title: Microbiota of Stool from patient SYN_8  PRE treatment [SF08]

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: 16s rRNA v3-v4 sequencing of human Stool

data_processing:
library strategy: 16s rRNA v3-v4 paired-end (2x300) amplicon sequencing
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
primer check and trimming: qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 --verbose >Log_di_cutadapt.txt
quality check: qiime demux summarize  --i-data trimmed-seqs.qza --o-visualization demux.qzv
quality trimming, pair merging and ASV table creation: qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 264 --p-trunc-len-r 179 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
taxonomic assignment: qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
further analyses: R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: NA
Supplementary files format and content: feature_table.csv: CSV text file containing the abundance table
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence
Supplementary files format and content: dna-sequences.fasta: txt file containing the ASV names and sequences

source_name: Stool

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

value: Stool

tag: patient id

tag: treatment time

value: PRE

tag: treatment type

value: Placebo

tag: condition

value: Obese

value: Unknown

tag: gender

value: F

tag: smoker

value: Yes


title: Microbiota of Stool from patient SYN_9  PRE treatment [SF9]

status: Public on May 03 2023

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

value: Probiotic

tag: age

value: No


title: Microbiota of Stool from patient SYN_40  POST treatment [SF80]

value: POST


title: Microbiota of Stool from patient SYN_38  POST treatment [SF78]

value: M


title: PDC2_2

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
Library strategy: ChEC-seq
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
paired end alignment to S288C_R64 with bowtie2 (-p8 --local --very-sensitive --trim-to 30 --dovetail)
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)

organism: Saccharomyces cerevisiae

source_name: budding yeast culture at OD=4

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD4 in SC medium with glucose

extract_protocol:
Phenol chlorofrom extraction
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. 2015

tag: genetic information

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PDC2 MNase

tag: tagged tf

tag: variant-type

value: TF


title: PDC2_nonDBD_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PDC2 Δ72 138 MNase

value: nonDBD


title: Liver, MetRNA, LCMV, Rep17

city: Grand Rapids

first: Zach

middle: B

last: Madaj

state: MI

address: 333 Bostwick Ave NE

department: Bioinformatics and Biostatistics Core

country: USA

institute: Van Andel Research Institute

library_source: transcriptomic

data_processing:
RNA libraries were normalized, pooled, and sequenced on Illumina NovaSeq S1 flow cell using paired end, 50 base pair reads to an average depth of 50 M reads per sample
Base calling was performed by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0
Adapters and low-quality bases (Phred>30) were trimmed from raw reads using Trim_Galore
Trimmed reads were then aligned to the GRCm38 reference genome using the STAR aligner v2.7
Aligned read counts were imported into edgeR wherein library sizes were normalized using the trimmed mean of M values method and pairwise comparisons for differential expression were performed using the quasi-likelihood approach
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts and ENSEMBL gene IDs. Each column is a replicate, where matching numbers in the column names indicate matched liver samples fomr the same animal.

molecule: total RNA

organism: Mus musculus

source_name: Hepatic

extract_protocol:
RNA was isolated directly from frozen liver tissue (RNA) or from post-metabolite extracted liver tissue (MetRNA). Samples were pulverized using QIAzol Lysis Reagent and a Tissue Lyser II. RNA was then purified from the lysates using RNeasy Plus Universal Mini Kit column-based isolation per manufacturers’ instructions. Isolated RNA was quantified by Promega Quantus and measured for integrity using Agilent Bioanalyzer.
Stranded RNA libraries were prepared from 500 ng RNA using the KAPA - mRNA Hyper Prep (08098140702, Roche)

treatment_protocol:
At eleven weeks of age, mice were randomly selected to receive an intraperitoneal injection of lymphocytic choriomeningitis virus (LCMV) (Armstrong strain, 2x105 PFU by intravenous injection) or PBS vehicle (Veh). 2.5 days post-infection, mice were anesthetized with an isoflurane vaporizer. While anesthetized, the liver was removed and snap-frozen in liquid N2 for later processing.
Frozen livers were pulverized to a fine powder using a mortar and pestle pre-chilled in liquid N2. Being careful to avoid thawing of powdered liver, two roughly 30 mg aliquots of each liver were rapidly weighed into liquid N2 chilled tubes. One aliquot was weighed into a liquid N2 chilled 1.5 mL Eppendorf tube for later RNA extraction. The other aliquot was weighed in to a 2.0 mL Omni Bead Ruptor (19-627, Omni) tube for metabolite extraction. Precise weights were then recorded, and samples were stored at –80°C until processing.

value: Hepatic

tag: fraction

value: MetRNA

tag: treatment

value: LCMV


title: PDC2_1


title: Microbiota of Stool from patient SYN_36  POST treatment [SF76]

value: Stool

value: Ex


title: Microbiota of Stool from patient SYN_37  POST treatment [SF77]

value: Obese


title: Liver, RNA, Veh, Rep15

value: RNA

value: Veh


title: Liver, MetRNA, Veh, Rep15


title: MSN1_nonDBD_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MSN1 Δ278 356 MNase


title: Liver, RNA, Veh, Rep14


title: MSN1_nonDBD_4


title: MSN1_nonDBD_1


title: MSN1_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MSN1 MNase


title: Liver, MetRNA, Veh, Rep14


title: Microbiota of Stool from patient SYN_34  POST treatment [SF74]

value: Placebo


title: MOT3_d2_75_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MOT3 Δ2 75 SV40 NLS MNase::kanMX

value: Truncation


title: MOT3_d2_341_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MOT3 Δ2 341 SV40 NLS MNase::kanMX

value: DBD


title: MOT3_d2_341_2


title: MOT3_d2_75_4


title: Liver, RNA, Veh, Rep13


title: Microbiota of Stool from patient SYN_31  POST treatment [SF71]

value: POST

value: M

value: No


title: MOT3_d2_75_3


title: Microbiota of Stool from patient SYN_33  POST treatment [SF73]

value: Probiotic

value: F


title: Microbiota of Stool from patient SYN_28  POST treatment [SF68]

value: Stool

value: Yes


title: Liver, MetRNA, LCMV, Rep11

value: Hepatic

value: MetRNA

value: LCMV


title: Liver, RNA, LCMV, Rep12

value: RNA


title: MOT3_d2_341_3


title: Microbiota of Stool from patient SYN_32  POST treatment [SF72]

value: Obese


title: Microbiota of Stool from patient SYN_25  POST treatment [SF65]

value: Ex


title: MOT3_d2_300_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MOT3 Δ2 300 SV40 NLS MNase::kanMX


title: MOT3_d2_300_1

value: Truncation


title: Liver, RNA, LCMV, Rep10


title: Liver, RNA, LCMV, Rep11


title: Liver, MetRNA, LCMV, Rep12


title: MOT3_d2_75_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MOT3 Δ2 75 SV40 NLS MNase::kanMX


title: Microbiota of Stool from patient SYN_35  POST treatment [SF75]

value: Placebo


title: Microbiota of Stool from patient SYN_29  POST treatment [SF69]

value: POST


title: MOT3_d2_200_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MOT3 Δ2 200 SV40 NLS MNase::kanMX


title: MOT3_d2_300_2


title: Microbiota of Stool from patient SYN_24  POST treatment [SF64]

value: No


title: Liver, MetRNA, Veh, Rep13

value: Veh


title: MOT3_d2_250_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MOT3 Δ2 250 MNase::kanMX


title: MSN1_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MSN1 MNase

value: TF


title: MOT3_d2_341_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MOT3 Δ2 341 SV40 NLS MNase::kanMX

value: DBD


title: MOT3_d2_300_3


title: MOT3_d2_150_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MOT3 Δ2 150 SV40 NLS MNase::kanMX


title: MOT3_d2_150_1


title: MIG1_nonDBD_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MIG1 Δ34 94 MNase::kanMX

value: nonDBD


title: Microbiota of Stool from patient SYN_23  POST treatment [SF63]

value: Stool

value: Obese

value: F

value: Yes


title: Liver, MetRNA, LCMV, Rep10

value: Hepatic

value: MetRNA

value: LCMV


title: MOT3_d2_200_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MOT3 Δ2 200 SV40 NLS MNase::kanMX

value: Truncation


title: Microbiota of Stool from patient SYN_22  POST treatment [SF62]

value: POST

value: Probiotic

value: M

value: No


title: MIG1_d95_504_6

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MIG1 Δ95 504 SV40 NLS MNase::kanMX

value: DBD


title: Liver, RNA, LCMV, Rep9

value: RNA


title: MIG1_nonDBD_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MIG1 Δ34 94 MNase::kanMX

value: nonDBD


title: Microbiota of Stool from patient SYN_21  POST treatment [SF61]

value: Stool

value: Obese

value: Ex


title: MIG1_d95_504_3


title: Microbiota of Stool from patient SYN_6  PRE treatment [SF6]

value: PRE


title: Liver, MetRNA, LCMV, Rep9

value: Hepatic

value: MetRNA


title: Liver, RNA, Veh, Rep7

value: Veh


title: Microbiota of Stool from patient SYN_19  POST treatment [SF59]


title: MIG1_d95_504_5


title: MIG1_d95_504_4


title: MIG1_d451_504_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MIG1 Δ451 504 SV40 NLS MNase::kanMX

value: Truncation


title: Liver, MetRNA, Veh, Rep8


title: MIG1_d95_504_1


title: Microbiota of Stool from patient SYN_15  POST treatment [SF55]

value: POST

value: Placebo

value: F


title: MIG1_d95_504_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MIG1 Δ95 504 SV40 NLS MNase::kanMX


title: MIG1_d401_504_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MIG1 Δ401 504 SV40 NLS MNase::kanMX


title: Liver, RNA, Veh, Rep6

value: RNA


title: MIG1_d401_504_2


title: Microbiota of Stool from patient SYN_14  POST treatment [SF54]

value: M

value: No


title: Liver, MetRNA, Veh, Rep6


title: MIG1_d351_504_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MIG1 Δ351 504 SV40 NLS MNase::kanMX


title: MIG1_d301_504_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MIG1 Δ301 504 SV40 NLS MNase::kanMX


title: MIG1_d351_504_2


title: Microbiota of Stool from patient SYN_13  POST treatment [SF53]

value: Stool

value: Probiotic

value: Obese


title: Liver, MetRNA, Veh, Rep7

value: Hepatic

value: MetRNA


title: MIG1_d451_504_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MIG1 Δ451 504 SV40 NLS MNase::kanMX


title: MIG1_d301_504_3

value: Truncation


title: MIG1_d301_504_2


title: Liver, RNA, Veh, Rep5

value: Veh


title: Liver, MetRNA, Veh, Rep5


title: MIG1_d201_504_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MIG1 Δ201 504 SV40 NLS MNase::kanMX


title: Microbiota of Stool from patient SYN_12  POST treatment [SF52]

value: POST

value: Placebo

value: F


title: MIG1_d201_504_4


title: Microbiota of Stool from patient SYN_9  POST treatment [SF49]


title: MIG1_d201_504_1


title: MGA1_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MGA1 MNase

value: TF


title: Liver, RNA, Veh, Rep8

value: RNA


title: MGA1_1


title: Microbiota of Stool from patient SYN_6  POST treatment [SF46]

value: M

value: No


title: Microbiota of Stool from patient SYN_18  POST treatment [SF58]

value: Stool

value: Yes


title: MBP1_d751_833_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MBP1 Δ751 833 SV40 NLS MNase


title: Liver, RNA, Veh, Rep3

value: Hepatic


title: Microbiota of Stool from patient SYN_5  POST treatment [SF45]

value: Probiotic

value: Obese

value: Ex


title: MBP1_d651_833_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MBP1 Δ651 833 SV40 NLS MNase

value: Truncation


title: MBP1_d651_833_2


title: MBP1_d751_833_1


title: Microbiota of Stool from patient SYN_4  POST treatment [SF44]

value: POST


title: MBP1_d451_833_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MBP1 Δ451 833 SV40 NLS MNase


title: Liver, MetRNA, LCMV, Rep2

value: MetRNA

value: LCMV


title: Liver, RNA, LCMV, Rep2


title: Microbiota of Stool from patient SYN_11  POST treatment [SF51]

value: Placebo

value: F


title: Liver, MetRNA, Veh, Rep4

value: Veh


title: Liver, RNA, Veh, Rep4

value: RNA


title: Microbiota of Stool from patient SYN_5  PRE treatment [SF5]

value: Stool

value: PRE

value: M


title: MBP1_d451_833_1


title: Liver, MetRNA, Veh, Rep3

value: Hepatic


title: MBP1_d351_833_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MBP1 Δ351 833 SV40 NLS MNase


title: Microbiota of Stool from patient SYN_3  POST treatment [SF43]

value: Probiotic

value: Obese

value: No


title: MBP1_d351_833_1

value: Truncation


title: MBP1_d251_833_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MBP1 Δ251 833 SV40 NLS MNase


title: Liver, MetRNA, LCMV, Rep1


title: MBP1_d251_833_1


title: MBP1_d151_833_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MBP1 Δ151 833 SV40 NLS MNase

value: DBD


title: MBP1_d151_833_2


title: Microbiota of Stool from patient SYN_2  POST treatment [SF42]

value: POST


title: Microbiota of Stool from patient SYN_1  POST treatment [SF41]


title: Microbiota of Stool from patient SYN_40  PRE treatment [SF40]

value: Placebo

value: Yes


title: 49633_Het_256

city: Duarte

first: Keane

last: Lai

state: CA

address: 1500 E Duarte Rd

department: Molecular Medicine BRI

institute: City of Hope National Medical Center

description:
counts_klai_220919_mm10.txt
RPKM_klai_220919_mm10.txt

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
Sequences were aligned to mm10 using STAR with default settings
Gene expression level of Refseq coding genes were quantified using HTSeq
Assembly: mm10
Supplementary files format and content: tab delimited text file gene expression counts

source_name: liver

extract_protocol:
The collected mice liver tissues were stored up to 1 week at 4'C in RNAlater (from Sigma), and frozen at -80'C for longer storage or went to RNA extraction. RNA was extracted with the Quick-RNA Miniprep kit (Zymo Research) and treated with DNase I.
RNA-seq libraries were constructed by using KAPA mRNA HyperPrep kits ( Roche )

value: liver

tag: Sex

value: male

tag: strain

tag: genotype

value: Midn hemizygotes

value: high-fat-fructose-cholesterol diet for 25 weeks


title: IXR1_d2_300_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 IXR1 Δ2 300 SV40 NLS MNase


title: MBP1_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MBP1 MNase

value: TF


title: Microbiota of Stool from patient SYN_4  PRE treatment [SF4]

value: Stool

value: PRE

value: Probiotic

value: F

value: Ex


title: 49630_Het_241


title: MBP1_2


title: IXR1_d2_300_4


title: Microbiota of Stool from patient SYN_38  PRE treatment [SF38]

value: Obese

value: M

value: No


title: MBP1_d251_833_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MBP1 Δ251 833 SV40 NLS MNase

value: Truncation


title: Liver, RNA, LCMV, Rep1

value: Hepatic

value: RNA

value: LCMV


title: IXR1_d2_300_1

value: DBD


title: 49629_wt_240

value: liver

value: male

value: wild type

value: high-fat-fructose-cholesterol diet for 25 weeks


title: IXR1_d2_300_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 IXR1 Δ2 300 SV40 NLS MNase


title: Microbiota of Stool from patient SYN_37  PRE treatment [SF37]

value: Stool

value: PRE

value: Probiotic


title: IXR1_d2_200_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 IXR1 Δ2 200 SV40 NLS MNase


title: IXR1_d2_200_1


title: 49628_wt_239


title: Microbiota of Stool from patient SYN_36  PRE treatment [SF36]

value: Placebo

value: Obese

value: M

value: Ex


title: IXR1_d2_100_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 IXR1 Δ2 100 SV40 NLS MNase

value: Truncation


title: Microbiota of Stool from patient SYN_35  PRE treatment [SF35]

value: F

value: Yes


title: 49626_wt_237

value: liver


title: Microbiota of Stool from patient SYN_34  PRE treatment [SF34]


title: INO2_d2_65_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 INO2 Δ2 65 SV40 NLS MNase


title: INO2_d2_65_3


title: INO2_d2_200_5

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 INO2 Δ2 200 SV40 NLS MNase

value: DBD


title: 49625_wt_235

value: male

value: wild type

value: high-fat-fructose-cholesterol diet for 25 weeks


title: 49631_Het_244

value: Midn hemizygotes


title: Microbiota of Stool from patient SYN_33  PRE treatment [SF33]

value: Stool

value: PRE

value: Probiotic

value: No


title: LC3_581_M

city: Philadelphia

first: Kathleen

last: Boesze-Battaglia

state: PA

address: 240 South 40th St

institute: University of Pennsylvania

data_processing:
Raw data was demuliplexed with the Illumina processing pipeline yeilding trimmed fastq files per sample
Fastq data was mapped to the mouse transciptiome defined in Gencode version M26
Transcipt counts were summarized to the gene level with the bioconductor package tximeta
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm39
Assembly: gencode M26 gene models
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Retinal pigment epithelium cells

extract_protocol:
Total RNA was isolated by RNAEasy Plus Micro kit (QIAgen) per manufacturer’s instructions. RNA concentration and sample quality was determined using an Agilent bioanalyzer.
15 ng of total RNA was used for library preparation using NEB Ultra II stranded mRNA library kit as per manufacturer’s instructions and assessed for quality.
Libraries were subjected to 100 bp single read sequencing on a NovaSeq SP flow cell using a NovaSeq 6000 sequencing system by the Next-Generation Sequencing Core of the University of Pennsylvania.

value: Male

tag: cell type

value: Retinal pigment epithelium cells

value: LCb-/-

value: 24 months


title: INO2_d2_130_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 INO2 Δ2 130 SV40 NLS MNase

value: Truncation


title: Microbiota of Stool from patient SYN_31  PRE treatment [SF31]

tag: patient id

value: Placebo

value: Obese

value: M


title: INO2_d2_130_5


title: IXR1_d2_100_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 IXR1 Δ2 100 SV40 NLS MNase


title: Microbiota of Stool from patient SYN_32  PRE treatment [SF32]

tag: treatment time


title: LC3_579_F3

value: Female


title: 49627_wt_238

value: liver

value: male

value: wild type

value: high-fat-fructose-cholesterol diet for 25 weeks


title: INO2_d2_200_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 INO2 Δ2 200 SV40 NLS MNase

value: DBD


title: INO2_d2_130_1


title: LC3_579_F1


title: Microbiota of Stool from patient SYN_3  PRE treatment [SF3]

value: Stool

value: PRE

tag: treatment type

value: Probiotic

value: F

value: No


title: HOT1_d2_500_5

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 HOT1 Δ2 500 SV40 NLS MNase::kanMX


title: INO2_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 INO2 MNase

value: TF


title: INO2_2


title: Microbiota of Stool from patient SYN_29  PRE treatment [SF29]

tag: condition

value: Obese

value: M


title: HOT1_d2_500_3


title: C57_567_M1

value: Male

value: Retinal pigment epithelium cells

value: WT

value: 24 months


title: C57_567_F3

value: Female


title: Microbiota of Stool from patient SYN_28  PRE treatment [SF28]

value: Placebo

tag: gender

value: Yes


title: C57_567_F2


title: HOT1_d2_500_2

value: DBD


title: HOT1_d2_500_1


title: HOT1_d2_100_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 HOT1 Δ2 100 SV40 NLS MNase::kanMX

value: Truncation


title: Microbiota of Stool from patient SYN_27  POST treatment [SF67]

value: Stool

value: POST

value: Probiotic

value: Unknown

value: F

tag: smoker


title: INO2_d2_200_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 INO2 Δ2 200 SV40 NLS MNase


title: HCM1_d451_564_7

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 HCM1 Δ451 564 SV40 NLS MNase


title: HOT1_d2_500_6

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 HOT1 Δ2 500 SV40 NLS MNase::kanMX


title: Microbiota of Stool from patient SYN_25  PRE treatment [SF25]

tag: tissue

value: PRE

value: Obese

value: Ex


title: HCM1_d451_564_6


title: C57_567_F1

value: Female

value: Retinal pigment epithelium cells

value: WT

tag: age

value: 24 months


title: HOT1_d2_100_1

tag: genetic information

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 HOT1 Δ2 100 SV40 NLS MNase::kanMX


title: CD45-Ter119- cells from the bone marrow of PyMT-N tumor-resected mice, 28 days after resection

city: Houston

first: Xiang

last: Zhang

state: Texas

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Tumor-resected

library_source: transcriptomic single cell

data_processing:
The mm10 genome was used for reads mapping. Raw sequencing files were imported into 10x Genomics Cell Ranger toolkit (v3.1.0) with default settings for quantifications.
Assembly: mm10
Supplementary files format and content: Compressed .gz files contains the filtered_feature_bc_matrix output folder from Cellranger. Each .gz file contains a .mtx file which is the count matrix and two .tsv files that list the feature names and sample annotations.

source_name: Bone marrow

extract_protocol:
To isolate the BM niche and HSPC cells, the muscle tissue on the tibia and femur were completely removed, then flushed out the BM cells. The remaining bone were cut and crashed into fragments and digest in DMEM containing 1 mg/mL Collagenase 1, 1 mg/mL Collagenase 2 , 4 mg/mL Dispase 2 , 0.1 mg/mL DNase 1 , 1 mg/mL BSA, 1% HEPES and antibiotics for 45 min at 37°C. Flushed BM cells also incubate in the same digest buffer for 15 min at 37°C. After digestion, bone cells and BM cells are filtered through a 70 µm strainer and resuspended in RBC lysis buffer, then combined into one sample (per mouse) for subsequent step analysis. Lin-cKit+ or CD45-Ter119- from the same batch of experiment were sorted into single-cell suspension and immediately submitted to the Single Cell Genomics Core at Baylor College of Medicine.
The single-cell gene expression library was prepared according to the Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics).

value: Bone marrow niche cells

tag: inoculated tumor cell line

value: PyMT-N


title: Microbiota of Stool from patient SYN_16  POST treatment [SF56]

value: Stool

value: POST

value: Placebo

value: M

value: No


title: HCM1_d351_564_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 HCM1 Δ351 564 SV40 NLS MNase

tag: tagged tf

tag: variant-type

value: Truncation


title: HCM1_d251_564_6

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 HCM1 Δ251 564 SV40 NLS MNase

value: DBD


title: HCM1_d251_564_3


title: CD45+Lin-c-Kit+ cells from the bone marrow of Naïve mice, 28 days after Sham surgery

description: Tumor-free

value: Hematopoietic stem cells and progenitor cells


title: Microbiota of Stool from patient SYN_23  PRE treatment [SF23]

value: PRE

value: Obese

value: F

value: Yes


title: Microbiota of Stool from patient SYN_24  PRE treatment [SF24]


title: HCM1_d251_564_5


title: HCM1_d351_564_2


title: Microbiota of Stool from patient SYN_21  PRE treatment [SF21]

value: Probiotic

value: Ex


title: Microbiota of Stool from patient SYN_22  PRE treatment [SF22]


title: HCM1_d251_564_2


title: C498_LPS_2

city: qingdao

first: jing

last: Xv

address: East Hong Kong Road

country: China

institute: Ocean  University of China

description: TPM

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software. The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/) in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples/groups, the expression level of each gene was calculated according to the transcripts per million reads (TPM) method.
RSEM (http://deweylab.biostat.wisc.edu/rsem/)was used to quantify gene abundances.
Assembly: ENSMUSG
Supplementary files format and content: gene_id, gene_name, sample name, etc

source_name: peritoneal macrophages

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent  according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). RNA degradation and contamination was monitored on 1% agarose gels. Then RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥8.0, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
The ranscriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer (2 × 150bp read length).

value: peritoneal macrophages

tag: treatment


title: HCM1_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 HCM1 MNase

value: TF


title: MIG1_d301_504_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MIG1 Δ301 504 SV40 NLS MNase::kanMX


title: HCM1_2


title: GLN3_nonDBD_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 GLN3 Δ307 340 MNase::kanMX

value: nonDBD


title: C498_LPS_1

description: TPM


title: GLN3_nonDBD_1


title: CD45-Ter119- cells from the bone marrow of Naïve mice, 28 days after Sham surgery

description: Tumor-free

value: Bone marrow niche cells


title: CD45+Lin-c-Kit+ cells from the bone marrow of PyMT-N tumor-resected mice, 28 days after resection

description: Tumor-resected

value: PyMT-N


title: C498_2

description: TPM


title: GLN3_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 GLN3 MNase::kanMX


title: GLN3_4


title: HCM1_d251_564_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 HCM1 Δ251 564 SV40 NLS MNase

value: DBD


title: GLN3_1


title: C498_1

description: TPM


title: LPS_1

description: TPM

value: LPS


title: GIS1_nonDBD_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 GIS1 Δ828 889 MNase


title: Microbiota of Stool from patient SYN_2  PRE treatment [SF2]

value: Stool

value: PRE

value: Obese

value: F

value: No


title: GIS1_d2_700_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 GIS1 Δ2 700 SV40 NLS MNase


title: Microbiota of Stool from patient SYN_18  PRE treatment [SF18]

value: Placebo

value: M

value: Yes


title: LPS_2

description: TPM

value: peritoneal macrophages


title: GIS1_nonDBD_2

value: nonDBD


title: Microbiota of Stool from patient SYN_19  PRE treatment [SF19]

value: Probiotic


title: GIS1_d2_700_2


title: Microbiota of Stool from patient SYN_15  PRE treatment [SF15]


title: Microbiota of Stool from patient SYN_7  POST treatment [SF47]

value: POST

value: Unknown


title: CTRL_1

description: TPM

value: DMSO


title: CTRL_2

description: TPM


title: GIS1_d2_400_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 GIS1 Δ2 400 SV40 NLS MNase

value: Truncation


title: Microbiota of Stool from patient SYN_27  PRE treatment [SF27]

value: Stool


title: Microbiota of Stool from patient SYN_14  PRE treatment [SF14]

value: PRE


title: GLN3_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 GLN3 MNase::kanMX

value: TF


title: GIS1_d2_310_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 GIS1 Δ2 310 SV40 NLS MNase


title: GIS1_d2_400_1


title: -WS.2

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

description: OG2 MEFs of passages 1-3 were seeded into 6-well plates at density of 2.5 x 10^4 cells/plate. On the next day, medium was changed to reprogramming medium. Medium was changed every 2 days. For reprogramming day 4 to 8, the medium was renewed every day.  Indicated small molecule was removed from the medium in day 8-12 and RNA-seq samples were collected on day 12.

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the mouse genome (mm10) using HISAT2 (v2.2.1) with the default parameter settings.
Gene expression based on GENCODE vM25 annotations was determined using stringtie (v2.0) with the default parameter settings.
Fragments per Kilobase per Million (FPKM) were calculated for representing the expression of each gene.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene FPKM for every gene and every sample

source_name: Reprogramming intermediate

growth_protocol: iPSCs were seeded on Feeder and maintained in mESC medium. mESC medium contains 47% DMEM/F12, 47% Neural basal medium, 1 x N2 supplement, 1 x B27 supplement, 1% Glutamax, 1% nonessential amino acids (NEAA), 0.055 mM 2-mercaptoethanol (β-ME), 1% P/S, 1000 units/mL mLIF, 3 μM CHIR99021 and 0.2 μM PD0325901. MEFs were cultured in MEF medium, containing DMEM Basic, 10% fetal bovine serum (FBS), 1% penicillin and streptomycin (P/S).

extract_protocol:
RNA was isolated using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme) according to the manufacture’s instruction.
RNA-seq library preparation and sequencing were performed by Novogene. The RNA-seq libraries were sequenced on the Illumina NovaSeq 6000 with read length of 150 bp.

treatment_protocol: FCR: OG2 MEFs of passages 1-3 were seeded into 6-well plates at density of 2.5 x 10^4 cells/plate. On the next day, medium was changed to reprogramming medium. Medium was changed every 2 days. For reprogramming day 4 to 8, the medium was renewed every day.  TFR: OG2 MEFs of passages 1-3 were seeded into 6-well plates. The OG2 MEFs were infected with lentivirus expressing Oct4, Sox2, Klf4, and c-Myc when cells were about 60% confluence. 24h after infection, the OG2 MEFs were replated into 24-well plates (1 × 10^5 cells/plate). On the next day, medium was changed to reprogramming medium, containing DMEM Basic, 10% fetal bovine serum (FBS), 10% knockout serum replacement (KSR), 1% nonessential amino acids (NEAA),  1% penicillin and streptomycin (P/S), 0.055 mM 2-mercaptoethanol (β-ME), with 2 ug/ml doxycycline. Medium was renewed every 2 days.

value: Reprogramming intermediate


title: FKH2_nonDBD_8

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 FKH2 Δ340 425 MNase::kanMX


title: FKH2_nonDBD_7


title: GIS1_d2_190_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 GIS1 Δ2 190 SV40 NLS MNase


title: Microbiota of Stool from patient SYN_13  PRE treatment [SF13]

value: Obese

value: F

value: No


title: GIS1_d2_190_2


title: FKH2_nonDBD_4

value: nonDBD


title: Microbiota of Stool from patient SYN_7  PRE treatment [SF07]

value: Placebo

value: M


title: -WS.1


title: FKH2_nonDBD_6


title: -VC.2


title: Microbiota of Stool from patient SYN_16  PRE treatment [SF16]

value: Unknown


title: Microbiota of Stool from patient SYN_12  PRE treatment [SF12]


title: -VC.1


title: Microbiota of Stool from patient SYN_11  PRE treatment [SF11]


title: FKH2_d701_861_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 FKH2 Δ701 861 SV40 NLS MNase::kanMX


title: FKH2_d701_861_3

value: Truncation


title: FKH2_d601_861_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 FKH2 Δ601 861 SV40 NLS MNase::kanMX


title: FKH2_d701_861_1


title: -PD.2


title: FKH2_d601_861_3


title: FKH2_d701_861_2


title: FKH2_d601_861_2


title: -PD.1


title: FKH2_d601_861_1


title: MIG1_d201_504_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 MIG1 Δ201 504 SV40 NLS MNase::kanMX


title: Microbiota of Stool from patient SYN_1  PRE treatment [SF1]

value: Stool

value: PRE

value: Probiotic


title: CT.2

value: Reprogramming intermediate


title: Microbiota of Saliva from patient CRC69

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-H12-FAS-69S-T0

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
primer check and trimming: qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 8 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose >Log_di_cutadapt.txt
quality check: qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
quality trimming, pair merging and ASV table creation: quality trimming, pair merging and ASV table creation: qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 261 --p-trunc-len-r 184  --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
taxonomic assignment: qiime feature-classifier classify-consensus-vsearch --i-query rep-seqs.qza --i-reference-reads silva-138-99-seqs.qza --i-reference-taxonomy silva-138-99-tax.qza --p-perc-identity 0.99 --p-threads 8 --o-classification taxonomy_vsearch.qza --o-search.results vsearch_hits.qza --verbose
further analyses: R software (see the relative script publicly available at github.com/LeandroD94)
Supplementary files format and content: rep_sequences.fasta: representative ASV sequences in fasta fomat (sequence names correspond to row names of the feature_table.tsv file)
Supplementary files format and content: feature_table.tsv: TSV text file containing the abundance table
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence
Library strategy: amplicon sequencing

source_name: Saliva

value: Saliva

tag: Sex

value: Adenocarcinoma

tag: tumor type

tag: stadiation

value: III


title: FKH2_d501_861_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 FKH2 Δ501 861 SV40 NLS MNase::kanMX


title: FKH2_d501_861_1


title: FKH2_d451_861_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 FKH2 Δ451 861 SV40 NLS MNase::kanMX

value: DBD


title: -CHIR.2

tag: cell type

tag: genotype


title: CT.1


title: MA009-10, biological replicate 2

city: Tianjin

first: Feiyu

last: Fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

description:
2G clean data
MA008-3, Pk2365:: PPkFBA1-EcSthA-TPkINO1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Pichia kudriavzevii CY902 genome using Bowtie 2 (version 2.2.5) .Detailed parameters for reads mapping: bowtie2 -x Index -1 sample_1.fq -2  sample_2.fq --no-mixed -p 2 -S sample.sam
The aligned reads were stored in SAM format, and the raw counts for reads mapped to unique genes were then tallied using the HTSeq-count script (0.6.0) in intersection-non-empty resolution mode.
The gene expression level was calculated using the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method
Assembly: Pichia kudriavzevii CY902 nuclear and mitochondrial genome sequences (CP039612.1-CP039617.1)
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample; CDS.fas (The CDS sequence corresponding to each gene)

molecule: polyA RNA

organism: Pichia kudriavzevii

source_name: Yeast cells

growth_protocol: Yeast cells grown overnight were used to inoculate a 250 ml flask with 50 ml rich medium (55 g/L glucose, 10 g/L yeast extract, 2 g/L peptone, and 0.4 mg/L biotin) to an OD600 of 0.1 and cultivated at 30°C and 250 rpm. Samples were collected after 18 hours of incubation by centrifugation at 6000g for 5 minutes and washed twice with phosphate buffered saline (PBS). Subsequently, yeast cells were flash-frozen and total RNA were extracted and used to generate Illumina RNA-seq libraries from polyA-selected mRNA.

extract_protocol:
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Yeast cells

value: MA008-3, Pk2365::PPkFBA1-EcSthA-TPkINO1

tag: time


title: Microbiota of Saliva from patient AP66

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-H09-FAS-66S-T0

tag: patient id

value: F

tag: condition

value: Adenoma

value: Proximal

value: Unknown


title: -CHIR.1


title: CF1-iPSC.2

description: iPSCs were seeded on Feeder and maintained in mESC medium. mESC medium contains 47% DMEM/F12, 47% Neural basal medium, 1 x N2 supplement, 1 x B27 supplement, 1% Glutamax, 1% nonessential amino acids (NEAA), 0.055 mM 2-mercaptoethanol (β-ME), 1% P/S, 1000 units/mL mLIF, 3 μM CHIR99021 and 0.2 μM PD0325901.

source_name: iPSC

value: iPSC


title: MA009-5, biological replicate 3

description:
2G clean data
MA008-3, ΔPk2365

value: 50 ml rich medium (55 g/L glucose, 10 g/L yeast extract, 2 g/L peptone, and 0.4 mg/L biotin)


title: CF1-iPSC.1


title: Microbiota of Colon biopsy from patient AP40

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-H06-FAS-40B-T0

source_name: Colon biopsy

value: Colon biopsy

value: M

value: Distal


title: FKH2_d451_861_3


title: FKH2_d451_861_1


title: Microbiota of Stool from patient SYN_8  POST treatment [SF48]

value: Stool

tag: treatment time

value: POST

tag: treatment type

value: Placebo

value: Obese

tag: gender

tag: smoker

value: Yes


title: Microbiota of Colon biopsy from patient AP60

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-H08-FAS-60B-T0

tag: tissue


title: MA009-5, biological replicate 2

description:
2G clean data
MA008-3, ΔPk2365


title: MA009-5, biological replicate 1

description:
2G clean data
MA008-3, ΔPk2365


title: CF1-D12.2

description: CF1 MEFs of passages 1-3 were seeded into 6-well plates at density of 2.5 x 10^4 cells/plate. On the next day, medium was changed to reprogramming medium. Medium was changed every 2 days. For reprogramming day 4 to 8, the medium was renewed every day.

value: Reprogramming intermediate


title: Microbiota of Stool from patient CRC69

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-G12-FAS-69F-T0

value: Adenocarcinoma

value: III


title: FKH2_d2_300_3

tag: genetic information

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 FKH2 Δ2 300 SV40 NLS MNase::kanMX

tag: tagged tf

value: Truncation


title: Microbiota of Stool from patient AP67

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-H05-FAS-67F-T0

value: F

value: Adenoma

value: Proximal


title: Microbiota of Colon biopsy from patient CRC34

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-G11-FAS-34B-T0

value: Unknown


title: FKH2_d2_300_2

tag: variant-type


title: CF1-D12.1


title: MA009-10, biological replicate 3

value: Yeast cells

value: MA008-3, Pk2365::PPkFBA1-EcSthA-TPkINO1

tag: treatment

value: 50 ml rich medium (55 g/L glucose, 10 g/L yeast extract, 2 g/L peptone, and 0.4 mg/L biotin)


title: MA009-10, biological replicate 1


title: Microbiota of Stool from patient AP66

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-G09-FAS-66F-T0

value: Stool

tag: Sex

tag: tumor type


title: CF1-D8.1

tag: cell type


title: FKH2_d2_300_1


title: FKH2_d451_861_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 FKH2 Δ451 861 SV40 NLS MNase::kanMX

value: DBD


title: P10_set2_rep1

city: New York

first: Andrew

last: Ji

state: NY

address: 1428 Madison Ave.

institute: Icahn School of Medicine at Mount Sinai

data_processing:
library strategy: Spatial Transcriptomics
Libraries were sequenced on NextSeq2000 (Illumina) with a 28-10-10-150 setup (for patient 3 and patient 10 Set 1) and NovaSeq6000 (Illumina) with a 28-10-10-120 setup (patient 10 Set 2). Between 218 and  346 million raw reads were generated per sample. Following demultiplexing of bcl files, read 2 fastq files were trimmed using Cutadapt (Martin, 2011) to remove full-length or truncated template switch oligo (TSO) sequences from the 5’ end (beginning of read 2) and polyA homopolymers from the 3’ end (end of read 2). The TSO sequence (AAGCAGTGGTATCAACGCAGAGTACATGGG) was used as a non-internal 5’ adapter with a minimum overlap of 5, meaning that partial matches (up to 5 base pairs) or intact TSO sequences were removed from the 5’ end. The error tolerance was set to 0.1 for the TSO trimming to allow for a maximum of 3 errors. For the 3’ end homopolymer trimming, a sequence of 10 As was used as a regular 3’ adapter to remove potential polyA tail products regardless of its position in the read, also with a minimum overlap of 5 base pairs. The trimmed data was processed with the spaceranger pipeline (version 1.0.0, 10X Genomics) and mapped to the GRCH38 v93 genome assembly.
Genome_build: GRCh38 v93
Supplementary_files_format_and_content: 10X spaceranger v1.0.0 pipeline outputs from /filtered_feature_bc_matrix/ and /spatial/ folders  including genes by barcode counts matrices (.mtx, .tsv), PNG of all replicate images, JSON of scaling factors, and Visium tissue position lists per replicate (.csv)

source_name: Skin

extract_protocol:
For Visium, two sections per patient were cut at 10 µm thickness and mounted onto Visium slide capture areas. Sequencing libraries were prepared following the manufacturer’s protocol, again with the Hematoxylin staining time adapted to 4 minutes. After tissue staining, bright-field images were taken as described in the Spatial Transcriptomics procedure. Tissue permeabilization was performed for 14 minutes, as established in the TO assay.
The Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics) was used to generate sequencing libraries for Visium samples.

value: Normal Skin


title: Microbiota of Saliva from patient AP60

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-G08-FAS-60S-T0

value: Saliva

value: M

tag: stadiation


title: P10_set2_rep2


title: Microbiota of Saliva from patient AP21

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-G06-FAS-21S-T0


title: FKH2_d2_300_4


title: CF1-D4.2

value: Reprogramming intermediate

tag: genotype


title: CF1-D4.1


title: P10_set1_rep2


title: P10_set1_rep1


title: FKH2_d2_250_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 FKH2 Δ2 250 SV40 NLS MNase::kanMX


title: FKH2_d2_250_1


title: FKH2_d2_250_4


title: Microbiota of Colon biopsy from patient AP67

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-G05-FAS-67B-T0

value: Colon biopsy


title: Microbiota of Stool from patient AP60

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-F08-FAS-60F-T0


title: CF1-D0.2

description: MEFs were cultured in MEF medium, containing DMEM Basic, 10% fetal bovine serum (FBS), 1% penicillin and streptomycin (P/S).

source_name: MEF

value: MEF


title: CF1-D0.1


title: P3_rep1


title: P3_rep2


title: FKH2_d2_200_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 FKH2 Δ2 200 SV40 NLS MNase::kanMX

value: Truncation


title: CF1-D8.2


title: Microbiota of Stool from patient AP21

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-F06-FAS-21F-T0

value: Adenoma

value: Proximal


title: scAT, SV_9

city: Milan

first: Letizia

last: Messa

address: Piazza Leonardo Da Vinci 32

department: Electronics, Informatics and Bioengineering

institute: Politecnico di Milano

data_processing:
Quality control of the raw data output were examined on FastQC software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt software. UMI were detected and extracted with UMI tools
Trimmed sequence reads were mapped to GRCh38.p13 using STAR
Read count extraction was performed using FeatureCounts
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files for each Sample

source_name: Periumbilical subcutaneous adipose tissues, Severe obesity (BMI-z score >3 )

growth_protocol: Periumbilical subcutaneous adipose tissues (scAT) were surgically collected from 20 prepubertal male children (range 1-12 years old), enrolled at the Buzzi Children’s Hos-pital (Milano, Italy), for the study of the gene expression profile

extract_protocol:
Total RNA was extracted from SAT using Trizol reagent (Invitrogen, Carlsbad, CA), according to the manufacturer's instructions. RNA quantity and integrity were estimated using the Qubit instrument (Invitrogen, Carlsbad, CA) and the Agilent 4200 TapeStation System (Agilent, Santa Clara, CA).
RNA libraries were performed using the CORALL total RNA-Seq library Prep Kit (Lexogen, Vienna, Austria) and the RiboCop rRNA De-pletion Kit (Lexogen, Vienna, Austria) was used to remove rRNA. Libraries qualities were assessed with High Sensitivity D1000 ScreenTape Assay using the 4200 TapeStation System (Agilent, Santa Clara, CA, USA) and quantified with Qubit dsDNA HS Assay Kit (Invitrogen, Carlsbad, CA).

tag: phenotype

value: SV


title: FKH2_d2_200_1


title: FKH2_d2_100_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 FKH2 Δ2 100 SV40 NLS MNase::kanMX


title: scAT, SV_8

value: Periumbilical subcutaneous adipose tissue


title: 4F-TFR-iPSC.1

value: iPSC


title: Microbiota of Colon biopsy from patient AP21

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-E06-FAS-21B-T0

tag: patient id

value: Unknown


title: Microbiota of Saliva from patient CRC59

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-D12-FAS-59S-T0

tag: condition

value: Adenocarcinoma

value: Distal

value: III


title: scAT, OB_26

source_name: Periumbilical subcutaneous adipose tissues, obesity (3≤BMI-z score ≤2)

value: OB


title: FKH2_d2_100_1


title: scAT, OB_10


title: 4F-TFR-D7.2

description: For TFs-mediated reprogramming, OG2 MEFs of passages 1-3 were seeded into 6-well plates. The OG2 MEFs were infected with lentivirus expressing Oct4, Sox2, Klf4, and c-Myc when cells were about 60% confluence. 24h after infection, the OG2 MEFs were replated into 24-well plates (1 × 10^5 cells/plate). On the next day, medium was changed to reprogramming medium, containing DMEM Basic, 10% fetal bovine serum (FBS), 10% knockout serum replacement (KSR), 1% nonessential amino acids (NEAA),  1% penicillin and streptomycin (P/S), 0.055 mM 2-mercaptoethanol (β-ME), with 2 ug/ml doxycycline. Medium was renewed every 2 days.

value: Reprogramming intermediate


title: scAT, OB_7


title: Microbiota of Stool from patient CRC59

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-C12-FAS-59F-T0

value: Stool

value: M


title: 4F-TFR-D4.2


title: 4F-TFR-D7.1


title: FKH1_nonDBD_5

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 FKH1 Δ303 388 MNase

value: nonDBD


title: 4F-TFR-D4.1


title: scAT, OB_6


title: scAT, OB_3


title: Microbiota of Stool from patient CRC71

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-C06-FAS-71F-T0

value: I


title: FKH1_nonDBD_4


title: FKH1_nonDBD_3


title: Microbiota of Colon biopsy from patient CRC48

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-B09-FAS-48B-T0

value: Colon biopsy

value: F


title: 4F-TFR-D2.2


title: 4F-TFR-iPSC.2

description: iPSCs were seeded on Feeder and maintained in mESC medium. mESC medium contains 47% DMEM/F12, 47% Neural basal medium, 1 x N2 supplement, 1 x B27 supplement, 1% Glutamax, 1% nonessential amino acids (NEAA), 0.055 mM 2-mercaptoethanol (β-ME), 1% P/S, 1000 units/mL mLIF, 3 μM CHIR99021 and 0.2 μM PD0325901.


title: 4F-TFR-D2.1


title: Microbiota of Saliva from patient CRC65

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-C08-FAS-65S-T0

value: Saliva


title: FKH1_d2_280_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 FKH1 Δ2 280 SV40 NLS MNase

value: DBD


title: 4F-TFR-D0.2

value: MEF


title: Microbiota of Stool from patient CRC65

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-B08-FAS-65F-T0


title: FKH1_d2_280_2


title: Microbiota of Saliva from patient AP40

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-B07-FAS-40S-T0

value: Adenoma

value: Unknown


title: Microbiota of Saliva from patient CRC71

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-D06-FAS-71S-T0

value: Adenocarcinoma

value: Proximal


title: FKH1_d2_280_1


title: scAT, OW_21

source_name: Periumbilical subcutaneous adipose tissues, overweight (1≤BMI-z score <2 )

value: OW


title: scAT, OW_4

value: Periumbilical subcutaneous adipose tissue


title: Microbiota of Colon biopsy from patient CRC71

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-B06-FAS-71B-T0


title: FKH1_d2_280_4


title: scAT, NORMO_25

source_name: Periumbilical subcutaneous adipose tissues, normal weight (-2≤BMI-z score <1)

value: NW


title: Microbiota of Colon biopsy from patient AP66

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-A10-FAS-66B-T0


title: FKH1_d2_150_4

source_name: budding yeast culture at OD=4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 FKH1 Δ2 150 SV40 NLS MNase

value: Truncation


title: 4F-TFR-D0.1


title: scAT, OB_2

value: OB


title: FKH1_d2_150_3


title: DOT6_nonDBD_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 DOT6 Δ75 117 MNase

value: nonDBD


title: Microbiota of Saliva from patient CRC48

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-A09-FAS-48S-T0

value: F


title: scAT, NORMO_20


title: Microbiota of Colon biopsy from patient CRC65

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-A08-FAS-65B-T0

value: Colon biopsy

value: Distal

value: III


title: DOT6_nonDBD_3


title: scAT, NORMO_18


title: DOT6_nonDBD_2


title: scAT, NORMO_16


title: Microbiota of Stool from patient AP40

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-A07-FAS-40F-T0

source_name: Stool

value: Stool

value: M


title: DOT6_nonDBD_1


title: scAT, OW_1


title: Microbiota of Saliva from patient CRC18

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-H08-FAS-18S-T0

value: Saliva

value: Unknown


title: DOT6_d551_670_8

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 DOT6 Δ551 670 SV40 NLS MNase


title: ATACseq, iPSC (myeloid) differentiated, iMonocyte, biol rep 2

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

data_processing:
Seq2science ATAC-seq analysis.
Sequence reads were trimmed using default fastp.
Trimmed sequence reads were mapped to hg38 using BWA-MEM2. Peaks were called with MACS2
Assembly: hg38
Supplementary files format and content: NarrowPeak file include ATAC-seq peaks for each Sample

growth_protocol:
hiPS cells were maintained in mTeSR™ Plus (STEMCELL™ Technologies) supplemented with 1% Penicillin/Streptomycin on Vitronectin XF™ (STEMCELL™ Technologies) coated 6-well plates at 37 °C.
For CD34+ progenitor differentiation, STEMdiff™ Hematopoietic Kit (STEMCELL™ Technologies) was used. After 12 days the cells residing in the supernatant are transferred to 6-well plates and the medium was replaced by Stemline® II Hematopoietic Stem Cell Expansion Medium (Sigma-Aldrich) supplemented with 1% Penicillin/Streptomycin, 1:100 insulin-transferrin-selenium-ethanolamine (ITS-X) (Thermo Fisher Scientific) and cytokines (50 ng/mL IL-3, 50 ng/mL FLT3-L, 50 ng/mL SCF, 50 ng/mL M-CSF, 10 ng/mL TPO) (Miltenyi Biotec B.V.) to induce myelo-monocyte differentiation.

extract_protocol:
Approximately 50.000 nuclei were isolated per sample. DNA was tagmented using Tn5.
ATAC libraries for ATAC-seq were prepared using Nextera primers.

treatment_protocol: On day 6, and afterwards routinely every second day (day 8, 10, 12, etc.), doxycycline (16 ng/mL) was supplemented to induce MLL-AF9 expression.

tag: cell line

value: hiPSC

value: Untreated


title: Microbiota of Saliva from patient AP67

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID881-A06-FAS-67S-T0

value: Adenoma

value: Proximal


title: scAT, NORMO_5

value: Periumbilical subcutaneous adipose tissue

value: NW


title: ATACseq, iPSC (myeloid) differentiated, iMonocyte, biol rep 1


title: DOT6_d551_670_7

value: Truncation


title: Microbiota of Saliva from patient CRC51

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-H01-FAS-51S-T0

value: Adenocarcinoma


title: DOT6_d551_670_6


title: KO_WD_F_1

city: San Antonio

first: Travis

middle: R

last: Madaris

address: 7703 Floyd Curl

department: Medicine

institute: University of Texas Health San Antonio

description: Novogen Sequencing Strategy #PE150

data_processing:
Hisat2 v2.0.5 was used to align reads to reference genome mm10 (Mus musculus)
Mapped reads were counted using FeautureCounts v1.5.0-p3. The read count was corrected for gene length and sequencing depth to calculate the FPKM values. Consistency between biological relicates was examained using correlation analysis.
Differential gene expression analysis was conducted using DESeq2 v1.20.0; ClusterProfile was used to analyze KEGG pathways; and, Gene set enrichment analysis was conducted utilizing the GSEA tool from Broad Institute.
Benjamini-Hochberg method was used to calculate adjusted P-values. An adjusted P-value <0.05 was considered statistically significant.
NOTE REGARDING FINAL DATA IN MANUSCRIPT: Results in manuscript were generated from the processed data (FPKM values) by one of two normalization methods (Note, BOTH methods normalize each gene individually). These two methods are: 1) Heatmaps are generated using a row z-score normalization method in Excel (function: "STANDARDIZE") and have values ranging from negative to positive,  or 2) by normalizing each gene individually to the average (sample FPKM/mean FPKM) of all compared samples for that specific gene, this gives only a positive value.
Assembly: mm10
Supplementary files format and content: Processed File 1 (name contains deglist) is a tab delimited file of the differential expression analysis and includes significant and nonsignificant genes.
Supplementary files format and content: Processed File 2 (name contains KEGGenrich) is a tab delimited file of the KEGG analysis and includes both significant and nonsignificant pathways

source_name: Inguinal white adipose tissue, iWAT (lymph nodes removed)

growth_protocol: Mice were 13 weeks old when dietary treatment began. Dietary treatment was for 52 weeks before organs/tissue was harvested.

extract_protocol:
RNA is prepared from tissue using QIAzol/chlorofrom extraction and QIAGEN RNeasy Pls Universal Mini Kit (following manufaturer's suggestions). Homogenization was accomplished using a metal bead and a TissueRuptor. RNA is eluted in Invitrogen RNase-free water. Tissues were freshly harvested from the mice, rinsed well in ice cold DPBS (no Mg/Ca), and cut in smaller pieces and rinsed further. The lymph nodes were removed from the inguinal white adipose tissue (iWAT). Tissues were flash frozen in LN2. Tissues were kept at -80C storage until processing. Processing consisted of cryogenic crushing of whole liver or whole iWAT to generate a "powder" of the the whole organ. This powder was aliquoted based on weight and stored. Tissue remained at cryogenic temperatures at all times. 100mg of iWAT was used for RNA isolation and 50mg of liver was used for RNA isolation.
Libraries were constructed by Novogene using poly-T magnetic beads following by fragmentation, cDNA synthesis, adaptor ligation, and finally PCR. Quality control was conducted by removing low quality reads or those containing the adaptor or poly-N strings. Quality control was done by Novogene on intial samples, constructed library, and raw data.

treatment_protocol: Mice were fed a Western Diet or standard chow diet for 52 weeks.

value: Mrs2 KO

value: Western diet


title: WT_WD_F_1

description: Novogen Sequencing Strategy #PE150

value: Inguinal white adipose tissue, iWAT (lymph nodes removed)

value: WT


title: WT_WD_F_3

description: Novogen Sequencing Strategy #PE150


title: KO_WD_F_2

description: Novogen Sequencing Strategy #PE150


title: WT_WD_F_2

description: Novogen Sequencing Strategy #PE150


title: KO_WD_F_3

description: Novogen Sequencing Strategy #PE150


title: ATACseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 2

value: Doxycyclin (16ng/mL)


title: Microbiota of Colon biopsy from patient AP45

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-G12-FAS-45B-T0

value: Colon biopsy

value: F


title: KO_CD_F_2

description: Novogen Sequencing Strategy #PE150

value: Chow diet


title: KO_CD_F_1

description: Novogen Sequencing Strategy #PE150


title: KO_CD_F_3

description: Novogen Sequencing Strategy #PE150


title: DOT6_d551_670_5

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 DOT6 Δ551 670 SV40 NLS MNase


title: scRNAseq, iPSC (myeloid) differentiated, iMonocyte, 2

data_processing:
Seq2science scRNA-seq analysis.
Sequence reads were trimmed using default fastp.
Trimmed sequence reads were mapped to GRCh38 and quantified by running the kb-python wrapper for Kallisto bustools.
Pre-processing of raw scRNA-seq count matrices included cells with atleast 350 counts and 150 total features. Data was normalized, scaled, and saved to a RDS file.
Cluster with low anchor scores has been filtered.
Assembly: GRCh38
Supplementary files format and content: RDS file include cells with atleast 350 counts and 150 total features.

growth_protocol:
hiPS cells were maintained in mTeSR™ Plus (STEMCELL™ Technologies) supplemented with 1% Penicillin/Streptomycin on Vitronectin XF™ (STEMCELL™ Technologies) coated 6-well plates at 37 °C.
For CD34+ progenitor differentiation, STEMdiff™ Hematopoietic Kit (STEMCELL™ Technologies) was used. After 12 days the cells residing in the supernatant are transferred to 6-well plates and the medium was replaced by Stemline® II Hematopoietic Stem Cell Expansion Medium (Sigma-Aldrich) supplemented with 1% Penicillin/Streptomycin, 1:100 insulin-transferrin-selenium-ethanolamine (ITS-X) (Thermo Fisher Scientific) and cytokines (50 ng/mL IL-3, 50 ng/mL FLT3-L, 50 ng/mL SCF, 50 ng/mL M-CSF, 10 ng/mL TPO) (Miltenyi Biotec B.V.) to induce myelo-monocyte differentiation. At day 15 days were harvested for library preperation.

extract_protocol:
RNA was isolated using an in-house CELseq2 variant (RAID-plate-based_CELseq2_V1) without using barcodes.
RNA libraries for scRNA-seq were prepared using using an in-house CELseq2 variant (RAID-plate-based_CELseq2_V1) without using barcodes.

value: hiPSC

tag: plate id


title: scRNAseq, iPSC (myeloid) differentiated, iMonocyte, 1

value: Untreated


title: Microbiota of Colon biopsy from patient AP19

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-G09-FAS-19B-T0

value: Adenoma

value: Distal

value: Unknown


title: WT_CD_F_2

description: Novogen Sequencing Strategy #PE150


title: Microbiota of Colon biopsy from patient CRC54

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-G02-FAS-54B-T0

value: Proximal

value: I


title: DOT6_d551_670_3

value: Truncation


title: DOT6_d551_670_4


title: Microbiota of Stool from patient CRC51

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-G01-FAS-51F-T0

value: Stool

value: M

value: Adenocarcinoma


title: WT_CD_F_1

description: Novogen Sequencing Strategy #PE150

value: Inguinal white adipose tissue, iWAT (lymph nodes removed)

value: WT


title: ATACseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 1

value: Doxycyclin (16ng/mL)


title: Microbiota of Stool from patient CRC55

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-H02-FAS-55F-T0


title: KO_WD_L_3

description: Novogen Sequencing Strategy #PE150

source_name: Whole Liver

value: Whole Liver

value: Mrs2 KO

value: Western diet


title: DOT6_d451_670_6

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 DOT6 Δ451 670 SV40 NLS MNase


title: DOT6_d551_670_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 DOT6 Δ551 670 SV40 NLS MNase


title: RNAseq, iPSC (myeloid) differentiated, iMonocyte, biol rep 3, 3

data_processing:
Seq2science RNA-seq analysis.
Sequence reads were trimmed using default fastp.
Trimmed sequence reads were mapped to GRCh38 using STAR.
Assembly: GRCh38
Supplementary files format and content: tab-delimited value file include raw counts for each Sample

extract_protocol:
RNA was isolated using Mini RNA Isolation II Kit (Zymo Research). Between 25 and 1000 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using using KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems) with RNA fragmentation of approximately 300 bp fragments.

value: hiPSC

value: Untreated


title: Microbiota of Saliva from patient CRC54

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-F02-FAS-54S-T0

value: Saliva

value: F


title: KO_WD_L_1

description: Novogen Sequencing Strategy #PE150


title: Microbiota of Colon biopsy from patient CRC41

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-F11-FAS-41B-T0

value: Colon biopsy

value: Distal

value: Unknown


title: KO_WD_L_2

description: Novogen Sequencing Strategy #PE150


title: DOT6_d451_670_4

value: Truncation


title: Microbiota of Saliva from patient AP45

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-F12-FAS-45S-T0

value: Adenoma


title: WT_CD_F_3

description: Novogen Sequencing Strategy #PE150

value: Inguinal white adipose tissue, iWAT (lymph nodes removed)

value: Chow diet


title: DOT6_d451_670_5


title: scRNAseq, iPSC (myeloid) differentiated, iMLL-AF9, 1

value: Doxycyclin (16ng/mL)


title: scRNAseq, iPSC (myeloid) differentiated, iMLL-AF9, 2


title: scRNAseq, iPSC (myeloid) differentiated, iMLL-AF9, 3


title: WT_WD_L_3

description: Novogen Sequencing Strategy #PE150

value: Whole Liver

value: WT


title: Microbiota of Saliva from patient AP19

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-F09-FAS-19S-T0


title: WT_WD_L_2

description: Novogen Sequencing Strategy #PE150

value: Western diet


title: RNAseq, iPSC (myeloid) differentiated, iMonocyte, biol rep 3, 2


title: scRNAseq, iPSC (myeloid) differentiated, iMLL-AF9, 4


title: WT_WD_L_1

description: Novogen Sequencing Strategy #PE150


title: DOT6_d451_670_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 DOT6 Δ451 670 SV40 NLS MNase


title: Microbiota of Colon biopsy from patient CRC50

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-F01-FAS-50B-T0

value: M

value: Adenocarcinoma

value: II


title: DOT6_d551_670_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 DOT6 Δ551 670 SV40 NLS MNase


title: RNAseq, iPSC (myeloid) differentiated, iMonocyte, biol rep 3, 1

value: hiPSC

value: Untreated


title: DOT6_d351_670_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 DOT6 Δ351 670 SV40 NLS MNase


title: RNAseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 3, 3


title: Microbiota of Stool from patient CRC54

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-E02-FAS-54F-T0

value: Stool

value: F

value: Proximal

value: I


title: DOT6_d351_670_1

value: Truncation


title: KO_CD_L_3

description: Novogen Sequencing Strategy #PE150

value: Mrs2 KO

value: Chow diet


title: RNAseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 3, 2

value: Doxycyclin (16ng/mL)


title: RNAseq, iPSC (myeloid) differentiated, iMonocyte, biol rep 2, 4


title: RNAseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 3, 1


title: Microbiota of Colon biopsy from patient CRC25

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-C10-FAS-25B-T0

value: Colon biopsy

value: Distal

value: Unknown


title: DOT6_d251_670_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 DOT6 Δ251 670 SV40 NLS MNase


title: RNAseq, iPSC (myeloid) differentiated, iMonocyte, biol rep 2, 3


title: WT_CD_L_3

description: Novogen Sequencing Strategy #PE150

value: Whole Liver

value: WT


title: DOT6_d121_670_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 DOT6 Δ121 670 SV40 NLS MNase

value: DBD


title: KO_CD_L_1

description: Novogen Sequencing Strategy #PE150


title: DOT6_d121_670_3


title: WT_CD_L_2

description: Novogen Sequencing Strategy #PE150


title: Microbiota of Saliva from patient CRC52

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-C02-FAS-52S-T0

value: Saliva

value: Adenocarcinoma


title: RNAseq, iPSC (myeloid) differentiated, iMonocyte, biol rep 2, 2

value: hiPSC

value: Untreated


title: DOT6_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 DOT6 MNase

value: TF


title: WT_CD_L_1

description: Novogen Sequencing Strategy #PE150


title: RNAseq, iPSC (myeloid) differentiated, iMonocyte, biol rep 2, 1


title: Microbiota of Saliva from patient CRC41

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-E11-FAS-41S-T0

value: F


title: Sensitized, replicate 4, technical rep. B

city: Chicago

first: Anita

last: Chong

state: IL

address: 5841 S Maryland Ave

institute: University of Chicago

description: MatrixColumn: Sens4_b

data_processing:
Raw RNA-Seq reads were trimmed for adapter content and filtered for truncated reads using Cutadapt v3.4
Paired-end reads were aligned using STAR v2.6.1b against the GRCm39 (mm39) reference genome and transcriptome annotations, and non-uniquely mapping reads were removed.
Per-sample read counts for each gene were quantified sample using featureCounts v2.0.1
Assembly: GRCm39 (mm39)
Supplementary files format and content: .csv file, raw read counts for each gene

source_name: Spleen+Lymph Nodes

extract_protocol:
RNA-Seq libraries were generated and amplified according to the SmartSeq2 protocol (Picelli et al. 2014). 200 live cells per sample/subset were sorted into 96-well optical PCR plates containing 4μl of lysis buffer at 4°C.
cDNA sequencing libraries were generated using Nextera XT DNA Library Prep Kit and Nextera XT Index Kit (Illumina).
All libraries were sequenced in the same run in a 150 bp/150 bp paired-end configuration. An average of ~55 × 106 paired reads was generated per sample.

value: Spleen+Lymph Nodes

value: CD8+ T cells

value: Allogeneic Skin Graft


title: Sensitized, replicate 4, technical rep. A

description: MatrixColumn: Sens4_a


title: Microbiota of Colon biopsy from patient CRC47

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-C01-FAS-47B-T0

value: Colon biopsy

value: M

value: Proximal


title: RNAseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 2, 6

value: Doxycyclin (16ng/mL)


title: Microbiota of Colon biopsy from patient CRC38

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-B11-FAS-38B-T0

value: Distal

value: Unknown


title: Microbiota of Saliva from patient CRC50

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-E01-FAS-50S-T0

value: II


title: KO_CD_L_2

description: Novogen Sequencing Strategy #PE150

value: Whole Liver

value: Mrs2 KO

value: Chow diet


title: DOT6_d251_670_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 DOT6 Δ251 670 SV40 NLS MNase

value: Truncation


title: DOT6_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 DOT6 MNase

value: TF


title: Microbiota of Colon biopsy from patient CRC52

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-D02-FAS-52B-T0

value: F

value: Adenocarcinoma


title: DOT6_2


title: Microbiota of Stool from patient CRC50

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-D01-FAS-50F-T0

value: Stool


title: RNAseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 2, 5

value: hiPSC


title: Sensitized, replicate 3, technical rep. B

description: MatrixColumn: Sens3_b

value: Spleen+Lymph Nodes

value: CD8+ T cells

value: Allogeneic Skin Graft


title: Microbiota of Saliva from patient CRC25

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-B10-FAS-25S-T0

value: Saliva

value: M

value: Distal


title: Sensitized, replicate 3, technical rep. A

description: MatrixColumn: Sens3_a


title: RNAseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 2, 4

value: Doxycyclin (16ng/mL)


title: RNAseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 2, 3


title: CST6_nonDBD_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CST6 Δ416 449 MNase::kanMX

value: nonDBD


title: DOT6_1


title: Microbiota of Stool from patient CRC52

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-B02-FAS-52F-T0

value: Proximal

value: Unknown


title: Sensitized, replicate 2, technical rep. A

description: MatrixColumn: Sens2_a


title: RNAseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 2, 2


title: Sensitized, replicate 2, technical rep. B

description: MatrixColumn: Sens2_b


title: Microbiota of Stool from patient CRC47

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-B01-FAS-47F-T0


title: CST6_d2_200_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CST6 Δ2 200 SV40 NLS MNase::kanMX

value: Truncation


title: Microbiota of Saliva from patient CRC38

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-A11-FAS-38S-T0

value: F


title: CST6_d2_200_3


title: RNAseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 2, 1


title: RNAseq, iPSC (myeloid) differentiated, iMonocyte, biol rep 1, 3

value: Untreated


title: Microbiota of Colon biopsy from patient CRC18

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-A09-FAS-18B-T0

value: Colon biopsy

value: Adenocarcinoma


title: Sensitized, replicate 1, technical rep. B

description: MatrixColumn: Sens1_b

value: Spleen+Lymph Nodes


title: Sensitized, replicate 1, technical rep. A

description: MatrixColumn: Sens1_a

value: CD8+ T cells


title: CST6_d2_200_2


title: CST6_d2_200_1


title: Sensitized+Pregnant C4 (PD1-), replicate 6, technical rep. A

description: MatrixColumn: SPP6_Ba

value: Allogeneic Skin Graft+Semi-Allogeneic Pregnancy


title: Sensitized+Pregnant C4 (PD1-), replicate 6, technical rep. B

description: MatrixColumn: SPP6_Bb


title: RNAseq, iPSC (myeloid) differentiated, iMonocyte, biol rep 1, 1

value: hiPSC


title: Microbiota of Colon biopsy from patient CRC51

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-A02-FAS-51B-T0

value: M


title: Microbiota of Colon biopsy from patient CRC55

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-B03-FAS-55B-T0

value: Distal


title: RNAseq, iPSC (myeloid) differentiated, iMonocyte, biol rep 1, 2


title: CRZ1_nonDBD_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ570 619 MNase


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 6, technical rep. B

description: MatrixColumn: SPP6_7b


title: Microbiota of Stool from patient CRC46

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-A01-FAS-46F-T0

value: Stool


title: CRZ1_nonDBD_1

value: nonDBD


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 6, technical rep. A

description: MatrixColumn: SPP6_7a


title: RNAseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 1, 2

value: Doxycyclin (16ng/mL)


title: CRZ1_d2_50_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ2 50 SV40 NLS MNase


title: RNAseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 1, 1


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 6, technical rep. B

description: MatrixColumn: SPP6_5b


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 6, technical rep. A

description: MatrixColumn: SPP6_5a


title: CRZ1_d2_50_3


title: HIO-2 (without EECs)

city: Cincinnati

first: Heather

last: McCauley

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: 10x Genomics

data_processing:
Standard CellRanger Pipeline to generate FASTQ and generate filtered matrices
Filtered matrices were imported into Scanpy
Initial filtering only included cells min_genes=1000 in min_cells=2
Processed data filtering included n_genes < 8000 and percent_mito < 0.4
Differential expression analysis performed using standard Scanpy pipeline
Assembly: hg19
Supplementary files format and content: .h5ad

source_name: intestinal organoid

extract_protocol:
After 20 weeks of in vivo growth, HIOs were removed from the kidney of the host mouse. The surrounding kidney capsule was dissected and discarded and the HIO was opened to expose the lumen. Mucus was washed away. HIOs were shaken in 5mL TryPLe + 5uL y-27632 for 30 minutes at 4C, then the epithelium gently scraped from the mucosa using curved forceps. Cells were filtered through a 40um cell strainer, centrifuged at 200RPM for 5 minutes, and resuspended in 2% FBS in PBS without Mg++ or Ca++ with y-27632. Cells were stained with Sytox Blue viability dye and sorted on a FACS Aria cell sorter and 100,000 live cells were collected in 5mL PBS with 5% FBS, 0.5% BSA, 5uL y-27632.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: epithelial and mesenchymal

value: intestinal organoid

value: WA01 ES cell + NGN3 KO

tag: age

value: 20 weeks in vivo


title: Microbiota of Saliva from patient CRC36

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-H8-FAS-36S

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

value: Saliva

value: II


title: CRZ1_d2_500_2

data_processing:
Library strategy: ChEC-seq
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
paired end alignment to S288C_R64 with bowtie2 (-p8 --local --very-sensitive --trim-to 30 --dovetail)
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)

extract_protocol:
Phenol chlorofrom extraction
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ2 500 SV40 NLS MNase

value: DBD


title: Microbiota of Colon biopsy from patient AP24

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-H6-FAS-24B

value: Colon biopsy

value: Adenoma

value: Proximal

value: Unknown


title: CRZ1_d2_500_1


title: Sensitized+Pregnant C4 (PD1-), replicate 5, technical rep. B

description: MatrixColumn: SPP5_Bb

value: Spleen+Lymph Nodes

value: CD8+ T cells

value: Allogeneic Skin Graft+Semi-Allogeneic Pregnancy


title: Sensitized+Pregnant C4 (PD1-), replicate 5, technical rep. A

description: MatrixColumn: SPP5_Ba


title: Microbiota of Saliva from patient CRC55

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID728-A03-FAS-55S-T0

value: M

value: Adenocarcinoma

value: Distal


title: HIO-1B (with EECs)

description: 10x Genomics

value: epithelial and mesenchymal

value: intestinal organoid

value: WA01 ES cell


title: Microbiota of Saliva from patient CRC20

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-H5-FAS-20S

value: Saliva


title: Microbiota of Stool from patient CRC32

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-H7-FAS-32F

value: Stool


title: HIO-1A (with EECs)

description: 10x Genomics

value: 20 weeks in vivo


title: CST6_nonDBD_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CST6 Δ416 449 MNase::kanMX

value: nonDBD


title: CRZ1_d2_450_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ2 450 SV40 NLS MNase

value: Truncation


title: Microbiota of Stool from patient CRC13

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-H4-FAS-13F

value: Unknown


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 5, technical rep. B

description: MatrixColumn: SPP5_7b

value: Spleen+Lymph Nodes


title: RNAseq, iPSC (myeloid) differentiated, iMLL-AF9, biol rep 1, 3

value: hiPSC

value: Doxycyclin (16ng/mL)


title: Microbiota of Colon biopsy from patient CRC39

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-H9-FAS-39B

value: Colon biopsy

value: M


title: CRZ1_d2_450_1


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 5, technical rep. A

description: MatrixColumn: SPP5_7a

value: CD8+ T cells

value: Allogeneic Skin Graft+Semi-Allogeneic Pregnancy


title: Kar_E

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

data_processing:
Sequencing in 75 cycles produced 20 bp Read 1 (bases 6-11 sample barcode, bases 13-20 UMI) and 55 bp Read 2 (sequence derived from the mRNA).
Raw sequence data was filtered to remove reads shorter than 20 bp.
The original pipeline suggested in (Macosko EZ et al. Cell 2015; https://github.com/broadinstitute/Drop-seq) for processing of drop-seq data was used. Briefly, reads were additionally filtered to remove polyA tails of length 6 or greater, then aligned to the mouse (mm10) genome using STAR aligner, with default settings. Uniquely mapped reads were grouped according to the 1-12 barcode, and gene transcripts were counted by their Unique Molecular Identifiers (UMIs) to reduce bias emerging from the PCR amplification. Digital expression matrices (DGE) reported the number of transcripts per gene in a given sample (according to the distinct UMI sequences counted).
Differentially expressed genes were identified using edgeR
Supplementary_files_format_and_content: Digital Gene Expression (DGE): tab-delimited text file containing UMI read counts for each sample

source_name: SV40 cell line

growth_protocol: Human SV40 immortalized microglia cells (ABM, Cat#T0251) were cultured in DMEM GlutaMAX containing 4.5 g/l glucose (Gibco) supplemented with 10 % fetal bovine serum (FBS) (Gibco) and 1% penicillin-streptomycin (Gibco). The flasks were precoated with rat type I collagen (Gibco) in 20 mM acetic acid and washed with DPBS (Gibco).

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) and following manufacturer’s guidelines. Cells were homogenized with QIAshredder colums (Qiagen). RNA samples were stored at -70°C.
RNA sequencing method was designed based on the Drop-seq protocol described in (Macosko EZ et al. Cell 2015). Briefly, 10 ng of RNA was mixed with Indexing Oligonucleotides. After 5 minutes of incubation the RNA was combined with RT mix (1 x Maxima RT buffer, 1 mM dNTPs, 10 U/µl Maxima H- RTase, 1 U/µl RNase inhibitor and 2.5 µM Template Switch Oligo). Samples were incubated for 30 minutes at 22°C and 90 minutes at 52°C. The constructed cDNA was amplified by PCR. The PCR products were pooled together in sets of 12 samples containing different Indexing Oligos and purified with Agencourt AMPure XP Beads according to the manufacturer’s instructions. The 3’-end cDNA fragments for sequencing were prepared using the Nextera XT (Illumina) tagmentation reaction. The reaction was performed according to manufacturer’s instruction, with the exception of the P5 SMART primer that was used instead of S5xx Nextera primer. Each set of 12-18 samples that was pooled after the PCR reaction was tagmented with a different Nextera N7xx index. Subsequently, the samples were PCR amplified and purified twice using Agencourt AMPure Beads. The libraries were sequenced on a Illumina NextSeq 500, with a custom primer producing read 1 of 20 bp and read 2 (paired end) of 50 bp. Sequencing was performed at the Functional Genomics Unit of the University of Helsinki, Finland.

treatment_protocol: Preincubation of 1.4 µM of apoE2, apoE3 or apoE4 with or without 650 nM FH (Complement Technology, Inc.) was performed in 96-well round bottom plates (Thermo Fisher Scientific) for 30 min on ice. HiLyte488 TM Fluor-labeled Aβ1-42 was incubated in the dark at room temperature in PBS for three days and then mixed with microglial cells (2.5 × 106 cells/ml). The suspension was immediately pipetted into the wells containing the preincubated mixture of apoE and FH (final concentration of Aβ: 2 µM, final amount: 8.7 × 104 microglial cells per well). Samples were further incubated for 1 h at 37⁰C with gentle shaking in RPMI-1640 media (Gibco) supplemented with 0.05% human serum albumin (HSA, Sigma). For the mRNA sequence analysis, 3 × 104 cells were stabilized by RNAlater (Thermo Fisher).

value: immortalized microglia cells


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 5, technical rep. B

description: MatrixColumn: SPP5_5b


title: CRZ1_d2_400_6

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ2 400 SV40 NLS MNase


title: Kar_D


title: Kar_C


title: CRZ1_d2_400_5


title: Kar_B


title: Sensitized+Pregnant C4 (PD1-), replicate 4, technical rep. B

description: MatrixColumn: SPP4_Bb


title: CRZ1_d2_400_4


title: Microbiota of Stool from patient CRC4

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-H1-FAS-4F

value: Adenocarcinoma

value: Distal

value: III


title: Sensitized+Pregnant C4 (PD1-), replicate 4, technical rep. A

description: MatrixColumn: SPP4_Ba


title: Microbiota of Stool from patient CRC39

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-G9-FAS-39F

value: Stool


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 4, technical rep. B

description: MatrixColumn: SPP4_7b


title: Kar_A


title: CRZ1_d2_350_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ2 350 SV40 NLS MNase


title: CRZ1_d2_350_2


title: R1-2

description: expression-MEFs and iPSCs.txt

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data were trimmed by fastp (v0.20.1) to remove adapter sequence and reads with low sequencing quality.
Clean reads were aligned to the mouse genome (mm10) using HISAT2 (v2.1.0) with the default parameter settings.
Transcript assembly was performed by stringtie (v2.0) and expression of transcripts sharing each Ensembl_id was quantified as Fragments Per Kilobase Million (FPKM).
To calculate expression of transposable elements (TEs), in-house perl scripts were used to extract the read fragments in each TE duplicate and then transformed into FPKM, multiple reads alignment was counted reciprocally.
For RNA-degradation samples, FPKM was then converted to attomoles by linear fitting of the RNA ERCC spike-ins.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Mouse blastocyst

growth_protocol: OG2 cells were maintained with DMEM containing 10% fetal bovine serum (FBS) and 1× penicillin/ streptomycin, and cultured in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
ciPSC medium included KnockOut DMEM supplemented with 10% KSR, 10% FBS, 1% NEAA, 1% P/S, 0.055 mM β-ME, 20 ng ml-1 bFGF, and the small molecules VPA (0.5 mM), CHIR99021 (20 μM), 616452 (10 μM), Parnate (5 μM), Forskolin (50 μM), AM580 (0.5 μM), EPZ004777 (5 μM) and vitamin C (Vc) (250 μM).
Total RNA was isolated and purified using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme).
cDNA library construction and high-throughput sequencing were performed by Novogene.

treatment_protocol: We performed ciPSC reprogramming with or without CD addition (ActD-treated 0h, 4h, 8h) reprogramming intermediates; MEF, ciPSCs (DMSO and CD), and R1 mESCs.

value: Mouse blastocyst

value: R1 mESC

value: mouse ESC


title: Microbiota of Stool from patient AP24

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-G6-FAS-24F

value: Adenoma

value: Proximal

value: Unknown


title: MEF-2

description: expression-MEFs and iPSCs.txt

value: Mouse embryonic fibroblasts

value: WT shRNA

value: ciPSC reprogramming


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 4, technical rep. A

description: MatrixColumn: SPP4_7a

value: Spleen+Lymph Nodes

value: CD8+ T cells

value: Allogeneic Skin Graft+Semi-Allogeneic Pregnancy


title: Microbiota of Saliva from patient CRC32

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-G7-FAS-32S

source_name: Saliva

value: Saliva

value: M

value: Adenocarcinoma


title: Microbiota of Colon biopsy from patient CRC9

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-H3-FAS-9B

value: Colon biopsy

value: F

value: Distal

value: I


title: CRZ1_d2_300_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ2 300 SV40 NLS MNase

value: Truncation


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 4, technical rep. B

description: MatrixColumn: SPP4_5b


title: MEF-1

description: expression-MEFs and iPSCs.txt


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 4, technical rep. A

description: MatrixColumn: SPP4_5a


title: R1-1

description: expression-MEFs and iPSCs.txt

value: Mouse blastocyst

value: R1 mESC

value: mouse ESC


title: CRZ1_d2_250_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ2 250 SV40 NLS MNase


title: Microbiota of Colon biopsy from patient CRC17

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-G5-FAS-17B


title: Microbiota of Saliva from patient CRC7

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-H2-FAS-7S

value: III


title: CRZ1_d2_300_1


title: Microbiota of Saliva from patient CRC13

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-G4-FAS-13S

value: Unknown


title: CRZ1_d2_250_1


title: DMSP-iPSC-2

description: expression-MEFs and iPSCs.txt

value: Mouse embryonic fibroblasts

value: DMSO addition

value: ciPSC reprogramming


title: Sensitized+Pregnant C4 (PD1-), replicate 3, technical rep. B

description: MatrixColumn: SPP3_Bb

value: Spleen+Lymph Nodes

value: CD8+ T cells

value: Allogeneic Skin Graft+Semi-Allogeneic Pregnancy


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 5, technical rep. A

description: MatrixColumn: SPP5_5a


title: DMSP-iPSC-1

description: expression-MEFs and iPSCs.txt


title: CRZ1_d2_200_8

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ2 200 SV40 NLS MNase


title: Microbiota of Colon biopsy from patient AP35

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-G8-FAS-35B

value: Colon biopsy

value: F

value: Adenoma

value: Proximal


title: Microbiota of Stool from patient CRC9

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-G3-FAS-9F

value: Stool

value: Adenocarcinoma

value: Distal

value: I


title: CD-iPSC-1

description: expression-MEFs and iPSCs.txt

value: CD addition


title: Microbiota of Saliva from patient CRC4

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-G1-FAS-4S

value: Saliva

value: M

value: III


title: Microbiota of Colon biopsy from patient CRC6

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-G2-FAS-6B


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 3, technical rep. A

description: MatrixColumn: SPP3_5a


title: Microbiota of Saliva from patient CRC39

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-F9-FAS-39S

value: Unknown


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 2, technical rep. B

description: MatrixColumn: SPP2_7b

value: Spleen+Lymph Nodes


title: DMSO_8h-1

description: expression-degradation.txt

value: Mouse embryonic fibroblasts

value: DMSO addition

value: ciPSC reprogramming


title: Microbiota of Stool from patient AP35

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-F8-FAS-35F


title: CRZ1_d2_200_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ2 200 SV40 NLS MNase

value: Truncation


title: Microbiota of Colon biopsy from patient AP31

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-F7-FAS-31B

value: Colon biopsy

value: Adenoma


title: Sensitized+Pregnant C4 (PD1-), replicate 1, technical rep. B

description: MatrixColumn: SPP1_Bb

value: CD8+ T cells

value: Allogeneic Skin Graft+Semi-Allogeneic Pregnancy


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 2, technical rep. B

description: MatrixColumn: SPP2_5b


title: CRZ1_d2_200_3


title: DMSO_4h-1

description: expression-degradation.txt


title: CRZ1_d2_150_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ2 150 SV40 NLS MNase


title: Sensitized+Pregnant C4 (PD1-), replicate 2, technical rep. B

description: MatrixColumn: SPP2_Bb


title: DMSO_0h-2

description: expression-degradation.txt


title: Microbiota of Stool from patient CRC17

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-F5-FAS-17F

value: Stool

value: Adenocarcinoma

value: Distal

value: I


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 3, technical rep. A

description: MatrixColumn: SPP3_7a


title: DMSO_4h-2

description: expression-degradation.txt


title: CD-iPSC-2

description: expression-MEFs and iPSCs.txt

value: CD addition


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 1, technical rep. B

description: MatrixColumn: SPP1_7b


title: DMSO_0h-1

description: expression-degradation.txt


title: CRZ1_d2_200_7


title: CD_8h-2

description: expression-degradation.txt


title: Microbiota of Colon biopsy from patient CRC11

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-F4-FAS-11B

value: M

value: Unknown


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 1, technical rep. A

description: MatrixColumn: SPP1_7a

value: Spleen+Lymph Nodes


title: CRZ1_d2_100_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ2 100 SV40 NLS MNase


title: Microbiota of Saliva from patient CRC9

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-F3-FAS-9S

value: Saliva

value: F


title: Microbiota of Saliva from patient AP24

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-F6-FAS-24S

value: Proximal


title: CD_8h-1

description: expression-degradation.txt

value: Mouse embryonic fibroblasts

value: ciPSC reprogramming


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 1, technical rep. A

description: MatrixColumn: SPP1_5a

value: CD8+ T cells


title: Sensitized+Pregnant C4 (PD1-), replicate 1, technical rep. A

description: MatrixColumn: SPP1_Ba

value: Allogeneic Skin Graft+Semi-Allogeneic Pregnancy


title: CD_4h-2

description: expression-degradation.txt


title: CRZ1_d2_100_1

value: Truncation


title: CBF1_nonDBD_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CBF1 Δ223 271 MNase

value: nonDBD


title: CRZ1_d2_150_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ2 150 SV40 NLS MNase


title: Microbiota of Colon biopsy from patient CRC46

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-F10-FAS-46B

value: Colon biopsy

value: Adenocarcinoma

value: Distal


title: CRZ1_d2_150_3


title: Microbiota of Stool from patient CRC6

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-F2-FAS-6F

value: Stool

value: M

value: I


title: CD_0h-2

description: expression-degradation.txt

value: CD addition


title: Microbiota of Colon biopsy from patient CRC37

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-E9-FAS-37B

value: III


title: Naive+Pregnant C5 (PD1+CD73+), replicate 3, technical rep. B

description: MatrixColumn: NPP3_5b

value: Spleen+Lymph Nodes

value: Semi-Allogeneic Pregnancy


title: CBF1_nonDBD_2


title: Naive+Pregnant C1 (PD1-), replicate 3, technical rep. A

description: MatrixColumn: NPP3_Ba


title: CD_0h-1

description: expression-degradation.txt

value: Mouse embryonic fibroblasts

value: ciPSC reprogramming


title: CBF1_nonDBD_1


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 1, technical rep. B

description: MatrixColumn: SPP1_5b

value: CD8+ T cells

value: Allogeneic Skin Graft+Semi-Allogeneic Pregnancy


title: shCTR-2

description: shE3-shCTR-gene expression.txt

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data were trimmed by fastp (v0.20.1) to remove adapter sequence and reads with low sequencing quality.
Clean reads were aligned to the mouse genome (mm10) using HISAT2 (v2.1.0) with the default parameter settings. For strand-specific RNA-seq data of shExosc3 and shCTR cells, clean reads were aligned to the mouse genome using HISAT2 (v2.1.0) with parameters: --rna-strandness=FR -k 1.
Transcript assembly was performed by stringtie (v2.0) and expression of transcripts sharing each Ensembl_id (genes and lncRNAs) was quantified as Fragments Per Kilobase Million (FPKM).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was isolated and purified using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme).
cDNA library construction and high-throughput sequencing were performed by Novogene.

treatment_protocol:
We performed ciPSC reprogramming with or without CD-treated, Rxra-OE and shE3.
ciPSC medium included KnockOut DMEM supplemented with 10% KSR, 10% FBS, 1% NEAA, 1% P/S, 0.055 mM β-ME, 20 ng ml-1 bFGF, and the small molecules VPA (0.5 mM), CHIR99021 (20 μM), 616452 (10 μM), Parnate (5 μM), Forskolin (50 μM), AM580 (0.5 μM), EPZ004777 (5 μM) and vitamin C (Vc) (250 μM).

value: embryonic fibroblasts

value: WT shRNA


title: Microbiota of Stool from patient AP31

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-E7-FAS-31F

value: Adenoma

value: Unknown


title: Microbiota of Saliva from patient AP35

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-E8-FAS-35S

value: Saliva

value: F

value: Proximal


title: shCTR-1

description: shE3-shCTR-gene expression.txt


title: Naive+Pregnant C5 (PD1+CD73+), replicate 3, technical rep. A

description: MatrixColumn: NPP3_5a


title: Naive+Pregnant C1 (PD1-), replicate 2, technical rep. B

description: MatrixColumn: NPP2_Bb


title: Microbiota of Colon biopsy from patient CRC23

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-E6-FAS-23B

value: Colon biopsy

value: M

value: Adenocarcinoma

value: Distal


title: CBF1_d301_351_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CBF1 Δ301 351 SV40 NLS MNase

value: Truncation


title: Naive+Pregnant C1 (PD1-), replicate 2, technical rep. A

description: MatrixColumn: NPP2_Ba

value: Spleen+Lymph Nodes

value: Semi-Allogeneic Pregnancy


title: Naive+Pregnant C1 (PD1-), replicate 3, technical rep. B

description: MatrixColumn: NPP3_Bb

value: CD8+ T cells


title: shE3-2

description: shE3-shCTR-gene expression.txt

value: Exosc3 knockdown

value: ciPSC reprogramming


title: CBF1_d301_351_2


title: Microbiota of Saliva from patient CRC17

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-E5-FAS-17S

value: I


title: Naive+Pregnant C5 (PD1+CD73+), replicate 2, technical rep. B

description: MatrixColumn: NPP2_5b


title: shE3-1

description: shE3-shCTR-gene expression.txt

value: embryonic fibroblasts


title: CBF1_d301_351_4


title: CD_4h-1

description: expression-degradation.txt

value: Mouse embryonic fibroblasts

value: CD addition


title: CBF1_d301_351_1


title: Microbiota of Stool from patient CRC11

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-E4-FAS-11F

value: Stool

value: Unknown


title: Naive+Pregnant C5 (PD1+CD73+), replicate 2, technical rep. A

description: MatrixColumn: NPP2_5a


title: Microbiota of Colon biopsy from patient CRC8

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-E3-FAS-8B

value: Colon biopsy

value: F

value: Proximal


title: Microbiota of Colon biopsy from patient CRC3

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-F1-FAS-3B

value: M

value: Adenocarcinoma

value: Distal


title: CTR-2

description: Rxra-OE_CTR-gene expression.txt

value: WT OE


title: CRZ1_d2_200_6

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CRZ1 Δ2 200 SV40 NLS MNase

value: Truncation


title: CBF1_d2_50_5

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CBF1 Δ2 50 SV40 NLS MNase


title: CTR-1

description: Rxra-OE_CTR-gene expression.txt

value: ciPSC reprogramming


title: Microbiota of Saliva from patient CRC6

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-E2-FAS-6S

value: Saliva

value: I


title: Naive+Pregnant C1 (PD1-), replicate 1, technical rep. B

description: MatrixColumn: NPP1_Bb

value: Spleen+Lymph Nodes

value: CD8+ T cells

value: Semi-Allogeneic Pregnancy


title: CBF1_d2_50_2


title: Microbiota of Saliva from patient CRC47

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-E10-FAS-47S

value: Unknown