title: ccndx_sibling2

city: Kansas City

first: Shiyuan

middle: (Cynthia)

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
Raw sequencing data were processed using 10X Genomics Cell Ranger pipeline. Reads were demultiplexed into Fastq file format using cellranger mkfastq. Genome index was built by cellranger mkref using zebrafish genome danRer11, ensembl 98 gene model. Data were aligned by STAR aligner and cell counts tables were generated using cellranger count function with default parameters.
Assembly: danRer11
Supplementary files format and content: single cell  count matrix in hdf5 format, raw data in bam format.

organism: Danio rerio

growth_protocol: 5dpf zebrafish FACS sorted lateral line cells were used. Standard growing condition were used.

extract_protocol:
5 dpf zebrafish were anesthetized with Tricane then split between two 70mm cell strainers (Falcon) and placed in 0.25% Trypsin-EDTA (Gibco) on ice. The larvae from each strainer are then added to a 5ml round bottom tube (Falcon) and the tissue is broken up via slowly pipetting up and down using a pipette man and a glass pipette (VWR) keeping the tubes on ice. The total time from placing larvae in trypsin to finishing pipetting is approximately 8 minutes. The tissue is then filtered through 70mm filter (BD Biosciences), pelleted for 5 min at 2000rpm at 4oC and then the pellet is resuspended in 1xDPBS/0.04%BSA. The pelleting and resuspension in 1xDPBS/0.04%BSA is repeated two more times. After the final pellet the cells are resuspended in 0.5mL 1xDPBS/0.04%BSA then cells are combined and put through another 70mm filter into a 5ml round bottom tube. Cells are then incubated in Draq5 (1/200 dilution) for 5 minutes on ice. Draq5+/mCherry+ cells were sorted by the Stowers Institute Cytometry Core Facility using a BD Influx Cell Sorter (BD Biosciences, San Jose, CA. USA), with cells collected in tubes containing 10mL 1XDPBS/0.04% BSA. Cells were not fixed in methanol as in previous protocols as we found this gave inconsistent results with 10X Genomics version 3 kits. Sorted cells are then spun down at 350rcf at 4oC for 2 min in a swinging bucket centrifuge with slow deceleration. Most of the supernatant is removed and the cells are resuspended in approximately remaining 100mL.
Cells deemed to be at least 80% viable were loaded based on live cell concentration onto a Chromium X Series instrument (10x Genomics) and libraries prepared using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) according to manufacturer’s directions. Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific). With cells captured estimated at ~6,800-9,600 cells per sample, libraries were pooled and sequenced to a depth necessary to achieve at least 30,000 mean reads per cell on an Illumina NextSeq 2000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp.
scRNA-seq (10x Genomics)

treatment_protocol: All cells were collected during homeostasis, no treatments were performed.

value: Homostasis


title: JB21118

status: Public on Mar 31 2025

type: SRA

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

country: USA

institute: THE JACKSON LABORATORY

description:
pCoV26
JB21118

library_source: transcriptomic

data_processing:
Illumina basecall files (*.bcl) were converted to fastqs using cellranger v3.0.2 which uses bcl2fastq v2.17.1.14. FASTQ files were then aligned to hg19 genome and transcriptome using the cellranger v3.0.2 pipeline, which generates a gene - cell expression matrix.
For all single cell samples, R1 contains a 16bp cell barcode + 12bp UMI barcode.  For all samples, R2 contains a 91bp biological read.
Assembly: GRCh38
Supplementary files format and content: Transcriptomic counts matrices in Matrix Market CSR format.  Transcriptomic counts matrices in Matrix Market CSR format.    Rows correspond to features in the order provided in features.tsv/features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.

molecule: polyA RNA

organism: Homo sapiens

source_name: BLOOD

extract_protocol:
10% DMSO + 90% FBS. PBMCs were thawed quickly at 37oC and into DMEM supplemented with 10% FBS. Cells exhibiting a viability rate less than 70% were excluded. Cells were quickly spun down at 400 g, for 10 min. Cells were washed once with 1 x PBS supplemented with 0.04% BSA and finally re-suspended in 1 x PBS with 0.04% BSA. Viability was determined using trypan blue staining and measured on a Countess FLII.
12,000 single cells were loaded into one lane of a 10X Genomics Chromium [Controller, X], targeting 6,000 barcoded single cells. Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform, version [3, 3.1] chemistry. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and sequenced on an Illumina NovaSeq 6000  targeting 100,000 raw read pairs per cell.

tag: cells

value: PBMCs

tag: groups

tag: age (months)

tag: affection status

value: Covid+

tag: Sex

value: F

value: AA


title: CRISPRi_sgMIR23

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Libraries were mapped tomm9 genome using STAR.
Genes were quantified using Cuffquant.
Libraries were normalized using Cuffnorm.
Assembly: mm9
Supplementary files format and content: Tab delimieted text table containing the FPKM for every gene in every sample

molecule: total RNA

organism: Mus musculus

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured in LIF-serum medium comprised of DMEM  high  glucose  (Hyclone)  supplemented  with  15%  ES  cell  FBS  (Gibco),  2mM  L-glutamine (Gibco), 1X Pen-Strep (Gibco), 100 μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore). 2i cells were derived from ESC by culturing in NDiff227 basal media (TakaraBio) supplemented with 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore), 15 μM CHIR (Tocris) and 5 μM PD0325901 (Tocris) for at least 3 passages. EPSC were derived from ESC by culturing in EPSC media developed by (Yang et al 2017), comprising of DMEM/F12 (Invitrogen), 20% KnockOut Serum Replacement (Invitrogen), 1× GPS, 1× non-essential amino acids, 0.1 mM β-ME, 103 U ml−1 hLIF, 3 μM CHIR99021 (Tocris), 1 μM PD0325901 (Tocris), 4 μM JNK Inhibitor VIII (Tocris), 10 μM SB203580 (Tocris), 0.3 μM A-419259 (Santa Cruz) and 5 μM XAV939 (Sigma). RA cells were cultured in LIF-serum medium, supplemented with 1 retinoic acid for 48 hours. All cultures were maintained at 37°C with 5% CO2. All cells were maintained on plates pre-coated with 0.1% gelatine (porcine).

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen) and Monarch total RNA miniprep kit (NEB)
The RNA-Seq libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit (Catalog #: RS-122-2101) as per manufacturer's instructions.

treatment_protocol: Lipofectamine (Invitrogen) was used for transfection of shRNA or CRISPRi plasmids according to the manufacturer’s instructions. cells were harvested for experiments after 3 days of knockdown.

tag: shRNA

value: CRISPRi plasmid (ORIGENE,  GE100083)


title: ccndx_sibling1

last: Chen

library_source: transcriptomic single cell

source_name: 5dpf zebrafish FACS sorted lateral line cells

tag: cell type

tag: genotype

value: Wildtype


title: JB21117

description:
pCoV25
JB21117

value: H


title: HEK293_Mock_Parental_total_Rep1_Experiment3

city: San Francisco

first: Stefan

last: Oberlin

address: 505 Parnassus Ave

department: Department of Microbiology and Immunology

institute: University of California, San Francisco

description:
small RNA
total RNA
dsRNA_variants_miRNA_quant.csv

data_processing:
Illumina Casava1.8 software used for basecalling.
Trimming of reads with BBduk of the BBmap package using the following parameters ktrim=r k=23 mink=11 hdist=1
Mapping to the human genome (GRCh38) with STAR (--outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --alignIntronMax 500 --alignIntronMin 50 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 50)
Read counting to mirbase annotation with Rsubread (allowMultiOverlap=T, isPairedEnd=T, strandSpecific=2, countMultiMappingReads=T)
Read normalization with DEsep2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text files of count per million (CPM) values

growth_protocol: All HEK293T cell lines were maintained at 37 °C with 5% CO2 in Dulbecco’s Modified Eagle’s Medium (DMEM) (Thermo Scientific) containing 4500 g/mL glucose, further supplemented with 10% fetal bovine serum (FBS) (Sigma Aaldrich), 100 U/mL of penicillin and 100 μg/mL of streptomycin (Sigma Aaldrich).

extract_protocol:
Ago-pulldown: Ago Affinity Purification by Peptides was performed in accordance with an earlier described protocols (Hauptmann et al., 2015). Ago-pulldown quality was validated by miR16/21 RT-qPCR. RNA extraction: 1.5-3*10^6 cells were trypsinized and washed twice with PBS before proceeding with RNA extraction. RNA was extarcted using TRI reagent (Sigma Aaldrich) according to manufacturer's recmmendations. Total RNA integrity and quality was validated on the Nanodrop 2000 (Thermo Scientific) and on an 1% agarose gel.
Libraries were prepared with total RNA and Ago-purified RNA, from approximately 2-3*10^6 cells, with the Lexogen small RNA-Seq Library Prep kit (Lexogen) according to the manufacturer’s instructions.

treatment_protocol: All HEK293T cells were transfected with long dsRNA using Lipofectamine 3000 (Thermo Scientific) according to the manufacturers’ instructions.

tag: parental cell line

value: pOSI17 PKR knock-out

tag: cell line

value: Parental

tag: transfected long dsrna

value: Mock


title: ccndx_mutant2

value: Mutant


title: CRISPRi_sgMIR22


title: JB21116

description:
pCoV24
JB21116


title: CRISPRi_3sgMIR


title: HEK293_dsGFPc_Dicer knock-out_APP_Rep2_Experiment2

description:
small RNA
Ago-pulldown
AGO_DCR_miRNA_quant.csv

value: additional Dicer knock-out

value: dsGFPc


title: ccndx_mutant1


title: HEK293_dsGFPd_Dicer knock-out_APP_Rep2_Experiment2

value: dsGFPd


title: JB21115

description:
pCoV23
JB21115

value: M

value: As


title: CRISPRi_1sgScrmbl


title: mdEM, day 9, rep3

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

data_processing:
Total reads were aligned to hg19 AmpliSeq Transcriptome ERCCv1.
Aligned reads raw count data were analyzed.
Read count normalization and analyses were prformed using R studio_v2023.06.1+524 with the 'DESeq2' package.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

growth_protocol: Human iPSCs were maintained on iMatrix-511 (human laminin-511 E8 fragment, Nippi)-coated cell culture plates in StemFit AK03N medium (Ajinomoto) in a 37°C incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (QIAGEN) and treated with the RNase-Free DNase Set to eliminate genomic DNA contamination.  Subsequently, 10 ng of total RNA underwent reverse transcription to generate single-stranded cDNA, employing the SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific).
For NGS library construction targeting the Ion AmpliSeq Transcriptome, we utilized the Ion AmpliSeq Transcriptome Human Gene Expression Panel, Chef-Ready Kit (Thermo Fisher Scientific), and the Ion Chef (Thermo Fisher Scientific) instruments, following the manufacturer's protocol. Briefly, a reverse transcription master mix was prepared by combining 5X VILO Reaction Mix and 10X SuperScript III Enzyme Mix. The mix was then aliquoted into reaction plates, with 10 ng of total RNA added to each. The plates were loaded into a thermal cycler and subjected to incubation at 42°C for 30 min, followed by 85°C for 5 min, and then held at 10°C. During library preparation on the Ion Chef instruments, the following consumables and cartridges were loaded: Ion AmpliSeq Chef Solutions DL8 cartridge, Ion AmpliSeq Chef Reagents DL8 cartridge, Ion AmpliSeq Tip Cartridge L8, PCR Frame Seal, IonCode 96 Well PCR Plate, PCR Plate Frame, Empty Tip Cartridge L8, and Enrichment Cartridge. Notably, IonCode 96 Well PCR Plates used for reverse transcription reactions contained an IonCode barcode adapter. Additionally, the tube containing the Ion AmpliSeq Transcriptome Human Gene Expression Panel was inserted into an Ion AmpliSeq Chef Reagents DL8 cartridge. Multiplex PCR was performed in the thermal cycler within the Ion Chef, with 13 cycles of 16-minute annealing/extension reactions. Subsequent steps involved primer digestion with FUPA reagents, ligation of IonCode barcode adapters, library purification using magnetic beads, equalization of library concentrations, and mixing in a single tube.

treatment_protocol: For NCC induction in three-dimensional (3D) conditions, iPSCs were detached from the culture dish using Accutase (Innovative Cell Technologies) and dissociated into single cells. These cells were promptly reaggregated in 100 μl of StemFit Basic03 (equivalent to AK03N without bFGF, Ajinomoto) supplemented with 10 μM Y-27632 in 96-well V-bottom ultra-low-cell-adhesion plates (Sumitomo Bakelite) (1.0×104 cells/well). Cell numbers were determined using a Countess II FL (Thermo Fisher Scientific). Aggregation was facilitated by centrifugation at 1200 rpm for 3 min (day 0). For NCC induction, these cell aggregates were maintained in a 37°C incubator with 5% CO2. After 24 h (day 1), the culture medium was replaced with 150 μl of StemFit Basic03 containing 10 μM SB431542 (TGF-β inhibitor; FUJIFILM Wako) and 10 ng/m BMP4 (R&D Systems). After another 24 h (day 2), the aggregates were individually collected and transferred into 48-well non-coated plates (IWAKI) and cultured in 250 μl of StemFit Basic03 containing 10 μM SB431542 and 1 μM CHIR99021 (GSK-3 inhibitor, Axon Medchem) on an orbital shaker (CS-LR; TAITEC) at 120 rpm from day 2 to 5. To initiate the induction of mdEM, the NCC aggregates (day 5) were cultured in 350 μl of StemFit Basic03 supplemented with 100 ng/ml FGF8b (FUJIFILM Wako), 50 nM Endothelin-1 (PEPTIDE INSTITUTE), and 2.5 ng/ml BMP4 on an orbital shaker at 120 rpm from day 5 to 9.

value: iPSCs derived from PBMC

value: WT

tag: time

value: day 9


title: HEK293_Mock_Dicer knock-out_APP_Rep2_Experiment2


title: mdEM, day 9, rep1


title: HEK293_dsGFPd_Ago2 knock-out_APP_Rep2_Experiment2

value: additional Ago2 knock-out


title: shEV_E14_LS

value: pSuper shRNA plasmid


title: JB21113

description:
pCoV21
JB21113

value: PBMCs

value: Covid+

value: W


title: mdEM, day 9, rep2


title: shEV_E14_2i


title: HEK293_dsGFPc_Ago2 knock-out_APP_Rep2_Experiment2

value: pOSI17 PKR knock-out


title: Esrrb_sh2_E14_LS


title: JB21102

description:
pCoV20
JB21102

value: F

value: BR


title: HEK293_Mock_Ago2 knock-out_APP_Rep2_Experiment2

value: Mock


title: Esrrb_sh2_E14_2i


title: NCC aggregates, day 5, rep2

value: day 5


title: JB21101

description:
pCoV19
JB21101


title: NCC aggregates, day 5, rep3


title: JB21100

description:
pCoV18
JB21100


title: HEK293_dsGFPd_Ago1/2 knock-out_APP_Rep2_Experiment2

value: additional Ago1/2 knock-out


title: NCC aggregates, day 5, rep1


title: JB21099

description:
pCoV17
JB21099

value: AA


title: Esrrb_sh1_E14_2i


title: HEK293_dsGFPc_Parental_APP_Rep2_Experiment2

value: Parental

value: dsGFPc


title: iPSCs, day 0, rep2

value: iPSCs derived from PBMC

value: day 0


title: HEK293_Mock_Parental_APP_Rep2_Experiment2


title: EPSC_H3K27Ac_Input

library_source: genomic

data_processing:
Libraries were mapped to mm9 genome using STAR with the options –alignIntronMax and –AlignEndsType set to 1 and EndToEnd respectively.
bigwig files were produced by deeptools
Assembly: mm9
Supplementary files format and content: bigwig

molecule: genomic DNA

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% ES FBS (Gibco), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco) and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)). All the ESC cell lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 . Or N2B27 supplemented with 2iLIF. Or expanded potential stem cell medium (EPSCM)

extract_protocol:
10 million cells were cross-linked with 1% formaldehyde for 10 min at room temperature, with the formaldehyde then quenched by the addition of 200 mM glycine and cells then washed once with ice-cold PBS. Cell lysis was carried out with a buffer containing 10 mM Tris-Cl (pH 8), 100 mM NaCl, 10 mM EDTA, 0.25% Triton X-100 and protease inhibitor cocktail (Roche). Cells were then resuspended in 1% SDS lysis buffer containing 50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC and protease inhibitor cocktail. The suspension was nutated for 15 mins at 4°C before spinning down to collect the chromatin pellet. The pellet was then washed twice with 0.1% SDS lysis buffer containing 50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 0.1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC, 1 mM PMSF and protease inhibitor cocktail. Sonication was conducted using the Branson sonifier 250 on ice (11 cycles, power amplitude of 35%, 30s pulses on with 59.9 s pulses off). The chromatin solution was clarified by centrifugation at 20,000 g at 4°C for 45 mins and then pre-cleared with Dynabeads protein A (Life Technologies) for 2 hrs. The pre-cleared chromatin sample was incubated with 50 μl of Dynabeads protein A loaded with 5 μg antibody overnight. The beads were then washed three times with 0.1% SDS lysis buffer, once with 0.1% SDS lysis buffer/0.35 M NaCl, once with 10 mM Tris-Cl (pH 8), 1 mM EDTA, 0.5% NP40, 0.25 LiCl, 0.5% NaDOC, and once with TE buffer (PH8.0). The immunoprecipitated material was eluted from the beads by heating for 45 min at 68°C in 50 mM Tris-Cl (pH 7.5), 10 mM EDTA, 1% SDS. To reverse the crosslinks, samples were incubated with 1.5 μg/ml Pronase at 42°C for 2 hr followed by 67°C for 6 hr. The samples were then extracted with QIAGEN MiniElute column, and re-suspended in TE buffer.
The ChIP-Seq libraries were prepared using  in-house protocol with Illumina TruSeq adapters

tag: culture condition

value: EPSCM


title: Esrrb_sh1_E14_LS


title: EPSC_H3K27Ac

tag: antibody

value: Rabbit polyclonal to Histone H3 (acetyl K27) Cat:ab4729


title: HEK293_dsGFPc_Ago1/2 knock-out_APP_Rep2_Experiment2


title: JB21098

description:
pCoV16
JB21098

value: M


title: iPSCs, day 0, rep3

value: WT


title: 2D NCC CD271high

treatment_protocol: To evaluate the effects of FEDB on NCC aggregates, 1231A3 iPSC-derived NCC aggregates were cultured in 350 μl of StemFit Basic03 supplemented with 100 ng/ml FGF8b (FUJIFILM Wako), 50 nM Endothelin-1 (PEPTIDE INSTITUTE), and 2.5 ng/ml BMP4 (R&D Systems) (referred to as FEDB) on an orbital shaker at 120 rpm from day 5 to 9. To evaluate the effects of FEDB on 2D-induced NCCs under a 2D condition, CD271high+ sorted NCCs from 2D induction protocols were seeded onto fibronectin-coated plates at a density of 1.0 × 104 cells/cm2 and cultured with StemFit Basic03 supplemented with FEDB for 4 days.

tag: treatment

value: FEDB, day0


title: EPSC_H3K4Me3_Input


title: HEK293_dsGFPd_Parental_APP_Rep2_Experiment2

value: dsGFPd


title: HEK293_Mock_Ago1/2 knock-out_APP_Rep2_Experiment2

value: pOSI17 PKR knock-out


title: JB21097

description:
pCoV15
JB21097

value: PBMCs

value: Covid+

value: W


title: HEK293_dsGFPc_Dicer knock-out_APP_Rep1_Experiment2

value: additional Dicer knock-out


title: JB20121

description:
pCoV11
JB20121

value: F


title: NCC aggregates, FEDB

value: FEDB, day4


title: JB20138

description:
pCoV14
JB20138

value: AA


title: E14_H3K4Me3

value: ES

value: Rabbit polyclonal to Histone H3 (tri methyl K4) Cat:ab8580


title: JB21114

description:
pCoV22
JB21114


title: 2D NCC CD271high, FEDB

value: iPSCs derived from PBMC


title: HEK293_Mock_Dicer knock-out_APP_Rep1_Experiment2

value: Mock


title: EPSC_H3K4Me3

value: EPSCM


title: JB20120

description:
pCoV10
JB20120

value: As


title: JB20137

description:
pCoV13
JB20137

value: M

value: BR


title: HEK293_dsGFPd_Dicer knock-out_APP_Rep1_Experiment2

value: dsGFPd


title: JB20136

description:
pCoV12
JB20136

value: H


title: E14_H3K4Me3_Input


title: E14_H3K27Ac_Input


title: JB20079

description:
pCoV9
JB20079

value: PBMCs


title: E14_H3K27Ac

value: Rabbit polyclonal to Histone H3 (acetyl K27) Cat:ab4729


title: NCC aggregates

value: WT

value: FEDB, day0


title: iPSCs, day 0, rep1

value: day 0


title: 2i_H3K4Me3_Input


title: JB20077

description:
pCoV7
JB20077

value: Covid+

value: F

value: W


title: 2i_H3K4Me3

value: Rabbit polyclonal to Histone H3 (tri methyl K4) Cat:ab8580


title: Dental mesenchyme, day 17, rep3

treatment_protocol: To initiate the induction of mandibular prominence ectomesenchyme (mdEM), 1231A3 iPSC-derived NCC aggregates (day 5) were cultured in 350 μl of StemFit Basic03 (equivalent to AK03N without bFGF, Ajinomoto) supplemented with 100 ng/ml FGF8b (FUJIFILM Wako), 50 nM Endothelin-1 (PEPTIDE INSTITUTE), and 2.5 ng/ml BMP4 (R&D Systems) on an orbital shaker at 120 rpm from day 5 to 9. mdEM aggregates (day 9) were transferred into 96-well U-bottom ultra-low-cell-adhesion plates (Sumitomo Bakelite). For the induction of the distal cap domain, mdEM aggregates were cultured in 200 μl of StemFit Basic03 supplemented with 50 nM Endothelin-1, 20 ng/ml FGF2 (FUJIFILM Wako), and 25 ng/ml BMP4 from day 9 to 13, with a medium change on day 11. For the induction of the proximal-oral domain, mdEM were cultured in 200 μl of StemFit Basic03 supplemented with 100 ng/ml FGF8b, 400 nM SAG (Smoothened Agonist, Selleck), 10 μM BQ-123 (Endothelin A receptor antagonist, Selleck), and 500 nM LDN193189 (ALK2/3 inhibitor, TOCRIS) from day 9 to 13, with a medium change on day 11. Subsequently, for dental mesenchyme induction, the proximal-oral domain induction medium was replaced with 200 μl of StemFit Basic03 supplemented with 100 ng/ml FGF8b, 400 nM SAG, 3 μM CHIR99021 (GSK-3 inhibitor, Axon Medchem), and 30 ng/ml Activin A (R&D Systems). Dental mesenchyme induction was performed from day 13 to 17, with a medium change on day 15.

value: iPSCs derived from PBMC

value: day 17


title: JB20076

description:
pCoV6
JB20076


title: Dental mesenchyme, day 17, rep2


title: HEK293_dsGFPd_Ago2 knock-out_APP_Rep1_Experiment2

value: pOSI17 PKR knock-out

value: additional Ago2 knock-out


title: Proximal-oral, day 13, rep3

value: day 13


title: 2i_H3K27Ac_Input


title: HEK293_dsGFPc_Ago2 knock-out_APP_Rep1_Experiment2

value: dsGFPc


title: JB20078

description:
pCoV8
JB20078

value: M

value: As


title: Dental mesenchyme, day 17, rep1


title: JB20067

description:
pCoV4
JB20067

value: PBMCs

value: H


title: HEK293_Mock_Ago2 knock-out_APP_Rep1_Experiment2

value: Mock


title: 5_EPSC

description: ATAC-seq

data_processing:
Libraries were mapped to mm9 genome using STAR with the options –alignIntronMax and –AlignEndsType set to 1 and EndToEnd respectively.
peaks were called using MACS2 and bigiwg files were produced by deeptools
Assembly: mm9
Supplementary files format and content: bigwig file

extract_protocol:
Chormatin was using Illumina tagment DNA TDE1 Enzyme and Buffer kit as per manufacturer's instructions.
Library was prepared using Nextera DNA library preparation kit as per manufacturer's instructions.

value: ES


title: Distal cap, day 13, rep2

value: WT


title: HEK293_dsGFPc_Parental_APP_Rep1_Experiment2

value: Parental


title: 4_2i

description: ATAC-seq

value: EPSCM


title: HEK293_dsGFPd_Ago1/2 knock-out_APP_Rep1_Experiment2

value: additional Ago1/2 knock-out

value: dsGFPd


title: Proximal-oral, day 13, rep2

value: iPSCs derived from PBMC


title: HEK293_dsGFPc_Ago1/2 knock-out_APP_Rep1_Experiment2


title: JB20068

description:
pCoV5
JB20068

value: Covid+

value: AA


title: HEK293_Mock_Parental_APP_Rep1_Experiment2

value: pOSI17 PKR knock-out


title: 2i_H3K27Ac

value: Rabbit polyclonal to Histone H3 (acetyl K27) Cat:ab4729


title: mdEM, day 9, rep3

value: day 9


title: HEK293_Dicer knock-out_dsGFPd_total_Rep2_Experiment2

description:
small RNA
total RNA
AGO_DCR_miRNA_quant.csv

value: additional Dicer knock-out


title: Proximal-oral, day 13, rep1

value: day 13


title: 2_ES

description: ATAC-seq


title: HEK293_Mock_Ago1/2 knock-out_APP_Rep1_Experiment2


title: stressed sample, rep 3

city: Gembloux

first: Yordan

last: Muhovski

address: Chaussee de Charleroi

department: Life Sciences

country: Belgium

institute: CRAW

description: Library name: stressed_3

data_processing:
Low-quality raw RNA-seq reads were filtered using SOAPnuke
Sequencing Reads Filtering We define raw reads as reads which containing low-quality, adaptor-polluted and high content of unknown base(N) reads additionally, these noise reads should be removed before downstream analyses. We use internal software to filter reads, fllowed as: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 5%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 20 is greater than 40% in a read). After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ
Assembly: Trinity was used to perform de novo assembly with clean reads ( PCR duplication removed in order to improve the efficiency), then use Tgicl to cluster transcripts to Unigenes. Trinity contains three independent software modules: Inchworm, Chrysalis, and Butterfly. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Briefly, the process works as follow: Inchworm:Assembles the reads into the unique sequences of transcripts, often generating full-length transcripts for a dominant isoform, but then reports just the unique portions of alternatively spliced transcripts. Chrysalis:Clusters the Inchworm Contigs into clusters and constructs complete de Bruijn graphs for each cluster. Each cluster represents the full transcriptonal complexity for a given gene (or sets of genes that share sequences in common). Chrysalis then partitions the full read set among these disjoint graphs. Butterfly:Then processes the individual graphs in parallel, tracing the paths that reads and pairs of reads take within the graph, ultimately reporting full-length transcripts for alternatively spliced. Software parameters: Trinity: Version: v2.5.1 Parameters: --min_contig_length 150 --CPU 8 --min_kmer_cov 3 --min_glue 3 --SS_lib_type RF --bfly_opts '-V 5 -- edge-thr=0.1 --stderr ' Tgicl: Version: v2.5.1 Parameters: -l 40 -c 10 -v 25 -O '-repeat_stringency 0.95 -minmatch 35 -minscore 35'
Supplementary files format and content: Files include processed with FPKM values for each sample.

organism: Vicia faba

source_name: leaves

growth_protocol: The local faba bean (Vicia faba L. var. minor) variety Bachar, which is largely cultivated in different grain legume production semi-arid areas in Tunisia (Maazaoui et al., 2016), was used in this study. Seeds harvested in 2022 were obtained from the National Institute of Agronomic Research of Tunisia (INRAT, Tunisia). Dried seeds were sterilized with 25 mL L-1 sodium hypochlorite (NaOCl) for 15 min and then washed 3 times and soaked for 12 h in deionized water. Soaked seeds were sown in plastic pots (20 cm diameter and 30 cm depth) filled with 5 kg of air-dried soil. The soil had a sandy texture with 84.40% sand, 8.30% silt and 5.50% clay and contained organic matter of 9 g·kg−1, total organic carbon 5.20 g·kg−1, total N 2.80 g·kg−1, available P of 4.92 mg·kg−1, available K of 292 mg·kg−1, pH of 7.50 and EC of 4.02 dS m–1. Experiment was conducted at the Experimental Station of Biotechnology Center of Borj Cedria (35 Km South-east of Tunis; 36°42' N, 10° 28' E).

extract_protocol:
The collected leaf samples (stressed and control) were ground in liquid nitrogen and the resulting powder was then used for RNA extraction using NucleoSpin RNA Plant kit (Macherey-Nagel, Germany).
Library construction and  RNA sequencing were carried out at Beijing Genomics Institute (BGI), China, at a sequencing depth of 40 million paired end reads.

treatment_protocol: Four replicates of each treatment (control and drought stress), each replication with 10 pots with single seedling in each pot, were arranged in a simple randomized design in a controlled growth room at a 14 h day/10 h night cycle (270 μmol of photons/m2s light intensity), temperature of 23 ± 2 °C and relative humidity of 55%-65%. Firstly, the seedlings were watered daily with 200 mL at 10.00 a.m. for one month, and the drought-stressed plants group (stressed treatment) was then subjected to natural drought stress conditions by withholding water for 10 days. The plants of control and stressed plants were collected and samples from fully expanded third leaves were collected for physiological and biochemical analyses.

tag: tissue

value: leaves

value: Bachar

value: drought


title: JB20064

description:
pCoV1
JB20064

value: PBMCs

value: G1 (mild)

value: F


title: 6_EPSC

description: ATAC-seq

value: ES


title: HEK293_Dicer knock-out_dsGFPc_total_Rep2_Experiment2

value: dsGFPc


title: HEK293_dsGFPd_Parental_APP_Rep1_Experiment2

value: Parental

value: dsGFPd


title: Distal cap, day 13, rep3

value: iPSCs derived from PBMC

value: WT


title: JB20066

description:
pCoV3
JB20066

value: G2 (moderate)

value: Covid+

value: M

value: As


title: mdEM, day 9, rep1

value: day 9


title: JB20065

description:
pCoV2
JB20065

value: G3 (severe)

value: AA


title: ES_4

data_processing:
Libraries were mapped tomm9 genome using STAR
Genes were quantified using Cuffquant.
Libraries were normalized using Cuffnorm.
Assembly: mm9
Supplementary files format and content: Tab delimieted text table containing the FPKM for every gene in every sample

extract_protocol:
Total RNA was extracted using the Monarch Total RNA Miniprep Kit and treated with in column DNaseI
The RNA-Seq libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit (Catalog #: 20020594) as per manufacturer's instructions.


title: HEK293_Ago2 knock-out_dsGFPd_total_Rep2_Experiment2

value: pOSI17 PKR knock-out

value: additional Ago2 knock-out


title: NCC aggregates, day 5, rep2

value: day 5


title: control sample, rep 2

description: Library name: control_2

value: leaves

value: Bachar

value: water


title: Distal cap, day 13, rep1

value: day 13


title: 3_2i

description: ATAC-seq

value: EPSCM


title: ES_16

value: ES


title: stressed sample, rep 2

description: Library name: stressed_2

value: drought


title: HEK293_Dicer knock-out_Mock_total_Rep2_Experiment2

value: additional Dicer knock-out

value: Mock


title: mdEM, day 9, rep2

value: iPSCs derived from PBMC

value: WT


title: NCC aggregates, day 5, rep3


title: 1_ES

description: ATAC-seq


title: Clusters, day 38, rep2

treatment_protocol: To initiate the induction of mdEM, 1231A3 iPSC-derived NCC aggregates (day 5) were cultured in 350 μl of StemFit Basic03 supplemented with 100 ng/ml FGF8b (FUJIFILM Wako), 50 nM Endothelin-1 (PEPTIDE INSTITUTE), and 2.5 ng/ml BMP4 (R&D Systems) on an orbital shaker at 120 rpm from day 5 to 9. mdEM aggregates (day 9) were transferred into 96-well U-bottom ultra-low-cell-adhesion plates. The mdEM were cultured in 200 μl of StemFit Basic03 supplemented with 20 ng/ml EGF and FGF (FUJIFILM Wako), 50 ng/ml BMP2 (R&D Systems), 3 μM CHIR99021 (GSK-3 inhibitor, Axon Medchem), and 400 nM SAG (Smoothened Agonist, Selleck) for 3 days. On day 12, the differentiation medium was replaced with 200 μl MSCgo Osteogenic Differentiation Medium (SARTORIUS) and the clusters were cultured for 7 days. On day 19, the differentiation medium was replaced with 200 μl of StemFit Basic03 supplemented with 10 mM β-glycerophosphate disodium salt hydrate (Sigma), 250 μM L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma), 100 nM Dexamethasone (Sigma), 50 ng/ml BMP2 (R&D), 3 μM CHIR99021, and 400 nM SAG and the clusters were cultured for 7 days. From day 26 to 38, the clusters were cultured in MSCgo Osteogenic Differentiation Medium, with medium changes every 2 days.

value: day 38


title: stressed sample, rep 1

description: Library name: stressed_1


title: ES_2


title: EP_19


title: HEK293_Ago1/2 knock-out_dsGFPd_total_Rep2_Experiment2

value: additional Ago1/2 knock-out

value: dsGFPd


title: EP_12


title: control sample, rep 1

description: Library name: control_1


title: HEK293_Ago2 knock-out_dsGFPc_total_Rep2_Experiment2

value: pOSI17 PKR knock-out

value: dsGFPc


title: HEK293_Ago2 knock-out_Mock_total_Rep2_Experiment2

value: additional Ago2 knock-out


title: EP_7


title: NCC aggregates, day 5, rep1

value: day 5


title: Clusters, day 38, rep1


title: HEK293_Ago1/2 knock-out_Mock_total_Rep2_Experiment2


title: control sample, rep 3

description: Library name: control_3

value: leaves

value: Bachar


title: HEK293_Ago1/2 knock-out_dsGFPc_total_Rep2_Experiment2


title: Siberian Hamster, Kidney, PRL, Sample 5

city: Glasgow

first: Sayantan

last: Sur

address: University of Glasgow, Vet School, Garscube Campus, Bearsden Road

department: School of Biodiversity, One Health & Veterinary Medicine

country: United Kingdom

institute: University of Glasgow

description: Library name: Prl Kid 343

data_processing:
Raw reads were demultiplexed and basealled using guppy basecaller
Porechop was used to trim adapters
Filtlong used to select long reads (>25 reads)
Minimap2 used to align reads to Mus musculus genome (GCRm39)
Transcript expression levels generated using Salmon
Assembly: GCF_000001635.27
Supplementary files format and content: Comma Separated Values Files with expressed gene transcripts for each sample

organism: Phodopus sungorus

source_name: Kidney tissue

extract_protocol:
RNA was extracted using the Qiagen RNEasy plus mini-kit
RNA Libraries were constructed using the PCR_cDNA sequencing barcoding kit (SQK-DCS109, EXP-NBD104, Oxford Nanopore) as per manufacturers instructions

value: Kidney tissue

value: female

value: Prolactin treatment


title: 2i_6


title: Siberian Hamster, Kidney, PRL, Sample 6

description: Library name: Prl Kid 341


title: Siberian Hamster, Kidney, PRL, Sample 4

description: Library name: Prl Kid 342


title: 2i_5


title: mdEM, day 9, rep2

value: day 9


title: Siberian Hamster, Kidney, PRL, Sample 3

description: Library name: Prl Kid 344


title: mdEM, day 9, rep1


title: 2i_18


title: NCC induction, RA treatment, day 5

growth_protocol: Human 1231A3 iPSCs were maintained on iMatrix-511 (human laminin-511 E8 fragment, Nippi)-coated cell culture plates in StemFit AK03N medium (Ajinomoto) in a 37°C incubator with 5% CO2.

treatment_protocol: For NCC induction in three-dimensional (3D) conditions, iPSCs were detached from the culture dish using Accutase (Innovative Cell Technologies) and dissociated into single cells. These cells were promptly reaggregated in 100 μl of StemFit Basic03 (equivalent to AK03N without bFGF, Ajinomoto) supplemented with 10 μM Y-27632 in 96-well V-bottom ultra-low-cell-adhesion plates (Sumitomo Bakelite) (1.0×104 cells/well). Cell numbers were determined using a Countess II FL (Thermo Fisher Scientific). Aggregation was facilitated by centrifugation at 1200 rpm for 3 min (day 0). For NCC induction, these cell aggregates were maintained in a 37°C incubator with 5% CO2. After 24 h (day 1), the culture medium was replaced with 150 μl of StemFit Basic03 containing 10 μM SB431542 (TGF-β inhibitor; FUJIFILM Wako) and 10 ng/m BMP4 (R&D Systems). After another 24 h (day 2), the aggregates were individually collected and transferred into 48-well non-coated plates (IWAKI) and cultured in 250 μl of StemFit Basic03 containing 10 μM SB431542 and 1 μM CHIR99021 (GSK-3 inhibitor, Axon Medchem) on an orbital shaker (CS-LR; TAITEC) at 120 rpm from day 2 to 4. For HOX-negative NCC induction, the aggregates were cultured without medium change from day 4 to 5. For HOX-positive NCC induction, day 4 aggregates were cultured with 250 μl of StemFit Basic03 containing 10 μM SB431542, 1 μM CHIR99021, and 10 nM all-trans-Retinoic Acid (FUJIFILM Wako) from day 4 to 5.

value: NCC induction


title: NCC aggregates, day 5, rep2


title: HEK293_Parental_Mock_total_Rep2_Experiment2

value: Parental

value: Mock


title: Siberian Hamster, Kidney, PRL, Sample 1

description: Library name: Prl Kid 345


title: bc11_S288C

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

institute: Francis Crick Institute

description: Library name: sample 15

library_source: other

data_processing:
Read processing was performed using an adapted nf-core/clipseq pipeline with Nextflow. Read demultiplexing was performed using Ultraplex with parameters “--phredquality 15--min_length0” . Adaptor trimming was performed using Cutadapt with parameters “--minimum-length 20”. Bowtie2 was used for premapping to ribosomal and small RNAs. Genome mapping was performed using STAR, for mouse samples with GRCm38 (mm10) release-89 annotation, and for S288C samples with S. cerevisiae Ensembl R64-1-1 release-90 annotation. UMI-tools was used for deduplication. BedTools was used to identify the 5’-most nucleotide (tag) and for genome-wide comparative analyses.
Assembly: mouse samples with GRCm38 (mm10) release-89 annotation, and for yeast S288C samples with S. cerevisiae Ensembl R64-1-1 release-90 annotation
Supplementary files format and content: bedGraph

molecule: other

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast growth conditions S. cerevisiae BY4741 strain background (derived from S288C) was used for the analysis of the yeast part of the manuscript. Cells were grown in liquid cultures (YPD (1.0% (w/v) yeast extract, 2.0% (w/v) peptone, 2.0% (w/v) glucose, and supplemented with uracil (2.4 mg/l) and adenine (1.2 mg/l))) in incubator/shaker (30°C, 300 rpm) till the exponential phase.   mESCs culturing mESCs (HM1) were grown in 2i/LIF [49% DMEM/F12-/- (Gibco), 49% Neurobasal (Gibco), 1X N2 (Gibco), 1X B27 (Gibco), 0.05 mM 2-Mercaptoethanol (Gibco), 2mM L-Glutamine (Gibco), Recombinant mouse 50,000 units LIF (ESGRO), 1 µM PD03259010 (Stemgent), 3 µM CHIR 99021 (TOCRIS), 1% Penicillin/Streptomycin]]. Cell culture surfaces were coated with 0.15% gelatin in PBS, for a minimum of 10 minutes at 37°C for mESC culture. mESCs were maintained at 37°C, 5% CO2, and confirmed to be negative for mycoplasma. mESCs were passed every 2-3 days depending on colony size, with media change occurring in the intermediate days. To pass cells, one wash with PBS was performed, before incubating the cells with Accutase (Gibco) at 37ºC for exactly 3 minutes.

extract_protocol:
RNA was extracted from yeast as previously detailed (Chia et al. 2021). For RNA extraction from yeast grown in YPD, 24 optical density (OD) units for TSS-seq were collected by centrifugation, and snap-frozen in liquid nitrogen. Per 10 OD units, RNA was extracted with 1 ml Tris-EDTA-SDS (TES) buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS) and 1 ml Acid Phenol:Chloroform:Isoamyl alcohol (125:24:1, Ambion), by shaking at 65°C for 45 minutes at 1400 rpm. After centrifugation at 4°C, max speed, 10 minutes, the aqueous phase was transferred to cold ethanol with 0.3 M sodium acetate. Precipitation was carried out overnight at 4°C, before centrifugation at 4°C, max speed, 20 minutes. The pellet was washed once with 80% v/v ethanol, dried, and reconstituted in DEPC-treated sterile water. rDNase (Machery-Nagel) treatment was carried out for 20 minutes at 37°C, before spin column purification (Machery-Nagel).  RNA was extracted from mammalian cells using TRIzol (Thermo Fisher). For TRIzol RNA extraction, 1 ml of TRIzol was added per 10-cm dish. Chloroform (0.2 volume, Thermo Fisher) was added, and the mixture was shaken for 30 seconds before centrifugation was performed. The aqueous phase was mixed with 1.1 volumes of isopropanol (Thermo Fisher), and RNA was precipitated overnight at 4°C. After centrifugation, the pellet was washed with 85% (v/v) ethanol, dried, and reconstituted in DEPC-treated sterile water. rDNase (Qiagen) digestion was carried out at 37°C for 1 hour before purification by spin column (Qiagen) or by phenol:chloroform and ethanol precipitation.  For small RNA size selection, Monarch RNA Cleanup with a 1:3 ratio of sample: ethanol volume was used.                                                                                4SU RNA labelling 4SU labelling was carried out as detailed previously (Gregersen et al. 2020), with few modifications. Cell culture media was removed, and filtered, and 1 mM 4SU (Glentham Life Sciences) was added. The cells were returned to the incubator, and labelled with 4SU for 15 minutes before medium aspiration and TRIizol addition. 1/5 volume of chloroform was added, mixed, and then centrifuged at 12,000g for 15 minutes at 4°C. 1.1 volumes of isopropanol and 1 µl of glycoblue were mixed with the upper aqueous layer, precipitation then occurred overnight at -20°C. The pellet was washed once with 85% ethanol, dried, and resuspended.  RNA integrity was checked for a selection of samples using Bioanalyser (Agilent Technologies). 4SU incorporation was assessed using slot blot. Here, 5 µg of total RNA was mixed with 3 µl biotin buffer (833 mM Tris-HCl, pH 7.4, and 83.3 mM EDTA) and 50 µl of 0.1 mg/ml MTSEA biotin-XX linker (Biotium, dissolved in dimethylformamide; Sigma-Aldrich) to a total volume of 200 µl, and incubated in the dark for 30 minutes. RNA clean-up was performed by adding an equal volume of phenol/chloroform/isoamyl alcohol (25:24:1 (vol/vol/vol)), mixing, and centrifuging at 12,000g for 5 minutes at 4°C. The aqueous phase was mixed with 1.1 volumes of isopropanol, 1/10 volume of 5 M NaCl and 1 µl of glycoblue and precipitated at -20°C for at least 2 hours. The pellet was washed once with 85% ethanol, dried, and resuspended to 10 µl.
The TSS-seq protocol: total RNA was dephosphorylated with quickCIP (NEB, 1.2 U/µg RNA) 37°C, with RNasin Plus before heat inactivation. RNA was extracted using phenol/chloroform/isoamyl alcohol as before. RNA was treated with mRNA decapping enzyme (NEB, 0.7 U/µg RNA) at 37°C with RNasin Plus. RNA was extracted using phenol/chloroform/isoamyl alcohol as before. RNA and the 5’ adaptor (10 µM) were denatured for 2 minutes at 70°C, then cooled on ice for 2 minutes. Ligation was performed, 16°C using and T4 RNA ligase I (30 U), with RNasin Plus. RNAClean XP (1.8X ratio, Beckman Coulter) was used to remove unligated adaptors, according to the manufacturer’s instructions. The concentration of the samples was measured using Qubit RNA BR assay, and samples were multiplexed. polyA+ RNA was enriched using Dynabeads Oligo(dT)25 (Thermo Fisher). Yeast RNA was fragmented with alkaline fragmentation reagent (Ambion). RNeasy MinElute Clean-up columns, with 1.5x volume of Ethanol, were used to purify the samples. The 3’ ends were fixed by CIP treatment (NEB,30 U).  Ligation was carried out by T4 Rnl2tr (NEB,200 U) for 2 hours, 25°C then 16 hours, 16°C. RNAClean XP (1.8X ratio) was used to remove unligated adaptors. RNA, RT oligo (0.5 pmol) and dNTP (10 mM each) were denatured at 65°C, then cooled on. Reverse transcription was carried out by SuperScript III (2 µl), with RNasin Plus with the following conditions: 25°C for 5 minutes, 42°C for 20 minutes, 50°C for 40 minutes, 80°C for 5 minutes. Template RNA was removed by RNase H (10 U) for 37°C, 30 minutes. AMPure XP beads (Agencourt, Beckman Coulter) were used to clean up the cDNA. 3X beads and 1.7x isopropanol added to the reverse transcription reaction, and incubated for 5 minutes. Beads were washed twice with 85% ethanol, dried, and eluted twice in nuclease-free water. cDNA pre-amplification was performed with i5_s and i7_s (300 nM each) primers and Phusion HF PCR Mastermix (Thermo Fisher). 6 PCR cycles were carried out (98°C for 10 seconds, 65°C for 30 seconds, 72°C for 30 seconds, with 3 minutes at 72°C final extension). ProNex beads (Promega) with a 1:2.95 ratio to sample were used to remove sequences less than 55 nt (including primer dimers). Final amplification was carried out with NEBNext i50 and i70 primers (500 nM each) and Phusion HF PCR Mastermix, for 8 cycles. Amplification was checked by using Novex 6% TBE (Tris/Borate/EDTA) gel and staining with SYBR green. ProNex beads (Promega) with a 1:2.3 ratio to sample were used for purification. Library concentration was measured using Qubit High Sensitivity D1000. Libraries were sequenced with Illumina NovaSeq 6000 using 100 nt paired-end reads, with 50 million reads minimum per sample.

value: yeast

value: Mat a, his3D1, leu2D0, met15D0, ura3D0


title: HEK293_Dicer knock-out_dsGFPc_total_Rep1_Experiment2

value: additional Dicer knock-out


title: Siberian Hamster, Kidney, SAL, Sample 5

description: Library name: Prl Kid 323

value: Saline treatment


title: HEK293_Dicer knock-out_dsGFPd_total_Rep1_Experiment2

value: pOSI17 PKR knock-out

value: dsGFPd


title: HEK293_Parental_dsGFPd_total_Rep2_Experiment2


title: Siberian Hamster, Kidney, SAL, Sample 6

description: Library name: Prl Kid 322


title: bc10_S288C

description: Library name: sample 14


title: iPSCs, day 0

value: iPSCs derived from PBMC

value: WT


title: HEK293_Parental_dsGFPc_total_Rep2_Experiment2

value: dsGFPc


title: HEK293_Ago2 knock-out_dsGFPd_total_Rep1_Experiment2

value: additional Ago2 knock-out


title: Siberian Hamster, Kidney, SAL, Sample 3

description: Library name: Prl Kid 329

value: Kidney tissue


title: bc09_S288C

description: Library name: sample 13


title: Siberian Hamster, Kidney, PRL, Sample 2

description: Library name: Prl Kid 414

value: female


title: Siberian Hamster, Kidney, SAL, Sample 2

description: Library name: Prl Kid 328


title: HEK293_Ago2 knock-out_Mock_total_Rep1_Experiment2


title: bc07_S288C

description: Library name: sample 11


title: bc08_S288C

description: Library name: sample 12


title: NCC aggregates, day 5, rep1

value: day 5


title: bc12_S288C

description: Library name: sample 16


title: NCC induction, day 5, CD271high

treatment_protocol: For NCC induction in 3D conditions, iPSCs were detached from the culture dish using Accutase (Innovative Cell Technologies) and dissociated into single cells. These cells were promptly reaggregated in 100 μl of StemFit Basic03 (equivalent to AK03N without bFGF, Ajinomoto) supplemented with 10 μM Y-27632 in 96-well V-bottom ultra-low-cell-adhesion plates (Sumitomo Bakelite) (1.0×104 cells/well). Cell numbers were determined using a Countess II FL (Thermo Fisher Scientific). Aggregation was facilitated by centrifugation at 1200 rpm for 3 min (day 0). For NCC induction, these cell aggregates were maintained in a 37°C incubator with 5% CO2. After 24 h (day 1), the culture medium was replaced with 150 μl of StemFit Basic03 containing 10 μM SB431542 (TGF-β inhibitor; FUJIFILM Wako) and 10 ng/ml BMP4 (R&D Systems). After another 24 h (day 2), the aggregates were individually collected and transferred into 48-well non-coated plates (IWAKI) and cultured in 250 μl of StemFit Basic03 containing 10 μM SB431542 and 1 μM CHIR99021 (GSK-3 inhibitor, Axon Medchem) on an orbital shaker (CS-LR; TAITEC) at 120 rpm from day 2 to 5.  For NCC induction in two-dimensional (2D) conditions, iPSCs were seeded onto iMatrix-511-coated culture plates at a density of 3.6 × 103 cells/cm2 in StemFit AK03N medium and maintained in culture for 4 days. The cells were cultured in StemFit Basic03 supplemented with 10 μM SB431542 and 1 μM CHIR99021 for 10 days, with medium changes every 2 days.


title: bc06_S288C

description: Library name: sample 10


title: NCC induction, day 5, CD271high


title: HEK293_Ago1/2 knock-out_dsGFPd_total_Rep1_Experiment2

value: additional Ago1/2 knock-out


title: NCC induction, day 5

value: NCC induction


title: Siberian Hamster, Kidney, SAL, Sample 1

description: Library name: Prl Kid 324


title: bc05_S288C

description: Library name: sample 9


title: NCC induction, day 5


title: HEK293_Dicer knock-out_Mock_total_Rep1_Experiment2


title: NCC induction, day 4


title: Siberian Hamster, Kidney, SAL, Sample 4

description: Library name: Prl Kid 327


title: bc04_S288C

description: Library name: sample 8


title: NCC induction, day 3


title: Siberian Hamster, Kidney, SP28wk, Sample 3

description: Library name: SW Kid 165

value: male

value: Short 8L photoperiod (28wk)


title: NCC induction in 2D conditions, day 10, CD271high


title: HEK293_Ago2 knock-out_dsGFPc_total_Rep1_Experiment2


title: Siberian Hamster, Kidney, SP28wk, Sample 2

description: Library name: SW Kid 174


title: bc03_S288C

description: Library name: sample 7

value: yeast


title: NCC induction, day 2


title: HEK293_Parental_dsGFPd_total_Rep1_Experiment2

value: Parental


title: Siberian Hamster, Kidney, SP28wk, Sample 1

description: Library name: SW Kid 175


title: bc02_S288C

description: Library name: sample 6

value: Mat a, his3D1, leu2D0, met15D0, ura3D0


title: bc01_S288C

description: Library name: sample 5


title: iPSCs, day 0


title: Siberian Hamster, Kidney, SP28wk, Sample 4

description: Library name: SW Kid 162


title: Siberian Hamster, Kidney, SP12wk, Sample 4

description: Library name: SW Kid 280

value: Short 8L photoperiod (12wk)


title: Genomic DNA from 39 weeks IVF Sperm 6

type: genomic

city: Philadelphia

first: Eric

middle: Alejandro

last: Rhon Calderon

state: Pennsylvania

address: 3400 Civic Center Blvd, Bldg 421, Floor 9-175

department: Cell and Developmental Biology

institute: University of Pennsylvania

description:
Bisulfite treated
39wks_IVF_6

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Mouse285 Methylation BeadChip 12v1-0 using standard Illumina Protocol

scan_protocol: Illumina iScan System

data_processing:
SeSAMe R Package
Beta values of individual probe for each  sample. Probes that did not pass SeSAMe quality control pOOBAH approach is maksed with NA

label: Cy3 and Cy5

source_name: Sperm

label_protocol: Standard Illumina Protocol:

growth_protocol: All animals were housed in polysulfone cages containing drinking water and chow (Laboratory Irradiated Rodent Diet 5LG4, LabDiet) ad libitum.

extract_protocol: Genomic DNA was extracted and purified from Sperm samples using Phenol:Chloroform according to lab protocols. Then samples were Bisulfite-treated using Qiagen EpiTect Bisulfite Conversion Kit.

treatment_protocol: Sperm was collected from vas deferens and caudal epydidimis from 12 and 39 weeks mice, somatic cells were lysed, and sperm samples were snap frozen in liquid nitrogen and stored at -80C for DNA extraction.

value: Sperm

tag: age

tag: group

value: IVF


title: Siberian Hamster, Kidney, SP12wk, Sample 3

description: Library name: SW Kid 278


title: S288C-Original_decap

description: Library name: sample 4


title: HEK293_dsGFPd_PACT, TRBP knock-out_APP_Rep2_Experiment1

description:
small RNA
Ago-pulldown
PACT_TRBP_miRNA_quant.csv

value: pOSI17 PKR knock-out

value: additional PACT, TRBP knock-out

value: dsGFPd


title: Siberian Hamster, Kidney, SP12wk, Sample 2

description: Library name: SW Kid 292


title: S288C-Original_contro

description: Library name: sample 3


title: HEK293_dsGFPc_PACT, TRBP knock-out_APP_Rep2_Experiment1

value: dsGFPc


title: HEK293_Ago1/2 knock-out_dsGFPc_total_Rep1_Experiment2


title: Siberian Hamster, Kidney, SP12wk, Sample 1

description: Library name: SW Kid 277

value: Kidney tissue


title: Genomic DNA from 39 weeks IVF Sperm 5

description:
Bisulfite treated
39wks_IVF_5


title: Siberian Hamster, Kidney, LP, Sample 4

description: Library name: SW Kid 238

value: Long 16L photoperiod


title: Genomic DNA from 39 weeks IVF Sperm 3

description:
Bisulfite treated
39wks_IVF_3


title: NCC induction, day 1

value: iPSCs derived from PBMC

value: WT


title: Siberian Hamster, Kidney, LP, Sample 3

description: Library name: SW Kid 247


title: HEK293_dsGFPd_TRBP knock-out_APP_Rep2_Experiment1

value: additional TRBP knock-out


title: HEK293_Parental_dsGFPc_total_Rep1_Experiment2


title: Genomic DNA from 39 weeks IVF Sperm 2

description:
Bisulfite treated
39wks_IVF_2


title: HEK293_dsGFPc_TRBP knock-out_APP_Rep2_Experiment1


title: Heated seeds rep2

city: Fukuoka

first: Yushi

last: Ishibashi

state: Fukuoka

address: 744 Motooka, Nishi-ku

department: Department of Bioresource Sciences

institute: Kyushu University, Faculty of Agriculture

data_processing:
All read data were checked with FastQC (v0.11.7) and trimmed by Trimmomatic (v-0.38)
Trimmed reads were mapped to the transcript in the reference Os-Nipponbare-Reference-IRGSP-1.0 using Bowtie2 aligner within RSEM [R]. The abundance estimation of genes and isoforms with RSEM generated basic counts data (expected counts).
The raw read counts of all samples were processed through edgeR package (v3.26.3) of Bioconductor, and normalized CPM counts were generated.
Ditection of differentially expressed genes (DEGs)  were carried out with edgeR program. Normalized counts per million (CPM) values, log fold-changes (logFC) and p-values were obtained from the normalized CPM values.
Assembly: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Oryza sativa

source_name: incubate at 30 ℃

extract_protocol:
Total RNA was harvested using Phenol/Chloroform and LiCl.
The sequencing libraries were prepared from 1 ug of total RNA with TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer's instructions. Cluster amplification and 150 bp paired-end sequencing was performed according to the manufacturer’s protocol (Illumina) for NovaSeq (Illumina).

value: leaf

tag: cultivar

value: Nipponbare

value: incubate at 30 ℃


title: HEK293_Parental_Mock_total_Rep1_Experiment2

value: Parental

value: Mock


title: Heated seeds rep1


title: Siberian Hamster, Kidney, LP, Sample 1

description: Library name: SW Kid 417

value: male


title: HEK293_mock_TRBP knock-out_APP_Rep2_Experiment1

value: mock


title: Cotrol seeds rep2


title: HEK293_dsGFPd_PACT knock-out_APP_Rep2_Experiment1

value: additional PACT knock-out


title: Genomic DNA from 39 weeks Natural Sperm 5

description:
Bisulfite treated
39wks_Nat_5

value: Sperm

value: Natural


title: HEK293_dsGFPc_PACT knock-out_APP_Rep2_Experiment1

value: pOSI17 PKR knock-out


title: Genomic DNA from 39 weeks Natural Sperm 4

description:
Bisulfite treated
39wks_Nat_4


title: Genomic DNA from 39 weeks IVF Sperm 4

description:
Bisulfite treated
39wks_IVF_4

value: IVF


title: HEK293_mock_PACT, TRBP knock-out_APP_Rep2_Experiment1

value: additional PACT, TRBP knock-out


title: HEK293_Ago1/2 knock-out_Mock_total_Rep1_Experiment2

value: additional Ago1/2 knock-out


title: FOE-2

city: Nanjing

first: WenHan

last: Zhou

address: No. 1 Weigang, Xuanwu District

department: college of animal science & technology

country: China

institute: Nanjing Agricultural University

description:
Library name: sample11
FOE2

data_processing:
Illumina Casava software used for basecalling.
（1）Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted )（2）Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality).（3）Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HISAT v2.1.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DESeq2 was designed for differential gene expression analysis between two samples with biological replicates. Genes with q≤0.05 and |log2_Foldchange|≥1 are identified as differentially expressed genes. The GO （Gene Ontology, http://geneontology.org/）enrichment of DEGs was implemented by the hypergeometric test. GO terms with q<0.05 were considered to be significantly enriched. The KEGG PATHWAY enrichment of DEGs was implemented by the hypergeometric test. KEGG terms with q<0.05 were considered to be significantly enriched. genome build.
Assembly: Mus_musculus.GRCm38.99
Supplementary files format and content: tab-delimited text files include FPKM values for Sample1、Sample2……
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Musculus

growth_protocol: Mice were engineered with liver-specific knockout of Mettl14 using CRISPR/Cas9-mediated gene editing.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: AML12 cells (a murine hepatocyte line) were transfected with a Flag-Fam32a overexpression plasmid or empty plasmid.

value: hepatocyte


title: HEK293_mock_PACT knock-out_APP_Rep2_Experiment1


title: S288C-Optimized_control

description: Library name: sample 1

value: yeast

value: Mat a, his3D1, leu2D0, met15D0, ura3D0


title: S288C-Optimized_decap

description: Library name: sample 2


title: MEL-st cell 3  aligned reads

city: Leuven

first: Kim

last: De Keersmaecker

address: ON4 Herestraat 49 - bus 810

department: Oncology

institute: KUL

description: Library name: OHMX20240126_003.flair.aligned.bam

data_processing:
Obtained sequencing reads were basecalled and demultiplexed using the high-accuracy basecall model of Dorado. After removal of reads with a PHRED score below 9, a total number of 26.38 million reads were retained for downstream analysis (≥ 7.2 million reads per replicate). Isoform detection, quantification and de novo transcript detection was performed using Flair2. The raw data were mapped to the human genome using Minimap2 through the Flair align module. Misaligned splice sites were corrected with Flair correct using the genome annotation from GENCODE release 47. Lastly, Flair collapse was used to define high-confidence isoforms from the corrected reads. The output from the Flair correct step was concatenated to create GTF files containing the detected transcript isoforms. A count matrix of the merged samples was also generated to identify the main expressed isoform identified by FLAIR.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: GTF files for each sample

source_name: skin

growth_protocol: Mel-ST cells were grown in DMEM (cat # 41965039, Thermo Fisher Scientific) supplemented with 10% Fetal Bovine Serum (cat # 1017760, Thermo Fisher Scientific) in a humidified cell culture incubator at 37 °C with 5% CO2. Cells were regularly verified to be mycoplasma-free.

extract_protocol:
RNA from three replicates of Mel-ST cells taken on different days was extracted using an RNeasy Mini Kit (cat #74106, Qiagen)
To convert RNA fragments into cDNA and perform library preparation, the Direct cDNA Sequencing kit (SQK-LSK114, Oxford Nanopore Technologies) in combination with the Native Barcoding Expansion kit (SQK-NBD114.96, Oxford Nanopore Technologies) were used. The library pool was sequenced on a PromethION flow cell (FLO-PRO114M, Oxford Nanopore Technologies).

treatment_protocol: No treatments were done

value: skin

value: Mel-ST

value: Melanocytes

value: WT


title: FOE-1

description:
Library name: sample10
FOE1


title: Siberian Hamster, Kidney, LP, Sample 2

description: Library name: SW Kid 248

value: Kidney tissue

value: Long 16L photoperiod


title: Genomic DNA from 39 weeks Natural Sperm 3

description:
Bisulfite treated
39wks_Nat_3


title: MEL-st cell 2 aligned reads

description: Library name: OHMX20240126_002.flair.aligned.bam


title: MEL-st cell 1 aligned reads

description: Library name: OHMX20240126_001.flair.aligned.bam


title: C-3

description:
Library name: sample9
C3


title: C-2

description:
Library name: sample8
C2


title: HEK293_dsGFPc_Parental_APP_Rep2_Experiment1

value: Parental

value: dsGFPc


title: Genomic DNA from 39 weeks Natural Sperm 2

description:
Bisulfite treated
39wks_Nat_2

value: Sperm


title: Genomic DNA from 39 weeks Natural Sperm 6

description:
Bisulfite treated
39wks_Nat_6

value: Natural


title: HEK293_dsGFPd_Parental_APP_Rep2_Experiment1

value: pOSI17 PKR knock-out

value: dsGFPd


title: FOE-3

description:
Library name: sample12
FOE3


title: BAT-3, C57BL/6N mouse, 79 weeks

city: Osaka

first: Yung-Ting

last: Hsiao

address: 6-1 Kishibe-Shimmachi, Suita

institute: National Cerebral and Cardiovascular Center

data_processing:
These libraries were analyzed on a NextSeq500 with a NextSeq 500/550 High Output Kit v2 (Illumina).
TopHat 2 (version 2.0.13) was used for mapping reads to the reference genome (Ensembl GRCm38/mm10) with annotation data downloaded from the Ensembl Asia website (URL https://asia.ensembl.org/).
Assembly: mm10
Supplementary files format and content: Expression of each transcript was quantified as the number of fragments per kilobase of transcript per million fragments mapped (FPKM)
Supplementary files format and content: The expression was compared among 3 groups by Cuffdiff (included in Cufflinks version 2.2.1).

source_name: brown adipose tissue

extract_protocol:
Total RNA was isolated from tissue samples with an RNeasy Mini Kit (Qiagen, 74104) and its quality was assessed by using the Agilent 2100 Bioanalyzer with the Agilent RNA6000 pico Kit (Agilent Technologies).
The TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) was employed to construct four libraries according to the specifications of the manufacturer.

value: brown adipose tissue

tag: strain

tag: Stage

value: aged

value: 79 weeks


title: HEK293_mock_Parental_APP_Rep2_Experiment1

value: mock


title: Cotrol seeds rep1

source_name: incubate at 25 ℃

value: leaf

value: Nipponbare

value: incubate at 25 ℃


title: C-1

description:
Library name: sample7
C1

value: hepatocyte


title: Genomic DNA from 39 weeks Natural Sperm 1

description:
Bisulfite treated
39wks_Nat_1


title: BAT-2, C57BL/6N mouse, 79 weeks


title: Genomic DNA from 12 weeks IVF Sperm 5

description:
Bisulfite treated
12wks_IVF_5

value: IVF


title: HEK293_dsGFPd_PACT, TRBP knock-out_APP_Rep1_Experiment1

value: additional PACT, TRBP knock-out


title: WT-3-24

description:
Library name: sample6
WT324

source_name: liver

value: liver


title: Genomic DNA from 12 weeks IVF Sperm 4

description:
Bisulfite treated
12wks_IVF_4


title: BAT-1, C57BL/6N mouse, 79 weeks


title: HEK293_dsGFPc_PACT, TRBP knock-out_APP_Rep1_Experiment1


title: WT-2-24

description:
Library name: sample5
WT224


title: BAT-7, C57BL/6N mouse, 12 weeks

value: young

value: 12 weeks


title: Genomic DNA from 12 weeks IVF Sperm 3

description:
Bisulfite treated
12wks_IVF_3

value: Sperm


title: HEK293_mock_PACT, TRBP knock-out_APP_Rep1_Experiment1


title: BAT-6, C57BL/6N mouse, 12 weeks


title: Genomic DNA from 12 weeks IVF Sperm 2

description:
Bisulfite treated
12wks_IVF_2


title: HEK293_dsGFPd_TRBP knock-out_APP_Rep1_Experiment1

value: additional TRBP knock-out


title: KO-41-24

description:
Library name: sample3
KO4124


title: BAT-5, C57BL/6N mouse, 12 weeks


title: Genomic DNA from 12 weeks IVF Sperm 1

description:
Bisulfite treated
12wks_IVF_1


title: KO-34-24

description:
Library name: sample2
KO3424


title: BAT-4, C57BL/6N mouse, 12 weeks


title: HEK293_dsGFPc_TRBP knock-out_APP_Rep1_Experiment1

value: pOSI17 PKR knock-out

value: dsGFPc


title: Genomic DNA from 12 weeks Natural Sperm 6

description:
Bisulfite treated
12wks_Nat_6

value: Natural


title: BAT-3, C57BL/6N mouse, 13 weeks

value: brown adipose tissue

value: 13 weeks


title: Genomic DNA from 12 weeks Natural Sperm 5

description:
Bisulfite treated
12wks_Nat_5


title: HEK293_mock_TRBP knock-out_APP_Rep1_Experiment1

value: mock


title: KO-31-24

description:
Library name: sample1
KO3124


title: HEK293_dsGFPd_PACT knock-out_APP_Rep1_Experiment1

value: additional PACT knock-out

value: dsGFPd


title: BAT-2, C57BL/6N mouse, 13 weeks


title: Genomic DNA from 12 weeks Natural Sperm 4

description:
Bisulfite treated
12wks_Nat_4


title: HEK293_dsGFPc_PACT knock-out_APP_Rep1_Experiment1


title: BAT-1, C57BL/6N mouse, 13 weeks


title: Pseudomonas putida, Day 15, FeCl3 Control, rep 2

city: Newark

first: Mark

last: Blenner

state: DE

department: Chemical and Biomolecular Engineering

institute: University of Delaware

description:
KT2440; ATCC47054
Pp_FeCl3Con_D15_R2

data_processing:
Data processing was performed using the Palmetto Cluster and rStudio.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CutAdapt commands (v2.8) and fastQC analysis (v0.11.8) within Trim Galore (v0.6.5).
Trimmed sequence reads were aligned to ASM756v2 RefSeq annotation GCF_000007565.2 using HISAT2 (v2.2.1) following instructions for paired-end reads and preparing HISAT2 genome index.
Samtools (v1.4) was used for file conversion of aligned reads before transcripts were assembled using StringTie (v1.3.3b) using genome guided mapping.
tximport (v1.20.0) was used to estimate counts and transcript lengths for import into DESeq2 (v1.35.0) for differential expression analysis within rStudio.
ClusterProfiler (v4.0.2) was used for KEGG pathway and Gene Ontology analyses.
Assembly: ASM756v2; GCF_000007565.2
Supplementary files format and content: Pp_count_matrix.txt: Tab-delimited text file containing matrix of abundance, counts, and transcript lengths.

organism: Pseudomonas putida KT2440

source_name: bacterial

growth_protocol: P. putida KT2440 (ATCC47054) cells were grown in 100 L M9 minimal medium supplemented with 0.5% glucose (Sigma-Aldrich), 1% thiamine hydrochloride (Spectrum), and 1% (w/v) casamino acids (Bacto) at 28°C and shaking at 215 rpm overnight. When appropriate radionuclide sources were spiked into liquid growth medium prior to inoculation of overnight E. coli cultures to achieve an approximate absorbed dose rate of 9 mGy d-1.

extract_protocol:
Total RNA was harvested using RNeasy mini kit (Qiagen). Ribosomal RNA was removed from total RNA samples using either Ribo-Zero rRNA Removal Kit Bacteria (Illumina) or RiboMinus Bacteria 2.0 Transcriptome Isolation Kit following the manufacturer's instructions. Ethanol precipitation was used to purify depleted RNA. 100 ng of purified mRNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols for purified mRNA input and Low Sample Protocol.

treatment_protocol:
Radionuclide sources were added to growth flasks prior to inoculation. Final activity concentration of internal sources were as follows (approx): Pu-239 in 0.01 M HCl at 0.12 kBq mL-1; Tritiated water (HTO) at 3 uCi mL-1; Fe-55 in 0.5 M HCl at 4.9 uCi mL-1. Non-irradiated controls either contained no additional chemical addition or an equimolar amount of stable FeCl3 (2.47uM).
Cultures were irradiated continuously for 15 days with samples for RNA extraction taken at one and 15-days after inoculation/spike addition. Samples were spun down into cell pellets and flask frozen for storage at -80C.

value: bacterial

value: WT

value: Growth with FeCl3

tag: time point

value: Day 15


title: Genomic DNA from 12 weeks Natural Sperm 3

description:
Bisulfite treated
12wks_Nat_3


title: Pseudomonas putida, Day 15, FeCl3 Control, rep 1

description:
KT2440; ATCC47054
Pp_FeCl3Con_D15_R1


title: HEK293_mock_PACT knock-out_APP_Rep1_Experiment1


title: HEK293_dsGFPd_Parental_APP_Rep1_Experiment1

value: Parental


title: WT-1-24

description:
Library name: sample4
WT124

value: liver


title: Pseudomonas putida, Day 1, FeCl3 Control, rep 3

description:
KT2440; ATCC47054
Pp_FeCl3Con_D1_R3

value: Day 1


title: Genomic DNA from 12 weeks Natural Sperm 1

description:
Bisulfite treated
12wks_Nat_1

value: Sperm


title: tdTomato+ cells, KO, bio rep 2

city: Shanghai

first: Yuanyuan

last: Wei

address: No. 130, Dong'an Road

institute: Fudan University

data_processing:
Clean reads were obtained after adaptor removal and discarding low-quality and short reads using Trimmomatic (version 0.39). The count tables of mapped paired-end reads from STAR outputs were used for differential gene expression analysis with DESeq2 (version 1.32.0).
STAR (version 2.7.10a) software was used to align the sequences to the reference genome.
DEseq2 (version 1.32.0) software was used for statistical differences.
Assembly: GRCm38 with GENCODE gene annotation (version M25)
Supplementary files format and content: tab-delimited excel file includes raw counts for each sample

source_name: tdTomato+ cells FACS sorted from murine atherosclerotic plaques

extract_protocol:
Total RNA was extracted from aortic roots and tdTomato+ plaque cells using the miRNeasy Micro kit (Qiagen), while from BMDMs using the MiPure Cell/Tissue miRNA Kit (Vazyme), according to the manufacturer’s instructions.
Library construction was performed using the QuantSeq 3' mRNA-Seq Library Prep kit for Illumina (REV) with Custom Sequencing Primer (Lexogen, #016).

value: LysMCre, Srsf3flox, RosatdTomato, Apoe-/-

value: High cholesterol diet, 12 weeks


title: HEK293_dsGFPc_Parental_APP_Rep1_Experiment1

value: pOSI17 PKR knock-out

value: dsGFPc


title: Pseudomonas putida, Day 1, FeCl3 Control, rep 1

description:
KT2440; ATCC47054
Pp_FeCl3Con_D1_R1


title: tdTomato+ cells, KO, bio rep 1

value: tdTomato+ cells FACS sorted from murine atherosclerotic plaques


title: Pseudomonas putida, Day 15, FeCl3 Control, rep 3

description:
KT2440; ATCC47054
Pp_FeCl3Con_D15_R3


title: Pseudomonas putida, Day 1, FeCl3 Control, rep 2

description:
KT2440; ATCC47054
Pp_FeCl3Con_D1_R2


title: tdTomato+ cells, WT, bio rep 2

value: LysMCre, Srsf3wt, RosatdTomato, Apoe-/-


title: SH-SY5Y cells_RBEE  pre-treatment 24h_LPS induction 24h_rep2

type: RNA

city: Tsukuba

first: sharmin

last: Aktar

state: 茨城県

department: Life and Environmental Science

institute: University of Tsukuba

description: Gene expression data from SH-SY5Y cells, pre-treated with RBEE  for 24 h and then LPS-induced for 24h

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, human; Thermofisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (Thermofisher Scientific).

data_processing:
The raw image data was normalized following the SST-RMA method using the Transcriptome Analysis Console (TAC) software (ver. 4.0, Thermofisher Scientific) (Summarization: SST-RMA, Anova Method: eBays, DABG <0.05, Pos/Neg AUC Threshold: 0.7).
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CHP files ).
RMA (SST-RMA, Transcriptome Analysis Console, version 4)

label: biotin

source_name: SH-SY5Y cells were treated with 0.2 mg/mL RBEE  for 24 h and then induced with LPS solution (5 ng/mL) for 24 h

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol from 100 ng/ uL total RNA

growth_protocol: SH-SY5Y cells  were purchased from RIKEN BioResource Center (RIKEN BRC, Tsukuba, Ibaraki, Japan). SH-SY5Y cells were cultured in Dulbecco’s modified Eagle medium (DMEM) (Merck KGaA, Darmstadt, Germany) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Bio West, Nuaillé, France) and 1penicillin-streptomycin solution (Merck KGaA) at 37ºC in a humidified incubator containing 5% CO2 using 75cm2 flask (BD FALCON, Corning, NY, USA)

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: RBEE  was extracted with 70% Ethanol (1 mL) at room temperature under the dark for 2 weeks. After the extraction was completed, it was centrifuged at 1000 xg for 10 minutes and collected the supernatant. The supernatant of the extracted sample was filtered by using a 0.22 µm filter unit and stored at -20 ºC in the dark until use.  Lipopolysaccharide (LPS; E. coli O111:B4) was purchased from EMD Millipore Co. (Billerica, MA USA). 5 mg of LPS was dissolved in 2 ml of PBS (-), and stored at -80 ℃ under the dark until use. SH-SY5Y cells were seeded into a 96-well plate at density of 2.0×105 cells/mL and incubated at 37 °C for 24 h. The cells were treated with or without RBEE  at 37 °C for 24 h. After the RBEE  treatment, the LPS solution (5 ng/ml) was added to each well and incubated for 24h and 24 h at 37 °C.

value: SH-SY5Y cells (Resource No. RCB0535, RIKEN BRC, Tsukuba, Ibaraki, Japan)


title: tdTomato+ cells, WT, bio rep 1


title: HEK293_mock_Parental_APP_Rep1_Experiment1

value: mock


title: HEK293_PACT, TRBP knock-out_dsGFPc_total_Rep2_Experiment1

description:
small RNA
total RNA
PACT_TRBP_miRNA_quant.csv

value: additional PACT, TRBP knock-out


title: HEK293_PACT, TRBP knock-out_dsGFPd_total_Rep2_Experiment1

value: dsGFPd


title: 4_3D21-18_80plus_d21

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

country: Germany

institute: University of Ulm

hyb_protocol: Following fragmentation, 5.2 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained.

scan_protocol: GeneArray Scanner

data_processing:
Transcriptome Analysis Console by Thermo Fisher Scientific
RMA (Robust Multi-Array Average) was used for normalization.

source_name: 3D Human full thickness skin model

label_protocol: 5.5 µg ss-cDNA was end labelled

extract_protocol: Total RNA from 3D skin models was extracted with the Nucleo Spin RNA Kit (Macherey and Nagel, Düren, Germany), according to the manufacturer’s instructions.

value: 3D skin model


title: Pseudomonas putida, Day 15, Fe-55, rep 3

description:
KT2440; ATCC47054
Pp_Fe55_D15_R3

value: bacterial

value: WT

value: Fe-55 exposure


title: SH-SY5Y cells_RBEE  pre-treatment 24h_LPS induction 24h_rep1


title: oxBMDM, KO, bio rep 4

source_name: bone marrow-derived macrophages

value: bone marrow-derived macrophages

value: LysMCre, Srsf3flox, Apoe-/-

value: oxidized LDL treatment for 48 hours


title: Pseudomonas putida, Day 15, Fe-55, rep 2

description:
KT2440; ATCC47054
Pp_Fe55_D15_R2

value: Day 15


title: Pseudomonas putida, Day 15, Fe-55, rep 1

description:
KT2440; ATCC47054
Pp_Fe55_D15_R1


title: 1_3D42-20_20plus_d14


title: SH-SY5Y cells_No pre-treatment_LPS induction 24h_rep2

description: Gene expression data from SH-SY5Y cells, maintained in culture medium for 24 h and then LPS-induced for 24h

source_name: SH-SY5Y cells were maintained in culture medium for 24h and then induced with LPS solution (5 ng/mL) for 24 h


title: HEK293_PACT, TRBP knock-out_mock_total_Rep2_Experiment1

data_processing:
Illumina Casava1.8 software used for basecalling.
Trimming of reads with BBduk of the BBmap package using the following parameters ktrim=r k=23 mink=11 hdist=1
Mapping to the human genome (GRCh38) with STAR (--outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --alignIntronMax 500 --alignIntronMin 50 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 50)
Read counting to mirbase annotation with Rsubread (allowMultiOverlap=T, isPairedEnd=T, strandSpecific=2, countMultiMappingReads=T)
Read normalization with DEsep2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text files of count per million (CPM) values

extract_protocol:
Ago-pulldown: Ago Affinity Purification by Peptides was performed in accordance with an earlier described protocols (Hauptmann et al., 2015). Ago-pulldown quality was validated by miR16/21 RT-qPCR. RNA extraction: 1.5-3*10^6 cells were trypsinized and washed twice with PBS before proceeding with RNA extraction. RNA was extarcted using TRI reagent (Sigma Aaldrich) according to manufacturer's recmmendations. Total RNA integrity and quality was validated on the Nanodrop 2000 (Thermo Scientific) and on an 1% agarose gel.
Libraries were prepared with total RNA and Ago-purified RNA, from approximately 2-3*10^6 cells, with the Lexogen small RNA-Seq Library Prep kit (Lexogen) according to the manufacturer’s instructions.


title: HEK293_TRBP knock-out_dsGFPd_total_Rep2_Experiment1

value: additional TRBP knock-out


title: oxBMDM, KO, bio rep 3


title: Pseudomonas putida, Day 1, Fe-55, rep 3

description:
KT2440; ATCC47054
Pp_Fe55_D1_R3

value: Day 1


title: SH-SY5Y cells_No pre-treatment_LPS induction 24h_rep1


title: 2_3D42-20_80plus_d14


title: 3_3D42-20_20plus_d21


title: oxBMDM, KO, bio rep 2


title: HEK293_TRBP knock-out_dsGFPc_total_Rep2_Experiment1

value: pOSI17 PKR knock-out

value: dsGFPc


title: Pseudomonas putida, Day 1, Fe-55, rep 2

description:
KT2440; ATCC47054
Pp_Fe55_D1_R2


title: SH-SY5Y cells_RBEE  pre-treatment 24h_No_LPS induction 24h_rep2

description: Gene expression data from SH-SY5Y cells, pre-treated with RBEE  for 24 h and then no LPS-induced for 24h

source_name: SH-SY5Y cells were treated with 0.2 mg/mL RBEE  for 24 h and then induced with LPS solution (0 ng/mL) for 24 h


title: oxBMDM, KO, bio rep 1


title: Pseudomonas putida, Day 1, Fe-55, rep 1

description:
KT2440; ATCC47054
Pp_Fe55_D1_R1


title: oxBMDM, WT, bio rep 4

value: LysMCre, Srsf3wt, Apoe-/-


title: HEK293_TRBP knock-out_mock_total_Rep2_Experiment1


title: SH-SY5Y cells _RBEE  pre-treatment 24h_No_LPS induction 24h_rep1

value: SH-SY5Y cells (Resource No. RCB0535, RIKEN BRC, Tsukuba, Ibaraki, Japan)


title: SH-SY5Y cells _ No pre-treatment 24h_No_LPS induction 24h_rep1

description: Gene expression data from SH-SY5Y cells, no pre-treated with RBEE  for 24 h and then no LPS-induced for 24h

source_name: SH-SY5Y cells were treated with 0 mg/mL RBEE  for 24 h and then induced with LPS solution (0 ng/mL) for 24 h


title: Pseudomonas putida, Day 15, H-3, rep 3

description:
KT2440; ATCC47054
Pp_H3_D15_R3

value: H-3 exposure


title: HEK293_PACT knock-out_dsGFPd_total_Rep2_Experiment1

value: additional PACT knock-out


title: oxBMDM, WT, bio rep 3


title: Pseudomonas putida, Day 15, H-3, rep 2

description:
KT2440; ATCC47054
Pp_H3_D15_R2


title: SH-SY5Y cells _No pre-treatment 24h_No_LPS induction 24h_rep1


title: HEK293_PACT knock-out_dsGFPc_total_Rep2_Experiment1


title: oxBMDM, WT, bio rep 2


title: Pseudomonas putida, Day 15, H-3, rep 1

description:
KT2440; ATCC47054
Pp_H3_D15_R1


title: HEK293_PACT knock-out_mock_total_Rep2_Experiment1

value: mock


title: RNA_CJ_015 Bef Holstein p7

city: Bron

first: Bertrand

middle: Pierre-Yves

last: PAIN

address: 18, Avenue du  Doyen Lépine

country: France

institute: U1208, INSERM

description: Library name: RNA_CJ_015_R1.fq.gz

data_processing:
FastQ files were collected and preprocessed with fastp 0.20.1, which enabled UMI preprocessing and polyA trimming.
Reads were mapped to the transcriptome reference genome (Ens109, Bos_taurus.ARS-UCD1.2) using TopHat (v2.1.1) and Bowtie2 (v2.3.4.1). To generate the gene count table, featureCounts (v1.6.0) was used. Analysis of differential expression was performed using the DESeq2 package (v1.28.1) (Anders and Huber, 2010).
edgeR; shiny
Assembly: Bos taurus: Ens109, Bos_taurus.ARS-UCD1.2
Supplementary files format and content: Tab-delimited text file (cnt) includes raw counts for each sample
Supplementary files format and content: CSV file include FPKM values each sample

organism: Bos taurus

source_name: Dermal biopsy

growth_protocol: Thawed bovine embryos were placed in 24 wells containing mitomycine C treated BEF with N2B27 medium supplemented with inhibitors of GSK3 and MEK/ERK and WNT3. Once established, the 2iTS cells were routinely passaged every 3-4 days in TrypLe (Invitrogen) for adherent ones with a splitting ratio of around 1/6 and by dilution of 1/6 for the cells in suspension.

extract_protocol:
RNAs from bEF, 2iTS, adherent and non adherent cells, were extracted with TRIzol Reagent (Life Technologies, # 15596018) following the instructions provided by the manufacturers.
Libraries for RNAseq analysis were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) for sequencing on Illumina platforms according to the supplier protocol using the unique molecular identifier (UMI) option (6 nucleotides).

treatment_protocol: no treatment

value: Dermal biopsy

value: Fibroblast

value: Holstein


title: HEK293_Parental_dsGFPd_total_Rep2_Experiment1

value: Parental

value: dsGFPd


title: oxBMDM, WT, bio rep 1

value: bone marrow-derived macrophages


title: HEK293_Parental_dsGFPc_total_Rep2_Experiment1


title: Pseudomonas putida, Day 1, H-3, rep 3

description:
KT2440; ATCC47054
Pp_H3_D1_R3

value: bacterial

value: WT


title: RNA_CJ_014 Bef Holstein p5

description: Library name: RNA_CJ_014_R1.fq.gz


title: Pseudomonas putida, Day 1, H-3, rep 2

description:
KT2440; ATCC47054
Pp_H3_D1_R2


title: aortic root, KO, bio rep 4

source_name: aortic root

value: aortic root

value: LysMCre, Srsf3flox, Apoe-/-

value: High cholesterol diet, 12 weeks


title: aortic root, KO, bio rep 3


title: RNA_CJ_013 Bef Holstein p4

description: Library name: RNA_CJ_013_R1.fq.gz


title: HEK293_Parental_mock_total_Rep2_Experiment1

value: pOSI17 PKR knock-out


title: RNA_CJ_012 N°34 Surnageante p14

description: Library name: RNA_CJ_012_R1.fq.gz

source_name: Embryo

value: Embryo

value: Trophoblastic cell


title: Pseudomonas putida, Day 1, H-3, rep 1

description:
KT2440; ATCC47054
Pp_H3_D1_R1

value: H-3 exposure

value: Day 1


title: aortic root, KO, bio rep 2


title: Pseudomonas putida, Day 15, Pu-239, rep 3

description:
KT2440; ATCC47054
Pp_Pu239_D15_R3

value: Pu-239 exposure

value: Day 15


title: HEK293_PACT, TRBP knock-out_dsGFPc_total_Rep1_Experiment1

value: additional PACT, TRBP knock-out

value: dsGFPc


title: aortic root, KO, bio rep 1


title: RNA_CJ_010 N°34 Surnageante p10

description: Library name: RNA_CJ_010_R1.fq.gz


title: RNA_CJ_011 N°34 Surnageante p11

description: Library name: RNA_CJ_011_R1.fq.gz


title: HEK293_PACT, TRBP knock-out_dsGFPd_total_Rep1_Experiment1


title: aortic root, WT, bio rep 4

value: LysMCre, Srsf3wt, Apoe-/-


title: Pseudomonas putida, Day 15, Pu-239, rep 1

description:
KT2440; ATCC47054
Pp_Pu239_D15_R1


title: HEK293_PACT, TRBP knock-out_mock_total_Rep1_Experiment1

value: mock


title: aortic root, WT, bio rep 3


title: RNA_CJ_009 N°34 Adhérente p16

description: Library name: RNA_CJ_009_R1.fq.gz


title: HEK293_TRBP knock-out_dsGFPd_total_Rep1_Experiment1

value: additional TRBP knock-out

value: dsGFPd


title: aortic root, WT, bio rep 2


title: HEK293_TRBP knock-out_dsGFPc_total_Rep1_Experiment1


title: Pseudomonas putida, Day 1, Pu-239, rep 1

description:
KT2440; ATCC47054
Pp_Pu239_D1_R1

value: bacterial

value: WT


title: RNA_CJ_007 N°34 Adhérente p11

description: Library name: RNA_CJ_007_R1.fq.gz


title: HEK293_TRBP knock-out_mock_total_Rep1_Experiment1


title: RNA_CJ_006 N°20 Surnageante p16

description: Library name: RNA_CJ_006_R1.fq.gz


title: Pseudomonas putida, Day 1, Pu-239, rep 2

description:
KT2440; ATCC47054
Pp_Pu239_D1_R2


title: aortic root, WT, bio rep 1

value: aortic root


title: HEK293_PACT knock-out_dsGFPd_total_Rep1_Experiment1

value: additional PACT knock-out


title: RNA_CJ_005 N°20 Surageante p13

description: Library name: RNA_CJ_005_R1.fq.gz


title: HEK293_PACT knock-out_dsGFPc_total_Rep1_Experiment1

value: pOSI17 PKR knock-out


title: Pseudomonas putida, Day 15, Control, rep 3

description:
KT2440; ATCC47054
Pp_Con_D15_R3

value: Control


title: Pseudomonas putida, Day 15, Control, rep 2

description:
KT2440; ATCC47054
Pp_Con_D15_R2


title: gADSCs YAP_3

city: Hohhot

first: Dongjun

last: Liu

state: Inner Mongolia

address: 235 Daxue west road  Saihan District

institute: Inner Mongolia University

description: Library name: Sample 6

data_processing:
The libraries were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated.. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed 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: 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 .
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Capra hircus

source_name: Adipose mesenchymal stem cells

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Adipose mesenchymal stem cells

value: overexpressing YAP

value: adipogenic differentiation


title: RNA_CJ_004 N°20 Surageante p11

description: Library name: RNA_CJ_004_R1.fq.gz

value: Embryo

value: Trophoblastic cell


title: Pseudomonas putida, Day 15, Pu-239, rep 2

description:
KT2440; ATCC47054
Pp_Pu239_D15_R2

value: Pu-239 exposure

value: Day 15


title: gADSCs YAP_2

description: Library name: Sample 5


title: gADSCs YAP_1

description: Library name: Sample 4


title: HEK293_PACT knock-out_mock_total_Rep1_Experiment1


title: RNA_CJ_003 N°20 Adhérente p18

description: Library name: RNA_CJ_003_R1.fq.gz


title: Pseudomonas putida, Day 1, Control, rep 3

description:
KT2440; ATCC47054
Pp_Con_D1_R3

value: Day 1


title: RNA_CJ_008 N°34 Adhérente p12

description: Library name: RNA_CJ_008_R1.fq.gz


title: HEK293_Parental_dsGFPd_total_Rep1_Experiment1

value: Parental


title: gADSCs Control_2

description: Library name: Sample 2


title: gADSCs Control_3

description: Library name: Sample 3


title: Pseudomonas putida, Day 15, Control, rep 1

description:
KT2440; ATCC47054
Pp_Con_D15_R1


title: Pseudomonas putida, Day 1, Pu-239, rep 3

description:
KT2440; ATCC47054
Pp_Pu239_D1_R3


title: RNA_CJ_002 N°20 Adhérente p14

description: Library name: RNA_CJ_002_R1.fq.gz


title: HEK293_Parental_dsGFPc_total_Rep1_Experiment1

value: dsGFPc


title: Pseudomonas putida, Day 1, Control, rep 2

description:
KT2440; ATCC47054
Pp_Con_D1_R2


title: RNA_CJ_001 N°20 Adhérente p13

description: Library name: RNA_CJ_001_R1.fq.gz


title: Pseudomonas putida, Day 1, Control, rep 1

description:
KT2440; ATCC47054
Pp_Con_D1_R1


title: gADSCs Control_1

description: Library name: Sample 1


title: HEK293_Parental_mock_total_Rep1_Experiment1

value: mock


title: Tumor single-cell multiome ATAC

status: Public on Mar 30 2025

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

institute: Japanese Foundation for Cancer Research

description: 10x Genomics

library_source: genomic single cell

data_processing:
All analysises were performed using Cell Ranger Arc software 2.0.1
Assembly: mm10
Supplementary files format and content: h5 matrix and tab-separated fragment files

source_name: primary

extract_protocol:
Tumor cells were isolated from the cerebellum of adulthood using percoll gradient centrifugation. Nuclei isolation was performed according to the manufacturer’s protocol (CG000366 Rev C, 10x Genomics). Of note, the incubation with the lysis buffer was optimized to 3 minutes. Targeted Nuclei Recovery was 5000 or 10000, depending on the number of isolated nuclei.
Library preparation was performed according to the manufacturer’s protocol (CG000338 RevE, 10x Genomics).

value: primary

value: medulloblastoma


title: Tumor single-cell multiome RNA

description: 10x Genomics

molecule: cytoplasmic RNA


title: Chd7_KO H3K27me3 rep3

data_processing:
Fastq files were generated by RTA in Illumina NextSeq 550.
Adaptor sequence were trimmed by Skewer
Reads were mapped to mm10 genome by bowtie2
Peak call was performed by MACS2
Assembly: mm10
Supplementary files format and content: peak summit data
Library strategy: Cut&Tag

extract_protocol:
CUT&Tag library preparation was performed using percoll-purified tumor cells according to the online protocol from EpiCypher with minor modifications. Briefly, nuclei from 1 x 105 cells were used in each reaction.
Of note, wheat germ agglutinin beads (BP530, Bangs Laboratories) were used instead of Concanavalin A beads to absorb the nuclei. After the binding of primary antibodies and secondary antibody (EpiCypher), targeted chromatin tagmentation was achieved by CUTANA pAG-Tn5 (EpiCypher). Reaction was terminated by adding 1.66 μl of 0.5M EDTA, 0.5 μl of 10% SDS and 0.42 μl of 20 mg/ml Proteinase K directly into each reaction, followed by incubation at 55℃ for 1 hour. Then, DNA fragments were purified by Zymo DNA Clean & Concentrator-5 kit (D4014, Zymo). Transposed DNA fragments were amplified by a 2-step PCR amplification as described in ATAC-seq library preparation. Of note, the final concentration of primers used in library PCR was adjusted to 400 nM


title: Chd7_KO H3K27ac rep3


title: DKO single cell RNA

description:
Library name: DKO single cell RNA
10X Genomics

data_processing:
All analysises were performed using Cell Ranger software v8
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

value: Ptch1 and Chd7 double KO


title: Chd7_KO H3K4me1 rep3


title: Chd7_KO H3K27me3 rep2


title: Chd7_KO H3K27ac rep2


title: Chd7_KO H3K4me1 rep2


title: Chd7_KO H3K4me3 rep2


title: Chd7_KO H3K27me3 rep1


title: Chd7_KO H3K4me3 rep1


title: Chd7_KO H3K27ac rep1


title: Kmt2c_KO H3K27ac rep2


title: Kmt2c_KO H3K4me3 rep3


title: Kmt2c_KO H3K27ac rep3


title: Kmt2c_KO H3K4me1 rep3


title: Chd7_KO H3K4me1 rep1


title: Kmt2c_KO H3K27me3 rep3


title: Kmt2c_KO H3K27me3 rep2


title: Kmt2c_KO H3K4me1 rep2


title: Kmt2c_KO H3K4me3 rep1


title: Genomic DNA from 39 weeks IVF Sperm 1

description:
Bisulfite treated
39wks_IVF_1

source_name: Sperm

value: Sperm

value: IVF


title: Kmt2c_KO H3K4me1 rep1


title: Kmt2c_KO H3K27me3 rep1


title: NC H3K4me3 rep3

value: NC


title: NC H3K4me1 rep3


title: Kmt2c_KO H3K27ac rep1


title: NC H3K27me3 rep2


title: NC H3K27ac rep2


title: NC H3K27ac rep3


title: NC H3K4me3 rep2


title: NC H3K4me1 rep2


title: NC H3K4me3 rep1


title: NC H3K27me3 rep1


title: Tumor Chd7_KO rep2

data_processing:
Fastq files were generated by RTA in Illumina NextSeq 550.
Adaptor sequence were trimmed by Skewer
Reads were mapped to mm10 genome by bowtie2
PCR de-duplicate was performed by Picard
Peak call was performed by MACS2
Assembly: mm10
Supplementary files format and content: peak summit data

extract_protocol:
To isolate GNP and hyperplasia cells from P7 and P28 Atoh1EGFP cerebella, the tissues were dissociated, followed by percoll gradient centrifugation as previously described. For tumor cell isolation, tumor-bearing cerebella was dissociated with Trypsin/DNase and filtrated though 40 μm cell strainer (CORNING). Subsequently, the cells were suspended in cold DPBS containing 1% BSA for cell sorting of EGFP positive cells with FACSAriaTM sorters (BD Biosciences).
Libraries were prepared with the Omni-ATAC protocol.


title: Chd7_KO H3K4me3 rep3


title: Tumor ATAC_3


title: NC H3K27me3 rep3


title: NC H3K27ac rep1


title: Tumor ATAC_2


title: Tumor ATAC_1


title: Ptch1GNP ATAC_3

value: granule neuron progenitors


title: PNC ATAC_2

value: hyperplasia


title: PNC ATAC_3


title: PNC ATAC_1


title: Tumor Chd7_KO rep1


title: NC H3K4me1 rep1


title: Ptch1GNP ATAC_1


title: Ptch1GNP ATAC_2


title: GNP SAG(-) rep1

data_processing:
The row reads were trimmed to remove adaptor sequences using Skewer (v0.2.2).
The reads were mapped to the mm10 genome using STAR (v.2.7.8a).
The mapped reads were then counted using featureCounts (v.2.0.10).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts for each Sample

extract_protocol:
Total RNAs extracted with RNeasy Plus Mini Kit (74134, QIAGEN) were used for RNA-seq differential expression analysis in some experiments.
For RNA sequencing, 450-700 ng of the RNA was used to prepare each library using the SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara, 634874), according to the provided guidelines.

value: control


title: Group3 medulloblatoma rep3


title: Kmt2c_KO H3K4me3 rep2


title: GNP SAG(-) rep3


title: GNP SAG(-) rep2


title: Group3 medulloblatoma rep1


title: GNP SAG(+) rep1

value: SAG


title: sgPtch1-sgKmt2c tumors rep2


title: sgPtch1-sgKmt2c tumors rep3


title: sgPtch1-sgKmt2c tumors rep1


title: sgPtch1-sgChd7 tumors rep3


title: sgPtch1-sgChd7 tumors rep2


title: GNP SAG(+) rep3


title: GNP SAG(+) rep2


title: sgPtch1 induced tumors rep3


title: sgPtch1 induced tumors rep2


title: Atoh1EGFP,Ptch1+/- spontaneous tumor rep3


title: Atoh1EGFP,Ptch1+/- spontaneous tumor rep2


title: Black BrafCA/+ nevus skin, replicate 1, scRNAseq

city: Irvine

first: Anand

middle: K

last: Ganesan

state: CA

address: 839 Health Science Rd

institute: University of California, Irvine

data_processing:
FASTQ files were generated from Illumina’s binary base call raw output with Cell Ranger’s (v2.1.0; RRID:SCR_017344) ‘cellranger mkfastq’ command and the count matrix for each sample was produced with ‘cellranger count‘.
Downstream bioinformatic analysis was conducted using Seurat78. For quality control, cells with fewer than 200 detected genes and genes detected in less than 3 cells were discarded. We calculated the percent mitochondrial gene expression and kept cells with less than 15% mitochondrial gene expression, and cells with fewer than 4000 genes per cell.
Assembly: mm10
Supplementary files format and content: normalized count matrix, barcodes, and genes for two merged Seurat Objects ( whole skin tumor and skin in Fig2B, and NC-derived subset of transplanted tumors in Fig 3B)

source_name: skin

extract_protocol:
The mice were euthanized, shaved, and depilated. For non-tumor bearing samples, a 2 by 3 cm section of the back skin was retrieved, and the fat scraped off from the underside. For melanoma-bearing samples, the skin sample on top of the tumor piece was also collected, with the mouse-matched adjacent skin next to the tumor (termed “tumor-adjacent skin”) as sample-matched control. The tumor or skin sample was then physically minced, and suspended in a gentle-macs C-tube dissociation buffer (5mL of RPMI, 50 µL  of liberase 0.25 mg/mL, 116 µL of Hepes 23.2 mM, 116 µL of Sodium Pyruvate 2.32 mM, 500 µL of Collagenase :Dispase 1 mg/mL) for 50 min at 37°C incubation with gentle agitation at a speed of 85-90rpm. After initial 50 minute digestion i, 10 µL of DNaseI (23 µL was added for another 10 min of 37°C agitated incubation and then inactivated with 400 µL of fetal bovine serum and 10 µL of EDTA (1 mM). The tissue suspension was further dissociated mechanically with GentleMACS by running the setting m_imptumor_04.01 twice. The digested suspensions were filtered twice through a 70 mm strainer and dead cells removed by centrifugation at 300 x g for 15 min. The live cells were washed with 0.04% UltraPure BSA:PBS buffer, gently re-suspended in the same buffer, and counted using trypan blue and cell counter.
Libraries were prepared using the Chromium Single Cell 3’ v2 protocol (10X Genomics). Briefly, individual cells and gel beads were encapsulated in oil droplets where cells were lysed and mRNA was reverse transcribed to 10X barcoded cDNA. Adapters were ligated to the cDNA followed by the addition of the sample index. Prepared libraries were sequenced using paired end 100 cycles chemistry for the Illumina HiSeq 4000.

treatment_protocol: Conditional allele BrafCA, Tyr::CreER, and/or Ptenlox4-5/+ mice (RRID:MGI:5902125, from Dr. Martin McMahon) were backcrossed with C57BL/6J (JAX 000664) for greater than 5 generations. Conditional allele BrafCA, Tyr::CreER, and/or Ptenlox4-5/+ congenic C57BL/6J mice were then crossed with Albino B6(Cg)-Tyrc-2J/J (JAX 000058) to create albino BrafCA/+ melanoma and nevi bearing mice. Topical 4-hydroxytamoxifen (4-OHT; 25 mg/mL or 75 mg/mL in DMSO; 98% Z-isomer, Sigma-Aldrich) was administered to pups on their back at ages P2-P4. Mice were euthanized if the volume of their tumors exceeded 10% of total body volume, if tumors were significantly ulcerated, if mice were moribund, if they lost weight, if they were lethargic, or if they were unable to ambulate. All mouse procedures were approved by UCI’s IACUC.

value: skin

tag: sample location

value: mouse depilated back

tag: gender

value: Female

value: BrafCA/+; Cre+; mTmG+

tag: coat color

value: black


title: sgPtch1 induced tumors rep1

tag: cell type


title: Atoh1EGFP,Ptch1+/- spontaneous tumor rep1