title: Rxra-OE-2

description: Rxra-OE_CTR-gene expression.txt

value: embryonic fibroblasts

value: Rxra overexpression


title: CBF1_d2_50_1

status: Public on May 03 2023

type: SRA

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

library_source: genomic

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)

molecule: genomic DNA

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 CBF1 Δ2 50 SV40 NLS MNase

tag: tagged tf

tag: variant-type

value: Truncation


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

city: Chicago

first: Anita

last: Chong

state: IL

address: 5841 S Maryland Ave

country: USA

institute: University of Chicago

description: MatrixColumn: NPP1_Ba

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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.

tag: tissue

value: Spleen+Lymph Nodes

tag: cell line

tag: cell type

value: CD8+ T cells

tag: genotype

tag: treatment

value: Semi-Allogeneic Pregnancy


title: CBF1_d2_200_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CBF1 Δ2 200 SV40 NLS MNase


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

description: MatrixColumn: NPP1_5b


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

description: MatrixColumn: NPP1_5a


title: Microbiota of Stool from patient CRC3

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 Saliva
feature_table.csv
ID598-E1-FAS-3F

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

organism: Homo sapiens

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: Sex

value: M

tag: condition

value: Adenocarcinoma

tag: tumor type

value: Distal

tag: stadiation

value: I


title: Microbiota of Stool from patient CRC37

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-D9-FAS-37F

value: III


title: CBF1_d2_200_1


title: CBF1_nonDBD_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CBF1 Δ223 271 MNase

value: nonDBD


title: DMSO-1

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

country: China

institute: Zhejiang University

description: CD-DMSO-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

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:
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: DMSO addition

value: ciPSC reprogramming


title: DMSO-2

description: CD-DMSO-gene expression.txt

value: embryonic fibroblasts


title: CBF1_d2_150_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CBF1 Δ2 150 SV40 NLS MNase


title: Microbiota of Colon biopsy from patient AP33

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-D8-FAS-33B

source_name: Colon biopsy

value: Colon biopsy

value: F

value: Adenoma

value: Proximal

value: Unknown


title: Naive, replicate 2, technical rep. B

description: MatrixColumn: N2_b

value: Spleen+Lymph Nodes

value: CD8+ T cells


title: CBF1_d2_150_3

value: Truncation


title: Microbiota of Stool from patient CRC23

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-D6-FAS-23F

value: Stool

value: M

value: Adenocarcinoma

value: Distal


title: Microbiota of Saliva from patient AP31

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-D7-FAS-31S

source_name: Saliva

value: Saliva


title: CBF1_d2_150_1


title: Microbiota of Colon biopsy from patient CRC16

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-D5-FAS-16B

value: II


title: CD-1

description: CD-DMSO-gene expression.txt

value: CD addition

value: ciPSC reprogramming


title: Naive, replicate 2, technical rep. A

description: MatrixColumn: N2_a


title: ATAC WT Day3 rep1

city: Berlin

first: Pavel

last: Tsaytler

address: Ihnestrasse  63-73

country: Germany

institute: MPI Molecular Genetics

description:
in vitro differentiated cardiac mesoderm progenitors
ATAC_WT_Day3_rep1and2.bw

data_processing:
For RNA-Seq, reads were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using cutadapt (version 2.9) (Martin, https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences. Alignment was performed using Hisat2 (version 2.1.0) (Kim, 2019) with the following arguments: --no-mixed --no-discordant. The index files for Hisat2 were built using mm10 reference genome containing chromosomes 1-19, X, Y and M, and splice sites and exon data from refSeq annotations. The resulting sam format files were then converted to bam format, sorted and indexed using samtools (version 1.9) (Li, 2009). FPKM values were calculated using Cuffdiff (version 2.2.1) (Trapnell, 2010) with the following arguments: -u -no-effective-length-correction -b.
For ChIP-Seq, reads were trimmed to 50 bp length. The trimmed reads were aligned to the reference genome using bowtie2 (version 2.2.4) (Langmead, 2012) with the following arguments: -3 5 -I 100 -X 500 --no-discordant --no-mixed. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. For visualization, the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing CPM --extendReads 200 --smoothLength 9 -bs 3 -ignore chrM.
For ATAC-Seq, reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from biological replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 3 -ignore chrY chrM.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing density for ATAC-Seq and ChIP-Seq
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each RNA-Seq sample for refseq genes

source_name: in vitro differentiated ES cells

growth_protocol: ES cells were deprived of feeder cells and cultured for 24 hours. Cells were then dissociated, and 40,000 cell/ml cell suspension was plated onto tissue culture plates in 5 µl droplets. Plates were then inverted and incubated for 24 hours. Drops containing mES cell aggregates (corresponding to differentiation day 0, or ES) were then pooled and resuspended in differentiation medium: 48% (v/v) DMEM/F12 (ThermoFisher; 11320033), 48% (v/v) Neurobasal medium (ThermoFisher; 21103049), 1% (v/v) 200 mM L-glutamine (Lonza; BE17-605E), 1% (v/v) penicillin and streptomycin, 1% (v/v) B27 (Gibco; 17504044), 0.5% (v/v) N2 (Gibco; 17502048), 0,5% (v/v) 7.5% BSA fraction V (Gibco; 15260037), 0.1 mM thioglycerol (Sigma-Aldrich; M1753) supplemented with 20 ng/ml mouse recombinant Bmp4 (R&D Systems; 5020-BP-010). To start differentiation, mESC aggregates resuspended in differentiation medium containing Bmp4 were immediately plated on plates pre-coated with fibronectin (Calbiochem; 341631). Differentiation medium supplemented with Bmp4 was refreshed every 24 hours.

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-7 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.

treatment_protocol: The cells were trypsinized, and the trypsin was inactivated by washing with cold PBS containing 2% BSA. For each sample, 50,000 cells were collected, washed with 1 ml cold PBS and pelleted by centrifugation.

tag: strain

tag: differentiation stage

value: Day 3


title: CBF1_d2_100_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CBF1 Δ2 100 SV40 NLS MNase


title: Naive, replicate 1, technical rep. B

description: MatrixColumn: N1_b


title: ATAC WT Day3 rep2


title: Rxra-OE-1

description: Rxra-OE_CTR-gene expression.txt

value: embryonic fibroblasts

value: Rxra overexpression


title: Microbiota of Saliva from patient CRC11

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-D4-FAS-11S


title: CBF1_d2_100_1


title: Naive, replicate 3, technical rep. B

description: MatrixColumn: N3_b


title: Microbiota of Stool from patient CRC8

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-D3-FAS-8F

value: F

value: Proximal

value: I


title: Naive, replicate 1, technical rep. A

description: MatrixColumn: N1_a

value: Spleen+Lymph Nodes

value: CD8+ T cells


title: ATAC WT Day2 rep2

description:
in vitro differentiated cardiac mesoderm progenitors
ATAC_WT_Day2_rep1and2.bw

value: Day 2


title: CBF1_d276_351_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CBF1 Δ276 351 SV40 NLS MNase

value: DBD


title: ATAC WT Day2 rep1


title: Microbiota of Colon biopsy from patient CRC5

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-D2-FAS-5B

value: Colon biopsy

value: M

value: Adenocarcinoma

value: Distal


title: ChIP Control Eomes Day2

data_processing:
For ChIP-Seq, reads were trimmed to 50 bp length. The trimmed reads were aligned to the reference genome using bowtie2 (version 2.2.4) (Langmead, 2012) with the following arguments: -3 5 -I 100 -X 500 --no-discordant --no-mixed. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. For visualization, the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing CPM --extendReads 200 --smoothLength 9 -bs 3 -ignore chrM.
Assembly: mm10
Supplementary files format and content: bigWig files representing density for ChIP-Seq

source_name: ES cells

extract_protocol:
For sonication, complete protease inhibitors without EDTA (Roche) at 1x final concentration was added to all lysis buffers (LB) prior to use. Each pellet was resuspended in 2.5 ml LB1 (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.75% NP-40, 0.25% triton X-100) and rotated at 4°C for 20 minutes. The cell suspension was homogenized using a douncer. The chromatin was pelleted by centrifugation at 1400g and 4°C for 5 minutes and resuspended in 2.5 ml LB2 (10 mM Tris pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). After 10 minutes rotation at 4°C, the centrifugation step was repeated and each pellet was resuspended in 1.5 ml LB3 (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine), transferred to 15 ml Falcon tubes and sonicated using a W-450D Digital Sonifier (Branson) sonicator for 14 cycles of 10s on/50s off in a 4°C cold room with tubes chilled in ice water. After sonication, 150 μl of Triton X-100 was added per tube, transferred to two 1.5 ml Eppendorf tubes and debris was pelleted by centrifugation at 20,000g and 4°C for 10 minutes. The solubilized chromatin was then pooled and mixed thoroughly. After taking 50 μl as an input control, the chromatin was distributed into 1.5 ml aliquots, snap frozen and stored at -80°C until use.  The input was reverse-crosslinked with the addition of 50 μl 2x elution buffer (100 mM Tris pH 8, 20 mM EDTA pH 8, 2% SDS) and 13-15 hour incubation at 65°C. 100μl of TE buffer were added, and RNA was digested using 0.2 μg/ml RNase A at 37°C for 2 hours. Proteins were digested with the addition of 0.2 μg/ml proteinase K and incubation at 55°C for 2 hours. The DNA was purified with two subsequent phenol:chloroform:isoamyl alcohol (25:24:1, pH 8) extractions and a subsequent MinElute (Qiagen) purification. The input DNA was quantified using a NanoPhotometer (Implen).    For ChIP, 100 μl protein G-coated Dynal beads (Life Technologies) were washed 3x with 1 ml of blocking buffer (PBS, 0.5% BSA), resuspended in 500 μl of blocking solution containing 5 μg primary ChIP antibody (listed in the Key resources table) and rotated overnight at 4°C. Beads were then washed 3x with 1 ml of blocking buffer and resuspended in 100 μl blocking buffer. Chromatin equivalent to 5x107 cells was added and rotated overnight at 4°C. The following day, 6 washing steps (9 for T) with 1 ml RIPA buffer (50 mM Hepes pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and one washing step with 1 ml of TEN (10 mM Tris pH 8, 1 mM EDTA, 50 mM NaCl) were performed. The elution was performed in two subsequent steps using 100 μl of 1x elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) and incubation at 65°C while shaking for 10 minutes each. The eluates were combined and incubated for 13-15 hours at 65°C. 200 μl of TE were added and the ChIP DNA was purified as described for the input above. ChIP DNA was quantified using the Qubit (Life Technologies) DNA HS assay.
The ChIP-seq libraries were generated using the TruSeq ChIP library kit (Illumina) with the previously described modifications (Koch, 2017). After adapter ligation, 0.95x of AMPure XP beads (Beckman Coulter) were used for a single purification and the DNA was eluted using 14 μl of resuspension buffer (RSB, Illumina). After the addition of 1 μl primer mix (25 mM each) and 15 μl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 seconds at 98°C, 5 cycles of [15 seconds at 98°C, 30 seconds at 63°C and 30 seconds at 72°C] and a final 1 minute incubation at 72°C. The PCR products were purified using 0.95x of beads and eluted using 21 μl of RSB. Ligation products were then separated using a 1.5% agarose gel. Post-run staining was performed using SYBR Gold under agitation for 30 minutes. Gel slices corresponding to 250-400 bp fragment size were cut out. using a Dark Reader Transilluminator.  The gel extraction was performed using 5 gel volumes of QG buffer (Qiagen) with the addition of one gel volume of isopropanol. The MinElute (Qiagen) columns were washed once with QG buffer and twice with PE buffer, air-dried for at least 10 minutes and eluted using 21 μl of EB buffer. 19 μl of the eluate was used in the final amplification, with the addition of 1 μl primer mix and 20 μl 2x Kapa HiFi Hotstart premix. The same protocol as for the pre-amplification was used, with the exception of using 13 amplification cycles. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS Bioanalyzer chips.

treatment_protocol: Crosslinking was performed directly on differentiating cells in differentiation medium with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 50mM Hepes pH 7.8) for 10 minutes at room temperature, while shaking. The crosslinking reaction was quenched with the addition of 1/10th volume of 2.5M glycine and 5 minutes incubation. Cells were washed twice with cold PBS, scraped in cold PBS containing 0.05% Triton X-100, pelleted in aliquots of 50 million cells, snap frozen and stored at -80°C until sonication.

value: ES cells

value: Eomes KO

value: in vitro differentiated cardiac mesoderm progenitors


title: Naive, replicate 3, technical rep. A

description: MatrixColumn: N3_a


title: CBF1_d276_351_1


title: CD-2

description: CD-DMSO-gene expression.txt

value: embryonic fibroblasts

value: CD addition

value: ciPSC reprogramming


title: Microbiota of Saliva from patient CRC46

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-D10-FAS-46S

value: Saliva

value: Unknown


title: ATAC WT Day1 rep2

description:
in vitro differentiated cardiac mesoderm progenitors
ATAC_WT_Day1_rep1and2.bw

value: Day 1


title: ATAC WT Day1 rep1


title: Microbiota of Saliva from patient CRC3

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-D1-FAS-3S

value: I


title: CBF1_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CBF1 MNase

value: TF


title: CBF1_3


title: Microbiota of Saliva from patient CRC37

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-C9-FAS-37S

value: III


title: Sensitized, replicate 4

description:
MatrixColumn: Sens4
ATAC_RawPeakCounts.csv
B6Sens_peaks.bed

data_processing:
Raw ATAC-Seq reads were trimmed for adapter content and filtered for truncated reads using Cutadapt v3.4
Paired-end reads were aligned using Bowtie2 v2.2.9 against the GRCm39 (mm39) reference genome
Non-uniquely mapping reads and PCR duplicates were filtered with Bamtools v2.5 and Picard v2.21.8, respectively
Peaks corresponding to ATAC-Seq cut sites for each sample were called using Genrich v0.6.1 in ATAC-Seq mode
Finally, reproducibly identifiable peaks for each experimental group were identified via ChIP-R v1.2.0. Reproducibly identifiable peaks across all experimental groups were merged into a single reference peak set using Bedtools v2.27.1. Multibamsummary v3.5.1 from the Deeptools suite was used to generate per-sample read counts at each peak from the reference peak set
Assembly: GRCm39 (mm39)
Supplementary files format and content: .csv file, raw read counts for each peak
Supplementary files format and content: .bed file of reproducible peaks for each experimental group

extract_protocol:
Chromatin profiling was performed by ATAC-seq as described by buenrostro et al. ~3,000-50,000 sorted cells were washed in cold PBS and lysed to isolate intact nuclei. Transposition was performed at 37°C for 30min with the Tagment DNA Enzyme and Buffer kit (Illumina).
After purification of the transposed DNA with the MinElute PCR purification kit (Qiagen), material was amplified via PCR for 13-14 cycles with Nextera XT Index primers (Illumina). Final product was purified again via MinElute PCR purification kit (Qiagen).
Libraries were sequenced in the same 150 bp/150 bp Paired end run. An average of 75 × 106 paired reads was generated per sample.

value: Spleen+Lymph Nodes

value: CD8+ T cells

value: Allogeneic Skin Graft


title: ATAC WT ES rep2

description:
mouse embryonic stem cells
ATAC_WT_ES_rep1and2.bw

value: mESC


title: Sensitized, replicate 2

description:
MatrixColumn: Sens2
ATAC_RawPeakCounts.csv
B6Sens_peaks.bed


title: CBF1_1


title: ATAC WT ES rep1


title: RNA Smad4 KO Day2

description:
in vitro differentiated cardiac mesoderm progenitors
FPKM_Smad4_WT_KO_Day2.txt

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596043) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

treatment_protocol: The cells were trypsinized, and the trypsin was inactivated by washing with cold PBS containing 2% BSA. For each sample, 40,000 cells were collected, washed with 1 ml cold PBS and pelleted by centrifugation.

value: Day 2


title: BAS1_nonDBD_5

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ161 214 MNase

value: nonDBD


title: Sensitized, replicate 1

description:
MatrixColumn: Sens1
ATAC_RawPeakCounts.csv
B6Sens_peaks.bed


title: BAS1_nonDBD_4


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 4

description:
MatrixColumn: SPP4_c5
ATAC_RawPeakCounts.csv
B6SPP5_peaks.bed

value: Allogeneic Skin Graft+Semi-Allogeneic Pregnancy


title: RNA Smad4 KO Day1

description:
in vitro differentiated cardiac mesoderm progenitors
FPKM_Smad4_WT_KO_Day1.txt

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596041) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: Microbiota of Saliva from patient CRC23

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-C6-FAS-23S

value: M

value: Adenocarcinoma

value: Distal


title: Microbiota of Stool from patient CRC16

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-C5-FAS-16F

value: Stool

value: II


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 4

description:
MatrixColumn: SPP4_c7
ATAC_RawPeakCounts.csv
B6SPP7_peaks.bed


title: Microbiota of Colon biopsy from patient CRC30

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-C7-FAS-30B

value: Colon biopsy

value: Proximal


title: RNA Smad4 WT Day1

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596040) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: Day 1


title: Sensitized+Pregnant C4 (PD1-), replicate 4

description:
MatrixColumn: SPP4_B
ATAC_RawPeakCounts.csv
B6SPPB_peaks.bed


title: Microbiota of Colon biopsy from patient CRC10

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-C4-FAS-10B

value: Unknown


title: BAS1_nonDBD_3


title: Sensitized, replicate 3

description:
MatrixColumn: Sens3
ATAC_RawPeakCounts.csv
B6Sens_peaks.bed

value: Spleen+Lymph Nodes


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 3

description:
MatrixColumn: SPP3_c7
ATAC_RawPeakCounts.csv
B6SPP7_peaks.bed

value: CD8+ T cells


title: BAS1_nonDBD_1


title: RNA Eomes T dKO Day3

description:
in vitro differentiated cardiac mesoderm progenitors
FPKM_WT_Eomes_T_dKO_Day3.txt

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596039) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: Day 3


title: CBF1_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 CBF1 MNase

value: TF


title: Microbiota of Stool from patient AP33

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-C8-FAS-33F

value: F

value: Adenoma


title: BAS1_d751_811_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ751 811 SV40 NLS MNase

value: Truncation


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 3

description:
MatrixColumn: SPP3_c5
ATAC_RawPeakCounts.csv
B6SPP5_peaks.bed

value: Allogeneic Skin Graft+Semi-Allogeneic Pregnancy


title: Microbiota of Saliva from patient CRC8

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-C3-FAS-8S

value: Saliva

value: Adenocarcinoma

value: I


title: RNA Eomes T dKO Day2

description:
in vitro differentiated cardiac mesoderm progenitors
FPKM_WT_Eomes_T_dKO_Day2.txt

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596038) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: Day 2


title: Microbiota of Stool from patient CRC5

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-C2-FAS-5F

value: Stool

value: M

value: Distal

value: II


title: Sensitized+Pregnant C4 (PD1-), replicate 3

description:
MatrixColumn: SPP3_B
ATAC_RawPeakCounts.csv
B6SPPB_peaks.bed

value: Spleen+Lymph Nodes

value: CD8+ T cells


title: RNA T KO Day3

description:
in vitro differentiated cardiac mesoderm progenitors
FPKM_T_WT_KO_Day3.txt

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596037) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: Day 3


title: BAS1_d751_811_1


title: RNA Smad4 WT Day2

description:
in vitro differentiated cardiac mesoderm progenitors
FPKM_Smad4_WT_KO_Day2.txt

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596042) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: Microbiota of Colon biopsy from patient CRC44

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-C10-FAS-44B

value: Colon biopsy

value: Proximal


title: BAS1_d701_811_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ701 811 SV40 NLS MNase


title: RNA Eomes KO Day3

description:
in vitro differentiated cardiac mesoderm progenitors
FPKM_Eomes_WT_KO_Day3.txt

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596035) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: RNA T KO Day2

description:
in vitro differentiated cardiac mesoderm progenitors
FPKM_T_WT_KO_Day2.txt

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596036) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: Microbiota of Colon biopsy from patient CRC36

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-B9-FAS-36B


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 2

description:
MatrixColumn: SPP2_c5
ATAC_RawPeakCounts.csv
B6SPP5_peaks.bed


title: Microbiota of Colon biopsy from patient CRC1

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-C1-FAS-1B

value: Unknown


title: BAS1_d701_811_2

value: Truncation


title: RNA Eomes KO Day2

description:
in vitro differentiated cardiac mesoderm progenitors
FPKM_Eomes_WT_KO_Day2.txt

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596034) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: Microbiota of Saliva from patient AP33

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-B8-FAS-33S

value: F

value: Adenoma


title: BAS1_d701_811_3

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


title: Sensitized+Pregnant C4 (PD1-), replicate 2

description:
MatrixColumn: SPP2_B
ATAC_RawPeakCounts.csv
B6SPPB_peaks.bed

value: Allogeneic Skin Graft+Semi-Allogeneic Pregnancy


title: BAS1_d701_811_1


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 1

description:
MatrixColumn: SPP1_c7
ATAC_RawPeakCounts.csv
B6SPP7_peaks.bed


title: Microbiota of Stool from patient CRC30

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-B7-FAS-30F

value: Adenocarcinoma


title: BAS1_d651_811_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ651 811 SV40 NLS MNase


title: Sensitized+Pregnant C5 (PD1+CD73+), replicate 1

description:
MatrixColumn: SPP1_c5
ATAC_RawPeakCounts.csv
B6SPP5_peaks.bed


title: Microbiota of Colon biopsy from patient CRC20

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-B6-FAS-20B


title: BAS1_d651_811_2


title: Sensitized+Pregnant C4 (PD1-), replicate 1

description:
MatrixColumn: SPP1_B
ATAC_RawPeakCounts.csv
B6SPPB_peaks.bed


title: Microbiota of Saliva from patient CRC16

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-B5-FAS-16S

value: Saliva


title: Naive+Pregnant C5 (PD1+CD73+), replicate 3

description:
MatrixColumn: NPP3_c5
ATAC_RawPeakCounts.csv
B6NPP5_peaks.bed

value: Semi-Allogeneic Pregnancy


title: RNA WT Day2 rep1

description:
in vitro differentiated cardiac mesoderm progenitors
FPKM_WT_time_course.txt

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596030) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: Day 2


title: Microbiota of Stool from patient CRC10

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-B4-FAS-10F

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

value: M

value: Distal


title: Sensitized+Pregnant C7 (PD1+CD73-), replicate 2

description:
MatrixColumn: SPP2_c7
ATAC_RawPeakCounts.csv
B6SPP7_peaks.bed

value: Spleen+Lymph Nodes

value: CD8+ T cells


title: BAS1_d651_811_1


title: RNA WT Day1 rep2

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596029) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: Day 1


title: Microbiota of Colon biopsy from patient CRC7

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-B3-FAS-7B

value: Colon biopsy

value: III


title: Naive+Pregnant C1 (PD1-), replicate 3

description:
MatrixColumn: NPP3_B
ATAC_RawPeakCounts.csv
B6NPPB_peaks.bed


title: BAS1_d601_811_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ601 811 SV40 NLS MNase

value: Truncation


title: Naive+Pregnant C5 (PD1+CD73+), replicate 2

description:
MatrixColumn: NPP2_c5
ATAC_RawPeakCounts.csv
B6NPP5_peaks.bed


title: BAS1_d501_811_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ501 811 SV40 NLS MNase


title: Naive+Pregnant C1 (PD1-), replicate 2

description:
MatrixColumn: NPP2_B
ATAC_RawPeakCounts.csv
B6NPPB_peaks.bed


title: RNA WT Day3 rep2

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596033) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: Day 3


title: RNA WT Day1 rep1

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596028) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: RNA WT ES rep2

description:
mouse embryonic stem cells
FPKM_WT_time_course.txt

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596027) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: mESC


title: Microbiota of Stool from patient CRC44

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-B10-FAS-44F

value: Adenocarcinoma

value: Proximal

value: II


title: CRZ1_d2_200_5

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


title: RNA WT Day3 rep1

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596032) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: RNA WT Day2 rep2

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596031) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: Day 2


title: RNA WT ES rep1

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596026) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: Microbiota of Stool from patient CRC1

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-B1-FAS-1F

value: Stool

value: M

value: Unknown


title: Naive+Pregnant C5 (PD1+CD73+), replicate 1

description:
MatrixColumn: NPP1_c5
ATAC_RawPeakCounts.csv
B6NPP5_peaks.bed

extract_protocol:
Chromatin profiling was performed by ATAC-seq as described by buenrostro et al. ~3,000-50,000 sorted cells were washed in cold PBS and lysed to isolate intact nuclei. Transposition was performed at 37°C for 30min with the Tagment DNA Enzyme and Buffer kit (Illumina).
After purification of the transposed DNA with the MinElute PCR purification kit (Qiagen), material was amplified via PCR for 13-14 cycles with Nextera XT Index primers (Illumina). Final product was purified again via MinElute PCR purification kit (Qiagen).
Libraries were sequenced in the same 150 bp/150 bp Paired end run. An average of 75 × 106 paired reads was generated per sample.

value: Spleen+Lymph Nodes

value: CD8+ T cells

value: Semi-Allogeneic Pregnancy


title: BAS1_d451_811_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ451 811 SV40 NLS MNase


title: ChIP T Day3

description:
in vitro differentiated cardiac mesoderm progenitors
ChIP_T_Day3.bw

extract_protocol:
For sonication, complete protease inhibitors without EDTA (Roche) at 1x final concentration was added to all lysis buffers (LB) prior to use. Each pellet was resuspended in 2.5 ml LB1 (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.75% NP-40, 0.25% triton X-100) and rotated at 4°C for 20 minutes. The cell suspension was homogenized using a douncer. The chromatin was pelleted by centrifugation at 1400g and 4°C for 5 minutes and resuspended in 2.5 ml LB2 (10 mM Tris pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). After 10 minutes rotation at 4°C, the centrifugation step was repeated and each pellet was resuspended in 1.5 ml LB3 (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine), transferred to 15 ml Falcon tubes and sonicated using a W-450D Digital Sonifier (Branson) sonicator for 14 cycles of 10s on/50s off in a 4°C cold room with tubes chilled in ice water. After sonication, 150 μl of Triton X-100 was added per tube, transferred to two 1.5 ml Eppendorf tubes and debris was pelleted by centrifugation at 20,000g and 4°C for 10 minutes. The solubilized chromatin was then pooled and mixed thoroughly. After taking 50 μl as an input control, the chromatin was distributed into 1.5 ml aliquots, snap frozen and stored at -80°C until use.  The input was reverse-crosslinked with the addition of 50 μl 2x elution buffer (100 mM Tris pH 8, 20 mM EDTA pH 8, 2% SDS) and 13-15 hour incubation at 65°C. 100μl of TE buffer were added, and RNA was digested using 0.2 μg/ml RNase A at 37°C for 2 hours. Proteins were digested with the addition of 0.2 μg/ml proteinase K and incubation at 55°C for 2 hours. The DNA was purified with two subsequent phenol:chloroform:isoamyl alcohol (25:24:1, pH 8) extractions and a subsequent MinElute (Qiagen) purification. The input DNA was quantified using a NanoPhotometer (Implen).    For ChIP, 100 μl protein G-coated Dynal beads (Life Technologies) were washed 3x with 1 ml of blocking buffer (PBS, 0.5% BSA), resuspended in 500 μl of blocking solution containing 5 μg primary ChIP antibody (listed in the Key resources table) and rotated overnight at 4°C. Beads were then washed 3x with 1 ml of blocking buffer and resuspended in 100 μl blocking buffer. Chromatin equivalent to 5x107 cells was added and rotated overnight at 4°C. The following day, 6 washing steps (9 for T) with 1 ml RIPA buffer (50 mM Hepes pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and one washing step with 1 ml of TEN (10 mM Tris pH 8, 1 mM EDTA, 50 mM NaCl) were performed. The elution was performed in two subsequent steps using 100 μl of 1x elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) and incubation at 65°C while shaking for 10 minutes each. The eluates were combined and incubated for 13-15 hours at 65°C. 200 μl of TE were added and the ChIP DNA was purified as described for the input above. ChIP DNA was quantified using the Qubit (Life Technologies) DNA HS assay.
The ChIP-seq libraries were generated using the TruSeq ChIP library kit (Illumina) with the previously described modifications (Koch, 2017). After adapter ligation, 0.95x of AMPure XP beads (Beckman Coulter) were used for a single purification and the DNA was eluted using 14 μl of resuspension buffer (RSB, Illumina). After the addition of 1 μl primer mix (25 mM each) and 15 μl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 seconds at 98°C, 5 cycles of [15 seconds at 98°C, 30 seconds at 63°C and 30 seconds at 72°C] and a final 1 minute incubation at 72°C. The PCR products were purified using 0.95x of beads and eluted using 21 μl of RSB. Ligation products were then separated using a 1.5% agarose gel. Post-run staining was performed using SYBR Gold under agitation for 30 minutes. Gel slices corresponding to 250-400 bp fragment size were cut out. using a Dark Reader Transilluminator.  The gel extraction was performed using 5 gel volumes of QG buffer (Qiagen) with the addition of one gel volume of isopropanol. The MinElute (Qiagen) columns were washed once with QG buffer and twice with PE buffer, air-dried for at least 10 minutes and eluted using 21 μl of EB buffer. 19 μl of the eluate was used in the final amplification, with the addition of 1 μl primer mix and 20 μl 2x Kapa HiFi Hotstart premix. The same protocol as for the pre-amplification was used, with the exception of using 13 amplification cycles. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS Bioanalyzer chips.


title: Microbiota of Stool from patient CRC36

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-A9-FAS-36F

value: Distal


title: BAS1_d601_811_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ601 811 SV40 NLS MNase

value: Truncation


title: BAS1_d451_811_1


title: Microbiota of Colon biopsy from patient CRC32

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-A8-FAS-32B

value: Colon biopsy


title: BAS1_d401_811_6

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ401 811 SV40 NLS MNase


title: Microbiota of Saliva from patient CRC5

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-B2-FAS-5S

value: Saliva

value: Adenocarcinoma


title: Microbiota of Saliva from patient CRC30

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-A7-FAS-30S

value: Proximal

value: II


title: Sample 12_Mutant_Cisplatin_3

city: Pittsburgh

first: Rannar

last: Airik

address: 4401 Penn Avenue

institute: University of Pittsburgh

data_processing:
The Rsubread and limma-voom packages were used for the analysis of the RNA-Seq data in R
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Kidneys were removed, flash frozen on dry ice, and RNA was harvested using the RNeasy Mini Kit (Qiagen) in accordance to manufacturer's protocol. The integrity of the RNA was assessed using an Agilent Tapestation prior to library construction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cisplatin treated mice received a weekly intraperitoneal dose of 2 mg/kg of cisplatin for 5 weeks. Control mice received saline injections

tag: strain background

value: Mixed

tag: age

value: 8-12 weeks old

value: Cisplatin

value: Kidney


title: BAS1_d401_811_4

tag: genetic information


title: Naive, replicate 1

description:
MatrixColumn: N1
ATAC_RawPeakCounts.csv
B6N_peaks.bed

value: Spleen+Lymph Nodes


title: Sample 11_Mutant_Cisplatin_2


title: Naive, replicate 2

description:
MatrixColumn: N2
ATAC_RawPeakCounts.csv
B6N_peaks.bed

value: CD8+ T cells


title: Naive, replicate 3

description:
MatrixColumn: N3
ATAC_RawPeakCounts.csv
B6N_peaks.bed


title: BAS1_d351_811_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ351 811 SV40 NLS MNase

tag: tagged tf


title: Naive+Pregnant C1 (PD1-), replicate 1

description:
MatrixColumn: NPP1_B
ATAC_RawPeakCounts.csv
B6NPPB_peaks.bed

value: Semi-Allogeneic Pregnancy


title: Microbiota of Stool from patient CRC20

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-A6-FAS-20F

value: Stool

value: M

value: Distal


title: Microbiota of Colon biopsy from patient CRC13

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-A5-FAS-13B

value: Colon biopsy

value: Unknown


title: BAS1_d501_811_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ501 811 SV40 NLS MNase

tag: variant-type

value: Truncation


title: Sample 10_Mutant_Cisplatin_1

tag: tissue


title: Sample 9_Wildtype_Cisplatin_3

value: Wildtype


title: BAS1_d351_811_2


title: Microbiota of Saliva from patient CRC10

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-A4-FAS-10S

value: Saliva

value: Adenocarcinoma


title: Sample 8_Wildtype_Cisplatin_2

value: Mixed

value: 8-12 weeks old


title: BAS1_d351_811_3


title: Microbiota of Stool from patient CRC7

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-A3-FAS-7F

value: III


title: Microbiota of Colon biopsy from patient CRC4

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-A2-FAS-4B


title: BAS1_d301_811_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ301 811 SV40 NLS MNase


title: Sample 7_Wildtype_Cisplatin_1

value: Cisplatin

value: Kidney


title: ChIP P-Smad1/5/9 Day2

description:
in vitro differentiated cardiac mesoderm progenitors
ChIP_P-Smad-1-5-9_Day2.bw

value: Day 2


title: Lung KP DT (Diphtheria Toxin 48hr) sample #B1, visium

city: New York

first: Dana

last: Pe'er

state: NY

address: 417 E 68th St

department: Computational and Systems Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Processing of Visium spatial transcriptomics data was performed with the SpaceRanger pipeline from 10X genomics (v 1.3.1). The mkfastq function was used to generate FASTQ files from raw base calls and the count function was used in combination with a matched brightfield H&E stained image to align to a modified mm10 genome, perform tissue detection, and count unique molecular identifiers (UMI) for each spot. The modified genome consisted of Ensembl 100 annotations with an added transcript to detect DTR-GFP expressed from the Foxp3 promoter (sDTR-eGFP). UMI counts were summed by gene symbol and sDTR-eGFP reads were summed together with Foxp3.
Assembly: GRCm38
Supplementary files format and content: h5 file, spot by feature count matrix from SpaceRanger output after filtering.
Supplementary files format and content: csv file, metadata for spots, including spot barcode, type of tumor spot using tumor RNA fractions, tumor type modified for region definition, tumor region separated by type and connected components, module score of shared ifn genes across lineages, module score of shared inflammatory cytokine genes across lineages, unique lesion across tissue sections, immune response status, membership in signaling niche
Supplementary files format and content: h5 file, feature information from SpaceRanger
Supplementary files format and content: h5 file, raw spot by feature count matrix from SpaceRanger with no filtering
Supplementary files format and content: csv file, spatial enrichment file from SpaceRanger
Supplementary files format and content: csv file, cell type RNA fraction estimates from BayesPrism
Supplementary files format and content: csv file, cell type RNA fraction estimates from BayesPrism using scRNA-seq reference with added tumor data
Supplementary files format and content: jpg file, aligned fiducials for matched H&E image
Supplementary files format and content: jpg file, detected tissue image for matched H&E image
Supplementary files format and content: json file, scale factors for image from SpaceRanger
Supplementary files format and content: png file, high resolution H&E image
Supplementary files format and content: png file, low resolution H&E image
Supplementary files format and content: csv, spot positions on tissue
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

source_name: lung

extract_protocol:
For isolation of immune and stromal cells, lungs were perfused, placed into 5 ml Eppendorf tubes containing 400ml of cold serum-free RPMI and chopped with scissors (1-2 mm). Lung fragments were placed in 2-3 ml of pre-warmed digestion medium (RPMI 1640, 10 mM HEPES buffer, 1% penicillin–streptomycin, 1% L-glutamine, liberase (Sigma-Aldrich #05401020001) and 1 U/ml DNase I (Sigma-Aldrich #10104159001)) (2-3 ml) and incubated for 30 min at 37°C. After digestion supernatant was collected and cells were resuspended in ice-cold RPMI1640 containing 5% FCS (ThermoFisher #35010CV), 1mM HEPES (Corning #MT25060CI), 1% penicillin–streptomycin (Corning #MT30002CI) and 200mM L-glutamine (Corning #MT25005CI). After additional digestion for 1 hr of the remaining tissue, both digested cell fractions passed through a 100um strainer (Corning #07-201-432), washed and FACS sorted.
Bulk RNA seq - Cell populations were sorted straight into Trizol (ThermoFisher #15596018), RNA was precipitated with isopropanol and linear acrylamide, washed with 75% ethanol, and resuspended in RNase-free water. After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.4-2.0ng total RNA with RNA integrity numbers ranging from 1.0 to 9.9 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech #63488), with 12 cycles of amplification. Subsequently, 1.5-10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems #KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 or HiSeq 2500 in Rapid Mode in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit or HiSeq Rapid SBS Kit v2 (Illumina).  An average of 32 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 62% to 88%. scRNAseq- Single-cell RNA-Seq was performed on FACS sorted mouse lung KP cells or patient LuAd samples, on the Chromium instrument (10X genomics) following the user guide manual (CG00052 Rev E) for 3′ v2 and v3 as previously described46.  Briefly, sorted cells were washed once with PBS containing 0.04% bovine serum albumin (BSA) and resuspended in PBS containing 0.04% BSA to a final concentration of 700–1,200 cells per μl. Viability of cells was confirmed to be above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Then samples were encapsulated in microfluidic droplets at a dilution of ∼70 cells/μl (doublet rate ∼3.9%.). Encapsulated cells were subjected to reverse transcription (RT) reaction at 53°C for 60 min. After RT, the emulsion droplets were broken and barcoded-cDNA was purified with DynaBeads MyOne SILANE, followed by 14-cycles of PCR-amplification (98°C for 180 s; [98°C for 15 s, 67°C for 20 s, 72°C for 60 s] x 12-cycles; 72°C for 60 s). 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit and purified with SPRI beads to obtain an average fragment size of 600 bp. Next, the DNA library was ligated to the sequencing adaptor followed by indexing PCR (98°C for 45 s; [98°C for 20 s, 54°C for 30 s, 72°C for 20 s] x 10 cycles; 72°C for 60 s). An average of 5,000 cells were targeted for each tumor sample. The resulting DNA library was double-size purified (0.6-0.8X) with SPRI beads and sequenced on an Illumina NovaSeq platform (R1 – 26 cycles (KP) 28 cycles (LuAd), i7 – 8 cycles, R2 – 96 cycles (KP), 90 cycles (LuAd)) resulting in 184.5-186.1 million reads per sample (average reads per single-cell being 42,000 and average reads per transcript 4.40-7.14) (KP)

value: Diphtheria Toxin

value: lung

value: 21-25 weeks


title: Sample 6_Mutant_Control_3

value: Saline


title: Lung KP DT (Diphtheria Toxin 48hr) sample #A1, visium


title: Microbiota of Saliva from patient CRC44

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-A10-FAS-44S

value: M

value: Proximal

value: II


title: Lung KP DT (Diphtheria Toxin 48hr) sample #D2, visium


title: BAS1_d301_811_1

value: Truncation


title: Sample 4_Mutant_Control_1


title: Sample 5_Mutant_Control_2


title: BAS1_d251_811_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ251 811 SV40 NLS MNase

value: DBD


title: BAS1_d251_811_3


title: Lung KP DT (Diphtheria Toxin 48hr) sample #C2, visium


title: Lung KP control (PBS 48 hr) sample #C2, visium

value: PBS


title: Lung KP control (PBS 48 hr) sample #B1, visium


title: Sample 3_Wildtype_Control_3

value: Mixed

value: 8-12 weeks old

value: Wildtype


title: Lung KP control (PBS 48 hr) sample #A1, visium


title: BAS1_d351_811_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 Δ351 811 SV40 NLS MNase


title: Microbiota of Colon biopsy from patient AP70

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID1077-H12-16S-FAS-70B-T0

value: Colon biopsy

value: Adenoma

value: Unknown


title: Sample 2_Wildtype_Control_2

value: Kidney


title: BAS1_d251_811_1


title: Microbiota of Saliva from patient CRC1

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID598-A1-FAS-1S

value: Saliva

value: Adenocarcinoma

value: Distal


title: BAS1_d251_811_2


title: MYC-Tp53 Organoid Wntinib-treated-7day rep 2

first: Julia

middle: Nanyi

last: Zhao

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Trim Galore! (v6.5) has been used to trim the adapter sequences with a quality threshold of 20. Trimmed sequence reads were then mapped to GrCM38/mm10.
The alignment is performed by using STAR aligner (v2.7.5b). Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries. All samples have passed the quality control requirements with > 50% of reads uniquely mapping (>20M uniquely mapped reads for each library) using STAR aligner.
Assembly: mm10
Supplementary files format and content: comma-separated file includes TPM values for each Sample

source_name: HCC organoid

extract_protocol:
tumor organoids were grown in 24 well plates, and after drug treatment, were collected in Trizol. RNA was extracted using standard procedures and quality was assessed with a bioanalyzer. Libraries were built using the PerkinElmer NextFlex Rapid Directional RNA-Seq Kit 2.0 and sequenced with a NovaSeq 6000 (SE75).
Libraries were built using the PerkinElmer NextFlex Rapid Directional RNA-Seq Kit 2.0 and sequenced with a NovaSeq 6000 (SE75).

value: HCC organoid

value: HCC organoid cells

value: Wntinib

tag: time

value: Day 7


title: MYC-Tp53 Organoid Wntinib-treated-7day rep 1

tag: cell type


title: Microbiota of Saliva from patient CRC34

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID1077-H7-16S-FAS-34S-T0

value: M

value: Proximal


title: Microbiota of Saliva from patient CRC56

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID1077-G6-16S-FAS-56S-T0


title: BAS1_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 MNase

value: TF


title: Sample 1_Wildtype_Control_1

value: Mixed

value: 8-12 weeks old

tag: genotype

value: Wildtype

value: Saline


title: MYC-TP53 Organoid Wntinib-treated-1day rep 2

tag: treatment

value: Day 1


title: Microbiota of Saliva from patient AP12

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID1077-F9-16S-FAS-12S-T0

tag: patient id

value: Adenoma

value: Unknown


title: MYC-Tp53 Organoid Wntinib-treated-1day rep 1


title: BAS1_3


title: W156X_3D_microtissues_ex6A-KO

city: Padova

first: Milena

last: Bellin

state: PD

address: Via Ugo Bassi 58/B

department: Department of Biology

institute: University of Padova

data_processing:
Residual Illumina adapters were trimmed from the RNA sequences using cutadapt with parameter -m 20
Reads were aligned to the human genome (build 38, Ensembl version 96) using STAR
Exon counts were retrieved using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hiPSCs

extract_protocol:
Total RNA was isolated either from hiPSC-CMs on day 21 of differentiation using Nucleospin kit (Machery and Nagel) andd from MTs on day 21 of culture using RNeasy Micro Kit (Qiagen), according the manufacturers’ instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: scn5a genotype

value: 3D microtissues


title: Microbiota of Colon biopsy from patient CRC75

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID1077-H8-16S-FAS-75B-T0

value: Colon biopsy

tag: Sex

tag: condition

value: Adenocarcinoma


title: W156X_corrected_cardiomyocytes_ex6A-KO

value: Cardiomyocytes


title: Microbiota of Colon biopsy from patient AP12

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID1077-F9-16S-FAS-12B-T0

tag: tumor type

tag: stadiation


title: MYC-Tp53 Organoid Wntinib-treated-1hour rep 2

value: HCC organoid

value: HCC organoid cells

value: Wntinib

value: 1 Hour


title: Microbiota of Colon biopsy from patient CRC56

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID1077-F8-16S-FAS-56B-T0

value: M

value: Proximal


title: AZF1_nonDBD_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 AZF1 Δ593 702 MNase

value: nonDBD


title: Microbiota of Stool from patient CRC76

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID1077-E12-16S-FAS-76F-T0

value: Stool

value: Distal


title: AZF1_nonDBD_3


title: MYC-Tp53 Organoid Wntinib-treated-1hour rep 1


title: parental_cardiomyocytes_ex6A-KO


title: MYC-Tp53 Organoid DMSO control rep 2

value: DMSO

value: Day 7


title: W156X_3D_microtissues


title: Microbiota of Colon biopsy from patient CRC59

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID1077-D8-16S-FAS-59B-T0

value: III


title: AZF1_nonDBD_2


title: W156X_corrected_cardiomyocytes


title: Microbiota of Stool from patient CRC75

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID1077-D12-16S-FAS-75F-T0

value: Unknown


title: MYC-Tp53 Organoid DMSO control rep 1


title: AZF1_nonDBD_1


title: MYC-CTNNB1 Organoid Wntinib-treated-7day rep 2


title: parental_3D_microtissues

value: 3D microtissues


title: Microbiota of Saliva from patient CRC75

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID1077-C9-16S-FAS-75S-T0

value: Saliva

value: Adenocarcinoma


title: MYC-CTNNB1 Organoid Wntinib-treated-7day rep 1

value: HCC organoid


title: parental_cardiomyocytes

value: Cardiomyocytes


title: Microbiota of Colon biopsy from patient CRC76

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
ID1077-A9-16S-FAS-76B-T0

value: Colon biopsy


title: AZF1_d801_914_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 AZF1 Δ801 914 SV40 NLS MNase

value: Truncation


title: BAS1_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 BAS1 MNase

value: TF


title: MYC-CTNNB1 Organoid Wntinib-treated-1day rep 2

value: HCC organoid cells

value: Wntinib

value: Day 1


title: ZIKV-infected human microglial cells with metformin administration, 48 h, replicate 3, RNAseq [Met48_3]

city: Galveston

first: Lynn

last: Soong

state: TX

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

description: 2×150bp paired-endsequencing (PE150)

data_processing:
From the RNA sample to the final data, each step, including sample test, library preparation, and sequencing, influences the quality of the data, and data quality directly impacts the analysis results. To guarantee the reliability of the data, quality control (QC) is performed at each step of the procedure. RNA degradation and contamination was monitored on 1% agarose gels.  RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA,USA). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: Gene_counts.xls of raw gene counts

extract_protocol:
Cells (5×104/well) were seeded in 24-well-plates at 37°C and cultured overnight. Cells were pre-treated with metformin at specified concentration (5 mM) for 2 h, followed by ZIKV infection at MOI 3. After infection of 1.5 h, cells were washed three times with PBS. Medium containing metformin was again supplemented and maintained during the culture. The total RNA of samples at 16 and 48 h were extracted for RNA-seq analysis. Preparation of RNA library and transcriptome sequencing were conducted by Novogene (Sacramento, CA). The numbers of reads mapped to each gene were counted using HTSeq v0.6.1. The expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) of each gene was then calculated based on the length of the gene and the read count mapped to this gene.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis  Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp  in length, the library fragments were purified with AMPure XP system (Beckman Coulter,Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: cell line

value: Human microglial cells

value: ZIKV infection+metformin treatment


title: AZF1_d2_500_2

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 AZF1 Δ2 500 SV40 NLS MNase

value: DBD


title: MYC-CTNNB1 Organoid Wntinib-treated-1day rep 1


title: MYC-CTNNB1 Organoid Wntinib-treated-1hour rep 2

value: 1 Hour


title: AZF1_d2_500_1


title: ZIKV-infected human microglial cells with metformin administration, 48 h, replicate 1, RNAseq [Met48_1]

description: 2×150bp paired-endsequencing (PE150)


title: ZIKV-infected human microglial cells with metformin administration, 16 h, replicate 3, RNAseq [Met16_3]

description: 2×150bp paired-endsequencing (PE150)


title: ZIKV-infected human microglial cells with metformin administration, 48 h, replicate 2, RNAseq [Met48_2]

description: 2×150bp paired-endsequencing (PE150)


title: AZF1_d2_400_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 AZF1 Δ2 400 SV40 NLS MNase


title: AZF1_d801_914_2


title: ZIKV-infected human microglial cells with metformin administration, 16 h, replicate 2, RNAseq [Met16_2]

description: 2×150bp paired-endsequencing (PE150)


title: AZF1_d2_300_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 AZF1 Δ2 300 SV40 NLS MNase


title: MYC-CTNNB1 Organoid DMSO control rep 2

value: HCC organoid

value: DMSO

value: Day 7


title: MYC-CTNNB1 Organoid DMSO control rep 1


title: DMSO_8h-2

description: expression-degradation.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

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 embryonic fibroblasts

value: DMSO addition

value: ciPSC reprogramming


title: ZIKV-infected human microglial cells with metformin administration, 16 h, replicate 1, RNAseq [Met16_1]

description: 2×150bp paired-endsequencing (PE150)


title: AZF1_d2_300_1

value: Truncation


title: ZIKV-infected human microglial cells, 48 h, replicate 3, RNAseq [Z48_3]

description: 2×150bp paired-endsequencing (PE150)

value: ZIKV infection


title: AZF1_d2_200_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 AZF1 Δ2 200 SV40 NLS MNase


title: Rxra-CT-1

description:
Rxra-CT-1
Rxra-CT1_peaks.narrowPeak
Rxra-CT1.bw

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 Bowtie2 (v2.2.5) with options: --no-unal --no-mixed –nodiscordant --local --very-sensitive-local --phred33 -I 10 -X 700.
For peak calling, parameters used were macs2 (v2.1.2) callpeak: -p 1e-5 -f BAMPE --keep-dup all -g mm. For H3K27ac CUT&Tag data, parameters will add --broad.
The bigwig files were generated with bamCoverage function in deepTools (v3.4.3) with default parameter settings.
Assembly: mm10
Supplementary files format and content: bigwig, peakfile text file

extract_protocol:
CUT&Tag assay was performed using NovoNGS_ CUT&Tag High- Sensitivity Kit (Novoprotein) according to the manufacturer’s recommendation.
We used TruePrep DNA Library Prep Kit V2 for library construction.

treatment_protocol: We performed ciPSC reprogramming DMSO/CD and Flag-Rxra-OE treatment.

tag: chip antibody

value: Flag (Sigma-Aldrich, F1804)


title: MYC-CTNNB1 Organoid Wntinib-treated-1hour rep 1

value: HCC organoid cells

value: Wntinib


title: ZIKV-infected human microglial cells, 48 h, replicate 2, RNAseq [Z48_2]

description: 2×150bp paired-endsequencing (PE150)

value: Human microglial cells


title: AZF1_d2_400_2


title: AZF1_d2_100_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 AZF1 Δ2 100 SV40 NLS MNase


title: DMSO-H3K27ac-2

description:
DMSO-H3K27ac-2
K27ac_DMSO_peaks.broadPeak
K27ac_DMSO.bw

value: H3K27ac (Abcam, Ab4729)


title: DMSO-H3K27ac-1

description:
DMSO-H3K27ac-1
K27ac_DMSO_peaks.broadPeak
K27ac_DMSO.bw


title: ZIKV-infected human microglial cells, 48 h, replicate 1, RNAseq [Z48_1]

description: 2×150bp paired-endsequencing (PE150)


title: AZF1_d2_100_1


title: Rxra-CT-2

description:
Rxra-CT-2
Rxra-CT2_peaks.narrowPeak
Rxra-CT2.bw


title: ZIKV-infected human microglial cells, 16 h, replicate 3, RNAseq [Z16_3]

description: 2×150bp paired-endsequencing (PE150)


title: AZF1_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 AZF1 MNase

value: TF


title: AZF1_1


title: CD-H3K27ac-1

description:
CD-H3K27ac-1
K27ac_CD_peaks.broadPeak
K27ac_CD.bw


title: ZIKV-infected human microglial cells, 16 h, replicate 2, RNAseq [Z16_2]

description: 2×150bp paired-endsequencing (PE150)


title: ZIKV-infected human microglial cells, 16 h, replicate 1, RNAseq [Z16_1]

description: 2×150bp paired-endsequencing (PE150)


title: tumor tissues of CPC-Apc mice, replicate 5

type: RNA

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: NC-P

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Data were analyzed using the bioinformatics software GeneSpring 13.0 (Agilent)

source_name: colorectal tissue

label_protocol: 35 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated with TRIzol Reagent (Invitrogen) for mouse samples following the manufacturer’s protocol. RNA quality was assessed with NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies).

treatment_protocol: We performed treatment of the combination of miRNAs to mouse model of spontaneous colorectal cancer, using CDX2P-NLS Cre;Apc+/loxP (CPC-Apc) mice. CPC-Apc mice were treated twenty-four times with formulated miRNAs (miR-200c, miR-302 (-a,-b,-c,-d), and miR-369 (-3p, -5p)) or negative control miRNA, three times a week from 8 weeks of age. MiRNAs were injected via tail vein using super carbonate apatite (sCA) as a drug delivery system. Briefly, 350 μL of 1 M CaCl2 was mixed with 25 μg of each miRNA or with a commensurate amount of NC miRNA in 87.5 mL of serum-free bicarbonate (44 mM)-buffered inorganic solution per mouse, and subsequently the mixture was incubated at 37°C for 30 min. The solution was centrifuged at 12,000 rpm for 3 min, and the pellet was dissolved with saline containing 0.5% albumin. The products were sonicated (38 kHz, 80 W) in a water bath for 10 min to generate sCA+0.5% albumin, which were intravenously injected within 10 min. At the time of sacrifice, colorectal tissue was collected and divided into normal tissues and tumor tissues for both groups of mice.

value: colorectal tumor

tag: genotype/variation

value: CPC-Apc mice


title: M4.WT.P4

city: Boulder

first: Eduard

last: Casas

state: Colorado

address: Porter Biosciences, CU Campus

department: MCDB

institute: CU Boulder

data_processing:
Alignment with hisat2
Read summarization with featureCounts
Read normalization and differential expression using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts of reads per gene
Supplementary_files_format_and_content: Differential expression using DESeq2

source_name: Hind Limb Articular Cartilage

growth_protocol: H3K9M and H3WT chondrocyte cells were cultured (at 37°C and 5% CO2) on tissue culture plastic in DMEM-F12 (Gibco) containing 10% fetal bovine serum (Gibco), 1% penicillin-streptomycin (Gibco), 0.1% bovine serum albumin (Sigma), 50ug/mL ascorbate-2-phosphate (Sigma) for 16 population doublings and collected for analysis.

extract_protocol:
After 16 population doublings in culture, chondrocyte cells were lyzed with Quiazol. RNA was isolated using Zymo Research Direct-zol RNA Miniprep Kit (Cat No. R2050).
Libraries were prepared using Tecan Universal Plus mRNA –SEQ with NuQuant Library Kit (Cat No. 0520)

treatment_protocol: The transgene expression was induced by replacing the media every other day with 2µg/ml doxycycline (Sigma)

value: Embryonic chondrocyte cells

value: induced with 2µg/ml doxycycline for 16 population doublings

tag: strain

value: C57BL/6 x 129S4/SvJae

tag: age

value: Embryonic (day 18.5)

value: Control WT (H3WT)


title: ASH1_nonDBD_4

tag: genetic information

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ASH1 Δ499 536 MNase

tag: tagged tf

tag: variant-type

value: nonDBD


title: tumor tissues of CPC-Apc mice, replicate 2

description: NC-P

tag: tissue


title: tumor tissues of CPC-Apc mice, replicate 7

description: NC-P


title: PBS mock-infected human microglial cells, 48 h, replicate 3, RNAseq [N48_3]

description: 2×150bp paired-endsequencing (PE150)

tag: cell type

value: PBS

tag: time


title: tumor tissues of CPC-Apc mice, replicate 6

description: NC-P


title: tumor tissues of CPC-Apc mice, replicate 3

description: NC-P


title: ASH1_nonDBD_3


title: tumor tissues of CPC-Apc mice, replicate 4

description: NC-P


title: M2.WT.P4

tag: treatment

tag: genotype


title: PBS mock-infected human microglial cells, 48 h, replicate 2, RNAseq [N48_2]

description: 2×150bp paired-endsequencing (PE150)


title: CD-H3K27ac-2

description:
CD-H3K27ac-2
K27ac_CD_peaks.broadPeak
K27ac_CD.bw

value: Mouse embryonic fibroblasts


title: ASH1_nonDBD_2


title: M1.WT.P4


title: PBS mock-infected human microglial cells, 48 h, replicate 1, RNAseq [N48_1]

description: 2×150bp paired-endsequencing (PE150)


title: normal tissues of CPC-Apc mice, replicate 2

description: NC

value: colorectal normal


title: ASH1_nonDBD_1


title: U1610; blood; CD19+ B cells; 24 weeks

city: Erlangen

first: Simon

last: Schaefer

state: Bavaria

address: Glueckstr. 6

department: Genetics

institute: FAU Erlangen

data_processing:
Immcantation 4.3.0
pResto; Quality control, Read assembly
Change-O, V(D)J reference alignment
Supplementary files format and content:
fasta formated files after merging and UMI filtering
igblast output text files including filtered and annotated immune repertoires (i.e. quantified annotated data about antibody receptor sequences mapped to germline genes)

source_name: blood

extract_protocol:
RNA was isolated using the Rneasy Micro Plus kit from Qiagen; RNA was collected in 14 µl Rnase-free water and 11 µl were used for cDNA generation
Library was prepared according to "Werner, A., et al., Determining immunoglobulin-specific B cell receptor repertoire of murine splenocytes by next-generation sequencing. STAR Protocols, 2022. 3(2): p. 101277"

value: blood

value: CD19+ B cells

value: TCL1 x Siglecg-R26ki/ki

value: 24 weeks


title: U1518; blood; CD19+ B cells; 24 weeks

value: TCL1 x Siglecg-R26ki/ki mb1cre


title: U1515; blood; CD19+ B cells; 24 weeks


title: PBS mock-infected human microglial cells, 16 h, replicate 3, RNAseq [N16_3]

description: 2×150bp paired-endsequencing (PE150)

value: Human microglial cells


title: M3.K9.P4

value: H3K9 methylation suppressed (H3K9M)


title: ASH1_d2_50_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)

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ASH1 Δ2 50 SV40 NLS MNase

value: Truncation


title: PBS mock-infected human microglial cells, 16 h, replicate 2, RNAseq [N16_2]

description: 2×150bp paired-endsequencing (PE150)


title: U2517; blood; CD19+ B cells; 48 weeks

value: 48 weeks


title: tumor tissue of mice injected microRNAs, replicate 2

description: MR-P

value: colorectal tumor

value: injected microRNAs


title: normal tissues of CPC-Apc mice, replicate 1

description: NC

value: CPC-Apc mice


title: ASH1_d2_50_1


title: tumor tissues of CPC-Apc mice, replicate 1

description: NC-P


title: tumor tissue of mice injected microRNAs, replicate 1

description: MR-P


title: PBS mock-infected human microglial cells, 16 h, replicate 1, RNAseq [N16_1]

description: 2×150bp paired-endsequencing (PE150)


title: RRBS_iPSC_2

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 (GRCm39) using Bismark (v0.23.0) bowtie2 aligner with options: -N 1 -l 20 --non_directional.
Mapping was done independently for the two ends of each pair. Read pairs that were mapped uniquely to two different fragments or showing more than one unconverted non-CpG cytosine, which occurred at very low frequency were filtered out.
Methylation levels of CpGs in the promoters were performed with R package methylKit from the bioconductor project, CpGs covered by at least 5 distinct reads were retained to calculate the average methylation levels.
Genome_build: GRCm39
Supplementary_files_format_and_content: CpG methylation values txt files

source_name: MEF

growth_protocol: riPSCs 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).                                                                                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.

extract_protocol:
Genome DNA was extracted using Quick-DNA Miniprep (ZYMO) according to the manufacture’s instruction.
RRBS was carried out similar as described (Legault et al., 2019). 500 ng DNA was digested by 20 U MspI (NEB) overnight. Then, DNA fragments were added with Gap filling and A-tailing mix (5 U Klenow enzyme, 1 μl dNTP mixture (10 mM dATP, 1 mM dCTP, 1 mM dGTP)) followed by incubating for 20 min at 30 °C and 20 min at 37 °C. 64 μl VAHTS DNA Clean Beads were used to purify DNA fragments. Subsequently, adapter ligation mix (14 μl purified DNA fragments, 25 μl Quick ligase buffer (2×), 10 μl Methylated adapters (15 μM) and 1 μl Quick ligase) was prepared and incubated for 10 min at 25 °C. Then, with 3 μl of USER enzyme added to each sample, samples were incubated for 15 min at 37 °C. After that, 55 μl VAHTS DNA Clean Beads were used for purification. Bisulfite conversion were then conducted using EZ DNA Methylation-Gol Kit according to the manufacture’s instruction. The converted DNA was PCR amplified using NEBNext Multiplex Oligos (NEB) for 15 cycle numbers. Libraries were purified using 50 μl VAHTS DNA Clean Beads. The RRBS libraries were sequenced on the Illumina NovaSeq 6000 with read length of 150 bp.

treatment_protocol: Cells were cultured in indicated medium

value: 129XOG2 E13.5 embryo

value: iPSC


title: M5.K9.P4

value: Embryonic chondrocyte cells

value: induced with 2µg/ml doxycycline for 16 population doublings

value: C57BL/6 x 129S4/SvJae

value: Embryonic (day 18.5)


title: EG20

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1E

department: School of Medicine, Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
Blood from diagnosis, B-cell acute lymphoblastic leukemia, ETV6-RUNX1
L10

library_source: transcriptomic single cell

data_processing:
scRNA- and scADT-seq data was aligned with Cell Ranger 6.0 version to human reference (hg19) from 10x Genomics with default parameters.
Donor (and singlet/doublet) assignment by hashtag signals.
The VDJ-data for BCR and TCR were separately processed using Cell Ranger version 6.0 by alignment to VDJ-reference (hg20) with default parameters.
Assembly: hg19 (transcriptome), hg20 (VDJ sequencing)
Supplementary files format and content: CITE-seq: barcode annotation: 10x Cell Ranger filtered barcode list; feature annotation: 10x Cell Ranger feature list; count matrix: 10x Cell Ranger raw UMI count matrix, VDJ-seq: all_contig_annotations.csv

extract_protocol:
Bone marrow or blood cells were thawn from the viably cryopreserved samples. Cells were thawn in a 37C water bath, immediately after adding 0.5 ml RPMI 1640 media (Thermo Fisher Scientific) + 10% FBS (Gibco)+ 20 ul DNAse (Roche 100U/ul) on top, then moving cells to 15 ml Falcon and filling the volume drop-wise, gently swirling. If < 1 million cells were processed (mini protocol), 10 ul of DNAse was added, filling volume to 5 ml. Cells were washed two times, then centrifuged and re-suspended in 50 ul Cell Staining Buffer (BioLegend) for counting. 100 000-200 000 cells per sample were processed by blocking with 5ul of Human TruStain FcX Blocking Solution (BioLegend) for 10 min at 4C. Antibody pool (0.25 ug per million cells per specific antibody, except 0.125 ug for CD45 and CD8; 0.1 ug per hashtag antibodies) was added  and incubated for 30 min at 4C. Samples were washed three times with cell staining buffer, counted and assessed for viability using trypan blue staining with EVE analysis, and then sample pools were prepared, centrifuged and loaded to Chromium lanes. If post-stain viability was >70% for all samples, equal ratios were loaded aiming at 10 000 cells. Otherwise, loading ratio was adjusted such that half target cell count was used for samples with viability 50-70% and one fifth of viability was 20-50%.
The 5' gene expression, ADT- and VDJ (BCR and TCR) libraries were prepared following manufacturer instructions (10x Genomics). cDNA qualities were assessed using Bioanalyzer. For some samples, wetting failure occured and in this case run was repeated. Libraries were index barcoded and sequenced using Novaseq S1, S2 or S4 runs.
10x Chromium 5' kit for CITE-seq and VDJ-seq

tag: donor

tag: hashtag

tag: batch

value: blood

tag: disease

value: childhood B acute lymphoblastic leukemia

tag: disease state

value: diagnosis

tag: staining protocol

value: mini

tag: blast cell_percentage

tag: viability after_stain_(%)


title: RRBS_iPSC_1

tag: strain


title: EG19

description:
Blood from day 2 during induction therapy (NOPHO2008 protocol), B-cell acute lymphoblastic leukemia
L10

value: day 2

value: basic


title: normal tissue of mice injected microRNAs, replicate 1

description: MR

value: colorectal normal

tag: genotype/variation


title: normal tissue of mice injected microRNAs, replicate 2

description: MR


title: ASH1_d2_400_4

tag: genetic information

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ASH1 Δ2 400 SV40 NLS MNase

tag: tagged tf

value: DBD


title: RRBS_D12_2

value: Reprogramming intermediate


title: ASH1_d2_400_3

tag: variant-type


title: ASH1_d2_400_2


title: RRBS_D12_1

tag: cell type


title: M1.K9.P4

tag: age

value: H3K9 methylation suppressed (H3K9M)


title: U2313; blood; CD19+ B cells; 48 weeks

tag: tissue

value: CD19+ B cells

value: TCL1 x Siglecg-R26ki/ki

tag: time

value: 48 weeks


title: EG17

description:
Blood from diagnosis, B-cell acute lymphoblastic leukemia
L9

tag: donor


title: ASH1_d2_400_5


title: U1863; blood; CD19+ B cells; 48 weeks

tag: genotype


title: EG18

description:
Blood from day 2 during induction therapy (NOPHO2008 protocol), B-cell acute lymphoblastic leukemia, ETV6-RUNX1
L9

tag: hashtag

tag: batch


title: ASH1_d2_400_1


title: EG16

description:
Bone marrow from day 15 during induction therapy (NOPHO2008 protocol), B-cell acute lymphoblastic leukemia, ETV6-RUNX1
L8

source_name: bone marrow

value: bone marrow

tag: disease

tag: disease state

value: day 15


title: ASH1_d2_300_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ASH1 Δ2 300 SV40 NLS MNase

value: Truncation


title: RRBS_D10_1

value: 129XOG2 E13.5 embryo


title: U1861; blood; CD19+ B cells; 48 weeks

value: blood

value: TCL1 x Siglecg-R26ki/ki mb1cre


title: EG15

description:
Bone marrow from diagnosis, B-cell acute lymphoblastic leukemia
L8

value: childhood B acute lymphoblastic leukemia

value: diagnosis

tag: staining protocol

tag: blast cell_percentage


title: U1719; blood; CD19+ B cells; 48 weeks


title: RRBS_D10_2

tag: strain


title: U2421; blood; CD19+ B cells; 48 weeks


title: ASH1_d2_300_1


title: RRBS_D8_2


title: EG14

description:
Bone marrow from day 15 during induction therapy (NOPHO2008 protocol), B-cell acute lymphoblastic leukemia
L7

value: mini

tag: viability after_stain_(%)


title: ASH1_d2_200_4

tag: genetic information

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ASH1 Δ2 200 SV40 NLS MNase


title: U1666; blood; CD19+ B cells; 48 weeks


title: U2423; blood; CD19+ B cells; 48 weeks


title: Lung KP control (PBS 48 hr) sample #D2, visium

tag: treatment

value: PBS

value: lung

value: 21-25 weeks


title: U2422; blood; CD19+ B cells; 48 weeks

value: CD19+ B cells

value: Siglecg-R26ki/ki mb1cre


title: EG13

description:
Bone marrow from diagnosis, B-cell acute lymphoblastic leukemia, ETV6-RUNX1
L7

value: basic


title: ASH1_d2_200_2

tag: tagged tf

tag: variant-type


title: RRBS_D8_1

tag: cell type

value: Reprogramming intermediate


title: U1664; blood; CD19+ B cells; 48 weeks

tag: tissue

value: 48 weeks


title: RRBS_D6_2


title: U1663; blood; CD19+ B cells; 48 weeks

tag: time


title: EG12

description:
Bone marrow from day 15 during induction therapy (NOPHO2008 protocol), B-cell acute lymphoblastic leukemia
L6

tag: donor

value: bone marrow

value: day 15


title: EG11

description:
Bone marrow from diagnosis, B-cell acute lymphoblastic leukemia, ETV6-RUNX1
L6


title: ASH1_d2_200_1

value: Truncation


title: ASH1_d2_150_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ASH1 Δ2 150 SV40 NLS MNase


title: EG10

description:
Bone marrow from day 15 during induction therapy (NOPHO2008 protocol), B-cell acute lymphoblastic leukemia, ETV6-RUNX1
L5


title: RRBS_D6_1

value: 129XOG2 E13.5 embryo


title: U1662; blood; CD19+ B cells; 48 weeks

value: blood

tag: genotype

value: TCL1 x Siglecg-R26ki/ki


title: RRBS_D4_1


title: U1610; blood; CD19+ B cells; 48 weeks


title: RRBS_D4_2


title: EG9

description:
Bone marrow from diagnosis, B-cell acute lymphoblastic leukemia
L5

tag: hashtag

value: childhood B acute lymphoblastic leukemia

value: diagnosis


title: ASH1_d2_150_1


title: U1607; blood; CD19+ B cells; 48 weeks

value: TCL1 x Siglecg-R26ki/ki mb1cre


title: RRBS_D2_2


title: ASH1_d2_100_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ASH1 Δ2 100 SV40 NLS MNase


title: U1518; blood; CD19+ B cells; 48 weeks


title: U1556; blood; CD19+ B cells; 48 weeks


title: ASH1_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ASH1 MNase

value: TF


title: ASH1_d2_100_1