title: primary met_TCCC-OS93_RNA-seq

data_processing:
RNA was fragmented, reverse transcribed into cDNA, and ligated with Illumina sequencing adaptors.
The size selection for libraries was analyzed using the DNA 1000 tape Tapestation 4200 (Agilent).
The prepared libraries were pooled and sequenced using NextSeq 500 (Illumina)
The sequenced reads of RNA-seq experiments were aligned to human reference genome hg38/GRCh38 using STAR aligner
Gene expression was determined as fragments per kilobase million (FPKM) by counting the number of uniquely mapping fragments and normalizing it by the length coding sequence and the library size
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes RPKM content for all RNA-seq samples

source_name: osteosarcoma cells from patient-derived xenograft

extract_protocol:
RNA was isolated using RNeasy (QIAGEN) from biopsies of patient derived xenografts
The RNA libraries were prepared and sequenced at the University of Houston Seq-N-Edit Core per standard protocols. RNA libraries were prepared with QIAseq Stranded Total RNA library Kit (Qiagen) using 500 ng input RNA. mRNA was enriched with Oligo-dT probes attached to Pure mRNA beads (Qiagen).

tag: diseased state

value: primary met


title: IGF2BP1 siRNAneg Cntrl matched replicate 3, Cytoplasmic fraction, sequencing round 2

status: Public on Dec 09 2023

type: SRA

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

library_source: transcriptomic

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 (Illumina), CASAVA version 1.8+
Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v2.1, using minimum-length 18, error-rate 0.2, overlap 5, paired-output options.
Trimmed reads were mapped against the GRChr37/hg19 human reference genome modified to include the circRNA spike vector sequence, using the STAR spliced alignment algorithm (version 2.6.1d with default parameters and --chimSegmentMin 20, --quantMode GeneCounts).
Quantification of circRNA abundance was conducted utilising the chimeric junction file produced by the STAR aligner and processed by the CIRCexplorer2 Parse and Annotate functions.
Assembly: GRChr37/hg19
Supplementary files format and content: Tab separated circRNA abundance estimations from CircExplorer2

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: Breast

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 10% (v/v) fetal bovine serum (Gibco) and 1% (v/v) penicillin-streptomycin (Thermo Fisher) at 37°C in a 5% CO2 incubator and routinely tested for mycoplasma contamination

extract_protocol:
Fractionation of cytoplasmic and nuclear RNA was performed using digitonin. cells were washed in ice cold PBS before permeabilised in digitonin solution (50 μg/mL digitonin (MP Biomedicals), 100 mM NaCl, 10 mM Tris, pH 8.0, 40 U/mL RNaseOUT (Invitrogen), 1 x Protease inhibitor cocktail (Roche)) for 15 min on ice. Nuclear and cytoplasmic fractions were separated by centrifugation for 3 min at 1000 g at 4°C. RNA in each fraction was then recovered using RNeasy Mini Kit (Qiagen) according to manufacturer instructions.
Samples were treated with RNase H for ribosomal RNA depletion then purified with RNA beads (Axygen Ampure) following the standard bead clean up protocol. Samples were then treated with RNase R for 15 min at 37°C (0.2 μl RNase R and 2μl 10X buffer, Lucigen) to enrich for circRNA, followed by RNA bead purification (Axygen Ampure). Stranded RNA libraries were made using the KAPA RNA HyperPrep Kit (Roche)

treatment_protocol: Depletions of different factors were induced by reverse transfection using small interfering RNA and DharmaFECT1 transfection reagent (Dharmacon). Cells were harvested 48 hour and 72 hour post-transfection.

tag: tissue

value: Breast

tag: cell line

tag: cell type

value: Epithelial-like, adherent, triple negative breast cancer cell line

tag: treatment

value: Cntrl siRNA


title: primary met_TCCC-OS63_RNA-seq

city: Bryan

first: Irtisha

last: Singh

state: Texas

address: 8447 Riverside Pkwy

department: Cell Biology and Genetics

country: USA

institute: Texas A&M University Health Science Center

molecule: total RNA

value: osteosarcoma cells from patient-derived xenograft


title: BAY_C1_3

type: RNA

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_2_2.txt
Gene expression after 24 h exposure to 2.5 ug/ml of BAY

hyb_protocol: Labeled cRNA samples were hybridised onto the Agilent 2-colour 8x60k arrays according to the manufacturer's recommendations and hybridized for 17 hours at 65°C. After hybridization, slides were washed following the manufacturer's recommendations (Agilent).

scan_protocol: Slides were scanned with Agilent microarray scanner G2505C and data were extracted using the Agilent Feature Extraction software (V12.02.2)

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and data were normalized with quantile normalization. This experiment was performed as a two-colour experiment, but data were analyzed as single-channel arrays. Raw data files are available as a tar archive on the series record.

source_name: THP-1 monocytes differentiated into macrophages, BAY 2.5 ug/ml IC20 replicate 3

label_protocol: Samples were amplified using the T7 RNA polymerase method. cRNAs were labelled with Cy3 or Cy5 following the manufacturer's protocol (Agilent).

growth_protocol: THP-1 cells (ATCC TIB-202) were grown in culture flasks in  RPMI-1640 media ( supplemented with 10% FBS, Gibco). During culturing the cell density was kept below 1x10^6 cells/ml and they were seeded three times before culturing. Cells were PMA differentiated (25 nM) for 48 hours on 12-well plates (150 000 cells/well). After differentiation, media was replaced to RPMI supplemented with 1 % FBS and the cells rested for 24 hours before exposures.

extract_protocol: Cells were harvested and lysed with lysis buffer (Qiagen). Two samples of the same exposure and concentration were pooled together to increase the total amount of RNA. Total RNA was extracted and purified with the Rneasy Mini Kit by Qiagen following the kits' instructions.

treatment_protocol: Stock solution (1 mg /ml for BAY, CHT, MIT, SIG and SES, 0.5 mg/ml for NM400 and NM401) in 1 % FBS RPMI was sonicated in a bath sonicator at RT for 2 x 15 min (BAY, CHT, SIG, SES) or 3 x 15 min (MIT, NM400, NM401) and vortexed and diluted to final concentrations in 1 % FBS RPMI. Dilutions were further vortexed and sonicated for 5 minutes prior to exposure. Cells were exposed to rCNT for 24 hours. Untreated controls had the same treatment without the rCNTs. Exposures were performed as six replicates on two parallel plates for each exposure.

tag: differentiation

value: PMA differentiated macrophage

tag: dose

tag: dose unit

value: µg/ml

tag: exposure time

value: 24 hours

value: BAY

tag: samples prepared

tag: plate

tag: rin


title: BAY_C2_1

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_2_3.txt
Gene expression after 24 h exposure to 1 ug/ml of BAY

source_name: THP-1 monocytes differentiated into macrophages, BAY 1 ug/ml IC10 replicate 1


title: WCE_local_control_TCCC-OS22-WCE

library_source: genomic

data_processing:
followed the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline, first by mapping the sequenced reads to the human reference genome hg38/GRCh38 using the Bowtie2
filtered low-quality, duplicate, multimapping, unmapped reads along with reads mapping to the mitochondrial genome and the blacklisted regions
performed peak calling using MACS2 with a P value threshold of 10^-5
determined the fraction of reads mapping within 2-kb of an annotated promoter as a quality control measure
The H3K27ac heatmaps and metaplots were generated using R Bioconductor package genomation
Assembly: hg38
Supplementary files format and content: bed files containing histone peak calls
Supplementary files format and content: ChiP-seq histone peaks were called using MACS2 with a threshold of p < 10-5

molecule: genomic DNA

extract_protocol:
The chromatin was prepared by Diagenode ChIP-seq/ChIP-qPCR Profiling service using the iDeal ChIP- seq kit for Histones. Chromatin was sheared using Bioruptor® Pico sonication device  combined with the Bioruptor® Water cooler for 8 cycles using a 30’’ [ON] 30’’ [OFF] settings
Libraries were prepared using IP-Star® Compact Automated System from input and ChIP’d DNA using MicroPlex Library Preparation Kit v3.

tag: chip antibody


title: WCE_local_control_TCCC-OS32-WCE


title: TERT_C13_NPC3

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

data_processing:
RNA-seq data quality was monitored via the FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads pre-processing was performed by trim_galore (version 0.6.5-1, https://github.com/FelixKrueger/TrimGalore).
Mapping of RNA-seq reads was done using STAR_2.5.4a (Dobin et al. 2013) with default parameters for RNA-seq data
RSEM software (Li and Dewey 2011) were used to quantify the gene-level expression.
Deseq2  package (http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html) was utilised for differential gene expression analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

source_name: NPC

growth_protocol: hiPSCs were differentiated into spinal motor neuron progenitor cells and spinal motor neurons by treating them with CHIR99021 (4.25 μM) and LDN-193189 (0.5 μM) day 0 to day 10. Retinoic acid (1 μM) was added from day 3 to day 16 to induce caudalization, and purmorphamine (2 μM), a sonic hedgehog (SHH) activator, was added from day 11 to day 16 to promote ventralization. From day 17 onwards (D17 - D28), the cultures were supplemented with brain-derived neurotrophic factor (BDNF) (10 ng/ml), glial cell-derived neurotrophic factor (GDNF) (10 ng/ml), and ascorbic acid (200 μM) to facilitate neuronal maturation. To generate hiPSC-derived astrocytes,hiPSC were treated with neural induction media for 3 days (D0 - D3); N2B27 supplemented with 0.5μM LDN193189 and 4.25μM CHIR99021. On day 3, the neural progenitors were plated at 200,000 cells per well onto matrigel-coated 6-well plates. Media was changed to N2B27 supplemented with 10% FBS, 0.5μM LDN193189, 4.25μM CHIR99021 and 1μM retinoic acid (D3 - D10). On day 10, cells were treated with N2B27 supplemented with 10% FBS, 1μM of retinoic acid, 1μM purmorphamine (D10-D18). On day 18, glial progenitors are treated with media N2B27 supplemented with 10% FBS, 10ng/ml GDNF and 10ng/ml BDNF.

extract_protocol:
RNA from Day 10 NPCs, Day 28 motor neurons and D35 astrocytes was extracted using the RNeasy Mini Kit (Qiagen, Germany, #74104) with RNA clean-up. Day 28 motor neurons were enriched for neurons by magnetic cell sorting using MACS cell separation antibodies, microbeads, and reagents (Miltenyi Biotec) targeting CD171+-PSA+-NCAM+ cells.
The mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

value: NPC

tag: genotype


title: BAY_C3_1

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_1_4.txt
Gene expression after 24 h exposure to 0.5 ug/ml of BAY

source_name: THP-1 monocytes differentiated into macrophages, BAY 0.5 ug/ml IC5 replicate 1


title: P06-2-0h

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: isolated monocytes, anhydrous milk fat shake, baseline (t=0)

data_processing:
Sequencing reads that contained adapters and/or had low quality, aligned to rRNA were filtered off before mapping.
The tool Salmon (version 1.4.0) was used to map the cleaned reads to the GRCh38.p13 human genome assembly-based transcriptome sequences as annotated by the GENCODE consortium (release 37). Salmon parameters used: -i ./salmon_index_H37  --libType A --seqBias --numBiasSamples 10000000 --gcBias --biasSpeedSamp 5 --validateMappings --numGibbsSamples 100
The Salmon-obtained transcript abundance estimates and lengths were imported in R using the package tximport to estimate gene level counts.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table (TxImport.GeneLevel.counts.GEO.txt) with raw gene counts for every gene and every sample (gene level counts were calculated from the Salmon-obtained transcript abundance estimates)
Supplementary files format and content: R-object (txi.counts.annotated.Rdata; exported tximport object) containing gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was not transformed nor scaled (i.e. countsFromAbundance = "no"), and can be used for subsequent analysis in edgeR or DESeq2.
Supplementary files format and content: R object (txi.lengthScaledTPM.annotated.Rdata; exported tximport object) containing scaled gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was scaled using library size and transcript gene length (i.e. countsFromAbundance = "lengthScaledTPM"), and these scaled counts can be used for subsequent analysis in limma (voom function).

source_name: isolated human monocytes, before consumption of a anhydrous milk fat shake

growth_protocol: The human study was a randomized, double-blind crossover intervention trial and aimed at comparing the postprandial effects (6h) of formula vegetable fat (VEGE), anhydrous milk fat (AMF), and anhydrous milk fat plus milk fat globule membranes (CREAM) on the immune response. Participants, males and females, were aged 40–70 years, and had a BMI of 22–27 kg/m2. The study was conducted at Wageningen University, the Netherlands, from 07-01-2020 until 10-03-2020. The experimental protocol and procedures were approved by the Medical Ethical Committee of Wageningen University and were in accordance with the Helsinki Declaration of 1975 as revised in 1983. The study was registered at ClinicalTrials.gov with identifier NCT04178681.

extract_protocol:
At least 500,000 cells were collected from each subject for every intervention and both time points and used for total RNA isolation using a RNeasy Micro Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. RNA concentration was measured with a Nanodrop 1000 spectrometer and RNA integrity was determined using an Agilent 2100 Bioanalyzer with RNA 6000 microchips (Agilent Technologies).
Library construction and RNA sequencing on BGISEQ-500 were conducted at Beijing Genomics Institute (BGI) for pair-end 150bp runs. At BGI, Genomic DNA was removed with two digestions using Amplification grade DNAse I (Invitrogen). The RNA was sheared and reverse transcribed using random primers to obtain cDNA, which was used for library construction. The library quality was determined by using Bioanalyzer 2100 (Agilent Technologies). Then, the library was used for sequencing with the sequencing platform BGISEQ-500 (BGI).

treatment_protocol: The three intervention fat shakes were supplied by FrieslandCampina. Shake VEGE (vegetable-sourced lipids) is based on the vegetable lipid formula used in infant formula. To form the VEGE and anhydrous milk fat (AMF) shakes, 118g of the respective powdered formulas were mixed with 500mL skim milk, whereas for the CREAM shake 461mL skim milk plus 39mL water were added. Except for the presence of milk fat globule membranes (MFGM), shake AMF and shake CREAM contained the same milk-sourced lipids. All shakes contained 95g of fat, 21g of protein, and 42g of carbohydrates and provided slighly over 4600kJ. Forty participants were given three different shakes on three different days. There was at least one week for washout between interventions. On the test day, subjects arrived fasted, and the concentration of C-reactive protein (CRP) in the blood was determined via a finger prick using a QuickRead CRP test (Orion Diagnostica Oy) before any blood was collected. When the CRP concentration was below 10.0 mg/L, participants were qualified for the study, and a catheter cannula was inserted in an antecubital vein. After a 30-minute rest, fasted blood was drawn into EDTA-containing tubes to obtain a baseline (t=0h) sample. Subjects were then asked to consume a shake within 10 min. Blood was drawn again 6h post-shake consumption. Each subject consumed all three shakes in a randomized order. Whole blood was collected in CPT tubes, mixed by inverting, and centrifuged at room temperature for 20m at 1800RCF. The white cloudy cell layer was collected for PBMC purification. Cells were washed with cold PBS three times, and monocytes were isolated by MojoSort CD14 negative selection kits (Biolegend, California, United States) and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany).

value: isolated monocytes

tag: subjectid

tag: shakeid

tag: shake description

value: AMF

tag: sampling time (h)

tag: Sex

value: male

tag: age (yrs)

tag: bmi (kg/m2)


title: primary met_TCCC-OS54_RNA-seq

tag: cell type

tag: diseased state


title: P06-1-6h

description: isolated monocytes, vegetable fat shake, 6h after consumption

source_name: isolated human monocytes, 6h after consumption of a vegetable fat shake

value: VEGE


title: TERT_C13_NPC2


title: BAY_C1_2

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_1_3.txt
Gene expression after 24 h exposure to 2.5 ug/ml of BAY

source_name: THP-1 monocytes differentiated into macrophages, BAY 2.5 ug/ml IC20 replicate 2

tag: cell line

tag: differentiation

tag: dose

tag: treatment


title: histone_primary_met_TCCC-OS93-H3K27ac

value: H3K27ac (Diagenode C15410196)


title: TERT_C13_NPC1


title: P06-1-0h

description: isolated monocytes, vegetable fat shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a vegetable fat shake


title: lung met_TCCC-OS84_RNA-seq

value: lung met


title: primary met_TCCC-OS14_RNA-seq


title: BAY_C1_1

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_2_1.txt
Gene expression after 24 h exposure to 2.5 ug/ml of BAY

source_name: THP-1 monocytes differentiated into macrophages, BAY 2.5 ug/ml IC20 replicate 1

tag: dose unit

tag: exposure time

tag: samples prepared

tag: plate


title: histone_primary_met_TCCC-OS63-H3K27ac

tag: chip antibody


title: histone_primary_met_TCCC-OS54-H3K27ac


title: P05-3-6h

description: isolated monocytes, milk fat globule membrane shake, 6h after consumption

source_name: isolated human monocytes, 6h after consumption of a milk fat globule membrane shake

tag: subjectid

tag: shakeid

value: CREAM

value: female


title: lung met_TCCC-OS45_RNA-seq


title: histone_primary_met_TCCC-OS14-H3K27ac


title: WT_CTRL_NPC3

tag: genotype

value: WT


title: P05-2-0h

tag: shake description

tag: sampling time (h)

tag: Sex


title: localized_TCCC-OS94_RNA-seq

tag: cell type

value: localized


title: histone_lung_met_TCCC-OS84-H3K27ac

tag: diseased state


title: TERT_C16_MN2

source_name: Motor neuron

value: Motor neuron


title: localized_TCCC-OS75_RNA-seq

value: osteosarcoma cells from patient-derived xenograft


title: histone_lung_met_TCCC-OS45-H3K27ac


title: WT_CTRL_NPC2


title: P05-1-6h

tag: age (yrs)

tag: bmi (kg/m2)


title: histone_localized_TCCC-OS94-H3K27ac


title: localized_TCCC-OS57_RNA-seq


title: TERT_C16_MN1


title: local control_TCCC-OS74_RNA-seq

value: local control


title: histone_localized_TCCC-OS75-H3K27ac


title: P02-3-6h


title: local control_TCCC-OS73_RNA-seq


title: WT_CTRL_MN3


title: P02-3-0h

description: isolated monocytes, milk fat globule membrane shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a milk fat globule membrane shake


title: P05-3-0h


title: WT_CTRL_MN2


title: histone_local_control_TCCC-OS74-H3K27ac


title: P02-2-6h

description: isolated monocytes, anhydrous milk fat shake, 6h after consumption

source_name: isolated human monocytes, 6h after consumption of a anhydrous milk fat shake


title: TERT_C16_MN3


title: local control_TCCC-OS32_RNA-seq


title: local control_TCCC-OS22_RNA-seq


title: histone_local_control_TCCC-OS73-H3K27ac


title: TERT_C16_NPC3


title: P02-1-6h


title: histone_local_control_TCCC-OS32-H3K27ac


title: TERT_C16_NPC2


title: P02-1-0h


title: P05-1-0h


title: histone_local_control_TCCC-OS22-H3K27ac


title: plasma, PCH patient 3

city: Suzhou

first: jingyi

last: xu

state: Jiangsu

address: No. 242, Guangji Road, Suzhou City

country: China

institute: The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical Universit

data_processing:
Raw sequencing data generated form Illumina NextSeq 500 that pass the Illumina chastity filter are used to the following analysis.
Trimmed reads (trimmed 5’, 3’-adaptor bases) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
Based on alignment statistical analysis (mapping ratio, read length, fragment sequence bias), we determine whether the results can be used for subsequent data analysis. If so, the expression profiling and differentially expressed tsRNAs are calculated.
Principal Component Analysis (PCA), Venn plots, Pie plots, Scatter plots and Volcano plots are performed for the expressed tsRNAs in R or Perl environment for statistical computing and graphics.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: plasma

growth_protocol: 5 mL plasma was taken using EDTA vacuum anticoagulant blood vessels from the two groups just before treatment initiation. The blood samples were centrifuged at 1000 g for 10 min (4˚C), and then the plasma samples were collected and stored in the -80˚C fridge.

extract_protocol:
The total RNA was extracted with Trizol following the manufacturer’s instructions. 1-2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared following manufacturer's protocols.Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter.  The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100.

treatment_protocol: Plasma was sequenced within 2 weeks of collection.

tag: tissue

value: plasma

tag: disease state

value: concentric cardiomyocyte hypertrophy

tag: age


title: TERT_C16_NPC1


title: WT_CTRL_NPC1


title: histone_localized_TCCC-OS57-H3K27ac


title: primary_met_TCCC-OS93-ATAC

data_processing:
followed the ENCODE ATAC-seq pipeline
mapped the sequenced reads to the human reference genome hg38/GRCh38 using the Bowtie2
filtered low-quality, duplicate, multimapping, unmapped reads along with reads mapping to the mitochondrial genome and the blacklisted regions
performed peak calling using MACS2 with a P value threshold of 10−5
The chromatin accessibility heatmaps and metaplots were generated using R Bioconductor package genomation
Assembly: hg38
Supplementary files format and content: bed files containing peak calls corresponding to regions of open chromatin
Supplementary files format and content: performed peak calling using MACS2 with a P value threshold of 10−5

extract_protocol:
Conducted by Diagenode ATAC-seq Profiling service. 8.9-26.7 mg of tissue were chopped into small pieces (between 1-3 mm3) using a scalpel blade, homogenized with a Dounce homogenizer and precleared by filtration through a 40μm Nylon cell strainer (Corning). Nuclei were then isolated on an iodixanol gradient and counted. 5-50 counted nuclei were transferred to a new tube and were centrifuged at 500g. The nuclei isolation was optimized on 11 mg of tissue. Isolated nuclei from Mouse PDX (Human) snap frozen tissues using 0.1% of Igepal CA-630 in the lysis buffer.
Isolated nuclei were lysed and transposed for 30 minutes at 37°c using kit, Illumina, FC-121–1030. Transposed DNA was then purified on Diapure columns (Diagenode), Transposed purified DNA was then pre-amplified for 5 PCR Cycles using NEBNext High-Fidelity PCR MasterMix (NEB, M0541) and Illumina indexing primers. After the amplification, the libraries were size selected then purified using AMPure beads and eluted in Tris pH7.5-8.0. The purified libraries were quantified using the Qubit ds DNA HS kit.


title: plasma, PCH patient 1


title: BPR-ADU-S100-3

city: Pittsburgh

first: Jessica

last: Filderman

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

data_processing: NanoString

organism: Mus musculus

source_name: BPR (BRAFV600E Pten-/-) murine melanoma

extract_protocol: Resected tumors were enzymatically dissociated into single-cell suspensions and then frozen in RLT buffer at -80C. RNA was isolated from the cell lysates using the RNEasy Micro Plus Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Female C57Bl/6J mice (6-8 weeks old) were purchased from Jackson Laboratory (Bar Harbor, Maine, USA). Mice were injected subcutaneously (s.c.) in the right flank with  3.5 x 10^5 BPR20 melanoma cells in 100 uL of PBS and allowed to establish solid tumors. After ~10 days (as indicated in text), palpable tumors were measured with calipers and mice were randomized into treatment groups with comparable mean tumor sizes. Mice were then injected intratumorally (i.t.) with sterile phosphate-buffered saline (PBS) or 5 ug of endotoxin-free ADU-S100 (Cat. No: HY-12885B, MedChemExpress) resuspended in 50 ul of sterile PBS. Repeat injections were administered 4 days later. Where indicated, mice were additionally dosed by oral gavage with 0.3 mg CB1158, 0.3 mg L-NMMA, and 1.2 mg celecoxib in a 20% Kolliphor solution for 5 days beginning on day 1 of treatment.

tag: treatment

value: BPR

value: melanoma


title: primary_met_TCCC-OS63-ATAC

source_name: osteosarcoma cells from patient-derived xenograft


title: WT_CTRL_ASTR3

source_name: Astrocyte

value: Astrocyte


title: P02-2-0h

value: isolated monocytes

value: AMF


title: BPR-ADU-S100-1


title: BPR-ADU-S100-2


title: plasma, healthy control 4

value: healthy

value: male


title: primary_met_TCCC-OS54-ATAC


title: WT_CTRL_ASTR2


title: TERT_C16_ASTR3


title: plasma, healthy control 3


title: plasma, PCH patient 4


title: BPR-PBS-3

value: PBS


title: plasma, healthy control 2


title: TERT_C13_ASTR3


title: BPR-PBS-2


title: WT_CTRL_MN1


title: TERT_C16_ASTR2


title: TERT_C13_ASTR2


title: localized_TCCC-OS94-ATAC


title: BPR-PBS-1


title: localized_TCCC-OS75-ATAC


title: localized_TCCC-OS57-ATAC


title: F3-800um, replicate 3, MeDIPSeq

city: Nanjing

first: Mingkuan

last: Sun

state: jiangsu

address: 101 Longmian Ave

institute: Nanjing Medical University

data_processing:
High quality reads (Raw Data) were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. cutadapt software was used to for adaptor-trimming, low quality reads removing. After adaptor trimming, clean reads were aligned to the reference genome using BOWTIE software (V2.1.0) with default parameters. Peak calling was performed by MACS1.4 software. Differentially methylated regions (DMRs) were identified by diffReps software. The enriched peaks and DMRs were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation. And the enriched peaks were visualized on UCSC Genome Browser.
Assembly: dm6
Supplementary files format and content: bed files includes methylation peaks for each sample

organism: Drosophila melanogaster

source_name: adult head

extract_protocol:
Genomic DNA was extracted using a DNeasy kit (QIAGEN Inc., Germany).
Genomic DNA was sonicated to 100–300 bp.Adaptors were ligated to genomic DNA fragments following the Illumina protocol (Illumina, Inc., USA). A portion of ligated DNA (10%) was kept as input, and the remaining ligated DNA was immunoprecipitated using the GenSeq® 5 mC MeDIP kit (GenSeq Inc., China) following the manufacturer’s instructions.

value: adult head


title: B16-ADU-S100-3

source_name: B16.F10 murine melanoma


title: B16-ADU-S100-2


title: plasma, PCH patient 2


title: plasma, healthy control 1


title: Fibroblasts - 18GM00141

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2018_1 were also provide

source_name: Skin biopsy

growth_protocol: Primary explant cultures were established in 75 cm2 culture flasks in MEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a 5% CO2 atmosphere

extract_protocol:
Total RNA was extracted by a classical phenol-chloroform extraction protocol
Total RNA was captured using TruSeq Stranded Total RNA with Ribo-Zero Gold - Illumina

treatment_protocol: No treatment

value: Skin fibroblasts

value: M

value: healthy individual


title: F3-800um, replicate 1, MeDIPSeq

value: WT


title: local_control_TCCC-OS73-ATAC

value: osteosarcoma cells from patient-derived xenograft


title: lung_met_TCCC-OS84-ATAC


title: Fibroblasts - 18GM00140

value: F


title: F3-800um, replicate 2, MeDIPSeq


title: Fibroblasts - 18GM00139


title: local_control_TCCC-OS32-ATAC


title: F3-0um, replicate 2, MeDIPSeq


title: lung_met_TCCC-OS45-ATAC


title: F3-0um, replicate 3, MeDIPSeq


title: local_control_TCCC-OS22-ATAC


title: B16-PBS-3


title: F3-0um, replicate 1, MeDIPSeq


title: B16-PBS-2


title: MEEC+rJAG1+RO.3 RNA

status: Public on Dec 08 2023

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

data_processing:
Sequencing reads were pre-processed using FastQC and Cutadapt to remove Illumina adapter contamination.
Resulting reads were mapped against reference transcriptome GRCm38.91 and quantified using RSEM.
Expected expression counts calculated with RSEM were then processed with the Bioconductor package Limma for normalization (using TMM method).
Assembly: GRCm38.91
Supplementary files format and content: Normalized counts (TMM method) in each sample, for genes with at least 1 CPM in at least 3 samples.

source_name: MEEC

growth_protocol: MEECs were cultured on 0.1% gelatin-coated dishes and maintained in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. GFP-, Jag1- or Dll4-expressing OP9 cells were cultured on 0.1% gelatin-coated dishes and maintained in MEM Alpha (1X) supplemented with 20% FBS and 1% penicillin/streptomycin. Cultures were incubated at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA from cells was extracted with the PicoPure RNA Isolation Kit (ThermoFisher)
Total RNA was used to generate barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs)

treatment_protocol:
Co-culture with OP9 cells: To define the effect of Dll4- and Jag1-mediated cell-to-cell signaling, MEECs were co-cultured for 6h (50% confluency) and 24h (25% confluency) over GFP-, Jag1- or Dll4-expressing OP9 cells at 90% confluence. To define the effect of NICD nuclear translocation inhibition, MEECS were cultured with DMSO (vehicle) or 20 μM of the γ-secretase inhibitor RO4929097 for 24 h. Next, MEECs were co-cultured for 6h (50% confluency) over GFP-expressing OP9 cells at 90% confluence.
Culture with Recombinant Ligands: Recombinant NOTCH ligands DLL4-His (R&D Systems 1389-D4-050) and JAG1-Fc (R&D Systems 599-JG-100) were attached to 24 x well dishes as described in (Torregrosa-Carrión et al., 2019). Once MEEC were seeded, DMSO was added to control and recombinant-ligand stimulated cells, and 20 μM RO4929097 (Selleck Chemicals S1575) to inhibit Notch activity. After 24 h at 37 °C, cells were washed twice with PBS and incubated for an additional 14 h in serum-free DMEM together with RO4929097 or DMSO as appropriate.

tag: cell line

value: MEEC

value: Mouse embryonic endocardial cells

value: culture over rJAG1 with RO4929097

tag: time

value: 38 hours


title: B16-ADU-S100-1

value: melanoma


title: B16-PBS-1


title: Fibroblasts - 18GM00142

value: ID-ASD patient


title: MEEC+rDLL4+RO.2 RNA

value: culture over rDLL4 with RO4929097


title: MEEC+rDLL4+RO.3 RNA


title: MEEC+rDLL4+RO.1 RNA


title: MEEC+DMSO.2 RNA

value: culture with DMSO


title: MEEC+rJAG1.3 RNA

value: culture over rJAG1


title: MEEC+rJAG1+RO.1 RNA


title: MEEC+rJAG1.2 RNA


title: MEEC+rDLL4.2 RNA

value: culture over rDLL4


title: MEEC+rDLL4.1 RNA


title: MEEC+rDLL4.3 RNA


title: MEEC+DMSO.1 RNA


title: MEEC+OP9-GFP+RO_6h.3 RNA

value: coculture with OP9-GFP cells and RO4929097

value: 6 hours


title: MEEC+OP9-GFP+RO_6h.4 RNA


title: MEEC+OP9-GFP+RO_6h.2 RNA


title: MEEC+OP9-GFP+DMSO_6h.3 RNA

value: coculture with OP9-GFP cells and DMSO


title: MEEC+OP9-GFP+DMSO_6h.2 RNA


title: MEEC+rJAG1+RO.2 RNA


title: MEEC+OP9-GFP+DMSO_6h.4 RNA


title: MEEC+OP9-GFP+RO_6h.1 RNA


title: MEEC+OP9-GFP+DMSO_6h.1 RNA


title: MEEC+rJAG1.1 RNA


title: MEEC+DMSO.3 RNA


title: fibro_CYS1_1 [NormalCDME_F]

city: San Francisco

first: Swastika

last: Sur

state: CA

address: 513 Parnassus Ave

department: Surgery

institute: UCSF

description: In vitro system

hyb_protocol: Hybridization of samples was conducted on Agilent Whole Human Genome 4×44-k 60-mer oligonucleotide arrays (G4112F, Agilent Technologies), using 150ng of total RNA as template/sample.

scan_protocol: The arrays were scanned on an Agilent scanner and further processed using Agilent Feature Extraction Software (Agilent Technologies).

data_processing:
Agilent array data were processed and normalized using LOWESS in Gene Spring GX7.3 (Agilent Technologies).
The LOWESS normalized data were further analyzed using significance analysis of microarrays (SAM) for two-class unpaired data to detect expression differences based on q-values (<5%).45 The input for SAM was gene expression measurements from a set of microarray experiments, as well as a response variable from each experiment. SAM used simple median centering of the arrays is an unbiased statistical technique for finding significant genes in a set of microarray experiments. SAM uses repeated permutations of the data to determine whether the expression of each gene is significantly related to the response. Significance levels were set at a q-value of 5%. We used a cutoff of the absolute value of log2 red channel/green channel >0.5. Data were analyzed using GraphPad Prism software.  P-values were calculated using Student's t-test or One-way ANOVA and Tuckey’ test. Results were expressed as mean ± SD (number of experiments) and considered to be statistically significant when P < 0.05.

source_name: Skin Fibroblasts

label_protocol: Cy5 label was used for all the samples whereas C3 was used to label universal RNA control

growth_protocol: Human RPTECs and fibroblasts were isolated from 8 unique individuals with a biochemically, clinically and genetically confirmed diagnosis of nephropathic cystinosis (provided by Dr. Gahl); in addition, similar cell types, RPTEC (Cambrex Biosciences) and fibroblast (Coriell Cell Repositories) cell lines were commercially obtained as normal control cells.  All RPTECs were cultured in renal epithelial growth medium (REGM) (Lonza); fibroblast cells were cultured in Minimum Essential Media (MEM) with Earl’s salts, supplemented with 15% FBS, 2mM L- glutamine, 2X conc. of  non-essential AA, 100 μg/ml Penicillin, 100 U/ml Streptomycin and 0.5 μg/ml Fungizone (Invitrogen Corporation, Carlsbad, CA) at 37°C in a 5% CO2 atmosphere. The medium was changed every alternate day, and cultured cells were harvested with 0.05% Trypsin/EDTA (Lonza) and passaged. All cells were cultured in a 95% air/5% CO2 Thermo Forma incubator (Waltham, MA) at 37°C. All the experiments were performed between passage numbers 2-5.

extract_protocol: Cells were grown until 70-80% confluence and processed for total RNA extraction using RNeasy Midi Kit® (Qiagen Inc.). Total RNA concentration was measured by NanoDrop® ND-1000 (NanoDrop Technologies) and the integrity of the extracted total RNA was assessed with the Agilent 2100 Bioanalyzer using RNA Nano Chips (Agilent Technologies). Total RNA was stored at -80°C until preparation for the microarray experiments.

treatment_protocol: Both normal RPTECs and fibroblasts were treated with cysteine dimethyl ester (CDME) to artificially load lysosomes with cystine, as this method has been used previously as a disease model for cystine RPTEC loading. For CDME loading, cells were treated with 1mM CDME (Sigma-Aldrich) for 30 min.

tag: cells

value: Fibroblasts

tag: biosource

value: Skin

source_name: Universal RNA from Agilent

tag: tag

value: Mixture of human cell lines

value: universal RNA


title: fibro_CYS2_2 [NormalCDME_F]

description: In vitro system


title: fibro_CYS2_1 [NormalCDME_F]

description: In vitro system


title: fibro_CYS1_2 [NormalCDME_F]

description: In vitro system


title: FibroN2_1 [Normal_F]

description: In vitro system


title: CF3 [Cystinosis_F]

description: In vitro system


title: CF6 [Cystinosis_F]

description: In vitro system


title: fibro1 [Normal_F]

description: In vitro system


title: FibroN1_1 [Normal_F]

description: In vitro system


title: CF8 [Cystinosis_F]

description: In vitro system


title: FibroN1_2 [Normal_F]

description: In vitro system


title: CF5 [Cystinosis_F]

description: In vitro system


title: RPTE7 [Cystinosis_R]

description: In vitro system

source_name: Renal Proximal Tubular Epithelial Cells from Urine

value: RPTEC

value: Urine


title: RPTE5 [Cystinosis_R]

description: In vitro system


title: fibro2 [Normal_F]

description: In vitro system


title: RPTE_CYS2_1 [NormalCDME_R]

description: In vitro system


title: CF7 [Cystinosis_F]

description: In vitro system


title: CF1 [Cystinosis_F]

description: In vitro system


title: RPTE4 [Cystinosis_R]

description: In vitro system


title: FibroN2_2 [Normal_F]

description: In vitro system


title: CF2 [Cystinosis_F]

description: In vitro system


title: RPTE8 [Cystinosis_R]

description: In vitro system


title: RPTE3 [Cystinosis_R]

description: In vitro system


title: CF4 [Cystinosis_F]

description: In vitro system


title: RPTE_CYS1_2 [NormalCDME_R]

description: In vitro system


title: RPTE_CYS1_1 [NormalCDME_R]

description: In vitro system


title: RPTE6 [Cystinosis_R]

description: In vitro system


title: RPTE1 [Cystinosis_R]

description: In vitro system


title: MCviPI_FFA_3

type: genomic

city: Wilrijk

first: Claudia

last: Theys

state: Antwerpen (nl)

department: FBD

country: Belgium

institute: Universiteit Antwerpen

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

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

data_processing: Raw intensity data from IDAT files was read and processed in R (v. 4.2.0) via the minfi R package. Data pre-processing consisted of masking probes with poor design, control probes, X-/Y chromosome probes and non-cg and non-ch probes. For quality control, the ratio of log2 median intensities (methylated and unmethylated) along with β-value densities, were calculated. β-values were then further processed using ChAMP (v 2.21.1). The difference in signal intensity between the two-colour channels (dye bias correction) was corrected for using the beta mixture interquartile matrix (BMIQ) method.

label: Cy3, Cy5

source_name: HepG2 cells

label_protocol: Standard Illumina Protocol

growth_protocol: The Human hepatoma cells (HepG2) cell lines overexpressing mitochondria targeted DNMTs MCviPI or inactivated MCviPI (MCviPI mutant) were cultured in Dulbecco’s modified Eagle medium (DMEM, Gibco, Thermo Fisher Scientific, 41965039) supplemented with 10% foetal bovine serum (Gibco, Thermo Fisher Scientific, 10270106), 1% penicillin-streptomycin solution (Gibco, Thermo Fisher Scientific, 15140122) and 1mM pyruvate. Both cell lines were cultured in T75 or T25 flasks in a humidified atmosphere (37°C and 5% CO2).

extract_protocol: Genomic DNA was extracted and purified from fresh cell pellets using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: 24h treatment with 1mM FFA (Oleic acid and palmitic acid in a 2:1 ratio)

tag: genotype

value: MCviPI overexpressing

tag: cel type

value: FFA treatment

tag: replicate

value: biological replicate 3


title: RPTE2 [Cystinosis_R]

description: In vitro system


title: RPTE_CYS2_2 [NormalCDME_R]

description: In vitro system


title: MCviPI_FFA_2

value: biological replicate 2,


title: MCviPI_2

value: biological replicate 2


title: Mutant_FFA_3

value: MCviPI mutant overexpressing


title: MCviPI_3


title: MCviPI_FFA_1

value: biological replicate 1


title: Mutant_FFA_1


title: MCviPI_1


title: RPTEN2_2 [Normal_R]

description: In vitro system


title: RPTEN2_1 [Normal_R]

description: In vitro system


title: RPTE2_2 [Normal_R]

description: In vitro system


title: Mutant_1


title: RPTEN1_1 [Normal_R]

description: In vitro system


title: Control mouse 1; skin

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

data_processing:
The raw reads were processed with Ion Torrent RNASEQAnalysis pipeline (Torrent Suite version 5.0.4)
htseq-count, version 0.6.0, default parameters
DESeq2, version 1.18.1, normalization
Assembly: AmpliSeq Mouse Transcriptome v1
Supplementary files format and content: htseq normalized count

source_name: adjacent skin

extract_protocol:
Collected tissue samples were snap-frozen in liquid nitrogen and stored at -80°C  prior to analysis. For RNA isolation, the samples were homogenized in Fenozol (A&A Biotechnology, Gdansk, Polska) using a tissue homogenizer (OMNI International, Kennesaw, GA, USA).
Library was prepared using Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit according to the manufacturer’s protocol (Thermo Fisher Scientific)

treatment_protocol: Control and myeloid-deficient Mcpip1MKO mice were subjected to the 7,12-dimethylbenz[a]-anthracene (DMBA)/12-O-tetradecanoylphorbol-13-acetate (TPA) tumor induction regimen for 18 weeks.

value: adjacent skin

value: DMBA/TPA


title: Control mouse 4; skin


title: Control mouse 2; skin


title: Control mouse 2; papilloma

source_name: papilloma

value: papilloma


title: Control mouse 4; papilloma


title: Control mouse 1; papilloma


title: RPTEN1_2 [Normal_R]

description: In vitro system


title: UCB, DMSO, replicate 2

city: Philadelphia

first: Peter

middle: S

last: Klein

address: 3400 Civic Center Blvd

department: Medicine

institute: University of Pennsylvania School of Medicine

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation steps were carried out with Cell Ranger software (10xGenomics).
Assembly: hg38
Supplementary files format and content: Tab separated values files and matrix files

source_name: umbilical cord blood

growth_protocol: Human CD34+CD38-CD45RA-CD90+ cells from UCB were cultured for 2 days in StemSpan SFEM with vehicle (DMSO), CR, or CRCY. Freshly thawed cells (Day 0) and cultured cells were subjected to scRNA-seq per 10X Genomics as above.

extract_protocol:
described in detail above
Library was prepared according to 10XGenomics User's Guide using Chromium Single Cell 3' Reagent Kits v3 (10X Genomics). Library was prepared by the Center for Applied Genomics, Childrens' Hospital of Philadelphia.

treatment_protocol: See above.

value: umbilical cord blood

value: primary cells

value: hematopoietic

value: normal control

value: vehicle (DMSO) 2 days


title: UCB, Uncultured, replicate 2

value: uncultured


title: RPTE1_2 [Normal_R]

description: In vitro system

value: RPTEC

value: Urine

value: Mixture of human cell lines

value: universal RNA


title: Mcpip1(MKO) mouse 3;  skin


title: Mutant_FFA_2

value: FFA treatment


title: Mutant_3

value: biological replicate 3


title: UCB, CR, replicate 2

value: CR 2 days


title: UCB, CRCY, replicate 2

value: CRCY 2 days


title: Control mouse 3; skin

value: adjacent skin


title: Mcpip1(MKO) mouse 2;  skin

value: DMBA/TPA


title: UCB, Uncultured, replicate 1


title: UCB, CRCY, replicate 1


title: Mcpip1(MKO) mouse 4;  nevi.

source_name: melanocytic nevi

value: melanocytic nevi


title: Mcpip1(MKO) mouse 1;  skin


title: Control mouse 3; papilloma

value: papilloma


title: UCB, CR, replicate 1

value: umbilical cord blood

value: primary cells


title: Mcpip1(MKO) mouse 2;  nevi.


title: Mcpip1(MKO) mouse 3;  nevi.


title: Mutant_2

value: MCviPI mutant overexpressing

value: biological replicate 2


title: P195_Pre_Mosun

first: Andrei

last: Thomas-Tikhonenko

address: 3501 Civic Center Blvd, CTRB 4056

department: Children's Hospital of Philadelphia

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
RNA sequencing (RNA-seq) reads were first trimmed to remove adapters (BBTools version 38.96) and then aligned using STAR version 2.7.9a to the hg38 reference genome while providingQ18 known gene isoforms through the GENCODE annotation V32. In addition, we used STAR flags “–quantMode GeneCounts” and “–alignSJoverhangMin 8” to quantify genes and ensure that spliced reads had an overhang of at least 8 bases.
Junctionspanning reads were obtained from the STAR “*_SJ.out.tab” result files, and each entry was normalized by dividing by the total number of junction-spanning reads and multiplying by a factor of 1 million to obtain the junctions per million. Visualization and downstream analyses were conducted via R using the ggplot2 and tidyverse packages.
Transcripts per million (TPMs) for all samples were calculated using TPMCalculator42 version 0.0.3, followed by ComBat-seq43 batch correction as implemented in the R Bioconductor package sva (version 3.42.0).
Assembly: hg38
Supplementary files format and content: FFPE_samples_raw_read_counts.csv holds the raw gene counts for each sample

molecule: polyA RNA

source_name: Skin, Punch biopsy L medial knee

extract_protocol:
RNA was isolated using the Agencourt FormaPure Kit (Beckman Coulter LifeSciences, Indianapolis, IN)
Sequencing libraries were prepared using 100ng of RNA and the TruSeq RNA Exome kit (Illumina, Inc., San Diego, CA)

value: Skin, Punch biopsy L medial knee

tag: individual

value: DLBCL

value: B-NHL


title: P195_Post_Mosun

source_name: Skin, Punch Biopsy, Left Chest

value: Skin, Punch Biopsy, Left Chest

tag: cell type


title: P100_Post_Mosun

source_name: Lymph node, left cervical, core biopsy

value: Lymph node, left cervical, core biopsy

value: Follicular lymphoma


title: P100_Pre_Mosun

source_name: "Left back mass", excision.

value: "Left back mass", excision.


title: Mcpip1(MKO) mouse 4;  skin


title: GFP iCLIP2 biol rep 3

city: Oeiras

first: Tom

last: Laloum

address: Rua da Quinta Grande, 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

data_processing:
Reads were demultiplexed and sequencing adapters removed using Flexbar (3.5.0). Reads were then quality- and length-trimmed with Flexbar. A genome index was created using STAR (2.7.3a) with the Arabidopsis thaliana genome version TAIR10 and gene annotation from Araport (version 11). Reads were then mapped using STAR and the created genome index, allowing only softclipping of 3’ ends (--alignEndsType Extend5pOfRead1). PCR duplicates were removed using umi_tools (1.1.4). The uniquely mapped and deduplicated reads from each replicate were merged and peak called with PureCLIP (1.3.1) in standard mode.
Assembly: TAIR10
Supplementary files format and content: Bedgraph files for visualisation of iCLIP2 peaks using a genome viewer software
Library strategy: iCLIP2

organism: Arabidopsis thaliana

source_name: Pool of 44h germinated seeds treated during 2h with ABA or control

growth_protocol: Stratified seeds were grown on MS medium in continuous white light  (100 µmol/m2) at 21 ºC for 44h

extract_protocol:
Germinated seed tissues were UV-crosslinked (2000 mJ/cm2), frozen in liquid N2 and ground to a homogeneous powder before cell lysis. SR34a-GFP-RNA and GFP-RNA complexes were precipitated using GFP-trap agarose beads (Chromotek). After 3' end RNA linker ligation and 5'end radiolabelling, RNA-protein complexes were run on an SDS gel, transferred on a nitrocellulose membrane, and revealed by autoradiography. After a proteinase K treatment, protein-bound RNA was purified using phenol-chloroform and concentrated with the RNA Clean and Concentrator kit (Zymo Research, R1013).
Library preparation was performed exactly as in Buchbender et al., 2019 (doi:10.1016/j.ymeth.2019.10.003). Purified RNAs were reverse transcribed and 5' adaptors were ligated to the subsequent cDNAs. cDNAs were then PCR-amplified. 10 nM of each library was submitted to sequencing using the NextSeq 500 system (Illumina).

treatment_protocol: 44h germinated seeds from promSR34a:SR34a-GFP sr34a-1  were transferred to MS medium (Control) or MS medium supplemented with 0.5 µM ABA during 2h. 44h germinated seeds from prom35S:GFP sr34a-1 were transferred to MS medium (Control) or MS medium supplemented with 0.5 µM ABA during 2h and pooled together before iCLIP2.

value: prom35S:GFP in sr34a-1

value: Mix Control and ABA 0.5 µM


title: GFP iCLIP2 biol rep 2

value: Pool of 44h germinated seeds treated during 2h with ABA or control


title: GFP iCLIP2 biol rep 1


title: P73_Post_Mosun

source_name: Superior mediastinal lymph node, biopsy

value: Superior mediastinal lymph node, biopsy


title: P73_Pre_Mosun

source_name: Right neck mass, excisional biopsy

value: Right neck mass, excisional biopsy


title: SR34a-GFP iCLIP2 ABA biol rep 3

source_name: 44h germinated seeds + 2h ABA treatment

value: 44h germinated seeds + 2h ABA treatment

value: promSR34a:SR34a-GFP in sr34a-1

value: ABA 0.5 µM


title: SR34a-GFP iCLIP2 ABA biol rep 2


title: P29_Post_Mosun

source_name: Lymph node, left cervical, core biopsy.

value: Lymph node, left cervical, core biopsy.


title: SR34a-GFP iCLIP2 ABA biol rep 1


title: P29_Pre_Mosun

source_name: Lymph node, right deep jugular, excisional biopsy


title: SR34a-GFP iCLIP2 Control biol rep 3

source_name: 44h germinated seeds + 2h mock treatment

value: Control


title: UCB, DMSO, replicate 1

value: umbilical cord blood

value: primary cells

value: hematopoietic

value: normal control

value: vehicle (DMSO) 2 days


title: SR34a-GFP iCLIP2 Control biol rep 2

value: 44h germinated seeds + 2h mock treatment


title: SR34a-GFP iCLIP2 Control biol rep 1


title: Mcpip1(MKO) mouse 1;  nevi.

value: melanocytic nevi

value: DMBA/TPA


title: Jurkat-DMSO-3

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

data_processing:
Adapter sequence trimming was performed by TrimGalore
The tools Hisat2 and StringTie were used to perform sequence mapping and transcript assembling, respectively.
Read count information was obtained using the python script prepDE.py from StringTie.
For differential expression analysis, read counts were imported into the tool edgeR.
Assembly: GRCh38
Supplementary files format and content: Ensembl gene IDs and read counts are provided in tab-delimited text files as the processed data files.

source_name: peripheral blood

growth_protocol: Cells were grown in RPMI 1640 (ATCC Modification) Medium supplemented with 10% FBS and 1% PenStrep.

extract_protocol:
Cells were harvested, washed with PBS, and shipped on dry ice to Azenta Life Sciences, where total RNA was isolated using TRIzol
Azenta (www.azenta.com) performed library preparation using the NEBNext Ultra II RNA Library Prep kit. The HiSeq 4000 platform was used to sequence the libraries and generate the RNA-seq profiles.

treatment_protocol: Cells were treated with either 1uM EdC or 0.05% DMSO for 16hr.

value: peripheral blood

value: T-ALL Jurkat

value: T lymphoblast

value: DMSO


title: SUDHL10-DMSO-3

source_name: Lymph node

value: Lymph node

value: DLBCL SUDHL-10

value: B lymphocyte


title: SUDHL10-1uM-EdC-3

value: EdC


title: SUDHL10-DMSO-1


title: SUDHL10-1uM-EdC-1


title: SUDHL10-1uM-EdC-2


title: Jurkat-DMSO-1


title: Jurkat-DMSO-2


title: Jurkat-1uM-EdC-3


title: Jurkat-1uM-EdC-2


title: miRNA-Seq NM02

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

data_processing:
The raw reads were processed using mirDeep2 and HTSeq software to extract the count data.
Assembly: hg38
Supplementary files format and content: tab-delimited file of normalized read counts

source_name: Plasma cells

extract_protocol: miRNA was extracted using the Qiagen miRNeasy Micro Kit (217004). The library was prepared using small RNA library kit.

value: Plasma cells

value: Sorted Plasma Cells

value: control


title: miRNA-Seq NM03


title: Jurkat-1uM-EdC-1


title: JA.37,HA777,Atot,N1,ADU,26yo

city: Montreal

first: Jack

last: Antel

state: Quebec

address: 3801 Rue University

country: Canada

institute: McGill University

description: Raw readcounts

data_processing:
The GenPipes workflow was used for alignment to the GRCh38 human genome and read counting.
Assembly: GRCh38 human genome
Supplementary files format and content: FASTQ

source_name: Brain

growth_protocol: After the isolation procedure, human primary OLs were plated into a 6 well poly-L-lysine and extracellular matrix-coated  plates. Cultures were maintained for an initial 1 week under optimal conditions prior to subjecting to experimental conditions, to allow cell adherence and process formation.

extract_protocol:
RNA was extracted from hOLs after two days of treatment with defined medium for Ctrl, NG, IFNgamma, TNFalpha, or glutamate conditions.
A NEBNext® Single Cell/Low Input RNA Library Prep Kit

treatment_protocol: For metabolic experiments, cells were cultured in a less enriched medium [DMEM-F12 without N1 and supplementary factors, containing 0.25 g/l of glucose (LG) or with no glucose added (NG)]. We refer to these conditions as LG or NG. Mediators IFNgamma (2000 IU per ml) and TNFalpha (100 ng/ml) as well as glutamate (1 mM, Sigma) were diluted in defined medium. Bulk RNA seq studies were performed after 2 days of exposure.

value: Brain

value: Oligodendrocyte

value: N1-Ctrl media


title: JA.36,HA782,Atot,TNF,PED,4yo

description: Raw readcounts

value: TNFalpha


title: miRNA-Seq NM01


title: miRNA-Seq BM-9

value: WM


title: SUDHL10-DMSO-2


title: JA.35,HA782,Atot,N1,PED,4yo

description: Raw readcounts


title: miRNA-Seq BM-8


title: miRNA-Seq BM-6

value: MGUS


title: miRNA-Seq BM-7


title: JA.34,HA818,Atot,IFN,PED,15yo

description: Raw readcounts

value: IFNgamma


title: JA.32,HA818,Atot,GLUT,PED,15yo

description: Raw readcounts

value: Glutamate


title: JA.33,HA818,Atot,TNF,PED,15yo

description: Raw readcounts


title: JA.31,HA818,Atot,N1,PED,15yo

description: Raw readcounts


title: JA.30,HA814,Atot,NG,PED,4yo

description: Raw readcounts

value: No Glucose


title: miRNA-Seq BM-46


title: miRNA-Seq BM-39


title: miRNA-Seq BM-40


title: miRNA-Seq NM05


title: JA.38,HA777,Atot,NG,ADU,26yo

description: Raw readcounts


title: miRNA-Seq NM04


title: miRNA-Seq BM-44


title: JA.29,HA814,Atot,GLUT,PED,4yo

description: Raw readcounts


title: JA.28,HA814,Atot,N1,PED,4yo

description: Raw readcounts


title: miRNA-Seq BM-33


title: JA.27,HA819,Atot,NG,PED,8yo

description: Raw readcounts


title: JA.26,HA819,Atot,TNF,PED,8yo

description: Raw readcounts


title: JA.24,HA819,Atot,N1,PED,8yo

description: Raw readcounts


title: miRNA-Seq BM-32


title: JA.23,HA810,Atot,NG,PED,8yo

description: Raw readcounts


title: miRNA-Seq BM-30


title: JA.21,HA810,Atot,GLUT,PED,8yo

description: Raw readcounts


title: miRNA-Seq BM-26


title: JA.18,HA816,Atot,IFN,ADU,31yo

description: Raw readcounts


title: JA.17,HA816,Atot,TNF,ADU,31yo

description: Raw readcounts


title: JA.20,HA810,Atot,N1,PED,8yo

description: Raw readcounts


title: miRNA-Seq BM-25


title: miRNA-Seq BM-27


title: miRNA-Seq BM-24


title: JA.16,HA816,Atot,GLUT,ADU,31yo

description: Raw readcounts


title: JA.15,HA816,Atot,N1,ADU,31yo

description: Raw readcounts


title: miRNA-Seq BM-23


title: miRNA-Seq BM-45


title: miRNA-Seq BM-22


title: JA.13,HA779,Aneg,TNF,ADU,41yo

description: Raw readcounts


title: JA.12,HA779,Aneg,N1,ADU,41yo

description: Raw readcounts


title: JA.11,HA766,Aneg,TNF,ADU,70yo

description: Raw readcounts


title: Raji dRNA

data_processing:
Raw Fast5 files were converted to fastq with guppy (version 3.4.5), followed by alignment to the gencode version of hg38 (version 30) using minimap2 (version 2.18); the resulting bam file was visualized using the Integrative Genomics Viewer (version 2.11.0).
Stringtie version 2.2.1 was run with the following flags -L -p 2 -A to produce the processed files.
Assembly: hg38
Supplementary files format and content: Table of gene abundances as produced by stringtie: stringtie_Raji_dRNA_2022_12_17_gene_abundance_no_annotation.txt
Supplementary files format and content: GTF file of transcripts called by stringtie: stringtie_Raji_dRNA_2022_12_17_unstranded_no_annotation.gtf

source_name: Raji

extract_protocol:
Total RNA was isolated using the Maxwell® RSC simplyRNA Cells Kit (Promega).
500ng of mRNA was isolated from total RNA using Dyna-beads mRNA DIRECT kit (Invitrogen) and used for direct RNA (SQK-RNA002, ONT) library preparation
Nanopore long-read direct RNA sequencing

value: Raji


title: miRNA-Seq BM-18


title: JA.14,HA779,Aneg,NG,ADU,41yo

description: Raw readcounts


title: JA.10,HA766,Aneg,NG,ADU,70yo

description: Raw readcounts


title: miRNA-Seq BM-16


title: miRNA-Seq BM-28


title: miRNA-Seq BM-12


title: JA.9,HA766,Aneg,N1,ADU,70yo

description: Raw readcounts


title: miRNA-Seq BM-14


title: JA.8,HA766,Apos,TNF,ADU,70yo

description: Raw readcounts


title: JA.7,HA766,Apos,N1,ADU,70yo

description: Raw readcounts


title: JA.6,HA751,Aneg,IFN,ADU,43yo

description: Raw readcounts


title: JA.5,HA751,Aneg,N1,ADU,43yo

description: Raw readcounts


title: JA.3,HA724,Apos,N1,ADU,51yo

description: Raw readcounts


title: RNA-Seq NM04

data_processing:
The raw RNA-seq reads were processed through the Mayo Clinic RNA-seq bioinformatics pipeline, MAP-RSeq version 3.0, as previously described. Briefly, MAP-RSeq used the STAR tool to align reads to the reference human genome build hg38. Gene and exon expression quantification were performed using the Subread package to obtain raw counts. We further removed genes with a median count below. We next computed transcripts per million (TPM) for the expression data. For our gene expression clustering, we used the nonnegative matrix factorization (NMF) unsupervised clustering approach that ensure robustness of clustering. Only protein coding genes, with the exclusion of mitochondrial genes and sex chromosome genes, were used for the NMF and principal component analysis (PCA).
Assembly: hg38
Supplementary files format and content: tab-delimited file of normalized read counts

extract_protocol:
Total RNA was extracted using the Qiagen miRNeasy Micro Kit (217004). The library was prepared using the RNA access kit TruSeq Stranded Total RNA v2 from Illumina.
Total RNA was extracted using the Qiagen miRNeasy Micro Kit (217004). The library was prepared using the RNA access kit TruSeq Stranded Total RNA v2 from Illumina.


title: RNA-Seq NM05


title: RNA-Seq NM03


title: JA.2,HA722,Apos,TNF,ADU,36yo

description: Raw readcounts


title: JA.1,HA722,Apos,N1,ADU,36yo

description: Raw readcounts


title: G11_Ctrl_HelaMm rep1

city: Stony Brook

first: Adam

last: Master

state: NY

address: 101 Nicolls Rd

department: Department of Cancer Prevention

institute: The State University of New York

description: Control Mouse Hela cells

hyb_protocol: Once the hybridization was completed, the arrays were washed and stained in a GeneChip Fluidics 450 station.

scan_protocol: These arrays were then scanned in a GeneChip Scanner 3000 G7 controlled by Affymetrix GeneChip Command Console v 4.3.3.1616.

data_processing: Each transcript was measured with a median of 22 probes. Raw microarray data were analyzed with the Transcriptome Analysis Console (TAC) Software (ThermoFisher Scientific). Microarray data containing 22 206 tested transcripts were filtered at p-value<0.01 and top 2% up- and 2% down-regulated genes were taken for further analyses (figure.1A). Of these 22,206  transcripts, 19,696 (89%) are fully annotated, with known homology to human genes (HomoGene NCBI database) while 2,510 (11%) are partially annotated without clear homology to human genes. TAC software was used to perform a) Hierarchical Clustering (heat-map) along with Scatter and Volcano plots, b) search WikiPathways (integrated with TAC), and export excel data file for further analyses in a number of biological databases. The String tool (https://string-db.org) was used to check the network of proteins encoded by our top annotated and not annotated transcripts (MCL clustering with inflation    parameter: 1.9) as well as other functional enrichments in the network that included: String local network clustering, Reactome Pathways, KEGG Pathways, WikiPathways, Annotated Keywords (UniProt), Protein Domains (Pfam), Protein Domains and Features (InterPro), Subcellular Localization (compartments), Cellular Components (gene ontology), Molecular Function (gene otology), Biological Process (gene ontology).

label: biotin

source_name: Control cells

label_protocol: After each mouse was euthanized, isolated SN or DRG were immediately placed in 0.7 mL of TRIzol Reagent (ThermoFisher Scientific, CA), frozen in liquid nitrogen and stored at -80 °C until analyzed. Samples were homogenized in TRIzol, mixed with 0.2 mL of chloroform, vortexed 20 s and centrifuged at 12,000 × g at 4°C for 10 min. Pre-cleaned RNA, present in the upper aqueous phase, was transferred to a new tube on ice and processed using the RNeasy® Mini column kit (Qiagen, Valencia, CA) with DNase digestion during RNA purification. The total RNA was labeled using the Affymetrix GeneChip® WT PLUS Kit according to the manufacturer’s protocol.

growth_protocol: Male C57BL/6J mice (Jackson Laboratory, Bar Harbor, ME), 8 weeks old and weighing 20–30 g, were housed 4/cage randomly allocated to different treatment groups, with food and water available ad libitum. Experiments were performed during the light cycle (7:00 am to 7:00 pm) and animals were euthanized via CO2 asphyxiation. Experimenters were blinded to the identity of the treatment groups.  All studies were approved by the Institutional Animal Care and Use Committee of Stony Brook University and followed the NIH Guidelines for the Care and Use of Laboratory Animals. Animal studies are reported in compliance with the ARRIVE guidelines. The animal facility was AAALAC-accredited.

extract_protocol: Trizol + DNAse I + Silica column based Cleanup. RNA was callected from mouse sciatic nerve (SN) and DRG. Each group contained at least 3 animals (2 samples right and left DRG or SN were collected from each animal). Samples were immediately frozen in liquid nitrogen.

treatment_protocol: PIPN was induced in mice with 4 i.p. injections of paclitaxel 8 mg/kg every other day.

value: Control


title: G11_Ctrl_HelaMm rep2

description: Control Mouse Hela cells


title: RNA-Seq NM02


title: RNA-Seq NM01


title: H1.2sh_+Dox_RNASeq, rep2

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

institute: IBMB-CSIC

data_processing:
RNA-Seq reads were mapped to the reference genome (GRCh37/hg19) using HISAT2 v2.2.1 with default parameters and specifying strand-specific information (--rna-strandness RF).
SAMtools v1.11 was used to sort BAM files and filter for properly paired-end reads (-f 2).
Aligned reads were mapped to Ensembl GRCh37.87 gene annotation with TEtranscripts v2.1.4 (--sortByPos --mode multi –stranded reverse)
DESeq2 v1.26.0 was used to identify differentially expressed genes between control and H1.2 KD cells. Gene expression changes were considered significantly different if the absolute value of the log2(FC) was higher than 1.4 and the adjusted p-value was lower than 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: TXT file containing raw read counts for Ensembl GRCh37.87 gene annotation (hg19)

source_name: Breast cancer cell line

growth_protocol: Cells were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100µg/ml streptomycin.

extract_protocol:
Total RNA of T47D-MTVL H1.2sh Untreated or 6-days-Dox-treated cells was extracted with High Pure RNA Isolation kit (Roche)
Strand-Specific Transcriptome Library Construction Protocol  (DNBSEQ). According to the manufacturer’s instructions, the first step involves the removal of ribosomal RNA (rRNA) using target-specific oligos and RNase H reagents to deplete both cytoplasmic (5S rRNA, 5.8S rRNA, 18S rRNA and 28S rRNA) and mitochondrial ribosomal RNA (12S rRNA and 16S rRNA) from total RNA preparations. Following SPRI beads purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. This process removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. After UDG treatment, the incorporation of dUTP quenches the second strand during amplification. The products are enriched with PCR to create the final cDNA library. The libraries were assessed quality and quantity in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The qualified libraries were sequenced pair end on the BGISEQ-500/ MGISEQ-2000 System (BGI-Shenzhen, China).
RNA-Seq (DNBSeq LncRNA-Seq)

treatment_protocol: Initially, T47D-MTVL cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of H1.2 shRNA (pLVTHM). The inducible knocked-down cell line were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Doxycycline treatment. Then cells were amplified in the absence of Dox until an experiment was performed.  Doxycycline (Sigma) was added at 2.5 µg/ml when indicated and treated for 6 days.

value: Breast cancer ductal carcinoma

value: Treated with Dox (6 days)

value: H1.2 knock-down


title: SortedBFPnegative_MPP_24h

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

country: United Kingdom

institute: UK Dementia Research Institute at Cardiff University

description:
gene expression (counts and normalized data)
MPPbasal_normalized_data.tsv
MPPbasal_metadata.tsv

data_processing:
We used FastQC for as first Quality Control step and MultiQC for summarization
Fastq files were processed using the Mappa (v1.0) pipeline from Takara (demuxer and analyser).
We ran demuxer to label the reads per cell, where the cell is included in the header of the sequence.
We ran the analyser, which includes read trimming with Cutadapt, Genome alignment with STAR and counting with Subread
Count summarization was done for exons only and for intron and exons.
Assembly: GRCh38
Supplementary files format and content: gene counts are given in csv format (Exons only SAMPLE_genematrix.csv, or also including introns SAMPLE_incl_introns_genematrix.csv)
Supplementary files format and content: normalized data for all samples and corresponding metadata are given in tsv format (MPPbasal_normalized_data.tsv and MPPbasal_metadata.tsv)

source_name: cell line

growth_protocol: KOLF2-C1 (HPSI0114i-kolf_2) and genome edited KOLF2-C1 derivatives were maintained on Matrigel-coated plates in Essential 8 media (TeSR-E8, Stemcell Technologies). All PSCs were passaged via manual dissociation using Gentle Cell Dissociation Reagent (Stemcell Technologies) as described previously (Arber et al 2015). IPSC differentiation towards mDA fate follows a protocol combining key features of (Kriks et al 2019) and (Jagger et al 2019). Briefly, PSCs were pre-plated on growth factor-reduced matrigel in TeSR-E8.  Neural differentiation was initiated when cells reached >80% confluence by switching to DMEM-F12/Neurobasal (2:1) supplemented with N2 and B27 (N2B27). For the first 7 days, cultures were supplemented with SB431542 (10µM, 1614-10 Tocris), LDN-193189 (100nM, StemGene), SHH-C24II (200ng/ml, 1845-SH-500 BioTechne) and Purmorphamine (1µM, 540220-5 VWR). LDN was kept until day 11. On day 3 CHIR99021 (3 µM, SM13-10 Cambridge Bioscience) was added to the media until day 13. Cultures were treated with PD0325901 from day 5 to 9 (1µM, SM26-10 Cambridge Bioscience).  FGF8a was added from day 11 to day 20 (100ng/ml, 100-25A Peprotech). Cultures were dissociated at around day 16/17 to single cells using Accutase (00-4555-56 Thermo Fisher Scientific) and replated onto poly-D-lysine/laminin coated plates at a density of 250000 cells/cm2. B27 without vitamin A (125870 Thermo Fisher Scientific) was used for the first 25 days, followed by B27 (175040 Thermo Fisher Scientific) plus BDNF (10ng/ml, 450-02-1MG Peprotech), GDNF (10ng/ml, GFH2-100 Cell Guidance System), Ascorbic Acid (200µM, A4544 Sigma-Aldrich) and DAPT (10µM, 2634 Tocris) from day 21 onwards.

extract_protocol:
We prepared single cell preparations from fresh cultures by incubation with Accutase 10 min at 37C followed by gently pipetting the cells 3-4 times and an extra 2 min incubation at 37C. After dissociation and pelleting, cells were pipetted to single cells in 500 ul PBS and incubated for staining with Hoechst and PI for 20 min at 37C (ReadyProbes™ Cell Viability Imaging Kit, Blue/Red, R37610 Invitrogen). After washing, we re-suspended the cells in 1ml PBS and filtered through a nylon membrane to remove cell clumps. We used Countess II Automated cell counter (Invitrogen) to quantify cell numbers and cells were dispensed at a concentration of 30.000 cells/ml into ICELL8 Single-Cell System (Takara).
The cDNA libraries were generated using the SMART-Seq ICELL8 cx Application Kit protocol provided by the manufacturer

value: cell line

value: KOLF2-C1 human iPSC line

value: iPSC differentiated into dopaminergic neurons

tag: sorting status

value: Sorted

tag: differentiation day

tag: genetic modification

value: LMX1A Cre AAVS1 BFP

tag: type


title: RNA-Seq BM-9

tag: tissue

value: Plasma cells

value: Sorted Plasma Cells


title: SortedBFPpositive_MPP_24h


title: SortedBFPnegative_basal_24h


title: SortedBFPpositive_basal_24h


title: H1.2sh_+Dox_RNASeq, rep1


title: H1.2sh_Untreated_RNASeq, rep2

value: Untreated

value: control


title: NonSorted_MPP_24h

value: Non sorted (NS)

value: NS


title: RNA-Seq BM-8

value: WM


title: G11_Ctrl_HelaMm rep3

description: Control Mouse Hela cells


title: G8_Nai_SN rep2

description: Naive mouse, Sciatic nerve tissue

source_name: Sciatic Nerve

value: Naive


title: G8_Nai_SN rep1

description: Naive mouse, Sciatic nerve tissue


title: G8_Nai_SN rep3

description: Naive mouse, Sciatic nerve tissue


title: JA.4,HA724,Apos,TNF,ADU,51yo

description: Raw readcounts

value: Brain

tag: age

value: Oligodendrocyte

value: TNFalpha


title: RNA-Seq BM-7

tag: treatment


title: H1.2sh_Untreated_RNASeq, rep1

value: Breast cancer ductal carcinoma

tag: cell line


title: NonSorted_basal_24h

value: cell line


title: RNA-Seq BM-6

value: MGUS


title: G7_Nai_DRG rep1

description: Naive mouse, Dorsal Toot Ganglion tissue

source_name: Dorsal Root Ganglion


title: 293T_Mut_GD

city: Hefei

first: Xiaolin

last: Wang

address: Huangshan Road

institute: USTC

data_processing:
The adaptors were trimmed with Cutadapt to obtain clean reads. The data quality was then checked with FastQC and the low-quality (Q value ≤ 20) reads were removed.
Reads were aligned to the human reference genome (hg19 or mm10) with Bowtie2. For linear RNAs including lncRNAs and mRNAs, the corresponding reads were counted with BEDtools and read per million (RPM) was used to calculate levels for lncRNAs and mRNAs.
Assembly: hg19 and mm10
Supplementary files format and content: tab-delimited text files include reads for each Sample

source_name: HEK293T cells

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) according to the manufacturer’s instructions.

value: HEK293T cells

value: Human Embryonic Kidney 293T Cells

value: Glucose deprivation for 24h


title: G7_Nai_DRG rep2


title: G6_Ptx_DRG rep3

description: Paclitaxel treated mouse, Dorsal Toot Ganglion tissue

value: Paclitaxel


title: RNA-Seq BM-46

value: Plasma cells

value: Sorted Plasma Cells


title: 293T_WT_GD

value: WT


title: Gfi1b-GFP+ small intestine scRNA

city: New Haven

first: Craig

middle: B

last: Wilen

address: 789 Howard Avenue, Clinic Building Rm 438

department: Immunobiology

institute: Yale University

data_processing:
The Cell Ranger Single-Cell Software Suite (version 5.0.0) was used to perform sample demultiplexing, barcode processing and single-cell gene counting. Only genes with at least one UMI count detected in at least one cell were retained for analysis; single cells were excluded when >10% of reads mapped to mitochondrial RNA. Cells with fewer than 250 expressed genes or greater than 100,000 reads were also discarded. Data normalization was performed using a standard protocol in Seurat. We report no original code in this analysis. All analysis was performed using the Seurat platform (4.3.0) and R (4.2.2).
Assembly: mm10
Supplementary files format and content: rds, gz

source_name: Small intestine

extract_protocol:
10x scRNA-seq
CD45-EpCAM+GFP+ cells from each mouse specimen were pooled together and submitted for sequencing at the Stanford Functional Genomics Core facility. There, the 10X Genomics Chromium Single Cell 3’ v3.0 platform was used to prepare individually barcoded single-cell RNA-Seq libraries following the manufacturer’s protocol. Library size was confirmed with Agilent Bioanalyzer High Sensitivity DNA assay.

value: Small intestine

value: IECs

value: Gfi1b-GFP B6J


title: 293T_Mut_REG

value: Mock


title: 293T_WT_REG


title: RNA-Seq BM-44

value: WM


title: RNA-Seq BM-45


title: sample.hoxcep120homo_6

city: Saint Louis

first: Tao

last: Cheng

state: MO

address: MSB Room 880M, Nephrology Division,425 South Euclid Ave, Box 8126, St Louis, MO  63110

institute: Washington University in St. Louis

data_processing:
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Assembly: mm9
Supplementary files format and content: texcelsheet files
Supplementary files format and content: DEG, raw counts

source_name: kidney

extract_protocol:
For analysis of GFP-positive UB cells with and without centrosomes during embryogenesis, kidneys of wildtype and Hoxb7-Cep120 mice were isolated at E13.5 and dissociated into single cell suspension as previously described (Jain et al., 2014). Briefly, E13.5 embryonic kidneys were dissected and collected in 1.5 ml tube. Collected kidneys were suspended with Trypsin-EDTA solution (Sigma, T3924) with 200 g/ml DNase I (Sigma) and incubated for 10 min at 37°C. After the incubation the specimens were triturated with a P-200 pipette and rinsed once with DMEM/F12 containing 10% FCS to inactivate Trypsin. The cell preparation was then treated with collagenase dissolved in DMEM/F12 (1 mg/ml) and incubated at 37°C for 10 min. The specimens were again triturated and fully dissociated cells were rinsed twice in 500 µl of PBS/ 5% FCS and subjected to Fluorescence active cell sorting (FACS). FACS sorting (Sony Synergy-HAPS 1, 100 micron) was performed using the GFP channel.
ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol

value: kidney

value: kidney UB cells

value: epithelial cells

value: Cep120 KO

tag: developmental stage

value: Embryonic


title: G7_Nai_DRG rep3

value: Naive


title: 293T-TG

value: HEK293T cells

value: Human Embryonic Kidney 293T Cells

value: 300 nM TG  for 6 h


title: RNA-Seq BM-40

value: Plasma cells


title: sample.hoxcep120homo_4


title: 293T-GD

value: Glucose deprivation for 24h


title: G6_Ptx_DRG rep2

value: Paclitaxel


title: RNA-Seq BM-39

value: Sorted Plasma Cells


title: sample.hoxcep120homo_5


title: sample.hoxcep120homo_7


title: G5_Ptx_SN rep3

description: Paclitaxel treated mouse, Sciatic nerve tissue


title: sample.hoxcep120homo_2


title: G6_Ptx_DRG rep1


title: 293T-REG

value: WT


title: Pool 3 (Mice 7-9)

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
For each flowcell, libraries were demultiplexed using Cellranger mkfastq (v 6.1.1; All unambiguously demultiplexed reads for each sample were combined for downstream processing.
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10X Cell Ranger count (v. 6.1.1).
Barcodes were called as cells or background using default settings in 10X Cell Ranger (v. 6.1.1).
Assembly: Gex mm10
Supplementary files format and content: Sparse matrix HDF5 file with UMI counts per barcode per gene ID, and table of read characteristics for each UMI / barcode combination

source_name: Spleen

extract_protocol:
MRFP/FoxP3+ cells taken from splenic tissue from euthanized mice, sorted for CD4+ and stained for CD16/32. Cells were hashed based on treatment.
Cells were loaded onto a 10X Genomics GemCode Single-Cell Instrument per manufacturer instructions for nanodroplet single-cell capture, cell lysis, mRNA rtPCR, and cDNA barcoding within droplets.

value: Spleen

value: Regulatory T-cell


title: Pool 4 (Mice 10-12)


title: G5_Ptx_SN rep1


title: G5_Ptx_SN rep2


title: RNA-Seq BM-33

value: WM


title: sample.hoxcep120het_1

value: kidney


title: Pool 2 (Mice 4-6)


title: RNA-Seq BM-32


title: sample.hoxcep120het_2

value: kidney UB cells


title: APA-Seq, Biol rep 3

city: Berkeley

first: Marena

middle: Isabelle

last: Trinidad

address: 2151 Berkeley Way

institute: Innovative Genomics Institute

data_processing:
Cutadapt was used to trim adapter sequences
SAMtools was used to remove PCR duplicates and filter uniquely mapped reads.
Trimmed and filtered sequences were aligned to the human genome (hg38) using Hisat2
Deeptools was used to normalize BAMs to counts-per-million and generate BigWigs, which were visualized with IGV browser
Assembly: UCSC hg38
Supplementary files format and content: Alignments for all APA-seq replicates (Samples 1-3) were consildated with samtools, then CPM-normalized with DeepTools to generate APA_Union_CPM_NORM.bigWig

growth_protocol: NPCs were generated from hPSCs using the embryoid body protocol (Stem Cell Technologies) following manufacturer’s protocol. The surface of all cultureware used for the maintenance and propagation of hPSC-derived NPCs was coated with Corning Matrigel (Fisher Scientific) prior to cell seeding. Maintenance and propagation of hPSC-derived NPCs was performed following manufacturer’s instructions. Briefly, NPCs were maintained using complete STEMdiff™ Neural Progenitor Medium (Stem Cell Technologies) for 7-9 days, with medium change every other day. NPCs were passaged using Accutase (Stem Cell Technologies) and seeded onto Matrigel-coated cultureware at an initial concentration of 1.25x105 cells/mL.

extract_protocol:
Total RNA was extracted with Trizol following manufacturer's protocol.
RNA libraries for APA-Seq were prepared using 3' mRNA-Seq Library Prep Kit (Lexogen) using manufacturer's protocol.

treatment_protocol: NPCs were seeded at an initial concentration of 5x105 cells/mL in STEMdiff™ Neural Progenitor Medium (Stem Cell Technologies) and allowed to sit at 37 °C for 48 hrs. After 48 hrs, medium was changed to  fresh complete STEMdiff™ Neural Progenitor Medium for 2 hrs at 37 °C and then cells were collected by centrifugation

value: neural progenitor cells

value: undifferentiated


title: Pool 1 (Mice 1-3)


title: RNA-Seq BM-30

value: MGUS


title: sample.hoxcep120het_3

value: epithelial cells

value: Embryonic


title: APA-Seq, Biol rep 1


title: RNA-Seq BM-28


title: sample.hoxpkd1homo_1

value: Pkd1 KO


title: RNA-Seq BM-27


title: mRNA-Seq, NPC Undiff

data_processing:
Cutadapt was used to trim fastq files.
Trimmed and filtered  reads were aligned to the human genome (hg38) using Hisat2.
SAMtools was used to remove PCR duplicates and filter uniquely mapped reads.
HOMER was used to call peaks and motifs from deduplicated BAMS.
Deeptools was used to perform counts-per-million normalization and convert BAMs to BigWigs, then coverage for specific transcripts was visualized using the IGV browser.
For mRNA-seq samples, transcript counts were generated with Kallisto
Assembly: UCSC hg38
Supplementary files format and content: JHDC001G-Diff_Transcriptome_Hits.xlsx contains Kallisto results for differentiated cells (neuron forebrain early differentiation).
Supplementary files format and content: JHDC001H-Undiff_Transcriptome_hits.xlsx contains Kallisto results for undifferentiated, neural progenitor cells.
Supplementary files format and content: irCLIP alignments for differentiated cell replicates (Samples 1-3) were consolidated and CPM-normalized to generate Differentiated_Union_CPM_Norm_BOTH.bigWig
Supplementary files format and content: irCLIP alignments for undifferentiated cell replicates (Samples 4-6) were consolidated and CPM-normalized to generate UNDifferentiated_Union_CPM_Norm_BOTH.bigWig

extract_protocol:
Total RNA was extracted using Trizol (mRNA-Seq samples) and using neutral phenol chloroform (Quick-irCLIP samples) using the manufacturer's protocol.
RNA libraries for mRNA-Seq were prepared using NEBNext rRNA Depletion Kit v2 following the manufacturer's protocol. RNA Libraries for Quick-irCLIP samples were prepared using the SMARTer smRNA-Seq Kit for Illumina following the manufacturer's protocol.

treatment_protocol: For differentiation studies, hPSC-derived NPCs were seeded at an initial concentration of 5x105 cells/mL in STEMdiff™ Neural Progenitor Medium (Stem Cell Technologies) and allowed to sit at 37 °C for 48 hrs. After 48 hrs, medium was changed to complete STEMdiff™ Forebrain Neuron Differentiation medium (Stem Cell Technologies) (for differentiated NPCs) or to fresh complete STEMdiff™ Neural Progenitor Medium (for undifferentiated NPCs) for 2 hrs at 37 °C and collected by centrifugation.


title: D11_m24_cDC1

data_processing:
Base call quality-trimming step was applied to remove low-confidence base calls from the ends of read using trimmomatic v0.39 (LEADING:3 SLIDINGWINDOW:4:20 MINLEN:8)
Trimmed sequence read were mapped to GRCm38.91 using star (v2.7.11a)
Duplicates were removed from aligned reads using Picard (v3.1.0) and samtools (v1.16)
Gene counts were generated using htseq-count v2.0.2
Assembly: GRCm38.91
Supplementary files format and content: csv of raw gene counts

source_name: Lin- CD11c+ MHC II+ 33D1- CD8+ DCs

extract_protocol:
300 cells per population were sorted (FACS Aria II, Becton Dickinson) into lysis buffer, and cDNA was prepared using the SMART-Seq Ultra Low Input RNA Kit for Sequencing (Takara Bio).
Reverse transcription was performed followed by PCR amplification to generate full-length amplified cDNA.  Sequencing libraries were constructed using a modified protocol of the Nextera XT DNA Sample Preparation Kit (Illumina) to generate Illumina-compatible barcoded libraries

value: Lin- CD11c+ MHC II+ 33D1- CD8+ DCs

tag: mouseid

value: Fc.Mut24 IL-2/LPS


title: D12_m24_cDC2

source_name: Lin- CD11c+ MHC II+ 33D1+ DCs

value: Lin- CD11c+ MHC II+ 33D1+ DCs


title: D10_m23_cDC2


title: sample.hoxpkd1homo_2


title: Quick-irCLIP, NPC Undiff, Biol rep 3


title: RNA-Seq BM-26

value: Plasma cells


title: mRNA-Seq, NPC Diff

value: neuron forebrain early differentiation


title: D9_m23_cDC1


title: RNA-Seq BM-25

value: Sorted Plasma Cells


title: sample.hoxpkd1het_1

value: WT


title: D8_m22_cDC2


title: Quick-irCLIP, NPC Undiff, Biol rep 2


title: sample.hoxpkd1het_2


title: RNA-Seq BM-24


title: Quick-irCLIP, NPC Undiff, Biol rep 1


title: D6_m21_cDC2


title: D7_m22_cDC1


title: RNA-Seq BM-23


title: sample.hoxcep120homo_p15_1

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
Assembly: mm9
Supplementary files format and content: excelsheet files
Supplementary files format and content: DEG

extract_protocol:
For analysis of gene expression changes in fibrocystic kidneys of postnatal mice, whole kidneys were isolated from wildtype and Hoxb7-Cep120 animals at P15. The kidneys were weighed and then grounded using pestle and mortar in liquid N2 bath and then lysed in Trizol, then total RNA was isolated using Direct-zolTM RNA MiniPrep Plus (Zymo Research).
ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol

value: whole kidney

value: whole kidney cells

value: Cep120 KO


title: Quick-irCLIP, NPC Diff, Biol rep 3


title: APA-Seq, Biol rep 2


title: Quick-irCLIP, NPC Diff, Biol rep 2


title: D5_m21_cDC1


title: RNA-Seq BM-18


title: sample.hoxcep120homo_p15_2

value: kidney


title: Quick-irCLIP, NPC Diff, Biol rep 1

value: neural progenitor cells


title: D2_m19_cDC2


title: sample.hoxpkd1homo_3

value: kidney UB cells


title: sample.hoxcep120het_p15_1


title: RNA-Seq BM-16

value: WM


title: C10_m17_cDC2


title: sample.hoxpkd1het_3

value: epithelial cells


title: HEK293T, Control-sh control-plasmid S96 Rep2

city: London

first: Pradeepa

middle: M

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

institute: Queen Mary University of London

data_processing:
150bp paired-end reads for the CUT&Tag-seq were trimmed for adapters using the Trimmomatic tool and aligned to the hg38 genome through local Bowtie2 (version 2.4.5) with these parameters for pair-end mapping: --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. The bam files were sorted and indexed using the samtools (version 1.9) sort and the samtools index. Merging of multiple replicates was performed using samtools merge.
The sorted bam files were used to generate bed, bedgraph and bigwig formats for individual modifications. Sorted bam files were subjected to bigwig generation via deepTools (version 3.5.1) bamCoverage tool with --binSize 20 --scaleFactor=1.0 --smoothLength 60 --extendReads 150 --centerReads options. The corresponding bigwig files were normalized by log2raio option for Antibody against IgG.
Peak-calling and analyses The reads were extracted from the bam to bed by the bedtools bamtobed option. Further reads were processed as mentioned in the SEACR (version 1.3) manual to get the bedgraph. These bedgraph files were subjected to peak calling through SEACR keeping IgG as a background with the norm and relaxed options for individual replicates. Peaks consistenet in both replicates were reatins and the coordinates were merged.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: HEK293T cells were grown on 100 mm culture dishes (Corning Falcon product number: 353003 ) in Delbecco's Modified Eagle's Medium (Gibco, 41966-029) supplemented with 100 U/ml penicillin-streptomycin (Gibco, 15140122) and 10% FBS (Sigma, F7524). The cells were passaged every 3-4 days. All the cell lines were tested for Mycoplasma contamination using EZ-PCR Kit (Geneflow, K1-0210).

extract_protocol:
CUT&Tag was performed according to the protocol of Kaya-Okur et al (1) with modifications to tissue processing as described below. ~100,000 cells were pelleted by centrifugation for 3 min at 600 x g at room temperature and resuspended in 500μl of ice-cold NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 1% Triton X-100, and 20 % glycerol and cOmplete EDTA free protease inhibitor tablet) and was let to sit for 10 min on ice. Nuclei were pelleted by centrifugation for 4 min at 1300 x g at 4°C, resuspended in 500μl of wash buffer and held on ice until beads were ready. Required amount of BioMag Plus Concanavalin-A-conjugated magnetic beads (ConA beads, Polysciences, Inc) were transferred into binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1mM CaCl2 and 1mM MnCl2), washed once in the same buffer, each time placing them on a magnetic rack to allow the beads to separate from the buffer and resuspended in binding buffer. 10 μl of beads was then added to each tube containing cells and rotated on an end-to-end rotator for 10 minutes. After a quick spin to remove liquid from the cap, tubes were placed on a magnet stand to clear, the liquid was withdrawn and 800μl of antibody buffer containing 1μg of primary antibodies: normal rabbit IgG (Santa Cruz Cat no sc-2027), PSIP1 (Bethyl Laboratory, A300-848A), S9.6 (Millipore, MABE 1095), YH2AX (Abcam, ab81299) was added and incubated at 4ºC overnight in a nutator. Secondary antibodies (guinea pig α-rabbit antibody, Antibodies online, ABIN101961) were added 1:100 in Dig-wash buffer (5% digitonin in wash buffer) and 100 µL was squirted in per sample while gently vortexing to allow the solution to dislodge the beads from the sides and incubated for 60 min on a nutator. Unbound antibodies were washed in 1 ml of Dig-wash buffer three times. 100 μl of (1:250 diluted) protein-A-Tn5 loaded with adapters in Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine with Roche cOmplete EDTA free protease inhibitor) was added to the samples, placed on nutator for 1 hour and washed three times in 1 ml of Dig-300 buffer to remove unbound pA-Tn5. 300 µL Tagmentation buffer (Dig-300 buffer + 5 mM MgCl2) was added while gentle vortexing and samples were incubated at 37ºC for 1 hr on an incubator. Tagmentation was stopped by adding 10 µL 0.5M EDTA, 3 µL 10% SDS and 2.5 µL 20 mg/mL Proteinase K to each sample. Samples were mixed by full speed vortexing for ~2 seconds and incubated for 1 hr at 55ºC to digest proteins. DNA was purified by phenol: chloroform extraction using phase-lock tubes (Quanta Bio) followed by ethanol precipitation.
Libraries were prepared using NEBNext HiFi 2x PCR Master mix (M0541S) with a 72ºC gap-filling step followed by 13 cycles of PCR with 10-second combined annealing and extension for the enrichment of short DNA fragments. Libraries were sequenced in Novaseq 6000 (Novogene) with 150bp paired-end reads.

treatment_protocol: Control or RNASEH overexpressing plasmid transfected HEK293T cells were transduced with either control shRNA or PSIP1 shRNA and grown in a medium containing 2ug/ml puromycin.

value: Human Embryonic Kidney cells with large T antigen

tag: antibody

value: S9.6(Millipore, MABE 1095)


title: C9_m17_cDC1

value: Lin- CD11c+ MHC II+ 33D1- CD8+ DCs


title: sample.hoxcep120het_p15_2


title: RNA-Seq BM-14


title: RNA-Seq BM-22


title: sample.hoxcep120het_p15_3


title: HEK293T, Control-sh control-plasmid PSIP1 Rep1

value: PSIP1(Bethyl Laboratory, A300-848A)


title: OVX.END4

city: Columbia

first: Mitzi

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Rd

department: PMI

institute: University of South Carolina School of Medicine

description:
predicted_metagenomes.L3_L3.txt
table_mc17612_sorted_L6.txt

data_processing:
Sequenced data by Illumina Miniseq system in FASTQ files along with mapfile in excel format were uploaded to the online 16s analysis platform, Nephele (https://nephele.niaid.nih.gov/) supported by Cyber Infrastructure and Computational Biology (OCICB), National Institute of Allergy and Infectious Diseases (NIAID), NIH.
The 16S metagenomics was analyzed through 16S Paired-end QIIME method, the groups of related DNA se-quences were assigned to operational taxonomic units (OTUs), and Nephele-generated output pipeline files were analyzed to determine targeted tissue-microbial compositions.
The default setting of Nephele was excluding any samples with the median OUT less than 0.2 OUT fractions of the highest sample in the same run in order to increase the quality of the reads, and then the generated FASTA files were blasted into Greengenes_99 database at 70% cutoff similarity.
Assembly: Greengenes_99
Supplementary files format and content: Text file includes raw total counts of OTUs for each sample
Supplementary files format and content: Text file includes raw counts of OTUs for each predicted metagenomic metabolism process
Library strategy: 16S ribosomal RNA sequencing

organism: mouse gut metagenome

source_name: Colonic contents

extract_protocol:
Colon flush was performed of the excised whole colon using sterile PBS. Bacterial genomic DNA was isolated from colon contents using QIAamp DNA Stool Mini Kit (Qiagen, Valencia, CA) and quantified using a Qubit 4 Fluorometer (ThermoFisher, Waltham, MA). Purified DNA was used in the library preparation for 16S ribosomal RNA sequencing using 16S Metagenomic Sequencing Library Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions. Briefly, the purified DNA was amplified by PCR using bacterial/archaeal sense 319 F primer and anti-sense 806 R primer to amplify the V3-V4 hypervariable regions of 16S rRNA. After clean-up, the amplified PCR products were then amplified again by PCR using dual indices and sequencing adaptors for 16S rRNA sequencing.
Purified DNA was used in the library preparation for 16S ribosomal RNA sequencing using 16S Metagenomic Sequencing Library Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Mature Balb\c mice were used in current experimental design. All the experimental mice were housed and managed at same condiotions with no restriction in standard food or drink. Some Balb\c mice were kept as naive and some underwent ovariectomy (OVX) under isoflurane anasthesia and then 7 days later some of these OVX mice assigned as donor mice and the rest was assigned as recipient mice (OVX) in rate of one donor for every 2 recipients mice. The donor mice went through euthanasia by using overdose of isoflurane to collect the uterie horns to appeal the endometrial tissue for transplantation. Naive and OVX then divided into four groups. Naïve group, mice of this group were kept as control wihtout any treatment to normalized collected data. Naive+END group, mice of this group are having intact ovaries but received endometrial tissue transplant taken from ovariectomized donor mice. OVX mice received either intraperitoneal load of endometrial tissue (END) in normal saline and assigned as OVX+END or received intraperitoneal injection of normal saline namely, OVX+VEH. At the endpoint of the experiment, the uterine horns, blood samples, peritoneal wash and colonic fulshes were collected for downstream analysis.

value: Colonic contents

tag: strain

value: Balb\c

value: Mice of this group exposed to ovariectomy procedure at the beginning of experiment and then at day 7 post operational procedure, each mouse of this group received intraperitoneal five mg of endometrial tissue transplants loaded in normal saline. Endometrial tissue transplant (END) was collected from ovariectomized-donor mice and then transplanted intraperitoneally into ovariectomized recipient mice (OVX). Intramuscular injection of Diethylstilbestrol to replace natural estrogen was given  every 5 days started from day of ovariectomy till the end of the experiment.


title: HEK293T, Control-sh control-plasmid PSIP1 Rep2


title: OVX.END3


title: sample.hoxpkd1homo_p15_1

tag: genotype

value: Pkd1 KO


title: C7_m16_cDC1


title: OVX.END2


title: sample.hoxpkd1homo_p15_2


title: HEK293T, Control-sh control-plasmid IgG Rep1

value: IgG(Abcam, ab4729)


title: D1_m19_cDC1

value: Fc.Mut24 IL-2/LPS


title: OVX.END1


title: sample.hoxpkd1homo_p15_3

value: whole kidney

value: whole kidney cells


title: sample.hoxcep120homo_p15_3

value: kidney

value: Cep120 KO


title: HEK293T, Control-sh control-plasmid YH2AX Rep2

value: YH2AX(Abcam, AB81299)


title: HEK293T, Control-sh control-plasmid S96 Rep1