title: DamID-seq, Neuruloid, Dam-Lhx1, rep 3

city: Westmead

first: Riley

last: McMahon

address: 214 Hawkesbury Road

country: Australia

institute: Children's Medical Research Institute

data_processing:
The FastQC v0.11.9 was used for quality control of 150 bp paired end DamID-Seq fastq files.
The fastq files were trimmed using trimmomatic (version 0.39) with the following parameters (ILLUMINACLIP:TruSeq2-PE.fa:2:20:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:20 MINLEN:50).
The package bwa mem (v0.7.17) was used for aligning the reads to mouse reference genome (mm10) with default parameters. Samtools (version 1.12) was used for sorting and indexing the bam files.
MACS2 callpeak (version 2.2.7.1) was used for peak calling from duplicated removed bam files with parameters [-f BAMPE -g mm --nomodel --keep-dup all –broad]. The control Dam-only peaks are subtracted from Dam-Lhx1 peaks to identify LHX1 specific binding.
Assembly: mm10
Supplementary files format and content: bigwig files
Library strategy: DamID-seq

source_name: Day 4 neuruloid

growth_protocol: Approximately 2.5 x 106  ESCs and 0.5 x 106 XEN cells were mixed and placed in each well of a 24-well plate on AggreWell™ 400 24-wells (Stem Cell Technologies) with 2 mL of N2B27 media, and then spun at 400 g for three minutes. The cells were cultured in wells for 48 hours, and next transferred to low adhesion plates on a shaking platform with a 24-hour pulse of 3 µM CHIR99021. CHIR99021 was then removed, and neuruloids were collected after a further 24 hours of culture

extract_protocol:
Genomic DNA was extracted with the Quick-gDNA MicroPrep (ZymoResearch) kit. Extracted gDNA was digested with DpnI and DamID adapters were then ligated using T4 DNA Ligase. After ligation, the DNA was digested with DpnII and the DamID fragments of interest were amplified with the KAPA HiFi Polymerase. Following PCR amplification, the samples were cleaned up using Wizard SV Gel and PCR Clean-Up System (Promega) and eluted into 90 µL dH20 + 10 µL CutSmart buffer (NEB). Samples were sonicated with a Bioruptor Plus (Diagenode) for 5 minutes, high power, 30s on/30s off. 10% of the sample was ran on a 0.8% gel to check fragment sizes then the DNA was digested with AlwI overnight at 37°C.
Following clean-up with AMPure XP beads, 500 ng of each sample was used for Library preparation with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

value: Day 4 neuruloid

value: R1 ESC

value: mouse embryonic stem cell

value: ROSA26 Neo-Dam-Lhx1 expressing


title: 3dpf_fibroblasts_sort_500_cells_injury_sample2

status: Public on Oct 01 2025

type: SRA

city: Shenzhen

first: Zhao

last: Shizheng

address: Shenzhen

department: LIFS

country: China

institute: Undefined

description: Library name: Injury-fibroblast-2

library_source: transcriptomic

data_processing:
STAR(v2.7.10a)
Assembly: Zebrafish reference genome (GRCz11.111)
Supplementary files format and content: csv files with TPM value of each sample

molecule: polyA RNA

organism: Danio rerio

extract_protocol:
The fibroblasts were isolated by FACS sorting and cDNA library was constructed by Smartseq2 protocol.
In this experiment, we have conducted acetic acid corrosion in four trunk sites in 2 dpf embryos,cut the trunk region at 3 dpf, dissociated the embryos into single cell suspension and performed FACS sorting of dsRed positive fibroblasts. In each biological replicate, around 30 embryos were harvested and 500 fibroblsts were sorted into lysis buffer. Smartseq2 protocol was utilized for double strand cDNA library construction. After acquiring the cDNA from sorted fibroblasts, 0.5 ng cDNA input was tagmented using the TruePrep DNA Library Prep Kit V2 for Illumina (TD503, Vazyme). Following tagmentation, the samples were amplified using the TruePrep Index Kit V2 for Illumina (TD202, Vazyme) for 12 cycles and subsequently purified using Ampure XP beads (A63881, Beckman Coulter). The quality of the libraries was evaluated using the Agilent Fragment Analyzer System and then sent to Novogene for Illumina Hiseq X Ten 150-bp paired-end sequencing, with an average sequencing depth of 8 × 10^6 raw reads per sample.

tag: tissue

tag: cell type

value: fibroblast

tag: genotype

value: WT

tag: treatment


title: DamID-seq, Neuruloid, Dam-Lhx1, rep 2

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line


title: 3dpf_fibroblasts_sort_500_cells_injury_sample1

description: Library name: Injury-fibroblast-1


title: 3D7_treated_exp1

city: Glasgow

first: Katarzyna

middle: Kinga

last: Modrzynska

state: Glasgow (City of)

address: B627 Sir Graeme Davies Building, 120 University Place

country: United Kingdom

institute: Wellcome Trust Centre for Molecular Parasitology

data_processing:
The quality of the raw sequencing reads were assessed using FastQC and MultiQC platforms.
The RNA-seq reads (FASTQ) was mapped against Plasmodium falciparum reference genome (downloaded from PlasmoDB ver 56) using splice-aware aligner hisat2 (v. 2.2.1). Resulting BAM files were sorted, indexed and filtered for the mapping quality (only reads with MAPQ>10 were kept) using samtools suite (v. 1.17) and visually inspected using IGV genome browser.
Initially a featureCounts function from subread software has been used in a -J mode to count the number of reads supporting each splicing junction. All identified splicing events were used to construct a genome feature file with all mapped junctions. Next featureCounts was used again to in –nonSplitOnly mode to count the number of reads covering the junctions (not spliced).
R software with data table package was used to combine data from all samples, with reads spanning each intron or covering it forming separate columns. Only the introns supported by >15 spliced reads between all the samples and present within the annotated genes were carried forward to further analysis. .
The edgeR package statistical framework has been adapted to splicing analysis as described previously (PMID: 29333247). The resulting table containing log-fold changes of the proportion of the reads spliced and P-values with Bonferroni correction was generated and used to filter the differentially spliced intron. Introns with >25% changes in splicing proportions between the conditions and q values <0.01 were considered as differentially spliced/retained.
Assembly: 3D7
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: "*spliced.txt" is tab-delimited text file including the number of reads supporting each of the splicing junctions detected in each of the samples."*non_spliced.txt" files cotain number of non-spliced reads spanning each of these junctions

organism: Plasmodium falciparum 3D7

source_name: 30_hpi trophozoites

growth_protocol: Asexual blood stage 3D7 Plasmodium falciparum parasites were grown in RPMI media supplemented with 0.5% Albumax II, 0.292g/L L-glutamine, 0.05g/L hypoxanthine, 2.3g/L sodium bicarbonate, 0.025g/L gentamicin, 5.957g/L HEPES and 4g/L dextrose in human O+ anonymous male blood donor maintained at 4% haemtocrit maintained at 37 degrees celsuis.

extract_protocol:
RNA was isolated using Rneasy mini kit according to the manufactirer's instructions.
Using 500ng of RNA for each sample, libraries were prepared for sequencing using Roche’s KAPA RNA Hyperprep kit (part No. KK8540). The samples were then paired-end multiplex sequenced (2x 150 base pairs) on the illumina HiSeq 2500 platform, and at least 30 million reads were generated for each sample.

treatment_protocol: Previously synchronised 30-hpi old trophozoites were treated with 1𝛍M selective PfCLK3 inhibitor TCMDC135051 for 1-hour at 37 degrees celsius

tag: strain

value: 30_hpi trophozoites


title: NOA_1_12_6

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

institute: Southern Medical University

description: Sample 49

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For bisulfite-seq data, Trim Galore (v0.3.3) was used to remove the first 6 bases of random primer, adaptor sequences and low quality bases; for RNA-seq data, each single cell was separated by unique cell barcode, then template switch oligo (TSO), ployA tails, adaptors and low quality bases were removed.
For bisulfite-seq data, clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; for RNA-seq data, clean reads were mapped to human genome hg19 with Tophat (v2.0.14), and then unique UMI counts were calculated by HTSeq.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include UMI counts of RefSeq genes. While WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

organism: Homo sapiens

source_name: testis

extract_protocol:
An individual cell was picked into the cell lysis buffer with vitro methylation (IVM) mixture containing 4 U RNase inhibitor (TAKARA, Cat. 2313B), 0.25% IGEPAL CA-630 (SIGMA, Cat. I3021), 1X GC reaction buffer and 2 U M. CviPI (NEB, Cat. M0227L). After gently vortexed for 10 sec, the cell lysate was incubated at 37 °C for 20 min and then at 65 °C for 25 min. Then, the cell lysate could be directly processed for RNA/DNA separation or stored at -80 °C.
For RNA part, a modified Smart-seq2 protocol was applied for single-cell RNA-seq. For DNA part, Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

tag: gender

value: male

tag: age

tag: condition

value: nonobstructive azoospermia (NOA)

tag: testis

value: testis


title: 3dpf_fibroblasts_sort_500_cells_control_sample3

description: Library name: Ctrl-fibroblast-3


title: NOA_1_12_4

description: Sample 47


title: NOA_1_12_5

description: Sample 48


title: ZNF808-KO, S6, 3

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

institute: University of Exeter Medical School

data_processing:
Stranded paired end 150bp RNA-seq reads were aligned to the hg19 genome using STAR and quantified against Gencode v36 release liftover to hg19 by RSEM using the RSEM-STAR pipeline, with additional options “--seed 1618 --calc-pme --calc-ci --estimate-rspd --paired-end”. RSEM estimated read counts per sample were rounded.
Assembly: hg19
Supplementary files format and content: tab delimited file with raw counts for each gene

growth_protocol: Human embryonic stem cells (hESC) (WA01/H1 line, Wicell) were cultured on Matrigel-coated plates (BD Biosciences) in Essential 8 (E8) medium (Life technologies, A1517001) and passaged using EDTA. To carry out the differentiation experiments, hPSC were dissociated using EDTA, then seeded on new Matrigel-coated plates in E8 medium supplemented with 10 µM Rho-Associated kinase inhibitor (ROCKi, catalog no. Y-27632; Selleckchem catalog no. S1049) at a density of 0.21 million cells cm-1. After 24 h, the differentiation was started by washing the cells with PBS, then changing the medium to D0 medium. The differentiation was carried out using our optimized seven-stage protocol as previously described in doi:10.1038/s41587-022-01219-z.

extract_protocol: RNA extraction and library preparation for stranded polyA+ RNA-seq libaries was performed by NovoGene Co Ltd.

value: human embryonic stem cells (hESC)

tag: Stage

tag: replicate


title: DamID-seq, Neuruloid, Dam-Lhx1, rep 1


title: WT-H1, S6, 3


title: NOA_1_12_3

description: Sample 46


title: ZNF808-KO, S5, 3


title: DamID-seq, Neuruloid, Dam, rep 3

value: ROSA26 Neo-Dam expressing


title: WT-H1, S5, 3


title: 3dpf_fibroblasts_sort_500_cells_control_sample1

description: Library name: Ctrl-fibroblast-1


title: DamID-seq, Neuruloid, Dam, rep 2


title: rad14_cdc13-1_cellular_NoUV_48hr_rep1

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

country: USA

institute: Washington State University

description:
Library name: rad14_cdc13-1_cellular_NoUV_48hr_rep1
Replicate 1

data_processing:
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences were trimmed, as well as the 3' nucleotide of the sequencing read, using a custom perl script
Fastq files were aligned to the Saccharomyces cerevisiae genome (saccer3) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to cytosine bases in dipyrimidine sequence contexts (i.e., TC, CT, CC), corresponding to deaminated CPD lesions, were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools or custom perl script
Assembly: saccer3
Supplementary files format and content: WIG files containing counts of DNA dCPD lesion reads filtered for only cytosines in dipyrimidine mapping sequences. For the NoUV samples, just the nucleotide counts for the putative lesion sites associated with dCPD-seq reads is indicated.
Library strategy: dCPD-seq

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: rad14∆ cdc13-1 yeast were grown overnight in rich (YPD or YPDA) medium at a permissive temperature (~23C), diluted ~1:7 with pre-warmed (37C) fresh YPDA medium, and incubated with shaking at 37C for six hours to induce G2/M arrest.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with approximately equal volumes of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 7.5-8.0, 1 mM EDTA) and PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and approximately 0.5 volumes of acid-washed glass beads. Beads were vortexed vigorously twice for about 2 min each time. After adding TE (10mM Tris-HCl, pH 7.5-8.0, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 2.5-3 volumes of 100% ethanol and stored at -20C to allow DNA precipitiation to occur.  DNA pellets were washed with 75-80% ethanol, dissolved in mixture of 1xTE (pH7.5) and 0.2 μg/μl RNase A, and incubated at 37C for 15 minutes. The purified genomic DNA was then used for each sequencing library preparation.
The dCPD-seq protocol was adapted from the CPDseq 2.0 method (Duan et al. PNAS 2024, 121 (4) e2310854121). Briefly, approximately 250mg of yeast gDNA (measured by NanoDrop spectrophotometry) was incubated with TdT (NEB) and either ddATP or ddGTP to block free 3’ OH ends. After phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation, the DNA was resuspended in water and 10x CPD photolyase buffer (100mM NaCl, 50mM Tris HCl pH 7.5, 20mM DTT, 1mM EDTA, 50% glycerol) to a final concentration of ~1x buffer, and E. coli CPD photolyase and UDG were added to reverse CPDs and excise uracil bases. Reactions were incubated under 365nm light (Spectroline EA-160) to reverse CPDs and then phenol:chloroform:isoamyl alcohol extracted and ethanol precipitated. APE1 (NEB) was then used to cleave the abasic sugar backbone to yield free 3’OH ends that were ligated to a biotinylated splint adaptor that labeled with biotin on the complementary 5’ end. Up to six different barcoded A adaptors were used to generate the library.  Ligated DNA was captured with streptavidin beads (Invitrogen), washed with 1x SCC (saline sodium citrate) buffer to remove nonspecific binding, and the non-biotinylated strand containing the ligated 3’ A adaptors was eluted with 0.15M NaOH. After synthesis of the complementary strand with EconoTaq (Lucigen) and preparation of DNA ends with NEBNext end repair and NEBNExt dA-tailing modules, a second adaptor ligation with trP1 adaptors was performed. The library was then amplified 7 cycles in a PCR reaction with primers complimentary to the A and trP1 adaptors. Libraries were submitted to the WSU LBB1 Core Facility for Ion Torrent sequencing.

treatment_protocol: Cells were washed with water and exposed to ~600 J/m^2 UVC radiation. Cells were then incubated in the dark at 37C for a designated deamination timepoint (0h, 6h, 24h, or 48h), before spinning down the cells to obtain cell pellets.

value: Yeast cells

value: rad14 cdc13-1

value: No UV (0 J/m2)

tag: deamination time


title: ZNF808-KO, S7, 2


title: NOA_1_12_1

description: Sample 44


title: DamID-seq, Neuruloid, Dam, rep 1


title: WT-H1, S6, 2


title: NOA_1_11_5

description: Sample 43


title: rad14_cdc13-1_cellular_48hr_rep1

description:
Library name: rad14_cdc13-1_cellular_48hr_rep1
Replicate 1

value: UV irradiated 600 J/m2

value: 48 hr


title: rad14_cdc13-1_cellular_6hr_rep1

description:
Library name: rad14_cdc13-1_cellular_6hr_rep1
Replicate 1

value: 6 hr


title: ZNF808-KO, S6, 2


title: NOA_1_11_4

description: Sample 42


title: DamID-seq, E7.75 embryo, Dam, rep 2

source_name: E7.75 chimeric mouse embryo

growth_protocol: ARC/s female and homozygous dsRed.T3 expressing male mice were time mated 2.5 days prior to 8-cell embryo collection. 8-cell embryos were injected with either Dam or Dam-Lhx1 expressing ESCs. The chimeric embryos were collected at E7.75 and imaged using SteREO Lumar.V12 Microscope for brightfield and dsRed.T3 expression. Embryos with high contribution of ESC cells were used to collect DNA.

value: E7.75 chimeric mouse embryo

value: R1 ESC

value: Injected into 8cell embryo and collected at E7.75


title: rad14_cdc13-1_cellular_0hr_rep1

description:
Library name: rad14_cdc13-1_cellular_0hr_rep1
Replicate 1

value: 0 hr


title: NOA_1_11_2

description: Sample 41


title: DamID-seq, E7.75 embryo, Dam, rep 1

value: mouse embryonic stem cell


title: ZNF808-KO, S5, 2


title: 3dpf_fibroblasts_sort_500_cells_control_sample2

description: Library name: Ctrl-fibroblast-2

value: fibroblast

value: WT


title: rad14_cdc13-1_cellular_24hr_rep1

description:
Library name: rad14_cdc13-1_cellular_24hr_rep1
Replicate 1

value: 24 hr


title: TF_lib_plasmid

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens St

institute: Gladstone-UCSF Institute of Genomic Immunology

description: high_low_MOI_screens_D1_D2_D3_2022-04-23.count.txt

data_processing:
A table of individual guide abundance in each sample was generated using the count command in MAGeCK version 0.5.8
Assembly: None
Supplementary files format and content: Count of guide RNAs, raw counts

organism: synthetic construct

growth_protocol: Cells were grown in RPMI (Sigma, Cat # R0883) with 10% FCS (Sigma, Cat # F0926), with 100U/mL Pen-Strep (Gibco, Cat # 15140-122), 2mM L-Glutamine (Sigma, Cat # G7513), 10mM HEPES (Sigma, Cat # H0887), 1X MEM Non-essential Amino Acids (Gibco, Cat # 11140-050), 1mM Sodium Pyruvate (Gibco, Cat # 11360-070), and 50 U/mL IL-2 (Amerisource Bergen, Cat #10101641) at a concentration of 1E6 cells/mL.

extract_protocol:
After sorting, cells were washed with PBS, counted, pelleted, and resuspending at up to 5E6 cells per 400 µl of lysis buffer (1% SDS, 50 mM Tris, pH 8, 10 mM EDTA). The remaining protocol reflects additives/procedures performed per each 400 µl of sample. 16µl of NaCl (5M) was added, and the sample was incubated on a heat block overnight at 66°C. The next morning, 8µl of RNAse A (10mg/ml, resuspended in ddH2O) (Zymo, Cat #E1008) was added, and the sample was vortexed briefly, and incubated at 37°C for 1 hour. Next, 8µl of Proteinase K (20mg/ml) (Zymo, Cat #D3001) was added, the sample was vortexed briefly, and incubated at 55°C for 1 hour. A phase lock tube (Quantabio, Cat #2302820) was prepared for each sample by spinning down the gel to the bottom of the tube at 20,000g for 1 minute and then 400µl of Phenol:Chloroform:Isoamyl Alcohol (25:24:1) was added to each tube. 400µl of the sample was then added to the phase lock tube and the tube was shaken vigorously. The sample was centrifuged at maximum speed at room temperature for 5 minutes. The aqueous phase was transferred to a low-binding eppendorf tube (Eppendorf, Cat #022431021) and then 40µl of Sodium Acetate (3M), 1µl GlycoBlue (Invitrogen, Cat # AM9515), and 600µl of room temperature isopropanol was added. The sample was then vortexed and stored at -80°C for 30 minutes or until the sample had frozen solid. Next the sample was centrifuged at maximum speed at 4°C for 30 minutes, the pellet was washed with fresh 70% room temperature Ethanol, and allowed to air dry for 15 minutes. Pellets were then resuspended in Zymo DNA elution buffer (Zymo, Cat No: D3004-4-10), and placed on the heat block at 65°C for 1 hour to completely dissolve the genomic DNA.
sgRNA was amplified and barcoded from the genomic DNA according to the protocol by Joung et al. (Joung et al. 2017). Up to 2.5 µg of genomic DNA were added to each 50 µL reaction, which included 25 µL of NEBNext Ultra II Q5 master mix (NEB, Cat #M0544L), 1.25 µL of the 10 µM forward primer and 1.25 µL of the 10 µM reverse primer, and H2O to 50 uL. The following PCR cycling conditions were used: 98°C for 3 minutes, followed by 23 cycles at 98°C for 10 seconds, 63°C for 10 seconds, and 72°C for 25 seconds, and ending with 2 minutes at 72°C. Samples were then cleaned and concentrated in Zymo Spin-V columns (Zymo, Cat #C1016-50) following Joung et al., and eluted in 150 uL of Zymo DNA elution buffer. Up to 2 µg of each library were loaded on a 2% agarose gel, and the band at ~250 base pairs was extracted using the Zymoclean Gel DNA recovery kit (Zymo, Cat #D4008). The concentration of each sample was then measured using the Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific, Cat #Q32854). Samples were then sequenced on an Illumina HiSeq 4000 using 10-30% PhiX (Illumina, Cat #15017872), and a custom sequencing primer.
CRISPR sequencing

treatment_protocol: CD4+CD25- T cells were infected with lentivirus containing a 6000 guide RNA CRISPR library. Cas9 ribonucleoprotein complex was electroporated. 6 days after electroporation, FACS was performed to isolate CD25 high and low expressing cells.

tag: expressing


title: ZNF808-KO, S6, 1


title: WT-H1, S5, 2


title: WT-H1, S6, 1


title: NOA_1_12_2

description: Sample 45

value: male

value: nonobstructive azoospermia (NOA)

value: testis


title: NOA_1_10_7

description: Sample 38


title: HT-22 cells, LPS4

city: beijing

first: Haina

last: Gao

address: fucheng road

institute: beijing technology and business university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to gossypium hirsutum using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

source_name: HT-22 Mouse Hippocampal Neuronal Cell

extract_protocol:
RNA was harvested using Trizol reagent.NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L) was used with 0.4 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: HT-22 Mouse Hippocampal Neuronal Cell

value: LPS


title: HT-22 cells, LPS5


title: HT-22 cells, LPS3


title: DamID-seq, E7.75 embryo, Dam-Lhx1, rep 2

value: ROSA26 Neo-Dam-Lhx1 expressing


title: NOA_1_10_3

description: Sample 37


title: WT-H1, S5, 1

value: human embryonic stem cells (hESC)


title: DamID-seq, E7.75 embryo, Dam-Lhx1, rep 1

value: ROSA26 Neo-Dam expressing


title: HT-22 cells, LPS2


title: NOA_1_11_1

description: Sample 40


title: NOA_1_10_1

description: Sample 36


title: H1, S7, input

data_processing:
Reads from each library were mapped on hg19 using Bowtie2 version 2.4.4 with the ‘very-sensitive-local’ setting. Mapped reads were compressed in BAM files and indexed using SAMtools version 1.1841. We used MACS2 2.2.7.1 to call peaks using the corresponding input datasets as background controls
Assembly: hg19
Supplementary files format and content: broadPeak Files

extract_protocol: Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® following to the manufacturer’s instructions.

tag: chip antibody


title: HT-22 cells, LPS1


title: H1, ZNF808KO, S7, input


title: NOA_1_10_8

description: Sample 39


title: NOA_1_1_7

description: Sample 34


title: NOA_1_1_8

description: Sample 35


title: CHAT-Con-CORTEX-A18

type: RNA

city: Shanghai

first: Youwen

last: Si

address: North Zhongshan Road Campus: 3663 N. Zhongshan Rd., Shanghai

institute: East China Normal University

description:
Gene expression for Cortex in 2-month-old Cre--PS1flox/flox-PS2+/- (Con) mice
Con-CORTEX-replicate 2

hyb_protocol: Labeled cRNA was hybridized to the Agilent SurePrint G3 Mouse Gene Expression v2 8x60K Microarray (Design ID: 074809) according to the manufacturer's protocol. Hybridization was performed at 65°C for 17 hours in an Agilent hybridization oven.

scan_protocol: After hybridization, the slides were washed and scanned using the Agilent Scanner G2505C (Agilent Technologies) following the manufacturer’s instructions.

data_processing: Raw data were extracted using Feature Extraction software version 10.7.1.1 (Agilent Technologies). The extracted data were normalized using the quantile normalization method in GeneSpring GX software version 14.9 (Agilent Technologies). Probes detected in at least 75% of samples in any group were retained. Differential expression was determined using a two-tailed t-test with a threshold of fold change ≥ 2.0 and p-value ≤ 0.05.

source_name: Con-CORTEX

label_protocol: Total RNA was reverse transcribed into double-stranded cDNA, which was then transcribed in vitro to synthesize cRNA labeled with Cyanine-3-CTP (Cy3) using standard Agilent protocols.

extract_protocol: Total RNA was extracted using standard RNA isolation protocols. RNA concentration was determined with a NanoDrop ND-2000 spectrophotometer (Thermo Scientific), and RNA integrity was assessed using the Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Total RNA was extracted from the basal forebrain and cerebral cortex of three 2-month-old control (Con) mice and three 2-month-old double knockout (DKO) mice. Mice were sacrificed by cervical dislocation, and tissues were immediately dissected and snap-frozen in liquid nitrogen.

value: Brain


title: HT-22 cells, ctrl4

value: control


title: H1, ZNF808KO, S6, input


title: NOA_1_1_6

description: Sample 33


title: H1, S6, input


title: ZNF808-KO, S5, 1


title: H1, ZNF808KO, S5, input


title: NOA_1_1_5

description: Sample 32


title: HT-22 cells, ctrl2


title: H1, S5, input


title: NOA_1_1_2

description: Sample 31


title: CHAT-Con-CORTEX-A34

description:
Gene expression for Cortex in 2-month-old Cre--PS1flox/flox-PS2+/- (Con) mice
Con-CORTEX-replicate 3


title: HT-22 cells, ctrl1


title: CHAT-DKO-CORTEX-A26

description:
Gene expression for Cortex in 2-month-old ChatCre-PS1flox/flox-PS2-/-(DKO) mice
cDKO-CORTEX-replicate 1

source_name: cDKO-CORTEX


title: CHAT-Con-Basal Forebrain-A34

description:
Gene expression for Basal Forebrain in 2-month-old Cre--PS1flox/flox-PS2+/- (Con) mice
Con-Basal Forebrain-replicate 3

source_name: Con-Basal Forebrain


title: CHAT-Con-CORTEX-A1

description:
Gene expression for Cortex in 2-month-old Cre--PS1flox/flox-PS2+/- (Con) mice
Con-CORTEX-replicate 1


title: CHAT-Con-Basal Forebrain-A18

description:
Gene expression for Basal Forebrain in 2-month-old Cre--PS1flox/flox-PS2+/- (Con) mice
Con-Basal Forebrain-replicate 2


title: NOA_1_1_1

description: Sample 30


title: HT-22 cells, BL99_EV5

value: EV


title: CHAT-DKO-CORTEX-A31

description:
Gene expression for Cortex in 2-month-old ChatCre-PS1flox/flox-PS2-/-(DKO) mice
cDKO-CORTEX-replicate 2


title: H1, S7, H3K27ac

value: Histone H3K27ac antibody (mAb) - Catalog number 39685, Active Motif


title: RNA_Normal_4_7

description: Sample 29

value: Normal


title: CHAT-DKO-CORTEX-A32

description:
Gene expression for Cortex in 2-month-old ChatCre-PS1flox/flox-PS2-/-(DKO) mice
cDKO-CORTEX-replicate 3


title: H1, ZNF808KO, S7, H3K27ac


title: HT-22 cells, ctrl5


title: RNA_Normal_4_6

description: Sample 28


title: HT-22 cells, ctrl3


title: HCMV-72hpi HELF cells CAGE-seq

city: Shenyang

first: Yang

address: No. 36. Sanhao street, Heping District

description:
Library name: HELF_72h
HCMV infected HELF cells were collected at 72 hours post-infection (hpi).

data_processing:
Quality control and adapter/low-quality trimming were performed.
Trimmed reads were aligned to the human reference genome GRCh38/hg38 (unique mappers retained; multi-mappers discarded).
The 5′ ends of aligned reads were extracted to define CAGE transcription start sites (CTSSs); per-sample CTSSs were merged to form transcript clusters (TCs).
CTSS/TC tag counts were generated and normalized as tags-per-million (TPM); consensus clusters across samples were computed for differential TSS-usage analysis between HCMV-infected and mock groups.
Assembly: GRCh38/hg38
Supplementary files format and content: BED6 file of CAGE transcript clusters (TCs) detected
Supplementary files format and content: Tab-delimited table with per-TC quantification and annotation

source_name: embryonic lung

growth_protocol: HELF (human embryonic lung fibroblast) cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified 5%CO₂ atmosphere at 37°C.

extract_protocol:
Total RNA was isolated from each condition using a column-based purification with on-column DNase treatment; 1 µg total RNA per sample was used to construct CAGE-seq libraries.
For CAGE-seq, 1 µg total RNA was treated with T4 polynucleotide kinase and Terminator 5′-phosphate-dependent exonuclease to enrich capped transcripts. Reverse transcription was primed with a randomized hexamer carrying the 3′ adaptor, followed by template switching to append the 5′ adaptor. cDNA was PCR-amplified and size-selected (≈250–500 bp). Libraries were sequenced on an Illumina HiSeq X Ten with 150-nt paired-end reads.

treatment_protocol: Cells were infected with human cytomegalovirus (HCMV) HAN strain(moi=3) and harvested at 72 hours post-infection (hpi).

value: embryonic lung

value: human embryonic lung fibroblasts

value: HELF cells were infected with HCMV clinical strain HAN, which was isolated from a urine sample of a 5-month-old infant hospitalized in Shengjing Hospital of China Medical University, at a multiplicity of infection (MOI) of 3.


title: HT-22 cells, BL99_EV3


title: HT-22 cells, BL99_EV4


title: RNA_Normal_4_4

description: Sample 26


title: HT-22 cells, BL99_EV2


title: CHAT-Con-Basal Forebrain-A1

description:
Gene expression for Basal Forebrain in 2-month-old Cre--PS1flox/flox-PS2+/- (Con) mice
Con-Basal Forebrain-replicate 1


title: H1, S6, H3K27ac

value: WT


title: RNA_Normal_4_5

description: Sample 27

value: male


title: H1, ZNF808KO, S5, H3K27ac


title: mock-infected HELF cells CAGE-seq

institute: Shengjing Hospital of China Medical University

description:
Library name: HELF_U
Mock-infected cells were harvested as control.

value: HELF cells were mock-infected.


title: H1, ZNF808KO, S6, H3K27ac


title: RNA_Normal_4_3

description: Sample 25

value: testis


title: HT-22 cells, BL99_EV1

value: HT-22 Mouse Hippocampal Neuronal Cell


title: CHAT-DKO-Basal Forebrain-A32

description:
Gene expression for Basal Forebrain in 2-month-old ChatCre-PS1flox/flox-PS2-/-(DKO) mice
cDKO-Basal Forebrain-replicate 3

source_name: cDKO-Basal Forebrain


title: Sample_iHTM_2

city: Qingdao

first: xuejiao

last: Yang

address: #16 Jiangsu Rd.

institute: the affiliated hospital of Qingdao University

data_processing:
To identify differentially expressed genes, pair‐end FASTQ read files were mapped to GRCh38 genomes with hisat2. Differentially expression testing was performed using the R package DESeq2. Only genes with P‐value ≤ .05 and fold change ≥2 or ≤1/2 were considered statistically significant.
Assembly: GRCh38
Supplementary files format and content: processed_data_files.txt: Tab-delimited text file.

source_name: iHTM

growth_protocol: Cells were cultured in Medium of Nutrient Mixture F‐12 (DMEM/F12; Gibco, Invitrogen) that contained 15% fetal bovine serum (FBS; Gibco, Invitrogen) at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted by using the manufacturer's protocol of mirVana miRNA Isolation Kit (Ambion). Agilent 2100 Bioanalyzer (Agilent Technologies) was used to evaluate the RNA integrity. Samples with RNA integrity number ≥ 7 were reserved further analysis. TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) was used to construct libraries according to the manufacturer's instructions. Then, these libraries were sequenced on the Illumina sequencing platform (Illumina HiSeq X Ten) and 150 bp paired‐end reads were generated.

value: iHTM

value: normal trabecular meshwork cells


title: MUT_scRNAseq

first: Yuxin

last: Dai

state: Guangdong

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger software, specifically version 7.1.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values (TSV) files and matrix files

source_name: Melanoma lung metastasis tissue

extract_protocol:
Tumor tissues from B16-IRF7-WT/MUT tumor-bearing mice were prepared into a single-cell suspension using collagenase II (1 mg/ml) and collagenase IV (2 mg/ml) at 37 °C for 30 minutes. Red blood cells were removed using lysis buffer, and the suspension was resuspended in flow staining buffer. Live immune cells (CD45 positive and 7-AAD negative) were isolated by FACS and resuspended in sample buffer for single-cell capture. These live CD45+ immune cells were then captured using the BD Rhapsody™ system and lysed.
Single-cell suspension was added to the 10x Chromium chip following the instructions provided for the 10X Genomics Chromium Single-Cell 3' Kit (V3), with the goal of capturing 8,000 cells. cDNA amplification and library construction were performed according to standard protocols. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end sequencing, 150 bp) at a minimum depth of 20,000 reads per cell.

value: Melanoma lung metastasis tissue

value: melanoma cell

value: IRF7-C435A mutant


title: WT_scRNAseq

value: wild-type


title: CHAT-DKO-Basal Forebrain-A26

description:
Gene expression for Basal Forebrain in 2-month-old ChatCre-PS1flox/flox-PS2-/-(DKO) mice
cDKO-Basal Forebrain-replicate 1

value: Brain


title: RNA_Normal_4_1

description: Sample 23


title: Sample_iHTM_3


title: H1, ZNF808KO, S6, H3K9me3

value: human embryonic stem cells (hESC)

value: Histone H3K9me3 antibody (pAb) - Catalog number 39161, Active Motif


title: MUTIFN3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM and count valuve for each sample

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: IFNα stimulation.


title: H1, S7, H3K9me3


title: CHAT-DKO-Basal Forebrain-A31

description:
Gene expression for Basal Forebrain in 2-month-old ChatCre-PS1flox/flox-PS2-/-(DKO) mice
cDKO-Basal Forebrain-replicate 2


title: RNA_Normal_3_7

description: Sample 21

value: Normal


title: H1, ZNF808KO, S7, H3K9me3


title: Sample_GTM3_2

value: glaucomatous trabecular meshwork cells


title: Sample_GTM3_3


title: RNA_Normal_3_8

description: Sample 22


title: RNA_Normal_3_6

description: Sample 20


title: MUTIFN2


title: RNA_Normal_4_2

description: Sample 24


title: H1, ZNF808KO, S5, H3K9me3


title: Sample_GTM3_1


title: MUTIFN1


title: WTIFN3


title: H1, S5, H3K27ac

value: WT

value: Histone H3K27ac antibody (mAb) - Catalog number 39685, Active Motif


title: H1, S6, H3K9me3


title: H1, S5, H3K9me3


title: RNA_Normal_3_5

description: Sample 19

value: male


title: Stage 13-16 Embryos, CrebA protein-null, scRNA-seq

city: Baltimore

first: Da

last: Peng

state: Maryland

address: 733 North Broadway, MRB 653

institute: Johns Hopkins University

description: Library name: Sample 3

data_processing:
Alignment and gene quantification were done using CellRanger (version 6.1.2).
Biological replicates were combined using Seurat and underwent bacth correction using Harmony.
Assembly: dmel r6.33
Supplementary files format and content: raw counts matrix
Supplementary files format and content: seurat objects

organism: Drosophila melanogaster

source_name: whole embryo

extract_protocol:
Embryos were collected and aged to appropriate stages on apple juice caps seeded with yeast paste. Embryos were harvested in collection baskets, soaked in 50% bleach for 3 minutes to remove the outer chorion, then rinsed thoroughly and transferred to Dounce homogenizers containing 1 ml ice-cold 1X PBS.  Embryos were disrupted using 20 strokes (up and down) of the loose “B” pestle.  The material was then transferred to a 1.5 ml microfuge tube and pelleted by a 3 minute spin in a tabletop centrifuge set at 4000 RPM at 4°C. Supernatant was removed and material was resuspended in 1 ml fresh ice-cold 1X PBS, then passaged 20 times through a 22 gauge needle, and 4X through a 23 gauge needle. The cell suspension is then passed through a 40 μm cell strainer into a 1.5 mL microcentrifuge tube. Cells were pelleted by a 3 minute spin in a tabletop centrifuge set at 6000 RPM at 4°C, then resuspended in 100 μL 1X ice cold PBS and immediately brought to the sequencing center for viability counts and library preparation for 10X Genomics sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: whole embryo

value: CrebA protein-null

tag: developmental stage

value: stage 13-16

tag: batch

value: rep 1


title: RNA_Normal_3_4

description: Sample 18

value: testis


title: WTIFN2

value: melanoma cell


title: WTIFN1


title: Drosophila-head-WT-female-with-TDO2i--2

city: Beer Sheva

first: Debra

last: Toiber

state: Israel

address: Ben Gurion Road #1, Building 40, room 205

country: Israel

institute: Ben Gurion University of the Negev

description: Library name: WT_F_TDO2_REP2

data_processing:
Raw reads were processed into gene expression counts using the nf-core/rnaseq pipeline (v3.14.0) with "--aligner star_salmon" option. Reads were first filtered and trimmed with TrimGalore! (v0.6.7), then mapped to the Drosophila BDGP6.46 reference genome using STAR (v2.7.9a). Transcript expression was quantified using Salmon (v1.10.1) and aggregated at the gene level using the tximport package (v1.12.0).
Assembly: BDGP6.46
Supplementary files format and content: comma-delimited text file include row expression counts for each sample

source_name: Head

growth_protocol: Flies were maintained under non-crowding conditions on standard cornmeal diet 5g dextrose, 2.5% yeast extract, 8.6% cornmeal, 2% agar, 0.1% ortho-phosphoric acid, and 0.1% propionic acid) and grown at 25oC with 12h light/dark cycle. Age-matched flies were used for all experiments.

extract_protocol:
RNA was extracted from single head of 21 days old verging female w1118 / SIRT6 KO Drosophila fed with 100µM TDO2 inhibitor/ DMSO for 21 days.  RNA was extracted using BioTri RNA (Bio-Lab, catalogue number 959758027100), according to the manufacturer’s manual followed by cleaning step using RNA Clean & Concentrator MagBead (Zymo Research, catalogue number R1081). Sample QC -Total RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. The next steps included performing rRNA depletion using QIAGEN FastSelect rRNA HMR or Fly Kit (Qiagen, Germantown, MD, USA), which was conducted following the manufacturer’s protocol. RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). Azenta US, Inc. 2910 Fortune Circle West, Suite E, Indianapolis, IN 46241 | Tel: (858)527 - 7080 . The sequencing libraries were multiplexed and clustered on the flowcell. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration.

treatment_protocol: TDO2 inhibitor 680C91 (Tocris Bioscience, Bristol, UK) was dissolved in dimethyl sulfoxide (DMSO). TDO2 inhibitor / DMSO were added to the yeast extract in the diet to a final concentration of 100 µM (680C91) . Flies were introduced to the inhibitor-supplemented media upon eclosion; supplemented media were changed every other day. Files were snaped freeze in liquid nitrogen at the age of 21 days for further process.

tag: tissue

value: Head

tag: Sex

value: female

value: 100uM TDO2 inhibitor (680C91)


title: RNA_Normal_3_3

description: Sample 17


title: Drosophila-head-WT-female-with-TDO2i--3

description: Library name: WT_F_TDO2_REP3

tag: genotype


title: RNA_Normal_3_2

description: Sample 16


title: aorta, Bmp2+/+ KlothoKl/Kl , female, replicate 4

city: Newark

first: Melissa

middle: B.

last: Rogers

state: NJ

address: 185 south orange ave.

department: Biochem. & Molec. Biology

institute: Rutgers NJMS

description: Library name: FDK201-ao_S8_R1_001

data_processing:
Partek Flow
sequence reads were trimmed based on quality score Phred <20 (default)
trimmed sequence reads were aligned with StarAligner 2.78a and mapped to mm39
read counts and TPM normalization were done using Partek Flow
Assembly: mm39
Supplementary files format and content: txt file includes TPM normalization for each sample

source_name: aorta

growth_protocol: Mice were made fully congenic on the 129S1/SvlmJ (129) by backcrossing more than 10 times.  Heterozygote-by-heterozygote breeding produced both control mice and mutant homozygotes.  After weaning, moistened mouse chow (LabDiet PicoLab Rodent Diet 20; Lab Supply, Fort Worth, TX) was placed on the bottom of the cage to ensure that the smaller and weaker KLOTHO-deficient mice had access to food.

extract_protocol:
miRNeasy Mini Kit (Qiagen Inc.)
New England Biolabs Ultra Directional RNA Library Prep Kit.
cDNA libraries purified with AmpureXP beads, quantified on the Agilent Bioanalyzer,  Qubit Fluorometric Quantification

treatment_protocol: aortas were flash frozen after dissection

value: aorta

tag: disease state

value: renal disease

value: 50 days

value: Bmp2+/+ KlothoKl/Kl


title: Stage 10-12 Embryos, CrebA protein-null, Replicate 2, scRNA-seq

description: Library name: Sample 2

value: stage 10-12

value: rep 2


title: MUTCTRL2

tag: cell line

tag: cell type

value: IRF7-C435A mutant

tag: treatment

value: Control


title: WTCTRL3

value: wild-type


title: RNA_Normal_3_1

description: Sample 15

tag: gender

value: male

tag: age

value: Normal


title: aorta, Bmp2+/+ KlothoKl/Kl , female, replicate 3

description: Library name: FDK267-ao_S6_R1_001

tag: strain

value: 53 days


title: MUTCTRL1


title: aorta, Bmp2+/+ KlothoKl/Kl , female, replicate 1

description: Library name: deltaK77-ao_S2_R1_001

value: 45 days


title: Drosophila-head-WT-female-with-DMSO--3

description: Library name: WT_F_DMSO_REP3

value: DMSO


title: Stage 10-12 Embryos, CrebA protein-null, Replicate 1, scRNA-seq

description: Library name: Sample 1

value: whole embryo

value: CrebA protein-null

value: rep 1


title: Drosophila-head-SIRT6-KO-female-with-TDOi-3

description: Library name: S6_F_TDO2_REP3

value: Head

value: female

value: SIRT6 KO

value: 100uM TDO2 inhibitor (680C91)


title: RNA_Normal_2_2

description: Sample 12

tag: condition

tag: testis

value: testis


title: RNA_Normal_2_4

description: Sample 14


title: Drosophila-head-WT-female-with-DMSO--2

description: Library name: WT_F_DMSO_REP2


title: WTCTRL2

value: melanoma cell


title: MUTCTRL3

value: IRF7-C435A mutant


title: RNA_Normal_2_3

description: Sample 13


title: aorta, Bmp2+/+ KlothoCtrl , female, replicate 4

description: Library name: deltaK11-ao_S3_R1_001

value: aorta

value: healthy renal function

value: Bmp2+/+ Klotho+/Kl


title: WTCTRL1

value: wild-type

value: Control


title: aorta, Bmp2+/+ KlothoKl/Kl , female, replicate 2

description: Library name: deltaK22-ao_S4_R1_001

value: renal disease

value: 45 days

value: Bmp2+/+ KlothoKl/Kl


title: Drosophila-head-SIRT6-KO-female-with-TDOi-2

description: Library name: S6_F_TDO2_REP2


title: Drosophila-head-WT-female-with-DMSO--1

description: Library name: WT_F_DMSO_REP1

value: DMSO


title: aorta, Bmp2+/+ KlothoCtrl , female, replicate 3

description: Library name: deltaK76-ao_S1_R1_001


title: Drosophila-head-WT-female-with-TDO2i--1

description: Library name: WT_F_TDO2_REP1


title: RNA_Normal_1_7.2_5

description: Sample 10

value: male

value: Normal


title: Drosophila-head-SIRT6-KO-female-with-TDOi-1

description: Library name: S6_F_TDO2_REP1

value: Head

value: female


title: aorta, Bmp2+/+ KlothoCtrl , female, replicate 2

description: Library name: FDK266-ao_S5_R1_001

value: 53 days


title: aorta, Bmp2+/+ KlothoCtrl , female, replicate 1

description: Library name: FDK202-ao_S7_R1_001

value: 50 days


title: WT_Th2_3

city: Bethesda

first: Tom

last: Hill

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

institute: NIAID

data_processing:
Reads were mapped to the mouse genome (mm10 assembly) using Bowtie 0.12.8. Distributions of fragment sizes were similar to previously published data (data not shown). Reads whose fragment lengths were less than 175 bp were kept and only one mapped read per a unique genomic region was used to call peaks. Regions of open chromatin were identified by MACS (version 1.4.2) using a p-value threshold of 1 × 10−5.
In all cases, redundant reads were removed using FastUniq, and customized Python scripts were used to calculate the fragment length of each pair of uniquely mapped paired-end (PE) reads.
Assembly: mm10
Supplementary files format and content: bigWig files
Supplementary files format and content: Peak bed files

source_name: Spleen

extract_protocol:
Sorted naïve CD4 T cells were activated and expanded using anti-CD3 (1ug/mL) and anti-CD28 (3ug/mL) in complete IMDM media in presence of antigen presenting cells (mitomycin C treated T-cell depleted splenocytes)
Ten thousand cells were pelleted and washed with 50 μL 1 × PBS. After lysis, nuclei were pelleted by centrifuging at 500 × g for 10 min, and re-suspended in 50 μL transposase mixture (25 μl of 2x TD buffer, 2.5 μl of TDE1, 0.5 μl of 1% digitonin, 22 μl of nuclease-free water) (#20034197, Illumina; #G9441, Promega) for incubattion at 37°C with shaking at 300 rpm for 30 min. The tagmentated DNAs were then purified using a QIAGEN MinElute kit and amplified with 10 or 11 cycles of PCR based on the amplification curve

treatment_protocol: Th2 polarized cells were generated by activating naïve CD4 T cells and differentiating in the presence of IL-4 and anti-IL12.

value: Spleen

value: WT


title: WT_Th2_1

growth_protocol: Sorted naïve CD4 T cells were activated and expanded using anti-CD3 (1ug/mL) and anti-CD28 (3ug/mL) in complete IMDM media in presence of antigen presenting cells (mitomycin C treated T-cell depleted splenocytes)


title: WT_Th2_2


title: Mut_Th2_3

value: Mut


title: Drosophila-head-SIRT6-KO-female-with-DMSO--2

description: Library name: S6_F_DMSO_REP2

value: SIRT6 KO


title: RNA_Normal_1_4

description: Sample 7

value: testis


title: RNA_Normal_1_5

description: Sample 8


title: Drosophila-head-SIRT6-KO-female-with-DMSO--3

description: Library name: S6_F_DMSO_REP3


title: aorta, Bmp2+/+ KlothoKl/Kl , male, replicate 4

description: Library name: FDK250-ao_S12_R1_001

value: aorta

value: 48 days


title: Mut_Th2_2


title: aorta, Bmp2+/+ KlothoKl/Kl , male, replicate 3

description: Library name: FDK68_ao_S2_R1_001

value: renal disease

value: 47 days


title: RNA_Normal_1_2

description: Sample 5


title: Mut_Th2_1


title: aorta, Bmp2+/+ KlothoKl/Kl , male, replicate 2

description: Library name: deltaK140_ao_S3_R1_001

value: 45 days

value: Bmp2+/+ KlothoKl/Kl


title: RNA_Normal_2_1

description: Sample 11

value: male


title: RNA_Normal_1_3

description: Sample 6

value: Normal


title: C. elegans, wildtype, replicate D

city: Seattle

first: Brian

last: Kraemer

address: 1660 S Columbian Way

department: Medicine

institute: University of Washington

description: Library name: N2-D

data_processing:
FASTQ files were pre-processed with FASTP (version 0.24.0)  and aligned with STAR two-pass-mapping (version 2.7.11b) against the C. elegans genome WBcel235 (version 113). Gene read counts were produced with featureCounts (version 2.0.6).
Assembly: WBcel235
Supplementary files format and content: .txt read counts

organism: Caenorhabditis elegans

source_name: whole animal

extract_protocol:
RNA was purified from flash-frozen, developmentally synchronized C. elegans populations grown at 20 C following hypochlorite treatment using TRIzol Reagent.
Novogene mRNA library preparation

value: whole animal

value: wildtype

value: D

value: hermaphrodite

value: Day 1 adult


title: C. elegans, wildtype, replicate C

description: Library name: N2-C

value: C


title: RNA_Normal_1_1

description: Sample 4


title: Bisulfite-seq_KO3

first: Huali

last: Shen

address: 130 Dongan Road

institute: Fudan University

data_processing:
Clean data were processed using Trim Galore. Read mapping and methylcytosine calling were analysed by bismark with Hisat2 (Krueger F, Andrews SR.Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.
Assembly: mm10

source_name: brain

extract_protocol:
Total RNAs were isolated by TRIzol reagent from 40mg tissues after homogenization with a dounce homogenizer. Poly-A tailed RNAs were enriched by a GenElute mRNA Miniprep Kit (Sigma-Aldrich). Treated mRNAs with 0.5% unmethylated RNA controls in vitro transcribed from lambda genome were treated using EZ RNA Methylation Kit (Zymo Research), with the following modifications: 500 ng of mRNAs were bisulfited using two cycles of 10 min denaturation at 70 °C followed by 45 min at 54 °C.
Strand-specific libraries were constructed with VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (vazyme), and sequenced using NovaSeq 6000 (Illumina).

treatment_protocol: We utilized five 3-month-old male wild-type and five Nsun5-KO mice from the same litter. The mice were anesthetized using 2% pentobarbital sodium (50 mg/kg, intraperitoneal), brain tissues were meticulously extracted through a cryogenic procedure.

value: brain


title: C. elegans, wildtype, replicate B

description: Library name: N2-B

value: B


title: aorta, Bmp2∆UCS/∆UCS KlothoKl/Kl , male, replicate 4

description: Library name: FDK175_ao_S11_R1_001

value: Bmp2deltaUCS/deltaUCS KlothoKl/Kl


title: RNA_Normal_1_6

description: Sample 9

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For bisulfite-seq data, Trim Galore (v0.3.3) was used to remove the first 6 bases of random primer, adaptor sequences and low quality bases; for RNA-seq data, each single cell was separated by unique cell barcode, then template switch oligo (TSO), ployA tails, adaptors and low quality bases were removed.
For bisulfite-seq data, clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; for RNA-seq data, clean reads were mapped to human genome hg19 with Tophat (v2.0.14), and then unique UMI counts were calculated by HTSeq.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include UMI counts of RefSeq genes. While WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

source_name: testis

extract_protocol:
An individual cell was picked into the cell lysis buffer with vitro methylation (IVM) mixture containing 4 U RNase inhibitor (TAKARA, Cat. 2313B), 0.25% IGEPAL CA-630 (SIGMA, Cat. I3021), 1X GC reaction buffer and 2 U M. CviPI (NEB, Cat. M0227L). After gently vortexed for 10 sec, the cell lysate was incubated at 37 °C for 20 min and then at 65 °C for 25 min. Then, the cell lysate could be directly processed for RNA/DNA separation or stored at -80 °C.
For RNA part, a modified Smart-seq2 protocol was applied for single-cell RNA-seq. For DNA part, Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

value: testis


title: RNA_NOA_3

description: Sample 3

value: nonobstructive azoospermia (NOA)


title: C. elegans, wildtype, replicate A

description: Library name: N2-A

value: A


title: Bisulfite-seq_KO1


title: aorta, Bmp2∆UCS/∆UCS KlothoKl/Kl , male, replicate 3

description: Library name: deltaK55_ao_S10_R1_001

value: aorta

value: renal disease


title: C. elegans, dib-1 mutant, replicate D

description: Library name: dib-1-D


title: Drosophila-head-SIRT6-KO-female-with-DMSO--1

description: Library name: S6_F_DMSO_REP1

value: Head

value: female

value: SIRT6 KO

value: DMSO


title: RNA_NOA_2

description: Sample 2

value: male


title: RNA_NOA_1

description: Sample 1


title: C. elegans, dib-1 mutant, replicate C

description: Library name: dib-1-C

value: whole animal


title: Bisulfite-seq_WT3

value: WT


title: Bisulfite-seq_WT2


title: aorta, Bmp2∆UCS/∆UCS KlothoKl/Kl , male, replicate 2

description: Library name: delta94_ao_S12_R1_001

value: 48 days


title: Bisulfite-seq_KO2


title: aorta, Bmp2+/+ KlothoCtrl , male, replicate 4

description: Library name: deltaK63-ao_S9_R1_001

value: healthy renal function

value: 44 days

value: Bmp2+/+ Klotho+/Kl


title: KD3

city: SHANGHAI

first: ZHENG

last: YANG

address: FENGLIN STREET

department: ZHONGSHAN HOSPITAL

institute: FUDAN UNIVERSITY

description:
Library name: SAMPLES 6
FPKM_K3

data_processing:
RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer
RNA integrity was assessed using the Agilent 2100 Bioanalyzer
Raw reads of fastq form were processed using fastp to obtain the clean reads
The clean reads were mapped to the reference genome using HISAT2
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: NCBI
Supplementary files format and content: EXCEL

organism: Rattus norvegicus

source_name: Heart

growth_protocol: NRVMs were isolated from Sprague-Dawley rats within the first three days postnatal (Animal Care and Use Committee of Zhongshan Hospital, Fudan University) by using a cardiomyocyte isolation kit (Miltenyi Biotec, #130-098-373) . The isolated cells were cultured in a humidified 5% CO2 incubator at 37(°C for 2h. After collecting the supernatant which containing cardiomyocytes, we transferred it into another culture dish with Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin-streptomycin (Gibco) for 24h. NRVMs were then subjected to subsequent experiments.

extract_protocol:
Total RNA was extracted using the TRIzol reagent
VAHTS Universal V6 RNA-seq Library Prep Kit

treatment_protocol: NC or sh-Decr1

value: Heart

value: NRVMs

value: Sprague-Dawley


title: KD2

description:
Library name: SAMPLES 5
FPKM_K2


title: aorta, Bmp2∆UCS/∆UCS KlothoKl/Kl , male, replicate 1

description: Library name: FdeltaK36_ao_S9_R1_001

value: 47 days

value: Bmp2deltaUCS/deltaUCS KlothoKl/Kl


title: aorta, Bmp2+/+ KlothoKl/Kl , male, replicate 1

description: Library name: FdeltaK28-ao_S10_R1_001

value: aorta

value: renal disease

value: 45 days

value: Bmp2+/+ KlothoKl/Kl


title: C. elegans, dib-1 mutant, replicate A

description: Library name: dib-1-A

value: A

value: hermaphrodite

value: Day 1 adult


title: aorta, Bmp2+/+ KlothoCtrl , male, replicate 3

description: Library name: FDK167_ao_S1_R1_001

value: male


title: Ribo-seq_KO4

data_processing:
Tophat2
Assembly: mm10
Library strategy: Ribo-seq

extract_protocol:
For RNA extraction, we employed the TRIzol method, a robust approach ensuring the purity and quality of RNA.
The lysate solution first underwent nucleic acid digestion and separated ribosome bounding RNA from free mRNA. RPFs were obtained by enrichment of ribosome-mrna complex. After the rRNA was removed and purified by PAGE glue, the target RNA fragments were obtained. End repair, add 5 'and 3' joints directly to both ends. cDNA was synthesized by reverse transcription and PAGE gel was purified. The initial library was obtained by PCR enrichment with sequencing splices.

value: brain


title: C. elegans, dib-1 mutant, replicate B

description: Library name: dib-1-B

value: whole animal

value: B


title: C. elegans, tau transgenic with dib-1 mutant, replicate D

description: Library name: tau-dib-1-D

value: D


title: aorta, Bmp2+/+ KlothoCtrl , male, replicate 2

description: Library name: FDK249-ao_S11_R1_001

value: healthy renal function

value: 48 days

value: Bmp2+/+ Klotho+/Kl


title: Ribo-seq_KO3


title: CTL3

description:
Library name: SAMPLES 3
FPKM_C3

value: Heart

value: NRVMs

value: Sprague-Dawley

value: NC


title: C. elegans, tau transgenic with dib-1 mutant, replicate C

description: Library name: tau-dib-1-C

value: C


title: CTL2

description:
Library name: SAMPLES 2
FPKM_C2


title: C. elegans, tau transgenic with dib-1 mutant, replicate B

description: Library name: tau-dib-1-B


title: aorta, Bmp2+/+ KlothoCtrl , male, replicate 1

description: Library name: deltaK143_ao_S4_R1_001

value: aorta

value: 45 days

value: Bmp2+/+ Klotho+/+


title: aorta, Bmp2∆UCS/∆UCS KlothoCtrl , male, replicate 4

description: Library name: deltaK138_ao_S8_R1_001

value: 47 days

value: Bmp2deltaUCS/deltaUCS Klotho+/Kl


title: Sample_iHTM_1

value: iHTM

value: normal trabecular meshwork cells


title: Bisulfite-seq_WT1

value: brain

value: WT


title: C. elegans, tau transgenic, replicate D

description: Library name: tau-D

value: whole animal

value: D

value: hermaphrodite

value: Day 1 adult


title: Ribo-seq_WT4


title: CTL1

description:
Library name: SAMPLES 1
FPKM_C1

value: Heart

value: NRVMs


title: aorta, Bmp2∆UCS/∆UCS KlothoCtrl , male, replicate 3

description: Library name: FdeltaK24_ao_S7_R1_001

value: male

value: healthy renal function


title: aorta, Bmp2∆UCS/∆UCS KlothoCtrl , male, replicate 1

description: Library name: deltaK125_ao_S6_R1_001

value: aorta

value: 48 days


title: C. elegans, tau transgenic, replicate C

description: Library name: tau-C

value: C


title: KD1

description:
Library name: SAMPLES 4
FPKM_K1

value: Sprague-Dawley


title: Ribo-seq_WT2


title: C. elegans, tau transgenic with dib-1 mutant, replicate A

description: Library name: tau-dib-1-A

value: A


title: A998-MenSC

first: Peilin

last: Liao

address: No. 382, Waihuan East Road, University Town, Panyu District, Guangzhou, Guangdong Province

institute: South China University of Technology

description: Library name: Sample 13

data_processing:
mapping software: hisat2.
counts analysis:featureCounts.
counts data analysis: DESeq2 package, ggplot2.
Assembly: mRatBN7.2
Supplementary files format and content: Excel file contains counts data of all each sample.

source_name: uterus

extract_protocol:
RNA was harvested using TRNzol Universal Reagent(DP424).
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 (Cat.No.RK20306).

value: uterus


title: 129S1/SvlmJ kidney, KlothoKl/Kl, female, replicate 4

description: Library name: kid_Fdk49_S4_R1_001 sample 16

source_name: kidney

growth_protocol: Animals are congenic

treatment_protocol: kidneys flash frozen after perfusion and dissection

value: kidney

value: female

value: renal disease

value: Kl/Kl


title: A997-SP

description: Library name: Sample 12


title: A999-MenSC

description: Library name: Sample 14


title: Ribo-seq_KO2

value: brain


title: 129S1/SvlmJ kidney, KlothoKl/Kl, female, replicate 3

description: Library name: kid_Fdk108_S5_R1_001 sample 15

value: 54 days


title: RNA-seq_KO4

data_processing:
All further analyses were conducted using this clean data. For the mapping phase, we employed the HISAT2 algorithm version 2.0.5 to construct the index of the reference genome and to align the data.
Assembly: mm10

extract_protocol:
For RNA extraction, we employed the TRIzol method, a robust approach ensuring the purity and quality of RNA.
NEBNext® Ultra™ RNA Library Prep Kit for Illumina®


title: Ribo-seq_KO1


title: C. elegans, tau transgenic, replicate A

description: Library name: tau-A

value: whole animal

value: hermaphrodite

value: Day 1 adult


title: A996-SP

description: Library name: Sample 11


title: 129S1/SvlmJ kidney, KlothoKl/Kl, female, replicate 2

description: Library name: kid_DK77_S8_R1_001 sample 14

value: 45 days


title: A1000-MenSC

description: Library name: Sample 15


title: hct116_wt_rep4

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

description: Library name: hct116_wt_rep4

data_processing:
Micro-C reads were mapped to the GRCh38 genome using BWA-MEM (version 0.7.17). Aligned reads were processed with Pairtools (version 1.0.3) using the parse2 function to rescue complex walks, with the options --min-mapq 1 --report-position outer --max-inter-align-gap 30. The resulting pairs files were sorted, converted to FAN-C pairs format (version 0.9.18), and deduplicated. Quality control metrics were then extracted. From these processed pairs, FAN-C .hic files were generated. Principal Component Analysis (PCA) was performed on the merged .hic files using FAN-C. Because biological replicates clustered consistently across all stages, replicate .hic files were combined. To estimate the optimal resolution at each stage, we applied a custom Python script (following Rao et al., Cell 2014) to identify the bin size at which 80% of bins contained more than 1,000 reads. Finally, the merged FAN-C .hic files were converted to balanced cooler (version 0.8.6; Abdennur and Mirny, 2020) .mcool files using cooler zoomify with mad-max set to 0.
Assembly: GRCh38
Supplementary files format and content: mcool files containing normalized matrix for each genotype

growth_protocol: HCT116 (CCL-247; ATCC), were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal calf serum (FCS; Eurobio Scientific) and 100 µg/mL penicillin/streptomycin (Corning) at 37°C, 5% CO2. ES-E14TG2a mESCs (CRL-1821; ATCC) were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Sigma) supplemented with 13% fetal calf serum (FCS; Sigma), 0.32% 2-mercaptoethanol (Gibco), and 100 µg/mL penicillin/streptomycin (Corning). Media was freshly supplemented with 1000 units/mL recombinant mouse LIF protein (ESGRO®), 1 µM of the MEK/ERK inhibitor PD0325901 (Sigma), and 3 µM of the GSK inhibitor CHIR99021 (Sigma) (2i). Cells were plated at a density of 2.65 x 105 cells per cm2 on plates coated with 0.2% gelatin from porcine skin (Sigma). Cells were grown at 37°C, 8% CO2, and passaged every 48 hours using 0.05% Trypsin-EDTA for detachment (Gibco). Cells were frozen in fetal calf serum (FCS; Sigma) supplemented with 10% DMSO (Gibco).

extract_protocol:
HCT116 Micro-C experiments were placed at 65°C overnight to reverse crosslinking. The following day, phenol:chloroform:isoamylalcohol DNA extraction was carried out followed by RNA removal through RNase A treatment. DNA concentrations were quantified using Qubit.
Total DNA was carried over into the final library construction phase, and after amplification, size selection for the appropriate di-nucleosomal band (350-500bp) was carried out with a two-sided cleanup using AMPure XP (Beckman Coulter) beads. Libraries were generated using approximately 1-2 million cells per individual library as described in Maziak N. et al. (in revision).

value: Human colon cancer cell line


title: aorta, Bmp2∆UCS/∆UCS KlothoCtrl , male, replicate 2

description: Library name: FdeltaK31_ao_S5_R1_001

value: aorta

value: male

value: healthy renal function

value: Bmp2deltaUCS/deltaUCS Klotho+/Kl


title: RNA-seq_KO3


title: A995-SP

description: Library name: Sample 10


title: RNA-seq_KO2


title: Ribo-seq_WT3

value: WT


title: hct116_wt_rep3

description: Library name: hct116_wt_rep3


title: 129S1/SvlmJ kidney, KlothoKl/Kl, female, replicate 1

description: Library name: kid_FdK22_S2_R1_001 sample 13


title: hct116_wt_rep2

description: Library name: hct116_wt_rep2


title: A994-Model

description: Library name: Sample 9

value: uterus


title: 129S1/SvlmJ kidney, KlothoCtrl, female, replicate 4

description: Library name: kid_Fdk48_S3_R1_001 sample 12

value: kidney

value: 48 days


title: RNA-seq_KO1


title: A993-Model

description: Library name: Sample 8


title: 129S1/SvlmJ kidney, KlothoCtrl, female, replicate 3

description: Library name: kid_Fdk84_S6_R1_001 sample 11

value: female

value: 49 days


title: hct116_wt_rep1

description: Library name: hct116_wt_rep1


title: C. elegans, tau transgenic, replicate B

description: Library name: tau-B

value: B


title: Ribo-seq_WT1

value: brain


title: RNA-seq_WT4


title: A992-Model

description: Library name: Sample 7


title: hct116_tko_rep2

description: Library name: hct116_tko_rep2


title: hct116_tko_rep3

description: Library name: hct116_tko_rep3


title: A991-Gel

description: Library name: Sample 6


title: 129S1/SvlmJ kidney, KlothoCtrl, female, replicate 1

description: Library name: kid_FdK33_S1_R1_001 sample 9


title: RNA-seq_WT3


title: A990-Gel

description: Library name: Sample 5


title: hct116_tko_rep1

description: Library name: hct116_tko_rep1


title: 129S1/SvlmJ kidney, KlothoKl/Kl, male, replicate 5

description: Library name: kid_Fdk69_S10_R1_001 sample 8

value: renal disease

value: 47 days

value: Kl/Kl


title: hct116_dko_rep4

description: Library name: hct116_dko_rep4


title: A989-Gel

description: Library name: Sample 4


title: RNA-seq_WT1


title: 129S1/SvlmJ kidney, KlothoKl/Kl, male, replicate 4

description: Library name: kid_Fdk153_S9_R1_001 sample 7

value: 44 days


title: hct116_dko_rep3

description: Library name: hct116_dko_rep3

value: Human colon cancer cell line


title: IL_restraint_cko6

first: Bing

last: Liu

address: No. 280, South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were aligned to the mouse reference genome (version mm10) using Bowtie2 RNASeq alignment software. HTSeq (version 2.0.2) was used to generate read counts of each gene. Normalized counts were obtained by normalizing raw counts with size factors using the median ratio method in DESeq2 1.36.0 package.
Assembly: mm10
Supplementary files format and content: Matrix of read counts, with each row representing a gene and each column representing a sample.

source_name: pituitary intermediate lobe

extract_protocol:
The intermediate lobe tissue was obtained using laser capture microdissection (LCM) from frozen pituitary sections. LCM-collected tissues in 10 μL lysis buffer with RNase inhibitor were submitted for RNA isolation using TRIzol (Sigma).
Samples with appropriate size distribution were selected for sequencing library construction using TruePrep RNA Library Prep Kit V2 for illumina (Vazyme, China). The final library was sequenced using an Illumina Novaseq 6000 sequencer, generating an average of approximately 20 million 150-bp paired-end reads per sample.

value: pituitary intermediate lobe

value: cko

value: restraint


title: A988-Con

description: Library name: Sample 3


title: RNA-seq_WT2


title: 129S1/SvlmJ kidney, KlothoKl/Kl, male, replicate 3

description: Library name: kid_DK54_S16_R1_00 sample 6

value: male

value: 45 days


title: 129S1/SvlmJ kidney, KlothoKl/Kl, male, replicate 2

description: Library name: kid_DK75_S14_R1_001 sample 5


title: IL_restraint_cko5


title: A987-Con

description: Library name: Sample 2

value: uterus


title: hct116_dko_rep2

description: Library name: hct116_dko_rep2


title: A986-Con

description: Library name: Sample 1


title: hct116_dko_rep1

description: Library name: hct116_dko_rep1


title: 129S1/SvlmJ kidney, KlothoCtrl, female, replicate 2

description: Library name: kid_DK76_S7_R1_001 sample 10

value: kidney

value: healthy renal function


title: 129S1/SvlmJ kidney, KlothoKl/Kl, male, replicate 1

description: Library name: kid_FdK28_S12_R1_001 sample 4


title: RA3

city: Beijing

first: Shi

last: Cuige

address: 12 Dahuisi road

institute: National Research Institute for Family Planning

data_processing:
Quality control and mapping
Gene-level quantification, analysis of differentially expressed genes (DEGs), cluster  analysis, GO and KEGG enrichment
Transcript-level quantification, analysis of differentially expressed transcript (DEGs),  cluster analysis, GO and KEGG enrichment
Gene structure extension and novel transcripts identification
Alternatively splicing analysis and SNP-INDEL calling
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Hippocampus

extract_protocol:
A.Add 600 μL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μL  miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting  the tube several times. Leave the mixture on ice for 10 min.  B.  Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume  before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum  speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the  aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh  tube.  C.  Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase.  D.  Pipet the lysate/ethanol mixture (from the previous step) onto the Filter  Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge  for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the  flow-through. E.  Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for  30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace  the Filter Cartridge into the same Collection Tube.  F.  The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then  the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15  min.  G.  Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for  30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace  the Filter Cartridge into the same Collection Tube.  H.  Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw  it through the Filter Cartridge as in the previous step. Repeat with a second 500 μL  aliquot of Wash Solution 2/3.  I.  Spin the assembly for 1 min to remove residual fluid from the filter. Transfer  the Filter Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C)  Elution Solution to the center of the filter. Leave it at the room temperature for 2 min.  Spin for ~20–30 sec at maximum speed to recover the RNA. Collect the eluate (which  contains the RNA) and store it at –70°C.
Purify and Fragment mRNA， Synthesize First Strand cDNA，Synthesize Second Strand cDNA，Adenylate 3’Ends， Ligate Adapters，Enrich DNA Fragments， Purification， Validate library

value: Hippocampus

value: 22 months

value: Sprague Dawley


title: 129S1/SvlmJ kidney, KlothoCtrl, male, replicate 3

description: Library name: kid_DK79_S15_R1_001 sample 3

value: 46 days

value: +/Kl


title: IL_restraint_cko2


title: RA2


title: MB231_shPRMT5H1

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

description: Library name: RNA_seq_MB231_shPRMT5H1

data_processing:
FastQC was used for quality assessment of raw Fastq reads.
Fastq files were mapped to human GRCh38 genome using STAR aligner.
For RNA-seq feature counts was used to count the reads numbers mapped to each gene.
Assembly: GRCh38
Supplementary files format and content: Tab delimited text files with raw counts for each sample.

growth_protocol: MDA-MB-231 cells were cultured in media recommended by European Collection of Authenticated Cell Cultures in a humidified incubator at 37 ⁰C and 5% CO2

extract_protocol:
For RNA-seq, total RNA was extracted from shControl and shPRMT5 cells using TRIzol (Invitrogen, 15596026).
mRNA enrichment method was used as the library preparation strategy . Library was prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®

treatment_protocol: MDA-MB-231 shControl or shPRMT5 cells were kept under Hypoxia (1% oxygen) before performing RNA-seq

value: Breast cancer

value: shPRMT5 Hypoxia


title: IL_restraint_cko1


title: MB231_shPRMT5H2

description: Library name: RNA_seq_MB231_shPRMT5H2


title: RA1


title: IL_restraint_wt6

value: wt


title: MB231_shControlH2

description: Library name: RNA_seq_MB231_shControlH2

value: ShControl Hypoxia


title: 129S1/SvlmJ kidney, KlothoCtrl, male, replicate 1

description: Library name: kid_FdK19_S11_R1_001 sample 1


title: RY3

value: 4 months


title: IL_restraint_wt5

value: pituitary intermediate lobe


title: RY2


title: IL_restraint_wt4

value: restraint


title: IL_restraint_cko4

value: cko


title: hct116_wt_si11_144h_rep2

description: Library name: hct116_wt_si11_144h_rep2

data_processing:
ChIP-seq datasets were processed to remove the Illumina adapters using Cutadapt (v4.4) with the parameters “--poly-a -q 25 -m 25 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT”121. The resulting filtered reads were aligned to reference human genome using bowtie2 aligner (v2.5.1) with the parameter “--very-sensitive” (Bowtie2). The alignment file was sorted by coordinate, indexed and filtered for mitochondrial reads using SAMtools (v1.17). The filtered alignment file was further processed to keep only uniquely mapped, non-duplicated reads using sambamba (v1.0.1).
For visualization, filtered BAM files from above were converted into normalized bigWig signal tracks using bamCoverage module of the deepTools package (v3.5.5). Parameters used were “--effectiveGenomeSize 2913022398 --binSize 1 --normalizeUsing RPGC --extendReads 150 --outFileFormat bigwig”. For each condition, signal mean was calculated using bigwigAverage module.
Assembly: The reference genomes for human (GRCh38; annotation version 108) and mouse (GRCm39; annotation version 112) were obtained from ENSEMBL
Supplementary files format and content: bigWig
Supplementary files format and content: hct116_exon_counts_si11_vs_ctrl_144h.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.

extract_protocol:
1% formaldehyde in DMEM was added to HCCT116 WT, DKO or TKO cells for 10 min, and quenched with 0.1 M glycine. Isolated nuclei were lysed and sonicated using a Bioruptor® Pico ultrasonic cell disruptor (Diagenode) to shear genomic DNA to an average fragment size of 200 bp. 20 μg of chromatin was diluted to a total volume of 500 μl with ChIP buffer (16.7 mM Tris pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100) and pre-cleared with 10 μl packed sepharose beads for 2 h at 4°C. Pre-cleared chromatin was incubated with ChIP-grade antibodies against H3K9me3 or H3K27me3 overnight. 20 ng of D. melanogaster S2 chromatin and 0.5 μg of H2Av antibody were added as spike-in to each sample. Dynabeads™ Protein A (Invitrogen, 10002D) or G (Invitrogen, 10004D) were added. After 4 h at 4°C, beads were pelleted, washed, and bound chromatin eluted with 1% SDS, 100 mM NaHCO3. After digestion with Proteinase K (Thermo Scientific) at 50°C for 3 h and reversion of cross-linking (65°C, overnight), DNA was purified with phenol/chloroform, ethanol precipitated and quantified by qPCR. To prepare samples for RNA-seq, 2 individual batches of cells were plated on the same day and further processed in parallel. Freshly harvested cells were lysed with 500 µL of QIAzol lysis reagent (QIAGEN #79306) and mixed by gentle pipetting. Subsequently, 100 µL of chloroform (Sigma) was added, samples were vortexed for 10 s and spun at 12’000 x g for 15 s at 4°C. The upper phase was transferred into a new tube, 600 μL of isopropanol (Sigma) added and samples incubated O/N at -20°C. After centrifugation at 16’000 x g for 10 min at 4°C, the RNA pellet was washed in 75% ethanol and resuspended in RNase-free water (Invitrogen). DNase digestion of RNA was performed using RNase-Free DNase Set (QIAGEN) following the manufacturer’s instructions. RNA was then precipitated by adding sodium acetate (Sigma) to a final concentration of 0.3 M, and adding 3 volumes of 100% ethanol O/N at -20°C. RNA was recovered by centrifugation at 16’000 x g for 10 min and washed two times with 70% ethanol. RNA was dissolved in RNase-free water (Invitrogen). To prepare ATAC-seq samples, 3 individual batches of cells were plate on the same day in 6-wells (for si-11) or 10 cm plates (for KO cells). Cell batches were then further processed in parallel, during all subsequent steps. For harvest, cells were washed twice with 1x PBS and detached using 0.5 mM EDTA in 1x PBS. Cells were counted and 80’000 cells were pelleted. Pellets were resuspended in 200 µL of freezing medium (10% DMSO in FCS) and slowly frozen at -80°C. ATAC-seq was performed at QuickBiology (Monrovia, California). Here, cells were washed and lysed to generate a crude preparation of nuclei. This crude extract was then treated with Tn5 Transposase. Tn5 transposase tagmentation simultaneously fragments the genome and tags the resulting DNA with Illumina sequencing adapters. DNA fragments were PCR-amplified and subsequently purified using the MinElute PCR Purification Kit (Qiagen, Maryland, USA).
For ChIP-seq analyses, the quantity of the isolated DNA was determined with Qubit® 4 Fluorometer (Life Technologies). Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep for Illumina (New England Biolabs, E7645S and E7645L), following the manufacturer’s protocol. Briefly, ChIP and input samples (15 ng) were end-repaired and polyadenylated. The adapters containing the index for multiplexing were then ligated. The quality and quantity of the enriched libraries were validated using 4200 TapeStation System (Agilent).

value: Human colon cancer cell line


title: MN01Control_Aorta

city: Riverside

first: Changcheng

last: Zhou

state: California

address: 900 University Avenue

department: School of Medicine

institute: University of California, Riverside

description:
Library name: MN01Control_Aorta
10× Genomics

data_processing:
Raw sequencing reads were demultiplexed using Cell Ranger and reads were aligned to the mouse genome (mm10).
Low-quality cells and doublets were removed based on UMI counts, mitochondrial gene percentage, and gene number thresholds.
Gene expression matrices were generated using Cell Ranger count.
Dimensional reduction, clustering, and analysis of scRNA-sequencing data were performed with the R package Seurat.
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz (gene expression count matrix)
Supplementary files format and content: features.tsv.gz (gene annotation)
Supplementary files format and content: barcodes.tsv.gz (cell barcode list)

source_name: Aorta

growth_protocol: 4-week-old LDLR⁻/⁻ male mice were orally gavaged with MPs for 9 weeks.

extract_protocol:
A single-cell suspension of aortic cells was prepared using enzymatic digestion. Briefly, whole aortas from three mice were pooled, minced, and digested in 1× aortic dissociation enzyme solution (125 U/mL collagenase type XI, 60 U/mL hyaluronidase type I-S, 60 U/mL DNase I, and 450 U/mL collagenase type I) for 1 hour at 37 °C. The suspension was then passed through a 30-μm filter.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell kit according to the manufacturer’s protocol.

treatment_protocol: 4-week-old LDLR-/- mice were fed ad libitum with semisynthetic low-fat AIN76 diet (4.2% fat and 0.02% cholesterol; Research Diet) and were administered with 10 mg/kg BW of MPs or vehicle control (ultrapure water) by oral daily gavage for 9 weeks.

value: Aorta

value: LDLR KO

value: microplastics treatment oral gavage (10mg/kg)


title: hct116_wt_si11_144h_rep1

description: Library name: hct116_wt_si11_144h_rep1


title: IL_restraint_wt3


title: MB231_shControlH1

description: Library name: RNA_seq_MB231_shControlH1


title: hct116_wt_ctrl_144h_rep2

description: Library name: hct116_wt_ctrl_144h_rep2


title: DDC + DT 3

city: Edinburgh

first: Wei-Yu

last: Lu

address: 4-5 Little France Drive

department: Institute for Regeneration and Repair

institute: University of Edinburgh

description: Library name: Sample 7

data_processing:
ROSALIND
Assembly: mm9
Supplementary files format and content: txt file including raw counts for each sample

source_name: Liver

extract_protocol:
RNA was harvested using PicoPure™ RNA Isolation Kit (ThermoFisher). 100ng total RNA was used for the construction of sequencing library
Library was constructed using Lexogen Quantseq FWD Library Prep Kit following manufacturer's protocol

value: Liver

value: EpCAM+ cholangiocytes

value: DT


title: RY1

value: Hippocampus

value: male

value: Sprague Dawley


title: IL_restraint_wt2


title: tcx5/6, D45, FT, LD, RNA-seq, rep3

city: Berkeley

first: Dawei

address: 2151 Berkeley Way

institute: University of California, Berkeley

description:
Library name: tcx5/6_D45_FT_LD_rep3
150x 150

data_processing:
Adapters were trimmed using cutadapt and Trim Galore 0.6.6 (Babraham Bioinformatics) by trimming 9 bp from the 5’-end of reads and enforcing a 3’-end quality of > 25%
Reads were mapped to the Araport11 genome using STAR 2.7.1a, permitting 0.05 mismatches as a fraction of total read length and discarding reads that did not map uniquely
Normalization of reads count was performed by running htseq-count of HTSeq 2.0  and DESeq2 1.40.1.
Assembly: Araport11
Supplementary files format and content: Tab-delimited txt file includes normalized reads count for all samples.

organism: Arabidopsis thaliana

source_name: First true leaves

extract_protocol:
Total RNA was isolated using a QIAGEN RNeasy plant mini kit.
Non-stranded libraries from poly-A-tailed RNA were generated according to the manufacturer’s instructions (Illumina).

value: First true leaves

tag: background

value: grown under long day conditions (16h light/ 8 h dark)


title: DDC + DT 2

description: Library name: Sample 6


title: hct116_wt_ctrl_144h_rep1

description: Library name: hct116_wt_ctrl_144h_rep1


title: IL_restraint_wt1

value: wt


title: tcx5/6, D45, FT, LD, RNA-seq, rep2

description:
Library name: tcx5/6_D45_FT_LD_rep2
150x 150


title: DDC + DT 1

description: Library name: Sample 5


title: IL_control_cko6

value: control


title: tcx5/6, D45, FT, LD, RNA-seq, rep1

description:
Library name: tcx5/6_D45_FT_LD_rep1
150x 150


title: DDC4

description: Library name: Sample 4

value: PBS


title: SOX17+Achilles-_R3

city: London

first: Silvia

middle: DM

last: Santos

address: 1 Midland Road

institute: The Francis Crick Institute

description:
Library name: S17_3
SOX17+Achilles-_R3

data_processing:
nf-core Nextflow RNAseq pipeline, revision 3.14.0 (https://github.com/nf-core/rnaseq), with STAR aligner and RSEM quantification - all other parameers as default
Assembly: Ensembl GRCh38 release-86
Supplementary files format and content: raw count matrix of sequencing reads

source_name: H1 FOXC1-Achilles reporter

growth_protocol: H1 FOXC1-Achilles hESCs were maintained in mTeSR1 (Stem Cell Technologies, #85850) and on GFR Matrigel (Corning, #354230). Cells were passaged every 3 days with Gentle Cell Dissociation Reagent (Stem Cell Technologies, #100-0485).

extract_protocol:
Sorted samples were initially lysed by treatment with 100µL specified lysis buffer to cell pellets [10 mM Tris-HCl (pH 7.9), 50 mM EDTA (pH 7.9), 0.2 M NaCl, 2.2% SDS, +1:100 RNAsin Plus (Promega) and 1000 µg/ml proteinase K (NEB)] at 55°C for 1hour. 500µL TRI reagent (ThermoFisher, #AM9738) was added to each sample and RNA was extracted according to manufacturers protocol using Qiagen MaXtract tubes (Qiagen, #129056). Extracted RNA was resuspeneded in RNAse free water and quantified by Qubit.
Watchmaker RNA Ribo/Globin depletion

treatment_protocol: Control cells were maintained in mTeSR1. Differentiated cells were seeded (1:24) 24 hours prior to differentiation and treated with Activin A (Cambridge Biosciences, #GFH6-10) 100 ng/mL, BMP4 (LifeTechnologies, PHC9534) 10 ng/mL, FGF2 (LifeTechnologies, PHG0026) 20 ng/mL, LY29004 (Cambridge Biosciences, CAY70920) 1 µM and Insulin (Sigma, I1882) in TeSR-E5 (Stem Cell Technologies, #5916). After 72 hours cells were harvested with Accutase (Gibco, #A1110501) for 5 mins at 37oC. Dissociated cells were centrifuged at 1500g and resuspended in 4% PFA (ThermoFisher, #28908) for 15 minutes rocking on ice with 1:1000 RNAsin plus  (Promega, N2611). Cells were diluted in PBS+0.5%BSA, centrifuged at 1400g and cell pellets resuspended in PBS + 0.5% BSA and 0.1% Triton-X100 and 1:3000 dillution of anti-SOX17 (CST, 81778) primary antibody and incubated for 1.5 hours at room temperature. Cells were washed in PBS + 0.5% BSA and 0.1% Triton-X100 and centrifuged at 1500g and resuspended with Alexa-647 secondary antibody 1:1000 (LifeTechnologies #A31573) for 40 minutes. Stained samples were washed and resuspended in PBS + 0.5% BSA and RNAsin Plus for cell sorting. Samples were sorted on the BD Aria III FACS system into specified populations and collected in PBS + 0.5% BSA and RNAsin Plus.

value: H1 FOXC1-Achilles reporter

value: Embryonic stem cells

value: Activin 100 ng/mL BMP4 10 ng/mL

tag: repeat


title: MN01MPs_Aorta

description:
Library name: MN01MPs_Aorta
10× Genomics

value: Aorta


title: tcx5/6, D30, FT, LD, RNA-seq, rep3

description:
Library name: tcx5/6_D30_FT_LD_rep3
150x 150


title: DDC3

description: Library name: Sample 3


title: SOX17-Achilles+_R3

description:
Library name: A_3
SOX17-Achilles+_R3


title: tcx5/6, D30, FT, LD, RNA-seq, rep2

description:
Library name: tcx5/6_D30_FT_LD_rep2
150x 150


title: SOX17+Achilles+_R3

description:
Library name: DP_3
SOX17+Achilles+_R3


title: DDC2

description: Library name: Sample 2


title: IL_restraint_cko3

value: pituitary intermediate lobe

value: cko

value: restraint


title: IL_control_cko5


title: IL_control_cko4


title: SOX17-Achilles-_R3

description:
Library name: DN_3
SOX17-Achilles-_R3


title: mTeSR1_R3

description:
Library name: C_3
mTeSR1_R3


title: DDC1

description: Library name: Sample 1

value: Liver

value: EpCAM+ cholangiocytes


title: IL_control_cko3


title: CTFL-GFPplus

city: Toulouse

first: Florence

last: Tatin

address: 1 avenue Jean Poulhès

country: France

description:
Library name: sample1
10X genomics

data_processing:
Demultiplexing and barcoded processing were made by cellranger-4.0.0.
Assembly: mm10-2020
Supplementary files format and content: scRNA_cell_metadata.csv.gz. UMAP coordinated and cluster information for each cell.
Supplementary files format and content: scRNA_count_matrix.csv.gz. Raw counts per gene per cell

source_name: dorsal skin

growth_protocol: LEC isolated from dorsal skin

extract_protocol:
Dorsal skin (around 2g) was placed in HBSS in 10cm dishes and transferred in digestion medium (1 U/mL Dispase II, 0,8 U/ml Liberase DH, 10U/mL DNase in Hanks’ Balanced Salt Solution solution) during 15 min at 37C. The dorsal skin was scraped and cell solution was incubated under agitation during 15 min at 37C. This two-step was repeated once and total cell solution was inhibited with DMEM with 10% FBS. Cells were washed, LEC were isolated as CD31 and GFP positive cells by FACS analysis
Single-cells were captured using the Chromium Controller and the Chromium Next GEM single cell 3' v3.1 kit (10x Genomics, Inc.). The library was profiled with the HS NGS kit for the Fragment Analyzer (Agilent Technologies) and quantified using the KAPA library quantification kit (Roche Diagnostics). The library was sequenced on the Illumina NextSeq550 instrument using the High Output 150 cycles kit (Illumina). The sequencing parameters were 28, 10, 10, 90 cycles (read 1, index 1, index 2, read 2). A minimum of 125406 mean reads/cell were obtained

value: dorsal skin

value: Lymphatic endothelial cells

value: 20 weeks

value: pooled male and female


title: tcx5/6, D23, FT, LD, RNA-seq, rep3

last: Dai

description:
Library name: tcx5/6_D23_FT_LD_rep3
150x 150

value: First true leaves

value: grown under long day conditions (16h light/ 8 h dark)


title: cortex_WT_control_rep3

city: Philadelphia

first: Emily

last: Feierman

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Paired end sequencing reads were processed using 10X Genomics Cellranger v5.0.1. Reads were aligned to the mm10 genome optimized for single cell sequencing through a hybrid intronic read recovery approach.
Raw matrices for each individual replicate per condition were converted to Seurat objects using Seurat 5.0.1 and filtered to remove UMIs with thresholds of > 200 minimum features, > 250 genes detected per nuclei, < 20% mitochondrial reads, and < 2% ribosomal reads.
Pseudobulk differentially expressed genes were identified using DElegate with a fold change threshold of 1.5 and Benjamini-Hochberg adjusted p value ≤ .05. Counts were aggregated by individual mice per condition under the orig.ident identity, then pairwise comparisons were computed using quasi-likelihood dispersion with glmQLFit through the findDE function.
Assembly: mm10
Supplementary files format and content: tab separated values files and matrix files
Supplementary files format and content: Seurat object

molecule: nuclear RNA

source_name: cortex

extract_protocol:
Cortical tissue was mechanically homogenized in a sucrose solution and nuclei were isolated through a sucrose gradient and ultracentrifugation
single-nucleus Drop-seq; Nuclei were captured and libraries were prepared for sequencing using the sNucDrop-seq protocol described in Hu et al. 2017

treatment_protocol: Seizures were induced via intraperitoneal injection of pentylenetetrazol.

value: cortex

value: WT

value: control


title: SOX17-Achilles+_R2

description:
Library name: A_2
SOX17-Achilles+_R2

value: H1 FOXC1-Achilles reporter

value: Embryonic stem cells


title: tcx5/6, D23, FT, LD, RNA-seq, rep1

description:
Library name: tcx5/6_D23_FT_LD_rep1
150x 150


title: cortex_KO_control_rep3


title: IL_control_cko1

city: Shanghai


title: tcx5/6, D23, FT, LD, RNA-seq, rep2

description:
Library name: tcx5/6_D23_FT_LD_rep2
150x 150


title: IL_control_wt6

value: wt


title: SOX17+Achilles+_R2

description:
Library name: DP_2
SOX17+Achilles+_R2

value: Activin 100 ng/mL BMP4 10 ng/mL


title: cortex_KO_seizure_rep2

value: seizure


title: IL_control_wt5

value: pituitary intermediate lobe


title: tcx5/6, D18, FT, LD, RNA-seq, rep2

description:
Library name: tcx5/6_D18_FT_LD_rep2
150x 150


title: IL_control_wt4


title: cortex_KO_control_rep2


title: tcx5/6, D30, FT, LD, RNA-seq, rep1

description:
Library name: tcx5/6_D30_FT_LD_rep1
150x 150


title: mTeSR1_R2

description:
Library name: C_2
mTeSR1_R2


title: cortex_KO_seizure_rep1


title: tcx5/6, D13, FT, LD, RNA-seq, rep3

description:
Library name: tcx5/6_D13_FT_LD_rep3
150x 150


title: SOX17+Achilles-_R1

description:
Library name: S17_1
SOX17+Achilles-_R1


title: cortex_KO_control_rep1


title: SOX17+Achilles-_R2

description:
Library name: S17_2
SOX17+Achilles-_R2