title: S7.Msi.IP.TSTRLT

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

data_processing:
Fastq quality check:FastQC,v0.11.8
Fastq trimming: Trimmomatic, v0.39
Alignment: STAR, version 2.7.1a
Assembly: Mus musculus GRCm39.104
Supplementary files format and content: counts

extract_protocol:
Pituitaries from sighted FVB males and females (FVB.129P2‐Pde6b+Tyrc‐ch/Ant, The Jackson Laboratory) were collected and placed into DBPS with RNase inhibitor to be stored at -20 degrees C.
Libraries for RNAseq were prepared using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina Inc) according to the supplier’s protocol.

treatment_protocol: Musashi1 was immunoprecipitated from lysate from six adult 8-10 week old control mouse pituitaries equally split between Musashi1 antibody (Abcam, ab52865) plus Musashi2 antibody (Abcam, ab114107) or control rabbit IgG (Millipore Sigma PP64) as per the kit supplier’s protocol (Invitrogen Dynabeads Protein A IP kit, Fisher Scientific, catalog # 10006).  Musashi IP was done with both antibodies pooled together. Protein was degraded, and RNA was isolated, precipitated and utilized for RNAseq.  The immunoprecipitation experiments were performed on six separate occasions (three for male pituitaries, three for female pituitaries).

value: pituitary

tag: rip antibody

value: 8-10 weeks

tag: Sex

value: Male


title: S7.IgG.TSTRLT

status: Public on Jul 31 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Pituitaries from sighted FVB males and females (FVB.129P2‐Pde6b+Tyrc‐ch/Ant,

tag: tissue

value: IgG

tag: age


title: MCF10A_shANCO1_#3_2D_2

city: Washington

first: Meng

last: Yuan

state: DC

address: 3970 Reservoir Road NW

department: Lombardi Comprehensive Cancer Center

institute: Georgetown University

data_processing:
Quality check: fastqc
Alignment to GRCh38: hisat2
Sorting: samtools
Expression count calculation: featureCounts
Expression data statistical analysis: edgeR
Plotting: Heatplus, dplyr, ggplot2, ggrepel
Signaling enrichment analysis: GSEA, IPA
Visualization: UCSC genome browser
Assembly: GRCh38
Supplementary files format and content: Processed files are raw read counts for each condition (2D/3D, shGFP and shANCO1). ShGFP is shCTRL. Sh14 is shANCO1_#1. Sh209 is shANCO1_#2. Sh474 is shANCO1_#3. Sh34 is shANCO1_#4. Bigwig files for display in genome browser.

organism: Homo sapiens

growth_protocol: MCF10A and MCFDCIS cells were maintained in DMEM/F12 (1:1) medium (Gibco, 11039-021) with 5% horse serum, 20 µg/ml epidermal growth factor (EGF), 100 µg/ml hydrocortisone, 10 µg/ml insulin, and 100 ng/ml cholera toxin.

extract_protocol: RNA was extracted from 2D-cultured cells or 3D-cultured spheres with DNase digestion using the RNeasy Mini Kit (Qiagen, 74106) following manufacturer’s instructions.

treatment_protocol: ANCO1 knockdown lines were generated by lentiviral infection.

tag: cell line

tag: cell type

value: Mammary epthelial cells

tag: genotype

value: ANCO1 knockdown


title: MCFDCIS_shANCO1_#2_2D_2

source_name: MCFDCIS

value: MCFDCIS

value: Ductal carcinoma in situ cells derived from mammary epthelial cells


title: MCF10A_shANCO1_#3_2D_1


title: S6.Msi.IP.TSTRLT

value: Female


title: S6.IgG.TSTRLT


title: S5.Msi.IP.TSTRLT


title: MCF10A_shANCO1_#2_2D_2


title: MCF10A_shANCO1_#2_2D_3


title: MCF10A_shANCO1_#2_2D_1


title: MCF10A_shANCO1_#1_2D_3


title: MCF10A_shANCO1_#1_2D_2


title: MCF10A_shANCO1_#1_2D_1


title: S3.IgG.TSTRLT


title: DKO GC #3

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
S257_20190409115059_11
DKO_GC_3_unique
Transcriptome profile of knockout, GC biological rep3

data_processing: Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq. Sequence reads were trimmed BBDuk (sourceforge.net/projects/bbmap/) to remove adapter sequences and low-quality end bases (Q < 20). Alignment was performed with STAR 2.6.0a(1) on the Hg38 reference provided by UCSC Genome Browser (2). Alignment to mm10, and rn6 reference genome assembly (1), and counting by gene (3) using Ensembl assembly (release 93). Gene expression levels were determined with HTseq-count 0.9.1(3). Differential expression analyses were performed using edgeR (4) a statistical package based on generalized linear models, suitable for multifactorial experiments. The threshold for statistical significance chosen was False Discovery Rate (FDR)<0,05.

organism: Rattus norvegicus

source_name: INS-1E_TFEB/TFE3 DKO_GC

growth_protocol: Cells were grown in 10cm dishes using RPMI 1640; 10%FBS; 10mM Hepes; 1mM PyrNa; 2mM Glutamine; 0,05 mM beta-mercaptoethanol, PenStrep.

extract_protocol:
Total RNA was quantified using the Qubit 2.0 fluorimetric Assay (Thermo Fisher Scientific). For RNA-seq analysis, library preparation was performed with a total of 100ng of RNA from each sample using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen) according to manufacturer's instructions. Amplified fragmented cDNA of 300bp in size was sequenced in single-end mode by NovaSeq 6000 (Illumina) with a read length of 100bp
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the Novaseq6000 (Illumina) with a read length of 100 bp

treatment_protocol: Cells were plated on 12-well plates and treated with full medium (GC) or Minimum Essential Medium (Fast) for 16h (overnight)

value: rat insulinoma derived cell line

tag: genotype/variation

value: TFEB/TFE3 DKO

tag: treatment

value: growing conditions (GC)


title: Control Fast #4

description:
S257_20190409115059_8
WT_Fast_4_unique
Transcriptome profile of wild type , Fast biological rep4

value: control

value: Fasting conditions (Fast)


title: Control Fast #3

description:
S257_20190409115059_7
WT_Fast_3_unique
Transcriptome profile of wild type , Fast biological rep3


title: S2.IgG.TSTRLT


title: DKO Fast #3

description:
S257_20190409115059_15
DKO_Fast_3_unique
Transcriptome profile of knockout, Fast biological rep3

source_name: INS-1E_TFEB/TFE3 DKO_Fast


title: DKO Fast #2

description:
S257_20190409115059_14
DKO_Fast_2_unique
Transcriptome profile of knockout, Fast biological rep2


title: DKO Fast #4

description:
S257_20190409115059_16
DKO_Fast_4_unique
Transcriptome profile of knockout, Fast biological rep4


title: DKO GC #1

description:
S257_20190409115059_9
DKO_GC_1_unique
Transcriptome profile of knockout, GC biological rep1


title: DKO GC #4

description:
S257_20190409115059_12
DKO_GC_4_unique
Transcriptome profile of knockout, GC biological rep4


title: S3.Msi.IP.TSTRLT


title: S2.Msi.IP.TSTRLT


title: S5.IgG.TSTRLT


title: DKO Fast #1

description:
S257_20190409115059_13
DKO_Fast_1_unique
Transcriptome profile of knockout, Fast biological rep1


title: MCF10A_shCTRL_2D_3

value: shGFP control


title: Control Fast #1

description:
S257_20190409115059_5
WT_Fast_1_unique
Transcriptome profile of wild type , Fast biological rep1


title: D6-g1-3

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

department: School of Medicine

country: Turkey

institute: Koç University

data_processing:
RNA-seq: Transcriptome alignment with STAR
RNA-seq: Quantification using Salmon
RNA-seq: tximport for gene-level quantification
RNA-seq: DESeq2 for normalisation
Assembly: GENCODE GRCh38
Supplementary files format and content: Raw gene-level abundance,counts and lengths matrix in .csv format

source_name: Fibroblast differentiated from H1 ESC

extract_protocol:
RNA from cells was harvested using Trizol reagent.
TruSeq Stranded mRNA

value: Fibroblast differentiated from H1 ESC

value: USP22 gRNA and Cas9 expressing cells were transduced by OSKM factors.


title: D6-g1-2

value: USP22 targeting gRNA and Cas9 expressing cells were transduced by OSKM factors.


title: E3.5_KLF4

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

country: China

institute: Peking University

library_source: genomic

data_processing:
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad"
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bigwig files.

molecule: genomic DNA

source_name: E3.5 embryo

growth_protocol: Mouse embryos were extracted from pregnant female mice.

extract_protocol:
To minimize potential cell loss, the digested single cells from E3.5 embryos or E12.5 heart were firstly conjugated to activated Concanavalin A coated magnetic beads at RT for 15 min, followed by fixation via 0.5% formaldehyde on ice for 5 min. Then, the formaldehyde was quenched by adding 2.5 M glycine and incubating on ice for 5 min. The slightly fixed cells could be cryopreserved in 90% methanol at -80°C for up to half a year, or be incubated with the primary antibody at 4°C for at least 4 h to perform in situ ChIP directly. After binding with the primary antibody, the samples were briefly washed and incubated with the secondary antibody. The cell-bead mixture was then incubated with 9 μg/ml purified PAT-MEA/B and wash twice in Dig-wash buffer, which containing 300 mM NaCl to reduce noises. Tagmentation and lysis were performed as before, and the tagmented gDNA was amplified using Nextera i5 and i7 index primer.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: The embryos without zona pellucida were dissociated with DPBS without Ca2+ and Mg2+ for 10 min at 37℃ to dissociate blastomeres. Later, the cells were fixed via 0.5% formaldehyde on ice for 5 min. Then, the formaldehyde was quenched by adding 2.5 M glycine and incubating on ice for 5 min. The slightly fixed cells could be cryopreserved in 90% methanol at -80°C for up to half a year.

value: embryo

tag: developmental stage


title: E3.5_KLF2


title: E12.5_KLF2

source_name: E12.5 heart

value: heart


title: Control GC #3

description:
S257_20190409115059_3
WT_GC_3_unique
Transcriptome profile of wild type , GC biological rep3


title: DKO GC #2

description:
S257_20190409115059_10
DKO_GC_2_unique
Transcriptome profile of knockout, GC biological rep2


title: MCF10A_shCTRL_2D_2


title: Control Fast #2

description:
S257_20190409115059_6
WT_Fast_2_unique
Transcriptome profile of wild type , Fast biological rep2


title: MCF10A_shCTRL_2D_1


title: D6-NT-3

value: Non-targeting gRNA and Cas9 expressing cells were transduced by OSKM factors (Control samples).


title: 50 μM BPS 48h_rep 1

city: MONTRÉAL

first: Barbara

last: Hales

state: QC

address: 3655 Promenade Sir-William-Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

data_processing:
Base calling was performed using Illumina CASAVA (v1.8)
Sequences were filtered for reads containing adapter or of low quality, then mapped to mm10 using STAR (v2.5, mismatch=2)
Quantification was performed using HTSeq (v0.6.1, -m union)
Differential analysis was performed using DESeq2 (v2_1.6.3, q-value < 0.05)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table containing raw count, FPKM value, and normalized abundance output (from DESeq2) of each gene for each sample and each treatment group

source_name: Embryonic forelimb

growth_protocol: Forelimbs of each gestational day 13 embryo were excised, pooled, and placed in glass bottles containing 6 mL of a culture medium consisting of 75% BGJb medium (Gibco, ThermoFisher Scientific), 25% salt solution, supplemented with ascorbic acid (0.16 mg/mL) and gentamycin (50 mg/mL, Wisent Bioproducts, QC, Canada). Limbs from male and female embryos were cultured together.

extract_protocol:
Total RNA was extracted using the Rneasy Mini kit (Qiagen). The concentration and purity of extracted RNA was assessed using NanoDrop 2000 spectrophotometer (Thermofisher).
mRNA was purified from 1ug of total RNA using poly-T oligo-attached magnetic beads and fragmented randomly in a fragmentation buffer. First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-); second-strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3' ends of DNA fragments, NEBNext Adaptor was ligated to prepare for hybridization. The library fragments were purified with AMPure XP system. The final library was obtained by PCR amplification and purification of PCR products using AMPure XP beads.

treatment_protocol: Culture bottles were gassed for two minutes with 5% CO2, 50% O2 balanced with N2. Each bottle subsequently received one of two treatments: dimethyl sulfoxide (DMSO, vehicle control) or bisphenol S (BPS 10 or 50 μM).  Limbs were then cultured at 37° for 3, 24, or 48 hours.

tag: strain

tag: gestation day

value: GD 13

value: limb bud

value: 50 uM BPS

tag: treatment length

value: 48 hours


title: 50 μM BPS 48h_rep 5


title: flor-1_Ext_C

city: London

first: Michalis

last: Barkoulas

address: SAF Building, South Kensington

country: United Kingdom

institute: Imperial College London

data_processing:
Reads were aligned to C. elegans genome WS283
Reads were counted using Kallisto
Transcript abundance was quantified using the Sleuth and Wald test
Assembly: WormBase Release WS283
Supplementary files format and content: H5 files having raw TPM counts for all genes

organism: Caenorhabditis elegans

source_name: flor-1(icb93) L4 + Extract

growth_protocol: All strains were prepared by bleaching gravid adults to isolate embyros which were grown until L4 stage

extract_protocol:
TRIzol (Life Technologies)
By BGI (Hongkong) and Novogene (Cambridge)

treatment_protocol: Nematode Growth Media agar plates supplemented with E. coli OP50 at 20°C

value: Whole animal


title: PBMC_day28_s456

city: Los Angeles

first: Matteo

last: Pellegrini

state: California

address: 610 Charles E. Young Drive South TLSB room 5146, Pellegrini Lab

department: Molecular, Cell, and Developmental Biology

institute: University of California, Los Angeles

data_processing:
Adapter sequences were removed using cutadapt (v2.10) for the demultiplexed FastQ files
BSBolt (v1.3.0) was used to align the reads to the reference GRCh38 genome
Samtools was used to remove PCR duplicates using the markdup function
methylation calling was performed using the BSBolt CallMethylaiton function
grch38 genome
Assembly: csv, day 0 (pre-vaccination) methylation calling matrix
Supplementary files format and content: csv, day 28 (post-vaccination) methylation calling matrix

source_name: blood

extract_protocol:
the standard phenol-chloroform extraction method for blood samples
For the TBS-seq library preparation, adapter ligation and dA-tailing were performed using the NEBNext Ultra II Library prep kit and custom pre-methylated adapters (IDT). Purified libraries were then hybridized to the biotinylated probes. Under the following conditions: 2 min at 98°C; 14 cycles of (98°C for 20 sec; 60°C for 30 sec; 72°C for 30 sec); 72°C for 5 minutes; hold at 4°C, PCR amplification was performed after bisulfite treatment on captured DNA using KAPA HiFi Uracil+. Library quality control was conducted on the high-sensitivity D1000 assay on a 2200 Agilent TapeStation.

value: blood

value: PBMC

value: post-vaccination

tag: dob

tag: gender

value: M

value: White/Caucasian

tag: bmi

tag: vaccine

value: Standard Dose

value: Y


title: flor-1_Ext_A


title: Control GC #4

description:
S257_20190409115059_4
WT_GC_4_unique
Transcriptome profile of wild type , GC biological rep4

value: rat insulinoma derived cell line

value: control

value: growing conditions (GC)


title: 50 μM BPS 48h_rep 3


title: Control GC #2

description:
S257_20190409115059_2
WT_GC_2_unique
Transcriptome profile of wild type , GC biological rep2


title: Control GC #1

description:
S257_20190409115059_1
WT_GC_1_unique
Transcriptome profile of wild type , GC biological rep1


title: flor-1_Ext_B


title: 50 μM BPS 48h_rep 2


title: 50 μM BPS 48h_rep 4


title: PBMC_day28_s395

value: F


title: PMBC_day0_s395

value: pre-vaccination


title: PMBC_day0_s456


title: DMSO control 48h_rep 1

value: GD 13

value: DMSO


title: PBMC_day28_s282

value: Hispanic


title: flor-1_B

source_name: flor-1(icb93) L4


title: DMSO control 48h_rep 5

value: limb bud

value: 48 hours


title: flor-1_A

value: Whole animal


title: DMSO control 48h_rep 4


title: PMBC_day0_s282

value: blood

value: PBMC


title: D6-NT-2

value: Fibroblast differentiated from H1 ESC

value: Non-targeting gRNA and Cas9 expressing cells were transduced by OSKM factors (Control samples).


title: DMSO control 48h_rep 2


title: DMSO control 48h_rep 3


title: PBMC_day28_s281

value: post-vaccination

value: White/Caucasian

value: Standard Dose


title: PMBC_day0_s281

value: Y


title: Tyrosol-3.

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of C. auris B8441
The DESeq algorithm (StrandNGS software) was used to obtain normalized gene transcription values.
Gene transcription differences between treated and control groups were compared by a moderated t test; the Benjamini-Hochberg false discovery rate was used for multiple-testing correction, and a corrected P value of <0.05 was considered significant.
Assembly: genome: https://fungi.ensembl.org/_candida_auris_gca_002759435/Info/Index; features: http://www.candidagenome.org/download/gff/C_auris_B8441/archive/C_auris_B8441_version_s01-m01-r11_features_with_chromosome_sequences.gff.gz
Supplementary files format and content: excell file includes  p corrected values, p values, fold change values and raw data for each Sample

organism: Candidozyma auris

source_name: fungal cells

growth_protocol: YPDA medium (1% yeast extract, 2% mycological peptone, 2% glucose, 2% agar, pH 5.6)., 140 rpm, 37 °C

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.

treatment_protocol: 15 mM tyrosol treated and untreated exponentially growing phase cultures

value: fungal cells

value: Isolate 12

value: Tyrosol treated


title: PBMC_day28_s267

value: M

value: Black/African American


title: 10 μM BPS 48h_rep 2

value: GD 13

value: 10 uM BPS


title: 10 μM BPS 48h_rep 1

value: limb bud

value: 48 hours


title: Tyrosol-2.


title: PBMC_day28_s264

value: blood

value: F


title: PMBC_day0_s267

value: PBMC

value: pre-vaccination


title: 10 μM BPS 48h_rep 4


title: PMBC_day0_s264


title: Control-2.

value: untreated


title: PBMC_day28_s263

value: post-vaccination

value: Asian


title: 10 μM BPS 48h_rep 3


title: 10 μM BPS 48h_rep 5


title: 50 μM BPS 24h_rep 2

value: 50 uM BPS

value: 24 hours


title: flor-1_C

value: Whole animal


title: Control-3.

value: fungal cells

value: Isolate 12


title: PDAC060 Gem-Pac treated [GC125137]

city: Wilrijk

first: Maxim

last: Le Compte

state: Antwerp

address: Campus Drie Eiken, Universiteitsplein 1, T457

country: Belgium

institute: University of Antwerp, Center for Oncological Research

data_processing:
CLC Genomics Workbench v 11.0.1
Trimmed secuence reads were mapped to GrCM38/mm10 using CLC benchwork.
Assembly: mm10
Supplementary files format and content: Tab-delimited tekst file includes raw counts for each sample

source_name: PDAC060 Gem-Pac treated

growth_protocol: Patient-derived tumor organoids were grown in ADF+++ supplemented with the traditional organoid growth factors (Wnt, Noggin, RSPONDIN, FGF10 B27 Nicotinamide, NAC..)

extract_protocol:
RNA was harvested using the Rneasy mini plus kit (Qiagen)
RNA libraries were prepared using the The QuantSeq 3' FWD Kit according to the manufacturer's protocol

treatment_protocol: For the treated organoids, RNA was collected after treatment with 400nM Gemcitabine and 80nM Paclitaxel

value: PDAC

value: PDAC060 Gem-Pac treated

value: Organoid

value: KRAS Mutant

value: Gem-Pac 400:80 nM


title: PMBC_day0_s263

value: blood

value: Standard Dose

value: Y


title: PBMC_day28_s262

value: PBMC

value: F

value: White/Caucasian


title: PDAC060 Gem-Pac treated [GC125136]


title: PDAC044 Gem-Pac treated [GC125135]

source_name: PDAC044 Gem-Pac treated

value: PDAC044 Gem-Pac treated


title: 50 μM BPS 24h_rep 5

value: GD 13

value: limb bud

value: 50 uM BPS


title: 50 μM BPS 24h_rep 4

value: 24 hours


title: PMBC_day0_s262

value: pre-vaccination


title: Tyrosol-1.

value: fungal cells

value: Isolate 12

value: Tyrosol treated


title: PBMC_day28_s260

value: post-vaccination


title: PDAC044 Gem-Pac treated [GC125134]

value: PDAC

value: Organoid

value: KRAS Mutant

value: Gem-Pac 400:80 nM


title: PDAC002 Gem-Pac treated [GC125133]

source_name: PDAC002 Gem-Pac treated

value: PDAC002 Gem-Pac treated


title: PMBC_day0_s260

value: blood

value: PBMC

value: F

value: Standard Dose

value: Y


title: PDAC002 Gem-Pac treated [GC125131]


title: 50 μM BPS 24h_rep 3

value: GD 13

value: limb bud

value: 50 uM BPS


title: PDAC002 Gem-Pac treated [GC125132]


title: PBMC_day28_s251

value: Black/African American


title: PBMC_day28_s252

value: M

value: Hispanic, Asian


title: 50 μM BPS 24h_rep 1

value: 24 hours


title: DMSO control 24h_rep 1

value: DMSO


title: DMSO control 24h_rep 4


title: PDAC087 baseline [GC125128]

source_name: PDAC087 baseline

value: PDAC

value: Organoid

value: untreated


title: PDAC087 baseline [GC125129]

value: KRAS Mutant


title: DMSO control 24h_rep 3


title: PMBC_day0_s251

value: blood

value: pre-vaccination


title: 10 μM BPS 24h_rep 2

value: 10 uM BPS


title: PDAC082 baseline [GC125127]

source_name: PDAC082 baseline


title: PMBC_day0_s249

value: PBMC

value: F

value: White/Caucasian

value: Standard Dose


title: 10 μM BPS 24h_rep 1

value: GD 13

value: limb bud


title: PDAC082 baseline [GC125126]


title: PDAC082 baseline [GC125125]


title: PBMC_day28_s244

value: post-vaccination

value: Black/African American

value: Y


title: PMBC_day0_s244


title: DMSO control 24h_rep 2

value: DMSO

value: 24 hours


title: PDAC087 baseline [GC125130]

value: PDAC

value: Organoid


title: 10 μM BPS 24h_rep 5


title: 10 μM BPS 24h_rep 4


title: PDAC070 baseline [GC125124]

source_name: PDAC070 baseline

value: KRAS Mutant

value: untreated


title: PBMC_day28_s238

value: blood


title: PMBC_day0_s252

value: pre-vaccination

value: M

value: Hispanic, Asian


title: PDAC070 baseline [GC125123]


title: PBMC_day28_s249

value: PBMC

value: F

value: White/Caucasian


title: PDAC070 baseline [GC125122]


title: PMBC_day0_s238

value: Standard Dose


title: PDAC068 baseline [GC125121]

source_name: PDAC068 baseline


title: DMSO control 24h_rep 5

value: GD 13

value: limb bud


title: 50 μM BPS 3h_rep 2

value: 50 uM BPS

value: 3 hours


title: PBMC_day28_s227

value: post-vaccination

value: Y


title: 50 μM BPS 3h_rep 1


title: 50 μM BPS 3h_rep 5


title: PDAC068 baseline [GC125120]

value: PDAC

value: Organoid


title: PDAC060 baseline [GC125119]

source_name: PDAC060 baseline

value: KRAS Mutant

value: untreated


title: PBMC_day28_s224

value: blood


title: 50 μM BPS 3h_rep 4


title: PMBC_day0_s224

value: pre-vaccination


title: PBMC_day28_s221


title: PDAC060 baseline [GC125118]


title: PDAC060 baseline [GC125117]


title: 50 μM BPS 3h_rep 3


title: DMSO control 3h_rep 2

value: DMSO


title: 10 μM BPS 24h_rep 3

value: 10 uM BPS

value: 24 hours


title: DMSO control 3h_rep 1


title: PMBC_day0_s221

value: PBMC

value: F

value: White/Caucasian


title: DMSO control 3h_rep 5

value: GD 13

value: limb bud


title: DMSO control 3h_rep 4

value: 3 hours


title: PDAC052 baseline [GC125115]

source_name: PDAC052 baseline


title: PMBC_day0_s220

value: Standard Dose


title: PDAC052 baseline [GC125114]


title: PDAC044 baseline [GC125113]

source_name: PDAC044 baseline


title: PMBC_day0_s227

value: Y


title: Control-1.

value: fungal cells

value: Isolate 12


title: PBMC_day28_s220

value: post-vaccination


title: DMSO control 3h_rep 3


title: PMBC_day0_s219

value: M


title: PDAC044 baseline [GC125112]

value: PDAC

value: Organoid

value: KRAS Mutant

value: untreated


title: 10 μM BPS 3h_rep 2

value: 10 uM BPS


title: PBMC_day28_s215

value: blood

value: PBMC


title: 10 μM BPS 3h_rep 1


title: PMBC_day0_s215

value: pre-vaccination

value: F

value: White/Caucasian


title: PDAC002 baseline [GC125110]

source_name: PDAC002 baseline


title: 10 μM BPS 3h_rep 5

value: GD 13

value: limb bud

value: 3 hours


title: 10 μM BPS 3h_rep 4


title: PDAC002 baseline [GC125109]


title: 10 μM BPS 3h_rep 3


title: PMBC_day0_s214

value: Standard Dose

value: Y


title: PDAC002 baseline [GC125108]


title: PBMC_day28_s219

value: post-vaccination


title: PBMC_day28_s213

value: M


title: MCFDCIS_shCTRL_input_3

data_processing:
Quality check: fastqc
alignment to GRCh38: bwa
Sorting and deduplication: Samtools
Peak calling: csaw
Gene annotation: ChIPpeakAnno
Motif enrichment analysis: Homer
Visualization: UCSC Genome Browser
Assembly: GRCh38
Supplementary files format and content: Bed files containing H3K27Ac peaks after normalization to respective input controls or directly comparing shANCO1 and shCTRL (shGFP) groups. Bigwig files for display in genome browser and calculation of detection q values.

source_name: MCFDCIS

extract_protocol:
DNA fragments were purified from de-crosslinked chromatin using the PCR Purification Kit (Qiagen, 28106) following manufacturer’s instructions.
Library preparation was done using the NEBNext Ultra II DNA Library Prep Kit and Multiplex Oligos for Illumina (Biolabs, E7645S, E7335S)

treatment_protocol: ANCO1 knockdown lines were generated by lentiviral infection. Cells were crosslinked in dishes with 1% Formaldehyde and chromatin was sonicated and incubated with H3K27Ac antibody. Input control samples were not immunoprecipitated. Reversal of crosslinnk was then performed.

value: MCFDCIS

value: Ductal carcinoma in situ cells derived from mammary epthelial cells

tag: chip antibody

value: shGFP control


title: MCFDCIS_shCTRL_input_2


title: PBMC_day28_s207


title: PMBC_day0_s213


title: 5 μM BPAF 48h rep 5

description:
AF05485
AF5_48vsAFC_48.txt

source_name: Embryonic forelimb

treatment_protocol: Culture bottles were gassed for two minutes with 5% CO2, 50% O2 balanced with N2. Each bottle subsequently received one of two treatments: dimethyl sulfoxide (DMSO, vehicle control) or bisphenol A (BPAF 1 or 5 μM).  Limbs were then cultured at 37° for 3, 24 or 48 hours.

value: 5 uM BPAF

value: 48 hours


title: MCFDCIS_shCTRL_input_1


title: 5 μM BPAF 48h rep 1

description:
AF05481
AF5_48vsAFC_48.txt


title: 5 μM BPAF 48h rep 4

description:
AF05484
AF5_48vsAFC_48.txt


title: PBMC_day28_s214

value: blood


title: PDAC044 baseline [GC125111]

value: PDAC

value: Organoid

value: KRAS Mutant

value: untreated


title: MCFDCIS_shANCO1_input_3

value: ANCO1 knockdown


title: male, FLExDUX4, 13-weeks-old, quadriceps rep3

first: Yi-Wen

last: Chen

state: District of Columbia

address: 111 Michigan Ave NW

department: Center for Genetic Medicine Research

institute: Children's National Hospital

data_processing:
Reads were processed using cutadapt v1.16, analyzed using FastQC v0.11.7, and aligned to the spike-in complemented Ensembl release 90 of the Mus musculus assembly GRCh38 from the Genome Reference Consortium using the splice-aware aligner STAR version 2.5.3a.
Alignments were quantified based on the annotations of Ensembl GRCm38.90 and the spike-in specific annotations of Lexogen with the featureCounts software program version 1.6.2 of the subread analysis package
Assembly: Ensembl release 90 of the Mus musculus assembly GRCh38 from the Genome Reference Consortium
Supplementary files format and content: tab-delimited text files including non-normalzied read counts for each sample, counts of all samples normalized for sequencing depth, and outputs from DEseq2

source_name: Quadriceps

extract_protocol:
Frozen quadriceps were homogenized in mL trizol reagent for RNA extraction. RNA was separated with chloroform, precipitated with isopropanol, and washed with 75% ethanol. Total RNA was suspended in RNase Free water.  Total RNA was submitted to Lexogen Gmbh (Vienna, Austria) for 3’ mRNA sequencing.
Sequencing-ready libraries were produced using a QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (015UG009V0252) using 50 ng RNA per sample.
Sequencing was performed on an Illumina NextSeq 500 sequencer with a v2 SR75 High Output kit at Lexogen GmbH.

value: Quadriceps


title: male, FLExDUX4, 13-weeks-old, quadriceps rep1


title: male, WT, 13-weeks-old, quadriceps rep3

value: WT


title: male, FLExDUX4, 13-weeks-old, quadriceps rep2


title: PMBC_day0_s207

source_name: blood

value: PBMC

value: pre-vaccination

value: White/Caucasian

value: Standard Dose


title: PBMC_day28_s203

value: post-vaccination

value: M

value: Asian

value: Y


title: 5 μM BPAF 48h rep 3

description:
AF05483
AF5_48vsAFC_48.txt

value: GD 13

value: limb bud

value: 5 uM BPAF

value: 48 hours


title: PMBC_day0_s203

value: blood


title: 5 μM BPAF 48h rep 2

description:
AF05482
AF5_48vsAFC_48.txt


title: MCFDCIS_shANCO1_input_1

value: MCFDCIS

value: Ductal carcinoma in situ cells derived from mammary epthelial cells


title: PBMC_day28_s196

value: Hispanic

value: High Dose


title: male, WT, 13-weeks-old, quadriceps rep2

value: Quadriceps

value: WT


title: control 48h rep 2

description:
AF00482
AFC_48vsAFC_3.txt

value: DMSO


title: male, WT, 13-weeks-old, quadriceps rep1


title: MCF10A_shANCO1_#1_3D_3

value: Mammary epthelial cells

value: ANCO1 knockdown


title: control 48h rep 1

description:
AF00481
AFC_48vsAFC_3.txt


title: MCFDCIS_shCTRL_H3K27Ac_3

value: H3K27Ac (Active Motif, 39135)

value: shGFP control


title: KO97-35039

city: Suita

first: Shugo

last: Sasaki

state: Osaka

address: 2-2 Yamadaoka, Suita-shi

department: Metabolic Medicine

country: Japan

institute: Osaka University

data_processing:
Linux Ubuntu operating system version 14.04 LTS was used for analyses. Fastq files from each sample were concatenated. ENSEMBL Mus musculus genome GRCm38p.4 fastq and gtf annotation file were used for alignments. STAR v2.4.0.1 230 was utilized to index the genome fastq files, align sample transcriptomes against the genome, and output as sorted by coordinate BAM files. Counts were generated from BAM files with HTSeq against annotated genes from GRCm38p.4. Finally, differential gene analysis was performed between control and experimental samples using DESeq2, with an FPKM criteria of ≥5 in two or more samples, applying a Wald test on p-valueP values from genes passing filtering, and adjusted for multiple testing via Benjamini and Hochberg procedure. Panther pathway analysis performed for differentially expressed genes.
Assembly: GRCm38p.4
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: Islet

extract_protocol:
An islet RNA was isolated with TRIzol, DNase treated (Turbo DNAse Free; Thermo Fisher Scientific). Samples were rRNA depleted utilizing the RiboGone Mammalian-Low Input Ribosomal RNA Removal Kit (Takara Bio USA Inc., Mountain View, CA, USA), and Agencourt AMPure XP SPRI beads (Beckman Coulter). rRNA depleted total RNA were was assessed for rRNA depletion, RNA integrity, size distribution, and concentration prior to library generation with the Agilent RNA Pico 6000 kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
rRNA depleted RNA passing quality control were was used in the SMARTer Stranded RNA-Seq Kit (Takara Bio USA). Following RNA incubation with stranded N6 primer, buffer, and water, samples were incubated at 94°C for 4 minutes, appropriate for samples with RIN values between 4-7. Following purification of first-strand cDNA, libraries were PCR amplified in accordance with their input RNA amount and purified. Final adapter-ligated cDNA was quantitated by Qubit 3.0 dsDNA high-sensitivity assay kit (Thermo Fisher Scientific) together with qPCR amplification using standard curves of a known concentration of adapter-ligated libraries. Sequencing was performed on the NextSeq 500 with the High Output Reagent Cartridge v2 150 cycles (75bp x 2) (Illumina, San Diego, CA, USA).

value: Islet

value: 18 week

value: Knockout


title: control 48h rep 5

description:
AF00485
AFC_48vsAFC_3.txt

value: GD 13

value: limb bud


title: MCFDCIS_shCTRL_H3K27Ac_2


title: MCFDCIS_shCTRL_H3K27Ac_1


title: KO94-35037


title: PBMC_day28_s194

value: blood

value: PBMC

value: post-vaccination

value: M

value: White/Caucasian

value: Standard Dose

value: Y


title: PMBC_day0_s194

value: pre-vaccination


title: KO96-35038


title: MCFDCIS_shANCO1_input_2

value: MCFDCIS

value: Ductal carcinoma in situ cells derived from mammary epthelial cells


title: KO82-35036


title: control 48h rep 3

description:
AF00483
AFC_48vsAFC_3.txt

value: DMSO

value: 48 hours


title: control 48h rep 4

description:
AF00484
AFC_48vsAFC_3.txt


title: PBMC_day28_s190


title: 1 μM BPAF 48h rep 2

description:
AF01481
AF1_48vsAFC_48.txt

value: 1 uM BPAF


title: KO81-35035

value: Islet

value: 18 week


title: 1 μM BPAF 48h rep 1

description:
AF01482
AF1_48vsAFC_48.txt

value: GD 13


title: MCFDCIS_shANCO1_H3K27Ac_1

value: H3K27Ac (Active Motif, 39135)

value: ANCO1 knockdown


title: CT95-35044

value: Floxed control


title: MCF10A_shCTRL_input_3

value: Mammary epthelial cells

value: shGFP control


title: PBMC_day28_s188

value: blood

value: PBMC

value: post-vaccination

value: F

value: White/Caucasian


title: PMBC_day0_s196

value: pre-vaccination

value: M

value: Hispanic

value: High Dose

value: Y


title: MCF10A_shCTRL_input_2


title: CT90-35043

value: Islet

value: 18 week


title: PMBC_day0_s188

value: Standard Dose


title: PBMC_day28_s185


title: MCFDCIS_shANCO1_H3K27Ac_2

value: MCFDCIS

value: Ductal carcinoma in situ cells derived from mammary epthelial cells

value: H3K27Ac (Active Motif, 39135)

value: ANCO1 knockdown


title: MCFDCIS_shANCO1_H3K27Ac_3


title: CT83-35041

value: Floxed control


title: MCF10A_shCTRL_input_1

value: Mammary epthelial cells

value: shGFP control


title: CT89-35042


title: CT80-35040


title: PBMC_day28_s184

value: blood

value: PBMC

value: post-vaccination


title: Sick mouse 6

city: Linköping

first: Sandra

last: Lilja

address: Sandbäcksgatan 7

department: BKV

country: Sweden

institute: Linköping University

data_processing:
Processed of scRNA-seq data into digital gene expression matrices following James Nemesh, McCarrol’s lab Drop-seq Core Computational Protocol (version 1.0.1) (http://mccarrolllab.com) using bcl2fastq conversion and Picard software. The indexed reference for alignment of the reads was generated from GRCm38 (June 2017, Ensembl) using STAR software. NCBI Gene Symbols were used for annotation.
Quality control, where cells with less than 10,000 reads, 400 transcripts, or 200 genes, or more than 20% mitochondrial genes were sorted out.
Genes expressed in less than three cells were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with transcript counts of each gene (rows) within each cell (columns).

molecule: polyA RNA

extract_protocol:
The bam files were extracted following all the steps of James Nemesh, McCarrol’s lab Drop-seq Core Computational Protocol (version 1.0.1) (http://mccarrolllab.com), using bcl2fastq conversion and Picard software. The fastq files from the same sample (multiple sequencing rounds) were merged after bcl2fastq extraction.
Libraries were prepared from GRCh38 (April 2017, Ensembl) using STAR software.

treatment_protocol: After pre-sensitization to mBSA, antigen induced arthritis (AIA) was triggered in 8 weeks old, female mice. The healthy control mice were injected with phosphate-buffered saline. One week after triggering, the mice were sacrificed. Successful AIA was ensured among the sick mice by immunohistochemistry, and whole joints were prepared for scRNA-seq using the Seq-Well method. To increase read coverage, each sample was sequenced multiple times.

value: 8 weeks old

tag: Sex

value: female

tag: disease

value: Sick

value: Joint


title: PMBC_day0_s184

tag: tissue

value: pre-vaccination

tag: age

value: M

value: White/Caucasian

value: High Dose

value: Y


title: 5 μM BPAF 24h rep 2

description:
AF05242
AF5_24vsAFC_24.txt

value: GD 13

value: limb bud

value: 5 uM BPAF

value: 24 hours


title: 1 μM BPAF 48h rep 3

description:
AF01483
AF1_48vsAFC_48.txt

value: 1 uM BPAF

value: 48 hours


title: 1 μM BPAF 48h rep 5

description:
AF01485
AF1_48vsAFC_48.txt


title: 5 μM BPAF 24h rep 1

description:
AF05241
AF5_24vsAFC_24.txt


title: PDAC052 baseline [GC125116]

value: PDAC

tag: cell line

tag: cell type

value: Organoid

value: KRAS Mutant

value: untreated


title: MCF10A_shANCO1_input_1

value: Mammary epthelial cells

tag: genotype

value: ANCO1 knockdown


title: 5 μM BPAF 24h rep 5

description:
AF05245
AF5_24vsAFC_24.txt

tag: treatment


title: 1 μM BPAF 48h rep 4

description:
AF01484
AF1_48vsAFC_48.txt


title: MCF10A_shCTRL_H3K27Ac_3

value: H3K27Ac (Active Motif, 39135)

value: shGFP control


title: MCF10A_shANCO1_input_3


title: 5 μM BPAF 24h rep 4

description:
AF05244
AF5_24vsAFC_24.txt


title: PMBC_day0_s190

value: blood

value: PBMC

value: pre-vaccination

value: M

value: White/Caucasian

value: Standard Dose


title: MCF10A_shANCO1_input_2


title: MCF10A_shCTRL_H3K27Ac_2


title: Sick mouse 5

value: 8 weeks old

value: female

value: Sick

value: Joint


title: PMBC_day0_s185

value: F

value: High Dose

value: Y


title: Sick mouse 4


title: PBMC_day28_s181

value: post-vaccination


title: 5 μM BPAF 24h rep 3

description:
AF05243
AF5_24vsAFC_24.txt

value: GD 13

value: limb bud

value: 5 uM BPAF

value: 24 hours


title: Sick mouse 3


title: Sick mouse 1


title: control 24h rep 2

description:
AF00242
AFC_48vsAFC_24.txt

value: DMSO


title: MCF10A_shANCO1_H3K27Ac_3

value: Mammary epthelial cells

value: H3K27Ac (Active Motif, 39135)

value: ANCO1 knockdown


title: MCF10A_shCTRL_H3K27Ac_1

value: shGFP control


title: PBMC_day28_s179

value: blood

value: PBMC

value: White/Caucasian

value: Standard Dose


title: PMBC_day0_s179

value: pre-vaccination

value: F


title: Healthy mouse 2

value: 8 weeks old

value: female

value: Healthy

value: Joint


title: PMBC_day0_s177

value: M

value: High Dose

value: Y


title: PBMC_day28_s177

value: post-vaccination


title: Healthy mouse 4


title: control 24h rep 1

description:
AF00241
AFC_48vsAFC_24.txt

value: GD 13

value: limb bud

value: DMSO

value: 24 hours


title: Healthy mouse 1


title: PBMC_day28_s170

value: blood

value: PBMC


title: MCF10A_shANCO1_H3K27Ac_1

value: Mammary epthelial cells

value: H3K27Ac (Active Motif, 39135)

value: ANCO1 knockdown


title: Healthy mouse 3

value: 8 weeks old


title: control 24h rep 3

description:
AF00243
AFC_48vsAFC_24.txt


title: PC9-GR

city: New Taipei

first: Shiao-Ya

last: Hong

address: 362, Zhongzheng Rd., Xindian Dist.

country: Taiwan

institute: Cardinal Tien Hospital

data_processing:
Low quality bases and sequencing adapters in raw data which generated from Illumina sequencer was removed using program Trimmomatic
The reads were aligned to reference transcript sequences using Bowtie2.
Clean RNA-seq data was further analyzed using the CLC genomics workbench software version 11.0 (Qiagen, Hilden, Germany).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Non-small cell lung cancer

growth_protocol: All cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (Gibco™, Grand Island, NY, USA) and 1% penicillin/streptomycin (Gibco™, NY, USA), and incubated at 37°C with 5% CO2 in an incubator.

extract_protocol:
RNA was extracted using GENEzol reagent. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using TruSeq stranded mRNA library prep Kit (cat# RS-122-2101, Illumina, San Diego, CA , USA) following manufacturer’s recommendations.

treatment_protocol: Gefitinib was used to select for resistance in HCC827 and PC9 cells, while osimertinib was used to select for resistance in H1975 cells. During the selection process, the concentration of TKIs was gradually increased as the cells began to proliferate to ensure that cells had developed acquired resistance to TKIs and were not killed at the given concentration. After 90-days incubation with the TKIs, the IC50 of the TKIs at the selection endpoint was much higher than at the beginning of selection. The selected resistant cells were designated as HCC827-GR (gefitinib resistant), PC9-GR (gefitinib resistant), or H1975-OR (osimertinib resistant). To test whether the selected cells were indeed resistant to EGFR-TKIs compared with their parental cells, cell viability assays were performed after 72h incubation with serial dilutions of gefitinib (for HCC827 and PC9) or osimertinib (for H1975). HCC827-GR, PC9-GR and H1975-OR cells demonstrated higher viability at high concentrations of TKIs. Moreover, the IC50 of the TKIs increased from 0.016-0.07 to 4.288-12.485 µM in HCC827-GR, PC9-GR, and H1975-OR cells, indicating that these cells were resistance to TKIs under TKI selection.

value: Human

value: Lung

tag: egfr mutation status

tag: tki response

value: Resistant

value: Gefitinib selected


title: H1975-OR

tag: strain

value: Osimertinib selected


title: PMBC_day0_s171

value: pre-vaccination

value: F

value: American Indian

value: High Dose

value: Y


title: PBMC_day28_s171

value: post-vaccination


title: MCF10A_shANCO1_H3K27Ac_2


title: PC9

value: Sensitive

value: Nontreated


title: control 24h rep 5

description:
AF00245
AFC_48vsAFC_24.txt

tag: gestation day

value: GD 13

value: limb bud

value: DMSO

tag: treatment length

value: 24 hours


title: PMBC_day0_s181

value: blood

value: PBMC

tag: dob

tag: gender

value: White/Caucasian

value: Standard Dose


title: PMBC_day0_s170

tag: bmi

tag: vaccine


title: 1 μM BPAF 24h rep 1

description:
AF01241
AF1_24vsAFC_24.txt

value: 1 uM BPAF


title: control 24h rep 4

description:
AF00244
AFC_48vsAFC_24.txt


title: 1 μM BPAF 24h rep 2

description:
AF01242
AF1_24vsAFC_24.txt


title: 1 μM BPAF 24h rep 5

description:
AF01245
AF1_24vsAFC_24.txt


title: 1 μM BPAF 24h rep 4

description:
AF01244
AF1_24vsAFC_24.txt


title: PBMC_day28_s169

value: M


title: H1975

value: Human

value: Lung


title: HCC827-GR

value: Resistant

value: Gefitinib selected


title: PMBC_day0_s169

value: pre-vaccination

value: High Dose

value: Y


title: 1 μM BPAF 24h rep 3

description:
AF01243
AF1_24vsAFC_24.txt

value: GD 13


title: HCC827

value: Sensitive

value: Nontreated


title: PBMC_day28_s166

value: post-vaccination


title: CRPC-ne EPCaT, PC-3 5:1 coculture with BJ-5ta fibroblasts, Day 15

city: Auburn University

first: Elizabeth

middle: A

last: Lipke

state: AL

address: 212 Ross Hall

institute: Auburn University

description: PC-3 5:1 EPCaT

data_processing:
Partek flow data analysis software was used to normalize RNAseq data.
The FastQC tool was employed in a quality control check on RNAseq raw reads.
RNAseq reads were mapped to the human genome using the STAR aligner tool.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file containing normalized gene counts.

source_name: 3D in vitro Engineered Prostate Cancer Tissue

growth_protocol: PC-3 cells were cultured in F-12K culture media supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) Pen-Strep. BJ-5ta normal human fibroblasts were cultured in 4 parts of DMEM containing 4 mM L-glutamine, 4.5 g/L glucose and 1.5 g/L sodium bicarbonate, and 1 part of Medium 199, supplemented with 0.01 mg/mL hygromycin B, and 10% (v/v) FBS. All cells were maintained in a humidified atmosphere with 5% CO2 and a constant temperature of 37 C; culture media was renewed twice weekly. EPCaTs were formed by encapsulating PC-3 and BJ-5ta cells within a poly(ethylene glycol)-fibrinogen matrix at a concentration of 20 x 10^6 cells/mL and a cell ratio of 5:1 PC-3 cancer cells to BJ-5ta fibroblasts; the PF matrix was modulated with excess PEGDA at volumetric ratios of 96:4 (1% w/v), 92:8 (2% w/v), and 88:12 (3% w/v) to tune EPCaT mechanical properties to mimic prostate cancer xenograft tumors. EPCaTs were maintained in PC-3 culture media in a humidified atmosphere with 5% CO2 and a constant temperature of 37 C; culture media was renewed twice weekly.

extract_protocol:
Total RNA was extracted using QIAshredder and an Rneasy kit, according to manufacturer protocols.
Libraries were constructed using a TruSeq RNA Sample Preparation kit v2, according to manufacturer protocols.

value: PC-3 and BJ-5ta

value: Prostate cancer, fibroblast


title: 5 μM BPAF 3h rep 2

description:
AF05032
AF5_3vsAFC_3.txt

value: limb bud

value: 5 uM BPAF

value: 3 hours


title: ADPC EPCaT, LNCaP monoculture, Day 15

description: LNCaP monoculture EPCaT

value: 3D in vitro Engineered Prostate Cancer Tissue

value: LNCaP

value: Prostate cancer


title: CRPC-ne EPCaT, PC-3 monoculture, Day 15

description: PC-3 monoculture EPCaT


title: 5 μM BPAF 3h rep 1

description:
AF05031
AF5_3vsAFC_3.txt


title: PMBC_day0_s161

value: blood

value: PBMC

value: M

value: White/Caucasian

value: Standard Dose


title: 5 μM BPAF 3h rep 5

description:
AF05035
AF5_3vsAFC_3.txt

value: GD 13


title: PBMC_day28_s161

value: Y


title: PBMC_day28_s155

value: N


title: 5 μM BPAF 3h rep 4

description:
AF05034
AF5_3vsAFC_3.txt


title: 5 μM BPAF 3h rep 3

description:
AF05033
AF5_3vsAFC_3.txt


title: PMBC_day0_s166

value: pre-vaccination


title: Human healthy peripheral blood mononuclear cells

type: RNA

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

scan_protocol: GeneChips were scanned using  Affymetrix® Scanner 3000 7G.

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm  using Partek Genomics Suite 6.6 software.

label: biotin

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

value: Mononuclear cells

value: peripheral blood (PB)


title: Wild-type (Kabuki syndrome type 2 differential analysis) replicate 6 [8-21_wt]

city: Baltimore

first: Leandros

last: Boukas

address: 733 North Broadway

institute: Johns Hopkins University

data_processing:
Reads were mapped to the mm10 mouse assembly.
Duplicates were removed with the MarkDuplicates function from Picard, and mitochondrial reads were removed with samtools
Samples from the same genotype were merged, and peaks were called on these merged meta-samples using MACS2
The peaks from each meta-sample were unionized to yield a final set of genomic intervals. The number reads from each sample that map onto each of these intervals were counted using the featureCounts function from the Rsubread package.
Assembly: mm10
Supplementary files format and content: The processed data file is a matrix (in csv format), with rows corresponding to the genomic intervals obtained after unionizing the peaks called from the individual meta-samples (each interval has its unique coordinates), and columns to samples (each sample name contains information about genotype). The entries in the matrix are counts, as obtained using the featureCounts function from the Rsubread R package.

source_name: Wild-type

extract_protocol:
Hippocampal neurons were isolated using a protocol adapted from the INTACT (Mo et al., 2015) and Omni-ATAC (Corces et al., 2017) protocols. Dentate gyrus was microdissected as previously described (Carosso et al., 2019) and placed into ice cold 1xHBS (1x HBS-B, 1M sucrose, 500mM EDTA, 10\% IGEPAL; 1x HBS-B was initially prepared as 6xHBS with 1MCaCl2, 1MMgAc, 1M Tris pH7.8, 1mM BME). Samples were homogenized in a 2mL glass dounce, pestle A until resistance went away (approximately 15 strokes) and pestle B until the tissue looked homogenized (approximately 8 strokes). Samples were then spun through a discontinuous iodixanol gradient. Gradients were made by diluting homogenized sample 1:1 with 50% iodixanol solution for a final concentration of 25% iodixanol (60% iodixanol solution + HBS), and overlayed on a 30%-35%  iodixanol gradient in 15 mL conical tubes (30% iodixanol solution: 1xHBS, 30% iodixanol solution, 160mM sucrose; 35% iodixanol solution: 1xHBS, 35% iodixanol solution, 160mM sucrose). Gradients were spun for 5000g 20min 4’ with no break in swinging bucket centrifuge. Nuclei were collected at the 30-35% interface, transferred to a new tube and diluted with 1xHBS. Samples were spun for 10min 4’ 1000g, aspirated, then resuspended in 200uL 1xHBS. Nuclei were then stained for NeuN (NeuN-488, EMD Millipore MAB377X) and incubated 30min in dark. DNA was counterstained with Hoechest 33342 and sorted on NeuN+ to collect neurons (to avoid glia). 5000 nuclei were collected for most samples, though some variation was present.
Samples were resuspended in tagmentation reaction mix for 30 min (2.5uL TD1, 1X TD Buffer, Illumina Nextera DNA, FC-121-1030; .25uL 1% digitonin, Promega G9441; 1xPBS) gently shaking (300rpm on Eppendorf thermomixer) at 37’. We purified reactions using Zymo DNA Clean and Concentrator-5 kit (Zymo D4013) following manufacturer protocols and eluted with 10.5uL water to recover 10uL. Each reaction was then amplified and indexed per standard ATAC-seq protocol. After indexing and amplification, we purified samples using Select-A-Size purification columns (Zymo D4080) with a cutoff of 150bp to remove adapter dimers to allow for efficient sequencing on patterned flow cells, checked library size on BioAnalyzer using DNA High Sensitivity reagents (Agilent 5067-4626) and determined concentration using Qubit dsDNA HS Assay Kit (ThermoFisher Q32851).

value: NeuN+ hippocampal neurons from the dentate gyrus

value: Wild-type

tag: strain background


title: Wild-type (Kabuki syndrome type 2 differential analysis) replicate 3 [10-5-4_wt]


title: Kabuki syndrome type 2 replicate 4 [10-5-9_KS2]


title: Wild-type (Kabuki syndrome type 2 differential analysis) replicate 4 [8-16_wt]


title: Wild-type (Kabuki syndrome type 2 differential analysis) replicate 5 [8-19_wt]


title: Human healthy mobilized peripheral blood mononuclear cells

label_protocol: In accordance with manufacturer's protocols

value: mobilized peripheral blood (MPB)


title: Human healthy bone marrow mononuclear cells

value: bone marrow (BM)


title: PMBC_day0_s155


title: ADPC EPCaT, LNCaP 5:1 coculture with BJ-5ta fibroblasts, Day 15

description: LNCaP 5:1 EPCaT

value: 3D in vitro Engineered Prostate Cancer Tissue

value: LNCaP and BJ-5ta

value: Prostate cancer, fibroblast


title: Kabuki syndrome type 2 replicate 3 [10-5-3_KS2]


title: RKO1 ZEB1 siRNA 1

city: Barcelona

first: Antonio

last: Postigo

address: Villarroel 170

department: Oncology and Hematology

country: Spain

institute: IDIBAPS

data_processing:
RNA-seq reads were mapped against Homo sapiens reference genome with STAR (ENCODE parameters)
Genes were quantified with RSEM (default parameters)
Normalization and differential expression was performed with edgeR R package
GO/KEGG enrichment analysis was performed with DAVID
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file containing RSEM expected counts

source_name: Colorectal adenocarcinoma

growth_protocol: DMEM (Lonza) + 10% FBS (Sigma-Aldrich) + 1%P/S (Lonza)

extract_protocol:
Cells were detached with trypsin/EDTA, centrifuged at 1.500rpm for 5 min, PBS washed, centrifuged and total RNA was extracted following RNAzol® RT extraction protocol (Sigma-Aldrich, R4533). Sequencing was done with HS2000, 2x75bp using >2ug of total RNA with a sequencing depth of >20M reads.
RNA libraries were prepared with TruSeq®Stranded mRNA LT Sample Prep Kit

treatment_protocol: small interference RNA transfection following Lipofectamine RNAiMax protocol (ThermoFisher).

value: Colorectal adenocarcinoma

tag: kras genotype

value: WT

tag: braf genotype

tag: small interference rna


title: RKO1 ZEB1 siRNA 3


title: RKO1 ZEB1 siRNA 2


title: control 3h rep 2

description:
AF00032
AFC_24vsAFC_3.txt

tag: tissue

value: limb bud

value: DMSO

value: 3 hours


title: RKO1 Ctl siRNA 3

tag: cell type

value: control


title: PBMC_day28_s151

value: blood

value: PBMC

value: post-vaccination

tag: age

value: F

value: White/Caucasian

value: Standard Dose

value: Y


title: Wild-type (Kabuki syndrome type 2 differential analysis) replicate 2 [10-5-2_wt]

value: NeuN+ hippocampal neurons from the dentate gyrus

tag: genotype

value: Wild-type


title: PMBC_day0_s151

tag: treatment

value: pre-vaccination


title: RKO1 Ctl siRNA 2


title: Kabuki syndrome type 2 replicate 2 [10-5-11_KS2]


title: control 3h rep 1

description:
AF00031
AFC_24vsAFC_3.txt

value: GD 13


title: RKO1 Ctl siRNA 1

value: Colorectal adenocarcinoma


title: Ls174T ZEB1 siRNA 3

value: WT


title: PBMC_day28_s149

value: M


title: control 3h rep 4

description:
AF00034
AFC_24vsAFC_3.txt

value: limb bud

value: DMSO


title: Kabuki syndrome type 2 replicate 1 [10-5-1_KS2]


title: Wild-type (Kabuki syndrome type 2 differential analysis) replicate 1 [10-5-10_wt]


title: control 3h rep 3

description:
AF00033
AFC_24vsAFC_3.txt

value: 3 hours


title: PMBC_day0_s149

value: blood


title: Ls174T ZEB1 siRNA 2


title: Ls174T ZEB1 siRNA 1


title: 1 μM BPAF 3h rep 2

description:
AF01032
AF1_3vsAFC_3.txt

value: 1 uM BPAF


title: PBMC_day28_s65

value: PBMC

value: post-vaccination

value: Hispanic


title: PMBC_day0_s65

value: F

value: Standard Dose


title: 1 μM BPAF 3h rep 1

description:
AF01031
AF1_3vsAFC_3.txt


title: Wild-type (Kabuki syndrome type 1 differential analysis) replicate 5 [9-6_wt]

value: NeuN+ hippocampal neurons from the dentate gyrus


title: Kabuki syndrome type 1 replicate 7 [9-3_KS1]


title: Ls174T Ctl siRNA 3

value: control


title: 1 μM BPAF 3h rep 5

description:
AF01035
AF1_3vsAFC_3.txt

value: 10 uM BPA


title: Kabuki syndrome type 1 replicate 6 [9_2-4_KS1]


title: PBMC_day28_s64

value: White/Caucasian

value: Y


title: 1 μM BPAF 3h rep 4

description:
AF01034
AF1_3vsAFC_3.txt

value: GD 13


title: control 3h rep 5

description:
AF00035
AFC_24vsAFC_3.txt


title: PBMC_day28_s58


title: 1 μM BPAF 3h rep 3

description:
AF01033
AF1_3vsAFC_3.txt


title: PMBC_day0_s58

value: pre-vaccination


title: Kabuki syndrome type 1 replicate 5 [9_2-25_KS1]


title: Ls174T Ctl siRNA 1

value: Colorectal adenocarcinoma

value: WT


title: 50 μM BPA 48h_rep 1

description:
A50_48vsAC_48.txt
A50481

treatment_protocol: Culture bottles were gassed for two minutes with 5% CO2, 50% O2 balanced with N2. Each bottle subsequently received one of two treatments: dimethyl sulfoxide (DMSO, vehicle control) or bisphenol A (BPA 10 or 50 μM).  Limbs were then cultured at 37° for 3 hours.

value: limb bud

value: 50 uM BPA

value: 48 hours


title: PBMC_day28_s55

value: blood

value: PBMC

value: M


title: Kabuki syndrome type 1 replicate 3 [9_2-17_KS1]


title: Kabuki syndrome type 1 replicate 8 [9-8_KS1]


title: 50 μM BPA 48h_rep 5

description:
A50_48vsAC_48.txt
A50485


title: Ls174T Ctl siRNA 2


title: 50 μM BPA 48h_rep 4

description:
A50_48vsAC_48.txt
A50484


title: PMBC_day0_s55


title: Wild-type (Kabuki syndrome type 1 differential analysis) replicate 4 [9_2-12_wt]

value: Wild-type


title: PMBC_day0_s64

value: F

value: Standard Dose


title: Wild-type (Kabuki syndrome type 1 differential analysis) replicate 3 [9_2-11_wt]

value: NeuN+ hippocampal neurons from the dentate gyrus


title: SKBR3, PVRL4 siRNA #2, rep3

city: Tokyo

first: Kiyoshi

last: Yamaguchi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Clinical Genome Research

institute: The University of Tokyo

description:
Ion AmpliSeq Transcriptome
siPVRL4_2_3

data_processing:
The sequencing reads were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program (TMAP).
QC metrics and normalized read counts per gene were obtained using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Assembly: hg19
Supplementary files format and content: A tab-delimited text file includes RPM values for each sample.

growth_protocol: SKBR3 cells were maintained in DMEM supplimented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kits (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using an Ion AmpliSeq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific) according to the manufacturer's instructions.

treatment_protocol: The cells were transfected with 10 nM of control (ON-TARGETplus Non-targeting Control, Horizon Discovery ) or PVRL4 siRNAs (Integrated DNA Technologies) using Lipofectamine RNAiMAX (Thermo Fisher Scientific).

tag: cell line

value: breast cancer

value: PVRL4 siRNA #2 for 48 h


title: SKBR3, PVRL4 siRNA #2, rep1

description:
Ion AmpliSeq Transcriptome
siPVRL4_2_1


title: SKBR3, PVRL4 siRNA #2, rep2

description:
Ion AmpliSeq Transcriptome
siPVRL4_2_2


title: 50 μM BPA 48h_rep 3

description:
A50_48vsAC_48.txt
A50483

tag: strain


title: SKBR3, PVRL4 siRNA #1, rep2

description:
Ion AmpliSeq Transcriptome
siPVRL4_1_2

value: PVRL4 siRNA #1 for 48 h


title: PMBC_day0_s47

value: White/Caucasian

value: High Dose

value: Y


title: PBMC_day28_s37

value: post-vaccination


title: SKBR3, PVRL4 siRNA #1, rep1

description:
Ion AmpliSeq Transcriptome
siPVRL4_1_1


title: Wild-type (Kabuki syndrome type 1 differential analysis) replicate 2 [9-2_wt]


title: Kabuki syndrome type 1 replicate 4 [9_2-20_KS1]


title: Kabuki syndrome type 1 replicate 2 [9-14_KS1]


title: SKBR3, siCTRL, rep3

description:
Ion AmpliSeq Transcriptome
siCTRL_3

value: Control RNA for 48 h


title: control 48h_rep 2

description:
AC_48vsAC_3.txt
A00482

tag: gestation day

value: GD 13

value: limb bud

value: DMSO


title: Wild-type (Kabuki syndrome type 1 differential analysis) replicate 1 [9-10_wt]


title: control 48h_rep 1

description:
AC_48vsAC_3.txt
A00481

tag: treatment length

value: 48 hours


title: PMBC_day0_s37

value: blood

value: PBMC

value: pre-vaccination

tag: dob


title: SKBR3, siCTRL, rep2

description:
Ion AmpliSeq Transcriptome
siCTRL_2


title: Kabuki syndrome type 1 replicate 1 [9-1_KS1]


title: PBMC_day28_s47

tag: gender

value: F


title: PBMC_day28_s34

tag: bmi

value: Standard Dose


title: SKBR3, PVRL4 siRNA #1, rep3

description:
Ion AmpliSeq Transcriptome
siPVRL4_1_3

value: breast cancer


title: SKBR3, siCTRL, rep1

description:
Ion AmpliSeq Transcriptome
siCTRL_1


title: PMBC_day0_s34

tag: vaccine


title: Wild-type (Kabuki cohorts) replicate 5 [63T-WT]

extract_protocol:
T cells were isolated at the same time as B cells (Luperchio, Boukas et al. 2021). Specifically, flow through from binding and washing of CD19+ cells on Miltenyi separation columns was collected on ice. These CD19+ depleted samples were then spun and the supernatant was aspirated, resuspended and incubated with 2x (20uL) CD90.2+ microbeads (Miltenyi Biotec 130-121-278). CD90.2+ T cells were bound, washed and eluted per manufacturer protocol, then counted and aliquoted on ice for subsequent processing. Further processing of the T cell samples and ATAC sequencing was done in parallel with B cells.
Samples were resuspended in tagmentation reaction mix for 30 min (2.5uL TD1, 1X TD Buffer, Illumina Nextera DNA, FC-121-1030; .25uL 1% digitonin, Promega G9441; 1xPBS) gently shaking (300rpm on Eppendorf thermomixer) at 37’. We purified reactions using Zymo DNA Clean and Concentrator-5 kit (Zymo D4013) following manufacturer protocols and eluted with 10.5uL water to recover 10uL. Each reaction was then amplified and indexed per standard ATAC-seq protocol. After indexing and amplification, we purified samples using Select-A-Size purification columns (Zymo D4080) with a cutoff of 150bp to remove adapter dimers to allow for efficient sequencing on patterned flow cells, checked library size on BioAnalyzer using DNA High Sensitivity reagents (Agilent 5067-4626) and determined concentration using Qubit dsDNA HS Assay Kit (ThermoFisher Q32851).

value: CD90.2+ T cells from peripheral blood

value: Wild-type

tag: strain background


title: Wild-type (Kabuki cohorts) replicate 11 [49_CD90-2]


title: control 48h_rep 5

description:
AC_48vsAC_3.txt
A00485


title: Wild-type (Kabuki cohorts) replicate 12 [65_CD90-2]


title: control 48h_rep 3

description:
AC_48vsAC_3.txt
A00483


title: 10 μM BPA 48h_rep 1

description:
A10_48vsAC_48.txt
A10482

value: 10 uM BPA


title: 10 μM BPA 48h_rep 2

description:
A10_48vsAC_48.txt
A10481


title: control 48h_rep 4

description:
AC_48vsAC_3.txt
A00484


title: 50 μM BPA 48h_rep 2

description:
A50_48vsAC_48.txt
A50482

value: 50 uM BPA


title: Wild-type (Kabuki cohorts) replicate 10 [37_WT_CD90-2]


title: ChIP_INPUT_SG2M

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

data_processing:
Sequence reads of mouse with fly spike-in samples were mapped to the mouse + fruit fly genome (mm9+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1.
SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each experiment. Height of the profiles was normalized by the total number of reads mapped over the spike-in genome.
Assembly: mm9
Supplementary files format and content: Genome-wide profiles (Bedgraph)

growth_protocol: Briefly, ESCs were growth in serum-free medium N2B27 media (DMEM/F12:Neurobasal 1:1, 0.5x N-2 supplement, 1x B-27 serum-free supplement, 50 µM 2-mercaptoethanol; Bovine Albumin Fraction V 0.033%; 1X Glutamax; 1X MEM non-essential aminoacids; 1X Penicillin-Streptomycin; all from Gibco) supplemented with 1 µM PD0325901 (Tocris), 3 uM CHIR99021 (Tocris) and Leukemia Inhibitory Factor (LIF).

extract_protocol:
ChIP-seq: ChIP experiments were carried out adapting with modifications a standard protocol in the lab (PubMed ID 34473698)
Libraries were prepared according to Illumina instructions.

value: mouse Embryonic Stem Cells (mESCs)

tag: chip antibody

value: none (input)


title: ChIP_P53_G1

value: NCL-L-p53-CM5 (Leica)


title: ChIP_INPUT_G1


title: ChIP_P53_SG2M


title: PMBC_day0_s22

value: M

value: White/Caucasian

value: Y


title: 10 μM BPA 48h_rep 5

description:
A10_48vsAC_48.txt
A10485

extract_protocol:
Total RNA was extracted using the Rneasy Mini kit (Qiagen). The concentration and purity of extracted RNA was assessed using NanoDrop 2000 spectrophotometer (Thermofisher).
mRNA was purified from 1ug of total RNA using poly-T oligo-attached magnetic beads and fragmented randomly in a fragmentation buffer. First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-); second-strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3' ends of DNA fragments, NEBNext Adaptor was ligated to prepare for hybridization. The library fragments were purified with AMPure XP system. The final library was obtained by PCR amplification and purification of PCR products using AMPure XP beads.

value: GD 13

value: limb bud

value: 48 hours


title: PBMC_day28_s29

value: blood

value: PBMC

value: post-vaccination


title: Wild-type (Kabuki cohorts) replicate 9 [27_CD90-2]


title: Wild-type (Kabuki cohorts) replicate 8 [26_WT_CD90-2]


title: 10 μM BPA 48h_rep 4

description:
A10_48vsAC_48.txt
A10484


title: SPF_Kpn_4

first: Jing

last: Li

address: Beilishi Road 167, Xicheng District,

department: Department of Hypertension Center

institute: FuWai Hospital, National Center for Cardiovascular Diseases,  Peking Union Medical College & Chinese Academy of Medical Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database  of splice junctions based on the gene model annotation file and thus a better mapping  result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining  differential expression in digital gene expression data using a model based on the  negative binomial distribution. The resulting P-values were adjusted using the  Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes  with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially  expressed
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: aorta

extract_protocol:
Aorta tissues were collected, and RNA was extracted using the RNeasy (Qiagen) kit with DNase. RNA quality was assessed on a NanoPhotometer spectrophotometer and Agilent 2100 bioanalyzer. Total RNA underwent mRNA enrichment with the NEBNext Poly (A) mRNA Magnetic Isolation Module, followed by library preparation with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina. Libraries were validated with the MultiNA Bioanalyzer, and barcoded samples were pooled to equimolar concentrations before sequencing. Cluster generation was performed with HiSeq 2500. Paired-end sequencing was performed at Novogene Bioinformatics Technology Co., Ltd. Cleaned RNA sequencing reads were obtained through quality control and blasted with a mice genome in HISAT2 software
Library preparation was performed with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina

value: aorta

value: Kpn

tag: time

value: Week 8


title: Wild-type (Kabuki cohorts) replicate 7 [24_WT_CD90-2]

value: CD90.2+ T cells from peripheral blood

value: Wild-type


title: SPF_Kpn_3


title: 10 μM BPA 48h_rep 3

description:
A10_48vsAC_48.txt
A10483

data_processing:
Base calling was performed using Illumina CASAVA (v1.8)
Sequences were filtered for reads containing adapter or of low quality, then mapped to mm10 using STAR (v2.5, mismatch=2)
Quantification was performed using HTSeq (v0.6.1, -m union)
Differential analysis was performed using DESeq2 (v2_1.6.3, q-value < 0.05)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table containing raw count, FPKM value, and normalized abundance output (from DESeq2) of each gene for each sample and each treatment group

value: 10 uM BPA


title: SPF_Kpn_2


title: PMBC_day0_s17

extract_protocol:
the standard phenol-chloroform extraction method for blood samples
For the TBS-seq library preparation, adapter ligation and dA-tailing were performed using the NEBNext Ultra II Library prep kit and custom pre-methylated adapters (IDT). Purified libraries were then hybridized to the biotinylated probes. Under the following conditions: 2 min at 98°C; 14 cycles of (98°C for 20 sec; 60°C for 30 sec; 72°C for 30 sec); 72°C for 5 minutes; hold at 4°C, PCR amplification was performed after bisulfite treatment on captured DNA using KAPA HiFi Uracil+. Library quality control was conducted on the high-sensitivity D1000 assay on a 2200 Agilent TapeStation.

value: pre-vaccination

value: Standard Dose


title: PMBC_day0_s29

value: F


title: PBMC_day28_s16

value: Hispanic


title: PBMC_day28_s22

value: M

value: White/Caucasian

value: Y


title: 50 μM BPA 24h_rep 2

description:
A50_24vsAC_24.txt
A50242

value: GD 13

value: limb bud

value: 50 uM BPA

value: 24 hours


title: SPF_Kpn_1

value: aorta


title: Wild-type (Kabuki cohorts) replicate 6 [21_WT_CD90-2]


title: PMBC_day0_s16

value: blood

value: PBMC


title: Wild-type (Kabuki cohorts) replicate 2 [104T-WT]

value: CD90.2+ T cells from peripheral blood


title: SPF_5

value: SPF

value: Week 8


title: 50 μM BPA 24h_rep 1

description:
A50_24vsAC_24.txt
A50241


title: PBMC_day28_s14

value: post-vaccination


title: PMBC_day0_s14

value: pre-vaccination

value: Standard Dose


title: PBMC_day28_s17


title: 50 μM BPA 24h_rep 5

description:
A50_24vsAC_24.txt
A50245


title: 50 μM BPA 24h_rep 4

description:
A50_24vsAC_24.txt
A50244


title: PBMC_day28_s5

value: F


title: 50 μM BPA 24h_rep 3

description:
A50_24vsAC_24.txt
A50243


title: Wild-type (Kabuki cohorts) replicate 3 [32T-WT]

value: Wild-type


title: SPF_3


title: Kabuki syndrome type 2 replicate 5 [42T-KDM6a]


title: SPF_2


title: PBMC_day28_s1

value: White/Caucasian


title: SPF_1


title: Kabuki syndrome type 2 replicate 4 [106T-KDM6a]


title: control 24h_rep 2

description:
AC_48vsAC_24.txt
A00242

value: DMSO


title: control 24h_rep 1

description:
AC_48vsAC_24.txt
A00241

value: GD 13


title: Wild-type (Kabuki cohorts) replicate 4 [40T-WT]


title: PMBC_day0_s1

value: Y


title: control 24h_rep 5

description:
AC_48vsAC_24.txt
A00245

value: limb bud


title: SW620 cells, ELAPOR1 group 3

city: Shanghai

first: Chunzhi

last: Qin

address: 1508 Longhang Road, Jinshan District

institute: Jinshan Hospital, Fudan University

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Assembly: GRCh38
Supplementary files format and content: excel files include RPKM values for each Sample
Supplementary files format and content: differentially expressed mRNAs before and after ELAPOR1 overexpression in SW620 cells

growth_protocol: SW620 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: To construct stable transgenic cells, ELAPOR1 were inserted into pLVX-IRES-Puro (Takara, Mountain View, CA, USA) to construct pLVX-IRES-Puro-ELAPOR1 plasmid; empty vector was used as the negative control. Afterwards, the plasmids were packed into lentiviruses using HEK293T cells, and the lentiviruses were harvested and purified. Next, cells were infected by lentivirus at multiplicity of 20. The stably-transfected cells were elected by puromycin (Merck) at 2ug/ml.

value: colorectal cancer

value: ELAPOR1 overexpression


title: SPF_4

value: aorta


title: Kabuki syndrome type 2 replicate 3 [103T-KDM6a]


title: Wild-type (Kabuki cohorts) replicate 1 [101T-WT]


title: MG_LPS_input_2

first: Adriana

last: Ramos

address: 600 North Wolfe Street

data_processing:
DNA libraries were generated using the DNA SMARTTM ChIP-Seq Kit (Clontech) and sequenced using paired end HiSeq2500 (Illumina). FastQC was used to quality control sequencing reads. The reads were aligned to the mm10 genome with bowtie2. Peak finding was performed by MACS14 with default parameters. Peak annotation was performed with Peak Annotation and Visualization
Genome_build: mm10
Supplementary_files_format_and_content: bed files for called peaks and summits are provided

source_name: Cortical microglia_Input

growth_protocol: Microglia cells were isolated from cortical tissue of LPS treated mice using Mylteny adult dissociation kit (Miltenyi Biotec, 130-107-677) to generate an initial single cell suspension, and microglia was subsequently isolated using Cd11b beads (Myltenyi Biotech, 130-049-601)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
DNA libraries were generated using the DNA SMARTTM ChIP-Seq Kit (Clontech) and sequenced using paired end HiSeq2500 (Illumina).

treatment_protocol: Mice were intraperitoneally tretaed with LPS for 4 consecutive days.

value: Mouse intraperitoneally exposed to LPS

tag: tissue/cell type

value: Ex-vivo Cortical microglia


title: MG_LPS_ChIP_2

source_name: Cortical microglia_LPS

value: AceGAPDH (Millipore Sigma 07-2184)


title: Kabuki syndrome type 2 replicate 1 [100T-KDM6a]

value: CD90.2+ T cells from peripheral blood


title: SW620 cells, ELAPOR1 group 1


title: Kabuki syndrome type 1 replicate 5 [84T-KMT2D]


title: PMBC_day0_s5

data_processing:
Adapter sequences were removed using cutadapt (v2.10) for the demultiplexed FastQ files
BSBolt (v1.3.0) was used to align the reads to the reference GRCh38 genome
Samtools was used to remove PCR duplicates using the markdup function
methylation calling was performed using the BSBolt CallMethylaiton function
grch38 genome
Assembly: csv, day 0 (pre-vaccination) methylation calling matrix
Supplementary files format and content: csv, day 28 (post-vaccination) methylation calling matrix

tag: tissue

value: blood

value: PBMC


title: control 24h_rep 3

first: Barbara

last: Hales

address: 3655 Promenade Sir-William-Osler

institute: McGill University

description:
AC_48vsAC_24.txt
A00243

value: 24 hours


title: MG_LPS_ChIP_1


title: MG_LPS_input_1


title: Kabuki syndrome type 1 replicate 4 [79T-KMT2D]

tag: cell type


title: NLF cells, siTBX2-AS1, replicate 3

city: Philadelphia

first: Sharon

last: Diskin

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Sample and read quality was assessed using FastQC.
Reads were mapped to hg19 using STAR_2.4.2a.
Read counts and gene expression quantification was identified using StringTie 1.3.3.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: neuroblastoma

growth_protocol: NLF neuroblastoma cell lines were  grown in RPM1-1640 with HEPES, L-glutamine and phenol red, supplemented with 10% FBS, 1% L-glutamine in an incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the miRNeasy kit (Qiagen). 1000 ng/sample was used as input for library preparation.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit from Illumina (with Ribo-Zero treatment).

treatment_protocol: NLF cells were treated for 48hours with siTBX2-AS1, siTBX2, and non-targeting control samples, siNTC, (three biological replicates per condition).

value: neuroblastoma

value: NLF

value: neural crest

value: WT


title: SW620 cells, vector group 3

value: empty vector


title: 10 μM BPA 24h_rep 1

description:
A10_24vsAC_24.txt
A10241

value: GD 13

value: 10 uM BPA


title: NLF cells, siTBX2, replicate 3


title: SW620 cells, vector group 2

value: colorectal cancer


title: Kabuki syndrome type 1 replicate 3 [6T-KMT2D]


title: NLF cells, siNTC, replicate 3

value: siNTC


title: 10 μM BPA 24h_rep 5

description:
A10_24vsAC_24.txt
A10245

value: limb bud


title: Kabuki syndrome type 1 replicate 7 [31_Mut_CD90-2]


title: SW620 cells, vector group 1


title: 10 μM BPA 24h_rep 4

description:
A10_24vsAC_24.txt
A10244


title: NLF cells, siTBX2-AS1, replicate 2


title: control 24h_rep 4

description:
AC_48vsAC_24.txt
A00244

value: DMSO


title: Kabuki syndrome type 1 replicate 6 [29_Mut_CD90-2]


title: NLF cells, siTBX2, replicate 2


title: LX2_Co rep2

city: Nanjing

first: Peiliang

last: Shen

address: Xianlin Road 138#

institute: Nanjing university of Chinese Medcine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hepatic stellate  cell

value: culture in a tumor-om-a-chip with HCCLM3


title: LX2_Co rep3


title: 10 μM BPA 24h_rep 2

description:
A10_24vsAC_24.txt
A10242


title: 50 μM BPA 3h_rep 2

description:
A50_3vsAC_3.txt
A50032

value: 50 uM BPA


title: LX2_Co rep1


title: Kabuki syndrome type 1 replicate 1 [23T-KMT2D]

value: CD90.2+ T cells from peripheral blood

value: Wild-type


title: NLF cells, siTBX2-AS1, replicate 1


title: LX2 rep3

value: culture in a tumor-om-a-chip alone


title: 50 μM BPA 3h_rep 1

description:
A50_3vsAC_3.txt
A50031

value: 24 hours


title: 50 μM BPA 3h_rep 5

description:
A50_3vsAC_3.txt
A50035


title: Enteric glial cells scATAC-seq

first: Vassilis

last: Pachnis

address: 1 Midland Rd

department: Development and Homeostasis of the Nervous System Laboratory

institute: The Francis Crick Institute

data_processing:
Reads for EGCs and neural crest cells (E9.5) were aligned to the mm10 genome using 10x Genomics Cell Ranger ATAC 1.2.0.   Fragment files (output from 10x Genomics Cell Ranger ATAC 1.2.0) for the fresh cortex from adult mouse brain (P50) data were obtained from 10x genomics (https://www.10xgenomics.com/resources/datasets?menu%5Bproducts.name%5D=Single%20Cell%20ATAC&page=1&configure%5Bfacets%5D%5B0%5D=chemistryVersionAndThroughput&configure%5Bfacets%5D%5B1%5D=pipeline.version&configure%5BhitsPerPage%5D=500).
Downstream analysis was performed using ArchR. Initially each dataset was investigated separately. Cells predicted to be doublets; cells with <= 10000 fragments; and cells with a TSS enrichment less than 4 were filtered from further analysis from each dataset. Iterative Latent Semantic Indexing (LSI) was performed and the first 30 dimensions used as input to the UMAP algorithm.
Cell types for the cortical and neural crest data were determined by label transfer using the Seurat FindTransferAnchors() function through the ArchR interface. For the cortical dataset we downloaded annotated adult mouse cortical scRNA-seq data from the Allen Institute for Brain Science from https://www.dropbox.com/s/kqsy9tvsklbu7c4/allen_brain.rds in the form of a Seurat object. Single cell neural crest data was processed as in the section "Analysis of neural crest data". EGC1 and EGC2 clusters in the scATAC EGC data were similarly inferred using our C1 fuidigm scRNA-seq EGC data.
For further analysis, cells labelled as oligodendrocytes and astrocytes from the cortical dataset were selected, and those labelled as belonging to the autonomic lineage were selected from the neural crest dataset. Iterative Latent Semantic Indexing (LSI) was performed on the entire dataset and the first 30 dimensions used to integrate the selected cortical, neural crest and EGC data using the Harmony algorithm via the ArchR interface. Clustering was performed using the Louvain algorithm (resolution 1). Two small outlying clusters were removed and iterative LSI, integration using harmony and dimensionality reduction using UMAP were performed on this filtered dataset.
Assembly: mm10
Supplementary files format and content: Zipped folder containing ArchR project (see https://www.archrproject.com/).

source_name: Enteric nervous system

growth_protocol: Mice used in this study were maintained according to standard practices and all procedures were approved by The Francis Crick Institute Animal Ethics Committee and conformed to UK Home Office requirements (ASPA 1986) and the ARRIVE guidelines.

extract_protocol:
Nuclei were isolated and scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics;10xGenomics.com CG000496 Rev A). Briefly, after counting, nuclei concentrations were adjusted to the desired capture number 10,000 based on the number of available nuclei and the desired multiplet rate (described on 10X protocol). To minimize potential multiplets, we typically aimed to capture <6,000 nuclei per channel. Next, 5 μl of the resulting resuspended nuclei were combined with ATAC Buffer and ATAC Enzyme (10x Genomics PN-1000390) to form a transposition mix, which was then incubated for 60 min at 37 °C.  A master mix composed of Barcoding Reagent, Reducing Agent B and Barcoding Enzyme (10X PN-1000390) was then added to the same tube as transposed nuclei. The resulting solution was loaded onto a Chromium Chip H(10x Genomics; PN-1000161). Vortexed Chromium Single Cell ATAC Gel Beads and Partitioning Oil were also loaded onto the same Chromium Chip H before attaching a 10x Gasket and placed. into a Chromium Single Cell Controller instrument (10X genomics). Resulting single-cell GEMs were collected at the completion of the run (~17 min) and linear amplification was performed on AB cycler: 72 °C for 5 min, 98 °C for 30 s, cycled 14×: 98 °C for 10 s, 59 °C for 30 s and 72 °C for 1 min. Emulsions were coalesced using the Recovery Agent (10x Genomics; 220016), then subjected to Dynabeads (2000048) and SPRIselect reagent (Beckman Coulter;B23318) bead clean-ups.
Indexed sequencing libraries were constructed by combining the barcoded linear amplification product with a sample index PCR mix comprising SI-PCR Primer B, Amp Mix and Chromium i7 Sample Index Plate N, Set A (10x Genomics; 3000262). Amplification was performed on an AB cycler: 98 °C for 45 s, for 12 cycles: 98 °C for 20 s, 67 °C for 30 s, 72 °C for 20 s, with a final extension of 72 °C for 1 min. The sequencing libraries were subjected to a final bead clean-up SPRIselect reagent and quantified by Qubit and TapeStation HS1000. Sequencing libraries were loaded on an Illumina Novaseq sequencer with 2 × 50 paired-end kits using the following read length: 51 bp read 1N, 8 bp i7 index, 24 bp i5 index (trimmed later on) and 51 bp read 2N using a loading molarity of 280 pM (Standard loading) or 180 pM (Xp loading).

treatment_protocol: nGFP+ cells were isolated from tunica muscularis preparations from 8 week old Sox10CreERT2(SER93);Rosa26-nuclearGFP mice that had been injected with tamoxifen (2 doses of tamoxifen at 100 μg/g of body weight 10 days prior isolation).

value: Enteric nervous system

value: Enteric glial cells

value: tamoxifen injections


title: 50 μM BPA 3h_rep 4

description:
A50_3vsAC_3.txt
A50034


title: 50 μM BPA 3h_rep 3

description:
A50_3vsAC_3.txt
A50033


title: Pt-19_GEX

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

description:
single-cell 5' Gene Expression
10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Gene expression reads were aligned to the human reference genome version gex-GRCh38-2020-A, while V(D)J reads were mapped to vdj-GRCh38-alts-ensembl-7.0.0, both available from the 10X Genomics website. Matrices from each separate sample were aggregated without read-depth normalization using the Cell Ranger aggr (v6.0.0) pipeline using the “normalize=None”.
Secondary analysis was carried out primarily using Loupe Browser (10X Genomics). Dead cells (% mitochondrial reads > 10%) and cells with the number of genes expressed less than 200 were also filtered out. Doublets were removed using a R package ‘Scrublet’. ScRNA-Seq Data was normalized, logarithm transformed and scaled. Principle component analysis (PCA) was run with 50 components using the top 4000 genes of each sample. The nearest neighbor algorithm was run with 50 PCAs and clustered in UMAP projections using Leiden clustering. All additional analyses were performed using Loupe Browser (10X Genomics) and the Python toolkit Scanpy. Immune cells clusters were defined using the set of markers and UMAP clusters: T cells (CD3+, TCR+, NCAM-), NK cells (CD3-, NCAM+), B cells (CD20+, CD79A+, IgKC low), PCs (JChainhi, IgKChi), myeloid cells (CD14+, CSF1R+), mast cells (CPA3+, GATA2+), fibroblasts (FAP+, ACTA2+, PDGFRA1+), epithelial cells (CK19+, CK18+, CK5+, CK14+).
Assembly: GRCh38
Supplementary files format and content: Gene expression: Single cell 5' cell/gene matrices in .mtx format generated by Cell Ranger for individual samples and for all samples aggregated.  V(D)J analysis: annotated contig files in .csv format and assembled contig sequences in FASTA format for all detected BCR sequences output by cellranger vdj.

source_name: resection

extract_protocol:
Live immune cells were sorted by EpCAM- /CD45+ (Biolegend, # clone 2D1 and 9C4) on a Sony SH800 cell sorter, stained with AO/PI (acridine orange / propidium iodide, Nexcelom ViaStain), and checked for viability > 80% using a Countess FL II Automated Cell Counter.
Gene expression (GEX) and V(D)J BCR libraries were constructed according to the manufacturer’s instructions (Single Cell 5’ Gene Expression V1 protocol, 10x Genomics). Libraries were sequenced on a combination of Illumina NextSeq500 (for GEX and V(D)J) and MiSeq (for V(D)J) flow cells.

tag: patient diagnosis

value: PDAC

value: resection

tag: age


title: HCC_Co rep3

value: hepatoma cell

tag: genotype

value: WT

tag: treatment

value: culture in a tumor-om-a-chip with LX2


title: Kabuki syndrome type 2 replicate 2 [102T-KDM6a]


title: control 3h_rep 2

city: MONTRÉAL

description:
AC_24vsAC_3.txt
A00032

tag: strain

value: GD 13

value: limb bud

value: 3 hours


title: HCC_Co rep2

tag: cell line


title: Kabuki syndrome type 1 replicate 2 [27T-KMT2D]


title: WT m4

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

data_processing:
Paired-end reads were aligned to the mouse genome mm10 using the STAR aligner
Raw gene counts for each sample were generated from the subsequent bam files using HTSeq and RPKM matrix calculated in R package edgeR
Assembly: mm10
Supplementary files format and content: RPKM matrix containing RPKM values by gene per sample

source_name: Pancreatic islets

growth_protocol: Mice were housed with free access to regular mouse chow and water under standard conditions

extract_protocol:
RNA was isolated using the Norgen All-in-one kit per manufacturer's instructions.
polyA

treatment_protocol: Islets were isolated from adult male mice by ductal collagenase (Roche) injection and Ficoll (Histopaque-1077; Sigma) gradient as previously described (Alonso et al, Diabetes 2007). Islets were hand picked on ice, flash frozen, and stored at -80 for future RNA isolation.

value: Pancreatic islets

value: IRS2+/+; CDK4 wt/wt

value: Flash frozen after isolation


title: SW620 cells, ELAPOR1 group 2

value: colorectal cancer

value: ELAPOR1 overexpression


title: KO m3

value: IRS2-/-; CDK4 wt/wt


title: Pt-17_GEX


title: KO m2


title: RRKO m2


title: Pt-8_GEX


title: NLF cells, siTBX2, replicate 1

value: neuroblastoma

value: NLF

value: neural crest


title: HCC_Co rep1


title: WT m3


title: control 3h_rep 5

description:
AC_24vsAC_3.txt
A00035

tag: gestation day

value: DMSO

tag: treatment length


title: control 3h_rep 1

description:
AC_24vsAC_3.txt
A00031


title: HCC rep3

value: culture in a tumor-om-a-chip alone


title: Pt-19_BCR

description:
single-cell BCR
10x Genomics

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Gene expression reads were aligned to the human reference genome version gex-GRCh38-2020-A, while V(D)J reads were mapped to vdj-GRCh38-alts-ensembl-7.0.0, both available from the 10X Genomics website. Matrices from each separate sample were aggregated without read-depth normalization using the Cell Ranger aggr (v6.0.0) pipeline using the “normalize=None”.
Secondary analysis was carried out primarily using Loupe Browser (10X Genomics). Dead cells (% mitochondrial reads > 10%) and cells with the number of genes expressed less than 200 were also filtered out. Doublets were removed using a R package ‘Scrublet’. ScRNA-Seq Data was normalized, logarithm transformed and scaled. Principle component analysis (PCA) was run with 50 components using the top 4000 genes of each sample. The nearest neighbor algorithm was run with 50 PCAs and clustered in UMAP projections using Leiden clustering. All additional analyses were performed using Loupe Browser (10X Genomics) and the Python toolkit Scanpy. Immune cells clusters were defined using the set of markers and UMAP clusters: T cells (CD3+, TCR+, NCAM-), NK cells (CD3-, NCAM+), B cells (CD20+, CD79A+, IgKC low), PCs (JChainhi, IgKChi), myeloid cells (CD14+, CSF1R+), mast cells (CPA3+, GATA2+), fibroblasts (FAP+, ACTA2+, PDGFRA1+), epithelial cells (CK19+, CK18+, CK5+, CK14+).
Assembly: GRCh38
Supplementary files format and content: Gene expression: Single cell 5' cell/gene matrices in .mtx format generated by Cell Ranger for individual samples and for all samples aggregated.  V(D)J analysis: annotated contig files in .csv format and assembled contig sequences in FASTA format for all detected BCR sequences output by cellranger vdj.
Library strategy: scBCR-seq

value: PDAC

value: resection


title: control 3h_rep 4

description:
AC_24vsAC_3.txt
A00034


title: LX2 rep1

value: hepatic stellate  cell

value: WT


title: RRKO m1


title: Pt-17_BCR

description:
single-cell BCR
10x Genomics


title: HCC rep2

value: hepatoma cell


title: control 3h_rep 3

description:
AC_24vsAC_3.txt
A00033

value: GD 13

value: limb bud

value: 3 hours


title: WT m1

value: Pancreatic islets

value: IRS2+/+; CDK4 wt/wt

value: Flash frozen after isolation


title: KO m1

value: IRS2-/-; CDK4 wt/wt


title: NLF cells, siNTC, replicate 1

value: neuroblastoma

value: siNTC


title: 10 μM BPA 3h_rep 2

description:
A10_3vsAC_3.txt
A10032

value: 10 uM BPA


title: 8plex-SSNseq-CAR-T-in-vivo, mRNA-derived cDNA

city: Houston

first: Pawel

last: Mazur

state: Texas

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

description:
mRNA
Sample 4-1
Exp4_barcodes.tsv.gz
Exp4_features.tsv.gz
Exp4_matrix.mtx.gz

data_processing:
Gene expressing reads were aligned to the GRCh38 genome (human) and/or mm10 genome (mouse) using the 10x Genomics Cell Ranger, with the pipeline cellranger count. Small RNA counts were retrieved through cellranger count using the pattern containing group barcodes and sequences derived from constant regions of corresponding small RNAs.
Assembly: GRCh38, mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: SSN-Seq

source_name: Human CAR T cells

extract_protocol:
Lentiviral barcoded multi-type cell lines and/or primary T cells were pooled and loaded into a Chromium Controller (10X Genomics).
10x Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (with Feature Barcoding technology for CRISPR Screening) was used to construct the mRNA and small RNA libraries, according to the manufacturer’s protocol (CG000205 Rev D).

value: Human CAR T cells


title: Pt-8_BCR

description:
single-cell BCR
10x Genomics


title: AU565-cap-1

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

data_processing:
RNA-seq libraries were prepared using Illumina’s TruSeq protocol and were sequenced on an Illumina NextSeq 500. Reads were aligned to the hg38 genome using Rsubread v1.5.3. Gene counts were quantified by Entrez Gene IDs using featureCounts and Rsubread’s built-in annotation. Gene symbols were provided by NCBI gene annotation. Genes with count-per-million above 0.5 in at least 3 samples were kept in the analysis. Differential expression analysis was performed using limma-voom
Assembly: hg38
Supplementary files format and content: CSV files containing read counts values for each Sample

source_name: epithelium

growth_protocol: AU565 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol extraction method
RNA-seq libraries were prepared using Illumina’s TruSeq protocol

treatment_protocol: liquid overlay + 5% matrigel following trastuzumab treatment, 96 hours incubation prior to rna extraction

value: epithelium

tag: condition

value: AU565 cells, Capsule


title: HCC rep1

value: culture in a tumor-om-a-chip alone


title: AU565-cap-3

value: 5% matrigel following trastuzumab treatment, 96 hours incubation prior to rna extraction


title: 8plex-SSNseq-CAR-T-in-vitro, SSN-derived cDNA

description:
small RNA
Sample 3-2
Exp3_barcodes.tsv.gz
Exp3_features.tsv.gz
Exp3_matrix.mtx.gz


title: AU565-cap-2

value: WT


title: 10 μM BPA 3h_rep 1

description:
A10_3vsAC_3.txt
A10031

source_name: Embryonic forelimb