title: 9-AB_Control

city: Pittsburgh

first: Annalisa

last: Baratta

state: PA

address: 3501 Fifth Ave

institute: University of Pittsburgh

hyb_protocol: cRNA was hybridized to the Mouse LncRNA Array v4.0 (8 x 60K, Arraystar) in Agilent's SureHyb Hybridization Chambers

scan_protocol: Slides were scanned with the Agilent DNA Microarray scanner

data_processing: Data was extracted using Agilent Feature Extraction software and normalization was performed using the Agilent GeneSpring GX v12.1 software.

source_name: Expression control

label_protocol: RNA was amplified and transcribed into Cy3 fluorescent cRNA

extract_protocol: Whole brain was collected immediately following the final day of exposure. Extracellular vesicles were isolated by differential ultracentrifugation. Total RNA was isolated using the SeraMir EV RNA Purification Kit (SBI) and ~3ug of total RNA were sent to Arraystar for analysis

treatment_protocol: Animals underwent either chronic intermittent ethanol vapor exposure or room air exposure for 8h a day, 5 days a week, for 4 weeks.

value: brain-derived extracellular vesicles

value: Control

tag: Sex

value: male


title: minimally cystic tissue_3

status: Public on Jan 23 2022

type: RNA

city: Toronto

first: York

middle: PC

last: Pei

state: Ontario

address: 8N838, 585 University Avenue

department: Department of Medicine

country: Canada

institute: University of Toronto

description:
PKD1 control tissue
MCT3

hyb_protocol: Standard Illumina DASL hybridisation protocol

scan_protocol: Standard Illumina DASL scanning protocol

data_processing: The raw data were normalized using quantile normalization with BeadStudio 3.4 (Illumina). The normalized intensities and detection p-values were exported and further adjusted for batch effect with the R package ComBat.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Minimally cystic tissue from PKD1 patient, batch2

label_protocol: Standard Illumina DASL label protocol

growth_protocol: The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.

extract_protocol: Total RNA containing miRNA was extracted from each sample using miRNeasy Mini Kit (Qiagen) with an on-column DNA digestion step to minimize genomic DNA contamination

treatment_protocol: All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80°C freezer

tag: diagnosis

value: PKD1 patient

tag: tissue

value: Minimally cystic renal tissue


title: 6-AB_Control

country: USA

organism: Mus musculus

tag: treatment

tag: strain


title: minimally cystic tissue_2, replicate

description:
PKD1 control tissue
MCT2_re


title: 8-AB_CIE

source_name: Expression after CIE

value: chronic intermittent ethanol (CIE) vapor exposure


title: 4-AB_Control


title: 1-AB_Control


title: Sample8_Expression after CIE

value: female


title: Sample3_Control expression

source_name: Control expression


title: Sample5_Control expression


title: Sample10_Expression after CIE


title: Sample6_Expression after CIE


title: 5-AB_CIE


title: Sample1_Control expression


title: Sample7_Expression after CIE


title: 2-AB_CIE


title: 3-AB_CIE


title: Sample9_Control expression


title: Sample2_Control expression


title: minimally cystic tissue_2

description:
PKD1 control tissue
MCT2

source_name: Minimally cystic tissue from PKD1 patient, batch1


title: 10-AB_CIE


title: Sample4_Expression after CIE


title: 7-AB_Control


title: minimally cystic tissue_1

description:
PKD1 control tissue
MCT1


title: PKD1 renal cyst, medium cyst_5, 50 ml

description:
PKD1 renal cyst
LC1

source_name: Renal cyst from PKD1 patient, large single cyst, batch1

value: renal cyst


title: PKD1 renal cyst, large cyst_3, 50 ml

description:
PKD1 renal cyst
LC4


title: PKD1 renal cyst, medium cyst_3, 20 ml, replicate

description:
PKD1 renal cyst
MC3_re

source_name: Renal cyst from PKD1 patient, medium single cyst, batch2


title: PKD1 renal cyst, large cyst_2, 60 ml

description:
PKD1 renal cyst
LC3


title: PKD1 renal cyst, large cyst_1, 100 ml

description:
PKD1 renal cyst
LC2

source_name: Renal cyst from PKD1 patient, large single cyst, batch2


title: PKD1 renal cyst, small cyst_8*, 3 ml

description:
PKD1 renal cyst
SC8*

source_name: Renal cyst from PKD1 patient, small single cyst, batch1


title: PKD1 renal cyst, medium cyst_2, 30 ml

description:
PKD1 renal cyst
MC2

source_name: Renal cyst from PKD1 patient, medium single cyst, batch1


title: PKD1 renal cyst, small cyst_9*, 5 ml

description:
PKD1 renal cyst
SC9*

source_name: Renal cyst from PKD1 patient, small single cyst, batch2


title: PKD1 renal cyst, medium cyst_3, 20 ml

description:
PKD1 renal cyst
MC3


title: PKD1 renal cyst, small cyst_7*, 1.5 ml

description:
PKD1 renal cyst
SC7*


title: PKD1 renal cyst, small cyst_6*, 3 ml

description:
PKD1 renal cyst
SC6*


title: PKD1 renal cyst, small cyst_5, < 1ml

description:
PKD1 renal cyst
SC5


title: PKD1 renal cyst, small cyst_4, < 1ml

description:
PKD1 renal cyst
SC4


title: PKD1 renal cyst, small cyst_8*, 3 ml, replicate

description:
PKD1 renal cyst
SC8*_re


title: NGN2_RNA_seq_line_12_CRISPR_AA_well_H2

type: SRA

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

description: NGN2_RNA_seq_line_12_CRISPR_AA_well_H2 [CD0000012]

library_source: transcriptomic

data_processing:
All raw sequence reads generated by Illumina HiSeq 2000 had been demultiplexed at the University of Minnesota Genomics Center and provided as 2×75 bp paired-end fastq files (targeting 60 M reads per sample).
Adapter remnants, low-quality reads, and low QSEQ short sequences near either end of reads were processed by Trimmomatic (ILLUMINACLIP:NexteraPE-PE.fa:2:30:7, SLIDINGWINDOW:3:18, MINLENGTH:26).
The processed sequences were separated into paired-end and single-end fastq files per sample and only paired-end reads were retained for subsequent mapping. The fastq files were individually mapped against the human genome reference file including decoy sequences (GRCh38p7.13/hg38, 1000 Genome Project) using bowtie2 (-x 2000, -mm --qc-filter –met 1 –sensitive –no-mixed -t) and subsequently merged and sorted as BAM-formatted files using samtools, with only uniquely mapped reads (MAPQ > 30) retained. Picard tools MarkDuplicate was then used to remove all PCR and optical duplicated reads from the BAM file.
To further eliminate allelic bias towards reference alleles during the aligning step, we performed WASP calibration on the generated raw BAM files 55. Briefly, we first called the VCF file profiles on all SNP sites that were not reference alleles of all 20 samples individually using GATK HaplotypeCaller, and subsequently collapsed the individual VCF files into one summary VCF file containing all non-reference sites of all 20 individuals. Subsequently, this SNP list was used as the basis of WASP calibration and re-alignment, and a new WASP-calibrated new BAM file set was collected as the final output for the following peak calling and ASoC SNP call 55.
In order to increase sample size and sensitivity for peak detection, the BAM files of the processed reads of each sample were first sub-sampled to 30 M paired-end reads per sample (the smallest sample size) and the 20 sub-sampled BAM files were merged as the source file for peak calling. MACS2 26 was used to generate peak files (narrowPeak format) with recommended settings at FDR = 0.05 (-f BAMPE, --nomodel, --call-summits --keep-dup-all -B). Peaks that fell within the ENCODE blacklisted regions were removed. Also, we removed peaks falling within chromosomes X and Y, and the mitochondrial genome regions.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: .narrowPeak, MACS2 peak file

extract_protocol:
For RNA-Seq, at the day of harvesting the culture media was removed by aspiration and the cells were washed twice using 1 ml PBS each with aspiration. Subsequently, 600 µl of RLT Plus reagent was directly added into each well to homogenise cells in situ. Qiagen RNEasy plus kit was used for the extraction of total RNA according to the manufacturer’s protocol. Extracted RNAs were eluted into 50 µl of RNA-free water and the concentration was determined by nanodrop. Approximately 5 µg total RNA was recovered from each well.
Total RNAs isolated by using MirVana kit (Thermofisher) were used in RNA-seq. After QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, 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. Subsequently, terminal repair and sequencing adaptor ligation were applied to the templates. The double-stranded cDNA library is completed through size selection and PCR enrichment.

tag: cell type

value: Glutamatergic, NGN2-induced, day-20 neuron

tag: rutgers university cell and dna repository rucdr-nimh stem cell center index id

tag: disease status

value: case

tag: gender

value: Male

tag: age


title: NGN2_RNA_seq_line_12_CRISPR_AA_well_C9

description: NGN2_RNA_seq_line_12_CRISPR_AA_well_C9 [CD0000012]


title: PKD1 renal cyst, small cyst_3, < 1ml

description:
PKD1 renal cyst
SC3


title: PKD1 renal cyst, small cyst_2, < 1ml

description:
PKD1 renal cyst
SC2


title: NGN2_RNA_seq_line_12_CRISPR_AA_well_D2

description: NGN2_RNA_seq_line_12_CRISPR_AA_well_D2 [CD0000012]


title: NGN2_RNA_seq_line_12_CRISPR_AA_well_F3

description: NGN2_RNA_seq_line_12_CRISPR_AA_well_F3 [CD0000012]


title: PKD1 renal cyst, small cyst_1, < 1ml

description:
PKD1 renal cyst
SC1


title: NGN2_RNA_seq_line_12_CRISPR_AA_well_C3

description: NGN2_RNA_seq_line_12_CRISPR_AA_well_C3 [CD0000012]


title: NGN2_RNA_seq_CD12_AG_sample2

description: NGN2_RNA_seq_CD12_AG_sample2 [CD0000012]


title: NGN2_RNA_seq_CD12_AG_sample1

description: NGN2_RNA_seq_CD12_AG_sample1 [CD0000012]


title: PKD1 renal cyst, medium cyst_1, 25 ml

description:
PKD1 renal cyst
MC1


description: NGN2_RNA_seq_line_11_CRISPR_GG_well_H6_sample_2 [CD0000011]

value: Female


title: WT3+Bacitracin

city: Paris

first: Pascale

last: Cossart

address: 25 rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
Raw sequence files (fastq) were cleaned of 3' adapter sequences, and low quality (cutoff 28) and short sequence (15 nt) reads were removed using AdapterRemoval v1.5.2 software
Reads were aligned against the reference genome (NC_003210) with bowtie v1.0.0 using default parameters
Raw counts were generated with HTSeq v0.6.0
Differential expression analysis was performed with DeSeq2 software package with default parameters
Genome_build: NC_003210
Supplementary_files_format_and_content: WT_vs_WT_plusBacitracin.complete.txt ; counts, fold-change

organism: Listeria monocytogenes

source_name: WT bacitracin

growth_protocol: the wt bacteria were grown in BHI (Difco) from an overnight preculture.

extract_protocol:
Bacterial pellets from 10 ml cultures were re-suspended in 500 ul of 20 mM Tris-HCl buffer pH 8.0 containing 50 mM EDTA. The suspensions were added to 500 ul of acid-saturated phenol:chloroform, pH 4.5 (with isoamyl alcohol, 125:24:1) (Ambion) and transferred to 2 ml Lysing Matrix Tubes (MP Biomedicals, 6911). Bacteria were mechanically lysed in a FastPrep apparatus (two cycles of 45 sec, speed 6.0 with one minute pause on ice). Subsequently tubes were centrifuged at 4°C at maximum speed for 15 min in a tabletop centrifuge. Lysates were transferred to new 2ml Eppendorf tubes containing 500 ul phenol and 500 ul chloroform, vigorously vortexed and centrifuged at 4°C at maximum speed for 15 min. The upper aqueous phase was transferred to new 1.5 ml tubes and RNA was precipitated with 500 ul isopropanol in the presence of 0.3 M sodium acetate pH 5.5 for 5 min at -80°C followed by 15 min at -20°C. RNA was pelleted by centrifugation at maximum speed for 30 min at 4°C. Pellets were washed with 75% ethanol, air dried and re-suspended in 50-70 ul water.
The input total RNAs had RNA integrity numbers of typically 9.8-10 as defined with 2100 Bioanalyser instrument (Agilent). Total RNA were diluted to 200 ng/ml and treated with TURBO DNase (Ambion) for 15 min at 37°C. DNase was removed with DNase inactivation reagent according to manufacturer’s instructions. 4 mg of TURBO DNase-treated RNA was depleted for ribosomal RNA with Ribo-Zero™ Magnetic kit (Epicentre). Zymo-Spin IC columns were used for RNA purification. RNA was subsequently fragmented for 5 min at 70°C using Ambion Fragmentation Reagent and purified with Zymo-Spin columns. Fragmented RNAs were treated with Antarctic phosphatase (New England Biolabs) for 30 min at 37°C followed by 5 min at 65°C for phosphatase inactivation. 5’-ends of the fragmented RNAs were then phosphorylated with polynucleotide kinase (New England Biolabs) for 60 min at 37°C in the presence of RNaseOUT™ ribonuclease inhibitor (Thermo Fischer Scientific). cDNA libraries were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina®  (New England Biolabs) according to manufacturers’ instructions. Libraries were purified with AMPure XP beads (Agencourt) and checked for quality with Bioanalyzer DNA High Sensitivity Chips (Agilent). Sequencing was performed on a MiSeq (Illumina) in a multiplexed single read using a MiSeq Reagent Kit v3 (Illumina). Raw sequence files (fastq) were cleaned of 3' adapter sequences, and low quality (cutoff 28) and short sequence (15 nt) reads were removed using AdapterRemoval v1.5.2 software (51). Reads were aligned against the reference genome (NC_003210) with bowtie v1.0.0 (52) using default parameters. Typically 94% reads were aligned. Reads were counted with HTSeq v0.6.0 and normalized to reads per million. Differential expression analysis was performed with DeSeq2 software package
Directional libraries were constructed with the use of a custom ligation based protocol (adapted from NEBNext® Small RNA Library Prep Set for Illumina®, #E7330)

treatment_protocol: For the bacitracin treatment, the wild-type strain was grown in BHI to OD600 ∼0.3, bacitracin was added to a final concentration of 50 μg/ml and bacteria were grown for further 30 min to OD600 ∼0.7, and sample was collected. The same protocol without bacitracin treatment was applied for the WT-BHI sample. 10 ml of culture were rapidly centrifuged at room temperature, and bacterial pellets were flash-frozen and stored at -80°C for further RNA isolation.

tag: genotype

value: WT

tag: agent

value: Bacitracin


title: WT1+Bacitracin


title: WT2+Bacitracin


description: NGN2_RNA_seq_line_11_CRISPR_GG_well_G7_sample_2 [CD0000011]


description: NGN2_RNA_seq_line_11_CRISPR_GG_well_B11_sample_2 [CD0000011]


title: WT2

source_name: WT BHI


description: NGN2_RNA_seq_line_11_CRISPR_GG_well_G7_sample_1 [CD0000011]


description: NGN2_RNA_seq_line_11_CRISPR_GG_well_H6_sample_1 [CD0000011]


description: NGN2_RNA_seq_line_11_CRISPR_AA_well_H12_sample1 [CD0000011]


description: NGN2_RNA_seq_line_11_CRISPR_AA_well_A11_sample2 [CD0000011]


description: NGN2_RNA_seq_line_11_CRISPR_AA_well_H12_sample2 [CD0000011]


title: WT1


description: NGN2_RNA_seq_line_11_CRISPR_GG_well_B11_sample_1 [CD0000011]


title: WT BHI 2

description: WT BHI 2

data_processing:
Raw sequence files (fastq) were cleaned of 3' adapter sequences, and low quality (cutoff 28) and short sequence (15 nt) reads were removed using AdapterRemoval v1.5.2 software
Reads were aligned against the reference genome (NC_003210) with bowtie v1.0.0 using default parameters
Raw counts were generated with HTSeq v0.6.0
Differential expression analysis was performed with DeSeq2 software package with default parameters
Genome_build: NC_003210
Supplementary_files_format_and_content: WT_vs_VirR.complete.txt, counts, fold-change

growth_protocol: the bacteria were grown in BHI (Difco) from an overnight preculture.

treatment_protocol: the mutant and the wild-type strains were grown in BHI to exponential phase (OD600 0.5-0.7), pelleted and stored at -80°C till further RNA isolation. Three biological replicates (individual colonies) of wild type and mutant strains were grown on different days.

tag: genotype/variation

value: wildtype


title: WT BHI 1

description: WT BHI 1


title: WT BHI 3

description: WT BHI 3


description: NGN2_RNA_seq_line_11_CRISPR_AA_well_A11_sample1 [CD0000011]


title: delta-VirR BHI 3

description: delta-VirR BHI 3

source_name: delta-VirR BHI

value: delta-VirR


title: NGN2_RNA_seq_CD11_AG_sample1

description: NGN2_RNA_seq_CD11_AG_sample1 [CD0000011]


title: delta-VirR BHI 1

description: delta-VirR BHI 1


description: NGN2_ATAC_seq_line_11_CRISPR_GG_mixed_culture [CD0000011]

library_source: genomic

molecule: genomic DNA

growth_protocol: Briefly, on Day 0, 5 × 105 hiPSCs were dissociated using Accutase (STEMCELL) and replated in 1.2 ml mTeSR Plus media containing 5 µM ROCK inhibitor, rtTA virus and Ngn2-puro or Ngn2-Hygro virus on 6-well plates. On Day 1, media was refreshed with mTeSRPlus containing 2 µg/ml doxycycline. From days 2 to 4, media was refreshed daily with Neuralbasal Medium supplemented with 1× Glutamax/B27, 2 µg/ml doxycycline, and 2 µg/ml puromycin or 200 µg/ml hygromycin. On day 5, cells were dissociated with Accutase and resuspended in Neuralbasal Medium supplemented with 1× Glutamax/B27, 2 µg/ml doxycycline, and 10ng/ml BDNF/GDNF/NT-3. Cells were replated at 2 × 105/cm2 on 0.1% PEI/Matrigel coated 12-well plates. For morphological immunostaining, 5 × 104 iNs were replated onto 12 mm coverslips (with 5 × 104 rat astrocytes pre-cultured) in Neuralbasal Medium supplemented with 1× Glutamax/B27, 2 µg/ml doxycycline, 10 ng/ml BDNF/GDNF/NT-3, and 1% FBS. From Day 6, media was refreshed every three days with a half volume change. Doxycycline was withdrawn from Day 14 onwards. ATAC-seq samples were harvested at Day 20

extract_protocol:
For ATAC-seq, we harvested 50,000 cells by centrifugation at 500 g x 5 min at 4C. We washed cells once with PBS buffer and resuspended the cell pellets in 50 uL of cold lysis buffer (10 mM Tris-HCl, pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA- 630). We collected cell pellets, discarded the supernatants, and immediately continued to transposition reaction in 50 uL transposition reaction mix. We incubated the transposition reaction at 37C for 30 min, immediately followed by purification through a QIAGEN MinElute Kit. We stored the purified DNAs at  20 C until generating sequencing library.
The library was generated and sequenced at University of Minnesota Genomic Center.We have followed the protocol as previously described (Buenrostro et al., 2013) with minor modifications. Specifically, we thawed the transposed and purified DNAs and carried out PCR in 50 uL of reaction with NEBNext High Fidelity 2X Master mix and 5 ul of 25 mM Forward/Reverse ATAC-seq index, i.e., standard barcoded primers of Nextera kit (FC-121-1030), for each sample. After reaction, we purified samples with SPRI beads and eluted the PCR products in 12 uL elution buffer. We checked the DNA library by picogreen quantification and the size of the fragments with an Agilent High Sensitivity DNA chip. Libraries were diluted to 2 nM and pooled for downstream sequencing.


title: HostAM 1 [RNA-seq]

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

institute: INSERM

description:
Pool of 3 mice
mRNA
Replicate 1

data_processing:
Samples were aligned to mouse genome version mm10 using Bowtie aligner.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: rawcount_rna_seq.txt: A table of raw counts on exons was generated using htseq-count (v 0.6.1) and R (v 3.3).

source_name: Whole lung sorted: FSC-A/SSC-A, SiglecF+, CD11c+, singlets, CD45.1+

growth_protocol: 8 weeks old WT C57BL/6 mice for isolation and expansion of AM and 8 weeks old WT C57Bl/6-Ly5.1 mice were used for transplantation of AM.

extract_protocol:
RNA was extracted using the Qiagen miRNeasy Kit.
Amplified cDNA was prepared from 2 ng of total RNA using the Ovation RNA-seq system V2 (NuGEN Technologies, Inc.) following manufacturer's instructions. Briefly, first-strand cDNA was prepared from total RNA using a combination of random and poly-T DNA/RNA chimeric SPIA primers and reverse transcriptase, resulting in a cDNA/mRNA hybrid molecule. Priming sites created by a heating fragmentation of the mRNA within the cDNA/mRNA complex were used to synthesize the second strand cDNA using a DNA polymerase. The resulting double-stranded cDNA with a unique RNA/DNA heteroduplex at one end was purified using Agencourt RNAClean XP beads (Beckman Coulter Inc.). The purified product was then used as the substrate of a linear amplification process, SPIA (single primer isothermal amplification). During the amplification step, RNase H degrades RNA in DNA/RNA heteroduplex at the 5'end of the first cDNA strand, creating a binding site for the DNA/RNA SPIA chimeric primer, then DNA polymerase starts replication at the 3'end of the primer displacing the existing forward strand. The process including SPIA DNA/RNA primer binding, DNA replication, strand displacement and RNA degradation is repeated and results in rapid generation of microgram quantities of amplified cDNA. Amplified cDNA was purified using AMPure XP beads (Beckman Coulter Inc.) and 500 ng was fragmented by sonication using a Covaris E210 instrument (with duty cycle: 10X, intensity: 5 and cycle/burst: 200 for 180 seconds).
The next steps of RNA-Seq Library preparation were performed using Ovation Ultralow Library System kit (NuGEN Technologies, Inc.) according to manufacturer's instructions. Briefly, in this system 100 ng of amplified cDNA were blunted, phosphorylated and ligated to indexed adapter dimers. The libraries were then enriched by PCR amplification (2 min at 72 degrees Celsius; [30 sec at 94 degrees Celsius, 30 sec at 60 degrees Celsius, 1 min at 72 degrees Celsius] x 6 cycles; 5 min at 72 degrees Celsius) and surplus PCR primers were removed by purification using AMPure XP beads. DNA libraries were checked for quality using 2100 Bioanalyzer (Agilent) and quantified using Kapa Sybr Fast Light Cycler 480 qPCR Kit (Kapa Biosystems) following manufacturer's instructions.

treatment_protocol: Mice were injected I.T with 80-100 µl PBS or 0.8 - 1.0 x 10ˆ6 exAM. At the indicated time after injection, lungs were harvested and Live, SiglecF+, CD11c+, CD45.1+ or CD45.2+ AM were FACS-sorted. Samples are from a pool of 3 mice.

value: Host AM

value: Host alveolar macrophages


title: NGN2_RNA_seq_CD11_AG_sample2

description: NGN2_RNA_seq_CD11_AG_sample2 [CD0000011]


title: HostAM 2 [RNA-seq]

description:
Pool of 3 mice
mRNA
Replicate 2


title: exAM 2 [RNA-seq]

description:
Pool of 3 mice
mRNA
Replicate 2

source_name: unsorted

value: AM ex vivo 2 months culture

value: culture expanded alveolar macrophages


title: NGN2_ATAC_seq_line_11_CRISPR_GG_well_G7

description: NGN2_ATAC_seq_line_11_CRISPR_GG_well_G7 [CD0000011]


title: texAM 2 [RNA-seq]

description:
Pool of 3 mice
mRNA
Replicate 2

source_name: Whole lung sorted: FSC-A/SSC-A, SiglecF+, CD11c+, singlets, CD45.2+

value: Transplanted expanded AM 4 months in vivo

value: transplanted expanded alveolar macrophages


title: texAM 1 [RNA-seq]

description:
Pool of 3 mice
mRNA
Replicate 1


title: tAM 2 [RNA-seq]

description:
Pool of 3 mice
mRNA
Replicate 2

value: Transplanted AM 4 months in vivo

value: transplanted alveolar macrophages


title: delta-VirR BHI 2

description: delta-VirR BHI 2


description: NGN2_ATAC_seq_line_11_CRISPR_GG_well_B11 [CD0000011]


title: NGN2_ATAC_seq_line_11_AG_sample2

description: NGN2_ATAC_seq_line_11_AG_sample2 [CD0000011]


title: SPF_104w_F_3

city: Freiburg im Breisgau

first: Omar

last: Mossad

address: Breisacher str 64

department: Institute of Neuropathology

country: Germany

institute: University Hospital Freiburg

data_processing:
Illumina CASAVA1.8.2 software used for basecalling.
Quality of sequencing reads stored in FASTQ files was assessed using FastQC (0.67) and trimmed using Trim Galore! (0.4.3). Strandedness of the library preparations was estimated for each sample using RSeQC (2.6.4)
Reads were mapped on the mouse genome version mm10 (UCSC) using STAR aligner (2.5.2) with RefGene annotation and index with 100 bp splice junction overhang. The number of reads mapped to each gene (counts) was extracted from the BAM files using Feature-Count (1.5.3) with the annotation version mm10 from UCSC and the following parameters: exon feature file, unstranded, a minimum mapping quality per read of 12, a minimum overlap of 1bp and other parameters set to default. A quality report of each step was generated using MultiQC (1.5.0). The process to extract the gene counts from FASTQ files was run on Galaxy. Three samples with a low mapping rate (< 75%) were removed.
A differential expression analysis was performed with DESeq2 (1.32.0) with a design model integrating the different factors (microbiota and age) and their interactions. The addition of each factor and interactions were tested beforehand and the number of genes with significant adjusted p-values for the LRT (Likelihood Ratio Test) was reported as the percentage of variables' effect on transcriptomic profile. An exploratory analysis and visualization of variance stabilizing transformation (VST) calculated by the DESeq2 model were performed. After that, normalized counts generated by DESeq2 were assessed for artifacts or contamination by other cell types. The list of genes used was based on single-cell RNA-sequencing data previously obtained by our group57. 30 marker genes of non-microglial cell types were removed. R version 4.1.0 was used to perform the Ward error sum of squares hierarchical clustering method and principal components analyses (PCA). Using the DESeq2 model, the differentially expressed genes (DEGs) showing adjusted p-values (Wald test) of less than 0.05 and absolute fold change greater than 1.5 were identified.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables with normalized gene counts for every gene and every sample

source_name: whole brain

extract_protocol:
Total RNA was extracted from FACS sorted CD11b+CD45lowLin- microglia cells using The ARCTURUS PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. The SMARTer v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) was used to generate first strand cDNA from 500 to 750 pg total-RNA. Double stranded cDNA was amplified by LD PCR (11 cycles) and purified via magnetic bead clean-up.
Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposase. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step, 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems). Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3.

value: Microglia

tag: microbiota

value: SPF


title: SPF_104w_F_2


description: NGN2_ATAC_seq_line_11_CRISPR_AA_well_A11 [CD0000011]

value: Glutamatergic, NGN2-induced, day-20 neuron

value: case


description: NGN2_ATAC_seq_line_11_CRISPR_AA_well_H12 [CD0000011]

value: Female


title: SPF_8w_F_4

value: 6-10 weeks


title: NGN2_RNA_seq_CD11_AG_sample3

description: NGN2_RNA_seq_CD11_AG_sample3 [CD0000011]


description: NGN2_ATAC_seq_line_11_CRISPR_AA_well_mixed_culture [CD0000011]


title: SPF_8w_F_3


title: SPF_8w_F_1


title: SPF_104w_F_1


title: NGN2_RNA_seq_line_19

description: NGN2_RNA_seq_line_19 [CD0000019]

growth_protocol: Briefly, on Day 0, 5 × 105 hiPSCs were dissociated using Accutase (STEMCELL) and replated in 1.2 ml mTeSR Plus media containing 5 µM ROCK inhibitor, rtTA virus and Ngn2-puro or Ngn2-Hygro virus on 6-well plates. On Day 1, media was refreshed with mTeSRPlus containing 2 µg/ml doxycycline. From days 2 to 4, media was refreshed daily with Neuralbasal Medium supplemented with 1× Glutamax/B27, 2 µg/ml doxycycline, and 2 µg/ml puromycin or 200 µg/ml hygromycin. On day 5, cells were dissociated with Accutase and resuspended in Neuralbasal Medium supplemented with 1× Glutamax/B27, 2 µg/ml doxycycline, and 10ng/ml BDNF/GDNF/NT-3. Cells were replated at 2 × 105/cm2 on 0.1% PEI/Matrigel coated 12-well plates. For morphological immunostaining, 5 × 104 iNs were replated onto 12 mm coverslips (with 5 × 104 rat astrocytes pre-cultured) in Neuralbasal Medium supplemented with 1× Glutamax/B27, 2 µg/ml doxycycline, 10 ng/ml BDNF/GDNF/NT-3, and 1% FBS. From Day 6, media was refreshed every three days with a half volume change. Doxycycline was withdrawn from Day 14 onwards. RNA-seq samples were harvested at Day 30

value: control

value: Male


title: NGN2_RNA_seq_line_18

description: NGN2_RNA_seq_line_18 [CD0000018]


title: NGN2_RNA_seq_line_17

description: NGN2_RNA_seq_line_17 [CD0000017]


title: GF_104w_F_1

value: GF


title: NGN2_RNA_seq_line_15

description: NGN2_RNA_seq_line_15 [CD0000015]


title: NGN2_RNA_seq_line_16

description: NGN2_RNA_seq_line_16 [CD0000016]


title: GF_104w_F_3


title: NGN2_RNA_seq_line_20

description: NGN2_RNA_seq_line_20 [CD0000020]


title: GF_104w_F_2


title: GF_8w_F_5


title: exAM 1 [RNA-seq]

description:
Pool of 3 mice
mRNA
Replicate 1


title: NGN2_RNA_seq_line_21

description: NGN2_RNA_seq_line_21 [CD0000021]


title: GF_8w_F_3


title: NGN2_ATAC_seq_line_11_AG_sample1

description: NGN2_ATAC_seq_line_11_AG_sample1 [CD0000011]


title: GF_8w_F_2


title: tAM 1 [RNA-seq]

description:
Pool of 3 mice
mRNA
Replicate 1


title: NGN2_RNA_seq_line_13

description: NGN2_RNA_seq_line_13 [CD0000013]


title: CML_4

data_processing:
Illumina CASAVA1.8.2 software used for basecalling.
Quality of sequencing reads stored in FASTQ files was assessed using FastQC (0.67) and trimmed using Trim Galore! (0.4.3). Strandedness of the library preparations was estimated for each sample using RSeQC (2.6.4).
Reads were mapped on the mouse genome version mm10 (UCSC) using STAR aligner (2.5.2) with RefGene annotation and index with 100 bp splice junction overhang. The number of reads mapped to each gene (counts) was extracted from the BAM files using Feature-Count (1.5.3) with the annotation version mm10 from UCSC and the following parameters: exon feature file, unstranded, a minimum mapping quality per read of 12, a minimum overlap of 1bp and other parameters set to default. A quality report of each step was generated using MultiQC (1.5.0). The process to extract the gene counts from FASTQ files was run on Galaxy. Three samples with a low mapping rate (< 75%) were removed.
A differential expression analysis was performed with DESeq2 (1.32.0) with a design model integrating the different factors (microbiota and age) and their interactions. The addition of each factor and interactions were tested beforehand and the number of genes with significant adjusted p-values for the LRT (Likelihood Ratio Test) was reported as the percentage of variables' effect on transcriptomic profile. An exploratory analysis and visualization of variance stabilizing transformation (VST) calculated by the DESeq2 model were performed. After that, normalized counts generated by DESeq2 were assessed for artifacts or contamination by other cell types. The list of genes used was based on single-cell RNA-sequencing data previously obtained by our group57. 30 marker genes of non-microglial cell types were removed. R version 4.1.0 was used to perform the Ward error sum of squares hierarchical clustering method and principal components analyses (PCA). Using the DESeq2 model, the differentially expressed genes (DEGs) showing adjusted p-values (Wald test) of less than 0.05 and absolute fold change greater than 1.5 were identified.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: norm_counts_*.txt: Matrix tables with normalized gene counts for every gene and every sample for microbiota & cml.

value: 10 weeks

value: CML


title: NGN2_RNA_seq_line_14

description: NGN2_RNA_seq_line_14 [CD0000014]


title: NGN2_RNA_seq_line_12

description: NGN2_RNA_seq_line_12 [CD0000012]


title: CML_3


title: NGN2_RNA_seq_line_11

description: NGN2_RNA_seq_line_11 [CD0000011]


title: NGN2_RNA_seq_line_10

description: NGN2_RNA_seq_line_10 [CD0000010]


title: CML_1


title: NGN2_RNA_seq_line_08

description: NGN2_RNA_seq_line_08 [CD0000008]


title: NGN2_RNA_seq_line_07

description: NGN2_RNA_seq_line_07 [CD0000007]


title: CML_2


title: NGN2_RNA_seq_line_09

description: NGN2_RNA_seq_line_09 [CD0000009]


title: PBS_3

value: PBS


title: NGN2_RNA_seq_line_06

description: NGN2_RNA_seq_line_06 [CD0000006]


title: NGN2_RNA_seq_line_05

description: NGN2_RNA_seq_line_05 [CD0000005]


title: PBS_2


title: NGN2_RNA_seq_line_04

description: NGN2_RNA_seq_line_04 [CD0000004]


title: GF_104w_M_4


title: PBS_1


title: NGN2_RNA_seq_line_03

description: NGN2_RNA_seq_line_03 [CD0000003]


title: GF_104w_M_5


title: Input iSLK-UR

city: Amherst

first: Daniel

last: MacVeigh-Fierro

state: MA

address: 639 N Pleasant St, Morrill Iv North

department: Microbiology

institute: UMass Amherst

data_processing:
Only the forward (R1" reads were used for the analysis.
Bam and bigWig files for each of the IP and input libraries to vizualize read alignment, KSHV genome is added as an extra genome for comparison
Eclipse used PureCLIP (https://pureclip.readthedocs.io/en/latest/) to identify m6A sites with a single nucleotide resolution. This algorithm identifies crosslink sites in eCLIP experiments, and it is not specifically trained to call m6A sites or required to ensure that crosslink site calls correspond to Adenosines. Therefore, as a part of the evaluation, we assessed enrichment of DRACH motif relative to reads starts in IP and input libraries, as well as calculated what fraction of identified crosslink sites are positioned on DRACH
Supplementary_files_format_and_content: Two files containing the PureCLIP start and stop locations of m6A sites. Labeled with the chromosome, strand, gene, Ensembl ID and feature. It also features the read start fold change. One file are the UR iSLK.219s and the other the 48R iSLK.219 sample

source_name: iSLK.219 cells

growth_protocol: ISLK.219 cells were grown were grown in Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen) supplemented with 10% fetal bovine serum (FBS), and were harvested  in their latent phase or 48h post reactivation.

extract_protocol:
Total RNA was harvested using TRIzol according to the manufacturer's protocol. Samples were sent to Eclipse Bio for m6A eCLIP enrichment then subsequent RNA seq and processing
samples were processed by EclipseBio as described in their user guide, performing 150 Paired End run on NovaSeq6000 on was PolyA selected RNA

treatment_protocol: Lytic reactivation cells were induced by the addition of 0.2 μg/ml doxycycline (BD Biosciences) and 110 μg/ml sodium butyrate for 48 h

value: iSLK.219 cells


title: Input iSLK-48R

value: Lytic reactivation cells were induced by the addition of 0.2 μg/ml doxycycline (BD Biosciences) and 110 μg/ml sodium butyrate for 48 h


title: iSLK-UR

description: m6A eCLIP-RNA seq


title: iSLK-48R

description: m6A eCLIP-RNA seq


title: GF_104w_M_3


title: Infect_2

city: New York

first: Brad

middle: R

last: Rosenberg

state: NY

address: 1 Gustave L Levy Place, Box 1124

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Fastq files were mapped and quantified using cellranger (v3.1.0, 10X Genomics) count to a combined human (GrCh38) and SARS-CoV-2 reference. The SARS-CoV-2 reference was derived from empirically defined RNAs sequenced with long-read direct RNA Nanopore sequencing published by Kim et al, Cell 2020. These were downloaded from the UCSC Genome Table Browser after filtering for TRS-dependent transcripts and score > 900 and exporting to gtf format. Transcripts for previously unknown ORFs were excluded and an additional annotation for genomic RNA covering the entire length of the SARS-CoV-2 genome was added. Modifications the reference were made to match the USA/WA01 SARS-CoV-2 strain. To minimize redundancy in the SARS-CoV-2 annotation of subgenomic RNAs (sgmRNAs) and thereby mitigate the exclusion of “ambiguous” sequence reads from scRNAseq quantification (i.e. reads derived from viral sgmRNAs mapping to redundant 3′ transcription regions), the 3′ region of each sgmRNA was truncated at the most distal 5′ start of the subsequent ORF immediately downstream.
Genome_build: custom build described above
Supplementary_files_format_and_content: h5: gene x cell matrix output by cellranger

source_name: Human pancreatic islets

growth_protocol: Human pancreatic islets for research purposes from non-diabetic cadaveric donors were obtained through Prodo Laboratories, Inc (Aliso Viejo, CA). Upon receipt, islets were rested overnight in Prodo Islet Media (Transport) / PMI(T) (5.8 mM D-glucose) at 37°C and 5% CO2 before transfer to complete RPMI 1640 (11.1 mM D-glucose) with 10% fetal bovine serum, 1% penicillin-streptomycin, 25 mM HEPES and GlutaMAX supplement (Gibco ThermoFisher) for subsequent culture.

extract_protocol:
Islets were gently dissociated into a single cell suspension in 500 μl Accutase (Innovative Cell Technologies) for up to 10 minutes at 37°C. Cells were then washed with PBS, passed through a 70 μm strainer and resuspended in a final volume of 200 μl. Cell viability and number of cells were determined using Trypan Blue Stain and a Countess Automated Cell Counter (ThermoFisher). 8,000 cells per sample were loaded onto the 10X Genomics Chromium Controller according to the 10X Genomics protocol.
cDNA was prepared according to the 10X reverse transcriptase protocol as per manufacturer's instructions, and samples were stored at -80°C for concurrent library preparation and sequencing. Libraries were prepared according to the manufacturer's protocol for 10X Genomics Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1. Libraries were pooled in equimolar concentration and sequenced to a targeted depth of 25,000 reads per cell with the Illumina NovaSeq SP 100 cycle kit with run parameters (read 1 28, index read i7 8, index read i5 0, read 2 60).

treatment_protocol: Primary human islets were infected in non-TC-treated 24-well plates at 3,000-4,000 islet equivalents per 500 μl complete RMPI 1640 (5.5 mM D-glucose) in the absence (mock infection) or presence of 2 x 10^4 pfu/well SARS-CoV-2 (USA-WA1/2020) for 48 hours.

tag: infection

value: SARS-CoV-2 (USA-WA1/2020)

tag: donor

value: Donor 2

value: Human pancreatic islets


title: Infect_1

value: Donor 1


title: Infect_3

value: Donor 3


title: NGN2_RNA_seq_line_02

description: NGN2_RNA_seq_line_02 [CD0000002]

value: Glutamatergic, NGN2-induced, day-20 neuron


title: GF_104w_M_2

value: Microglia


title: NGN2_ATAC_seq_line_21

description: NGN2_ATAC_seq_line_21 [CD0000021]

value: case


title: Mock_2

value: Mock


title: PBS_4

value: SPF


title: Idiopathic Intermediate Uveitis [SystUviIU012]

city: Utrecht

first: Jonas

last: Kuiper

address: Heidelberglaan 100

department: Ophthalmology

country: Netherlands

institute: Universitair Medisch Centrum Utrecht

data_processing:
FastQC for quality check
STAR aligner for genome indexing and alignment of reads
Htseq to generate count data
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: .count data in processed directory. Contains the read counts generated using Htseq count (python) module.

source_name: Idiopathic Intermediate Uveitis

extract_protocol: NOT PROVIDED; REQUESTED

value: female

tag: age @ sampling

tag: subject group

value: Active uveitis, without systemic inflammatory disease, systemic treatment free


title: GF_104w_M_1

tag: Sex

value: Male

value: GF


title: Idiopathic Intermediate Uveitis [SystUviIU011]

value: male


title: Mock_3


title: NGN2_ATAC_seq_line_20

description: NGN2_ATAC_seq_line_20 [CD0000020]


title: NGN2_ATAC_seq_line_19

description: NGN2_ATAC_seq_line_19 [CD0000019]

value: control


title: Idiopathic Intermediate Uveitis [SystUviIU009]


title: NGN2_ATAC_seq_line_18

description: NGN2_ATAC_seq_line_18 [CD0000018]

value: Female


title: Idiopathic Intermediate Uveitis [SystUviIU007]


title: Idiopathic Intermediate Uveitis [SystUviIU008]


title: Idiopathic Intermediate Uveitis [SystUviIU006]


title: SPF_104w_M_7


title: SPF_104w_M_8


title: Idiopathic Intermediate Uveitis [SystUviIU003]


title: NGN2_ATAC_seq_line_17

description: NGN2_ATAC_seq_line_17 [CD0000017]


title: SPF_104w_M_5


title: Idiopathic Intermediate Uveitis [SystUviIU001]


title: Healthy blood donor [SystUviHC017]

source_name: Healthy blood donor

value: No History of inflammatory eye disease, no  systemic inflammatory condition


title: NGN2_ATAC_seq_line_15

description: NGN2_ATAC_seq_line_15 [CD0000015]


title: Healthy blood donor [SystUviHC018]


title: Healthy blood donor [SystUviHC016]


title: Idiopathic Intermediate Uveitis [SystUviIU002]


title: Mock_1


title: Healthy blood donor [SystUviHC014]


title: NGN2_ATAC_seq_line_14

description: NGN2_ATAC_seq_line_14 [CD0000014]


title: SPF_104w_M_6


title: Healthy blood donor [SystUviHC015]


title: SPF_104w_M_14


title: SPF_104w_M_13


title: SPF_104w_M_9


title: Healthy blood donor [SystuviHC012]


title: Healthy blood donor [SystUviHC011]


title: NGN2_ATAC_seq_line_13

description: NGN2_ATAC_seq_line_13 [CD0000013]


title: Healthy blood donor [SystUviHC010]


title: SPF_104w_M_12


title: SPF_104w_M_11


title: Healthy blood donor [SystUviHC007]


title: Healthy blood donor [SystUviHC006]


title: NGN2_ATAC_seq_line_11

description: NGN2_ATAC_seq_line_11 [CD0000011]


title: Healthy blood donor [SystUviHC005]


title: SPF_104w_M_10


title: NGN2_ATAC_seq_line_16

description: NGN2_ATAC_seq_line_16 [CD0000016]


title: NGN2_ATAC_seq_line_12

description: NGN2_ATAC_seq_line_12 [CD0000012]


title: Healthy blood donor [SystUviHC004]


title: Healthy blood donor [SystUviHC002]


title: NGN2_ATAC_seq_line_10

description: NGN2_ATAC_seq_line_10 [CD0000010]


title: Healthy blood donor [SystUviHC003]


title: NGN2_ATAC_seq_line_09

description: NGN2_ATAC_seq_line_09 [CD0000009]


title: SPF_104w_M_2


title: HLA-A29-positive Birdshot Uveitis [SystUviBS011]

source_name: HLA-A29-positive Birdshot Uveitis


title: SPF_104w_M_4


title: HLA-A29-positive Birdshot Uveitis [SystUviBS009]

value: Active uveitis, without systemic inflammatory disease, prednisolone  oral <10mg


title: HLA-A29-positive Birdshot Uveitis [SystUviBS008]


title: NGN2_ATAC_seq_line_08

description: NGN2_ATAC_seq_line_08 [CD0000008]


title: HLA-A29-positive Birdshot Uveitis [SystUviBS010]


title: HLA-A29-positive Birdshot Uveitis [SystUviBS006]


title: HLA-A29-positive Birdshot Uveitis [SystUviBS007]


title: NGN2_ATAC_seq_line_06

description: NGN2_ATAC_seq_line_06 [CD0000006]


title: HLA-A29-positive Birdshot Uveitis [SystUviBS005]


title: HLA-A29-positive Birdshot Uveitis [SystUviBS003]


title: NGN2_ATAC_seq_line_05

description: NGN2_ATAC_seq_line_05 [CD0000005]


title: SPF_8w_M_3

value: 6-10 weeks


title: SPF_8w_M_4


title: SPF_8w_M_2


title: HLA-A29-positive Birdshot Uveitis [SystUviBS001]


title: NGN2_ATAC_seq_line_04

description: NGN2_ATAC_seq_line_04 [CD0000004]


title: HLA-B27-positive acute anterior uveitis [SystUviAU008]

source_name: HLA-B27-positive acute anterior uveitis


title: HLA-B27-positive acute anterior uveitis [SystUviAU009]


title: NGN2_ATAC_seq_line_03

description: NGN2_ATAC_seq_line_03 [CD0000003]


title: HLA-B27-positive acute anterior uveitis [SystUviAU007]


title: GF_8w_M_1


title: HLA-B27-positive acute anterior uveitis [SystUviAU004]


title: HLA-B27-positive acute anterior uveitis [SystUviAU005]


title: SPF_104w_M_1


title: NGN2_ATAC_seq_line_02

description: NGN2_ATAC_seq_line_02 [CD0000002]


title: WTC11_AFTER3

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

description: WTC11 hiPSCs, passage 45+32

data_processing:
Illumina bcl2fastq (v2.20.0.422) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.12) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
HTSeq (v0.13.5) were perfomed for counting reads with the GENCODE (version 35) annotation gtf file.
To normalized read counts, R (v3.6.1) and its package DESeq2 (v1.26.0) were performed.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file including DESeq2 nomalized count values for each sample.

source_name: Human iPSC

growth_protocol: Human pluripotent stem cells were maintained in StemFiT AK02N media (Ajinomoto) on iMatrix-511-coated plates at 37 ºC in a humidified incubator with 20% O2 and 5% CO2.

extract_protocol:
RNA was prepared using the miReasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified with the Agilent 2100 Bioanalyzer (Agilent Technologies).
Illumina TruSeq Stranded Total RNA Library Prep

tag: cell line

tag: passage

value: AFTER


title: GF_8w_M_3

tag: treatment


title: HLA-B27-positive acute anterior uveitis [SystUviAU003]


title: HLA-B27-positive acute anterior uveitis [SystUviAU006]


title: HLA-B27-positive acute anterior uveitis [SystUviAU002]


title: NGN2_ATAC_seq_line_07

description: NGN2_ATAC_seq_line_07 [CD0000007]

tag: cell type


title: WTC11_AFTER2

description: WTC11 hiPSCs, passage 45+31


title: HLA-B27-positive acute anterior uveitis [SystUviAU001]


title: 271364-ai [ECA-6]

city: fuzhou

first: yangfan

last: zhang

address: Fujian Normal University Qishan Campus, College Town, Fuzhou, Fujian Province

country: China

institute: FJNU

description: tumor 6

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg38 whole genome using Hisat2
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: esophagus

extract_protocol:
The total RNA was extracted by RNA extraction kit (Qiagen)
The RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject/sample id

tag: tissue

value: esophagus

tag: tissue subtype

value: ESCC tumor


title: 271364-zhengchang [Normal-6]

description: normal 6

value: adjacent normal tissue


title: WTC11_AFTER1

description: WTC11 hiPSCs, passage 45+30


title: HLA-A29-positive Birdshot Uveitis [SystUviBS002]

tag: gender


title: MeDIP_siBDH2_IP

city: Changsha

first: Xiaofei

last: Gao

address: NO.139 Renmin Middle Road

institute: The Second Xiangya hospital of Central South University

data_processing:
For RNA-seq data, lllumina Hiseq was used for basecalling. The raw data were firstly processed through Seqtk. The RNA-seq data were then mapped to the mouse reference genome mm10 with Hisat2(version:2.0.4). Stringtie(version:1.3.0) was used to count the number of fragments per gene after Hisat2 matching. The differential analysis was performed using DESeq.
For MeDIP-seq and hMeDIP-seq, low quality bases were trimmed by using Trimmomatic(version: 0.36). Clean reads were mapped to human reference genome (hg19) using Bowtie2(version:2.3.4.3) with default parameters. MACS2(version: 2.1.2) software was used to call peaks representing enriched binding sites from filtered alignment file with default parameters.
Genome_build: mm10;hg19
Supplementary_files_format_and_content: For RNA-seq data, matrix table with raw gene counts for every gene and every sample; For MeDIP-seq/hMeDIP data, the Integrative Genomics Viewer (IGV) software was used for data visualization.

source_name: naive CD4

growth_protocol: All human studies were permitted by the Ethics Committee of the Second Xiangya Hospital of Central South University, China, all participants subscribed written informed consent. All animal procedures were approved by the Animal Care and Use Committee of the Laboratory Animal Research Center at the Second Xiangya Medical School, Central South University

extract_protocol:
Total RNA was extracted from Tfh cells using TRIzol reagent (MRC) for RNA-sequencing, including total RNA sample detection, mRNA enrichment, synthesis of double-stranded cDNAs, End Repair/dA-Tailing Module, fragment selection, and PCR amplification, library detection, and Illumina sequencingselection, and PCR amplification, library detection, and Illumina sequencing.
DNA was isolated from induced Tfh cells. 1 microgram of original genomic DNA was fragmented to a mean size of 300 bp. The methylated DNA fractions were immunoprecipitated using the Magnetic Methylated DNA Immunoprecipitation Kit (Diagenode) according to the instructions. The hydroxymethylated DNA fractions were immunoprecipitated using the hMeDIP kit (Active Motif) according to the instructions. After that, the immunoprecipitated products were then treated with protease K and purified with ZYMO DNA Clean & Concentrator-5 (ZYMO). Finally, the MeDIP seq and hMeDIP-seq libraries were constructed by PCR amplification with the enriched DNA as templates.
RNA libraries were prepared for sequencing using standard Illumina protocols
MeDIP-seq/hMeDIP libraries were sequenced using Illumina platform with PE150 read length.

treatment_protocol:
For murine Tfh cell polarization, splenic naive CD4+ T cells were isolated from the WT and miR-21 cKO mice, and then cultured under the Tfh-polarized condition for 5 days. After 5 days of polarization, cells were collected for RNA-sequencing to compare gene expression between WT Tfh cells and miR-21 cKO Tfh cells induced in vitro.
For human Tfh cell polarization, human naïve CD4+ T cells were isolated from peripheral blood of healthy donors. Naïve CD4+T cells were transfected with Agomir-21/Agomir-NC, or siRNA-BDH2/siNC and then cultured under Tfh-cell polarized conditions for 3 days.

value: Blood

value: Tfh cell polarization

tag: genotype


title: MeDIP_siNC_IP

value: siNC


title: GF_8w_M_4

value: Microglia

tag: age


title: MeDIP_Agomir21_IP


title: 271121-ai [ECA-5]

description: tumor 5


title: hMeDIP_siNC_IP

data_processing:
Library strategy: hMeDIP-seq
For RNA-seq data, lllumina Hiseq was used for basecalling. The raw data were firstly processed through Seqtk. The RNA-seq data were then mapped to the mouse reference genome mm10 with Hisat2(version:2.0.4). Stringtie(version:1.3.0) was used to count the number of fragments per gene after Hisat2 matching. The differential analysis was performed using DESeq.
For MeDIP-seq and hMeDIP-seq, low quality bases were trimmed by using Trimmomatic(version: 0.36). Clean reads were mapped to human reference genome (hg19) using Bowtie2(version:2.3.4.3) with default parameters. MACS2(version: 2.1.2) software was used to call peaks representing enriched binding sites from filtered alignment file with default parameters.
Genome_build: mm10;hg19
Supplementary_files_format_and_content: For RNA-seq data, matrix table with raw gene counts for every gene and every sample; For MeDIP-seq/hMeDIP data, the Integrative Genomics Viewer (IGV) software was used for data visualization.


title: WTC11_BEFORE2

description: WTC11 hiPSCs, passage 46

value: BEFORE


title: 6 months old-Cortex-Tau4RΔK-AP-Female TL16

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

description:
6 months old-Cortex-Tau4RΔK-AP-Female
scRNA-Seq

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat V3 was used to perform downstream analysis following the standard pipeline.
Genome_build: mm10

source_name: scRNA-Seq - TL16

extract_protocol: scRNA-Seq following 10x V3.0 guideline

tag: strain

value: Cerebral cortex

value: 6 months old


title: 271116-zhengchang [Normal-4]

description: normal 4


title: 6 months old-Cortex-APP;PS1-Female TL15

description:
6 months old-Cortex-APP;PS1-Female
scRNA-Seq

source_name: scRNA-Seq - TL15


title: 6 months old-Cortex-Tau4RΔK-Female TL14

description:
6 months old-Cortex-Tau4RΔK-Female
scRNA-Seq

source_name: scRNA-Seq - TL14


title: WTC11_BEFORE1

description: WTC11 hiPSCs, passage 45


title: 6 months old-Cortex-WT-Female TL13

description:
6 months old-Cortex-WT-Female
scRNA-Seq

source_name: scRNA-Seq - TL13


title: WTB6_AFTER3

description: WTB6 hiPSCs, passage 49+32


title: hMeDIP_siBDH2_IP


title: WTB6_AFTER2

description: WTB6 hiPSCs, passage 49+31


title: 270954-zhengchang [Normal-3]

description: normal 3


title: hMeDIP_Agomir21_IP


title: 270954-ai [ECA-3]

description: tumor 3


title: 12 months old-Cortex-Tau4RΔK-AP-Female TL12

description:
12 months old-Cortex-Tau4RΔK-AP-Female
scRNA-Seq

source_name: scRNA-Seq - TL12

value: 12 months old


title: WTB6_AFTER1

description: WTB6 hiPSCs, passage 49+30


title: SK-N-BE2 shSAPCD2_rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al.. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample …

source_name: Neuroblastoma cells

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neuroblastoma cells

tag: transfected with


title: 271121-zhengchang [Normal-5]

description: normal 5


title: 12 months old-Cortex-APP;PS1-Female TL11

description:
12 months old-Cortex-APP;PS1-Female
scRNA-Seq

source_name: scRNA-Seq - TL11

value: Female


title: WTB6_BEFORE3

description: WTB6 hiPSCs, passage 51


title: WTC11_BEFORE3

description: WTC11 hiPSCs, passage 47


title: MeDIP_Agomirnc_IP

value: Agomirnc


title: 12 months old-Cortex-Tau4RΔK-Female TL10

description:
12 months old-Cortex-Tau4RΔK-Female
scRNA-Seq

source_name: scRNA-Seq - TL10


title: WTB6_BEFORE2

description: WTB6 hiPSCs, passage 50


title: 12 months old-Cortex-WT-Female TL9

description:
12 months old-Cortex-WT-Female
scRNA-Seq

source_name: scRNA-Seq - TL9


title: WTB6_BEFORE1

description: WTB6 hiPSCs, passage 49


title: SK-N-BE2 shScb_rep1

value: scramble shRNA


title: 271116-ai [ECA-4]

description: tumor 4


title: 12 months old-Cortex-Tau4RΔK-AP-Female TL4

source_name: scRNA-Seq - TL4


title: 154836-zhengchang [Normal-1]

description: normal 1


title: 154836-ai [ECA-1]

description: tumor 1


title: 12 months old-Cortex-APP;PS1-Female TL3

source_name: scRNA-Seq - TL3


title: hMeDIP_Agomirnc_IP


title: 12 months old-Cortex-WT-Female TL1

source_name: scRNA-Seq - TL1


title: WT2

description: wild type

value: Spleen

value: wildtype


title: JKD6008 ∆sRNA275::sRNA275 (repaired) RNA-seq (no vancomycin) replicate 2

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

data_processing:
Trimming - BBTrim from BBTools
RNase III-CLASH: Merging paired reads: BBMerge from BBTools
RNase III-CLASH: Calling RNase III binding sites: pyCRAC (Webb et al Genome Biol 2014)
RNase III-CLASH: Calling RNA-RNA interactions: hyb (Travis et al Bioinformatics 2013)
dRNA-seq: Mapping, calling RNA 5' ends: ANNOgesic (Yu, Vogel, Forstner Gigascience, 2018)
Term-seq: Read mapping/alignment: bowtie2
Term-seq: 3' end mapping: bedtools genomecov
Term-seq: Statistical filtering: Custom R scripts inspired by Dar & Sorek Science 2016.
RNA-seq: Read mapping/alignment: bowtie2
RNA-seq: Statistical analysis: DESeq2 (Bioconductor)
Genome_build: NC_017341.1
Genome_build: NZ_LR027876.1
Supplementary_files_format_and_content: BEDGRAPH format, files contain mapped read depth representing RNase III-RNA interaction sites (binding sites)
Supplementary_files_format_and_content: BEDGRAPH, RNA 3' end depth (reverse complement read 5' ends)

organism: Staphylococcus aureus subsp. aureus str. JKD6008

growth_protocol: Muller-Hinton media, grown at 37C to an OD600 of 3.0

extract_protocol:
Total RNA was extracted using a GTC Phenol extraction protocol (Tollervey and Mattaj, EMBO J 1987)
Total RNA-seq libraries were constructed by NovoGene.

treatment_protocol: 3ug/ml vancomycin for 10 mins at OD600 where indicated | 10ug/ml chloramphenicol was added to cultures with pSD-1 and derivatives

value: {delta}sRNA275::sRNA275 (repaired)


title: Los

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

institute: University of Calgary

description: # FACS sorted cells: 15,000 cells; Recovered: 5,702 cells

data_processing:
All raw FASTQs reads were aligned to the human referene genome GRCh38 (primary assembly) using the STAR algorithm and quantified through the 10X Genomics cellranger v3.0.1 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat (v3) R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes was obtained and used to calculate up to 50 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. Significant PCs were used to run and plot a tSNE plot for all cells. Expression of selected marker genes across cell clusters identified by graph based clustering was used to identify cell clusters for all subsequent analysis.
Genome_build: Homo_sapiens : GRCh38
Supplementary_files_format_and_content: Filtered gene/feature - barcode matrix output from CellRanger

molecule: polyA RNA

source_name: Los

extract_protocol:
Kidney organoids were dissociated to single cells using TrypLE Select (Thermo Fisher Scientific) at 37°C with mechanical trituration. Single cell suspensions were visually inspected under a microscope, counted using an automated hand-held cell counter (Scepter™ 2.0 Cell Counter), and resuspended at a concentration of 15,000 single-cells in 50 microliters of FACS buffer (0.1% BSA–PBS). All four samples were processed according to 10X Genomics ChromiumTM Next GEM Single Cell 3' Reagent Kits v3.1 as per manufacturer’s protocol.
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3.1 Chemistry as per the manufacturer’s protocol. Briefly, single cells were partitioned together with barcoded Gel Bead-In-EMulsions (GEMs) using 10x GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent D1000 ScreenTape System. Libraries were pooled and first sequenced on NovaSeq 100 (plus 25 additional) Cycle SP dual lane flow cell to approximate the number of recovered cells in each sample. We recovered 4,235 cells in Control, 5,702 cells in Losartan-alone, 5,800 cells in Angiotensin II-alone, and 5,855 cells in Angiotensin II plus Losartan treated groups with an estimated doublet rate of ≈4%. Based on these, we determined proportions for Illumina NovaSeq 100 (plus 25 additional) Cycle S2 dual lane flow cell with a targeted sequencing depth of ~30,000 reads per cell. Illumina sequencer's BCL files were demultiplexed using cellranger mkfastq (a wrapper around Illumina's bcl2fastq). Downstream barcode processing, alignment to pre-built GRCh38, and single-cell 3′ gene counting were performed using CellRanger software version 3.0.1 (10X Genomics). All four libraries were aggregated using cellranger aggr (with mapped normalization). The resulting filtered feature-barcode matrix was imported into Seurat v3 for quality control, dimensionality reduction, cell clustering, and differential expression analysis using default or recommended parameters.

treatment_protocol: Culturing of iPSC : Human iPSC derived from cryopreserved human dermal fibroblast (Cell Applications, Inc. Cat. #106-05n, lot #1481 using CytoTune™-iPS 2.0 Sendai reprogramming kit (Life Technologies cat. #A16517) at the Harvard Stem Cell Institute iPS Core Facility was a gift from Dr. Martin Pollak. iPSC were confirmed to be of normal karyotype. iPSC were maintained in with daily medium changes of mTeSR1 medium in 6 well plates coated with Matrigel. Cells were passaged using GCDR and transferred to T25 flasks coated with Matrigel prior differentiation. iPSC were routinely tested and confirmed negative for mycoplasma.     Generation of kidney organoids: Kidney organoids were differentiated using the protocol developed by Takasato et al. with minor modifications. APEL2 medium supplemented with 5% PFHM-II was used in replacement of APEL and will be hereon referred to as APEL2. Cell were treated with 8 µM CHIR99021 for 4 days followed by recombinant human FGF-9 (200 ng/mL) and heparin (1 μg/mL) for an additional 3 days. At day 7, cells were dissociated into single cells using trypsin for 2 min and one million cells were pellet at 400 x g for 2 min. The pellet was transferred onto a six-well transwell plate (Corning cat. # 07-200-170) with two pellets per well.  Pellets were incubated with a pulse of 5 µM CHIR99021 in APEL2 + PFHM medium for 1 h at 37 °C, 5% CO2. After 1 hr, the medium was changed to APEL2 + PFHM supplemented with FGF-9 (200 ng/mL) and heparin (1 μg/mL) for an additional 5 days, and then were maintained in APEL2 + PFHM medium for 14 days with medium change every other day.

tag: infection

value: kidney organoids

tag: agent

value: angiotensin II receptor blockers (ARB) losartan


title: Ang + los

description: # FACS sorted cells: 15,000 cells; Recovered: 5,855 cells

source_name: Ang + los

value: Ang II plus losartan


title: JKD6008 ∆sRNA275::sRNA275 (repaired) RNA-seq (no vancomycin) replicate 3


title: JKD6008 ∆sRNA275::sRNA275 (repaired) RNA-seq (no vancomycin) replicate 1


title: 270678-zhengchang [Normal-2]

description: normal 2

value: esophagus

value: adjacent normal tissue


title: Ang

description: # FACS sorted cells: 15,000 cells; Recovered: 5,800 cells

source_name: Ang

value: angiotensin II


title: 68722: d12 RX WT SOX17neg34pos43pos 3

status: Public on Jan 22 2022

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

institute: Australian Institute for Bioengineering and Nanotechnology

data_processing:
Illumina TruSeq adapters were removed and basic quality trimming was carried out with cutadapt version 1.18 with Python 2.7.13. Cutadapt arguments were: cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a ATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A ATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a TCGGAAGAGCACACGTCTGAACTCCAGTCAC -A TCGGAAGAGCACACGTCTGAACTCCAGTCAC -a CGGAAGAGCACACGTCTGAACTCCAGTCAC -A CGGAAGAGCACACGTCTGAACTCCAGTCAC --minimum-length 19 --trim-n --no-indels -e 0.05 --quality-cutoff 10 -o /{}_R1.fastq -p /{}_R2.fastq /{}_R1.fastq /{}_R2.fastq (where {} is a file name).
Individual fastq files were aligned to the reference genome (GRCh38 assembly and ENSEMBL version 91) with Rsubread 1.20.6 with default settings in R version 3.2.2.
Reads were quantified with featureCounts as part of the Rsubread 1.20.6 library.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited text files include raw counts and TMM scaled RPKM Log2 values. An offset of 1 was added to values before taking the log to avoid log errors.

source_name: Embryonic stem cell (H9 Cell Line)

growth_protocol: Growth and media were different for the endoderm and mesoderm differentiation. Please refer to the “Overall design” for an overview and “Media” column to see the growth protocol per sample.

extract_protocol: TruSeq

value: Embryonic stem cell (H9 Cell Line)

tag: parental cell type

value: Embryonic stem cell

tag: final cell type

value: Mesoderm

tag: genetic modification

value: SOX17 mCHERRY/w RUNX1C GFP/w

tag: facs profile

tag: media

value: STAPEL, d0-4 BMP4 20ng/ml ACTIVIN A 7.5ng/ml,  VEGF 25ng/ml SCF 50mg/ml, FGF2 10ng/ml, d2-4 SB431542 3µM, CHIR 99021 3µM, d4-8 VEGF 25ng/ml SCF 50mg/ml, FGF2 10ng/ml, IGF2 25ng/ml


title: Cnt

description: # FACS sorted cells: 15,000 cells; Recovered: 4,235 cells

source_name: Cnt

value: control


title: 12 months old-Cortex-Tau4RΔK-Female TL2

source_name: scRNA-Seq - TL2

value: Cerebral cortex

value: 12 months old

tag: Sex

value: Female


title: miR21_cKO2

source_name: naive CD4

value: Spleen

tag: treatment

value: Tfh cell polarization


title: 68723: d12 RX KO SOX17pos34pos43neg 4

tag: cell line

value: SOX17 mCHERRY/w RUNX1C GFP/w RUNX1 -/- (knockout of RUNX1, deletion of DNA binding domain)


title: 270678-ai [ECA-2]

description: tumor 2

source_name: esophagus

tag: subject/sample id

tag: tissue

value: ESCC tumor


title: SK-N-BE2 shSAPCD2_rep1

tag: cell type

value: Neuroblastoma cells


title: 68717: d7 RX KO SOX17pos34pos43neg 4


title: 68719: d12 RX WT SOX17pos34pos43neg 4


title: SK-N-BE2 shScb_rep2

value: scramble shRNA


title: 68715: d7 RX WT SOX17pos34pos43neg 4


title: 68716: d7 RX WT SOX17neg34pos43neg 4


title: 68713: d12 RX KO SOX17pos34pos43neg 3


title: 68707: d7 RX KO SOX17pos34pos43neg 3


title: 68710: d12 RX WT SOX17pos34pos43pos 2


title: WT1

description: wild type

tag: genotype

value: wildtype


title: miR21_cKO1


title: 68706: d7 RX WT SOX17neg34pos43neg 3


title: 68714: d12 RX KO SOX17neg34pos43neg 1


title: 68709: d12 RX WT SOX17pos34pos43neg 3


title: 68703: d12 RX KO SOX17pos34pos43neg 2


title: 68699: d12 RX WT SOX17pos34pos43neg 2


title: 68702: d12 RX WT SOX17neg34pos43pos 1


title: 68687: d7 RX KO SOX17pos34pos43neg 1


title: 68698: d7 RX KO SOX17neg34pos43neg 2


title: 68693: d12 RX KO SOX17pos34pos43neg 1


title: 68718: d7 RX KO SOX17neg34pos43neg 3


title: 68689: d12 RX WT SOX17pos34pos43neg 1


title: 68685: d7 RX WT SOX17pos34pos43neg 1


title: 68705: d7 RX WT SOX17pos34pos43neg 3


title: 68686: d7 RX WT SOX17neg34pos43neg 1


title: 68696: d7 RX WT SOX17neg34pos43neg 2


title: 32010: d7 RX WT Unsorted Endoderm 3

value: Endoderm

value: Unsorted

value: d0 Act A 100ng/ul, CHIR 2uM, PI-103 50nM, d1-7 Act A 100ng/ul, DMH-1 1uM


title: 68690: d12 RX WT SOX17pos34pos43pos 1

value: Embryonic stem cell (H9 Cell Line)

value: Embryonic stem cell

value: Mesoderm


title: 68695: d7 RX WT SOX17pos34pos43neg 2

value: SOX17 mCHERRY/w RUNX1C GFP/w

value: STAPEL, d0-4 BMP4 20ng/ml ACTIVIN A 7.5ng/ml,  VEGF 25ng/ml SCF 50mg/ml, FGF2 10ng/ml, d2-4 SB431542 3µM, CHIR 99021 3µM, d4-8 VEGF 25ng/ml SCF 50mg/ml, FGF2 10ng/ml, IGF2 25ng/ml


title: 68684: d4 RX WT Unsorted Endoderm 3


title: 68712: d12 RX WT SOX17neg34pos43pos 2


title: 68688: d7 RX KO SOX17neg34pos43neg 1


title: 32009: d7 RX WT Unsorted Endoderm 2


title: 32003: d4 RX WT Unsorted Endoderm 1


title: 32005: d4 RX WT Unsorted Endoderm 2


title: 32008: d7 RX WT Unsorted Endoderm 1


title: 32001: d2 RX WT Unsorted Endoderm 1


title: 32002: d2 RX WT Unsorted Endoderm 2


title: 32004: d2 RX WT Unsorted Endoderm 3


title: 31999: d0 RX WT Undifferentiated 1


title: 32006: d0 RX WT Undifferentiated 3


title: 32000: d0 RX WT Undifferentiated 2


title: 68697: d7 RX KO SOX17pos34pos43neg 2


title: 31322: d2 RX KO Unsorted 4


title: EB_Hypoxia_16h 1

city: Daejeon

first: Lee

last: Sunwoo

address: #211, Next2Vill, 278-2, Jangdae-dong, Yuseong-gu

country: South Korea

institute: GenomicWorks

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Hybridization signals were detected with a DNA microarray scanner G2505B (Agilent Technologies, Santa Clara, CA, USA)

data_processing: scanned images were analyzed using Agilent feature extraction software (v9.5.3.1). Data were analyzed using GeneSpring GX 7.3.1 software (Agilent Technologies) and normalized as follows: (i) values below 0.01 were set to 0.01; (ii) to make comparisons between one-color expressions profiles, each measurement was divided by the 50th percentile of all measurements from the same species.

source_name: EB

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

growth_protocol: Undifferentiated C57-mESCs were cultured on mitomycin C-treated mouse embryonic fibroblast feeder layers in DMEM with 20% FBS, 1% penicillin/streptomycin, 0.1 mM β-mercaptoethanol, 1% non-essential amino acids, 2 mM L-glutamine, and 1000 U/ml LIF. EBs were formed by the hanging drop method in the absence of LIF and feeder cells.

extract_protocol: Total RNA was prepared using a Trizol extraction Kit (Invitrogen, Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: mESCs cultured for 16 h under normoxia, EBs cultured for 16 h under normoxia, EBs cultured for 16 h under hypoxia

tag: sample type

value: cultured cell

value: 16h under hypoxia


title: EB_norm_16h 2

value: 16h under normoxia


title: mESC_norm_16h 1

source_name: mESC


title: EB_norm_16h 1


title: mESC_norm_16h 2


title: 31321: d0 RX KO Unsorted 4


title: 31323: d4 RX KO Unsorted 4


title: 31320: d4 RX WT Unsorted 4


title: 31318: d0 RX WT Unsorted 4


title: 31319: d2 RX WT Unsorted 4


title: CD8_Tfc_2

city: Livermore

first: Dina

last: Weilhammer

state: California

address: 7000 East Ave

institute: Lawrence Livermore National Laboratory

data_processing:
trimmomatic
Rsubread
featureCounts
edgeR
limma
Genome_build: GRCm38
Supplementary_files_format_and_content: raw data

source_name: CD8+ CXCR5+PD-1hi

extract_protocol:
TruSeq Stranded Total RNA (illumina)
TruSeq RNA Library Prep (illumina)

tag: strain

value: BALB/c

value: lymph nodes and spleen

tag: age

value: 15-16 days old

value: CD8 T cells


title: 31305: d4 RX KO Unsorted 3


title: 31304: d2 RX KO Unsorted 3


title: CD8_Tfc_1


title: CD4_Tfh_2

source_name: CD4+ CXCR5+PD-1hi

value: CD4 T cells


title: CD4_Tfh_1


title: EB_Hypoxia_16h 2


title: 0.1% EtOH, 48 h, rep2

city: Kuopio

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
Ethanol
EtOH_48h_R2

data_processing:
Read alignment and quantification via nf-core/rnaseq STAR-Salmon pipeline 3.0 (http://doi.org/10.5281/zenodo.4323183)
Filtering for protein coding genes, read counts normalization via EdgeR 3.32.1 (TMM-normalized CPM)
Genome_build: hg38, Aligned to Ensembl annotation version 103, final annotation (via Biomart) to Ensembl version 104
Supplementary_files_format_and_content: Excel table of TMM-normalized read counts (CPM; EdgeR pipeline)

source_name: PBMC

growth_protocol: RPMI 1640 medium supplemented with 10% charcoal-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and were at 37 °C in a humidified 95% air/5% CO2 incubator.

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: treatment for 4 h, 8 h, 24 h or 48 h with either 10 nM 1,25(OH)2D3 (Sigma-Aldrich) or solvent (0.1% EtOH)

value: PBMC

value: 0.1percent ethanol

tag: time point


title: 31303: d0 RX KO Unsorted 3

value: SOX17 mCHERRY/w RUNX1C GFP/w RUNX1 -/- (knockout of RUNX1, deletion of DNA binding domain)

value: Unsorted


title: 31301: d2 RX WT Unsorted 3

value: Embryonic stem cell (H9 Cell Line)


title: 31287: d4 RX KO Unsorted 2

value: Embryonic stem cell


title: 31300: d0 RX WT Unsorted 3

value: Mesoderm


title: 10 nM 1,25(OH)2D3, 48 h, rep3

description:
1α,25-dihydroxyvitamin D3
125D_48h_R3

tag: agent


title: 31302: d4 RX WT Unsorted 3

tag: parental cell type

value: SOX17 mCHERRY/w RUNX1C GFP/w


title: 0.1% EtOH, 48 h, rep1

description:
Ethanol
EtOH_48h_R1


title: 31285: d0 RX KO Unsorted 2

tag: final cell type

value: STAPEL, d0-4 BMP4 20ng/ml ACTIVIN A 7.5ng/ml,  VEGF 25ng/ml SCF 50mg/ml, FGF2 10ng/ml, d2-4 SB431542 3µM, CHIR 99021 3µM, d4-8 VEGF 25ng/ml SCF 50mg/ml, FGF2 10ng/ml, IGF2 25ng/ml


title: 31286: d2 RX KO Unsorted 2

tag: genetic modification


title: 10 nM 1,25(OH)2D3, 48 h, rep2

description:
1α,25-dihydroxyvitamin D3
125D_48h_R2


title: 10 nM 1,25(OH)2D3, 48 h, rep1

description:
1α,25-dihydroxyvitamin D3
125D_48h_R1


title: 31284: d4 RX WT Unsorted 2

tag: facs profile


title: 0.1% EtOH, 24 h, rep2

description:
Ethanol
EtOH_24h_R2


title: 0.1% EtOH, 24 h, rep1

description:
Ethanol
EtOH_24h_R1


title: 31282: d0 RX WT Unsorted 2

tag: media


title: 0.1% EtOH, 24 h, rep3

description:
Ethanol
EtOH_24h_R3


title: 31283: d2 RX WT Unsorted 2


title: 10 nM 1,25(OH)2D3, 24 h, rep3

description:
1α,25-dihydroxyvitamin D3
125D_24h_R3


title: 10 nM 1,25(OH)2D3, 24 h, rep2

description:
1α,25-dihydroxyvitamin D3
125D_24h_R2


title: 31267: d0 RX KO Unsorted 1


title: 31266: d4 RX WT Unsorted 1


title: 0.1% EtOH, 48 h, rep3

description:
Ethanol
EtOH_48h_R3


title: 31268: d2 RX KO Unsorted 1


title: 31269: d4 RX KO Unsorted 1


title: 0.1% EtOH, 08 h, rep2

description:
Ethanol
EtOH_08h_R2

value: 8 h


title: 0.1% EtOH, 08 h, rep3

description:
Ethanol
EtOH_08h_R3


title: 10 nM 1,25(OH)2D3, 24 h, rep1

description:
1α,25-dihydroxyvitamin D3
125D_24h_R1


title: 31265: d2 RX WT Unsorted 1


title: SM9

city: Nashville

first: Masoud

last: Ghamari-Langroudi

state: TN

address: 8435 MRB #IV, 2215 Garland ave

institute: Vanderbilt University

description:
SM9
SkM_SFN

data_processing:
1. Data Quality Control: filtering reads containing adapter or with low quality.
2. Statistics Analysis of Data Production and Quality.
3. Mapping Reads to Reference Genome.
4. Gene Expression Quantification.
5. Correlation analysis (for biological replicates only).
6. Differential Expression Analysis (two or more groups of samples).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: FPKM_all_samples.xlsx
Supplementary_files_format_and_content: Differentially_Expressed_Genes_SFN_effects_all_tissues.xlsx

extract_protocol:
Total RNA samples from each tissue were prepared with Trizol.
mRNA library preparation (poly A enrichment).

treatment_protocol: Male 12-week-old C57/BJ wild type mice were fed with high fat diet for 16-20 weeks. Around 28 weeks of age, mice were treated with daily ip injections of either SFN (5 mg/kg) or vehicle for one week.

value: Skeletal Muscle

tag: Sex

value: Male

value: wild type

tag: body weight

value: diet-induced obesity

value: Sulforaphane

tag: mouse id


title: SM10

description:
SM10
SkM_SFN

tag: treatment


title: SM8

description:
SM8
SkM_SFN

tag: tissue


title: 10 nM 1,25(OH)2D3, 08 h, rep3

description:
1α,25-dihydroxyvitamin D3
125D_08h_R3

tag: cell type


title: 0.1% EtOH, 08 h, rep1

description:
Ethanol
EtOH_08h_R1


title: 10 nM 1,25(OH)2D3, 08 h, rep2

description:
1α,25-dihydroxyvitamin D3
125D_08h_R2


title: SM6

description:
SM6
SkM_SFN

tag: genotype


title: SM7

description:
SM7
SkM_SFN


title: SM5

description:
SM5
SkM_Veh

value: vehicle


title: 10 nM 1,25(OH)2D3, 08 h, rep1

description:
1α,25-dihydroxyvitamin D3
125D_08h_R1


title: SM4

description:
SM4
SkM_Veh


title: SM3

description:
SM3
SkM_Veh


title: 0.1% EtOH, 04 h, rep3

description:
Ethanol
EtOH_04h_R3

value: 4 h


title: SM1

description:
SM1
SkM_Veh


title: L10

description:
L10
Liv_SFN

value: Liver


title: L9

description:
L9
Liv_SFN


title: 0.1% EtOH, 04 h, rep2

description:
Ethanol
EtOH_04h_R2

value: PBMC

value: 0.1percent ethanol


title: 0.1% EtOH, 04 h, rep1

description:
Ethanol
EtOH_04h_R1


title: 10 nM 1,25(OH)2D3, 04 h, rep3

description:
1α,25-dihydroxyvitamin D3
125D_04h_R3


title: L8

description:
L8
Liv_SFN


title: Healthy B-LCL RPMI-8866

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

country: Spain

institute: Hospital Clinico Universitario Virgen de la Arrixaca

hyb_protocol: Agilent Gene Expression Hybridization kit protocol following the manufacturer's instructions

scan_protocol: Agilent G2565CA scanner, Agilent Scan Control software, scanning at 3 µm

data_processing: Agilent Feature Extraction software version 11.0.1.1

source_name: Mix of EBV-transformed B-LCL and NK cell lines (Reference sample)

label_protocol: Agilent Two Color Quick Amp Labeling and RNA Spike-In kits protocols following the manufacturer's instructions

growth_protocol: B-LCL were cultured IMDM supplemented with 10% fetal calf serum, 50 U/ml penicillin, 50 U/ml streptomycin, and 2 mM L-glutamine

extract_protocol: RNAs were isolated using the miRNeasy mini kit (Qiagen) protocol following the manufacturer's instructions

treatment_protocol: B-LCL were obtained by culture of patients' purified blood B lymphocytes with supernatants of the marmoset EBV-leukocyte cell line B95-8

tag: reference

value: Mix of EBV-transformed B lymphoblastoid cell lines and NK cell lines

source_name: EBV-transformed healthy B-LCL cell line RPMI-8866 (Test sample)

tag: cell line


title: L5

description:
L5
Liv_Veh

tag: strain


title: L6

description:
L6
Liv_SFN


title: 10 nM 1,25(OH)2D3, 04 h, rep1

description:
1α,25-dihydroxyvitamin D3
125D_04h_R1

tag: time point


title: L1

description:
L1
Liv_Veh


title: Healthy B-LCL WEWAK

source_name: EBV-transformed healthy B-LCL cell line WEWAK (Test sample)


title: Healthy B-LCL TRAL

source_name: EBV-transformed healthy B-LCL cell line TRAL (Test sample)


title: Healthy B-LCL R69

source_name: EBV-transformed healthy B-LCL cell line R69 (Test sample)


title: Healthy B-LCL DMAR

source_name: EBV-transformed healthy B-LCL cell line DMAR (Test sample)


title: Healthy B-LCL GUS

source_name: EBV-transformed healthy B-LCL cell line GUS (Test sample)


title: iW10

description:
iW10
iWAT_SFN

value: inguinal white adipose tissue


title: Healthy B-LCL LG-15

source_name: EBV-transformed healthy B-LCL cell line LG-15 (Test sample)


title: PMM2-CDG B-LCL JAPe

description: JAPe-LCL

source_name: EBV-transformed PMM2-CDG B-LCL cell line JAPe (Test sample)


title: PMM2-CDG B-LCL SBS

description: SBS-LCL

source_name: EBV-transformed PMM2-CDG B-LCL cell line SBS (Test sample)


title: iMSC_senescent_5

city: Odense

first: Eduardo

last: Fernandez-Rebollo

address: Campusvej 55

department: Functional Genomics and Metabolism

country: Denmark

institute: University of Southern Denmark

description:
Sample_20
Induced pluripotent stem cells redifferentiated back into induced mesenchymal stromal cells in senescent passages.
processed data file: FPKM_iMSCs_manuscript.txt

data_processing:
Pair-end reads were quality-checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and low-quality reads were removed using TrimGalore.
Reads were mapped to the GRCh38 assembly of the human genome using Tophat2, version 2.0.10, and reassembled with Cufflinks.
Differential gene expression was analyzed using the DESeq2 package, version 1.10.1.
Significance of transcriptomic changes was estimated using the R limma package with an adjusted paired p-value <0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM_iMSC_manuscript.txt: Tab-delimited text file includes FPKM.

source_name: iPSC-derived mesenchymal stromal cells

growth_protocol: MSCs and iMSCs were cultured in basal medium consisting of Dulbecco’s Modified Eagle Medium (DMEM, 1g/L glucose; PAA, Pasching, Austria) with 1% penicillin/streptomycin (PAA) and 1% L-glutamine, and supplemented with 10% human platelet lysate (HPL). Induced pluripotent stem cells were reprogrammed from the same MSC donors that were used for experiments with primary MSCs. Reprogramming was performed with episomal plasmids. iPSCs were cultured on tissue culture plastic coated with vitronectin (0.5 µg/cm²) in StemMACS iPS-Brew XFe96 (all Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). iPSCs were re-differentiated toward iMSCs under MSC culture conditions as described by Frobel et al., 2014. After one week, differentiated iPSCs were maintained on 0.1% gelatine-coated TCP or HPL-gel and passaged every further week using trypsin-EDTA 0.25% (Gibco/Thermo Fisher Scientific).

extract_protocol:
RNA was isolated from the samples using the NucleoSpin RNA extraction kit (Macherey-Nagel, Düren, Germany).
Library preparation was performed with the Illumina TruSeq Stranded Total RNA Sample Preparation Kit, with a total input amount of 1 µg, following the standard protocol with ribosomal depletion (Illumina Ribo-Zero Gold rRNA removal kit) and the NextSeq 500/550 High Output Kit v2 (carried out by the Core Genomics-facility IZKF, RWTH Aachen University).

value: induced mesenchymal stromal cells

tag: passage

tag: donor

value: Donor 5

tag: gender

value: Female

tag: age


title: PMM2-CDG B-LCL MML

description: MML-LCL

source_name: EBV-transformed PMM2-CDG B-LCL cell line MML (Test sample)


title: iMSC_senescent_4

description:
Sample_19
Induced pluripotent stem cells redifferentiated back into induced mesenchymal stromal cells in senescent passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: Donor 4


title: iW8

description:
iW8
iWAT_SFN


title: iW9

description:
iW9
iWAT_SFN


title: PMM2-CDG B-LCL 3

source_name: EBV-transformed PMM2-CDG B-LCL cell line 3 (Test sample)


title: iMSC_senescent_3

description:
Sample_18
Induced pluripotent stem cells redifferentiated back into induced mesenchymal stromal cells in senescent passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: Donor 3


title: L4

description:
L4
Liv_Veh


title: iW7

description:
iW7
iWAT_SFN


title: L2

description:
L2
Liv_Veh


title: PMM2-CDG B-LCL NESI

description: NESI-LCL

source_name: EBV-transformed PMM2-CDG B-LCL cell line NESI (Test sample)


title: iW5

description:
iW5
iWAT_Veh


title: iW6

description:
iW6
iWAT_SFN


title: L3

description:
L3
Liv_Veh


title: iMSC_senescent_2

description:
Sample_17
Induced pluripotent stem cells redifferentiated back into induced mesenchymal stromal cells in senescent passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: Donor 2


title: iW4

description:
iW4
iWAT_Veh

value: Male


title: PMM2-CDG B-LCL 2

source_name: EBV-transformed PMM2-CDG B-LCL cell line 2 (Test sample)


title: p_50gy_02

city: Dresden

first: Claudia

last: Peitzsch

data_processing:
Raw sequencing data was processed following the DKFZ/ODCF RNAseq workflow (version 1.3.02). FASTQ reads for individual samples were aligned by a 2-pass alignment using the STAR aligner (version 2.5.3a, https://www.ncbi.nlm.nih.gov/pubmed/23104886). Reads were aligned to a STAR index generated from the 1000 genomes assembly, gencode 19 gene models and for sjdbOverhang of 200.
Duplicate marking of the resultant main alignment file was done with sambamba (version 0.6.5, https://www.ncbi.nlm.nih.gov/pubmed/25697820).
The Chimeric file was sorted using samtools sort (version 1.6, https://www.ncbi.nlm.nih.gov/pubmed/19505943), and then duplicates were marked using sambamba. BAM indexes were generated using sambamba.
Quality control analysis was performed using the samtools flagstat command, and the rnaseqc tool (version 1.1.8, https://www.ncbi.nlm.nih.gov/pubmed/22539670) with the 1000 genomes assembly (hs37d5 with the PhiX sequence added, see ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/PhiX/Illumina/RTA/PhiX_Illumina_RTA.tar.gz) and gencode 19 gene models.
Depth of Coverage analysis for rnaseqc was turned off. Featurecounts (subread version 1.5.1, https://www.ncbi.nlm.nih.gov/pubmed/24227677) was used to perform gene specific read counting over exon features based on the gencode 19 gene models. Both reads of a paired fragment were used for counting.
Genome_build: 1000 genomes assembly (hs37d5 with the PhiX sequence added, see ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/PhiX/Illumina/RTA/PhiX_Illumina_RTA.tar.gz) and gencode 19 gene models.
Supplementary_files_format_and_content: A file containing Featurecounts for all genes is provided separately for each sample.

source_name: prostate

growth_protocol: To estimate ALDH+ cells within prostate cancer cell cultures, cells were stained using the Aldefluor kit (Stem cell technologies; Cat#01700) according to the manufacturer’s instructions. The Aldefluor buffer was supplemented with 5 % fetal bovine serum (FBS), 1 % 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffer (Sigma Life Science) and 1 mM ethylene-diaminetetraacetic acid (EDTA) (Sigma Life Science). The ALDH inhibitor DEAB was add to each sample as control to define the ALDH negative gate. Viability dye 7-aminoactinomycin D (7-AAD) (0.002µg/µl Sigma Life Science; A9400-1MG) was used to exclude dead cells. Flow cytometry was performed with the BD Celesta (Beckton, Dickinson and Company) and cell sorting with BD FACSAria™ III (Beckton, Dickinson and Company) using the 100 µm nozzle. The purity of the sorted populations was routinely assessed by re-analyses.

extract_protocol:
RNA isolation was performed using the RNAeasy Mini Kit (Qiagen).
Illumina TruSeq® Stranded mRNA Library Prep kit with Oligodt bead-enrichment and IDT for Illumina – TruSeq RNA UD indexes was used. Library preparation was carried out following the manufacturer's instructions using 500ng RNA input.

treatment_protocol: Eight to ten weeks old male NMRI-Foxn1 nu/nu immune-deficient, outbred mice were bred in-house (OncoRay or Center for Regenerative Therapies Dresden (CRTD), Faculty of Medicine, Technische Universität Dresden) and kept under specific pathogen-free conditions. One day prior to tumor cell injection, mice received whole body irradiation (WBI) with 4 Gy using the Yxlon Maxishot (Yxlon Y. TU 320, 0.5 mm Cu filter) with a dose rate of 1.1 Gy/min at 200 kV and 20 mA. For tumor control doses 50 (TCD50) analyses, 1000 purified ALDH+ or ALDH- DU145 cells were embedded in 100 µl media-matrigel mixture (1:1) and injected subcutaneously to the right hind leg. Mice with tumors larger than 7 mm in length received total irradiation doses of 0 and 50 Gy within 30 fractions (0 and 1.67 Gy per fraction) and five fractions per week. Tumors were cut frozen on dry ice, weighted, and dissociated using the Gentle MACS dissociator (Miltenyi Biotec) before RNA isolation.

value: DU145 xenograft tumor

tag: aldh expression

value: ALDH+

value: irradiated

tag: mouse strain

value: NMRI-Foxn1 nu/nu immune-deficient


title: iMSC_senescent_1

description:
Sample_16
Induced pluripotent stem cells redifferentiated back into induced mesenchymal stromal cells in senescent passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: Donor 1


title: p_50gy_03

institute: Center for Regenerative Therapies Dresden (CRTD)


title: iW3

description:
iW3
iWAT_Veh

tag: Sex

value: wild type

value: diet-induced obesity

value: vehicle


title: p_50gy_01


title: H7

description:
H7
Hyp_SFN

value: Hypothalamus

tag: body weight

value: Sulforaphane


title: iW1

description:
iW1
iWAT_Veh

value: inguinal white adipose tissue

tag: mouse id


title: H9

description:
H9
Hyp_SFN

tag: treatment


title: iMSC_5

description:
Sample_15
Induced pluripotent stem cells redifferentiated back into induced mesenchymal stromal cells in early passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: induced mesenchymal stromal cells

value: Donor 5


title: iMSC_4

description:
Sample_14
Induced pluripotent stem cells redifferentiated back into induced mesenchymal stromal cells in early passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: Donor 4

value: Female


title: H6

description:
H6
Hyp_SFN

tag: tissue


title: iMSC_2

description:
Sample_12
Induced pluripotent stem cells redifferentiated back into induced mesenchymal stromal cells in early passages.
processed data file: FPKM_iMSCs_manuscript.txt

tag: cell type

value: Donor 2


title: H10

description:
H10
Hyp_SFN

value: Male

tag: genotype


title: H5

description:
H5
Hyp_Veh


title: p_control_03

value: DU145 xenograft tumor

value: control


title: PMM2-CDG B-LCL 1

tag: reference

value: Mix of EBV-transformed B lymphoblastoid cell lines and NK cell lines

source_name: EBV-transformed PMM2-CDG B-LCL cell line 1 (Test sample)


title: p_control_02

value: ALDH+

value: NMRI-Foxn1 nu/nu immune-deficient


title: iMSC_1

description:
Sample_11
Induced pluripotent stem cells redifferentiated back into induced mesenchymal stromal cells in early passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: Donor 1


title: H2

description:
H2
Hyp_Veh

value: wild type

value: diet-induced obesity


title: H3

description:
H3
Hyp_Veh

value: Hypothalamus

value: vehicle


title: iMSC_3

description:
Sample_13
Induced pluripotent stem cells redifferentiated back into induced mesenchymal stromal cells in early passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: Donor 3


title: H8

description:
H8
Hyp_SFN

value: Sulforaphane


title: m_50gy_03

value: ALDH-

value: irradiated


title: p_control_01


title: L7

description:
L7
Liv_SFN

value: Liver


title: iW2

description:
iW2
iWAT_Veh

value: inguinal white adipose tissue


title: MSC_senescent_5

description:
Sample_10
Bone marrow isolated mesenchymal stromal cells in senescent passages.
processed data file: FPKM_iMSCs_manuscript.txt

source_name: bone marrow derived mesenchymal stromal cells

value: mesenchymal stromal cells

value: Donor 5

value: Female


title: m_50gy_02

value: DU145 xenograft tumor


title: eW10

description:
eW10
eWAT_SFN

value: epididymal white adipose tissue

value: Male


title: eW9

description:
eW9
eWAT_SFN


title: H4

description:
H4
Hyp_Veh


title: MSC_senescent_4

description:
Sample_9
Bone marrow isolated mesenchymal stromal cells in senescent passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: Donor 4


title: m_50gy_01

value: NMRI-Foxn1 nu/nu immune-deficient


title: MSC_senescent_3

description:
Sample_8
Bone marrow isolated mesenchymal stromal cells in senescent passages.
processed data file: FPKM_iMSCs_manuscript.txt


title: MSC_senescent_1

description:
Sample_6
Bone marrow isolated mesenchymal stromal cells in senescent passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: Donor 1


title: m_control_03

value: control


title: m_control_02


title: eW5

description:
eW5
eWAT_Veh

value: wild type

value: diet-induced obesity

value: vehicle


title: 31264: d0 RX WT Unsorted 1

source_name: Embryonic stem cell (H9 Cell Line)

value: Embryonic stem cell (H9 Cell Line)

tag: parental cell type

value: Embryonic stem cell

tag: final cell type

value: Mesoderm

tag: cell line

tag: genetic modification

value: SOX17 mCHERRY/w RUNX1C GFP/w

tag: facs profile

value: Unsorted

tag: media

value: STAPEL, d0-4 BMP4 20ng/ml ACTIVIN A 7.5ng/ml,  VEGF 25ng/ml SCF 50mg/ml, FGF2 10ng/ml, d2-4 SB431542 3µM, CHIR 99021 3µM, d4-8 VEGF 25ng/ml SCF 50mg/ml, FGF2 10ng/ml, IGF2 25ng/ml


title: MSC_5

description:
Sample_5
Bone marrow isolated mesenchymal stromal cells in early passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: mesenchymal stromal cells

tag: passage

tag: donor

value: Donor 5

tag: gender

value: Female

tag: age


title: eW6

description:
eW6
eWAT_SFN

tag: strain

value: epididymal white adipose tissue

tag: Sex

value: Male

tag: body weight

value: Sulforaphane


title: MSC_senescent_2

description:
Sample_7
Bone marrow isolated mesenchymal stromal cells in senescent passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: Donor 2


title: eW7

description:
eW7
eWAT_SFN

tag: tissue

tag: treatment

tag: mouse id


title: eW2

description:
eW2
eWAT_Veh

tag: genotype


title: eW3

description:
eW3
eWAT_Veh


title: m_control_01

value: DU145 xenograft tumor

tag: aldh expression

value: ALDH-

value: control

tag: mouse strain

value: NMRI-Foxn1 nu/nu immune-deficient


title: BAT10

description:
BAT10
BAT_SFN

value: Brown Adipose Tissue

value: wild type

value: diet-induced obesity


title: MSC_4

description:
Sample_4
Bone marrow isolated mesenchymal stromal cells in early passages.
processed data file: FPKM_iMSCs_manuscript.txt

tag: cell type

value: Donor 4


title: BAT8

description:
BAT8
BAT_SFN