: CIR24HG8

description:
2
Gill-028


title: Mycth_90344_A6h_1


title: CIR24HG9

description:
2
Gill-029


title: Dnmt3aVillin723, RNA

description: 2 X 50 bp


title: Dnmt3aVillin722, RNA

description: 2 X 50 bp


title: CIR24HG7

description:
2
Gill-027


title: W.MP345N

description: Bisulfite treated


title: Dnmt3aVillin721, RNA

description: 2 X 50 bp

value: Dnmt3a fl/fl


title: CIR24HG5

description:
1
Gill-025

value: Spleen


title: W.MP355N

description: Bisulfite treated


title: W.MP342N

description: Bisulfite treated


title: CIR24HG6

description:
2
Gill-026

value: K


title: W.MP330N

description: Bisulfite treated


title: Dnmt3aVillin720, RNA

description: 2 X 50 bp


title: CIR24HG4

description:
1
Gill-024

value: G


title: CIR24HG3

description:
1
Gill-023

value: non-QTL


title: CIR24HG1

description:
1
Gill-021

value: Day 4


title: CIR24HG2

description:
1
Gill-022


title: Dnmt3aVillin719, RNA

description: 2 X 50 bp


title: IRG9

description:
2
Gill-019

value: 5 hpe

value: 1x infected


title: IRG10

description:
2
Gill-020


title: Dnmt3aVillin718, RNA

description: 2 X 50 bp


title: W.MP317N

description: Bisulfite treated


title: W.MP315N

description: Bisulfite treated


title: Dnmt3aVillin717, RNA

description: 2 X 50 bp


title: W.MP313N

description: Bisulfite treated


title: IRG6

description:
2
Gill-016

value: T


title: Ai-α4 KO BAT5

city: Kumamoto

first: masaji

last: sakaguchi

address: 1-1-1 Honjo, Chuoku

department: Metabolic Medicine

country: Japan

institute: Kumamoto University

data_processing:
Base calls were generated in real-time on the NovaSeq6000 instrument (RTA 3.3.3). Bcl2fastq2 v2 20 Conversion Software (Illumina) was used to generate demultiplexed Fastq files. Sequencing was performed on a NovaSeq-6000 (Illumina) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol.
Sequence reads were aligned to genome mm10 using STAR v2.5.3a.
The expression profile obtained by transcript quantification of each sample was extracted with FPKM, which is the normalization value considering read count and transcript length and depth of coverage.The reads were mapped and annotated using Genedata Profiler Genome v11.0.8 (Genedata).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and raw gene counts for each sample.

source_name: BAT (Brown adipose tissue)

extract_protocol:
Adipose tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Sample Prep Kit following manufacturer's protocols.

tag: tissue

value: BAT (Brown adipose tissue)

value: KO

tag: treatment

value: Tamoxifen


title: IRG5

description:
1
Gill-015


title: IRG7

description:
2
Gill-017


title: IRG4

description:
1
Gill-014

value: R


title: W.MP323N

description: Bisulfite treated

value: White

value: Myometrium


title: Ai-α4 KO BAT4


title: IRG3

description:
1
Gill-013


title: IRG2

description:
1
Gill-012


title: Ai-α4 KO BAT3


title: IRG1

description:
1
Gill-011


title: CIR5HG10

description:
2
Gill-010


title: W.MP308N

description: Bisulfite treated


title: W.MP319N

description: Bisulfite treated


title: Ai-α4 KO BAT2


title: W.MP306N

description: Bisulfite treated


title: W.MP305N

description: Bisulfite treated


title: IRG8

description:
2
Gill-018

value: Excluded


title: CIR5HG9

description:
2
Gill-009

value: Uninfected


title: W.MP323F

description: Bisulfite treated

value: Fibroid


title: Ai-α4 KO BAT1


title: W.MP100N

description: Bisulfite treated


title: CIR5HG6

description:
2
Gill-006

value: Spleen


title: CIR5HG7

description:
2
Gill-007

value: K


title: CIR5HG5

description:
1
Gill-005

value: G


title: Ai-α4 Control BAT5

value: WT


title: CIR5HG4

description:
1
Gill-004

value: non-QTL


title: Ai-α4 Control BAT4


title: CIR5HG3

description:
1
Gill-003

value: 5 hpe


title: CIR5HG2

description:
1
Gill-002


title: ISREINFECTS10

description:
2
Spleen-180

value: Gill

value: QTL

value: Day 20

value: 1x infected


title: CIR5HG1

description:
1
Gill-001


title: CIR5HG8

description:
2
Gill-008


title: ISREINFECTS9

description:
2
Spleen-179


title: ISREINFECTS8

description:
2
Spleen-178


title: ISREINFECTS7

description:
2
Spleen-177


title: Ai-α4 Control BAT3

value: BAT (Brown adipose tissue)

value: Tamoxifen


title: Ai-α4 Control BAT2


title: ISREINFECTS6

description:
2
Spleen-176

value: A


title: ISREINFECTS4

description:
1
Spleen-174

value: R


title: Ai-α4 KO iWAT4

source_name: iWAT (Inguinal white adipose tissue)

value: iWAT (Inguinal white adipose tissue)

value: KO


title: ISREINFECTS3

description:
1
Spleen-173

value: Excluded


title: Ai-α4 KO iWAT3


title: ISREINFECTS1

description:
1
Spleen-171


title: ISREINFECTS2

description:
1
Spleen-172


title: Ai-α4 Control BAT1


title: GFP_mCherry_35

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

description: RNA expression value derived from Expression Console software; core- gene or -exon analysis

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse Gene ST 1.0 arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console v4.0 using default analysis settings for RNA analyses  for  gene default.CHP files for analyses.

label: biotin

source_name: Ba/F3 (DSMZ no.: ACC 300)

label_protocol: 150 ng total RNAwas amplified using the  WT Expression Kit and the WT Terminal Labeling Kit (Thermofisher, Darmstadt, Germany).

growth_protocol: All cells were grown at 37°C with 5% CO2 in a water saturated atmosphere in Dulbecco’s modified Eagle’s Medium (DMEM) high glucose culture medium (GIBCO®, Life Technologies, Darmstadt, Germany) with 10% fetal calf serum (GIBCO®, Life Technologies, Darmstadt, Germany) and 60 mg/l penicillin and 100 mg/l streptomycin (Genaxxon Bioscience GmbH, Ulm, Germany). Murine Ba/F3/gp130 cells were obtained from Immunex (Seattle, WA, USA) and grown in the presence of Hyper-IL-6, a fusion protein of IL-6 and soluble IL-6 receptor. 0.2% (10 ng/ml) of conditioned medium from a stable clone of CHO-K1 cells secreting Hyper-IL-6 in the supernatant (stock solution approximately 5 μg/ml as determined by ELISA) were used to maintain Ba/F3/gp130 cells and derivates thereof.

extract_protocol: Total RNA extraction was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: Ba/F3-gp130-VGmIFNAR1-VCmIFNAR2 cells were cultured as described before. Cells were washed four times with PBS to remove cytokines/synthetic cytokine ligands from the medium and then starved for 5 h in serum-free DMEM. Cells were stimulated for 240 min without cytokine or with 100 ng/ml GCCG or 100 U/ml IFNα4.

value: interleukin-3 or Hyper-Interleukin-6 dependent pro-B cell line

value: GFP-mCherry (100 ng/ml)


title: 27_GFP-mCherry


title: Ai-α4 KO iWAT5


title: 19_GFP-mCherry


title: ISREINFECTS5

description:
1
Spleen-175

value: K


title: IS1WS9

description:
2
Spleen-169

value: 2x infected


title: Ai-α4 KO iWAT2


title: IFNa_26

value: IFNα4 (100U/ml)


title: IFNa_18


title: 11_GFP-mCherry


title: IFNa_30


title: Ai-α4 KO iWAT1


title: IS1WS8

description:
2
Spleen-168

value: G


title: IS1WS5

description:
1
Spleen-165

value: Gill


title: IS1WS7

description:
2
Spleen-167

value: QTL


title: Ai-α4 Control iWAT5

value: WT


title: IS1WS6

description:
2
Spleen-166

value: Day 20


title: Ai-α4 Control iWAT4


title: IFNa_2


title: IS1WS4

description:
1
Spleen-164


title: IS1WS3

description:
1
Spleen-163


title: IS1WS10

description:
2
Spleen-170


title: 33_unst

value: untreated


title: IS1WS1

description:
1
Spleen-161


title: Ai-α4 Control iWAT3

value: Tamoxifen


title: CIS1WS10

description:
2
Spleen-160

value: Uninfected


title: unst_21


title: Whole Genome CRISPR Screen

city: Madrid

first: María José

last: Jiménez

state: Madrid

address: C. de Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: Spanish National Cancer Research Centre

library_source: genomic

data_processing:
CRISPR screen analysis:
Sequence deconvolution was performed with PoolQ (https://portals.broadinstitute.org/gpp/public/software/poolq). Raw counts were analyzed with the MAGeCK-VISPR pipeline v0.5.5 (https://bitbucket.org/liulab/mageck-vispr/src/master/).
Normalization was performed using a list of negative control sgrnas (norm_method=control).
Since samples were processed in different batches, batch correction of log2 normalized counts was performed. This screening had 2 batch levels according to the plate (A, B) and was corrected with limma v3.44.1 (https://bioconductor.org/packages/release/bioc/html/limma.html).
Comparisons were done using treatment versus control analysis via MAGeCK-RRA mode. Plots were drawn using MAGeCKFlute v1.8.0 (https://www.bioconductor.org/packages/release/bioc/html/MAGeCKFlute.html).
Assembly: GRCm38
Supplementary files format and content: Tabulated text file with raw counts obtained with PoolQ.

growth_protocol: BA/F3 cells were grown in RPMI containing 10% FBS, 1% penicillin/streptomycin and 10ng/mL recombinant murine IL3.

extract_protocol:
Genomic DNA was isolated using the NucleoSpin Blood XL-Maxi kit (Clontech Cat. # 740950) with RNase A (Clontech Cat. # 740505) treatment. DNA concentration was measured with the Quant-iT™ PicoGreen™ dsDNA Assay Kit (ThermoFisher Scientific, #P11496).
Whole genome CRISPR sgRNA pBrie library designed by Broad Genetic Perturbation Platform (GPP).
OTHER: CRISPR sequencing.

treatment_protocol: Where indicated, cells were grown in the absence of IL3 after washing for three times with PBS.

tag: cell line

value: IL3 dependent pro-B cell line

value: Empty Vector (EV) or CALR del 52

value: +IL3 or -IL3

tag: time

value: Day 11 or Day 21

tag: batch

value: A


title: CIS1WS9

description:
2
Spleen-159

tag: organ

value: R


title: Ai-α4 Control iWAT2

value: iWAT (Inguinal white adipose tissue)


title: Pooled CRISPR Screen

data_processing:
CRISPR screen analysis:
Sequence deconvolution was performed with PoolQ v3.3.2 (https://portals.broadinstitute.org/gpp/public/software/poolq). Raw counts were analyzed with the MAGeCK-VISPR pipeline v0.5.5 (https://bitbucket.org/liulab/mageck-vispr/src/master/).
Normalization was performed using a list of negative control sgrnas (norm_method=control). Sample EV#2 -_Day 21_without IL3 (positive control of unviability) was excluded from downstream analysis.
Since the remaining samples were processed in different batches, batch correction of log2 normalized counts was performed. This screening had 4 balanced batch levels and batch correction was performed with ComBat, included in sva package v3.36.0 (https://bioconductor.org/packages/release/bioc/html/sva.html).
Comparisons were done using treatment versus control analysis via MAGeCK-RRA mode. Plots were drawn using MAGeCKFlute v1.8.0 (https://www.bioconductor.org/packages/release/bioc/html/MAGeCKFlute.html).
Assembly: GRCm38
Supplementary files format and content: Tabulated text file with raw counts obtained with PoolQ.

extract_protocol:
Genomic DNA was isolated using the NucleoSpin Blood XL-Maxi kit (Clontech Cat. # 740950) with RNase A (Clontech Cat. # 740505) treatment. DNA concentration was measured with the Quant-iT™ PicoGreen™ dsDNA Assay Kit (ThermoFisher Scientific, #P11496).
Genes in N-glycosylation, protein secretion, UPR and protein arginine methylation were included.
OTHER: CRISPR sequencing.

value: Day 21


title: 1_unst

value: interleukin-3 or Hyper-Interleukin-6 dependent pro-B cell line


title: 25_unst


title: CIS1WS8

description:
2
Spleen-158

tag: genotype omy16

value: K

value: Excluded


title: CIS1WS7

description:
2
Spleen-157

value: Gill

tag: genotype omy17

value: QTL


title: Ai-α4 Control iWAT1

value: WT


title: IS1WS2

description:
1
Spleen-162

value: G

tag: status

value: Day 20

value: 2x infected


title: CIS1WS6

description:
2
Spleen-156

tag: timepoint

value: Uninfected


title: WT Rep2

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Assembly: not provided
Supplementary files format and content: bigWig files
Library strategy: 5hmC-seq

source_name: Lung smooth muscle cells

extract_protocol:
Genomic DNA extracted from cells were eluted in nuclease-free water. Illumina sequencing library was generated from 75 ng of genomic DNA using the NxSeq UltraLow DNA Library Kit (Lucigen) following the manufacturer’s instruction, but without PCR amplification. Glucosylation of half of the purified DNA library was performed in 21 µL reaction containing 1× Thermo Epi Buffer, 100 µM N3-UDP-Glc and 2 µL of T4 beta-glucosyltransferase (Thermo Fisher) at 37 °C for 1 hr. After glucosylation, 2.1 µl of Biotin-PEG4-DBCO (Click Chemistry Tools, 20 mM stock) was added directly to the reaction mixture, and the mixture was incubated at 37 ˚C for 2 hr. The biotinylated DNA was purified by (1.8× volume) paramagnetic DNA binding beads (Omega Bio-Tek) according to standard procedure. The purified DNA was incubated with 5 µl of C1 Streptavidin beads (Life Technologies) in B&W buffer (B&W buffer: 5 mM Tris [pH 7.5], 0.5 mM EDTA, and 1 M NaCl) according to the manufacture’s instruction, for 40 min at room temperature with rotation. The beads were subsequently undergone six 5-min washes with B&W buffer before finally eluted in 40 µL water.
The eluted enriched DNA libraries were PCR amplified with index primers and sequenced on an Illumina HiSeq 2000.

tag: strain

value: Lung smooth muscle cells


title: CIS1WS5

description:
1
Spleen-155

tag: no. of exposures


title: CIS1WS3

description:
1
Spleen-153


title: CIS1WS2

description:
1
Spleen-152


title: WT Rep1

tag: cell type


title: Tet3 Mut 2

value: Tet3 Mut


title: Galaxy376-[M_CR__M_CR_B69]

city: New York

first: Sasha

middle: Leilani

last: Fulton

state: NY

address: 3227 Broadway

institute: Columbia University

description: concatenated read data from 2 flow cells

data_processing:
fastq files were aligned to ensembl mouse reference genome mm10 using HISAT2 (Version 2.1.0).
BAM files resulting from the alignments were summarized to genes using the featureCounts (Version 2.0.1) algorithm
Expression data was normalized using DESEQ2 (Version 2.11.40.6) followed by normalizaton with RUVrseq estimation of variation (Version 1.24.0)
Differentially expressed genes (10% false discovery rate) were identified using DESEQ2 based on a model using the negative binomial distribution
Assembly: mm9
Supplementary files format and content: tab-delimited text files are raw featurecounts matrix for each sample

molecule: polyA RNA

source_name: adult (6-wk) hippocampus tissue - male

extract_protocol:
RNA was isolated using trizol-chloroform extraction followed by cleanup on the RNeasy Micro Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the Illumina Truseq RNA Library Prep Kit V2 , according to the manufacturer’s instructions.

treatment_protocol: In order to confirm relevance of Ts65Dn to human DS etiology, we first performed bulk RNA-seq profiling on E17.5 Ts65Dn vs. euploid forebrain tissues. Furthermore, in order to further evaluate the effects of Brwd1 rescue within the context of adult brain, we performed bulk RNA-seq on hippocampal tissues from 6-week-old male and female animals, comparing Ts65Dn vs. euploid and Ts65Dn;Brwd1+/– genotypes .

tag: background strain

value: DBA/2J x B6EiC3Sn/J

tag: Sex

value: male

tag: age

value: adult (6-wk)

value: hippocampus tissue


title: Galaxy376-[M_CR__M_CR_B94]

tag: genotype


title: CIS1WS1

description:
1
Spleen-151

value: R


title: Galaxy376-[M_CR__M_CR_T35]

tag: tissue


title: Galaxy376-[M_CR__M_CR_B51]


title: IS4DS9

description:
2
Spleen-149

value: Day 7

value: 1x infected


title: IS4DS8

description:
2
Spleen-148


title: AtSDR4L, mock ChIP

city: Vancouver

first: Liang

last: Song

state: British Columbia

address: 2231-6270 University Boulevard

department: Botany

country: Canada

institute: University of British Columbia

description: ChIP was carried out using HA antibody (CST3724,  lot 9). The ratio of antibody to nuclei lysate was 1:100 (v/v).

data_processing:
Basecalling was performed on NextSeq2000 with the built-in software RTA v3.9.2
Demultiplexing and adaptor trimming were performed on Basespace using bcl2fastq v2.20
ChIP-seq reads were aligned to Arabidopsis thaliana TAIR10 genome using Bowtie2 version 2.3.5.1 with the default parameters and filtered for mapping quality score greater than 10 on samtools version 1.7
Peaks were called using MACS2 version 2.2.7.1 using the mock treated sample (S002-3) as control, pair-end format "BAMPE", effective genome size of 120 Mb, q-value cutoff at 0.1 and the "--call-summits" option, the remaining parameters were the same as MACS2 default settings.
Reproducible peaks from replicates S002-1 and S002-2 were merged using IDR version 2.0.4.2 with q-value rank and "min" merge method
Genome_build: TAIR10
Supplementary_files_format_and_content: narrowPeak files (MACS2 output)
Supplementary_files_format_and_content: merged peak text file (IDR output)

organism: Arabidopsis thaliana

source_name: uninduced AtSDR4L-HA, control ChIP

growth_protocol: AtSDR4L-HA seeds were stratified at 4 °C in dark for 3 days and then sowed on 1X Linsmaier & Skoog (LS) basal medium supplemented with 1% sucrose and 1.5% agar. Seedlings were grown under 8 h dark/16 h light conditions at 22 °C for four days.

extract_protocol:
DNA crosslinked to AtSDR4L-HA were captured by the HA antibody (CST3724,  lot 9) and reserved crosslinked at 65 °C for 6 hours, followed by treatment of 150 µg/mL proteinase K at 55 °C for 2 hours before the phenol:chloroform:IAA (25:24:1 v/v, pH 8.0) extraction. DNA were precipited in the presence of 150 µg/mL glycoblue, 0.2M NaCl, and 3 vol. of ethanol and double-size selected using 0.6 vol. and 1.3 vol. AMPure XP beads, respectively, before library construction.
Libraries were constructed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®.

treatment_protocol: Seedlings were grown for 4 days on 1x LS plates either supplemented with or without 1 μM β-estradiol.

value: whole seedlings

tag: developmental stage

value: 4 days after imbibtion (DAI)

tag: eptitope tag

value: HA


title: CIS1WS4

description:
1
Spleen-154

value: Gill

value: K

value: Excluded


title: IS4DS7

description:
2
Spleen-147


title: Galaxy376-[M_CR__M_CR_B26]


title: AtSDR4L, ChIP rep2

source_name: β-Estradiol induced AtSDR4L-HA, ChIP rep2


title: IS4DS6

description:
2
Spleen-146

value: G

value: QTL


title: IS4DS5

description:
1
Spleen-145


title: Galaxy376-[M_CR__M_CR_B24]


title: IS4DS4

description:
1
Spleen-144


title: AtSDR4L, ChIP rep1

source_name: β-Estradiol induced AtSDR4L-HA, ChIP rep1


title: Galaxy376-[M_CR__M_CR_B138]


title: IS4DS10

description:
2
Spleen-150

value: A


title: IS4DS1

description:
1
Spleen-141


title: Tet3 Mut 1

value: Lung smooth muscle cells

value: Tet3 Mut


title: IS4DS2

description:
1
Spleen-142


title: CIS4DS10

description:
2
Spleen-140

value: Uninfected


title: Galaxy376-[M_CR__M_CR_B137]

value: DBA/2J x B6EiC3Sn/J

value: male

value: adult (6-wk)


title: Galaxy204-[F_TS__F_TS_T142]

source_name: adult (6-wk) hippocampus tissue - female

value: female

value: hippocampus tissue


title: CIS4DS9

description:
2
Spleen-139

value: Day 7


title: CIS4DS6

description:
2
Spleen-136


title: CIS4DS8

description:
2
Spleen-138


title: Galaxy204-[F_TS__F_TS_T141]


title: CIS4DS7

description:
2
Spleen-137

value: R


title: IS4DS3

description:
1
Spleen-143

value: 1x infected


title: CIS4DS5

description:
1
Spleen-135

value: Gill


title: CIS4DS4

description:
1
Spleen-134

value: K


title: Galaxy204-[F_TS__F_TS_T139]


title: Galaxy204-[F_TS__F_TS_B53]


title: CIS4DS3

description:
1
Spleen-133


title: CIS4DS2

description:
1
Spleen-132


title: CIS4DS1

description:
1
Spleen-131


title: IS24HS10

description:
2
Spleen-130

value: Day 4


title: Galaxy204-[F_TS__F_TS_B135]


title: Galaxy204-[F_TS__F_TS_B56]


title: IS24HS9

description:
2
Spleen-129

value: G


title: IS24HS8

description:
2
Spleen-128

value: QTL


title: Galaxy204-[F_TS__F_TS_B134]


title: IS24HS7

description:
2
Spleen-127

value: A


title: Galaxy204-[F_TS__F_TS_B103]


title: IS24HS6

description:
2
Spleen-126

value: Excluded


title: IS24HS4

description:
1
Spleen-124


title: IS24HS5

description:
1
Spleen-125


title: Galaxy179-[F_WT__F_WT_B65]

value: Euploid


title: IS24HS2

description:
1
Spleen-122


title: IS24HS3

description:
1
Spleen-123


title: Galaxy179-[F_WT__F_WT_B85]


title: IS24HS1

description:
1
Spleen-121


title: CIS24HS10

description:
2
Spleen-120

value: Uninfected


title: Galaxy179-[F_WT__F_WT_B21]

value: DBA/2J x B6EiC3Sn/J


title: CIS24HS9

description:
2
Spleen-119


title: CIS24HS7

description:
2
Spleen-118


title: Galaxy179-[F_WT__F_WT_B184]


title: CIS24HS6

description:
2
Spleen-116


title: CIS24HS8

description:
2
Spleen-117


title: CIS24HS4

description:
1
Spleen-115


title: Galaxy179-[F_WT__F_WT_B173]


title: CIS24HS5

description:
1
Spleen-114


title: CIS24HS3

description:
1
Spleen-113


title: CIS24HS2

description:
1
Spleen-112


title: Galaxy179-[F_WT__F_WT_B125]


title: CIS24HS1

description:
1
Spleen-111


title: Galaxy179-[F_WT__F_WT_B17]


title: ISS9

description:
2
Spleen-109

value: 5 hpe


title: Galaxy179-[F_WT__F_WT_B12]

value: adult (6-wk)


title: ISS8

description:
2
Spleen-108


title: ISS7

description:
2
Spleen-107


title: ISS10

description:
2
Spleen-110


title: ISS6

description:
2
Spleen-106


title: ISS5

description:
1
Spleen-105


title: Galaxy170-[M_WT__M_WT_B84]

value: male


title: genomic DNA from Cord Blood sample 490028_CU

city: New Orleans

first: Eric

last: Dumonteil

state: LA

address: 1440 Canal st.

department: Tropical Medicine

institute: Tulane University

description: Chagasic pregnancy

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Bioconductor R package Chip Analysis Methylation Pipeline (ChAMP)

label: Cy5 and Cy3

source_name: Cord blood sample 490028_CU

extract_protocol: genomic DNA was extracted and purified from cord blood samples using an automated Maxwell® RSC Instrument (Promega Benelux, Leiden, The Netherlands), according to standard instructions

value: cord blood

tag: disease status

value: exposed


title: genomic DNA from Cord Blood sample 490022_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490022_CU


title: ISS3

description:
1
Spleen-103

value: R


title: ISS2

description:
1
Spleen-102

value: 1x infected


title: Galaxy170-[M_WT__M_WT_B79]

value: hippocampus tissue


title: genomic DNA from Cord Blood sample 490074_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490074_CU


title: ISS1

description:
1
Spleen-101

value: Gill

value: K


title: genomic DNA from Cord Blood sample 490054_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490054_CU


title: CIS5HS9

description:
2
Spleen-099

value: G


title: CIS5HS10

description:
2
Spleen-100

value: QTL


title: Galaxy170-[M_WT__M_WT_B139]


title: Galaxy170-[M_WT__M_WT_B122]


title: Galaxy170-[M_WT__M_WT_B95]


title: ISS4

description:
1
Spleen-104


title: genomic DNA from Cord Blood sample 490043_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490043_CU


title: CIS5HS8

description:
2
Spleen-098


title: CIS5HS6

description:
2
Spleen-096

value: A


title: CIS5HS5

description:
1
Spleen-095


title: Galaxy170-[M_WT__M_WT_B80]


title: CIS5HS4

description:
1
Spleen-094

value: Excluded


title: Galaxy170-[M_WT__M_WT_B110]

value: Euploid


title: Galaxy170-[M_WT__M_WT_B100]


title: CIS5HS3

description:
1
Spleen-093

value: Uninfected


title: genomic DNA from Cord Blood sample 490068_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490068_CU


title: genomic DNA from Cord Blood sample 490010_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490010_CU


title: Galaxy150-[M_TS__M_TS_B88]

value: DBA/2J x B6EiC3Sn/J


title: genomic DNA from Cord Blood sample 290010_CU

description: Chagasic pregnancy

source_name: Cord blood sample 290010_CU


title: genomic DNA from Cord Blood sample 490064_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490064_CU


title: genomic DNA from Cord Blood sample 490053_MG_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490053_MG_CU


title: CIS5HS7

description:
2
Spleen-097

value: 5 hpe


title: genomic DNA from Cord Blood sample 490034_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490034_CU


title: genomic DNA from Cord Blood sample 490072_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490072_CU


title: genomic DNA from Cord Blood sample 490082_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490082_CU


title: IRREINFS10

description:
2
Spleen-090

value: T

value: non-QTL

value: Day 20


title: Galaxy150-[M_TS__M_TS_B74]

source_name: adult (6-wk) hippocampus tissue - male

value: male

value: adult (6-wk)


title: genomic DNA from Cord Blood sample 390051_CU

description: Chagasic pregnancy

source_name: Cord blood sample 390051_CU

value: cord blood

value: exposed


title: IRREINFS9

description:
2
Spleen-089

value: Gill

value: 1x infected


title: IRREINFS8

description:
2
Spleen-088

value: K

value: R


title: genomic DNA from Cord Blood sample 490041_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490041_CU


title: IRREINFS7

description:
2
Spleen-087

value: G


title: genomic DNA from Cord Blood sample 590012_TM_CU

description: Chagasic pregnancy

source_name: Cord blood sample 590012_TM_CU


title: IRREINFS6

description:
2
Spleen-086


title: Galaxy150-[M_TS__M_TS_B45]

value: hippocampus tissue


title: IRREINFS5

description:
1
Spleen-085


title: genomic DNA from Cord Blood sample 490040_VK_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490040_VK_CU


title: IRREINFS3

description:
1
Spleen-083


title: IRREINFS4

description:
1
Spleen-084


title: Galaxy150-[M_TS__M_TS_B40]


title: genomic DNA from Cord Blood sample 490038_IG_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490038_IG_CU


title: IRREINFS2

description:
1
Spleen-082


title: CIS5HS1

description:
1
Spleen-091

value: A

value: QTL


title: genomic DNA from Cord Blood sample 490069_UE_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490069_UE_CU


title: IRREINFS1

description:
1
Spleen-081


title: IR1WS10

description:
2
Spleen-080

value: 2x infected


title: Galaxy150-[M_TS__M_TS_B25]

value: DBA/2J x B6EiC3Sn/J


title: genomic DNA from Cord Blood sample 490030_BQ_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490030_BQ_CU


title: Galaxy150-[M_TS__M_TS_B145]


title: genomic DNA from Cord Blood sample 290022_CU

description: Chagasic pregnancy

source_name: Cord blood sample 290022_CU


title: Galaxy146-[F_CR__F_CR_B181]

source_name: adult (6-wk) hippocampus tissue - female

value: female


title: IR1WS6

description:
2
Spleen-076

value: non-QTL


title: IR1WS7

description:
2
Spleen-077

value: T

value: Day 20


title: IR1WS9

description:
2
Spleen-079


title: Galaxy146-[F_CR__F_CR_B176]

value: adult (6-wk)


title: IR1WS5

description:
1
Spleen-075


title: IR1WS8

description:
2
Spleen-078


title: rS8: MEF_Fbxo4(-/-)+hnRNPK siRNA rep 2 [RPF]

city: Cleveland

first: J Alan

last: Diehl

state: Ohio

address: 2109 Adelbert Rd. SOM Wood/W402

department: Department of Biochemistry

institute: Case Western Reserve University

description: RNA sequencing & RPF sequencing in separate raw files

data_processing:
Basecalling with Ilumina Casava software
FASTQ Quality Filter module of FASTX-Toolkit
Read collapsing by UMI by Collapse module
UMI trimming by Cutadapt
Alignment to mm10 by STAR v2.5.3a
Bam file proccessd by RIboProfiling package v1.2.2
Coverage counts on coding region (CDS) obtained by RxDb.Mmusculus.UCSC.mm10.knownGene v3.10.0
DEseq2 pipeline version 1.26.0 for differential expressed gene analysis
Genome_build: mm10
Supplementary_files_format_and_content: Sample coding for RNA and RPF; cont_tab_sample.txt
Supplementary_files_format_and_content: normalized count from DEseq2; table_norCount_RNAandRPF.txt
Supplementary_files_format_and_content: raw count for total RNA sequencing; summary_gene_count_rpf_table.txt
Supplementary_files_format_and_content: raw count for RPF sequencing; summary_gene_count_rna_table.txt

growth_protocol: Murine Embryonic Fibroblasts (MEFs) were cultured in DMEM (Corning) media supplemented with 10% FBS (Gemini) and Penicillin-Streptomycin (Corning)

extract_protocol:
Cell extract was treated with MNase, CaCl2 (5mM final concentration), and Turbo DNAse I and incubated at 25°C for 30 minutes; the digestion was stopped with SUPERase-inhibitor and placing on ice.
The cell extract was loaded onto a 15%-45% sucrose gradient to separate the polysomes by ultra-centrifugation. The relevant fractions corresponding to the 80S monosome were collected and precipitated using ethanol and the RNA was isolated
Total RNA was isolated from each sample and subjected to the Turbo DNase I digestion and then RNA-seq libraries. The ribosome-protected fragments were subjected to denaturing polyacrylamide-mediated gel electrophoresis and were gel-extracted based on size (26-mers to 34-mers) followed by rRNA depletion by RiboMinus kit (Ambion)
For total RNA sequencing, libraries were constructed using Illumina’s TruSeq Stranded Total RNA kit. The ribosome protected fragment library was generated using NEXT-Flex smRNA-Seq Kit v3 (Perkin Elmer)

treatment_protocol: Fbxo4(+/+) or Fbxo4(-/-) cells were transfected with either non-targeting (Dharmacon-Horizon, cat#D-001810-01-20) or anti-hnRNPK siRNA (Dharmacon-Horizon, cat#L-048002-01-0020). RNAi was delivered by Lipofectamine RNAiMAX (Thermofisher) according to the manufacturer guide.

value: Murine Embrionic Fibroblasts

value: Fbxo4 knock-out

tag: treatment

value: hnRNPK knock-down


title: genomic DNA from Cord Blood sample 490056_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490056_CU

value: cord blood

value: exposed


title: CIS5HS2

description:
1
Spleen-092

tag: organ

value: Gill

value: K

value: 5 hpe

value: Uninfected


title: IR1WS4

description:
1
Spleen-074

tag: genotype omy16

value: R


title: rS7: MEF_Fbxo4(-/-)+hnRNPK siRNA rep 1 [RPF]


title: genomic DNA from Cord Blood sample 290026_GH_CU

description: Chagasic pregnancy

source_name: Cord blood sample 290026_GH_CU


title: genomic DNA from Cord Blood sample 490058_CR_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490058_CR_CU


title: Galaxy146-[F_CR__F_CR_B175]

value: hippocampus tissue


title: Galaxy146-[F_CR__F_CR_B167]

value: DBA/2J x B6EiC3Sn/J


title: rS6: MEF_Fbxo4(-/-)+non_targeting siRNA rep 2 [RPF]

value: control RNAi


title: IR1WS3

description:
1
Spleen-073

tag: genotype omy17

value: Excluded

value: 2x infected


title: Galaxy146-[F_CR__F_CR_B166]

value: female


title: rS5: MEF_Fbxo4(-/-)+non_targeting siRNA rep 1 [RPF]


title: rS4: MEF_wt+hnRNPK siRNA rep 2 [RPF]

value: Fbxo4 wt


title: genomic DNA from Cord Blood sample 490090_GD_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490090_GD_CU


title: IR1WS2

description:
1
Spleen-072

value: G

tag: status

value: non-QTL

value: Day 20


title: Galaxy146-[F_CR__F_CR_B136]

value: adult (6-wk)


title: Galaxy146-[F_CR__F_CR_B113]


title: rS2: MEF_wt+non_targeting siRNA rep 2 [RPF]

value: Murine Embrionic Fibroblasts


title: CIR1WS9

description:
2
Spleen-069

value: Gill

value: T

tag: timepoint


title: genomic DNA from Cord Blood sample 490023_VB_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490023_VB_CU

value: cord blood

value: exposed


title: CIR1WS10

description:
2
Spleen-070

value: K

value: Uninfected


title: TS7_10795_11_S27

source_name: E17.5 mouse forebrain tissue

value: DBA/2J x B6EiC3Sn/J

value: forebrain tissue


title: rS1: MEF_wt+non_targeting siRNA rep 1 [RPF]

tag: strain

value: control RNAi


title: TS6_10795_10_S26


title: S8: MEF_Fbxo4(-/-)+hnRNPK siRNA rep 2 [RNA]

value: Fbxo4 knock-out

value: hnRNPK knock-down


title: CIR1WS7

description:
2
Spleen-067

value: R

value: Excluded

tag: no. of exposures


title: genomic DNA from Cord Blood sample 490006_VP_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490006_VP_CU


title: IR1WS1

description:
1
Spleen-071

value: 2x infected


title: TS5_10795_6_S24


title: S7: MEF_Fbxo4(-/-)+hnRNPK siRNA rep 1 [RNA]

tag: cell type


title: CIR1WS6

description:
2
Spleen-066

value: G

value: non-QTL

value: Day 20


title: genomic DNA from Cord Blood sample 490007_TI_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490007_TI_CU


title: Galaxy150-[M_TS__M_TS_B52]

source_name: adult (6-wk) hippocampus tissue - male

tag: background strain

value: male

value: adult (6-wk)

value: hippocampus tissue


title: rS3: MEF_wt+hnRNPK siRNA rep 1 [RPF]

value: Murine Embrionic Fibroblasts

value: Fbxo4 wt


title: CIR1WS8

description:
2
Spleen-068

value: Gill

value: K

value: Uninfected


title: CIR1WS5

description:
1
Spleen-065


title: genomic DNA from Cord Blood sample 490012_DO_CU

description: Chagasic pregnancy

source_name: Cord blood sample 490012_DO_CU

value: cord blood

value: exposed


title: CIR1WS4

description:
1
Spleen-064


title: S5: MEF_Fbxo4(-/-)+non_targeting siRNA rep 1 [RNA]

value: Fbxo4 knock-out

value: control RNAi


title: TS3_10813_3_S15

value: DBA/2J x B6EiC3Sn/J

value: forebrain tissue


title: genomic DNA from Cord Blood sample 490054_NEG

description: Control pregnancy

source_name: Cord blood sample 490054_NEG

value: control


title: CIR1WS3

description:
1
Spleen-063

value: T

value: R

value: non-QTL


title: S4: MEF_wt+hnRNPK siRNA rep 2 [RNA]

value: hnRNPK knock-down


title: TS2_10813_2_S14


title: S3: MEF_wt+hnRNPK siRNA rep 1 [RNA]


title: S6: MEF_Fbxo4(-/-)+non_targeting siRNA rep 2 [RNA]


title: TS1_10813_1_S13


title: CIR1WS2

description:
1
Spleen-062

value: G

value: Day 20


title: TS4_10795_3_S22


title: EU8_10795_7_S25

value: euploid


title: S2: MEF_wt+non_targeting siRNA rep 2 [RNA]

value: Murine Embrionic Fibroblasts

value: Fbxo4 wt


title: genomic DNA from Cord Blood sample 490074_NEG

description: Control pregnancy

source_name: Cord blood sample 490074_NEG


title: genomic DNA from Cord Blood sample 490028_NEG

description: Control pregnancy

source_name: Cord blood sample 490028_NEG


title: genomic DNA from Cord Blood sample 490022_NEG

description: Control pregnancy

source_name: Cord blood sample 490022_NEG


title: genomic DNA from Cord Blood sample 490056_NEG

description: Control pregnancy

source_name: Cord blood sample 490056_NEG


title: EU7_10795_4_S23


title: CIR1WS1

description:
1
Spleen-061

value: Gill

value: K

value: Uninfected


title: IR4DS10

description:
2
Spleen-060

value: Day 7

value: 1x infected


title: IR4DS9

description:
2
Spleen-059


title: genomic DNA from Cord Blood sample 290002_UB_CU

description: Chagasic pregnancy

source_name: Cord blood sample 290002_UB_CU

value: cord blood

value: exposed


title: Galaxy146-[F_CR__F_CR_B133]

source_name: adult (6-wk) hippocampus tissue - female

value: DBA/2J x B6EiC3Sn/J

tag: Sex

value: female

value: adult (6-wk)

value: hippocampus tissue


title: EU5_10795_1_S20

tag: age

value: forebrain tissue


title: Screen3 VOA4627loss-of-function-meki-enhancer-data

city: Amsterdam

first: Katrien

last: Berns

state: Noord Holland

address: Plesmanlaan 121

department: Molecular Carcinogenesis

country: Netherlands

institute: The Netherlands Cancer Institute

description:
4754
CRISPR/Cas9 Brunello lentiCRISPRV2 (Addgene #73179)

data_processing:
sgRNA abundance in treated and untreated samples were analyzed using  DESeq2 (RRID:SCR_000154) and RRA MAGeCK tools. For sequence depth normalization, a relative total size factor was calculated for each sample, by dividing the total counts of each sample by the geometric mean of all totals as described. After normalization, a differential test between the treated and untreated condition for each sgRNA was performed using DESeq2 and the output was sorted in a specific order depending on the interest: depletion or enhancement. We used the MAGeCK Robust Rank Algorithm to determine for each gene whether its sgRNAs were enriched towards the top of the result list. The resulting enrichment P values were corrected for multiple testing using the Benjamini–Hochberg correction, resulting in a false-discovery rate (FDR)-corrected value.
Assembly: homo sapiens (hg38)
Supplementary files format and content: Processed data file is generated  in Excel (the README.txt file describes the generation of processed data from the raw multiplexed fastq's) and contains all the readcounts of the gRNA's of the indicated genes for the reference (T0), untreated (UT) and trametinib treated (TR) conditions performed in triplicate (r1,r2,r3).

source_name: Ovarian

growth_protocol: All cells were maintained in DMEM (Gibco) supplemented with 10% FBS and 100µg/ml penicillin/ streptomycin and 2mM L-glutamine (Gibco).

extract_protocol:
Cells were harvested and genomic DNA was isolated using a ZYMO gDNA isolation kit according to manufacturer’s protocol.
sgRNAs were amplified using a capture/two-step PCR protocol for next generation sequencing in an Illumina HiSeq-2500 as described (Jastrzebski K, Evers B, Beijersbergen RL. Pooled shRNA Screening in Mammalian Cells as a Functional Genomic Discovery Platform. Methods Mol Biol 2016;1470:49-73 doi 10.1007/978-1-4939-6337-9_5)
DNA seq Library ready for sequencing

treatment_protocol: Cells were treated with trametinib. Medium was replaced every three days.

value: Ovarian

tag: cell line

value: LGSOC

tag: genotype

value: RAS WT

value: T0, UT, TR (2nM trametinib)


title: genomic DNA from Cord Blood sample 490064_NEG

description: Control pregnancy

source_name: Cord blood sample 490064_NEG

tag: tissue

value: control


title: EU6_10795_2_S21

value: euploid


title: genomic DNA from Cord Blood sample 490041_NEG

description: Control pregnancy

source_name: Cord blood sample 490041_NEG


title: genomic DNA from Cord Blood sample 490043_NEG

description: Control pregnancy

source_name: Cord blood sample 490043_NEG


title: IR4DS8

description:
2
Spleen-058

value: Gill

value: K

value: R

value: Excluded


title: EU4_10813_8_S19


title: Screen2 VOA6406loss-of-function-meki-resistance-data

description:
5159
CRISPR/Cas9 Brunello lentiCRISPRV2 (Addgene #73179)

value: VOA-6406 derivative

value: NRAS Q61R

value: T0, UT, TR (5nM trametinib)


title: IR4DS7

description:
2
Spleen-057

value: G

value: non-QTL

value: Day 7

value: 1x infected


title: EU3_10813_6_S18

value: DBA/2J x B6EiC3Sn/J

value: forebrain tissue


title: genomic DNA from Cord Blood sample 490068_NEG

description: Control pregnancy

source_name: Cord blood sample 490068_NEG

value: cord blood


title: EU2_10813_5_S17

source_name: E17.5 mouse forebrain tissue


title: IR4DS6

description:
2
Spleen-056


title: EU1_10813_4_S16


title: RNA-Seq ICU_P63

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Reads were aligned to human genome (hg38) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against gene transcripts annotated by RefSeq.
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: hg38
Supplementary files format and content: Text; First column for entrz gene ID; second column for gene symbol; columns thereafter: expression values (log2(RPKM+1)+0.0001) for each sample

source_name: Blood

extract_protocol:
RNA from blood was extracted using Qiagen QIAamp RNA Blood Mini Kit (Qiagen, Germantown, MD) and purified by using an RNeasy Mini Kit (Qiagen, Valencia, CA) following manufacturer’s instructions.
RNA-Seq library were prepared by using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Wilmington MA, USA) with ribosomal/globin reduction and illumina compatible iTru adapters for the build following manufacturer’s instructions.

tag: disease state

value: COVID19 ICU


title: genomic DNA from Cord Blood sample 290010_NEG

description: Control pregnancy

source_name: Cord blood sample 290010_NEG

tag: disease status

value: control


title: RNA-Seq ICU_P64


title: RNA-Seq ICU_P57


title: genomic DNA from Cord Blood sample 490082_NEG

description: Control pregnancy

source_name: Cord blood sample 490082_NEG


title: genomic DNA from Cord Blood sample 490072_NEG

description: Control pregnancy

source_name: Cord blood sample 490072_NEG


title: genomic DNA from Cord Blood sample 490010_NEG

description: Control pregnancy

source_name: Cord blood sample 490010_NEG


title: Screen1 VOA6406gain-of-function-meki-resistance-data

description:
5048
CRISPR/Cas9 Synergistic Activation Mediator (SAM) (Addgene #1000000057)

value: Ovarian

value: LGSOC

tag: treatment


title: IR4DS5

description:
1
Spleen-055

tag: organ

value: Gill

value: T


title: S1: MEF_wt+non_targeting siRNA rep 1 [RNA]

value: Murine Embrionic Fibroblasts

value: Fbxo4 wt

value: control RNAi


title: IR4DS4

description:
1
Spleen-054

tag: genotype omy16

value: K


title: genomic DNA from Cord Blood sample 290025_NEG

description: Control pregnancy

source_name: Cord blood sample 290025_NEG


title: RB_5100

description: MxCre

data_processing:
RNA-seq processing:
Raw reads were analyzed with cluster_rnaseq pipeline (https://gitlab.com/bu_cnio/cluster_rnaseq), as follows:
Read adapters were removed with BBDuk v38.90 (ktrim=r k=23 mink=11 hdist=1 tpe tbo). Sequencing quality was checked with FastQC v0.11.9 and MultiQC v1.10.1.
Reads were aligned to the mouse reference genome (GRCm39) with STAR v2.7.9a (--outSAMtype BAM SortedByCoordinate). Read counts were obtained with HTSeq-count v0.12.4 (-m union -s no -i gene_name -f bam -r pos) using the mouse gene annotation from GENCODE (gencode.vM27.primary_assembly.annotation.gtf).
Differential expression was performed with DESeq2 v1.30.1, using a 0.05 FDR. Genes were ranked according to the shrunken log2 Fold Change (ype = "apeglm") and GSEAPreranked v4.1.0 was used to perform gene set enrichment analysis for Hallmarks, Biocarta, Reactome and KEGG v7.4 signatures, setting 1000 gene set permutations, a weighted enrichment statistic and a random seed of 123.
Assembly: GRCm39
Supplementary files format and content: Tabulated text file with normalized counts obtained with DESeq2.

source_name: MxCre

growth_protocol: MxCre or CalrD52/+ MxCre, pI:pC induced.

extract_protocol:
RNA was isolated from sorted cell pellets using PicoPure RNA isolation kits (Applied Biosystems, KIT0204).
Takara SMART-Seq v4 kit was used for cDNA synthesis, shearing was performed according to the Covaris Protocol and library preparation was done with Swift ACCEL-NGS™ 2S PLUS DNA kit.
Stranded RNA-seq.

treatment_protocol: 2 weeks after pIpC induction, mice were intraperitoneally treated with 750 mg/kg 2-DG for 18 days, followed by cell sorting for MEPs.

value: MxCre

value: Calr WT

value: Vehicle

value: Female


title: IR4DS3

description:
1
Spleen-053

tag: genotype omy17

value: G

value: non-QTL

value: Day 7

value: 1x infected


title: IR4DS1

description:
1
Spleen-051

tag: status


title: RNA-Seq ICU_P12

value: COVID19 ICU


title: RNA-Seq ICU_P21


title: RNA-Seq ICU_P05


title: RB_5093

description: CalrD52/+ Ki MxCre

value: Calr fl/+

value: Male


title: CIR4DS10

description:
2
Spleen-050

value: Gill

tag: timepoint

value: Uninfected


title: RNA-Seq ICU_P02


title: CIR4DS9

description:
2
Spleen-049

value: R

value: Excluded


title: RNA-Seq ICU_P13


title: RNA-Seq NonICU_P17

value: COVID19 NonICU


title: genomic DNA from Cord Blood sample 301002_NEG

description: Control pregnancy

source_name: Cord blood sample 301002_NEG

value: cord blood

value: control


title: genomic DNA from Cord Blood sample 490053_MG_NEG

description: Control pregnancy

source_name: Cord blood sample 490053_MG_NEG


title: genomic DNA from Cord Blood sample 290020_SD_CU

description: Chagasic pregnancy

source_name: Cord blood sample 290020_SD_CU

value: exposed


title: RB_5090

description: CalrD52/+ Ki MxCre

tag: strain

value: MxCre

value: Vehicle


title: genomic DNA from Cord Blood sample 490034_NEG

description: Control pregnancy

source_name: Cord blood sample 490034_NEG


title: CIR4DS7

description:
2
Spleen-047

value: K

value: G

tag: no. of exposures


title: RNA-Seq NonICU_P14


title: CIR4DS6

description:
2
Spleen-046

value: non-QTL

value: Day 7


title: TT_2562

description: MxCre

value: Calr WT

value: Female


title: RNA-Seq NonICU_P15


title: RNA-Seq NonICU_P10


title: genomic DNA from Cord Blood sample 590012_TM_NEG

description: Control pregnancy

source_name: Cord blood sample 590012_TM_NEG


title: GG_2721

description: CalrD52/+ Ki MxCre

value: Calr fl/+


title: RB_5095

description: CalrD52/+ Ki MxCre


title: RB_5091

description: CalrD52/+ Ki MxCre

value: Male


title: PPD6 mouse uterine transcriptome, myometrial PGR deficiency 4 [sw191]

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

data_processing:
Raw reads of 76 nucleotides, paired-end filtered for quality score > 20.
The reads passing the initial processing were aligned to the mouse reference genome (mm10) using HISAT2 version 2.2.1 with “--very-sensitive” option
The duplicated reads with the same sequence were removed
Assembly: mm10
Supplementary files format and content: Gene expression matrix with read count was calculated by counting the total number of paired-end reads mapped to each gene with HTSeq version 0.10.0.

organism: Mus

source_name: Uterus

extract_protocol:
RNA was extracted using TRIzol according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: myometrial PGR deficiency

tag: Stage

value: pseudopregnancy day 6

value: uterine tissues surrounding the embryo implantation sites


title: PPD6 mouse uterine transcriptome, myometrial PGR deficiency 3 [sw190]


title: RB_5092

description: CalrD52/+ Ki MxCre

tag: Sex


title: IR4DS2

description:
1
Spleen-052

data_processing:
All q-PCR assays exhibited efficiencies within 100% ± 5% so the simplified 2^-ΔΔCq method was used for analysing data (Livak and Schmittgen, 2001). For normalization and as internal calibrator the average of three genes (ARP, ELF1α and β-actin) was chosen by using NormFinder (Andersen et al., 2004). For gene expression analyses, all challenged groups were compared to non-exposed time point controls using Student’s t-test. We considered differences to be significant when regulations were at least two-fold and p < 0.05.
Target gene signals were normalized using the average of 3 housekeeping genes (ARP, b-actin and ELF 1a) as2^-ΔCt, where -ΔCt = -(Ct_Target − Ct_ average of 3 HKGs). Folds were calculated as  2^-ΔΔCt, where -ΔΔCt = -[ΔCt_infected -ΔCt_control].  First case of folds describes infected groups relative to the uninfected groups at the timepoints.  Second case  of folds describes non-QTL groups relative to the QTL groups at the timepoints.  Third case of folds (only relevant at day 20) describes 1x infected groups relative to the 2x infected groups  in both cases of non-QTL and QTL.

extract_protocol: RNAlater fixed samples from fish (gills, liver and spleen) were homogenized (Tissue-lyser II, Qiagen, Denmark) using a homogenization buffer with 2-mercaptoethanol (Sigma-Aldrich). RNA was extracted using the GenEluteTM mammalian RNA kit (RTN350, Sigma-Aldrich, Denmark). Liver samples were pre-treated by Proteinase K (cat.no.P4850, Sigma-Aldrich, Denmark). DNase I (AMPD1, Sigma-Aldrich, Denmark) treatment was applied to remove genomic DNA. The concentration of RNA was determined in a NanoDrop 2000 spectrophotometer (Saveen & Werner, Denmark). Quality of RNA was evaluated by agarose (cat.no. 16500100, ThermoFisher Scientific, Denmark) gel electrophoresis. RNA was kept at −80°C until cDNA synthesis.

value: Gill

value: 1x infected


title: genomic DNA from Cord Blood sample 490030_BQ_NEG

description: Control pregnancy

source_name: Cord blood sample 490030_BQ_NEG

value: cord blood

value: control


title: CIR4DS5

description:
1
Spleen-045

value: Uninfected


title: GG_2560

description: CalrD52/+ Ki MxCre

value: MxCre

value: Vehicle


title: RNA-Seq NonICU_P08

value: COVID19 NonICU


title: genomic DNA from Cord Blood sample 490040_VK_NEG

description: Control pregnancy

source_name: Cord blood sample 490040_VK_NEG


title: CIR4DS4

description:
1
Spleen-044

value: T

value: G

value: non-QTL


title: genomic DNA from Cord Blood sample 490058_CR_NEG

description: Control pregnancy

source_name: Cord blood sample 490058_CR_NEG


title: CIR4DS3

description:
1
Spleen-043

value: K

value: R

value: Excluded

value: Day 7


title: PPD6 mouse uterine transcriptome, myometrial PGR deficiency 1 [sw188]

value: myometrial PGR deficiency

value: pseudopregnancy day 6


title: genomic DNA from Cord Blood sample 490090_GD_NEG

description: Control pregnancy

source_name: Cord blood sample 490090_GD_NEG


title: genomic DNA from Cord Blood sample 490038_IG_NEG

description: Control pregnancy

source_name: Cord blood sample 490038_IG_NEG


title: TT_2528

description: MxCre

value: Calr WT

value: Female


title: GG_2344

description: CalrD52/+ Ki MxCre

value: Calr fl/+


title: RNA-Seq NonICU_P06

source_name: Blood


title: PPD6 mouse uterine transcriptome, myometrial PGR deficiency 2 [sw189]

value: uterine tissues surrounding the embryo implantation sites


title: genomic DNA from Cord Blood sample 490003_EN_NEG

description: Control pregnancy

source_name: Cord blood sample 490003_EN_NEG

value: cord blood

value: control


title: CIR4DS8

description:
2
Spleen-048

value: Gill

value: Uninfected


title: CIR4DS2

description:
1
Spleen-042


title: PPD6 mouse uterine transcriptome, control 4 [sw184]


title: SX_2024

description: MxCre

value: MxCre


title: PPD6 mouse uterine transcriptome, control 3 [sw183]


title: genomic DNA from Cord Blood sample 290026_GH_NEG

description: Control pregnancy

source_name: Cord blood sample 290026_GH_NEG


title: SX_2023

description: MxCre

value: Vehicle

value: Male


title: RNA-Seq Control_N77

value: Healthy


title: genomic DNA from Cord Blood sample 490023_VB_NEG

description: Control pregnancy

source_name: Cord blood sample 490023_VB_NEG


title: IR24HS10

description:
2
Spleen-040

value: T

value: R

value: non-QTL

value: Day 4

value: 1x infected


title: SX_1979

description: MxCre

value: Calr WT


title: genomic DNA from Cord Blood sample 490069_UE_NEG

description: Control pregnancy

source_name: Cord blood sample 490069_UE_NEG


title: CIR4DS1

description:
1
Spleen-041

value: G

value: Day 7


title: IR24HS9

description:
2
Spleen-039

value: K


title: PPD6 mouse uterine transcriptome, control 1 [sw181]

value: pseudopregnancy day 6

value: uterine tissues surrounding the embryo implantation sites


title: IR24HS8

description:
2
Spleen-038

value: Gill

value: Excluded


title: RNA-Seq Control_N72


title: PPD6 mouse uterine transcriptome, control 2 [sw182]

value: control


title: SX_1978

description: MxCre

source_name: MxCre

value: MxCre


title: SX_1977

description: MxCre

value: Vehicle

value: Male


title: IR24HS7

description:
2
Spleen-037


title: RNA-Seq Control_N68

value: Healthy


title: Hi-C of GD13 mouse uterus

data_processing:
Reads were mapped to the mouse genome (UCSC mm10) using HiCUP (v0.7.1)
Assembly: mm10
Supplementary files format and content: Chromatin loops were identified with Juicer tool

extract_protocol: by Arima Genomics

value: Gestation day 13

value: tissue


title: RNA-Seq NonICU_P01

value: COVID19 NonICU


title: RNA-Seq Control_P72


title: genomic DNA from Cord Blood sample 490012_DO_NEG

description: Control pregnancy

source_name: Cord blood sample 490012_DO_NEG

value: cord blood


title: Control_SST_total_2

city: Linköping

first: Susanne

last: Bauer

address: BKV, Cellbiologi Pl 10

department: BKV

country: Sweden

institute: Linköpings universitet

data_processing:
RNAseq data was analyzed with nf-core/rnaseq 3.0 pipeline, using default parameters. STAR/Salmon were used for alignment and quantification
Genome_build: Gencode M25 (GRCm38.p6)
Supplementary_files_format_and_content: transcript counts obtained from salmon are provided in raw_count.csv. DESeq2  (v 1.30.1) results are provided in files DEG_CJD.csv and DEG_FFI.csv. Results were obtained comparing RiboTag samples of by sample set (CJD vs. Control or FFI vs. Control).
Supplementary_files_format_and_content: raw counts per transcript for all samples, imported using tximport (v 1.18.0)
Supplementary_files_format_and_content: TPM counts per transcript for all samples, imported using tximport (v 1.18.0)
Supplementary_files_format_and_content: DGE analysis using DESeq2 (v 1.30.1) results comparing CJD and Control RiboTag samples by cell type and region.
Supplementary_files_format_and_content: DGE analysis using DESeq2 (v 1.30.1) results comparing FFI and Control RiboTag samples by cell type and region.

source_name: Cerebrum

extract_protocol:
Flash frozen brain hemispheres were homogenized and total RNA ("Input") was isolated from tissue homogenate using Trizol and purified using the Qiagen Rneasy Mini kit. For "RiboTag" samples, 12CA5 monoclonal anti-HA antibody (Roche) was coupled to protein G-coated dynabeads (Invitrogen) and incubated with tissue homogenate for 90 min to immunoprecipitate HA-tagged ribosomes and their attached mRNAs. Ribosome-bound mRNAs were isolated using Qiazol and purified using the Qiagen miRNeasy kit.
Libraries were prepared according to protovol using the Illumina TruSeq stranded mRNA kit

value: Control

tag: cell type

value: SST

tag: protocol

value: Input


title: RNA-Seq Control_N70


title: IR24HS6

description:
2
Spleen-036

value: K

value: R

value: Day 4

value: 1x infected


title: IR24HS5

description:
1
Spleen-035

value: Gill

value: G

value: non-QTL


title: Control_SST_IP_3

tag: genotype

value: RiboTag


title: HL-60 RIP_IgG_4

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

data_processing:
Trimmomatic, version 0.39, parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50
hisat2
optical duplicates removal, gatk-4.1.2.0, --OPTICAL_DUPLICATE_PIXEL_DISTANCE=40
htseq-count, version 0.6.0, parameters: --stranded=reverse
Genome_build: GRCh38
Supplementary_files_format_and_content: counts generated by htseq-count

growth_protocol: HL-60 cells grown in RPMI1640 with L-glutamine and  10% FBS

extract_protocol:
EZ-Magna RIP RNA-binding Protein Immunoprecipitation Kit (Sigma Aldrich) was used for immunoprecipitation with anti-HAX1 antibody (anti-HAX1 rabbit polyclonal antibody, Thermo Fisher Scientific)
cDNA libraries were prepared using TruSeq™ Stranded Total RNA Library Prep Gold (Illumina, USA) according to manufacturer’s procedure. The average size of the libraries was determined utilizing Agilent 2100 Bioanalyzer and High Sensitivity DNA Kit (Agilent Technologies, USA), while concentration was assessed using Qubit Fluorometer and dsDNA HS Assay Kit (Thermo Fisher Scientific, USA).  Uniquely indexed libraries were pooled, mixed with Illumina PhiX Control v3 Library (1% of total amount), and sequenced on HiSeq 1500 (Illumina) on Rapid Run Mode with single-read sequencing (1x 50 bp).

treatment_protocol: untreated, basic cell culture condtions

tag: cell line

tag: rip antibody

value: IgG


title: Control_SST_total_1


title: IR24HS4

city: Frederiksberg

first: Per

last: Kania

address: Stigbojlen 7

institute: University of Copenhagen

description:
1
Spleen-034

value: T


title: HL-60 RIP_IgG_3


title: exclude_4

value: exclude


title: IR24HS3

description:
1
Spleen-033


title: HL-60 RIP_IgG_2


title: genomic DNA from Cord Blood sample 290020_SD_NEG

description: Control pregnancy

source_name: Cord blood sample 290020_SD_NEG

tag: tissue

tag: disease status

value: control


title: HL-60 RIP_IgG_5


title: IR24HS2

description:
1
Spleen-032

tag: organ

value: Excluded


title: Control_SST_IP_1


title: Control_SST_IP_2


title: HL-60 RIP_HAX1_5


title: RNA-Seq NonICU_P07

tag: disease state

value: COVID19 NonICU


title: HL-60 RIP_IgG_1


title: IR24HS1

description:
1
Spleen-031

tag: genotype omy16

tag: genotype omy17


title: Control_VglutCb_total_2

source_name: Cerebellum

value: Control


title: Control_VglutCer_IP_6


title: HL-60 RIP_HAX1_3


title: genomic DNA from Cord Blood sample 490006_VP_NEG

description: Control pregnancy

source_name: Cord blood sample 490006_VP_NEG

value: cord blood


title: Control_VglutCb_total_1

value: Input


title: HL-60 RIP_HAX1_2


title: HL-60 RIP_HAX1_4


title: Control_VglutCb_IP_5


title: HL-60 RIP_HAX1_1


title: Control_VglutCer_IP_5


title: CIR24HS10

description:
2
Spleen-030

value: K

tag: status

tag: timepoint

value: Uninfected


title: HL-60 HAX1 KO #2 4

source_name: HL-60 HAX1 KO #2

extract_protocol:
RNA was extracted from cells via PureLink Mini Total RNA Isolation kit (Thermofisher, USA) , endogenous DNA was removed from samples via TURBO DNAse kit (Thermofisher, USA) , RNA quaility was assessed via Agilent 2100 Bioanalyzer using Agilent RNA 6000 Nano Kit (Agilent Technologies, USA)
cDNA libraries were prepared using TruSeq™ Stranded Total RNA Library Prep Gold (Illumina, USA) according to manufacturer’s procedure. The average size of the libraries was determined utilizing Agilent 2100 Bioanalyzer and High Sensitivity DNA


title: Control_VglutCb_IP_4


title: HL-60 HAX1 KO #2 3


title: HL-60 HAX1 KO #2 2


title: Control_VglutCer_total_3


title: Control_VglutCer_IP_4


title: CIR24HS8

description:
2
Spleen-028

value: Day 4

tag: no. of exposures


title: CIR24HS5

description:
1
Spleen-025

value: R


title: CIR24HS9

description:
2
Spleen-029

value: Gill


title: CIR24HS6

description:
2
Spleen-026

value: G


title: CIR24HS7

description:
2
Spleen-027

value: non-QTL


title: CIR24HS4

description:
1
Spleen-024


title: Control_VglutCb_IP_3

value: RiboTag


title: HL-60 HAX1 KO #1 4

source_name: HL-60 HAX1 KO #1


title: HL-60 HAX1 KO #2 1


title: CIR24HS2

description:
1
Spleen-022


title: CIR24HS3

description:
1
Spleen-023


title: Control_VglutCer_total_2


title: HL-60 HAX1 KO #1 3


title: CIR24HS1

description:
1
Spleen-021


title: IRS10

description:
2
Spleen-020

value: 5 hpe

value: 1x infected


title: Control_VglutCer_IP_3


title: genomic DNA from Cord Blood sample 490007_TI_NEG

description: Control pregnancy

source_name: Cord blood sample 490007_TI_NEG


title: HL-60 HAX1 KO #1 2


title: Control_VglutCb_IP_2


title: HL-60 HAX1 KO #1 1


title: IRS9

description:
2
Spleen-019


title: Control_VglutCer_total_1


title: IRS8

description:
2
Spleen-018


title: HL-60 WT 4

source_name: HL-60 WT

value: WT


title: IRS7

description:
2
Spleen-017


title: Control_VglutCer_IP_2


title: IRS6

description:
2
Spleen-016

value: T


title: HL-60 WT 3


title: Dnmt3aVillin722, DNA

hyb_protocol: For Caco-2 cells, bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Infinium Methylation EPIC Beadchip using standard Illumina protocol: For mice tissue, bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Mouse Methylation-12v1-0 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing:
DNA methylation data was analyzed using the Bioconductor package RnBeads (version 1.12.1) with human reference genome version hg19.
The signal intensity values were normalized using the dasen method. The human and mouse data were normalized separately.

source_name: intestinal epithelial cells

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated from Caco-2 cells, purified IECs and intestinal crypts using DNeasy Blood and Tissue Kit (Qiagen) according to manufacturer´s instructions.

treatment_protocol: For DSS experiments, mice were treated with 2%DSS for 5 days followed by 7 days of normal drinking water.

value: Steady state

value: intestinal epithelial cells

value: Dnmt3a {delta}IEC

tag: treatment

value: No treatment


title: Dnmt3aVillin723, DNA


title: Dnmt3aVillin724, DNA


title: HL-60 WT 2


title: Control_VglutCb_IP_1

value: Control


title: HL-60 WT 1


title: Control_VglutCer_IP_1


title: Control_PV_total_4

value: PV

value: Input


title: IRS5

description:
1
Spleen-015


title: IRS4

description:
1
Spleen-014


title: Control_PV_IP_6


title: IRS3

description:
1
Spleen-013

value: K


title: Myeloid_Week1_GFP_CordBlood_rep3

city: Seattle

first: Soheil

last: Meshinchi

state: Washington

address: 1100 Fairview Ave N.

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

data_processing:
mRNA libraries were sequenced on the Illumina HiSeq 2500  at the British Columbia Genome Sciences Center (BCGSC, Vancouver, BC)
Sequenced reads in fastq format were quantified using Kallisto v0.45.0 with a GRCh38 transcriptome reference prepared using the coding and noncoding transcript annotations in in Gencode v29 and RepBase v24.01
Gene-level counts and abundances were produced using tximport v1.16.1 from Kallisto h5 abundance files with the `scaledTPM` method
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with normalized transcipts per million (TPM)  abundance for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cord Blood

growth_protocol: The C/G oncofusion and the MND promoter were inserted into pRRLhPGK-GFP lentivirus vector upstream of the PGK promoter.  Human umbilical cord blood samples were obtained from normal deliveries at Swedish Medical Center (Seattle, WA).  Cells were thawed in IMDM supplemented with 20% FBS and 100 U/mL DNaseI and cultured on Notch ligand in Stem Span II supplemented with SCF, FLT3L and TPO.  Cells were transduced the following day with the C/G fusion/GFP construct at an MOI of 200 or GFP control construct at MOI 50. Transduced cells were grown on Notch ligand for 2 days prior to placement in EC co-culture or MC culture.

extract_protocol:
Total RNA from cultured cells were extracted with AllPrep DNA/RNA/miRNA Universal Kit using the QIAcube platform at 1 week, 6 weeks, and 12 weeks in culture. Total RNA (500ng) from cultured cells were prepared using the NEBNext rRNA Depletion Kit for Human/Mouse/Rat  (NEB, E6310X).
The rRNA depleted RNA samples underwent the NEBNext Ultra Directional Second Strand cDNA Synthesis protocol (NEB) that incorporates dUTP in the dNTP mix.  The 75bp strand-specific paired-end mRNA libraries were prepared using the ribodepletion (rRNA depleted) v2.0 protocol by the British Columbia Genome Sciences Center (Vancouver, BC) and sequenced on the Illumina HiSeq 2500.

value: Myeloid

value: GFP

tag: group


title: Myeloid_Week1_GFP_CordBlood_rep2


title: IRS2

description:
1
Spleen-012

value: Gill

value: G


title: Control_PV_total_3


title: Myeloid_Week1_GFP_CordBlood_rep1


title: Control_PV_IP_5

value: RiboTag


title: Dnmt3aVillin721, DNA

value: Dnmt3a fl/fl


title: IRS1

description:
1
Spleen-011

value: non-QTL

value: 5 hpe

value: 1x infected


title: EC_Week1_GFP_CordBlood_rep3

value: EC


title: CIR5HS10

description:
2
Spleen-010

value: T

value: Uninfected


title: EC_Week1_GFP_CordBlood_rep2


title: Dnmt3aVillin719, DNA

value: Steady state

value: intestinal epithelial cells

value: Dnmt3a {delta}IEC

value: No treatment


title: Control_PV_total_2

value: Control

value: PV

value: Input


title: Control_PV_IP_4


title: EC_Week1_GFP_CordBlood_rep1

value: GFP


title: Control_PV_IP_3


title: CIR5HS9

description:
2
Spleen-009

value: Gill

value: K

value: R

value: Excluded


title: CIR5HS8

description:
2
Spleen-008

value: G

value: non-QTL

value: 5 hpe


title: Dnmt3aVillin693, DNA

source_name: epithelial crypts

value: DSS-induced ulcerative colitis model

value: epithelial crypts

value: Dnmt3a fl/fl

value: DSS treatment for 5 days


title: Myeloid_Week6_CBFGLIS_CordBlood_rep3

value: Myeloid


title: CIR5HS7

description:
2
Spleen-007

value: Uninfected


title: Control_PV_IP_2

value: Control

value: RiboTag


title: Dnmt3aVillin718, DNA

value: Steady state

value: intestinal epithelial cells

value: No treatment


title: Dnmt3aVillin692, DNA

value: Dnmt3a {delta}IEC


title: Myeloid_Week6_CBFGLIS_CordBlood_rep2


title: Control_PV_total_1

value: PV

value: Input


title: Dnmt3aVillin720, DNA


title: Myeloid_Week6_CBFGLIS_CordBlood_rep1


title: CIR5HS5

description:
1
Spleen-005

value: Gill

value: T

value: G


title: Dnmt3aVillin691, DNA

value: DSS-induced ulcerative colitis model


title: CIR5HS6

description:
2
Spleen-006

value: non-QTL

value: 5 hpe


title: Control_PV_IP_1


title: Dnmt3aVillin643, DNA

value: epithelial crypts

value: Dnmt3a fl/fl

value: Recovery for 7 days after 5 day DSS treatment


title: Myeloid_Week1_CBFGLIS_CordBlood_rep3

value: Myeloid


title: genomic DNA from Cord Blood sample 290002_UB_NEG

description: Control pregnancy

source_name: Cord blood sample 290002_UB_NEG

value: cord blood

value: control


title: CIR5HS4

description:
1
Spleen-004

value: K

value: Uninfected


title: Control_GadCb_total_4

value: Control


title: CIR5HS3

description:
1
Spleen-003


title: Control_GadCb_IP_6

value: RiboTag


title: Myeloid_Week1_CBFGLIS_CordBlood_rep1


title: Dnmt3aVillin684, DNA

value: Dnmt3a {delta}IEC


title: Dnmt3aVillin690, DNA

value: DSS treatment for 5 days


title: CIR5HS2

description:
1
Spleen-002

value: Gill


title: Myeloid_Week1_CBFGLIS_CordBlood_rep2


title: Dnmt3aVillin673, DNA


title: Control_GadCer_IP_6


title: Dnmt3aVillin678, DNA


title: EC_Week6_CBFGLIS_CordBlood_rep4

value: EC


title: Dnmt3aVillin683, DNA

value: DSS-induced ulcerative colitis model


title: Dnmt3aVillin642, DNA


title: Dnmt3aVillin663, DNA


title: Dnmt3aVillin657, DNA


title: Control_GadCb_total_3

value: Input


title: Dnmt3aVillin672, DNA


title: Dnmt3aVillin660, DNA


title: Dnmt3aVillin675, DNA


title: Dnmt3aVillin656, DNA


title: Dnmt3aVillin662, DNA


title: EC_Week6_CBFGLIS_CordBlood_rep3


title: Dnmt3aVillin677, DNA


title: Control_GadCb_IP_5


title: Dnmt3aVillin666, DNA


title: EC_Week6_CBFGLIS_CordBlood_rep2


title: Dnmt3aVillin670, DNA


title: Control_GadCer_IP_5


title: EC_Week6_CBFGLIS_CordBlood_rep1


title: Control_GadCb_total_2


title: CIR5HS1

description:
1
Spleen-001

value: G

value: non-QTL

value: 5 hpe


title: EC_Week12_CBFGLIS_CordBlood_rep4


title: EC_Week12_CBFGLIS_CordBlood_rep3


title: T cells_KPC-SubQ_Ant08+PD1-2

city: Atlanta

first: Edmund K.

last: Waller

state: Georgia

address: 1365 Clifton Rd Building C

department: Hematology and Medical Oncology

institute: Emory University School of Medicine

description: Singlet cell suspensions of tumors were subjected to magnetic T cell isolation using EasySepTM Mouse CD90.2 Positive Selection kit II from STEMCELL technologies (Vancouver, Canada). Purity of T cells following isolation was 80-85%. Qiagen RNeasy Micro kit was used to extract RNA, and quantity and quality was assessed using the Nanodrop and Agilent 2100. RNA analyzed using the nCounter Metabolic Pathways Panel (Nanostring Technologies, Seattle, WA)

hyb_protocol: Probes and target transcripts were hybridized overnight at 65°C for at least 16 hours.   exceed 48 hours.s as described in the manufacturer’s protocol.

scan_protocol: Hybridized RNA was then diluted in molecular grade water and loaded into nCounter SPRINT cartridge (NanoString), placed into nCounter SPRINT Profiler, and quantified. RNA-conjugated probes were counted via NanoString Sprint Profiler technology. counts are quantified.

data_processing: Raw NanoString data (n=12) from both batches was exported from NSolver. Data quality was assessed with the help of QC plots using R package NanoStringNorm5. Raw files were imported and analyzed using R package NanoStringClustR6. Data was normalized using quantile normalization after background subtraction of mean2sd, and count thresholding.  Differential expression analysis was carried out using NanoStringClustR and genes were identified as significant with an FDR adjusted p-value of less than or equal to 0.05. Functional enrichment and network analysis for the principal comparison of interest was carried out using an ordered query on gProfiler7.

label: codeset probes

source_name: T cells_KPC-SubQ_Ant08+PD1-2

label_protocol: nCounter gene expression assays (NanoString Technologies) were performed for the NanoString metabolic pathways mouse panel. Samples were labelled with panel-specific codeset probes. nCounter® Metabolic Pathways Panel (NanoString Technologies) were performed. Samples were labelled with panel-specific codeset probes.

treatment_protocol: For the subcutaneous model, 5x105 KPC-Luc cells were injected subcutaneously near the right flank of female C57BL/6 mice. For the MT5 or Panc02 models, 5x105 were injected subcutaneously near the right flank of female C57BL/6 mice. For the orthotopic KPC-Luc model, mice were anesthetized, and the KPC-Luc cells were suspended in Matrigel and injected in the tail of the pancreas following laparotomy. 6-7 days after tumor implantation mice were randomized into 4 treatment groups and treatedwith VIP-R antagonist and/or anti-PD-1. While scram+IgG control mice received scrambled peptide and isotype IgG, the VIP-R antagonist, anti-PD-1 and VIP-R antagonist and anti-PD-1 groups received VIP-R antagonist and IgG; scrambled peptide and anti-PD-1; and VIP-R antagonist and anti-PD-1, respectively. The treatment regimen involved administering 10μg of scrambled or VIP-R antagonist: ANT008 or ANT308, subcutaneously every day and 200μg of IgG or anti-PD-1 intraperitoneally once every three days, for a total of 10 days.

value: T cells

tag: gender

value: Female

tag: strain


title: T cells_KPC-SubQ_Ant08+PD1-1

source_name: T cells_KPC-SubQ_Ant08+PD1-1

extract_protocol: Singlet cell suspensions of tumors were subjected to magnetic T cell isolation using EasySepTM Mouse CD90.2 Positive Selection kit II from STEMCELL technologies (Vancouver, Canada). Purity of T cells following isolation was 80-85%. Qiagen RNeasy Micro kit was used to extract RNA, and quantity and quality was assessed using the Nanodrop and Agilent 2100.

tag: cell type


title: Control_GadCer_total_3

tag: genotype

tag: protocol


title: T cells_KPC-SubQ_Ant08+PD1-3

source_name: T cells_KPC-SubQ_Ant08+PD1-3


title: Control_GadCb_IP_4


title: Dnmt3aVillin655, DNA

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

institute: Institute of Clinical Molecular Biology

value: epithelial crypts

value: Dnmt3a fl/fl

value: Recovery for 7 days after 5 day DSS treatment


title: EC_Week12_CBFGLIS_CordBlood_rep2


title: Dnmt3aVillin674, DNA


title: Control_GadCer_IP_4


title: EC_Week12_CBFGLIS_CordBlood_rep1


title: T cells_KPC-SubQ_PD1-3

source_name: T cells_KPC-SubQ_PD1-3


title: Dnmt3aVillin667, DNA


title: Control_GadCb_IP_3


title: Dnmt3aVillin668, DNA


title: Dnmt3aVillin661, DNA


title: EC_Week1_CBFGLIS_CordBlood_rep2


title: T cells_KPC-SubQ_Ant08-3

source_name: T cells_KPC-SubQ_Ant08-3


title: T cells_KPC-SubQ_Ant08-2

source_name: T cells_KPC-SubQ_Ant08-2


title: Control_GadCer_IP_3

source_name: Cerebrum


title: EC_Week1_CBFGLIS_CordBlood_rep1


title: SCC-9 cell IP replicate 2

city: Guangzhou

first: LiuTao

last: Chen

address: Waihuan West Road 132, University TownHigher Education Mega Center

institute: The Sun YAT-SEN UNIVERSITY

data_processing:
The fastp tool (https://github.com/OpenGene/fastp) was used to remove the low   quality reads and trim adaptors . Sequence quality of IP and input samples was  verified using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)   and RseQC (http://rseqc.sourceforge.net/) .
Clean reads were then mapped to the reference genome Homo sapiens (Version: v101) using HISAT2 (http://daehwankimlab.github.io/hisat2)
m6A peak calling and analysis of   differentially methylated peaks were performed by R package exomePeak2   (https://bioconductor.org/packages/release/bioc/html/exomePeak2.html) , and   peaks were annotated by intersection with gene architecture using R package   5  ANNOVAR (http://www.openbioinformatics.org/annovar/)
The MEME   (http://meme-suite.org) (30) and HOMER (http://homer.ucsd.edu/homer/motif) were   used for de novo and known motif finding, followed by localization of the motif with   respect to peak summit. The expression level of all transcripts and genes from input   libraries was analyzed through calculating FPKM (total exon fragments/mapped reads   (millions) × exon length (kb)) using StringTie (https://ccb.jhu.edu/software/stringtie)  (31). The R package edgeR (https://bioconductor.org/packages/edgeR) (32) was used   to identify differentially expressed transcripts and genes, and the threshold was set to  |log2fold change (FC)|≥1 and p value < 0.05.
The differentially expressed genes and differentially methylated coding genes were subjected to Gene Oncology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis
Supplementary files format and content: bigwig

source_name: oral

growth_protocol: DOK cells were maintained in RPMI-1640 medium, HOEC and SCC-9 cells were maintained in DMEM medium, supplemented with 10% FBS (GIBCO, Australia), 100 U/mL penicillin G and 100 μg/mL streptomycin, in a humidified atmosphere of 5% CO2 at 37 ◦C. About 5×107 cells were harvested for MeRIP-seq and RNA-seq.

extract_protocol:
total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and quantified. RNA integrity was evaluated by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) and fragmentedinto about 100nt using Magnesium RNA Fragmentation Module (NEB, USA). The RNA fragments weredivided into two portions, one was kept as input and the otherwas used to enrich m6A-methylated RNA fragments by immunoprecipitation with m6A-specific antibody (Synaptic Systems, Germany).
RNA-seq library preparation included double stranded cDNA synthesis, addition of A-tailing, adapter ligation, amplification of ligated products, and library purification. The paired-end sequencing (PE150) of libraries was performed on Illumina Novaseq™ 6000 platform

value: oral

tag: cell line

value: Squamous Cell

value: WT


title: T cells_KPC-SubQ_PD1-2

source_name: T cells_KPC-SubQ_PD1-2


title: T cells_KPC-SubQ_PD1-1

source_name: T cells_KPC-SubQ_PD1-1


title: Control_GadCb_total_1

source_name: Cerebellum

value: Control


title: SCC-9 cell IP replicate 1

tag: tissue

tag: rip antibody

value: m6A-specific antibody (Synaptic Systems, Germany)


title: Standard_inf_05

city: Spokane

first: Yiyong

last: Liu

state: WA

address: 412 E Spokane Falls Blvd

institute: Washington State University

description:
Retrived from SRA GSE122544
Standard_ctr_vs_inf_DE_result.csv

data_processing:
HiSeq Control Software (HCS v2.2.68) was used for base-calling.
bcl2fastq2 Conversion Software v2.17.1 was used to convert base-calling files to fastq files and to trim adaptors.
Bowtie2 v2.3.4 was used for alignment
featureCounts from Subread v2.0.3 was used to quantify gene expression.
DESeq2 v1.34.0 was used for differential gene expression analysis.
Genome_build: UCSC ce10
Supplementary_files_format_and_content: comma-delimited text files including read counts in genes and differential gene expression

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans was cultured under standard conditions and fed E. coli strain OP50.

extract_protocol:
Individual worms were mechanically lysed using TissueLyser LT (Qiagen) without pre-processing, followed by RNA extraction using the Rneasy Mini Kit (Qiagen).
cDNA synthesis was carried out using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio). Sequencing-ready libraries were prepared using the Nextera XT DNA Library Prep Kit (Illumina).

treatment_protocol: Synchronized L1 larvae were grown on E. coli OP50 at 20⁰C until they reached young adult stage.  The worms were transferred to NGM plates seeded with P. aeruginosa PA14 for 24 hrs at 25⁰C.  The worms were then collected and washed with M9 buffer.

value: wild-type

tag: agent

value: infected by P. aeruginosa


title: SCC-9 cell input replicate2

value: none (input)


title: T cells_KPC-SubQ_Ant08-1

source_name: T cells_KPC-SubQ_Ant08-1


title: EC_Week1_CBFGLIS_CordBlood_rep3

value: EC


title: Control_GadCer_IP_2

value: RiboTag


title: Control_GadCb_IP_2


title: Standard_inf_04


title: DOK cell IP replicate 2

value: DOK

value: human oral mucousa precancerous cell


title: SCC-9 cell input replicate1


title: Control_GadCer_total_2

value: Input


title: Standard_inf_03


title: T cells_KPC-SubQ_Control-2

source_name: T cells_KPC-SubQ_Control-2

value: T cells

value: Female


title: T cells_KPC-SubQ_Control-3

source_name: T cells_KPC-SubQ_Control-3


title: T cells_KPC-SubQ_Control-1

source_name: T cells_KPC-SubQ_Control-1


title: Control_GadCb_IP_1


title: Control_GadCer_total_1


title: Standard_inf_02


title: Standard_inf_01


title: DOK cell input replicate 2


title: DOK cell IP replicate 1


title: Control_GadCer_IP_1


title: Standard_ctr_05

value: uninfected control


title: DOK cell input replicate 1


title: Standard_ctr_04


title: CJD_SST_total_3

value: CJD

value: SST


title: CJD_SST_IP_5


title: CJD_SST_IP_4


title: Standard_ctr_02


title: HOEC cell IP replicate 1

value: oral

value: HOEC

value: Human oral epithelial cell


title: Standard_ctr_03


title: HOEC cell input replicate 2

value: WT


title: Single_worm_inf_05

description:
New
Single_worm_ctr_vs_inf_DE_result.csv

value: wild-type


title: CJD_SST_total_2


title: Standard_ctr_01


title: 96h_plus_4

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: cell line lenvatinib

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: cell line: HuH-7 cells were cultured in low-glucose DMEM supplemented with 10% fetal bovine serum and 100 units/mL penicillin-100 µg/mL streptomycin in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol: RNA samples were extracted from serum using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

treatment_protocol: cell line: HuH-7 cells were treated with 1.0 µM lenvatinib or without lenvatinib for 96 h.

tag: disease status

value: hepatocellular carcinoma


title: NHRI-HN2

city: Miaoli County

first: Ya-Wen

address: 35, Keyan Rd, Zhunan Town

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

description: Gene expression data from total RNA of mouse cell lines

hyb_protocol: Microarray analysis were conducted as followed the standard Affymetrix procedures.

scan_protocol: Hybridized slides were scanned by Affymetrix Gene Chip scanner 3000 7G system.

data_processing: Raw data were generated using Partek Genomics Suite version 7 software.

source_name: Derivation from M2-3 cells by sphere culture

label_protocol: Genome-wide gene expression analysis was performed using the Affymetrix Mouse Clariom S Assay.

growth_protocol: Cells were stably cultured in dishes with DMEM with 10% fetal bovine serum at 37°C in an incubator supplied with 5% CO2.

extract_protocol: Total RNA was extracted using Trizol reagent and purified using RNeasy mini kit.

value: oral cancer cell line


title: HOEC cell input replicate 1

value: none (input)


title: M2-3

source_name: Generation from a mouse tumor induced by 4-nitroquinoline 1-oxide (4-NQO)/arecoline


title: shALKBH3-rep3

city: Shanghai

first: Xiang

last: Gu

address: Zhizaoju Road

institute: shanghai ninth people hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low qualityreads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All thedownstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene wascalculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number ofFragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect ofsequencing depth and gene length for the reads count at the same time, and is currently the most commonlyused method for estimating gene expression levels.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue. < 0.05
GO and KEGG enrichment analysis of differentially expressed genes
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: 92.1 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

value: Ocular melanoma cells

value: ALKBH3 knockdown


title: HOEC cell IP replicate 2

value: m6A-specific antibody (Synaptic Systems, Germany)


title: Single_worm_inf_04

value: infected by P. aeruginosa


title: 96h_plus_2


title: shALKBH3-rep2


title: CJD_SST_IP_2

value: RiboTag


title: Single_worm_inf_03


title: 96h_plus_5


title: shALKBH3-rep1


title: 96h_plus_3


title: M1-2


title: CJD_SST_IP_1


title: CJD_SST_IP_3


title: NHRI-HN1

source_name: Derivation from M1-2 cells by sphere culture


title: Single_worm_inf_02


title: NC-rep3


title: CJD_VglutCb_total_4

value: Input


title: CJD_SST_total_1


title: 96h_minus_4

source_name: cell line control


title: 96h_plus_1


title: CJD_VglutCb_IP_6


title: NC-rep2


title: NC-rep1


title: CJD_VglutCer_IP_6


title: F_B18

city: Grand Rapids

first: Jose

last: Teixeira

address: 400 Monroe Ave NW

institute: Michigan State University

data_processing:
Reads were trimmed for quality and adapters using TrimGalore (version 0.6.5)
Trimmed reads were mapped to Homo sapiens (human) using STAR (version 2.7.9a)
Overlapping Ensembl annotations (version 99)
Analysis was performed using edgeR-robust
Assembly: GRCh38 (hg38)
Supplementary files format and content: txt file with the raw counts per gene

source_name: Uterus

extract_protocol:
Trizol
paired-end (2 × 100 bp) RNA-sequencing on an Illumina NextSeq 6000
Kapa RNA HyperPrep kit with ribosomal re-duction, pooled, and sequenced on flowcells to yield approximately 50–60 million reads/sample.

value: uterus

tag: tissue type

value: Fibroid

tag: race

value: Black


title: CJD_VglutCb_total_3

value: CJD


title: 96h_minus_5


title: 96h_minus_3


title: 96h_minus_2


title: F_B17


title: PBS rep 5

city: Columbus

first: Yuzhou

last: chang

state: OH

address: 1800 Cannon Drive, Lincoln Tower ,

institute: ohio state univeristy

data_processing:
Remove reads containing adapters; Remove reads containing N > 10% (N represents base that could not be determined); Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Filtered reads were mapped to GRCm38 using Hisat2
Alignment files were quantified using featureCounts
Assembly: GRCm38
Supplementary files format and content: Comma-delimited csv files include DEseq2 normalized values for each Sample

source_name: tumor

growth_protocol: MB-49 Bladder Cancer cells (1x10^5) were injected s.c. on the right flank of hLrrc32KI mice.

extract_protocol:
Total RNA was isolated by using RNeasy Kits (Qiagen) and verified by Agulent Bioanalyser
Libraries were prepared using NEBNext Ultra TM RNA Library Prep Kit for Illumina (NEB, USA), following manufacturer’s recommendations.

treatment_protocol: PIIO-1 was delivered (200 ug/mouse, i.p) on day 6 and 9.

value: tumor

value: MB-49 bladder cancer cell

value: Whole tumor

value: hLrrc32 knock-in mice

value: PBS


title: PBS rep 4


title: CJD_VglutCb_IP_5


title: Single_worm_ctr_02

value: wild-type

value: uninfected control


title: 96h_minus_1

value: hepatocellular carcinoma


title: PBS rep 3


title: F_B16


title: CJD_VglutCer_total_3

source_name: Cerebrum


title: Single_worm_ctr_01


title: PBS rep 2


title: F_B15


title: F2_B5


title: CJD_VglutCer_IP_5


title: Single_worm_ctr_04


title: MC0181

city: Rochester

first: Hu

last: Li

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Fastq files were mapped to the UCSC hg19 reference genome using STAR
gene-level counts were obtained from the alignment using HTSeq-count
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene counts for each sample

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) samples were isolated from 15 ml of whole blood before acamprosate treatment using Ficoll density gradient centrifugation. We lysed the cells in Trizol and extracted total RNA using the RNeasy mini kit (Qiagen, Valencia, CA, USA).
RNA-seq experiments were conducted by GENEWIZ using an Illumina HiSeq 4000 with eight samples in each lane using 100bp paired end index reads.

value: PBMC

value: non-relapse


title: PBS rep 1


title: Single_worm_ctr_03


title: MC0275


title: a4D3 rep 5


title: CJD_VglutCb_IP_4


title: MC0367


title: F2_B4


title: CJD_VglutCb_total_2


title: MC0436


title: F1_B4


title: a4D3 rep 3


title: CJD_VglutCer_IP_4


title: a4D3 rep 4


title: CJD_VglutCer_total_2


title: CJD_VglutCb_total_1


title: MC0444


title: a4D3 rep 2


title: F1_B3


title: MC0187


title: F1_B5


title: a4D3 rep 1


title: CJD_VglutCb_IP_3


title: MC0442


title: CJD_VglutCer_total_1


title: Single_worm_ctr_05