title: tof1_TrAEL_seq_rep_1

city: Brighton

first: Andrea

last: Keszthelyi

address: University of Sussex, Sussex House, Falmer

department: Genome Damage and Stability Centre

institute: University of Sussex

data_processing:
UMI deduplicated mapped reads from TrAEL-SEQ experiments were generated as described in  Kara, N., Krueger, F., Rugg-Gunn, P., and Houseley, J. (2021). Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq. PLoS Biol 19, e3000886. 10.1371/journal.pbio.3000886.
Mapped reads were then analysed using SeqMonk v1.47 (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Minimum mapping quality of 1 was applied, and reads were truncated to 1 nucleotide at the 5’ end
Running windows of probe size 10 bp and step size 10 bp were generated and the reads were exported to bedgraph file
Custom made R programs were then used generate wig files with read numbers
(R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database
Supplementary files format and content: WIG files containing read numbers
Library strategy: TrAEL-SEQ

source_name: Matα ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100 tof1Δ::hphNT1

growth_protocol: For exponential experiments in glucose for TrAEL-SEQ, cells were grown at 30 °C in YP media with 40 mg/l adenine + 2% glucose to mid-log phase (~107 cells/ml).

extract_protocol:
Extraction of DNA was performed as described in Kara, N., Krueger, F., Rugg-Gunn, P., and Houseley, J. (2021). Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq. PLoS Biol 19, e3000886. 10.1371/journal.pbio.3000886.
Libraries were constructed as described in Kara, N., Krueger, F., Rugg-Gunn, P., and Houseley, J. (2021). Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq. PLoS Biol 19, e3000886. 10.1371/journal.pbio.3000886.

value: Mat{alpha} ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100 tof1{delta}::hphNT1

tag: cell cycle_stage

value: exponential

tag: carbon source

value: glucose

tag: sequencing method

value: TrAEL-seq


title: salivary DNA from intervention post 49

status: Public on Oct 21 2024

type: genomic

city: Girona

first: Anna

last: Prats-Puig

state: Girona

address: Carrer del President Francesc Macià, 65, 17190 Salt, Girona

country: Spain

institute: University School of Health and Sport

description: salivary DNA from intervention post 49

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to human Illumina 900K (EPIC) microarray using standar Illumina protocol.

scan_protocol: Arrays were imaged using the BeadArray redader (HiScan) and the strandard recommended Illumina scanner setting.

data_processing: Rn Beads package in R environment.

molecule: genomic DNA

organism: Homo sapiens

source_name: saliva

label_protocol: Protocol outlined in manufacturer's instructions.

extract_protocol: Genomic DNA was extracted from saliva using the prepIT®•L2P reagent (PT-L2P-5; DNA Genotek, USA) and 500 μL of Oragene samples, according to the manufacturer’s instructions.

tag: tissue

value: saliva

tag: Sex

value: F

tag: control/intervention

value: intervention


title: salivary DNA from intervention pre 50

description: salivary DNA from intervention pre 50


title: tof1_TrAEL_seq_rep_2

type: SRA

country: United Kingdom

library_source: genomic

organism: Saccharomyces cerevisiae

tag: strain

tag: genotype


title: WT tRF OTTR Control Rep 1

city: Worcester

first: Oliver

last: Rando

state: Massachusetts

address: 364 Plantation St

department: BMP

country: USA

institute: University of Massachusetts

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt v2.9, when UMI was present reads were deduplicated with seqkit v0.14.0 and UMI sequence was trimmed with cutadapt.
Trimmed reads where then mapped to sacCer3 or mm10 with tRAX using default settings.
Assembly: mm10, sacCer3
Supplementary files format and content: Each processed data file contains information about read-start/stop site, coveage, and  misinicorporation rate.

molecule: total RNA

source_name: Yeast

growth_protocol: For full length tRNA experiments, yTG66 and yTG109 were grown overnight in selective synthetic media containing 2% dextrose, saturated cultures were diluted to OD600=0.1 and grown in selective synthetic media containing 2% dextrose until they reached OD600=0.5-07. For tRF experiments, yTG72 were grown overnight in selective synthetic media containing 2% raffinose. Saturated cultures were diluted to OD600=0.1 in selective synthetic media containing 2% raffinose and grown until early-midlog (OD600= 0.3-0.4). Cells were then centrifuged and diluted in selective synthetic media containing 2% galactose to an OD600 so that they reach OD600=0.5-0.7 in 360 minutes (“WT” samples were resuspended in selective synthetic media containing 2% galactose, centrifuged, and snap frozen immediately).

extract_protocol:
Mouse RNA was extracted using standard TRIZol protocol. Yeast RNA was extracted by beadbeating in TNE buffer (50 mM Tris-Cl pH7.4, 100 mM NaCl, 10 mM EDTA), followed by an acid Phenol extraction.
Libraries were constructed following published protocols.

tag: growth media

value: SC-Ura Galactose


title: wt_TrAEL_seq_rep_2

source_name: Matα ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100

value: Mat{alpha} ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100


title: KRAS MSPCS 4 Bones_22: KrasG12D mouse mesenchymal stem and progenitor cells, replicate 4

type: RNA

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description: Gene expression from KrasG12D mouse mesenchymal stem and progenitor cells

hyb_protocol: Labeled fragments were hybridized to Affymetrix Mouse Gene ST 1.0 arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

organism: Mus musculus

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: Rosa26Cre;LSL-KrasG12D mice and their single allele littermates were raised in the animal facility of the University Medical Center of Freiburg

extract_protocol: RNA was isolated from bone marrow niche cells. RNA isolation was performed using the Qiagen AllPrep DNA/RNA Micro Kit according to the manufacturer’s protocol

treatment_protocol: Rosa26Cre;LSL-KrasG12D mice and their single allele littermates were treated with a single dose of 1mg of tamoxifen via oral gavage to induce Cre-mediated KrasG12D expression. After 5.5 weeks, mice were sacrificed by cervical dislocation under anesthesia. Bone marrow niche cells were isolated out of bone and bone marrow cell suspensions using fluorescence-activating cell sorting.

tag: cell type

value: mesenchymal stem and progenitor cells

value: Bones


title: salivary DNA from intervention pre 48

description: salivary DNA from intervention pre 48


title: KRAS OBCs 4 Bones_26: KrasG12D mouse osteoblast cells, replicate 4

description: Gene expression from KrasG12D mouse osteoblast cells

source_name: KrasG12D mouse osteoblast cells

value: osteoblast cells


title: salivary DNA from intervention pre 49

description: salivary DNA from intervention pre 49


title: KRAS OBCs 1 Bons_23: KrasG12D mouse osteoblast cells, replicate 1


title: KRAS OBCs 2 Bones_24: KrasG12D mouse osteoblast cells, replicate 2


title: KRAS OBCs 3 Bones_25: KrasG12D mouse osteoblast cells, replicate 3


title: salivary DNA from intervention post 48

description: salivary DNA from intervention post 48


title: wt_TrAEL_seq_rep_1


title: KRAS MSPCS 3 Bones_21: KrasG12D mouse mesenchymal stem and progenitor cells, replicate 3

description: Gene expression from KrasG12D mesenchymal stem and progenitor cells


title: tof1627_exp_H2A

data_processing:
Illumina basespace (https://basespace.illumina.com/home/index) was used to generate FASTQ files from the sequencing reactions.
H2A and H2AP sequences were aligned without trimming to a reference genome (R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database) using Bowtie 2 (http://bowtie bio.sourceforge.net/bowtie2/index.shtml). RFA1 reads were aligned to the same reference genome but the LTR-retrotransposons were masked.
SAM files were then converted into sorted BAM files by using SAMtools (http://samtools.sourceforge.net/)
For RFA1 analysis duplicates were then removed using picard (https://broadinstitute.github.io/picard):
BAM files were used for Model-based Analysis of ChIP-SEQ (MACS2). We used the ‘call peak’ function which also generates genome wide score data. These were used to generate fold enrichment tracks.
The data then was sorted into 50 bp bins, normalized to have a mean value of 1, smoothed moving averages indicated at each figure and used for meta data analysis and plotting using custom made R programs.
Libraries for relative copy number determination were prepared as described for the input preparation for RFA1-ChIP. Reads were aligned LTR-retrotransposon masked reference genome, duplicates were removed using picard, and reads were summed to 50 bp bins using sam- to bincount program (https://github.com/yasukasu/sam-to-bincount).
Read per million values were calculated (rDNA values ignored) and values from forward and reverse strands were summed using custom R scripts.
Assembly: (R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database
Supplementary files format and content: Wig files for ChIP enrichment (H2AP over H2A or RFA1 over input) and wig files for read per million counts of input for copy number samples

source_name: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3 TOF1::tof1-codon-optimised-627–1238Δ (natNT2)

growth_protocol: For exponential ChIP-SEQ experiments in glucose, cells were grown at 25 °C in YP media with 40 mg/l adenine + 2% glucose to mid-log phase (~107 cells/ml).  For exponential ChIP-SEQ experiments in galactose, cells were grown to ~0.7 x 107 cells/ml at 25 °C in YP media with 40 mg/l adenine + 2% raffinose first, then 2% galactose was added, and cells were further incubated to reach ~107 cells/ml before collection. Cell synchronizations were performed as described previously Schalbetter, S.A., Mansoubi, S., Chambers, A.L., Downs, J.A., and Baxter, J. (2015). Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability. Proc Natl Acad Sci U S A 112, E4565-4570. 10.1073/pnas.1505356112.. Cultures were grown in YP media with 40 ml/l adenine + 2% raffinose to midlog phase, then 10 μg/ml alpha factor (Genscript) was added to arrest cells in G1 phase. After ~120 min, when 90% of cells were unbudded (G1 phase) 2% of galactose was added. 20 minutes later 50 μg/ml doxycycline (Sigma-Aldrich) and an additional 5 μg/ml alpha factor was added. After a further 10 minutes the temperature was shifted to 37°C for 1h. Cells were released from G1-block by 3x wash with YP + 40 mg/l adenine + 2% raffinose + 2% galactose 50 μg/ml doxycycline followed by resuspension in the same media. For mitotic arrested samples, nocodozole (Sigma-Aldrich) was added to cultures at 10 μg/ml 45 minutes after time 0 min (addition of the first wash), and cells were collected at 95 min. For G1 arrested samples, 10 μg/ml alpha factor was added after 70 min and cells were collected at 160 min. Cell cycle phases were confirmed by Flow cytometry analysis (FACS)

extract_protocol:
25 ml of cultures were used per each antibody used for ChIP. Cells were washed and resuspended in YP media, then 1% formaldehyde (Sigma-Aldrich) was added, and cells were incubated for 45 min at 25°C. To quench the formaldehyde 125 mM glycine (Alfa Aesar) was added followed by 5 min incubation. Cells were then washed with cold PBS, pelleted and frozen in liquid nitrogen. For a subset of experiments (Spiked with Schizosaccharomyces pombe) normalization by adding Schizosaccharomyces pombe (S. pombe) cells containing the HO-endonuclease inducible system (AW507). Primary cultures of AW507 (described in Watson et al., Regulation of gene expression at the fission yeast Schizosaccharomyces pombe urg1 locus, Gene, 2011) were grown in EMM media supplemented with leucine (100 μg/ml) at 30°C overnight, then kept at logarithmic phase for a day, before diluting to a secondary culture to reach logarithmic phase (5x106 cells) again the next day. Cells were then pelleted and re-suspended in pre-warmed EMM supplemented with leucine, histidine and uracil (100 μg/ml each) to induce HO endonuclease (Purg1loxON). After two hours of incubation at 30°C cells were fixed and collected as described above for S. cerevisiae cells.
Pellets from liquid nitrogen were resuspended in 500 μl SDS buffer (1% SDS, 10 mM EDTA, 5M Tris HCl, cOmplete Tablets, Mini EDTA-free EASYpack (Roche), PhosSTOP (Roche)), then lysed in a FASTPREP machine, 5 rounds of 1 min at 6.5 power, with 200 μl of 0.5 mm silica beads. Silica beards were then separated and discarded and IP buffer (0.1% SDS, 1.1% Triton-X-100, 1.2 mM EDTA, 16.7 mM TRIS HCl (pH8), cOmplete Tablets, Mini EDTA-free EASYpack (Roche), PhosSTOP (Roche)) was added to the lysate to a final volume of 1 ml. Focused-Ultrasonicator (Covaris, M220) was then used to sonicate the samples (Average incident power – 7.5 Watts, Peak Incident Power – 75 Watts, Duty Factor – 10 %, Cycles/Burst – 200, Duration – 20 min). For 50 ml starting culture the supernatant was diluted to 5 ml in total. 50-50 μl of protein A Dynabeads (Invitrogen) and protein G Dynabeads (Invitrogen) were mixed and washed 3 times in IP buffer then added to the samples and was incubated for 2 h at 4°C. After discarding the beads 2-2 ml of the supernatant was incubated with either H2A 1:500 (active motif) or 1.6 μg/ml H2AP (Abcam) on a rotating wheel at 4°C for 15 – 20 h. The rest of the sample was kept for input. If RFA1 ChIP-SEQ was also performed, the volume of the starting culture was increased to 75 ml and the sample after sonication was diluted to 7.5 ml in total and 75-75 μl of protein A and G Dynabeads were used to reduce unspecific binding and RFA1 antibody (1:10000, Agrisera) was added to 2 ml of the pre-cleaned sample followed by incubation on a rotating wheel at 4°C for 15 – 20 h. 30-30 μl of protein A and G Dynabeads were washed 3x with IP buffer and was added to each antibody reaction and incubated at 4°C for 4 h. Beads were then washed at 4°C for 6 min in TSE-150 (1% Triton-X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris HCl (pH8), 150 mM NaCl), followed by TSE-500 (1% Triton-X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris HCl (pH8), 500 mM NaCl), followed by LiCl wash (0.25 M LiCl, 1% NP-40, 1% dioxycholate, 1 mM EDTA, 10 mM Tris HCl (pH8)) and finally Tris-EDTA (TE pH8). Samples were then eluted in 400 μl elution buffer, for 30 min at room temperature. Input samples were prepared from 50 μl starting material mixed with 150 μl of elution buffer (200 μl final volume). For reverse crosslinking and protease treatment NaCl (500 mM final concentration) and proteinase K (Invitrogen, 500 μg/ml final concentration) was added and incubated at 65°C overnight. RNase treatment was then performed by adding DNase-free RNase (Roche, 25 μg/ml final concentration) followed by incubation at 37°C for 30 min. DNA was then purified with Qiagen PCR purification kit.
NGS libraries were prepared using NEBnext Ultra II library kit (NEB) with 13 cycles used for PCR enrichment. AMPure XP beads were used for size selection and PCR purification. DNA yield was measured by Qubit 2.0 Fluorometer (Life technologies). For input and RFA1 libraries 34 μl from the RFA1 IP samples and 1 ng DNA in 34 ul water from the input was used as starting material. To generate complementary strand for the ssDNA first 5 μl 10 x NEB2.1 buffer and 5 μl of random primers (8N, 3 mg/ml stock) were added and the samples were boiled at 95°C for 5 minutes and immediately placed to ice for 5 minutes. 5 μl 10 x dNTP with dUTP instead of dTTP (2 mM each) and 1 μl T4 polymerase (NEB) were then added, and the mixture was incubated at 37°C in a thermal cycler for 20 min. 5 μl 0.5 M EDTA (pH 8) was immediately added to stop the reaction. This was then used to generate libraries using Ultra II library kit (NEB) with 16 cycles for PCR enrichment. Paired end sequencing was performed using NextSeq 500 (42 bp reads from each side) system. For experiments with normalization using S. Pombe cells, aliquots (~2.5 x 109 cells) of S. pombe cell pellets were resuspended in 250 μl SDS buffer, and 1/1000 volume of the original S. cerevisiae culture (corresponding to 1:10 S. pombe to S. cerevisiae ratio) was added to each S. cerevisiae samples which were then processed the same way as described above.

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 TOF1::tof1-codon-optimised-627-1238{delta} (natNT2)

value: galactose

tag: spiked with_schizosaccharomyces_pombe

value: NO

value: ChIP-seq

tag: chip antibody


title: salivary DNA from intervention post 47

description: salivary DNA from intervention post 47


title: salivary DNA from intervention post 32

description: salivary DNA from intervention post 32


title: tof1627_exp_H2AP

value: H2AS129P (1.6 μg/ml final concentration, Abcam, ab181447)


title: salivary DNA from intervention pre 32

description: salivary DNA from intervention pre 32


title: salivary DNA from intervention post 31

description: salivary DNA from intervention post 31


title: KRAS MSPCS 2 Bones_20: KrasG12D mouse mesenchymal stem and progenitor cells, replicate 2


title: tof1627_exp_sp_H2A

value: YES


title: tof1627_exp_sp_H2AP

value: exponential


title: salivary DNA from intervention pre 31

description: salivary DNA from intervention pre 31


title: salivary DNA from intervention pre 30

description: salivary DNA from intervention pre 30

value: M


title: salivary DNA from intervention post 30

description: salivary DNA from intervention post 30


title: salivary DNA from intervention pre 47

description: salivary DNA from intervention pre 47


title: KRAS Endo Cells 4 Bones_18: KrasG12D mouse endothelial cells, replicate 3

description: Gene expression from KrasG12D mouse endothelial cells

source_name: KrasG12D mouse endothelial cells

value: endothelial cells


title: salivary DNA from intervention pre 29

description: salivary DNA from intervention pre 29

value: saliva


title: KRAS Endo Cells 3 Bones_17: KrasG12D mouse endothelial cells, replicate 2


title: KRAS MSPCS 1 Bones_19: KrasG12D mouse mesenchymal stem and progenitor cells, replicate 1


title: salivary DNA from intervention post 28

description: salivary DNA from intervention post 28

value: F


title: salivary DNA from intervention pre 28

description: salivary DNA from intervention pre 28

value: intervention


title: KRAS Endo Cells1 Bones_15: KrasG12D mouse endothelial cells, replicate 4


title: tof1997_exp_sp_H2A

source_name: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3 TOF1::tof1-codon-optimised-997–1238Δ (natNT2)

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 TOF1::tof1-codon-optimised-997-1238{delta} (natNT2)


title: tof1997_exp_H2AP


title: salivary DNA from intervention pre 27

description: salivary DNA from intervention pre 27


title: KRAS CaR Cells 4 BM_29: KrasG12D mouse CXCL12-abundant reticular cells, replicate 3

description: Gene expression from KrasG12D mouse CXCL12-abundant reticular cells

value: CXCL12-abundant reticular cells

value: Bone Marrow


title: salivary DNA from intervention post 27

description: salivary DNA from intervention post 27


title: tof1997_exp_H2A


title: salivary DNA from intervention pre 26

description: salivary DNA from intervention pre 26


title: KRAS Endo Cells 2 Bones_16: KrasG12D mouse endothelial cells, replicate 1

value: Bones


title: tof1997_exp_sp_H2AP


title: TOF1wt_exp_H2A

source_name: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3 TOF1::TOF1-codon-optimised-wildtype (natNT2)

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 TOF1::TOF1-codon-optimised-wildtype (natNT2)


title: salivary DNA from intervention post 25

description: salivary DNA from intervention post 25


title: salivary DNA from intervention pre 25

description: salivary DNA from intervention pre 25


title: salivary DNA from intervention post 29

description: salivary DNA from intervention post 29


title: salivary DNA from control pre 22

description: salivary DNA from control pre 22

value: control


title: salivary DNA from control post 22

description: salivary DNA from control post 22


title: KRAS CaR Cells 1 BM_27: KrasG12D mouse CXCL12-abundant reticular cells, replicate 1


title: KRAS CaR Cells 2 BM_28: KrasG12D mouse CXCL12-abundant reticular cells, replicate 2


title: TOF1wt_exp_H2AP

value: galactose


title: Contr OBCs 4 Bones_11: WT mouse osteoblast cells, replicate 4

description: Gene expression from WT mouse osteoblast cells

source_name: WT mouse osteoblast cells

value: osteoblast cells

value: WT


title: Contr OBCs 2 Bones_9: WT mouse osteoblast cells, replicate 3


title: salivary DNA from control pre 21

description: salivary DNA from control pre 21


title: salivary DNA from control pre 19

description: salivary DNA from control pre 19


title: salivary DNA from control post 19

description: salivary DNA from control post 19


title: TOF1wt_exp_sp_H2AP

value: ChIP-seq

value: H2AS129P (1.6 μg/ml final concentration, Abcam, ab181447)


title: salivary DNA from control post 21

description: salivary DNA from control post 21


title: Contr OBCs 1 Bones_8: WT mouse osteoblast cells, replicate 2


title: Contr OBCs  Bones3_10: WT mouse osteoblast cells, replicate 1


title: TOF1wt_exp_sp_H2A

value: exponential

value: YES


title: salivary DNA from control post 16

description: salivary DNA from control post 16


title: salivary DNA from intervention post 26

description: salivary DNA from intervention post 26


title: mrc1_exp_input

source_name: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3 mrc1∆::hphNT1

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 mrc1{delta}::hphNT1

value: NO


title: salivary DNA from control post 14

description: salivary DNA from control post 14

value: saliva

value: M


title: Treatment of MCF-7 cells with 2% O2 for 24 hours rep3

city: Shenyang

first: Huanyu

last: Wu

state: Liaoning

address: No. 77 Puhe Road

department: Pathology Teaching and Research Office of Basic Medical College

country: China

institute: China Medical University

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

tag: cell line

tag: group

value: Hypoxia

tag: treatment


title: salivary DNA from control pre 14

description: salivary DNA from control pre 14


title: salivary DNA from control post 13

description: salivary DNA from control post 13

value: F


title: mrc1_exp_RFA1


title: mrc1_exp_sp_input


title: salivary DNA from control pre 13

description: salivary DNA from control pre 13


title: salivary DNA from control post 10

description: salivary DNA from control post 10


title: salivary DNA from control post 9

description: salivary DNA from control post 9


title: mrc1_exp_sp_RFA1


title: salivary DNA from control pre 10

description: salivary DNA from control pre 10


title: mrc1_expglu_sp_input

value: glucose


title: salivary DNA from control pre 16

description: salivary DNA from control pre 16


title: salivary DNA from control pre 9

description: salivary DNA from control pre 9


title: Contr MSPCS 1 Bones_4: WT mouse mesenchymal stem and progenitor cells, replicate 1

description: Gene expression from WT mouse mesenchymal stem and progenitor cells

value: mesenchymal stem and progenitor cells

value: Bones


title: salivary DNA from control post 8

description: salivary DNA from control post 8

value: control


title: mrc1_expglu_sp_RFA1


title: salivary DNA from control pre 8

description: salivary DNA from control pre 8


title: salivary DNA from control pre 7

description: salivary DNA from control pre 7


title: tof1_exp_input

source_name: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3 tof1∆::hphNT1

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 tof1{delta}::hphNT1

value: galactose


title: salivary DNA from control post 6

description: salivary DNA from control post 6


title: salivary DNA from control post 7

description: salivary DNA from control post 7


title: Contr Endo Cell 4 Bones_3: WT mouse endothelial cells, replicate 3

description: Gene expression from WT mouse endothelial cells

source_name: WT mouse endothelial cells

value: endothelial cells

value: WT


title: Contr MSPCS 4 Bones_7: WT mouse mesenchymal stem and progenitor cells, replicate 4


title: Contr Endo Cell 2 Bones_2: WT mouse endothelial cells, replicate 2


title: salivary DNA from control pre 6

description: salivary DNA from control pre 6


title: Contr MSPCS 2 Bones_5: WT mouse mesenchymal stem and progenitor cells, replicate 2


title: tof1_exp_RFA1

value: ChIP-seq


title: salivary DNA from control pre 5

description: salivary DNA from control pre 5


title: salivary DNA from control post 4

description: salivary DNA from control post 4


title: salivary DNA from control pre 4

description: salivary DNA from control pre 4


title: tof1_exp_sp_RFA1

value: exponential


title: Microbiota of lung from DM120 mice

city: Florence

first: Sara

last: Bertorello

address: Viale Gaetano Pieraccini 6

country: Italy

institute: University of Florence

description:
106093_ID2881_120-DM120-A25-H3_S668
16s rRNA v3-v4 sequencing of mice lung
feature-table.tsv

data_processing:
Demultiplexing: From raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
Primer check and trimming: qiime cutadapt trim-paired --i-demultiplexed-sequences paired-end-demux.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACHVGGGTATCTAATCC --p-discard-untrimmed --o-trimmed-sequences  trim-seqs.qza --p-cores 7 --verbose
Quality check: qiime demux summarize --i-data trim-seqs.qza --o-visualization quality --p-n 100000
Quality trimming, pair merging and ASV table creation: qiime dada2 denoise-paired --i-demultiplexed-seqs trim-seqs.qza --p-trunc-len-f 228 --p-trunc-len-r 214 --o-table Featuredada.qza --o-representative-sequences data-trunc.qza --o-denoising-stats denoising-stats.qza --p-n-threads 0
Discard sequences from host (Mus Musculus): bowtie2 -x INDEXED_mouse_GRCm39_BOWTIE2/GRCm39 -U dna-sequences.fasta --un filtered.fasta -S Microplastic_mouse_SAM.txt  -f -p 5
Taxonomic assignment: qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads import_filtered.qza --o-classification taxonomy.qza
Further analyses: R phyloseq package
Assembly: SILVA 138 V3V4 BayesClassifier
Supplementary files format and content: feature-table.tsv: CSV text file containing the abundance table
Supplementary files format and content: taxonomy.csv: CSV text file containing the complete taxonomic classification of the reference sequence
Supplementary files format and content: filtered.fasta: fasta file containing the reference sequences used for taxonomy classification

source_name: Lung

growth_protocol: Samples were sored at -80 °C before the DNA extraction. After extraction, DNA were frozen at -20 °C until sequencing.

extract_protocol:
Genomic DNA from stool and oral swab was extracted using the DNeasy PowerLyzer PowerSoil Kit (Qiagen, Hilden, Germany), while the DNA from lung and colon fresh tissue with DNeasy Blood and Tissue kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
Amplicons of the variable V3-V4 region of the bacterial 16S rRNA gene were sequenced in paired-end (2x300)

value: Lung

value: male

value: Non exposed to nanoplastic after 28 days


title: tof1_exp_sp_input

value: YES


title: Microbiota of lung from DM119 mice

description:
106092_ID2881_119-DM119-A24-G3_S667
16s rRNA v3-v4 sequencing of mice lung
feature-table.tsv


title: salivary DNA from control pre 3

description: salivary DNA from control pre 3

value: saliva


title: salivary DNA from control post 2

description: salivary DNA from control post 2


title: Microbiota of stool from DM104 mice

description:
106091_ID2881_104-DM104-A9-H1_S666
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv

source_name: Stool

value: Stool

value: Exposed to nanoplastic after 28 days


title: Contr CaR Cells 4 BM_14: WT mouse CXCL12-abundant reticular cells, replicate 3

description: Gene expression from WT mouse CXCL12-abundant reticular cells

value: CXCL12-abundant reticular cells

value: Bone Marrow


title: salivary DNA from control post 3

description: salivary DNA from control post 3

value: F


title: Contr Endo Cell 1 Bones _1: WT mouse endothelial cells, replicate 1

value: Bones


title: salivary DNA from control post 5

description: salivary DNA from control post 5

value: control


title: Contr CaR Cells 2 BM_12: WT mouse CXCL12-abundant reticular cells, replicate 1


title: Contr CaR Cells 3 BM_13: WT mouse CXCL12-abundant reticular cells, replicate 2


title: tof1_expglu_sp_input

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 tof1{delta}::hphNT1

value: glucose


title: Contr MSPCS 3 Bones_6: WT mouse mesenchymal stem and progenitor cells, replicate 3

value: mesenchymal stem and progenitor cells

value: WT


title: tof1_expglu_sp_RFA1

value: exponential

value: ChIP-seq


title: salivary DNA from control post 1

description: salivary DNA from control post 1

value: M


title: salivary DNA from control pre 1

description: salivary DNA from control pre 1


title: Microbiota of oral swab from DM142 mice

description:
105691_ID2881_142-DM142-A47-F6_S657
16s rRNA v3-v4 sequencing of mice oral swab
feature-table.tsv

source_name: Oral Swab

value: Oral Swab

value: male


title: wt_exp_RFA1

source_name: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3

value: galactose

value: NO


title: Microbiota of oral swab from DM141 mice

description:
105690_ID2881_141-DM141-A46-E6_S656
16s rRNA v3-v4 sequencing of mice oral swab
feature-table.tsv

value: Exposed to nanoplastic after 28 days


title: salivary DNA from control pre 2

description: salivary DNA from control pre 2

value: saliva


title: wt_exp_sp_input_rep2

value: YES


title: Microbiota of oral swab from DM140 mice

description:
105689_ID2881_140-DM140-A45-D6_S655
16s rRNA v3-v4 sequencing of mice oral swab
feature-table.tsv


title: Microbiota of stool from DM95 mice

description:
106090_ID2881_95-DM95-A1-G12_S665
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv

value: Stool

value: Non exposed to nanoplastic after 28 days


title: RNA-seq WT arthroconidia arthroconidia Replicate 1 FigureS4

city: San Francisco

first: Christina

last: Homer

state: CA

address: 513 Parnassus Ave, S472

institute: University of California, San Francisco

data_processing:
For RNA-Seq: Estimated counts of each transcript were calculated for each sample by alignment-free comparison against the predicted mRNA for the published Silveira genome (de Melo Teixeira et al 2022, PMID 35137016) using KALLISTO version 0.46.2 (Bray et al 2016, PMID 27043002).
Assembly: Silveira genome (de Melo Teixeira et al 2022, PMID 35137016)
Supplementary files format and content: For RNA-Seq: Processed data are Kallisto output files with estimated counts per gene.

molecule: polyA RNA

organism: Coccidioides posadasii str. Silveira

source_name: liquid culture

growth_protocol: The wildtype Coccidioides posadasii strain Silveira (NR-48944) was used for growth experiments and as the background for the generation of the ryp1∆ mutant. All manipulation of live Coccidioides strains were performed in a biosafety level 3 facility. Standard spherulation conditions: polypropylene flasks containing Converse media were inoculated with 1 x 10^6/mL arthroconidia (unless otherwise stated) and placed at 39˚C, 10 % CO2, shaking at 120 rpm.  Where noted, spherulation was induced under the same conditions with different media: DMEM (UCSF Media Core) containing 20 % FBS (Corning) or RPMI (UCSF Media Core) containing 10 % FBS. For hyphal growth, polypropylene flasks containing Converse media were inoculated with 1 x 10^6 arthroconidia/mL and grown at 25˚C (Figures 2, S2) or room temperature (RT) (Figure 4, S4) shaking at 120 rpm. All growth experiments were performed in 125 mL polypropylene flasks with 50 mL of media except for experiments in Figures 2, S2, which were performed in 1 L flasks with 350 mL of media (except for replicate 3 of ryp1∆ mutant in spherulation conditions, which was placed in 300 mL of media given limited arthroconidia stock, to maintain the same concentration across all samples) and Figures 4, S4, which were performed in 1 L flasks with 330 mL Converse for wildtype and 500 mL flasks with 100 mL Converse for ryp1∆ mutant.Arthroconidia were generated on 2x GYE agar (2% Dextrose (Fisher), 1% Yeast extract (Gibco), 1.5% Bacto-Agar (BD)) + Penicillin/Streptomycin (100 U/ml penicillin and 100 g/ml streptomycin, UCSF Media Core) in T225 tissue culture flasks for 4-6 weeks at 30˚C, 25˚C, or 37˚C. Arthroconidia were then collected through scraping and washing as previously described (Mead et al 2020, PMID 32894648) and stocks were stored in PBS until use.

extract_protocol:
For RNA-Seq: RNA from arthroconidia were collected from the same arthroconidia stock in triplicate by placing 5x10^7 arthroconidia into Trizol LS (Ambion) and bead beating for 2 minutes. For all other samples, at indicated timepoints, RNA was extracted by pelleting cells by centrifugation at 1200 x g for 5 minutes at RT, removing supernatants, and flash freezing cell pellets in liquid nitrogen. Cell pellets were resuspended in Trizol, thawed, and bead beat for 2 minutes. Samples were stored at -80˚C until all samples at all timepoints in an individual experiment had been collected. RNA was extracted using the Direct-zol RNA Miniprep Plus isolation kit (Zymo) with on-column DNAse digestion step extended for 15-30 minutes.
For RNA-Seq: Sequencing libraries were prepared using the Ultra II Directional RNA Library Prep kit with dual-indexed multiplexing barcodes with polyA selection. Library quality and adaptor dimer contamination were analyzed using Agilent High Sensitivity DNA Chip. An additional round of library size selection was performed using homemade Serapure size selection beads (Rohland et al 2012, PMID 22267522) for libraries containing significant adaptor dimers.

treatment_protocol: No additional treatments aside from the differing growth conditions above.

value: fungal cell

tag: morphology

value: arthroconidia

tag: timepoint

tag: media

value: PBS

tag: figure of related microscopy data

tag: replicate


title: wt_exp_sp_RFA1_rep2

tag: cell cycle_stage

tag: carbon source

tag: sequencing method


title: wt_exp_input

tag: strain


title: Microbiota of oral swab from DM139 mice

description:
105688_ID2881_139-DM139-A44-C6_S654
16s rRNA v3-v4 sequencing of mice oral swab
feature-table.tsv

tag: tissue

tag: Sex


title: RNA-seq WT arthroconidia arthroconidia Replicate 3 FigureS4

tag: cell type

tag: genotype

value: WT


title: wt_exp_sp_input_rep1

value: exponential

tag: spiked with_schizosaccharomyces_pombe

tag: chip antibody


title: Microbiota of oral swab from DM137 mice

description:
105686_ID2881_137-DM137-A42-A6_S652
16s rRNA v3-v4 sequencing of mice oral swab
feature-table.tsv


title: RNA-seq WT spherules 8h Replicate 3 FigureS4

value: spherules

value: Converse


title: RNA-seq WT arthroconidia arthroconidia Replicate 2 FigureS4


title: RNA-seq WT spherules 8h Replicate 2 FigureS4


title: wt_exp_sp_RFA1_rep1

value: ChIP-seq


title: Microbiota of oral swab from DM138 mice

description:
105687_ID2881_138-DM138-A43-B6_S653
16s rRNA v3-v4 sequencing of mice oral swab
feature-table.tsv

value: Oral Swab

value: male


title: RNA-seq WT spherules 8h Replicate 1 FigureS4


title: RNA-seq WT hyphae 8h Replicate 2 FigureS4

value: hyphae


title: wt_expglu_sp_input

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3

value: glucose


title: RNA-seq WT hyphae 8h Replicate 3 FigureS4


title: RNA-seq Ryp1 spherules D1 Replicate 1 FigureS4


title: Microbiota of oral swab from DM136 mice

description:
105685_ID2881_136-DM136-A41-H5_S651
16s rRNA v3-v4 sequencing of mice oral swab
feature-table.tsv


title: RNA-seq WT hyphae 8h Replicate 1 FigureS4


title: wt_expglu_sp_RFA1


title: mrc1_M_copy_number_rep1

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 mrc1{delta}::hphNT1

value: M-phase (nocodazole block)

value: galactose

value: NO


title: Microbiota of oral swab from DM135 mice

description:
105684_ID2881_135-DM135-A40-G5_S650
16s rRNA v3-v4 sequencing of mice oral swab
feature-table.tsv

value: Non exposed to nanoplastic after 28 days


title: Microbiota of oral swab from DM134 mice

description:
105683_ID2881_134-DM134-A39-F5_S649
16s rRNA v3-v4 sequencing of mice oral swab
feature-table.tsv


title: mrc1_M_copy_number_rep2


title: Microbiota of oral swab from DM133 mice

description:
105682_ID2881_133-DM133-A38-E5_S648
16s rRNA v3-v4 sequencing of mice oral swab
feature-table.tsv


title: tof1_M_copy_number_rep2

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 tof1{delta}::hphNT1


title: RNA-seq Ryp1 arthroconidia arthroconidia Replicate 2 FigureS4

value: fungal cell

value: arthroconidia

value: PBS


title: RNA-seq Ryp1 arthroconidia arthroconidia Replicate 3 FigureS4


title: RNA-seq Ryp1 spherules D1 Replicate 3 FigureS4

value: spherules


title: wt_M_copy_number_rep2

source_name: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2)

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2)


title: RNA-seq WT spherules D4 Replicate 2 FigureS4

value: WT

value: Converse


title: Microbiota of lung from DM130 mice

description:
105679_ID2881_130-DM130-A35-B5_S645
16s rRNA v3-v4 sequencing of mice lung
feature-table.tsv

value: Lung

value: male

value: Exposed to nanoplastic after 28 days


title: RNA-seq Ryp1 spherules D1 Replicate 2 FigureS4


title: RNA-seq WT spherules D4 Replicate 3 FigureS4


title: RNA-seq Ryp1 hyphae D1 Replicate 1 FigureS4

value: hyphae


title: RNA-seq Ryp1 hyphae D1 Replicate 2 FigureS4


title: RNA-seq WT spherules D4 Replicate 1 FigureS4


title: RNA-seq Ryp1 hyphae D1 Replicate 3 FigureS4


title: RNA-seq Ryp1 arthroconidia arthroconidia Replicate 1 FigureS4


title: tof1_M_copy_number_rep1

value: ChIP-seq


title: Microbiota of oral swab from DM132 mice

description:
105681_ID2881_132-DM132-A37-D5_S647
16s rRNA v3-v4 sequencing of mice oral swab
feature-table.tsv

value: Oral Swab


title: Microbiota of oral swab from DM131 mice

description:
105680_ID2881_131-DM131-A36-C5_S646
16s rRNA v3-v4 sequencing of mice oral swab
feature-table.tsv


title: wt_M_copy_number_rep1

value: M-phase (nocodazole block)

value: galactose


title: mrc1_M_H2AP_rep2

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 mrc1{delta}::hphNT1

value: NO

value: H2AS129P (1.6 μg/ml final concentration, Abcam, ab181447)


title: mrc1_M_H2A_rep2


title: RNA-seq WT spherules D2 Replicate 2 FigureS4

value: fungal cell


title: Microbiota of lung from DM129 mice

description:
105678_ID2881_129-DM129-A34-A5_S644
16s rRNA v3-v4 sequencing of mice lung
feature-table.tsv


title: RNA-seq WT spherules D2 Replicate 1 FigureS4


title: RNA-seq WT spherules D2 Replicate 3 FigureS4


title: Microbiota of lung from DM126 mice

description:
105675_ID2881_126-DM126-A31-F4_S641
16s rRNA v3-v4 sequencing of mice lung
feature-table.tsv


title: RNA-seq WT hyphae D4 Replicate 3 FigureS4


title: RNA-seq WT hyphae D4 Replicate 2 FigureS4


title: mrc1_M_H2AP_rep1


title: Microbiota of lung from DM128 mice

description:
105677_ID2881_128-DM128-A33-H4_S643
16s rRNA v3-v4 sequencing of mice lung
feature-table.tsv


title: RNA-seq WT hyphae D4 Replicate 1 FigureS4


title: RNA-seq WT hyphae D2 Replicate 2 FigureS4


title: RNA-seq WT hyphae D2 Replicate 1 FigureS4


title: Microbiota of lung from DM127 mice

description:
105676_ID2881_127-DM127-A32-G4_S642
16s rRNA v3-v4 sequencing of mice lung
feature-table.tsv


title: mrc1_M_H2A_rep1


title: RNA-seq WT hyphae D2 Replicate 3 FigureS4


title: Microbiota of lung from DM125 mice

description:
105674_ID2881_125-DM125-A30-E4_S640
16s rRNA v3-v4 sequencing of mice lung
feature-table.tsv


title: RNA-seq WT spherules D1 Replicate 1 FigureS4


title: tof1_M_H2A_rep2

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 tof1{delta}::hphNT1


title: RNA-seq WT hyphae D1 Replicate 2 FigureS4


title: Microbiota of lung from DM124 mice

description:
105673_ID2881_124-DM124-A29-D4_S639
16s rRNA v3-v4 sequencing of mice lung
feature-table.tsv

value: Non exposed to nanoplastic after 28 days


title: RNA-seq WT spherules D1 Replicate 3 FigureS4

value: spherules


title: Microbiota of lung from DM122 mice

description:
105671_ID2881_122-DM122-A27-B4_S637
16s rRNA v3-v4 sequencing of mice lung
feature-table.tsv


title: RNA-seq WT hyphae D1 Replicate 3 FigureS4

value: WT


title: tof1_M_H2AP_rep1


title: tof1_M_H2AP_rep2


title: Inverted ter ΔmatP_2, Xer recombinase

city: Gif sur Yvette

first: Elena

last: ESPINOSA

address: 1, Avenue de la Terrasse

country: France

institute: CNRS

data_processing:
Cutadapt was used to trim adapter and transposon sequences. Also, Cutadapt was used to create the files with total reads and the files with the reads in which the reporter cassette was excised.
BWA software was used for the alignment of reads on genomes
MatLab was used to create the files with the transposon hits in the genome
Assembly: N16961.fa
Assembly: MCH1.fa
Assembly: EPV496.fa
Assembly: EPV487.fa
Supplementary files format and content: Two tables per sample containing the total transposon instertion positions  and the recombined positions at a besa pair resolution, respectively
Library strategy: HiSC2 (Adapted from Tn-seq)

organism: Vibrio cholerae

source_name: O1 biovar El Tor str. N16961

growth_protocol: V. cholerae transposon libraries were grown in M9 minimal medium supplemented with 0.2% fructose, 1 μg/ml thiamine and 0.1 mM of IPTG at 37°C until exponential phase

extract_protocol:
gDNA was extracted with GenElute bacterial genomics DNA kit (Sigma-Aldrich)
Briefly, gDNA was digested with MmeI, then, fragments containing Mariner transposon were size selected using Pippinprep and custom-made adpaters were ligated. Finally, libraries were amplified and size selected using Pippinprep.

treatment_protocol: V. cholerae transposon libraries were supplemented with arabinose up to a final concentration of 0.02% to induce recombinase expression

value: O1 biovar El Tor str. N16961

value: ChapR {delta}lacZ::PBAD-xerC-invPlac-aadA1 INV(attP-dif) matP::bla

tag: recombination cassette

value: short dif-dif


title: Microbiota of lung from DM121 mice

description:
105670_ID2881_121-DM121-A26-A4_S636
16s rRNA v3-v4 sequencing of mice lung
feature-table.tsv

value: Lung

value: male

tag: treatment


title: RNA-seq WT spherules D1 Replicate 2 FigureS4

tag: morphology

value: Converse


title: Microbiota of colon from DM118 mice

description:
105667_ID2881_118-DM118-A23-F3_S635
16s rRNA v3-v4 sequencing of mice colon
feature-table.tsv

source_name: Colon

value: Colon

value: Exposed to nanoplastic after 28 days


title: MCH1ΔmatP_2,  Cre recombinase

value: MCH1 ChapR {delta}lacZ::PBAD-cre-invPlac-ble matP::bla

value: short loxP-loxP


title: Tumor 5

city: Hamburg

first: Melanie

last: Schoof

address: Martinistr. 52

institute: Research Institute Childrens Cancer Center Hamburg

hyb_protocol: 200–500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). Then, the DNA was hybridized to Illumina Human EPIC Beadchip using standard protocols.

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

data_processing: Data was noob normalized and processed with Minfi

label: cy3, cy5

source_name: DNA from FFPE tumor material

label_protocol: Standard Illumina protocol

extract_protocol: genomic DNA was extracted from FFPE tumor samples using the Maxwell DNA extraction kit according to standard instructions

tag: disease

value: HGG-MYCN tumor


title: Microbiota of lung from DM123 mice

description:
105672_ID2881_123-DM123-A28-C4_S638
16s rRNA v3-v4 sequencing of mice lung
feature-table.tsv


title: ΔmatP_2, Cre recombinase


title: Microbiota of colon from DM117 mice

description:
105666_ID2881_117-DM117-A22-E3_S634
16s rRNA v3-v4 sequencing of mice colon
feature-table.tsv


title: Microbiota of colon from DM116 mice

description:
105665_ID2881_116-DM116-A21-D3_S633
16s rRNA v3-v4 sequencing of mice colon
feature-table.tsv


title: Tumor 1


title: mrc1_G1_H2A

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 mrc1{delta}::hphNT1

value: G1-phase (alpha-factor block)

value: galactose

value: NO

value: ChIP-seq


title: Tumor 2


title: MCH1_2, Xer recombinase


title: Tumor 4


title: tof1_M_H2A_rep1

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 tof1{delta}::hphNT1

value: M-phase (nocodazole block)


title: Microbiota of colon from DM115 mice

description:
105664_ID2881_115-DM115-A20-C3_S632
16s rRNA v3-v4 sequencing of mice colon
feature-table.tsv


title: Tumor 3


title: WT_2, Xer recombinase

value: O1 biovar El Tor str. N16961


title: RNA-seq WT hyphae D1 Replicate 1 FigureS4

value: fungal cell

value: WT

value: hyphae

tag: timepoint

tag: media


title: tof1_G1_H2A_rep1


title: tof1_G1_H2A_rep2


title: mrc1_G1_H2AP

value: H2AS129P (1.6 μg/ml final concentration, Abcam, ab181447)


title: Inverted ter_2, Xer recombinase

value: short dif-dif


title: MCH1_2, Cre recombinase


title: exo-2

city: shanghai

first: Yuqiong

last: Lei

state: 上海市

address: 600 Yishan Road

institute: Shanghai jiaotong university

data_processing:
STAR is used to align clean reads to reference genome.
Assembly: GRCh38（hg38）
Supplementary files format and content: Tab-delimited text files includes FPKM values for each sample to standardize.

source_name: cell line

extract_protocol:
Use Trizol (Thermo Fisher Scientific, 15596018) to extract RNA from the samples.
Use NEBNext UltraTM RNA Library Prep Kit (NEB #E7490) to build the library, and use beads to purify the library (AMPure XP system).

value: cell line

tag: cell line

value: lung squamous carcinoma cells

value: incubated with exosomes


title: tof1_G1_H2AP_rep2

tag: cell cycle_stage


title: exo-3


title: exo-1


title: MCH1ΔmatP_2,  Xer recombinase

value: MCH1 ChapR {delta}lacZ::PBAD-xerC-invPlac-aadA1 matP::bla


title: Ctrl-2

value: incubated without exosomes


title: Microbiota of colon from DM110 mice

description:
105659_ID2881_110-DM110-A15-F2_S627
16s rRNA v3-v4 sequencing of mice colon
feature-table.tsv

value: Colon

value: male

value: Non exposed to nanoplastic after 28 days


title: Microbiota of colon from DM114 mice

description:
105663_ID2881_114-DM114-A19-B3_S631
16s rRNA v3-v4 sequencing of mice colon
feature-table.tsv

value: Exposed to nanoplastic after 28 days


title: Ctrl-3


title: wt_G1_H2AP_rep2

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3

value: G1-phase (alpha-factor block)

tag: carbon source

value: galactose

value: NO

value: ChIP-seq


title: Ctrl-1

value: WT


title: 24hr SGC-GAK-1 1uM, U2932, rep 3

city: miami

first: Jonathan

middle: H

last: Schatz

state: Florida

address: 1580 NW 10th Ave 1st floor

department: Department of Medicine

institute: university of miami

data_processing:
Picard was used to analyze the reads.
STAR was used to align the reads to Hg38.
Cutadapt was used to process the data.
Assembly: Hg38
Supplementary files format and content: tab delimited text file containing raw counts for each sample

growth_protocol: All cells were grown at 37 °C in a 5% CO2 incubator. Ly1 cells were grown in Gibco Iscove’s Modified Dulbecco’s Medium (IMDM). U2932 cells were grown in Roswell Park Memorial Institute (RPMI) 1640 Medium. Both media were supplemented with 10% FBS, 1% penicillin/streptomycin, and plasmocin.

extract_protocol:
Total RNA was extracted using the Qiagen Symphony system and quantified with Qubit.
Total RNA was prepped with the Nugen Universal Plus mRNA-Seq with NuQuant (M01485 v6) using 500ng via Qubit and 14 cycles PCR. Libraries were sequenced on Illumina Novaseq 6000 across 2 runs.  Fastq files were combined for analysis.

treatment_protocol: Cells were treated in triplicate with either DMSO (vehicle control) or SGC-GAK-1 at a concentration of 1 µM for 12 and 24 hours.

value: DLBCL

value: ABC

value: 24hr SGC-GAK-1 1uM


title: Microbiota of colon from DM109 mice

description:
105658_ID2881_109-DM109-A14-E2_S626
16s rRNA v3-v4 sequencing of mice colon
feature-table.tsv


title: Vehicle (DMSO), U2932, rep 2

value: Vehicle (DMSO)


title: tof1_G1_H2AP_rep1

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 tof1{delta}::hphNT1

tag: sequencing method

value: H2AS129P (1.6 μg/ml final concentration, Abcam, ab181447)


title: Microbiota of colon from DM113 mice

description:
105662_ID2881_113-DM113-A18-A3_S630
16s rRNA v3-v4 sequencing of mice colon
feature-table.tsv


title: wt_G1_H2A_rep3

tag: strain


title: 24hr SGC-GAK-1 1uM, U2932, rep 1


title: 12hr SGC-GAK-1 1uM, U2932, rep 3

value: 12hr SGC-GAK-1 1uM


title: Microbiota of colon from DM112 mice

description:
105661_ID2881_112-DM112-A17-H2_S629
16s rRNA v3-v4 sequencing of mice colon
feature-table.tsv

tag: tissue

value: Colon


title: wt_G1_H2AP_rep3


title: WR_7

city: Nanjing

first: Ma

last: Ce

address: weigang

department: nanjingnongyedaxue

institute: Nanjing

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing following reads: (1) reads with 5’ adapter; (2) reads without 3’ adapter or insert sequence; (3) reads with more than 10% N; (4) reads with more than 50% nucleotides with Qphred<=20; (5) reads with ploy A/T/G/C. Adapter trimming for the removal of adapter sequences from the 3’ ends of reads was also performed. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Clean reads for each sample were first mapped to a reference genome with the software HISAT2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: R498_mbkbase
Supplementary_files_format_and_content: Matrix table with fpkm for every gene and every sample

organism: Oryza sativa

source_name: filling panicles

growth_protocol: All the tested lines were routinely planted in the experimental field of Dafeng base.

extract_protocol:
RNA library for lncRNA-seq was prepared as rRNA depletion and stranded method. Briefly, the ribosomal RNA was depleted from total RNA using the rRNA Removal Kit following manufacturer’s instruction. RNA was then fragmented into 250~300 bp fragments, and first strand cDNA was reversetranscribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP). RNA was degraded using RNase H, and second strand cDNA was synthesised using DNA polymerase I and dNTPs (dATP, dUTP, dCTP and dGTP). Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/ polymerase activities. After adenylation of 3’ ends of DNA fragments,  equencing adaptors were ligated to the cDNA. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Uridine digestion was performed using Uracil-N-Glycosylase, which was followed by the cDNA amplification using PCR
RNA librarys were prefared for secquencing using standard Illumina protocls

treatment_protocol: Three replicates were setted.

value: filling panicles

tag: line

value: WR (WFB X RFB)


title: WR_8


title: wt_G1_H2A_rep2


title: Vehicle (DMSO), U2932, rep 3

tag: cell type


title: 12hr SGC-GAK-1 1uM, U2932, rep 2

tag: genotype


title: Vehicle (DMSO), U2932, rep 1


title: Microbiota of colon from DM111 mice

description:
105660_ID2881_111-DM111-A16-G2_S628
16s rRNA v3-v4 sequencing of mice colon
feature-table.tsv

tag: Sex

value: male

value: Non exposed to nanoplastic after 28 days


title: WR_9


title: 24hr SGC-GAK-1 1uM, U2932, rep 2


title: 12hr SGC-GAK-1 1uM, U2932, rep 1


title: wt_G1_H2A_rep1

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3

value: G1-phase (alpha-factor block)

tag: spiked with_schizosaccharomyces_pombe

tag: chip antibody


title: Microbiota of colon from DM108 mice

description:
105657_ID2881_108-DM108-A13-D2_S625
16s rRNA v3-v4 sequencing of mice colon
feature-table.tsv

tag: treatment


title: mrc1_exp_H2AP

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 mrc1{delta}::hphNT1

value: exponential

value: galactose

value: NO


title: Microbiota of colon from DM107 mice

description:
105656_ID2881_107-DM107-A12-C2_S624
16s rRNA v3-v4 sequencing of mice colon
feature-table.tsv


title: wt_G1_H2AP_rep1

value: ChIP-seq


title: 12hr SGC-GAK-1 1uM, Ly1, rep 3

value: DLBCL

value: GCB


title: Microbiota of stool from DM103 mice

description:
105652_ID2881_103-DM103-A8-G1_S621
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv

value: Stool

value: Exposed to nanoplastic after 28 days


title: Microbiota of stool from DM102 mice

description:
105651_ID2881_102-DM102-A7-F1_S620
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv


title: mrc1_exp_H2A


title: 24hr SGC-GAK-1 1uM, Ly1, rep 2

value: 24hr SGC-GAK-1 1uM


title: WR_3

source_name: young seedlings

value: young seedlings


title: Microbiota of stool from DM106 mice

description:
105655_ID2881_106-DM106-A11-B2_S623
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv


title: WR_6

source_name: young panicles

value: young panicles


title: WR_5

value: WR (WFB X RFB)


title: Microbiota of stool from DM105 mice

description:
105654_ID2881_105-DM105-A10-A2_S622
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv

value: male


title: mrc1_exp_sp_H2A

value: YES


title: 24hr SGC-GAK-1 1uM, Ly1, rep 3


title: Vehicle (DMSO), Ly1, rep 3

value: Vehicle (DMSO)


title: WR_4


title: mrc1_exp_sp_H2AP

value: H2AS129P (1.6 μg/ml final concentration, Abcam, ab181447)


title: mrc1_expglu_sp_H2AP

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 mrc1{delta}::hphNT1

value: glucose


title: Vehicle (DMSO), Ly1, rep 2


title: mrc1_expglu_sp_H2A

value: exponential


title: WR_1


title: 12hr SGC-GAK-1 1uM, Ly1, rep 2

value: 12hr SGC-GAK-1 1uM


title: ARS517del_tof1_exp_H2A

source_name: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3  ars517∆::natNT2 tof1∆::hphNT1

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3  ars517{delta}::natNT2 tof1{delta}::hphNT1

value: galactose

value: NO

value: ChIP-seq


title: Microbiota of stool from DM101 mice

description:
105650_ID2881_101-DM101-A6-E1_S619
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv

value: Stool

value: Exposed to nanoplastic after 28 days


title: Microbiota of stool from DM100 mice

description:
105649_ID2881_100-DM100-A5-D1_S618
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv

value: Non exposed to nanoplastic after 28 days


title: RY308_9

value: filling panicles


title: Microbiota of stool from DM99 mice

description:
105648_ID2881_99-DM99-A4-C1_S617
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv


title: ARS517del_tof1_exp_sp_H2A


title: Microbiota of stool from DM98 mice

description:
105647_ID2881_98-DM98-A3-B1_S616
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv


title: RY308_8


title: RY308_7


title: ARS517del_tof1_exp_H2AP


title: Microbiota of stool from DM97 mice

description:
105646_ID2881_97-DM97-A2-A1_S615
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv


title: 12hr SGC-GAK-1 1uM, Ly1, rep 1

value: DLBCL

value: GCB


title: WR_2

value: young seedlings

value: WR (WFB X RFB)


title: Vehicle (DMSO), Ly1, rep 1

value: Vehicle (DMSO)


title: ARS517del_tof1_exp_sp_H2AP

value: YES

value: H2AS129P (1.6 μg/ml final concentration, Abcam, ab181447)


title: Microbiota of stool from DM96 mice

description:
105645_ID2881_96-DM96-A1-H12_S614
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv

value: male


title: ARS517del_exp_H2A

source_name: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3 ars517∆::natNT2

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 ars517{delta}::natNT2

value: exponential


title: ARS517del_exp_H2AP

value: galactose


title: RY308_5

value: young panicles


title: Microbiota of stool from DM94 mice

description:
105643_ID2881_94-DM94-A1-F12_S613
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv

value: Exposed to nanoplastic after one week


title: Microbiota of stool from DM93 mice

description:
105642_ID2881_93-DM93-A1-E12_S612
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv

value: Stool


title: 24hr SGC-GAK-1 1uM, Ly1, rep 1

value: 24hr SGC-GAK-1 1uM


title: ARS517del_exp_sp_H2A

value: ChIP-seq


title: Microbiota of stool from DM92 mice

description:
105641_ID2881_92-DM92-A1-D12_S611
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv


title: RY308_4


title: RY308_3


title: brain, ST multiple sclerosis, 9

city: Mannheim

first: Lucas

last: Schirmer

address: Theodor-Kutzer-Ufer 1-3

institute: University of Heidelberg

description:
Fresh Frozen ST 10X Genomics
ST_MS497I

data_processing:
*library strategy: Spatial Transcriptomics
The demultiplexing of the data was done using SpaceRanger software (10x – version 2.0.0), creating FASTQ files. These files were then used by SpaceRanger count to perform alignment with the human reference genome GRCh38-2020-A, tissue detection, fiducial detection and barcode/UMI counting generating a spatial gene count matrix per slide.
The cell2location (v0.1.3)74 package was used to calculate cell type abundances for each spot. Based on the annotated snRNA-seq atlas, reference expression signatures of major cell types were inferred leveraging regularized negative binomial regressions. Then, each slide was deconvoluted using hierarchical bayesian models with the following hyperparameters: N_cells_per_location=5 and detection_alpha=20. Afterwards, cell type proportions were calculated per spot by dividing the abundance of a given cell type by the total sum of abundances of a given spot.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values and matrix files

source_name: brain

extract_protocol:
After being imaged to do a general morphological analysis and for future spatial alignment of the data, the samples were enzymatically permeabilized for 18 min. This time was assessed using the 10x Visium Tissue Optimization kit (PN-1000191) and following the protocol CG000238 Rev D.
The generation of the libraries was performed according to the protocol CG000239 Rev D, using the Gene Expression Reagent kit (PN-1000186), the Library Construction Kit (PN-1000190) and the Dual Index Plate TT Set A (PN-1000215). To assess the correct amplification of the cDNA, QuantStudio 3 from ThermoFisher was used. For full length of cDNA and indexed libraries analysis 4200 TapeStation System from Agilent was used. The seven libraries were loaded at 300pM and sequenced on a NovaSeq 6000 System from Illumina with a sequencing depth of 250 million reads per sample. Sequencing was performed at Institute of Clinical Biology (IKMB, Kiel). The demultiplexing of the data was done using SpaceRanger software (10x – version 1.2.2), creating Fastq files. These files are then used by SpaceRanger count to perform alignment with the human reference genome, tissue detection, fiducial detection and barcode/UMI counting.

value: brain

value: Female

tag: age

value: Glial cells

tag: lesion type

value: Chronic Inactive

tag: condition

value: MS


title: ARS517del_exp_sp_H2AP


title: RY308_2

value: young seedlings


title: brain, ST multiple sclerosis, 10

description:
Fresh Frozen ST 10X Genomics
ST_MS497T


title: brain, ST multiple sclerosis, 11

description:
Fresh Frozen ST 10X Genomics
ST_MS549H

value: Male


title: brain, ST multiple sclerosis, 12

description:
Fresh Frozen ST 10X Genomics
ST_MS549T


title: RY308_1


title: tof1_exp_H2AP

source_name: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3 tof1∆::hphNT1

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 tof1{delta}::hphNT1

value: NO

value: H2AS129P (1.6 μg/ml final concentration, Abcam, ab181447)


title: RY308_6


title: RY998_9

value: filling panicles


title: tof1_exp_H2A

value: exponential

value: galactose


title: brain, ST multiple sclerosis, 8

description:
Fresh Frozen ST 10X Genomics
ST_MS411

value: Chronic Active


title: Microbiota of stool from DM89 mice

description:
105638_ID2881_89-DM89-A1-A12_S608
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv

value: Stool

value: male

value: Exposed to nanoplastic after one week


title: brain, ST multiple sclerosis, 7

description:
Fresh Frozen ST 10X Genomics
ST_MS377I

value: brain


title: brain, ST multiple sclerosis, 6

description:
Fresh Frozen ST 10X Genomics
ST_MS377T

value: Female


title: Microbiota of stool from DM88 mice

description:
105637_ID2881_88-DM88-A1-H11_S607
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv

value: Non exposed to nanoplastic after one week


title: RY998_7


title: tof1_exp_sp_H2AP_rep2

value: YES

value: ChIP-seq


title: tof1_exp_sp_H2A_rep1


title: RY998_6

value: young panicles


title: brain, ST multiple sclerosis, 4

description:
Fresh Frozen ST 10X Genomics
ST_MS229

value: Male

value: Glial cells

value: MS


title: Microbiota of stool from DM86 mice

description:
105635_ID2881_86-DM86-A1-F11_S605
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv


title: tof1_exp_sp_H2AP_rep1

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 tof1{delta}::hphNT1

value: H2AS129P (1.6 μg/ml final concentration, Abcam, ab181447)


title: Microbiota of stool from DM91 mice

description:
105640_ID2881_91-DM91-A1-C12_S610
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv


title: RY998_5


title: Microbiota of stool from DM90 mice

description:
105639_ID2881_90-DM90-A1-B12_S609
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv


title: brain, ST multiple sclerosis, 3

description:
Fresh Frozen ST 10X Genomics
ST_MS197U


title: tof1_expglu_sp_H2A

value: exponential

value: glucose


title: Microbiota of stool from DM84 mice

description:
105633_ID2881_84-DM84-A1-D11_S603
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv


title: RY998_4


title: tof1_exp_sp_H2A_rep2

value: galactose


title: wt_exp_H2A

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3

value: NO


title: Microbiota of stool from DM83 mice

description:
105632_ID2881_83-DM83-A1-C11_S602
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv

value: Stool

value: male


title: RY998_3

value: young seedlings


title: brain, ST control,6

description:
Fresh Frozen ST 10X Genomics
ST_CO96

value: brain

value: Female

value: Control


title: brain, ST multiple sclerosis, 2

description:
Fresh Frozen ST 10X Genomics
ST_MS197D

value: Chronic Active


title: shMETTL3, 3

city: Richmond

first: Daniel

last: Del Valle-Morales

state: VA

address: 417 N 11th St

department: Division of Pulmonary Diseases and Critical Care Medicine

institute: Virginia Commonwealth University

data_processing:
Raw sequencing reads in FASTQ format were quality trimmed, and adapters were removed using Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed reads were then mapped to the human genome (HG38 assembly) using HISAT2 (v2.1.0). Afterward, the mapped reads in SAM format were converted into BAM format, sorted (for coordinates), and indexed using Samtools (v1.12). Finally, gene quantification was performed by FeatureCounts (v2.0.0) using Gencode (v39) GTF annotation file.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes processed read counts in reads per million (RPM)

source_name: Lung

growth_protocol: A549 NSCLC cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), antibiotics, and plasmocin prophylactic in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Total RNA Purification Kit (NorgenBiotek). 2ug of RNA was used for library contruction.
RNA was converted into cDNA using TeloPrime Full-Length cDNA Amplification Kit V2 following manufacture's protocol. The resulting cDNA was used for library contruction with the 2S DNA turbo kit from Swift Biosciences followinf manufacture's protocol

treatment_protocol: A549 cells were syncronized overnight in RPMI with 0.5% FBS. The following day, cells were plated and incubated for 24 hrs

value: Lung

value: Non small cell lung cancer

value: METTL3 knockdown


title: brain, ST multiple sclerosis, 5

description:
Fresh Frozen ST 10X Genomics
ST_MS377N

value: Glial cells

value: MS


title: brain, ST multiple sclerosis, 1

description:
Fresh Frozen ST 10X Genomics
ST_MS94


title: RY998_8

value: filling panicles


title: tof1_expglu_sp_H2AP

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3 tof1{delta}::hphNT1

value: exponential

value: glucose

value: YES

value: ChIP-seq

value: H2AS129P (1.6 μg/ml final concentration, Abcam, ab181447)


title: Microbiota of stool from DM87 mice

description:
105636_ID2881_87-DM87-A1-G11_S606
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv

source_name: Stool

value: Stool

value: male

value: Non exposed to nanoplastic after one week


title: RY998_1

value: young seedlings


title: wt_exp_H2AP

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3

value: galactose

value: NO


title: brain, ST control,5

description:
Fresh Frozen ST 10X Genomics
ST_CO85

value: brain

value: Female

value: Control


title: brain, ST control,4

description:
Fresh Frozen ST 10X Genomics
ST_CO74

value: Glial cells


title: RY998_2


title: Microbiota of stool from DM85 mice

description:
105634_ID2881_85-DM85-A1-E11_S604
16s rRNA v3-v4 sequencing of mice stool
feature-table.tsv


title: wt_exp_sp_H2A_rep2


title: shMETTL3, 1

value: Lung

value: Non small cell lung cancer

value: METTL3 knockdown


title: shMETTL3, 2


title: WY308_9

value: filling panicles


title: shCtrl 3

value: sh- control


title: wt_exp_sp_H2AP_rep2

value: exponential

value: YES

value: ChIP-seq

value: H2AS129P (1.6 μg/ml final concentration, Abcam, ab181447)


title: WY308_8


title: brain, ST control,3

description:
Fresh Frozen ST 10X Genomics
ST_CO41

value: Male


title: wt_exp_sp_H2A_rep1

value: Mata, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3


title: shCtrl 2


title: WY308_7


title: shCtrl 1


title: wt_exp_sp_H2AP_rep1

value: galactose


title: wt_expglu_sp_H2AP

value: glucose


title: wt_expglu_sp_H2A


title: WY308_5

value: young panicles


title: S4KO_D4_Rep2

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using histat2 with parameters -p 4 --no-unal --qc-filter --dta-cufflinks
Stringtie was used for generated the expression level.The expression level of each gene was normalized to Fragments Per Kilobase Million of library size (FPKM)
R package DESeq2 was then used to identify differentially expressed genes (DEGs) between different conditions. To assess the significance of differential gene expression, the P-value threshold was set at 0.01 and the fold change was set at 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includesFPKM values for each sample

extract_protocol:
For RNA-Seq samples, 2 million ES or EB cells were collected at the indicated time point and extracted with PrepEase RNA spin kit (Affymetrix).
For RNA-Seq library construction, total RNA purified from mES and mEB was quantified by Ribogreen and quality assessed by Agilent BioAnalyzer 2000. 500ng RNA with integrity number (RIN) > 9.5 from each sample was used for library construction with TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s instructions.

value: Smad4 knockout

value: LIF removal and form EB for 4 days


title: WY308_6


title: brain, ST control,1

description:
Fresh Frozen ST 10X Genomics
ST_CO37

value: brain

value: Glial and immune cells

value: Control


title: S4KO_D4_Rep1


title: brain, snRNA-seq multiple sclerosis, 9

description:
snRNA-seq 10x Genomics
snRNA-seq_MS549H

library_source: transcriptomic single cell

data_processing:
Expression count matrices for each sample were generated using  Cell Ranger Count (v6.0.2) by performing alignment to the sequencing data against the GRCh38-2020-A reference transcriptome
Obtained count matrices were corrected for ambient mRNA using CellBender (v0.2.0)
The data processing and downstream analyses for the snRNA-seq datasets was done using the scanpy toolkit (v1.9.6)69 in Python (v3.10.0). Each sample was filtered separately to control for batch differences. Single nuclei were filtered by genes (< 200 genes), mitochondrial genes (percentage of mitochondrial genes < 5%) and gene counts (number counts < number counts 99th percentile). Genes were kept if they were expressed across different nuclei (number of expressed nuclei > 3). Afterwards, nuclei were filtered by doublet scores computed with scrublet70 (doublet score < 0.1). Finally, each nuclei raw expression was normalized by the median of total counts (target_sum = None) and log-transformed (log1p).
PCA was performed on the scaled log-transformed most variable genes across as many samples as possible. Depending on the number of cells, different numbers of variable genes were used: 4,096 genes (number of cells > 1e4), 2,048 genes (number of cells > 1e3) and 1,024 genes (number of cells < 1e3). PCs were integrated using harmony-py71, nearest neighbors were computed per nucleus by finding similarities in the corrected PC space (n_pcs = 50), and the obtained connectivities were used to generate a UMAP manifold and clustering with the Leiden algorithm (resolution = 1.0). Clusters were characterized by identifying marker genes using the rank_genes_groups (method = t-test_overstim_var) function from scanpy with the log-transformed counts (adjusted P < 0.05; abs(log2FC) > 0.5).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values and matrix files

extract_protocol:
For nuclei isolation, 20-30 mg of muscle tissue was chopped and homogenized using 2 ml lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl, 1 mM DTT, 0.5% Triton X100 in DEPC-treated water) and a glass Dounce homogenizer with a tight pestle on ice.
Libraries were generated according to the provided protocols according to the 10X Next GEM 3’ Kit v3.1 protocol. After recommended quality control, all libraries were pooled and sequenced on an Illumina NovaSeq 6000 system. Sequencing was performed at Institute of Clinical Biology (IKMB, Kiel).

value: Chronic Inactive

value: MS


title: WY308_4


title: brain, snRNA-seq multiple sclerosis, 8

description:
snRNA-seq 10x Genomics
snRNA-seq_MS497T

value: Female


title: ΔmatP

data_processing:
Custom-made adpters were removed using Cutadapt
Data were analized using HiC-Pro
Assembly: N16961
Supplementary files format and content: Matrix file

extract_protocol:
Cells were fixed with formaldehyde 3% and genome was digested with HpaII and religated.
3C libraries were sheared using a Covris S220 and sheared fragments were ligated with custom-made adapters.

value: O1 biovar El Tor str. N16961


title: S4KO_D0_Rep2

value: Undifferentiated mESC


title: WY308_3

value: young seedlings


title: S4KO_D0_Rep1


title: WT


title: brain, snRNA-seq multiple sclerosis, 6

description:
snRNA-seq 10x Genomics
snRNA-seq_MS411

value: Chronic Active


title: WY308_2


title: WY308_1


title: brain, snRNA-seq multiple sclerosis, 5

description:
snRNA-seq 10x Genomics
snRNA-seq_MS377I


title: wounding 16H, rep2

city: Montpellier

first: Anne-Sophie

last: PETITOT

address: 911 avenue Agropolis

department: UMR DIADE

institute: IRD

description:
wildtype-t16_2
wildtype-t16_2

data_processing:
The quality of each library was controlled using FastQC.
Reads were trimmed with CutAdapt using the following criteria: the first 10 bases of all reads were eliminated, contaminating adapters were removed, low quality bases (Q<30) were trimmed out from both the 5- and 3-ends of reads, and reads less than 50 nt were discarded.
Clean reads were mapped against the Oryza sativa subsp. japonica ‘Nipponbare’ reference genomes (MSU7 and RAP-DB) using HiSat2. Mapped reads were assembled into transcripts with StringTie using  reference annotations. Count files were generated from GTF files with an in-house script.
Assembly: msu7 and rapdb
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: leaves

growth_protocol: Seeds were sterilized in 70% ethanol for 1 minute, and then 30 minutes in 40% commercial bleach, following by 6-8 times rinsed in sterilized water. Disinfected seeds were then pregerminated on half‐strength Murashige & Skoog (MS) medium including Gamborg B5 vitamins medium (Duchefa Biochemie BV, Haarlem, the Netherlands) supplied with 0.7% plant agar (Duchefa Biochemie BV, Haarlem, the Netherlands) for 2 days. Seedlings with both coleoptile and primary root were then transferred into the square petri dish (one plant per plate) containing ½ MS including Gamborg B5 supplied with 0.7% plant agar (Duchefa Biochemie BV, Haarlem, the Netherlands) and allowed to growth for 7 days in the growth chamber at 26°C under a 12 : 12 h, light : dark photoperiod, humidity at 70%.

extract_protocol:
Total RNAs were extracted from rice leaves samples using the RNeasy Plant mini kit (Qiagen) with addition of an on-column DNase I digestion.
For each sample, 500 ng of the extracted total RNA was used for library construction. Libraries were constructed using Truseq RNA Sample Preparation Kit V2 (Illumina, CA, USA), following the manufacturer's instructions. Adapters with index sequences were attached to the libraries. After the average length of the libraries was confirmed, the concentration of each library was adjusted to 10 nM.

treatment_protocol: The first complete leaf was wound 3 times with the forceps. The wounded leaves were then sampled for RNA extraction, following a kinetic from 0-16 hours. A total of 10 samples were harvested for each biological replicate at 0, 1, 2, 4, 6, 8, 10, 12, 14, and 16 h. For each time point, 5 leaves were pooled.The experiment was repeated 3 times.

value: leaves

value: Kitaake

value: wounding 16H


title: brain, ST control,2

description:
Fresh Frozen ST 10X Genomics
ST_CO40

value: Glial cells


title: S2/3DKO_D4_Rep2

value: Smad2/3 double knockout


title: wounding 16H, rep3

description:
wildtype-t16_3
wildtype-t16_3


title: brain, snRNA-seq multiple sclerosis, 10

description:
snRNA-seq 10x Genomics
snRNA-seq_MS549T

value: Male


title: WY998_9

value: filling panicles


title: brain, snRNA-seq multiple sclerosis, 4

description:
snRNA-seq 10x Genomics
snRNA-seq_MS377T

value: brain


title: S2/3DKO_D4_Rep1

value: LIF removal and form EB for 4 days


title: wounding 14H, rep3

description:
wildtype-t14_3
wildtype-t14_3

value: wounding 14H


title: wounding 16H, rep1

description:
wildtype-t16_1
wildtype-t16_1


title: S2/3DKO_D0_Rep2


title: WY998_7


title: brain, snRNA-seq multiple sclerosis, 2

description:
snRNA-seq 10x Genomics
snRNA-seq_MS229

value: Glial and immune cells


title: S2/3DKO_D0_Rep1


title: brain, snRNA-seq multiple sclerosis, 7

description:
snRNA-seq 10x Genomics
snRNA-seq_MS497I

value: Chronic Inactive

value: MS


title: wounding 14H, rep2

description:
wildtype-t14_2
wildtype-t14_2


title: brain, snRNA-seq multiple sclerosis, 1

description:
snRNA-seq 10x Genomics
snRNA-seq_MS197D

value: Female


title: WY998_6

value: young panicles


title: WT_D4_Rep1

value: Wild type


title: WY998_5


title: wounding 14H, rep1

description:
wildtype-t14_1
wildtype-t14_1


title: brain, snRNA-seq control,6

description:
snRNA-seq 10x Genomics
snRNA-seq_CO85

value: Control


title: wounding 12H, rep3

description:
wildtype-t12_3
wildtype-t12_3

value: leaves

value: wounding 12H


title: WY998_8


title: brain, snRNA-seq multiple sclerosis, 3

description:
snRNA-seq 10x Genomics
snRNA-seq_MS377N

value: Chronic Active


title: WY998_4


title: WT_D0_Rep2

value: Undifferentiated mESC


title: brain, snRNA-seq control,4

description:
snRNA-seq 10x Genomics
snRNA-seq_CO45


title: brain, snRNA-seq control,5

description:
snRNA-seq 10x Genomics
snRNA-seq_CO74


title: WT_D0_Rep1


title: WY998_3

value: young seedlings


title: WY998_2


title: wounding 12H, rep1

description:
wildtype-t12_1
wildtype-t12_1

value: Kitaake


title: wounding 10H, rep3

description:
wildtype-t10_3
wildtype-t10_3

value: wounding 10H


title: WT_D4_Rep2


title: WY998_1


title: brain, snRNA-seq control,3

description:
snRNA-seq 10x Genomics
snRNA-seq_CO41

value: brain

value: Male


title: wounding 10H, rep2

description:
wildtype-t10_2
wildtype-t10_2


title: brain, snRNA-seq control,2

description:
snRNA-seq 10x Genomics
snRNA-seq_CO40


title: E12.5_mouse_distal_forelimb_WT_SUZ12_ChIPseq

city: Montréal

first: Fanny

last: GUERARD-MILLET

state: Quebec

address: 110 AVENUE DES PINS OUEST

country: Canada

institute: IRCM

data_processing:
ChIP-seq reads were aligned to the mm10 genome using bowtie v.2.3.1 with the following settings: bowtie2 -p 8 --fr --no-mixed --no-unal –x. Sam files were converted into bam files using Samtools v1.4.1. Duplicates were removed using Picard MarkDuplicates v.2.9.0. ChIP-seq data were visualized on the IGV software using BigWig files generated using bamCoverage tools using the following parameters : --normalizeUsing CPM -bs 1.
Mouse (MM10) and human (HG38) genome FASTA files were downloaded from the UCSC Genome Browser Website on September 15th 2022. Adapter sequences were removed from reads using robtools (https://github.com/francoisrobertlab/robtools) with the command “robtools trimmomatic --trimmers "ILLUMINACLIP:adapters.fa:2:30:10: TRAILING:3 MINLEN:25"” which requires Trimmomatic . Robtools version 2.0 and Trimmomatic version 0.36 was used. Reads were aligned to the genome using robtools with the commands “robtools bowtie2 -x mm10.fa.index -is -paired" and “robtools bowtie2 -x hg38.fa.index -is -paired" which require Bowtie2 (https://github.com/BenLangmead/bowtie2). Bowtie2 version 2.3.4.3 was used. Unmapped reads, low quality reads and duplicated reads were removed using robtools with the command “robtools filterbam” which requires samtools (https://github.com/samtools/samtools). Samtools version 1.9 was used. BAM files of replicates were merged together using robtools with the command “robtools mergebam --suffix -dedup” which requires samtools. Fragments were converted to BED format using robtools with the command “robtools bam2bed” which requires bedtools. Bedtools version 2.27.1 was used. Genome coverage files were generated using robtools with the command “robtools genomecov -g mm10.chrom.sizes --spike-suffix -human” which requires bedtools.
From the BED files containing the fragments, we counted the number of fragments per transcript for each category obtained from the SUZ12 and RING1B ChIP-seq data using a custom script called “TssFragmentCount.py” which requires bedtools. The number of fragments were scaled using a custom script called “TssScaleFragmentCount.py”. These custom scripts are available at https://github.com/francoisrobertlab/kmita-202210.
Peak calling was done using a custom script called macs2.py that requires MACS2. MACS2 version 2.2.7.1 was used. For each peak, TSSs from “knownGene.txt.gz” that are within a window size of 500bp around peak were keep for further analysis using a custom script called “TssWithPeaks.py”. Scaled number of fragments for each TSS were obtained using custom scripts “TssFragmentCount.py” and “TssScaleFragmentCount.py”. TSSs for which the EED mutant fragment count are between half and twice the WT counts are considered as maintained genes in the EED mutant. TSSs for which the EED mutant fragment count are above twice the WT counts are considered as gain genes in the EED mutant.
Scaled number of fragments for each TSS from “knownGene.txt.gz” were obtained using custom scripts “TssFragmentCount.py” and “TssScaleFragmentCount.py”. TSSs for which the WT fragment count is twice above the input fragment count were kept for further analysis. From these TSSs, only TSSs for which the WT fragment count is twice above the median of non-zero input fragment count of all TSSs were kept for further analysis. TSSs for which the EED mutant fragment count are between half and twice the WT counts were considered as additional maintained genes in the EED mutant.
Comparison of fragment counts were done using Perseus  version 1.6.14.0.
Assembly: mm10

source_name: distal forelimb

extract_protocol:
ChIP experiments were performed in dissected proximal and distal forelimb buds of CD1 (wild type) and Prrx1Cre; EedDel/Flox (Eedc/-) mice at E12.5 following the same conditions as previously described (Berlivet et al., 2013). Chromatin was cross-linked for 13 minutes using formaldehyde and sonicated using Fisher Scientific, Model 100 sonic dismembrator to obtain fragments between 100-600 bp. Protein A and Protein G Dynabeads (Invitrogen) were incubated for 6 hours at 4℃ with 5ug of antibody. The chromatin was coupled to the beads overnight at 4℃. The immunoprecipitated samples were then washed with different wash buffers depending on the antibody present. Lastly, the DNA was purified on QIAquick columns (Qiagen).
Library and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations and sequenced on Illumina Hiseq 2500 in a 50 cycles paired-end configuration.

value: distal forelimb

value: WT

tag: antibody

value: SUz12 cell signaling :3737


title: E12.5_mouse_proximal_forelimb_WT_SUZ12_ChIPseq

source_name: proximal forelimb

value: proximal forelimb


title: wounding 10H, rep1

description:
wildtype-t10_1
wildtype-t10_1


title: brain, snRNA-seq control,1

description:
snRNA-seq 10x Genomics
snRNA-seq_CO37

value: Glial and immune cells


title: WFB_8

value: filling panicles

value: WFB (Parent)


title: WFB_9


title: E12.5_mouse_distal_forelimb_EED_RYBP_ChIPseq

value: RYBP millipore Sigma :ab3637


title: WFB_7


title: wounding 12H, rep2

description:
wildtype-t12_2
wildtype-t12_2

value: leaves


title: wounding 8H, rep3

description:
wildtype-t8_3
wildtype-t8_3

value: wounding 8H


title: JHOS2 cells, HTO

city: Oulu

first: Alice

last: Dini

address: Aapistie 5A

department: Faculty of Biochemistry and Molecular Medicine

country: Finland

institute: University of Oulu

description:
Hashtag-derived oligonucleotides (HTO)/Antibody Capture
HTO/Antibody Capture counts are new features in addition to the standard per-gene features, and are output alongside gene counts in the feature-barcode matrix for the GEX (3' mRNA) library.
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

library_source: other

data_processing:
Raw FASTQ file preprocessing was performed using Cell Ranger (version 7.1.0, 10x Genomics) pipelines. Specifically, cellranger mkfastq was used to produce FASTQ (raw sequence data) files and cellranger count to perform alignment, filtering, and UMI counting. Alignment was performed against the GRCh38 (GENCODE v32/Ensembl 98) assembly of the human genome.
Assembly: GRCh38-2020-A (GENCODE v32/Ensembl 98)
Supplementary files format and content: Cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: JHOS2 (CVCL_4647)

extract_protocol:
JHOS2 cells were harvested according to standard cell culture procedures. After medium removal, the cells were washed with 6 ml of phosphate-buffered saline (PBS) and detached with 1 ml of TrypLE Express Enzyme (#12605010, Gibco™, Thermo Fisher Scientific) incubation for 10–15 minutes at 37°C and 5.0% CO2 before quenching with 5 ml of warm medium. During incubation, the pre-printed drugs in the 96-well plates were dissolved in 25 µl of medium while shaking for 15 minutes. The cell suspension was then transferred to a 15 ml tube and centrifuged at 300 g for 5 minutes. After removing the supernatant, the pellet was resuspended in 5 ml of warm medium before cell counting, which was performed as described before. The objective was to plate ~13,000 cells per well by adding 75 µl of the cell suspension to each well after dissolving the drugs, to obtain a final volume of 100 µl per well of each 96-well plate. Finally, cells were incubated for 24 hours at 37°C and 5.0% CO2 before harvesting for Cell Hashing. Live-cell labeling was performed as previously described by Stoeckius et al. (2017, DOI: 10.1186/s13059-018-1603-1) with pairwise combinations of 20 in-house produced antibody-oligo conjugates directed against β2microglobulin (#316302, BioLegend, San Diego, CA, USA), and CD298 (#341712, BioLegend). Single-cell gene expression profiles were studied using 10x Genomics Chromium Single Cell 3’RNAseq platform (10x Genomics, Pleasanton, CA, USA). The Chromium Single Cell 3’RNAseq run and library preparation were done using the Chromium Next GEM Single Cell 3' Gene Expression version 3.1 Dual Index chemistry with Feature Barcoding technology (see user guide #CG000317, 10x Genomics)
The Cell Hashing protocol described by Stoeckius et al. (2017, DOI: 10.1186/s13059-018-1603-1) was used to generate the HTO/Antibody Capture library and a 3' mRNA library. https://cite-seq.com/wp-content/uploads/2019/02/cite-seq_and_hashing_protocol_190213.pdf

tag: cell line

value: JHOS2 (CVCL_4647)

value: mixed sample (untreated (DMSO), treated)

tag: library type

value: HTO

tag: hto

value: row1, row2, row3, row4, row5, row6, row7, row8, column1, column2, column3, column4, column5, column6, column7, column8, column9, column10, column11, column12


title: wounding 8H, rep2

description:
wildtype-t8_2
wildtype-t8_2

value: Kitaake


title: WFB_6

value: young panicles


title: JHOS2 cells, GEX

description:
polyA mRNA
GEX (3' mRNA) library: R1 library contains cell barcode and UMI; R2 contains transcript; I1 contains i510X Genomics index reads; I2 contains i7 10X Genomics index reads.
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

value: mRNA


title: E12.5_mouse_distal_forelimb_EED_RING1B_ChIPseq

value: distal forelimb

value: RING1B active motif :39664


title: wounding 6H, rep3

description:
wildtype-t6_3
wildtype-t6_3

value: wounding 6H


title: wounding 8H, rep1

description:
wildtype-t8_1
wildtype-t8_1


title: WFB_5


title: 293T cells, PRMT1 KD, rep2

city: Daejeon

first: Kim

last: Hyoungmin

address: 291, Daehak-ro, Yuseong-gu, Daejeon, 34141, Rep. of KOREA

department: Department of Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
RNA-seq reads were filtered by FastQC (v0.11.4) and trimmed with TrimGalore (v0.6.10).
Reads were aligned to hg38 using STAR (v2.7.5a) with default parameters.
Bam file quantification was performed using featureCount (v1.5.0-p1) with parameter -Q 10.
DEG analysis was performed using DESeq2 (v1.36.0).
Assembly: hg38
Supplementary files format and content: Bigwig files include CPM values.
Supplementary files format and content: Tab-delimited text files include featureCount count values. These files are used for DESeq2 input.

extract_protocol:
Total RNA was prepared using TRIzol (Invitrogen).
RNA libraries were generated using TruSeq Stranded Total RNA Library Prep Gold (Illumina).

value: PRMT1 knockdown


title: 293T cells, PRMT1 KD, rep1


title: WFB_4


title: E12.5_mouse_INPUT

source_name: forlimb

value: forlimb

value: WT

value: none (input)


title: 293T cells, MLL2 KO, rep2

value: MLL2 knockout


title: WFB_3

value: young seedlings

value: WFB (Parent)


title: wounding 6H, rep1

description:
wildtype-t6_1
wildtype-t6_1

value: leaves


title: E12.5_mouse_distal_forelimb_WT_RYBP_ChIPseq

value: RYBP millipore Sigma :ab3637


title: wounding 4H, rep3

description:
wildtype-t4_3
wildtype-t4_3

value: wounding 4H


title: E12.5_mouse_distal_forelimb_WT_H3K27me3_ChIPseq

value: H3K27me3 millipore :07-449


title: E12.5_mouse_distal_forelimb_EED_H3K27me3_ChIPseq


title: WFB_2


title: E12.5_mouse_distal_forelimb_WT_RING1B_ChIPseq


title: E12.5_mouse_INPUT_Rx

source_name: forelimb

value: forelimb


title: E12.5_mouse_proximal_forelimb_WT_RING1B_ChIPseq

value: proximal forelimb


title: 293T cells, Control, rep2


title: wounding 4H, rep2

description:
wildtype-t4_2
wildtype-t4_2

value: Kitaake


title: E12.5_mouse_proximal_forelimb_WT_H3K27ac_ChIPseq

value: H3K27ac abcam :ab4729