title: genomic DNA from sample33

description: whole blood case sample


title: genomic DNA from sample32

status: Public on Dec 01 2024

type: genomic

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

description: whole blood control sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Microarray methylation analysis was performed in R. Quality control, including intensity read outs, filtering as well as beta value calculation was done using the minfi Bioconductor package. Functional normalization onto control probes was then used to normalized the raw intensity values across all the arrays and to remove part of the variance attributable to technical batches. We excluded any CpG containing SNPs or cross-hybridizing probes and CpGs with a detection p-value > 0.01 in at least 50% of the samples.
matrix processed value definition: Funnorm normalized

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

tag: diagnosis

value: control

tag: Sex

tag: age

tag: bmi

tag: cellcount-mono

tag: cellcount-gran

tag: cellcount-nk

tag: cellcount-bcell

tag: snp based principle component 1

tag: snp based principle component 2


title: genomic DNA from sample31

description: whole blood control sample


title: genomic DNA from sample27

description: whole blood case sample

value: case


title: genomic DNA from sample25

description: whole blood control sample


title: genomic DNA from sample45

description: whole blood case sample


title: genomic DNA from sample28

description: whole blood case sample


title: genomic DNA from sample29

description: whole blood control sample


title: genomic DNA from sample22

description: whole blood case sample


title: genomic DNA from sample24

description: whole blood control sample


title: genomic DNA from sample26

description: whole blood control sample


title: genomic DNA from sample30

description: whole blood control sample


title: genomic DNA from sample18

description: whole blood case sample


title: genomic DNA from sample17

description: whole blood case sample


title: genomic DNA from sample20

description: whole blood control sample


title: genomic DNA from sample21

description: whole blood case sample


title: genomic DNA from sample19

description: whole blood control sample


title: genomic DNA from sample15

description: whole blood case sample


title: genomic DNA from sample12

description: whole blood control sample


title: genomic DNA from sample13

description: whole blood control sample


title: genomic DNA from sample11

description: whole blood control sample


title: genomic DNA from sample10

description: whole blood control sample


title: genomic DNA from sample14

description: whole blood control sample


title: genomic DNA from sample16

description: whole blood case sample


title: genomic DNA from sample23

description: whole blood control sample


title: genomic DNA from sample9

description: whole blood control sample


title: genomic DNA from sample8

description: whole blood control sample


title: genomic DNA from sample6

description: whole blood control sample


title: genomic DNA from sample7

description: whole blood control sample


title: genomic DNA from sample35

description: whole blood case sample


title: genomic DNA from sample5

description: whole blood control sample


title: genomic DNA from sample3

description: whole blood case sample


title: Juvenile_253

type: SRA

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality bases removed, with resulting reads that were less than 25bp removed. Reads were then mapped to mm10 whole genome using STAR c2.7.5a
Number of reads aligned to each gene in the mm10 genome were quantified using HTSeq v0.6.1, using the following paratmers: --stranded=reverse -a 3, and the mm10 GTF file from ENSEMBL.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw number of counts aligned to every gene, each sample in an individual file

molecule: total RNA

organism: Mus musculus

source_name: Mammary gland

extract_protocol:
Right thoracic mammary gland fat pads were excised intact, snap frozen in liquid nitrogen, and RNA was harvested using the mirVANA RNA Isolation Kit. Illumina TruSeq RNA Sample Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina TruSeq RNA Sample Prep Kit v2 following standard Illumina protocols

tag: treatment group

value: 1mg/kg folic acid

tag: strain

tag: tissue

value: Mammary gland

value: post-natal day 84


title: genomic DNA from sample2

description: whole blood case sample


title: Juvenile_254


title: Juvenile_255


title: Juvenile_252


title: Juvenile_251


title: Juvenile_250


title: Juvenile_249

value: 5mg/kg folic acid


title: Juvenile_247


title: Juvenile_248


title: Juvenile_244


title: genomic DNA from sample1

description: whole blood case sample


title: genomic DNA from sample4

description: whole blood case sample


title: coral adult, shallow, rep2

city: Haifa

first: Jessica

last: Bellworthy

address: 199 Aba Khoushy Ave

country: Israel

institute: Haifa University

data_processing:
All read processing was conducted using the HIVE computer cluster at the University of Haifa, Israel.
Read quality was assessed with FastQC and compiled with MultiQC. Adapters were removed from the reads using Cutadapt (Martin, 2011) and reads with a quality score of less than 25 were discarded using Trimmomatic (Bolger et al., 2014).
Reads were then aligned to the S. pistillata host genome assembly (NCBI GCA_002571385.1) using Star (Dobin et al., 2013). MultiQC was then repeated; percentage successful alignment was 81.55 ± 0.07 % (mean ± standard deviation).
Differential expression analysis was conducted on the genome-mapped reads using DEseq2 (Love et al., 2014) based on host genes with ≥5 reads in ≥2 samples.
Assembly: NCBI GCA_002571385.1
Supplementary files format and content: RawGeneCounts.csv, comma separated file with raw gene counts for each sample; annotations for the gene ids can be found in DEG lisst-FPMvalues.xlsx
Supplementary files format and content: DEG lisst-FPMvalues.xlsx, excel file containing output FPM value and significance level for each gene identifed for pairwise comparison of all treatments. Merged with gene and protein ID.

organism: Stylophora pistillata

source_name: whole organism tissue

growth_protocol: Coral adult and planulae samples were taken from the natural reef. 8 day and 60 day samples were grown in situ, held in plastic settlement chambers.

extract_protocol:
Quick-DNA/RNA Miniprep Plus Kit, Zymo Research. Samples for RNAseq all had an RNA integrity number (RIN) >7.7
Sequencing libraries were prepared using a standard in house mRNA-Seq protocol at The Crown Genomics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Israel. The polyA fraction (mRNA) was purified from 500 ng of total RNA per sample, followed by fragmentation and the generation of double-stranded cDNA. Unique molecular identifiers were added prior to PCR amplification steps to reduce errors and quantitative bias introduced by amplification.
150 bp paired-end reads were sequenced on an Illumina NovaSeq SP with 100 cycles.

treatment_protocol: SS samples were sampled from the shallow reef and grown on the shallow reef (5m). SD were sampled form the shallow reef and translocated to grow on the mesophotic reef (45m).

value: whole organism tissue

value: adult

tag: treatment

value: shallow native


title: coral adult, deep, rep3

value: deep native


title: MT_SOD1_PSPC_treat5_rep2

type: RNA

city: Amsterdam

first: Andreia

last: Duarte

state: Select a State

address: Science Park 408

country: Netherlands

institute: VectorY

description:
nCounter Neuroinflammation Panel
S04087

hyb_protocol: Samples for the nCounter assay were treated as described in the nanoString technologies Gene expression hybridization protocol (Gene Expression CodeSet RNA Hybridization Protocol; MAN-10056-05) and 5 µL of sample (20 ng/ul) was used in each hybridization reaction. The entire hybridization reaction was used as input for the nCounter prep station and run on an nCounter MAX cartridge. Each nCounter cartridge was read on the nanostring digital analyzer (nCounter MAX/FLEX) with 280 fields of view (FOV). Finally, digital count files were generated for each sample run.

data_processing: All samples were verified regarding quality control (QC) parameters using Basic nSolver analysis software (101), applying default settings recommended by nanoString for binding density, mRNA content, mRNA positive normalization factor, mRNA content normalization facto and fields of view (FOV). Only transcripts with average counts ≥ 80 reads were considered as suitable housekeeping genes. Negative control probe reads were used to define minimum expression threshold (≥ 15 reads). Therefore, all transcripts with expression levels (Max counts) below the negative control limit were excluded from further analysis. Following QC, samples were clustered into the respective experiment groups. Pairwise ratios comparisons were applied to datasets on both panels to compare experimental groups. Fold-change (FC) was used as a readout for each possible combination.  Regression analysis (Coefficient of determination, R2) was used to analyze independent replicates, that showed R2 ≥ 0.95 across all datasets. Detailed information about the software, including the recommended ranges of values for the different QC parameters, creating experiments, normalization, and analyzing data, can be found at nSolver 4.0 Analysis Software User Manual (nanostring.com).

source_name: motor neurons, SOD1 mutation, exposed to PSPC treated with AAV6

growth_protocol: Human iPS-derived cell lines (iCell Motor Neurons and Astrocytes) were purchased from FujiFilm Cellular Dynamics International (FCDI, Madison, WI). Frozen vials were thawed and seeded according to manufacturer's instructions at a recommended of 100.000 live cells/cm2. iCell Motor neurons were cultured in a volume of 500 on a 12- (3513, Corning).

extract_protocol: Cell lysates were collected in QIAzol lysis reagent (79306, Qiagen). RNA isolation was performed using the miRNeasy Mini kit (217004, Qiagen) according to the manufacturer’s protocol for samples containing <1 μg total RNA. RNA concentrations were determined using NanoDrop ONEC (Thermo Scientific). Quality control analysis was executed with Bioanalyzer (Agilent RNA 6000 Nano), according to manufacturer's instructions. All the analyzed samples contained high quality RNA, with RNA integrity number (RIN) above 8.5, and clear ribosomal RNA (rRNA) 18/28S peaks.

treatment_protocol: PSPC/PONPC: Cells were treated with 25 µM and incubated for 24 hr. // AAV: Human iPS-derived cultures were transduced with different AAV constructs at a multiplicity of infection (MOI) of 10E6 and 107 in culturing media at seven days post-seeding. Half of the medium was removed from the wells before adding the AAV mixture. The same volume of fresh media was added to the cells 4 h post-transduction.

tag: phenotype

value: SOD1 (G93A) point mutation


title: MT_SOD1_PSPC_treat5_rep1

description:
nCounter Neuroinflammation Panel
S04086

source_name: motor neurons, SOD1 mutation, exposed to PSPC treated with AAV5


title: WT_SOD1_PONPC_rep2

description:
nCounter Neuroinflammation Panel
S04077

source_name: motor neurons, wild-type, exposed to PONPC

value: Apparently Healthy Neurons (AHN)


title: MT_SOD1_PONPC_treat5_rep2

description:
nCounter Neuroinflammation Panel
S04085

source_name: motor neurons, SOD1 mutation, exposed to PONPC treated with AAV5


title: WT_SOD1_PONPC_treat5_rep2

description:
nCounter Neuroinflammation Panel
S04079

source_name: motor neurons, wild-type, exposed to PONPC treated with AAV6


title: MT_SOD1_PSPC_rep2

description:
nCounter Neuroinflammation Panel
S04081

source_name: motor neurons, SOD1 mutation, exposed to PSPC


title: MT_SOD1_PONPC_rep1

description:
nCounter Neuroinflammation Panel
S04082

source_name: motor neurons, SOD1 mutation, exposed to PONPC


title: WT_SOD1_PONPC_treat5_rep1

description:
nCounter Neuroinflammation Panel
S04078

source_name: motor neurons, wild-type, exposed to PONPC treated with AAV5


title: MT_SOD1_PSPC_rep1

description:
nCounter Neuroinflammation Panel
S04080


title: coral adult, shallow, rep3


title: MT_SOD1_PONPC_treat5_rep1

description:
nCounter Neuroinflammation Panel
S04084


title: MT_SOD1_PONPC_rep2

description:
nCounter Neuroinflammation Panel
S04083


title: Juvenile_245


title: coral adult, shallow, rep1


title: Juvenile_246


title: coral adult, deep, rep2


title: MT_TDP-43 M337V__treat2_rep2

description:
nCounter Neuroinflammation Panel
S04069

source_name: motor neurons, TDP-43 mutation treated with AAV2

value: TDP-43 (M337V) point mutation


title: WT_SOD1_PSPC_rep2

description:
nCounter Neuroinflammation Panel
S04075

source_name: motor neurons, wild-type, exposed to PSPC


title: WT_SOD1_PSPC_rep1

description:
nCounter Neuroinflammation Panel
S04074


title: WT_SOD1_PONPC_rep1

description:
nCounter Neuroinflammation Panel
S04076


title: coral adult, deep, rep1


title: coral juvenile, shallow to deep, 60 days, rep3

value: 60 days

value: shallow to deep


title: MT_TDP-43 M337V__treat1_rep2

description:
nCounter Neuroinflammation Panel
S04067

source_name: motor neurons, TDP-43 mutation treated with AAV1


title: MT_TDP-43 M337V__treat1_rep1

description:
nCounter Neuroinflammation Panel
S04066


title: MT_TDP-43 M337V_rep3

description:
nCounter Neuroinflammation Panel
S04065

source_name: motor neurons, TDP-43 mutation


title: MT_TDP-43 M337V__treat2_rep1

description:
nCounter Neuroinflammation Panel
S04068


title: coral juvenile, shallow to deep, 60 days, rep2


title: coral juvenile, shallow control, 60 days, rep1

value: shallow control


title: coral planulae, deep, rep3

value: planulae


title: coral planulae, deep, rep2


title: coral juvenile, shallow control, 60 days, rep2


title: T5.415, normal PPLO medium repeat2

city: Wuhan

first: Jiongxi

last: Chen

address: No.1, Shizishan Street, Hongshan District

department: College of Animal Science & Technology

country: China

institute: Huazhong Agriclutural University

description:
Library name: T_50_2
T50_allSamples

data_processing:
The quality information of raw data in FASTQ format was calculated and then the raw data was filtered using fastp(0.22.0) software, clean data was obtained by removing reads containing adapter, reads containing ploy-N and low quality reads. All the subsequent analysis was based on high quality clean data
The reference genome and gene annotation files were downloaded from genome website. Reference genome index was built by Bowtie2(v2.5.1) and the filtered reads were mapping to the reference genome using Bowtie2
The gene read count value was counted using HTSeq(v0.9.1) as the original expression level of the gene. In order to make the gene expression levels of different genes and different samples comparable, FPKM(fragments per kilobaseof exon per million fragments mapped) is used to normalize the expression.
DESeq(v1.38.3) was conducted to analyze the differential expressed mRNA, transcripts with |log2FoldChange|>1 and P-value<0.05 were considered as differentially expressed mRNA.
we mapped all the genes to Terms in the Gene Ontology database and calculated the numbers of differentially enriched genes in each Term. Using topGO to perform GO enrichment analysis on the differential genes, calculate P-value by hypergeometric distribution method (the standard of significant enrichment is P-value <0.05), and find the GO term with significantly enriched differential genes to determine the main biological functions performed by differential genes. ClusterProfiler (v4.6.0) software was used to carry out the enrichment analysis of the KEGG pathway of differential genes, focusing on the significant enrichment pathway with P-value <0.05.
Assembly: GCF_000270525.1_ASM27052v1_genomic.fna
Supplementary files format and content: rawdata data is fastq Format file
Supplementary files format and content: This table contains the corresponding FPKM values for each gene identified on the genome for each sample

organism: Mycoplasmopsis bovis

source_name: bacterial cell

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies). Quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific) and a Bioanalyzer 2100 system (Agilent).
Zymo-Seq RiboFree Total RNA Library Kit was used to remove rRNA from total RNA. Random oligonucleotides and SuperScript III were used to synthesize the first strand cDNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). T

tag: cell type

value: bacterial cell

tag: genotype

value: inoculate under normal PPLO medium


title: T5.415, normal PPLO medium repeat3

description:
Library name: T_50_3
T50_allSamples


title: T5.415, 50 mM PPLO medium repeat3

description:
Library name: T_5415_3
T5.415_allSamples

value: inoculate under 50 mM PPLO medium


title: coral juvenile, shallow control, 60 days, rep3


title: T5.415, 50 mM PPLO medium repeat2

description:
Library name: T_5415_2
T5.415_allSamples


title: WT, 50 mM PPLO medium repeat3

description:
Library name: WT_50_3
WT50_allSamples

value: WT


title: coral planulae, shallow, rep3


title: coral planulae, deep, rep1


title: T5.415, normal PPLO medium repeat1

description:
Library name: T_50_1
T50_allSamples


title: WT_TDP-43_rep1

description:
nCounter Neuroinflammation Panel
S04061

source_name: motor neurons, wild-type


title: MT_TDP-43 M337V_rep1

description:
nCounter Neuroinflammation Panel
S04063


title: WT_TDP-43_rep2

description:
nCounter Neuroinflammation Panel
S04062


title: MT_TDP-43 M337V_rep2

description:
nCounter Neuroinflammation Panel
S04064


title: WT, 50 mM PPLO medium repeat1

description:
Library name: WT_50_1
WT50_allSamples


title: coral planulae, shallow, rep2


title: coral planulae, shallow, rep1


title: WT, 50 mM PPLO medium repeat2

description:
Library name: WT_50_2
WT50_allSamples


title: coral juvenile, shallow to deep, 8 days, rep3

value: 8 days


title: coral juvenile, shallow to deep, 8 days, rep2


title: WT, normal PPLO medium repeat3

description:
Library name: WT_3
WT_allSamples


title: WT, normal PPLO medium repeat2

description:
Library name: WT_2
WT_allSamples


title: WT, normal PPLO medium repeat1

description:
Library name: WT_1
WT_allSamples


title: coral juvenile, shallow to deep, 60 days, rep1


title: T5.415, 50 mM PPLO medium repeat1

description:
Library name: T_5415_1
T5.415_allSamples


title: coral juvenile, shallow to deep, 8 days, rep1


title: coral juvenile, shallow control, 8 days, rep3


title: Milk Replacer with Liquid Feed and Whey 9

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Sus Scrofa genome (11.1)
DEG assessed using DeSeq2
Assembly: Sscrofa11.1
Supplementary files format and content: excel file with count data and gene symbol for each sample

organism: Sus scrofa

source_name: Small Inestine

extract_protocol:
Total RNA was extracted using mRNAeasy kits (Qiagen)
Standard Illumina

value: Small Inestine

value: Milk Replacer with Liquid Feed and Whey


title: coral juvenile, shallow control, 8 days, rep2

value: whole organism tissue


title: Milk Replacer with Liquid Feed and Whey 8


title: coral juvenile, shallow control, 8 days, rep1


title: Milk Replacer with Liquid Feed and Whey 7


title: Milk Replacer with Liquid Feed and Whey 6


title: Milk Replacer with Liquid Feed and Whey 5


title: Milk Replacer with Liquid Feed and Whey 4


title: Milk Replacer with Liquid Feed and Whey 3


title: Scc1-PK ∆eco1 ∆wpl1 IP_rep2

city: Tokyo

first: Sao

middle: Anh

last: Nguyen

address: 1-1-1 Yayoi, Bunkyo-ku

department: Institute for Quantitative Biosciences

country: Japan

institute: University of Tokyo

library_source: genomic

data_processing:
Raw sequencing reads were mapped to S.cerevisiae and C.glabrata reference genomes by Bowtie (v.1.2.3) using default parameter.
Reads mapped to each reference genome were qualified using parse2wig in the DROMPAplus package (v.1.17.2). Number of non-redundant reads uniquely mapped to each reference genome in IP and input was used to calculate the Occupancy Ratio and Normalization Factor as described previously.
Non-redandunt reads mapped to S.cer were processed to bin data by parse2wig using the normalization factors calculated above, to produce bigwig files of read count per bin.
Fold-enrichment (FE) of ChIP/input ratio was executed using DROMPA peakcall PC_ENRICH, which produced bigwig file of FE per bin, and bed file of enriched peaks with enrichment threshold set to 2.
Assembly: Saccharomyces Genome Database (SGD), identical with sacCer3 Candida Genome Database (CGD)
Supplementary files format and content: bigwig (read counts): both IP and input
Supplementary files format and content: bigwig (fold enrichment): IP only
Supplementary files format and content: bed (peaks)

organism: Saccharomyces cerevisiae BY4741

source_name: G2/M, IP, rep2

growth_protocol: Budding yeast was cultured in YEPD supplemented with specific treatments as described in Method session of the manuscript.

extract_protocol:
S.cer and C.gla cells mixture  was crosslinked in 1% formaldehyde for 30min, then incubated at 4oC overnight. Cells were broken in lysis buffer using multi-beads shocker (Yasui-kikai). Cell extract was then processed to chromatin shearing by sonication (Sonifier Branson, 2508).
Sequencing library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Library was processed to double-sided size selection using AMPure XP Reagent (Beckman Coulter, A63881). Library was validated by Agilent High Sensitivity DNA kit and quantified by KAPA Library Quantification Kits.

tag: spike-in

value: Candida glabrata [NCYC No.388; SN50; SCC1-PK:NatMX]

tag: strain no

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 BY4741 wpl1{delta}::TRP1 eco1{delta}::LEU2 TIR1-9Myc:Aur1 SCC2-AID:KanMX6 SCC1-9PK:HIS3MX6Cgla:SCC1-PK:NatMX

value: EtOH


title: Scc1-PK ∆eco1 ∆wpl1 WCE_rep2

source_name: G2/M, input, rep2


title: Scc1-PK ∆eco1 ∆wpl1 Scc2-AID_G2/M IP

source_name: G2/M, IAA, IP

value: G2/M, IAA


title: Milk Replacer with Liquid Feed and Whey 2


title: Milk Replacer with Liquid Feed and Benzoic Acid 9


title: Scc1-PK ∆eco1 ∆wpl1 WCE_rep1

source_name: G2/M, input, rep1


title: Scc1-PK wt WCE_rep2

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 TIR1-9Myc:Aur1 SCC2-AID:KanMX6 SCC1-9PK:HIS3MX6Cgla:SCC1-PK:NatMX


title: Scc1-PK wt IP_rep2


title: Milk Replacer with Liquid Feed and Benzoic Acid 7


title: Milk Replacer with Liquid Feed and Whey 1


title: Milk Replacer with Liquid Feed and Benzoic Acid 6


title: Scc2-PK ∆eco1 ∆wpl1 IP_rep2

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 wpl1{delta}::TRP1 eco1{delta}::LEU2 SCC2-9PK:HIS3MX6Cgla:SCC1-PK:NatMX


title: Scc1-PK ∆eco1 ∆wpl1 IP_rep1

source_name: G2/M, IP, rep1


title: Scc2-PK ∆eco1 ∆wpl1 WCE_rep2


title: Milk Replacer with Liquid Feed and Benzoic Acid 5


title: Milk Replacer with Liquid Feed and Benzoic Acid 4


title: Milk Replacer with Liquid Feed and Benzoic Acid 3


title: Scc1-PK ∆eco1 ∆wpl1 Scc2-AID_G2/M WCE

source_name: G2/M, IAA, input


title: Milk Replacer with Liquid Feed and Benzoic Acid 2


title: WG334_OS-10min_rep2

city: Brighton

first: William

last: Gittens

state: I am not in the U.S. or Canada

address: Science Park Road

department: Genome Damage and Stability Centre

institute: University of Sussex

data_processing:
Paired-end reads that passed filter were aligned to Cer3H4L2 using bowtie2 (options: -X 1000 –no-discordant –very-sensitive –mp 5,1 –np 0), using MAPQ0 settings, then SAM files processed via terminalMapper (Perl, v5.22.1; https://github.com/Neale-Lab). Fragment midpoints (reflecting nucleosome midpoints) were computed in R. Two independent experiments were conducted, and the data were averaged to produce the supplementary files included in the series.
Assembly: Cer3H4L2
Supplementary files format and content: A table of counts of MNAse-seq fragment midpoints, reflecting nucleosome dyads. Three column format: Chr, Pos, Value.

organism: Saccharomyces cerevisiae

growth_protocol: For all experiments, cells were grown overnight to saturation in 4 mL YPD medium at 30 °C with shaking at 250 rpm, then diluted to OD600 0.5 in 500 mL YPD, or YP-Raffinose (for galactose induction experiments), and grown until OD600 2.0 in a 2 L baffled flask with antifoam 204 (Sigma A8311) added to 0.0001%. Alpha mating factor was added to a concentration of 20 µg/mL, and the cultures were incubated for a further 90 min. A second dose of alpha factor was added to a final total concentration of 26.6 µg/mL (including first dose), and the cultures were incubated for a further 30 min. At this point >99% of the cells were arrested in G1.

extract_protocol:
At untreated and treated time points following osmotic shock with 0.6M sorbitol, cells were fixed by addition of 17.5 mL of culture directly into prepared 50 mL Falcon tubes containing 2.5 mL of 16% paraformaldehyde (final 2% concentration). These were incubated for 15 min at 30˚C in a shaking incubator at 250 rpm, prior to quenching of the formaldehyde by addition of 10 mL 4.3 M TRIS pH 8.0 and subsequent incubation for 5 min at 30˚C. These fixed samples were maintained on ice until collection of all time points, whereupon they were centrifuged at 3500g for 5 min. The supernatant was aspirated, and the fixed cell pellet was resuspended in 1 mL ice-cold TBS and transferred to a microcentrifuge tube. Samples were centrifuged again at 3500g for 5 min, supernatant was aspirated, and the pellets were snap frozen in liquid nitrogen and stored at -80˚C. The following day, pellets were defrosted and spheroplasted with 1 mL spheroplasting buffer (1 M Sorbitol, 50 mM Tris pH 7.5, 5 mM β-mercaptoethanol, 2 mg/mL Zymolyase) at 37˚C for 30 min. Spheroplasts were pulse-pelleted by centrifugation at 20,000g for 15 seconds and the supernatant was removed. DNA was digested for exactly 10 min with 100 μL digestion buffer (1 M Sorbitol, 50 mM NaCl, 10 mM Tris pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.075% NP-40, 0.5 mM Spermidine, 1 mM β-mercaptoethanol) plus 3 μL MNase and 0.3 μL ExoIII (both NEB). Reactions were stopped by addition of 12.5 μL STOP buffer ( 50 mM EDTA, 50 mM EGTA) and mixing. RNA and protein were digested by incubation with 3 μL RNAse A (10 mg/mL) at 42˚C for 30 min, followed by incubation with 12.5 μL 10% SDS and 10 μL proteinase K (50 mg/mL) at 65˚C for 1 hour. DNA was purified using the Qiagen PCR purification kit, followed by elution in 25 μL 10 mM Tris pH 8.0. DNA digestion was checked by running a 2.5 μL sample on a 2% agarose gel. A clear primary mononucleosomal band was observed, with weaker di and trinucleosomal bands—indicating efficient digestion.
DNA 3´-termini were dephosphorylated by addition of 22.5 μL 2X CutSmart buffer and 1 μL shrimp alkaline phosphatase (NEB) and incubation at 37˚C for 10 min. DNA was re-purified with the Qiagen PCR purification kit, with elution in 25 μL Tris pH 8.0. DNA sequencing libraries were prepared using the NEBNext Ultra II kit (NEB) according to manufacturer’s instructions, except at half-scale, with 1 hour adaptor ligation times and a 20 min USER incubation. DNA libraries were PCR amplified with dual-end indexing primers (NEB) and 8 reaction cycles, prior to molarity measurement using Qubit (ThermoFisher Scientific) and TapeStation (Agilent). Libraries were pooled at equal molarity and sequenced using the NextSeq 1000 (Illumina).


title: WG335_OS-30min_rep2


title: Milk Replacer with Liquid Feed and Benzoic Acid 1


title: WG332_OS-3min_rep2


title: WG330_OS-1min_rep2


title: WG333_OS-5min_rep2


title: WG331_OS-2min_rep2


title: Milk Replacer with Liquid Feed 8

value: Milk Replacer with Liquid Feed


title: WG329_OS-30s_rep2


title: Milk Replacer with Liquid Feed 5


title: Milk Replacer with Liquid Feed 6


title: WG307_OS-30min_rep1


title: WG328_UT_rep2


title: Milk Replacer with Liquid Feed 4


title: Milk Replacer with Liquid Feed 3


title: Milk Replacer with Liquid Feed 2


title: Milk Replacer with Liquid Feed 1


title: Milk Replacer Only 6

value: Milk Replacer Only


title: WG304_OS-3min_rep1


title: Milk Replacer Only 7


title: Milk Replacer Only 5


title: WG301_OS-30s_rep1


title: WG302_OS-1min_rep1


title: WG300_UT_rep1


title: Milk Replacer with Liquid Feed 7


title: Milk Replacer Only 4


title: WG350_pdr1mut_VP16-30min_OS-2min_rep1

data_processing:
Multiplexed library pools were sequenced on the Illumina NextSeq 500 (Kit v2–75 cycles) or Illumina NextSeq 1000 (Kit P2–100 cycles), with paired-end read lengths of 42, or 51 bp, respectively. Paired-end reads that passed filter were aligned using bowtie2 (options: -X 1000 –no-discordant –very-sensitive –mp 5,1 –np 0), using MAPQ0 settings, then SAM files processed via terminalMapper (Perl, v5.22.1; https://github.com/Neale-Lab) that computes the coordinates of the protein-linked 5′-terminal nucleotide. The reference genome used in this study is our in-house Cer3H4L2 (S. cerevisiae) build, which we generated by inclusion of the his4::LEU2 and leu2::hisG loci into the Cer3 yeast genome build. Specifically, Cer3H4L2 is identical to the sacCer3 reference genome (R64-1-1), with the addition of two ectopic insertions: 1,173 bp of hisG sequence inserted at the LEU2 locus at position 91,965, and 3,077 bp of LEU2 sequence including 77 bp of associated unidentified bacterial sequence at position 65,684. All subsequent analyses were performed in R (Version 4.4) using RStudio (Version 2024.04.2+764), unless indicated otherwise. Yeast data sets were filtered to exclude the rDNA, the CUP1-2 locus, the mitochondrial genome and the 2-micron plasmid. Final averaged datasets used for generating figures are included in the supplementary files for the series accession.
Assembly: Cer3H4L2
Supplementary files format and content: FullMap files containing sparsely-formatted, 1bp histograms detailing the total number of Watson (+) and Crick (-) hits for all mapped base-pairs. 4-column format (Chr, Pos, Watson, Crick).
Library strategy: Top2 CC-seq

source_name: W303-1a pdr1{delta}::DBD-CYC8

extract_protocol:
CC-seq-v2 is an update of our prior published method that improves sensitivity by several orders of magnitude, enabling the detection of physiological Top2ccs in etoposide-unchallenged cells. Transient physiological Top2ccs were rapidly fixed by denaturation via the direct addition of 70 mL of culture to 150 mL of ethanol (-20˚C) in a 250 mL centrifuge vessel (NALGENE), which had been pre-chilled overnight at -20˚C. Mixtures were immediately vigorously shaken, resulting in a final concentration of 70% ethanol at ~0˚C, prior to incubation at -20˚C for 15 min. Tubes were centrifuged at 3500g for 3 min (4˚C) and the supernatant was aspirated fully. Cell pellets were resuspended in 1.2 mL spheroplasting buffer (1 M sorbitol, 50 mM NaHPO4 buffer pH 7.2, 10 mM EDTA) containing 400 μg/mL Zymolyase 100 T (AMS Biotech) and 1% β-mercaptoethanol (Sigma) for 20 min at 37 °C. The entire spheroplast suspension was transferred to 5 mL eppendorfs containing 3.773 ml of ethanol (-20˚C), shaken vigorously to mix, and pelleted by centrifugation at 1000g for 2 min. The ethanolic supernatant of each sample was fully aspirated prior to addition of 800 µL 1× STE buffer (2% SDS, 0.5 M Tris pH 8.1, 10 mM EDTA, 0.05% bromophenol blue). Cells were lysed using a small plastic pestle (VWR) before addition of a further 1600 µL 1× STE buffer, with mixing by inversion and incubation for 10 min at 65 °C. Samples were cooled on ice and 1250 µL Phenol-Chloroform-isoamyl alcohol (25:24:1; Sigma) was added. The mixtures were emulsified by shaking vigorously 30 times, prior to incubation at room temperature (RT) for 5 min. The mixtures were re-emulsified by shaking vigorously 30 times, prior to phase separation by centrifugation at 20,000 × g for 5 min. 2 mL of the aqueous phase was removed to a clean microcentrifuge tube, taking care not to disturb the interphase, and nucleic acids were precipitated with 3.5 mL ice-cold ethanol, pelleted by centrifugation, washed with 5 mL ice-cold 70% ethanol, and dissolved in 1 mL 1x TE buffer pH 7.5 overnight at 4 °C. 1 mL aliquots of nonproteolysed DNA (prepared as above) were fully resuspended by heavy vortexing and inversion on a rotation wheel for 15 min (RT), prior to sonication to an average fragment size of 300–400 bp with Covaris (duty cycle: 10%, intensity/peak power incidence: 75 W, cycles/burst: 200, time: 21 min). A sample of 12 uL was removed and incubated at 37˚C for 45 min with 3 uL of RNAse A (50 mg/mL). DNA shearing was checked by 1% agarose gel electrophoresis, and DNA was quantified in technical triplicate with the Qubit (ThermoFisher) and High Sensitivity reagents. Human-Lambda DNA spike was added to 950 uL of sample, then the total volume was made up to 1 mL with 1x TE (pH 7.5). Triton-X100, N-Lauroylsarcosine sodium salt and NaCl were then added to complete the binding buffer (final concentrations: 0.3 M NaCl, 0.2% Triton-X100, 0.1% N-Lauroylsarcosine sodium salt). Each sample was divided over two QIAquick silica fibre membrane spin columns (QIAGEN). Under these conditions, protein, but not nucleic acids, bind to the silica membrane, leading to selective retention of any CCs. The flowthrough was reapplied to the column to improve yield. Columns were washed six times with 600 µL of TEN (10 mM Tris pH 7.5, 1 mM EDTA, 0.3 M NaCl) per 1 min wash to remove any residual non-CC DNA fragments, prior to elution twice with 125 µL TES (10 mM Tris pH 7.5, 1 mM EDTA, 0.5% SDS). The SDS detergent in the elution buffer releases interactions between protein and silica, thereby releasing bound CCs.
Eluted products were pooled to 500 µL in TES and incubated with 1 mg/mL Proteinase K (Sigma) for 60 min at 50 °C, prior to overnight ethanol precipitation at −20 °C with 1.41 mL ethanol, 0.2 mg/mL glycogen and 200 mM NaOAc. The DNA-glycogen precipitate was pelleted by centrifugation at 20,000 × g for 1 h at 4 °C, washed once with 1.5 mL 70% ethanol without disturbing the pellet, and re-centrifuged for 15 min. The supernatant was aspirated, and the pellet was air-dried for 10 min at room temperature, prior to solubilisation in 26 µL 10 mM Tris-HCl pH 7.5. DNA concentration was measured in a 1 µL sample using a Qubit (ThermoFisher) and High Sensitivity reagents. The remaining 25 µL was used as input for one round of end repair and adapter ligation with NEBNext Ultra II DNA Library Preparation kit (NEB), according to manufacturer’s instructions, except all steps were conducted at half-scale and a custom P7 adapter was used. The use of custom adapters is to allow differentiation of the sheared end (P7 adapter) from the Top2cc end (P5 adapter). After ligation of the P7 adapter, TE was added to a final volume of 90 uL. DNA was isolated with AMPure XP beads (Beckman Coulter) according to manufacturer’s instructions (beads:input of 78:90 uL) and eluted in 85 µL water. Next, 10 uL of 10X Cutsmart buffer and 5 uL Shrimp Alkaline Phosphatase (rSAP; NEB) were added before incubation for 30 min at 37˚C. DNA was isolated again with AMPure XP beads (Beckman Coulter) according to manufacturer’s instructions (beads:input of 83:100 uL) and eluted in 50 µL 10 mM Tris-HCl. Samples were diluted twofold with 50 µL TDP2 reaction buffer (100 mM TrisOAc, 100 mM NaOAc, 2 mM MgOAc, 2 mM DTT, 200 µg/mL BSA) and incubated with 3 µL of 10 µM recombinant zebrafish TDP2 catalytic domain (Addgene plasmid #200512)  for 1 h at 37 °C. DNA was isolated again with AMPure XP beads (beads:input of 83:103) and eluted in 26 µL 10 mM Tris-HCl. Next, a second round of adapter ligation was conducted using a new custom adapter dp-P5 without prior end repair in order to prevent dephosphorylation of DNA 3′-phosphate termini which may be generated by TDP2 activity on 3′-CCs. After ligation of the dp-P5 adapter to the Top2-cleaved end, sample volume was adjusted to 90 uL with Tris-HCl, DNA was isolated with AMPure XP beads (beads:input of 78:90) and eluted in 16 µL 10 mM Tris-HCl. DNA concentration was measured in 1 µL using a Qubit. The remaining 15 µL was used as template for the NEBNext Ultra II PCR step using universal primer (P5 end) and indexed primers for multiplexing (P7 end), according to manufacturer’s instructions (12–15 cycles). PCR reactions were diluted with 50 µL 10 mM Tris-HCl, DNA was isolated with AMPure XP beads (beads:input of 83:100) and eluted in 30 µL 1 mM Tris-HCl pH 8.1, 100 uM EDTA. Sample DNA molarities were quantified using the Bioanalyzer or Tapestation (Agilent).

value: W303-1a pdr1{delta}::DBD-CYC8


title: Milk Replacer Only 3


title: Milk Replacer Only 2


title: WG349_pdr1mut_VP16-30min_rep1


title: WG348_pdr1mut_VP16-15min_OS-2min_rep1


title: Milk Replacer Only 1


title: WG347_pdr1mut_VP16-15min_rep1


title: human iPSC, islet-like organoids, lithium-nonresponsive patients, subject 3, rep3

city: beijing

first: xinyu

last: She

address: shuangqing road, haidian district

department: school of life sciences

institute: Tsinghua university

description:
Library name: NR_3
Gene_count_all.xlsx

data_processing:
Primary sequencing data, called as raw reads, is subjected to quality control (QC)to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences, QC of alignment is performed to determine if resequencing is needed. The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio. If alignment result passes QC, we will proceed with downstream analysis including gene expression and deep analysis based on gene expression (PCA/correlation/screening differentially expressed genes and so on). Further, we also can perform deep analysis based on DEGs, including Gene Ontology (GO) enrichment analysis, KEGG pathway enrichment analysis, cluster analysis, protein-protein interaction network analysis and finding transcription factor.
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25
Supplementary files format and content: Excel spreadsheet, gene count of all samples
Supplementary files format and content: Excel spreadsheet, FPKM for each sample

molecule: polyA RNA

source_name: human iPSC

growth_protocol: Quick-freeze samples immediately after collection and store at –80°C or in liquid nitrogen until RNA isolation.

extract_protocol:
1. Add 1 mL of TRIzol™ Reagent per 30 mg of ipsc derived neurons and islet-like organoids to the sample. 2. Pipet the lysate up and down several times to homogenize. 3. Incubate for 5 minutes to permit complete dissociation of the nucleoproteins complex. 4. Add 0.2 mL of chloroform per 1 mL of TRIzol™ Reagent used for lysis, then securely cap the tube. 5. Incubate on ice for 2–3 minutes. 6. Centrifuge the sample for 30 minutes at 12,000 × g at 4°C. The mixture separates into a lower red phenol-chloroform, and interphase, and a colorless upper aqueous phase. 7. Transfer the aqueous phase containing the RNA to a new tube. 8. Add 0.5 mL of isopropanol to the aqueous phase, per 1 mL of TRIzol™ Reagent used for lysis. 9. Incubate at -80 ℃ for 30 mins. 10. Centrifuge for 30 minutes at 12,000 × g at 4°C. Total RNA precipitate forms a white gel-like pellet at the bottom of the tube. 10. Discard the supernatant with a micropipettor. 11. Resuspend the pellet in 1 mL of 75% ethanol per 1 mL of TRIzol™ Reagent used for lysis. 12. Vortex the sample briefly, then centrifuge for 5 minutes at 7500 × g at 4°C. 13. Discard the supernatant with a micropipettor. 14. Air dry the RNA pellet for 5–10 minutes. 15. Resuspend the pellet in 20–50 µL of RNase-free water.16. Deliver the samples to the company using dry ice.
1)There are two methods to treat total RNA. Oligo(dT)magnetic beads are used to select mRNA with poly A tail, or hybridize the rRNA with DNA probe and digest the DNA / RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at5' end and stickiness 'A'at3'end, then ligate and adaptor with stickiness 'T'at3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6)Perform sequencing on prepared library.

tag: cell line

value: human iPSC

value: islet-like organoids

value: Bipolar I disorder

tag: gender

value: Female

tag: batch


title: WG346_pdr1mut_OS-2min_rep1


title: human iPSC, islet-like organoids, lithium-nonresponsive patients, subject 2, rep2

description:
Library name: NR_2
Gene_count_all.xlsx


title: human iPSC, islet-like organoids, MDD patient 5, rep5

description:
Library name: MDD_5
Gene_count_all.xlsx

value: Major depressive disorder


title: human iPSC, islet-like organoids, lithium-nonresponsive patients, subject 1, rep1

description:
Library name: NR_1
Gene_count_all.xlsx


title: WG306_OS-10min_rep1


title: WG305_OS-5min_rep1


title: WG303_OS-2min_rep1


title: ∆pilY1 bio rep 2

city: Johnson City

first: Chris

last: Pritchett

state: TN

address: 325 Treasure Lane

department: Health Sciences

country: USA

institute: East Tennessee State University

data_processing:
CLC Genomics workbench
reads were mapped to the Pseudomonas aeruginosa genome
The following settings were used for mapping the reads :mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8
RPKM values were using the default settings in CLC genomics
gene expression changes were determined using EDGE  (Extraction of Differential Gene Expression) analysis and Bonferroni correction
Assembly: PAO1 Pseudomonas.com
Supplementary files format and content: .txt file cotains raw counts for each sample
Supplementary files format and content: text files include RPKM values for each sample

organism: Pseudomonas aeruginosa PAO1

growth_protocol: ~109 cells were grown until log phase (OD600=0.4)

extract_protocol:
RNA was isolated using the RNA SNAP protocol and the  RNeasy Mini Kit (Qiagen) and DNase treated.
libraries were prepared using Illumina TruSeq library prep kit v.2. after rRNA depletion

value: pilY1 knockout

value: genetic modification


title: human iPSC, islet-like organoids, MDD patient 4, rep4

description:
Library name: MDD_4
Gene_count_all.xlsx


title: human iPSC, islet-like organoids, MDD patient 3, rep3

description:
Library name: MDD_3
Gene_count_all.xlsx


title: PAO1 bio repl 2

value: wild-type


title: PAO1 bio rep 3


title: ∆pilY1 bio rep 1


title: human iPSC, islet-like organoids, MDD patient 1, rep1

description:
Library name: MDD_1
Gene_count_all.xlsx


title: human iPSC, islet-like organoids, lithium-responsive patients, subject 3, rep3

description:
Library name: LR_3
Gene_count_all.xlsx


title: PAO1 bio repl 1


title: C57BL/6, IR, C9-3

city: Nantong

first: Jinyu

last: Ma

address: 19 Qixiu Road, Nantong 226001, China.

institute: Nantong University

description:
Library name: S-3
Column name in raw_counts_All_Samples.txt:S-3

data_processing:
Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT2) software was used to align the transcriptome sequencing Reads to the reference genome. Clean Reads were aligned to the reference genome to obtain the Alignment feature information and stored in SAM format (Sequence Alignment/Map format). The SAM sequence alignment format standard was formulated by sanger, which is mainly used for the display of sequence alignment to genomic information features. BAM file is a binary format of SAM file, which has smaller storage resources and is often used for subsequent calculation. Based on the alignment results, BCFtools was used to sort BAM files and filter duplicate Reads. Finally, the alignment results on the reference genome were statistically and plotted.
Reads Count was calculated using HTSeq
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.1).   DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution.   The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.   Genes with |log2(FoldChange)| > 1 and adjusted Pvalue <0.05 found by DESeq were assigned as differentially expressed.
Assembly: MM10
Supplementary files format and content: Transcripts Per Kilobase of exon model per Million mapped reads（TPM）

source_name: Kidney tissues

extract_protocol:
total RNA was extracted using RNA Extraction Reagent (Qiagen), total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Vazyme Stranded mRNA-Seq Library Prep Kit for illumina following manufactuter's protocols.

value: Kidney tissues

value: IR, C11

tag: time

value: Day 2

value: WT

tag: Sex

value: male


title: human iPSC, islet-like organoids, lithium-responsive patients, subject 2, rep2

description:
Library name: LR_2
Gene_count_all.xlsx


title: human iPSC, islet-like organoids, lithium-responsive patients, subject 1, rep1

description:
Library name: LR_1
Gene_count_all.xlsx


title: C57BL/6, IR-3

description:
Library name: I-3
Column name in raw_counts_All_Samples.txt:I-3

value: IR


title: human iPSC, islet-like organoids, healthy control group II, subject 4, rep4

description:
Library name: HCII_4
Gene_count_all.xlsx

value: Healthy control


title: C57BL/6, IR, C9-2

description:
Library name: S-2
Column name in raw_counts_All_Samples.txt:S-2

value: IR, C10


title: C57BL/6, IR, C9-1

description:
Library name: S-1
Column name in raw_counts_All_Samples.txt:S-1

value: IR, C9


title: C57BL/6, IR-2

description:
Library name: I-2
Column name in raw_counts_All_Samples.txt:I-2


title: human iPSC, islet-like organoids, healthy control group II, subject 5, rep5

description:
Library name: HCII_5
Gene_count_all.xlsx

value: human iPSC


title: human iPSC, islet-like organoids, healthy control group II, subject 3, rep3

description:
Library name: HCII_3
Gene_count_all.xlsx

value: islet-like organoids


title: ∆pilY1 bio rep 3


title: WG345_pdr1mut_UT_rep1

value: W303-1a pdr1{delta}::DBD-CYC8


title: human iPSC, islet-like organoids, healthy control group I, subject 4, rep4

description:
Library name: HCI_4
Gene_count_all.xlsx

value: Female


title: human iPSC, islet-like organoids, MDD patient 2, rep2

description:
Library name: MDD_2
Gene_count_all.xlsx

value: Major depressive disorder


title: human iPSC, islet-like organoids, healthy control group I, subject 3, rep3

description:
Library name: HCI_3
Gene_count_all.xlsx


title: human iPSC, islet-like organoids, healthy control group II, subject 1, rep1

description:
Library name: HCII_1
Gene_count_all.xlsx


title: human iPSC, islet-like organoids, healthy control group I, subject 1, rep1

description:
Library name: HCI_1
Gene_count_all.xlsx


title: day7 replicate2

city: Chavannes-près-Renens

first: Can

last: Aztekin

address: Swiss Federal Institute of Technology Lausanne (EPFL)

country: Switzerland

institute: EPFL

description: Library name: rep2_day7

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: h5 format
Supplementary files format and content: Contains the per molecule read information from Cell Ranger. The instructions to read the matrix in hdf5 format can be found here: https://support.10xgenomics.com/single-cell/software/pipelines/latest/advanced/h5_matrices

source_name: 129/SvEv mouse embryonic stem cells (mESCs)

extract_protocol:
Samples (day0 replicate1, day3 replicate1, day5 replicate1, day7 replicate1, day5 replicate2, day7 replicate2 and day12 replicate2), were collected, dissociated with 0.25% trypsin-EDTA, deactivated with mESC media without inhibitors (2i/Lif). Cells were collected, dissociated, centrifuged, resuspended in 1X PBS supplemented with 1% BSA, and filtered through a strainer. Samples were multiplexed using CellPlex, according to the manufacturer’s recommendations. Samples (Day2budoids and Day5budoids) were collected, washed with 1X PBS, dissociated with 0.25% trypsin-EDTA and deactivated with mESCs media without inhibitors (2i/Lif). Cells were collected, centrifuged, resuspended in 1X PBS supplemented with 0.04 % BSA and filtered. Please refer to the main text for more details.
Library was performed according to the manufacturer's instructions (3'GE v3.1).


title: day12 replicate2

description: Library name: rep2_day12

value: 129/SvEv mouse embryonic stem cells (mESCs)


title: scraped ileum WT, rep 4

city: Boston

first: Meenakshi

last: Rao

state: MA

address: 300 Longwood Ave

department: Pediatrics-Division of Gastroenterology

institute: Boston Children's Hospital

data_processing:
Readcounts table (Sample by gene count matrix) was generated by using trimmomatic to trim low quality reads. Subsequently, high-quality trimmed reads were aligned to the mouse reference genome mm10 using STAR aligner.Readcounts were made using featureCounts.
Differential analysis was conducted using DESeq2
Assembly: mm10
Supplementary files format and content: excel sheet containing samples in columns and raw counts in rows for each sample.

source_name: scraped ileal epithelium

extract_protocol:
RNA was extracted using phenol/chloroform extraction methods followed by a cleanup with the RNeasy Kit (Qiagen #74004)
Libraries were contructed and sequenced by Novogene using Illumina Novaseq 6000 platform.

value: scraped ileal epithelium

value: epithelium


title: day5 replicate2

description: Library name: rep2_day5


title: day12

description: Library name: Day5budoids


title: human iPSC, islet-like organoids, healthy control group I, subject 2, rep2

description:
Library name: HCI_2
Gene_count_all.xlsx


title: day9

description: Library name: Day2budoids


title: scraped ileum WT, rep 3


title: human iPSC, islet-like organoids, BDII patient 3, rep3

description:
Library name: BDII_3
Gene_count_all.xlsx

value: Bipolar II disorder


title: scraped ileum WT, rep 1


title: human iPSC, islet-like organoids, BDII patient 2, rep2

description:
Library name: BDII_2
Gene_count_all.xlsx


title: human iPSC, islet-like organoids, healthy control group II, subject 2, rep2

description:
Library name: HCII_2
Gene_count_all.xlsx


title: human iPSC, islet-like organoids, BDII patient 1, rep1

description:
Library name: BDII_1
Gene_count_all.xlsx


title: Medulloblastoma D458 cells treated with RVU120 for 48 hours_2

city: Aurora

first: Dong

last: Wang

state: CO

institute: University of Colorado, Anschutz Campus

data_processing:
Sequenced 150bp pair-end reads were mapped to the human genome (GRCh38) by STAR (v2.4.0.1), read counts were calculated by R Bioconductor package GenomicAlignments (v1.18.1), and differential expression was analyzed with DESeq2 (v1.22.2) in R. Further analysis by GSEA was performed using GSEA (v2.1.0) software with 1,000 data permutations and Cytoscape (v3.10.1).
Assembly: human genome (GRCh38)
Supplementary files format and content: text file of Deseq2 output

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries fro RNA-seq were prepared using SMARTER mRNA-Seq library Prep Kit following manufacturer's protocols

value: medulloblastoma


title: ileum, WT, rep 4

source_name: ileum

value: ileum

value: all cells


title: Medulloblastoma D458 cells treated with RVU120 for 48 hours_1


title: ileum, WT, rep 1

value: WT

value: male


title: Medulloblastoma D458 cells treated with DMSO_2


title: C57BL/6, IR-1

description:
Library name: I-1
Column name in raw_counts_All_Samples.txt:I-1

value: Kidney tissues

value: IR

value: Day 2


title: ileum, WT, rep 3


title: Duodenum, WT, rep 4

source_name: duodenum

value: duodenum


title: Medulloblastoma D458 cells treated with DMSO_1


title: Duodenum, WT, rep 2


title: Medulloblastoma D425 cells treated with RVU120 for 48 hours_2


title: human iPSC, islet-like organoids, BDII patient 5, rep5

description:
Library name: BDII_5
Gene_count_all.xlsx

value: human iPSC

value: islet-like organoids


title: Duodenum, WT, rep 3


title: scraped ileum WT, rep 2


title: human iPSC, islet-like organoids, BDII patient 4, rep4

description:
Library name: BDII_4
Gene_count_all.xlsx

value: Female


title: Duodenum, WT, rep 1


title: Medulloblastoma D425 cells treated with DMSO_2


title: Medulloblastoma D425 cells treated with RVU120 for 48 hours_1


title: Medulloblastoma D425 cells treated with DMSO_1


title: Colon, WT, rep 3

source_name: proximal colon

value: proximal colon


title: Medulloblastoma D458 cells, CRISPER-Cas9 knockout CDK8_3


title: Colon, WT, rep 2


title: ileum, WT, rep 2


title: Medulloblastoma D458 cells, CRISPER-Cas9 knockout CDK8_2


title: Colon, WT, rep 1


title: Medulloblastoma D458 cells, CRISPER-Cas9 negative control_3


title: scraped ileum Cre+, rep 2

value: Cre+


title: scraped ileum Cre+, rep 3

value: scraped ileal epithelium


title: Medulloblastoma D458 cells, CRISPER-Cas9 negative control_2


title: Medulloblastoma D458 cells, shRNA knockdown CDK8_3


title: Medulloblastoma D458 cells, CRISPER-Cas9 knockout CDK8_1


title: Medulloblastoma D458 cells, shRNA knockdown CDK8_2


title: scraped ileum Cre+, rep 4

value: epithelium


title: ileum, Cre+, rep 4


title: ileum, Cre+, rep 3


title: Medulloblastoma D458 cells, shRNA knockdown CDK8_1


title: scraped ileum Cre+, rep 1


title: ileum, Cre+, rep 2


title: Colon, WT, rep 4


title: Duodenum, Cre+, rep 4


title: Medulloblastoma D458 cells, shNull control_3


title: ileum, Cre+, rep 1


title: Medulloblastoma D458 cells, shNull control_2


title: Medulloblastoma D458 cells, shNull control_1


title: WT Control, 6 hours DMSO, Rep2 [Hi-C]

city: Evanston

first: vadim

last: backman

state: IL

address: 2170 Campus Drive, Silverman Hall 3627

department: Bioengineering

institute: Northwestern University

data_processing:
Samples were aligned to human reference genome GRCh38 (Ensembl) using Borrow-Wheeler Aligner version 0.7.17 and processed using the SLURM version of Juicer version 1.619 (https://github.com/aidenlab/juicer) on the Quest HPC provided by Northwestern University. Processing in the Juicer pipeline included removal of duplicates, exclusion of improperly ligated fragments, and mapping of Hi-C contacts with the GATC motif. Statistics generated for each replicate can be found in SI Fig. 2a. Individual replicates were checked for reproducibility using standard heuristics and combined as a mega map using Juicer’s Mega.sh script to increase sample resolution. TADs were identified using Juicer’s Arrowhead algorithm (https://github.com/aidenlab/juicer/wiki/Arrowhead). Loops were identified using Juicer’s HICCUPS algorithm (https://github.com/aidenlab/juicer/wiki/HiCCUPS). Compartment eigenvector analysis and Pearson correlation analysis were generated using Juicer’s Eigenvector and Pearsons scripts, respectively, or using built in functions in GENOVA. Aggregate TAD Analysis and Aggregate Peak Analysis were generated using GENOVA20 (https://github.com/robinweide/GENOVA). Contacts were dumped with Hi-C Straw (https://github.com/aidenlab/straw) and used for downstream analysis.
Assembly: hg38
Supplementary files format and content: compressed binarized .hic files with mapq > 30 (juicer output: inter_30.hic)

growth_protocol: HCT116-POLR2A-AID2, HCT116-POLR1A-AID, and HCT116 cells were grown in McCoy’s 5A Modified Medium  supplemented with 10% FBS and penicillin-streptomycin (100 μg/ml) All cells were cultured under recommended conditions at 37°C and 5% CO2. Lines in this study were maintained between passage 5 and 20. Cells were allowed at least 48 hours to re-adhere and recover from trypsin-induced detachment prior to experiments. All experiments  were performed at a confluence between 40–70%.

extract_protocol:
To wash the nuclei, samples were thawed and resuspended in 50 µL ice cold PB, followed by the addition of 150 µL ice-cold RNase-free water. 50 µL of Buffer C1 (Qiagen Epitect Hi-C Kit, #59971) was added to each sample and mixed. Samples were then centrifuged at 2500 x g and 4 ˚ C for 5 minutes. The supernatant was aspirated and the nuclear pellet was resuspended in 500 µL of RNase-free water, before being centrifuged again at 2500 x g and 4 ˚ C for 5 minutes. Library generation and subsequent steps used proprietary reagents from Qiagen’s Epitect Hi-C Kit. Washed nuclei were digested with according to the Epitect Hi-C protocol using a proprietary enzyme cocktail that cut at the GATC motif. Nuclei were end-labeled with biotin followed by ligation for 2 hours at 16 ˚C. Ligated chromatin was then de-crosslinked using 20 µL of Proteinase K solution at 56 ˚C for 30 minutes and then heated to 80 ˚C for 90 minutes. Ligated, decrosslinked DNA was purified using a Qiagen column kit (Qiagen Epitect Hi-C Kit, #59971).  and resuspended in 130 µL EB. Hi-C library samples were fragmented to a median size of between 400 and 600 bp using a Covaris E220 sonicator with a sample size of 130 µL. Samples were purified for fragments between 400 and 500 bp using a Qiagen bead purification size exclusion kit .
Reagents used in Hi-C library generation were supplied with Qiagen Epitect Hi-C Kit unless otherwise noted.  Hi-C samples were streptavidin-purified to enrich for properly ligated contact pairs using streptavidin beads and a magnetic bead rack. Beads were first washed in 100 µL of bead wash buffer, resuspended in 50 µL of bead resuspension buffer, and then mixed with 50 µL of Hi-C sample. The mixture was then incubated at room temperature for 15 minutes in a thermal mixer at 1000 RPM. Enriched bead-bound DNA was then end-repaired, phosphorylated, and poly-A tailed using a combined ER/A-tailing solution. The samples were incubated for 15 minutes at 20 ˚C followed by incubation at 65 ˚C for 15 minutes. Beads were then washed once with 100 µL of bead wash buffer, washed again with 95 µL of adapter ligation buffer, and resuspended in adapter ligation buffer in preparation for ligation of Illumina adapter sequences. Each sample was mixed with 5 µL of one of 6 Illumina adapter sequences (specified in the Qiagen protocol appendix) and 2 µL of ultralow input ligase. These samples were then incubated for 45 minutes. Following adapter ligation, each sample was washed three times before adding 400 µL of library amplification mixture to the beads. Samples were then distributed equally across 8 wells of a 96-well PCR plate and cycled using the following parameters on an Eppendorf Mastercycler x50s thermocycler

treatment_protocol: To induce expression of OsTIR1 in HCT116-POLR1A-AID, 1 μg/ml of doxycycline was added to cells 24 hours prior to auxin treatment. HCT116-POLR1A-AID cells were treated with 500 μM Indole-3-acetic acid sodium salt  to degrade endogenous POLR1A. HCT116-POLR2A-AID2 cells were treated with 1 µM  5-phenyl-indole-3-acetic acid to degrade endogenous POLR2A. HCT116 “WT” cells were treated with either 5 µg/mL Actinomycin D or % v/v DMSO equal to the highest DMSO concentration in each experiment. Treatment times varied between 1 hour and 8 hours.

value: human collecteral

value: DMSO


title: POLR2A, 6 hours 5-ph- IAA, Rep2 [Hi-C]

value: 1 µM 5-PH-IAA


title: Colon, Cre+, rep 4

value: all cells


title: Duodenum, Cre+, rep 3


title: WT Control, 6 hours DMSO, Rep1 [Hi-C]

value: WT


title: Medulloblastoma D458 cells, CRISPER-Cas9 negative control_1

value: medulloblastoma


title: Duodenum, Cre+, rep 1

value: male


title: Duodenum, Cre+, rep 2


title: POLR2A, 6 hours 5-ph- IAA, Rep1 [Hi-C]


title: ActD 5 ug/mL, 1 hour, Rep2 [Hi-C]

value: 5 µg/mL Actinomycin D


title: Colon, Cre+, rep 3


title: POLR1A, 6 hours IAA, Rep1 [Hi-C]

value: 500 µM IAA


title: ActD 5 ug/mL, 1 hour, Rep1 [Hi-C]


title: Colon, Cre+, rep 2


title: bleo, D14, IMres, rep2

city: Denver

last: Janssen

address: 1400 Jackson St

institute: National Jewish Health

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Gzipped, tab-separated values files and matrix files

extract_protocol:
Mice were euthanized and anti-CD45 antibody was instilled into the trachea. After 4 minutes, anti-CD45 solution was aspirated and bronchoalveolar lavage (BAL) was performed. Lungs were perfused by injecting 10 mL of PBS through the right ventricle during which lungs visibly blanched. Lung tissue was finely chopped with a razor blade and then incubated at 37C in 1 mL of 0.4 mg/mL Liberase TM for 25 min. Following incubation, tissue was pipetted rapidly up and down to further disaggregate, then filtered through 100 μm filters. Lung cells were pelleted and resuspended in then filter through 70 μm filters then resuspended HBSS containing 0.3% BSA and 0.3 mM EDTA. Cells were sorted using FACS into 3 bins: 1) CD45+ cells (live, CD45+), 2) resident IMs (live, CD45+, CD64+, CD88+, IT CD45-, tdT+), or 3) recruited IM (live, CD45+, CD64+, CD88+, IT CD45-, tdT-). Cells were manually counted using a hemocytometer and resuspended at 1x 1Mice were euthanized and anti-CD45 antibody was instilled into the trachea. After 4 minutes, anti-CD45 solution was aspirated and bronchoalveolar lavage (BAL) was performed. Lungs were perfused by injecting 10 mL of PBS through the right ventricle during which lungs visibly blanched. Lung tissue was finely chopped with a razor blade and then incubated at 37C in 1 mL of 0.4 mg/mL Liberase TM for 25 min. Following incubation, tissue was pipetted rapidly up and down to further disaggregate, then filtered through 100 μm filters. Lung cells were pelleted and resuspended in then filter through 70 μm filters then resuspended HBSS containing 0.3% BSA and 0.3 mM EDTA. Cells were sorted using FACS into 3 bins: 1) CD45+ cells (live, CD45+), 2) resident IMs (live, CD45+, CD64+, CD88+, IT CD45-, tdT+), or 3) recruited IM (live, CD45+, CD64+, CD88+, IT CD45-, tdT-). Cells were manually counted using a hemocytometer and resuspended at 1x 10^6 cells/ml in 0.06% BSA in PBS solution.^6 cells/ml in 0.06% BSA in PBS solution.
Library was contructed according to manufacturer's instructions. Single cells were captured using a Chromium Box (10x Genomics, Pleasanton, CA, USA). Libraries were sequenced using the Illumina NovaSEQ 6000 sequencer (Illumina, Inc., San Diego, CA). Sequencing was targeted to 5,000 cells in the CD45+ library, 3,000 cells in each of the IM sorts with sequencing depth of 100,000 reads per cell.

treatment_protocol: Intraperitoneal Tamoxifen (0.25 mg/g body weight) was given on days 1, 4, and 7 to lineage label interstitial macrophages.  4 weeks later, mice were treated with intratracheal E. coli O111:B4 LPS (20 μg) or intratracheal bleomycin (1.5U/kg body weight).

value: bleomycin

tag: flow sorting

value: IMres

tag: days after_treatment

tag: biological replicate


title: bleo, D14, IMres, rep3

description: 10X Genomics


title: shPP_LO_1

city: Guangzhou

first: xiang

last: zhang

state: Guangzhou

address: 58 Zhongshan Second Road, Yuexiu District

department: Department of General Surgery

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length<35 bp) and low quality reads using Cutadapt  v1.18 (non-default parameters: --max-n 0 --minimum-length 35) and Trimmomatic v0.35 (non-default parameters: SLIDINGWINDOW:4:15 LEADING:10 TRAILING:10 MINLEN:35). Then FastQC(with default parameters) is used to ensure high reads quality. The clean reads were mapped to the human genome (assembly GRCh38) using the HISAT2 v2.1.0(non-default parameters: --rna-strandness RF --dta) software.
Assembly: human genome (assembly GRCh38)
Supplementary files format and content: excel file includes raw counts for each sample

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies Corp.), and further treated with DNase to remove genomic DNA contamination. Isolation of mRNA was performed using the NEBNext PolyA mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA).
The mRNA was then used for RNA-Seq library preparation with the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA).

value: colerectal cancer cells

value: PPA2 knockdown

value: hypoxia


title: shPP_LO_2


title: bleo, D14, IMrec, rep3

description: 10X Genomics

value: IMrec


title: bleo, D14, IMres, rep1

description: 10X Genomics


title: shNT_LO_1


title: bleo, D14, IMrec, rep2

description: 10X Genomics


title: shPP_HO_2

value: normoxia


title: bleo, D14, IMrec, rep1

description: 10X Genomics


title: bleo, D14, CD45, rep3

description: 10X Genomics


title: shNT_HO_2


title: shPP_HO_1


title: bleo, D14, CD45, rep1

description: 10X Genomics


title: bleo, D14, CD45, rep2

description: 10X Genomics


title: bleo, D14, AM, rep3

description: 10X Genomics

value: AM


title: shNT_HO_1


title: Colon, Cre+, rep 1

value: proximal colon

value: Cre+


title: Female HH6 AVS, scRNAseq

city: La Jolla

first: Talia

last: Baddour

state: California

address: 9500 Gilman Dr.

institute: University of California San Diego

description: 10X Genomics

data_processing:
Cell Ranger software (v7.0.2) was used to demultiplex, align, filter, barcode and generate raw gene counts matrix files (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: hg19
Supplementary files format and content: tab-separated values files and matrix files

source_name: Aortic valve leaflet

extract_protocol:
Aortic valves were excised from human hearts (post-mortem interval < 48 hours) and washed with Earle’s Balanced Salt Solution (Cat. No. E2888). Briefly, valve leaflets were then digested with Liberase TM (Cat. No. 05401119001) for 30 minutes before quenching with media for centrifugation. The resulting cell pellet was treated with Red Blood Cell Lysis Buffer (Cat. No. 00433357) for 1 minute before quenching with media and centrifugation. Cells were counted manually with a hemacytometer before subsequent preparation for single cell sequencing.
Library preparation was performed using manufacturer's protocols (single cell 3' v3.1). Accordingly, valve cells were resuspended in a master mix and loaded with partitioning oil and gel beads into a Next GEM chip to create gel bead-in-emulsion (GEM). Poly-A mRNA from cell lysate was reverse transcribed (RT) to generate barcoded, full length cDNA. Silane magnetic beads were used to clean cDNA from RT mixture and then cDNA was amplified via PCR for library construction. Enzymatic fragmentation and size selection with SPRIselect reagent was used to extract the optimal cDNA amplicon size. Illumina R2 primer sequences, paired end sequences P5 and P7 and a sample index were added to each sample.

value: Aortic valve leaflet

value: female

tag: disease state

value: aortic valve stenosis


title: bleo, D14, AM, rep1

description: 10X Genomics


title: bleo, D07, IMres, rep3

description: 10X Genomics


title: bleo, D14, AM, rep2

description: 10X Genomics


title: HEK293,8hours,scRNA-Seq

city: Brisbane

first: Robin

middle: William

last: Palfreyman

state: QLD

address: Old Cooper Road

department: AIBN

country: Australia

institute: The University of Queensland

description: 10X Genomics

data_processing:
Cellranger v2.3.1 was used for demultiplexing, barcode processing and gene counting.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated files and matrix files

growth_protocol: A bioreactor was inoculated with exponentially growing HEK293F cells at a density of 0.4e6 cells/mL and viability >95%, and final volume of 550mL. Cells were cultured at 37C, 50% DO, and CO2 and NaHCO3 were used for pH control. Approximately 91 hours after inoculation, oxygen supply was turned off for hypoxic insult.

extract_protocol:
Freshly collected samples (of 1 mL) were centrifuged at 300xg for 3 mins before resuspending in ice-cold PBS and 10% DMSO and frozen at -80C using a Corning CoolCell container. Frozen samples were shipped on dry ice for ScRNA-Seq analysis.
Libraries were prepared using the manufacturer's protocol; NextGEM SC 3' v 3.1

treatment_protocol: Prior to removal of oxygen delivery, a sample was taken (TP00) to represent normoxia. When hypoxia was initiated, sample timing was started from when DO% reached 2% for the remaining samples.

value: cell line


title: shNT_LO_2

value: WT


title: Male HH4 AVS, scRNAseq

description: 10X Genomics

value: male


title: HEK293,4hours,scRNA-Seq

description: 10X Genomics


title: bleo, D07, IMres, rep2

description: 10X Genomics


title: bleo, D07, IMrec, rep2

description: 10X Genomics


title: bleo, D07, IMrec, rep3

description: 10X Genomics


title: HEK293,0.75hours,scRNA-Seq

description: 10X Genomics


title: HEK293,2hours,scRNA-Seq

description: 10X Genomics


title: bleo, D07, CD45, rep3

description: 10X Genomics


title: HEK293,0hours,scRNA-Seq

description: 10X Genomics


title: H_LPS

city: Memphis

first: Michael

middle: A

last: Dyer

state: Tennessee

address: 262 Danny Thomas

department: DNB

institute: St. Jude Children's Research Hospital

data_processing:
Data was processed using Cellranger v6.0.0
Assembly: mm10-mouse / GRCh38-human
Supplementary files format and content: barcode, feautres, and matrix files for each sample

source_name: retina

extract_protocol:
Papain (40U) was added to 400uL of papain buffer and incubate at 37°C for ~10 min. Retinal punches were added to papain and incubated at 37°C for 5-10 minutes while flicking. Dnase (40uL) was added as the retina began dissociating. The suspension was transferred into a 50-ml conical tube through a 40-μm mesh cell strainer and washed with PBS−/− and layered onto a 5 ml BSA cushion medium (4% BSA in Retinal Explant media). The sample were centrifuged at 500gfor 10 min at 4 °C and the cell pellets were resuspended in REM. Cells were counted and viability was confirmed on a hemocytometer.
Libraries were constructed using 10x Genomics Chromium Single Cell 3' Reagent Kit

treatment_protocol: Retina were dissected from the eye cup in Retinal Explant Media (REM). 1.5mm punches were taken from each eye using a biopsy punchand were placed on a Nuclepore 1.0uM membrane floating on 2mL of REM in a 12-well dish. The retinal punches were incubated for 24 hours (37C, 5% CO2) for culture control retina. Punches were harvested after 24 hours.

value: retina

value: Retina, 24 hour culture in REM + 0.2ug/mL LPS


title: H_Wildtype_5

value: Normal Retina_5


title: H_Control_4

value: Retina, 24 hour culture in REM_4


title: bleo, D07, CD45, rep1

description: 10X Genomics

value: bleomycin


title: H_2.3% O2

value: Retina, 24 hour culture in REM at 2.3% Oxygen


title: bleo, D07, CD45, rep2

description: 10X Genomics


title: H_33C

value: Retina, 24 hour culture in REM at 33 degrees Celcius


title: H_PH 7.15

value: Retina, 24 hour culture in REM pH7.15


title: bleo, D07, AM, rep3

description: 10X Genomics

value: AM


title: bleo, D07, AM, rep2

description: 10X Genomics


title: bleo, D03, IMres, rep2

description: 10X Genomics

value: IMres


title: bleo, D03, IMres, rep1

description: 10X Genomics


title: H_40C

value: Retina, 24 hour culture in REM at 40 degrees Celcius


title: bleo, D03, IMrec, rep2

description: 10X Genomics

value: IMrec


title: bleo, D07, AM, rep1

description: 10X Genomics


title: bleo, D03, CD45, rep3

description: 10X Genomics


title: H_Wildtype_4

value: Normal Retina_4


title: H_Control_3

value: Retina, 24 hour culture in REM_3


title: H_IFN

value: Retina, 24 hour culture in REM + 100U/mL IFN g


title: bleo, D03, IMrec, rep3

description: 10X Genomics


title: bleo, D03, CD45, rep2

description: 10X Genomics


title: H_Ouabain

value: Retina, 24 hour culture in REM + 70uM Ouabain


title: bleo, D07, IMrec, rep1

description: 10X Genomics


title: bleo, D03, IMrec, rep1

description: 10X Genomics


title: H_Glutamate

value: Retina, 24 hour culture in REM + 1mM Glutamate


title: bleo, D03, CD45, rep1

description: 10X Genomics


title: H_Wildtype_3

value: retina

value: Normal Retina_3


title: H_Wildtype_2

value: Normal Retina_2


title: LPS, D15, IMres, rep2

description: 10X Genomics

value: LPS


title: bleo, D03, AM, rep1

description: 10X Genomics

value: bleomycin


title: POLR1A, 6 hours IAA, Rep2 [Hi-C]

value: human collecteral

value: 500 µM IAA


title: bleo, D03, AM, rep3

description: 10X Genomics


title: LPS, D15, IMres, rep1

description: 10X Genomics


title: iPSC-EC, willd type, hypoxia, rep3

city: Chicago

first: Anna

last: Di Rienzo

department: Human Genetics

institute: University of Chicago

description:
10x Genomics
WT3-H

data_processing:
The scRNAseq data demultiplexing, barcoded processing, feature counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: Gencode 2019-09-05 transcriptome (GRCh38)
Supplementary files format and content: scRNAseq: tab separated values files and matrix files.

growth_protocol: For the Tibetan samples, peripheral whole blood samples were collected by venipuncture, and LCLs were generated using a standard protocol (Coriell Institute) for establishment of lymphoblastoid cell cultures from peripheral blood mononuclear cells (PBMCs). All Han Chinese samples used in the study were obtained from Coriell in the form of LCLs. Reprogramming of LCLs to iPSCs was performed in accordance with Thomas et al., 2015. All generation and maintenance of iPSCs were performed in atmospheric oxygen concentration. Cells were grown in culture at 37°C, 5% CO2 in a standard incubator. iPSCs were then differentiated into vascular endothelium. Our panel of TAC-CHB iPSCs were grown to confluence in batches of 4-8 lines (balanced for population and sex). On day 0 cells were detached using Cell Release, an EDTA-based solution, counted, and replated at a density of ~50,000 cells/cm2 in Essential 8 media supplemented with Rho-associated kinase (ROCK) inhibitor Y27632 (BioVision, 1994-1). On day 1, medium was replaced with N2B27 medium – a 1:1 mixture of DMEM:F12 (Life technologies, 11320-033) and Neurobasal media (Life technologies, 21103049) with glutaMAX (Life technologies, 35050038), β-Mercaptoethanol (0.097%) ( Life technologies, 21985023), N2(Life technologies, 17502048), and B27 minus vitamin A (Life technologies, 12587010)] this was supplemented with 8uM CHIR (Tocris, 4953) and 25ng/ml hBMP4 (PeproTech, 120-05ET) and added to the cells at high volume (i.e. 15 mL in 22.1cm dish). The cells were left undisturbed for 3 days. On day 4, media was exchanged for EC Induction Medium - StemPro-34 SFM medium (Life technologies, 10639-011) supplemented with 200 ng/mL VEGF165 (PeproTech, 100-20) and 2μM forskolin (Abcam, ab120058), and penicillin-streptomycin]. EC Induction Medium was refreshed on day 5, and on day 6 CD144+ cells were either isolated via pulldown or replated for subsequent single-cell sequencing.

extract_protocol:
RNA extraction was performed in 5 balanced batched of 8 (balanced for population, sex, and treatment) in a Qiagen Qiacube (9001292) using the Rneasy Plus Mini Kit. RNA was assessed for concentration prior to library preparation
500ng of each sample was used for library prep using Illumina TruSeq2 RNA-seq library prep kit and set A indexes (RS-122-2001). All libraries were assessed via bioanalyzer to be of sufficient quality, concentration, and fragment size for further processing.

treatment_protocol: For single cell sequencing, CRISPR-modified cells were subjected to differentiation, but were harvested prior to bead purification to avoid disturbing the microfluidic processes of single-cell sequencing. Instead on day 6 of differentiation, these cells were passaged to fibronectin coated plates and allowed to rest for 24 hours at which point they were moved to the hypoxia chamber (1% O2) for 48 hours. Cells were detached in hypoxic conditions after which they were kept on ice to prevent reperfusion response and processed according to 10x recommendations.

value: LCL-iPS

value: iPS-derived vascular endothelium

value: wild type

value: hypoxia


title: bleo, D03, AM, rep2

description: 10X Genomics

value: AM


title: H_Kcl

value: Retina, 24 hour culture in REM + 80mM Kcl


title: H_Wildtype_1

value: Normal Retina_1


title: LPS, D15, IMrec, rep2

description: 10X Genomics

value: IMrec


title: iPSC-EC, willd type, hypoxia, rep5

description:
10x Genomics
WT5-H


title: iPSC-EC, willd type, hypoxia, rep4

description:
10x Genomics
WT4-H


title: LPS, D15, IMrec, rep1

description: 10X Genomics


title: H_Glucose

value: Retina, 24 hour culture in REM + 20mM Glucose


title: iPSC-EC, knockout, hypoxia, rep3

description:
10x Genomics
KO3-H

value: ENH5 knockout


title: LPS, D15, CD45, rep2

description: 10X Genomics


title: iPSC-EC, willd type, hypoxia, rep1

description:
10x Genomics
WT1-H


title: iPSC-EC, knockout, hypoxia, rep5

description:
10x Genomics
KO5-H


title: iPSC-EC, knockout, hypoxia, rep2

description:
10x Genomics
KO2-H


title: LPS, D15, CD45, rep1

description: 10X Genomics


title: iPSC-EC, knockout, hypoxia, rep4

description:
10x Genomics
KO4-H


title: LPS, D06, IMres, rep2

description: 10X Genomics

value: IMres


title: LPS, D15, AM, rep2

description: 10X Genomics


title: split ePE3 with untethered MMLV-RTΔRH at EMX1 loci - Rep2 -I7

city: Hangzhou

first: Lijia

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

data_processing:
Traget site and protential off-target sites were amplified by PCR using the primer sequences (Table S1), then sequenced on an Illumina NovaSeq system. Deep sequencing data analysis was processed using CRISPResso2 and untreated cells were used as negative controls to exclude PCR amplification and sequencing errors. Reads were align to the amplicon sequence by crispresso2 using --max_paired_end_reads_overlap 140 --min_paired_end_reads_overlap     10 --exclude_bp_from_left 0 --exclude_bp_from_right 0 --plot_window_size 20 --min_frequency_alleles_around_cut_to_plot 0.2
On-target editing efficiencies, which are greater than 0.1%, were quantified as a percentage of (number of on-target reads) / (number of total reads).
Supplementary files format and content: xlsx files, percentage of total sequencing reads with on-target editing for all libraries, percentage of total sequencing reads with indels for ePE3-hepa.
Library strategy: Amplicon Sequencing

source_name: HEK293T cell

growth_protocol: HEK293T cell and Hepa1-6 cell were grown in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Gemini #900-108) and 1% GlutaMAX (Thermo #35050061). Cells were passaged every 2-3 days. After one day post-transduction, the medium was changed. Cells were harvested at 72 hours post-transduction.

extract_protocol:
Genomic DNA (gDNA) was isolated using TIANamp Genomic DNA Kit (TIANGEN #DP304) according to the manufacturer’s protocol.
The region that integrated with genomic DNA including RT template was PCR amplified from genomic DNA for HTS. For the first round of PCR, genomic sites of interest were amplified from 150 ng of genomic DNA using Q5 PCR Master Mix (New England Biolabs #M0544S) with the primers containing Illumina forward and reverse adapters. 50 uL of PCR 1 reaction was performed with forward and reverse primers each at 0.25 uM, ~1 uL of genomic DNA extract, and 25 uL of Q5 PCR Master Mix. To add a unique sequencing index, 50 uL of a given PCR 2 contained 2.5 uL of previous step unpurified PCR product; a unique forward or reverse primer pair, each at 0.25 uM; and 25 uL of Q5 PCR Master Mix. Primers are listed in Table S1. PCR 2 products were purified by DNA AMPure XP beads (Beckman Coulter #A63882) and eluted with 25 uL of water. DNA concentration was quantified by Nanodrop One (Thermo Fisher Scientific).

treatment_protocol: Cells were transfected at 60%-70% confluency using 3 uL of Lipofectamine 3000 (Thermo Fisher) with 1500 ng each half of the Split-PE. Three days post transfection, cells were collected.

value: HEK293T cell


title: split ePE3 with untethered MMLV-RTΔRH at EMX1 loci - Rep2 -I9


title: LPS, D15, AM, rep1

description: 10X Genomics


title: iPSC-EC, knockout, hypoxia, rep1

description:
10x Genomics
KO1-H


title: iPSC-EC, willd type, hypoxia, rep2

description:
10x Genomics
WT2-H


title: LPS, D06, IMres, rep3

description: 10X Genomics


title: LPS, D06, IMrec, rep2

description: 10X Genomics


title: split ePE3 with untethered MMLV-RTΔRH at EMX1 loci - Rep2 -I11


title: LPS, D06, IMres, rep1

description: 10X Genomics


title: split ePE3 with untethered MMLV-RTΔRH at EMX1 loci - Rep2 -I5


title: LPS, D06, IMrec, rep1

description: 10X Genomics


title: split ePE3 with untethered MMLV-RTΔRH at EMX1 loci - Rep2 -I1


title: split PE2 at EMX1- Rep 2- I9


title: LPS, D06, CD45, rep3

description: 10X Genomics


title: split PE2 at EMX1- Rep 2- I7


title: split PE2 at EMX1- Rep 2- I5


title: LPS, D06, CD45, rep2

description: 10X Genomics


title: LPS, D06, IMrec, rep3

description: 10X Genomics


title: split PE2 at EMX1- Rep 2- I1


title: LPS, D06, AM, rep2

description: 10X Genomics


title: LPS, D06, AM, rep1

description: 10X Genomics


title: LPS, D03, IMres, rep4

description: 10X Genomics


title: split PE2 at EMX1- Rep 1- I9


title: LPS, D03, IMres, rep3

description: 10X Genomics


title: split ePE3 with untethered MMLV-RTΔRH at EMX1 loci - Rep2 -I3


title: split PE2 at EMX1- Rep 1- I5


title: LPS, D03, IMres, rep1

description: 10X Genomics


title: split PE2 at EMX1- Rep 1- I3


title: LPS, D03, IMrec, rep4

description: 10X Genomics


title: LPS, D03, IMres, rep2

description: 10X Genomics


title: LPS, D06, CD45, rep1

description: 10X Genomics


title: split PE2 at EMX1- Rep 1- I1


title: split ePE3 with untethered MMLV-RTΔRH at EMX1 loci - Rep1 -I9


title: LPS, D03, IMrec, rep1

description: 10X Genomics


title: LPS, D03, CD45, rep3

description: 10X Genomics


title: LPS, D03, CD45, rep1

description: 10X Genomics


title: LPS, D03, IMrec, rep2

description: 10X Genomics


title: LPS, D03, AM, rep4

description: 10X Genomics


title: split ePE3 with untethered MMLV-RTΔRH at EMX1 loci - Rep1 -I1


title: split PE2 at EMX1- Rep 1- I7


title: LPS, D03, IMrec, rep3

description: 10X Genomics


title: split ePE3 with untethered MMLV-RTΔRH at EMX1 loci - Rep1 -I11


title: split ePE3 at multiple endogenous sites- Rep 3- I55


title: LPS, D06, AM, rep3

description: 10X Genomics


title: split ePE3 at multiple endogenous sites- Rep 3- I54


title: split ePE3 with untethered MMLV-RTΔRH at EMX1 loci - Rep1 -I7


title: LPS, D03, AM, rep3

description: 10X Genomics


title: split ePE3 with untethered MMLV-RTΔRH at EMX1 loci - Rep1 -I5


title: LPS, D03, AM, rep1

description: 10X Genomics


title: LPS, D03, CD45, rep2

description: 10X Genomics


title: split PE2 at EMX1- Rep 2- I3


title: split ePE3 with untethered MMLV-RTΔRH at EMX1 loci - Rep1 -I3


title: Homeostasis, D00, IMres, rep2

description: 10X Genomics


title: split ePE3 at multiple endogenous sites- Rep 3- I49


title: Homeostasis, D00, IMrec, rep3

description: 10X Genomics


title: split ePE3 at multiple endogenous sites- Rep 3- I53


title: split ePE3 at multiple endogenous sites- Rep 3- I52


title: split ePE3 at multiple endogenous sites- Rep 3- I47


title: Homeostasis, D00, IMres, rep1

description: 10X Genomics


title: split ePE3 at multiple endogenous sites- Rep 3- I46


title: split ePE3 at multiple endogenous sites- Rep 3- I45


title: Homeostasis, D00, IMres, rep3

description: 10X Genomics


title: Homeostasis, D00, CD45, rep2

description: 10X Genomics


title: split ePE3 at multiple endogenous sites- Rep 3- I51


title: split ePE3 at multiple endogenous sites- Rep 3- I48


title: Homeostasis, D00, IMrec, rep2

description: 10X Genomics


title: split ePE3 at multiple endogenous sites- Rep 3- I42


title: Creon3

city: GuangZhou

first: Xiaofan

last: Sun

address: 613 Huangpu Avenue, Tianhe District

institute: The First Affiliated Hospital of Jinan University

data_processing:
Personalbio Technologies
Assembly: The cells were then sent to Personalbio Technologies for RNA isolation and sequencing.
Supplementary files format and content: Approximately 1×106 MV4-11 cells (both including DMSO, 48 h HPA-12 and Creno at the indicated concentrations alone or in combination treatment groups) were collected and suspended in TRIzol reagent. The cells were then sent to Personalbio Technologies for RNA isolation and sequencing.

source_name: bone marrow

growth_protocol: All the media contained 10% fetal bovine serum (BI) plus 1% penicillin/streptomycin (Gibco). Cells were maintained in a 37 ℃ humidified atmosphere containing 5% CO2.

extract_protocol:
Crenolanib and (1R,3S)-HPA-12 were purchased from Selleck Chemicals (CP-868596, s2730, Houston, TX, USA) and TCI (Shanghai) Development Co., Ltd. (H1553-5MG, 383418-30-22, Shanghai, China), respectively.
Personalbio Technologies

value: bone marrow

value: AML

value: WT


title: split ePE3 at multiple endogenous sites- Rep 3- I44


title: LPS, D03, AM, rep2

description: 10X Genomics

value: LPS


title: HPA-12_3


title: Homeostasis, D00, CD45, rep3

description: 10X Genomics


title: split ePE3 at multiple endogenous sites- Rep 3- I43


title: split ePE3 at multiple endogenous sites- Rep 3- I41


title: DMSO3


title: Homeostasis, D00, AM, rep3

description: 10X Genomics


title: Homeostasis, D00, CD45, rep1

description: 10X Genomics


title: HPA-12_2


title: Combo3


title: Homeostasis, D00, IMrec, rep1

description: 10X Genomics


title: split ePE3 at multiple endogenous sites- Rep 3- I50


title: Homeostasis, D00, AM, rep2

description: 10X Genomics


title: split ePE3 at multiple endogenous sites- Rep 3- I39


title: NEAT1-WT; hSOD1G93A_4

city: Ngoya

first: Yu

last: Kawakami

address: Showaku, Tsurumai, 65

institute: Nagoya University

data_processing:
The quality of the raw paired-end sequence reads was assessed with FastQC (Version 0.11.7; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Low quality (< 20) bases and adapter sequences were trimmed using Trimmomatic software (Version 0.38) with the following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36. The trimmed reads were aligned to the reference genome by RNA-seq aligner HISAT2 (Version 2.1.0). The .sam files from the HISAT2 results were converted to .bam files with Samtools (Version 1.9). The .bam files were used to estimate the abundance of uniquely mapped reads using featureCounts (Version 1.6.3).
Assembly: mm10
Supplementary files format and content: Comma-separated text file

source_name: cervical spinal cord

extract_protocol:
Total RNAs isolated from cervical spinal cords of NEAT1-KO; hSOD1G93A (n=4) and NEAT1-WT; hSOD1G93A (n=3) mice at 8-week-old using the RNeasy Mini Kit (QIAGEN).
A library was independently prepared with 1.5ug of total RNA for each sample by the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490; NEB) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7530; NEB).

value: cervical spinal cord

value: NEAT1-WT; hSOD1G93A

tag: age

value: 8 weeks


title: Homeostasis, D00, AM, rep1

description: 10X Genomics


title: NEAT1-WT; hSOD1G93A_3

tag: tissue


title: split ePE3 at multiple endogenous sites- Rep 3- I40


title: Creon2


title: DMSO2


title: Combo1


title: HPA-12-1


title: split ePE3 at multiple endogenous sites- Rep 3- I38


title: Creon1


title: NEAT1-WT; hSOD1G93A_2


title: NEAT1-KO; hSOD1G93A_4

value: NEAT1-KO; hSOD1G93A


title: split ePE3 at multiple endogenous sites- Rep 3- I37


title: split ePE3 at multiple endogenous sites- Rep 3- I35


title: DMSO1


title: Gastric Mucin Oligosaccharides replicate 2

city: Ann Arbor

first: Nicholas

last: Pudlo

address: 1150 W. Medical Center Dr.

institute: University of Michigan

library_source: other

data_processing:
Fastq files were analyzed in SeqMan NGen 17 software (DNA Lasergene suite) and averaged RPKM, fold change and p-values exported by ArrayStar software.
Assembly: UGRO018.gff; awaiting genome submission
Supplementary files format and content: xlsx file contains locus tags, gene annotations, avg RPKM for each substrate, fold changes and significance (p-values).

molecule: other

organism: Erysipelotrichaceae bacterium DSM 116809

source_name: bacterial

growth_protocol: Hoskinsella mucinolytica DSM116809 was grown in biological replicate 5ml cultures to mid-log phase under anaerobic conditions at 37ºC on Depleted Medium (DM) containing either N-acetylgalactosamine, N-acetylglucosamine and cellobiose at 5mg/ml or gastric mucin oligosaccharides at 10mg/ml.

extract_protocol:
Samples were thawed and treated with 500 uL buffer (200 mM NaCl, 200 mM Tris, 20 mM EDTA at pH 8), 210 uL of 20% SDS and 500 uL phenol:choloroform:isoamyl alcohol (125:24:1, pH 4.3) followed by  bead beating for 3 minutes and centrifugation. Aqueous phase samples were subjected to a second phenol:choloroform:isoamyl alcohol mix and centrifugation prior to being precipitated with isopropanol, pellets resuspended, treated with DNaseI (NEB), and re-precipitated. Pellets were retained and resuspended in ultra pure water. Total RNA was confirmed to be DNA free (<0.5ng/ul) via quantitative PCR using universal 16S rRNA primers. If sequenced at the University of Michigan, rRNA was depleted with the MICROBExpress Bacterial mRNA Enrichment Kit (ThermoFisher). If sequenced at SeqCenter, total RNA was directly submitted.
Samples were multiplexed for sequencing on the Illumina NovaSeq platform at both the University of Michigan Advanced Genomics Core and SeqCenter.

treatment_protocol: At substrate-respective growth densities, cells were pelleted, resuspended in 1 mL of RNAprotect (Qiagen) and frozen at -80C until extraction.

value: bacterial

value: wild type

tag: treatment

value: 10mg/ml gastric mucin oligosaccharides


title: NEAT1-KO; hSOD1G93A_2


title: Gastric Mucin Oligosaccharides replicate 5


title: NEAT1-KO; hSOD1G93A_3


title: split ePE3 at multiple endogenous sites- Rep 3- I34


title: Gastric Mucin Oligosaccharides replicate 3


title: split ePE3 at multiple endogenous sites- Rep 3- I36


title: N-Acetylglucosamine replicate 1

value: 5mg/ml GlcNAc


title: N-Acetylglucosamine replicate 3


title: N-Acetylglucosamine replicate 2


title: split ePE3 at multiple endogenous sites- Rep 3- I32


title: Gastric Mucin Oligosaccharides replicate 1


title: split ePE3 at multiple endogenous sites- Rep 3- I33


title: mT4 cells treated with RT, anti-PD-L1, and olaparib, scRNAseq

first: Meredith

last: Morgan

state: Michigan

address: 1301 Catherin St

department: Radiation Oncology

description: 10x Genomics

data_processing:
Bcl2fastq2 Conversion Software for generating de-mulitplexed fastq files
CellRanger v7 Pipeline for read alignment and count matrices
Assembly: mm10
Supplementary files format and content: tab-seperated values files and matrix files

source_name: pancreatic tumor

growth_protocol: mT4 cells were grown in DMEM culture media with 10% fetal bovine serum. Cells were washed with PBS and trypsinized. Cells were collected and diluted to a concentration of 10 million cells/ml. 1 million cells were subcutaneously injected into 6-8 week old C57/Bl6 mice in 100ul injections.

extract_protocol:
6-8 tumors per treatment group were harvested, minced and digested in collagenase digest buffer (RPMI, Type I collagenase 0.1mg/ml, Type IV collagenase 0.1mg/ml, Dnase 2ul/ml) for 30 minutes at 37°C. Tissue digest was filtered using a 40um mesh filter and was quenched by washing with 2% FBS in PBS. Cells were counted and depleted of dying cells twice using the Dead Cell Removal kit from Miltenyi per manufacturer protocol. CD45 isolation kit from Miltenyi was used to seperate CD45- and CD45+ cells. Equal amounts of CD45- and CD45+ cells were mixed together in single cell suspension and counted once more. Samples were diluted to a final concentration of 700-1000cells/ul. Samples with greater then 85% viability were processed for sequencing. Single cell RNA-sequencing was performed at the University of Michigan Advanced Genomics Core Research Facility.
Single-cell 3' library generation was performed on the 10x Genomics Chromium Controller following the manufacturers protocol for the 3' v3.1 chemistry with NextGEM Chip G reagents (10x Genomics, Pleasanton, CA, USA). Library qualtiy was assessed by LabChip GXII HT (PerkinElmer) and wuantified by Qubit (Thermo Fisher Scientific).

treatment_protocol: Mice were treated with AZD1390 (20mg/kg) for 5 days starting on day 0, 1 dose of radiation (8Gy) on day 0, and 3 doses of anti-PD-L1 (100ug) once every three days starting on day -1. 6-8 tumors per treatment group were harvested on day 5.

value: pancreatic tumor

value: epithelial

tag: strain

value: 6-8 weeks

value: female


title: N-Acetylgalactosamine replicate 2

tag: cell type

value: 5mg/ml GalNAc


title: N-Acetylgalactosamine replicate 3

tag: genotype


title: Combo2

value: bone marrow


title: Cellobiose replicate 3

value: 5mg/ml Cellobiose


title: mT4 cells treated with RT and anti-PD-L1, scRNAseq

description: 10x Genomics


title: N-Acetylgalactosamine replicate 1


title: mT4 cells treated with RT, scRNAseq

description: 10x Genomics

value: RT


title: NEAT1-KO; hSOD1G93A_1


title: Cellobiose replicate 4


title: split ePE3 at multiple endogenous sites- Rep 3- I31

value: HEK293T cell


title: Gastric Mucin Oligosaccharides replicate 4


title: Cellobiose replicate 2


title: Cellobiose replicate 1