title: 40265_Chronic_TCRgd

description: non broad neutralizer


title: 40094_Chronic_TCRgd

status: Public on Jul 03 2024

type: SRA

city: silver spring

first: Dohoon

last: Kim

address: 503 BLDG, Walter Reed Army institute of research

country: USA

institute: Henry M Jackson Foundation

description: non broad neutralizer

library_source: transcriptomic

data_processing:
Quality control was performed on raw FASTQ files using FastQC to assess the quality of the sequencing data.
Adapters and low-quality bases were trimmed using Trimmomatic.
Cleaned reads were aligned to the reference genome using STAR aligner(ver. 2.6.1d) with default parameters.
Aligned reads were quantified to gene-level expression using RSEM(ver. 1.3.1).
Raw read counts and TPM (Transcripts Per Million) were generated for each sample.
Differential expression analysis was carried out using edgeR.
Assembly: hg38
Supplementary files format and content: The processed data files are in tab-delimited text format and include gene expression matrices (TPM and raw counts) and differential expression results (gene IDs, log2 fold changes, p-values, and FDR).

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: Cryopreserved PBMC were thawed, stained, and sorted directly without any culture

extract_protocol:
200 cells were directly sorted into 1x lysis buffer supplemented with 6U RNase inhibitor (both Takara Bio). Post sort, sample tubes were vortexed, incubated at RT for 2 minutes, and snap frozen on dry ice prior to storage at -80˚ C.
Upon thawing, cDNA synthesis was performed using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) as per the manufacturer’s instructions. A total of 150-300pg amplified cDNA was used as input for library preparation

treatment_protocol: Cells were not treated other than staining and sorting

tag: tissue

value: PBMC

tag: cell line

tag: cell type

value: gamma delta T cells

tag: genotype

tag: treatment


title: 40094_SetPoint_TCRgd

description: non broad neutralizer


title: 40094_Peak_TCRgd

description: non broad neutralizer


title: 40094_Pre-Infection_TCRgd

description: non broad neutralizer


title: 40139_Chronic_TCRgd

description: non broad neutralizer


title: 30156_Chronic_TCRgd

description: Broad neutralizer


title: 40139_SetPoint_TCRgd

description: non broad neutralizer


title: 40139_Peak_TCRgd

description: non broad neutralizer


title: 40139_Pre-Infection_TCRgd

description: non broad neutralizer


title: 20233_Chronic_TCRgd

description: non broad neutralizer


title: 40511_SetPoint_TCRgd

description: non broad neutralizer


title: 20178_Peak_TCRgd

description: non broad neutralizer


title: 20178_Chronic_TCRgd

description: non broad neutralizer


title: 20631_SetPoint_TCRgd

description: non broad neutralizer


title: 20178_Pre-Infection_TCRgd

description: non broad neutralizer


title: 20178_SetPoint_TCRgd

description: non broad neutralizer


title: 20233_Pre-Infection_TCRgd

description: non broad neutralizer


title: 30507_SetPoint_TCRgd

description: non broad neutralizer


title: 20233_Peak_TCRgd

description: non broad neutralizer


title: 30507_Peak_TCRgd

description: non broad neutralizer


title: 20355_Chronic_TCRgd

description: non broad neutralizer


title: 30507_Pre-Infection_TCRgd

description: non broad neutralizer


title: 20233_SetPoint_TCRgd

description: non broad neutralizer


title: 20631_Peak_TCRgd

description: non broad neutralizer


title: 20631_Chronic_TCRgd

description: non broad neutralizer


title: 20355_Peak_TCRgd

description: non broad neutralizer


title: 20631_Pre-Infection_TCRgd

description: non broad neutralizer


title: 30507_Chronic_TCRgd

description: non broad neutralizer


title: 20225_Chronic_TCRgd

description: non broad neutralizer


title: 20225_SetPoint_TCRgd

description: non broad neutralizer


title: 20225_Peak_TCRgd

description: non broad neutralizer


title: 20225_Pre-Infection_TCRgd

description: non broad neutralizer


title: 40503_Chronic_TCRgd

description: Broad neutralizer


title: 20355_Pre-Infection_TCRgd

description: non broad neutralizer


title: 40503_SetPoint_TCRgd

description: Broad neutralizer


title: 40503_Pre-Peak_TCRgd

description: Broad neutralizer


title: 40503_Peak_TCRgd

description: Broad neutralizer


title: 40436_SetPoint_TCRgd

description: Broad neutralizer


title: 40436_Peak_TCRgd

description: Broad neutralizer


title: 40436_Chronic_TCRgd

description: Broad neutralizer


title: 40363_Chronic_TCRgd

description: Broad neutralizer


title: 40363_Peak_TCRgd

description: Broad neutralizer


title: 40363_Pre-Infection_TCRgd

description: Broad neutralizer


title: 40363_SetPoint_TCRgd

description: Broad neutralizer


title: 30486_Chronic_TCRgd

description: Broad neutralizer


title: 30486_Peak_TCRgd

description: Broad neutralizer


title: 30124_SetPoint_TCRgd

description: Broad neutralizer


title: 30196_Chronic_TCRgd

description: Broad neutralizer


title: 30196_Peak_TCRgd

description: Broad neutralizer


title: 30124_Chronic_TCRgd

description: Broad neutralizer


title: Bacteria, No Flow, rep2

city: Princeton

first: Ashwin

last: Ramachandran

state: NJ

address: Department of Molecular Biology, Department of Mechanical and Aerospace Engineering

institute: Princeton University

description: See column Ra3 for counts per million

data_processing:
RNA-Seq analysis was performed by SeqCenter (Pennsylvania). Quality control and adapter trimming was performed with bcl-convert. Read mapping was performed with HISAT2. Read quantification was performed using Subread’s featureCounts functionality. Raw, quantified read counts loaded into R were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm. Subsequent values were then converted to counts per million (CPM).
Assembly: Pseudomonas aeruginosa PAO1 (RefSeq: GCF_000006765.1)
Supplementary files format and content: tab-delimited text file contains counts per million (CPM) for all samples as a single matrix table

organism: Pseudomonas aeruginosa PAO1

source_name: Planktonic bacteria

growth_protocol: P. aeruginosa PAO1 was grown in LB media at 25C on a floor shaker. Prior to experiments, overnight-grown cultures were diluted 1:200 in fresh media and grown to mid-exponential phase (OD of 0.4-0.5).

extract_protocol:
Total RNA was extracted from fixed cells using the Qiagen RNeasy Mini kit with the following modifications to the protocol. Fixed cells were spun down at 6000 ×g for 5 min and resuspended in an 80 µL volume containing 30 mM Tris-HCL (pH 8.0), 2 mM EDTA, and 0.1% Triton-X 100, and 20 mg/mL lysozyme. Lysis was performed at 37C for 20 min, followed by Proteinase K digestion at 65C for 1 h. In addition, on-column DNase digestion was performed during RNA extraction as per the Qiagen RNeasy protocol.
Libraries were prepared by SeqCenter (Pennsylvania) using llumina Stranded Total RNA library preparation and RiboZero Plus rRNA depletion

treatment_protocol: Planktonic bacteria was flowed in a microfluidic channel. A branched channel section near the device outlet was used to inject 37% Formaldehyde at a flow rate equal to 1/8th of the main channel to fix planktonic bacteria in a 4% Formaldehyde (final concentration) media solution after they flowed for 55 min within the device and prior to exiting the channel. No-flow control cells were incubated in the channel for the same duration as cells that were subject to flow.

tag: strain

value: Planktonic bacteria

value: WT

value: No Flow


title: 30486_Pre-Infection_TCRgd

description: Broad neutralizer


title: 30196_SetPoint_TCRgd

description: Broad neutralizer


title: 30196_Pre-Peak_TCRgd

description: Broad neutralizer


title: 30486_SetPoint_TCRgd

description: Broad neutralizer


title: 30112_Chronic_TCRgd

description: Broad neutralizer


title: 30124_Pre-Infection_TCRgd

description: Broad neutralizer


title: 30112_SetPoint_TCRgd

description: Broad neutralizer


title: 30124_Peak_TCRgd

description: Broad neutralizer


title: Bacteria, No Flow, rep1

description: See column Ra1 for counts per million


title: 30112_Peak_TCRgd

description: Broad neutralizer


title: Bacteria, Flow, rep1

description: See column Rc2 for counts per million

value: Flow


title: Th2_Input

city: Cambridge

first: Ana

last: Ferreira

address: Francis Crick Avenue, Cambridge Biomedical Campus

country: United Kingdom

institute: MRC - Laboratory of Molecular Biology

library_source: genomic

data_processing:
Pooled libraries were sequenced using an Illumina NextSeq 2000 (or Hiseq4000) running a pair-end 50bp protocol
Sequenced reads were aligned to the mouse genome (GRCm38) using Bowtie2 (v2.3.5.1) with default parameters
reads that could not be uniquely mapped were removed from further analysis
Peak calling analysis was performed using Macs2 (v2.1.2)
Assembly: GRCm38
Supplementary files format and content: macs2 output files with peak calling data

molecule: genomic DNA

organism: Mus musculus

source_name: spleen

growth_protocol: ILC2s Purified from MLN of IL-25 and IL-2/anti–IL-2 complex treated mice  were maintained for 7 days inRPMI-1640, 10% FCS plus penicillin/streptomycin and 2-mercaptoethanol, supplemented with IL-7 (10 ng/ml), IL-2 (10 ng/ml) and IL-33 (10 ng/ml). For Th2 cells, splenic naïve CD4+ T cells were sorted (CD4+ CD44lo CD62Lhi CD25–) and cultured on anti-CD3 coated, supplemented with anti-CD28 (2 mg/ml), IL-2 (10ng/ml), IL-4 (10ng/ml) and anti-IFN-g neutralising antibody (1 mg/ml) for 6 days (day 0-6).

extract_protocol:
Chromatin extracts from in vitro expanded ILC2 or Th2 (10 million) were prepared using truChIP Chromatin Shearing kit (Covaris), with 5 min of crosslink and optimized shearing conditions (peak power 75, duty factor 10.0, cycles/burst 200, duration 300 sec) to obtain fragments of ~500bp
Chromatin-antibody-bead complexes were then subjected to tagmentation, followed by DNA elution, and libraries amplification and purification, as described previously (Schmidl et al., 2015)

value: spleen

tag: chip antibody


title: Th2_anti-NFAT1_2


title: 20509_SetPoint_TCRgd

description: Broad neutralizer


title: Bacteria, Flow, rep2

description: See column Rc3 for counts per million


title: Nova-ST_MouseBrain_Rep6

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

description: Fresh frozen Nova-ST spatial transcriptome sequencing

data_processing:
Library strategy: Spatial Transcriptomics (Nova-ST)
Raw sequencing data was processed using bcl2fastq to generate fastq files
Nova-ST chip tiles were identified using a subset of data, and a witelist of barcodes was created from these tiles. Data was mapped and quantified against the mm10 using this whitelist and STARsolo
X/Y coordinates for barcodes with identified counts were normalised into a chip-based space and used alongside the expression data to create GEM files.
Assembly: mm10
Supplementary files format and content: tiff: H&E stained images
Supplementary files format and content: gem.gz: GEM formatted expression matrix including normalized X/Y coordinates of each cluster
Supplementary files format and content: BC_Coords.pickle: Python pickled dictionaries containing barcodes, tile information and X/Y coordinates used for whitelist creation.

molecule: polyA RNA

source_name: Brain

growth_protocol: Six to eight weeks old mice (C57BL/6J) used in the study were kept on a 14 h light, 10 h dark–light cycle from 7:00 to 21:00

extract_protocol:
Brains were dissected and immediately snap-frozen in isopentane for 10 min. Afterwards, brains were embedded in Tissue-Tek OCT cryo embedding compound, 10μm sections were cut using a cryostat and placed on the Nova-ST chips
Pepsin was used to permeabilise the sectioned tissue and Maxima Rtase for the reverse transcription. Samples were treated with endonuclease and then tissue was cleared with Proteinase K. Klenow Fragment was used for second strand synthesis and the resulting cDNA was amplified and prepared for sequencing by addition of indexes and Illumina flow cell attachment sites.

value: Brain


title: 20509_Pre-Infection_TCRgd

description: Broad neutralizer


title: Th2_anti-NFAT1_1


title: Th2_anti-Mef2d_2


title: 10220_Chronic_TCRgd

description: Broad neutralizer


title: 10220_SetPoint_TCRgd

description: Broad neutralizer


title: ILC2_Mef2d_KO_2

data_processing:
Pooled libraries were sequenced using an Illumina NextSeq 2000 running a paired-end 50bp protocol
Sequenced reads were aligned to the mouse genome (GRCm38) using Bowtie2 (v2.3.5.1) with default parameters
reads that could not be uniquely mapped were removed from further analysis
Assembly: GRCm38
Supplementary files format and content: dedup.bed

source_name: mLN

growth_protocol: ILC2s Purified from MLN of IL-25 and IL-2/anti–IL-2 complex treated mice  were maintained for 7 days inRPMI-1640, 10% FCS plus penicillin/streptomycin and 2-mercaptoethanol, supplemented with IL-7 (10 ng/ml), IL-2 (10 ng/ml)  and IL-33 (10 ng/ml)

extract_protocol:
FACS purified cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) to obtain nuclei extract
Nuclei were immediately used in the transposase reaction (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease- free water) for 30 min at 37 °C, followed by sample purification (Qiagen MinElute kit). Then, we amplified library fragments using Kappa HiFi HotStart Ready mix and 1.25 M of custom Nextera PCR primers. Libraries were purified using dual (0.5x-0.7x) SPRI Ampure XP beads (Beckman Coulter), pooled and were subjected to high-throughput sequencing

value: mLN


title: 10220_Pre-Infection_TCRgd

description: Broad neutralizer


title: aceE Rep 1

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

data_processing:
Short reads were quality-checked with FastQC and processed with fastp v0.23 (--length_required 50) to discard low-quality reads and to remove possible 3' adapters.
Processed reads were aligned against the P. putida KT2440 genome (NCBI reference sequence NC_002947.3) using RNA STAR v2.7.11a (--alignIntronMin 1) and default parameters for paired-end reads.
Unique aligned reads were assigned to bacterial genes from annotation release 110 (https://pseudomonas.com) with featureCounts v2.0.6 (-M --primary -p --countReadPairs -s 2)
Normalized counts and differential expression of genes between replicated samples were obtained using the Bioconductor package DESeq2 v1.40.2, applying default parameters.
Assembly: GCF_000007565.2
Supplementary files format and content: Tab-delimited text file containing raw counts for all samples
Supplementary files format and content: Tab-delimited text file containing normalized counts (DESeq2) for all samples

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa KT2440 aceE mutant

growth_protocol: Cells were cultured in rich LB medium supplemented with glucose, and collected at mid exponential phase.

extract_protocol:
RNA was purified using the RNeasy kit (QIAGEN) and residual DNA was eliminated with the RNase-free DNase Set Kit (QIAGEN).
RNA-seq library construction and deep-sequencing were carried out by Sistemas Genomicos S.L. (Valencia, Spain). Ribosomal RNA was eliminated using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina). RNA was chemically fragmented and directional (strand-specific) libraries were constructed using the Illumina mRNA Sequencing Sample Preparation Kit (TruSeq). Sequencing was performed using the Illumina HiSeq 2500 system (Illumina).

treatment_protocol: When cultures reached to a turbidity of 0.6, they were transferred to ice-cold tubes and cells were collected by centrifugation at 4°C.

value: aceE mutant


title: Th2_anti-Mef2d_1


title: 10220_Peak_TCRgd

description: Broad neutralizer


title: ILC2_LTC4_anti-NFAT1_3

growth_protocol: ILC2s Purified from MLN of IL-25 and IL-2/anti–IL-2 complex treated mice  were maintained for 7 days inRPMI-1640, 10% FCS plus penicillin/streptomycin and 2-mercaptoethanol, supplemented with IL-7 (10 ng/ml), IL-2 (10 ng/ml) and IL-33 (10 ng/ml)

extract_protocol:
Chromatin extracts from in vitro expanded ILC2 (10 million) were prepared using truChIP Chromatin Shearing kit (Covaris), with 5 min of crosslink and optimized shearing conditions (peak power 75, duty factor 10.0, cycles/burst 200, duration 300 sec) to obtain fragments of ~500bp
Chromatin-antibody-bead complexes were then subjected to tagmentation, followed by DNA elution, and libraries amplification and purification, as described previously (Schmidl et al., 2015)


title: ILC2_Cont_2


title: ILC2_Cont_1


title: Wild Type Rep 3

source_name: Pseudomonas aeruginosa KT2440 Wild Type

value: Wild Type


title: ILC2_Mef2d_KO_1


title: Nova-ST_MouseBrain_Rep7


title: aceE Rep 3


title: aceE Rep 2


title: Wild Type Rep 2


title: 30112_Pre-Infection_TCRgd

description: Broad neutralizer


title: ILC2_LTC4_anti-NFAT1_1


title: ILC2_anti-NFAT1_3


title: ILC2_LTC4_anti-NFAT1_2


title: ILC2_anti-NFAT1_2


title: Wild Type Rep 1


title: 20509_Peak_TCRgd

description: Broad neutralizer


title: ILC2_anti-NFAT1_1


title: KLF1 -/- mRNAseq rep 2

city: Brisbane

first: Stephen

last: Huang

state: Queensland

address: 37 Kent Street Woolloongabba

department: Mater Research institute

country: Australia

institute: University of Queensland

data_processing:
ChIP-Seq:
Base calling was performed with RTAv2
Bowtie2 was used to mapped PE sequencing reads with default parameters to the reference genome (mm9)
Duplicate reads were removed using Picard with the MarkDuplicates function
ChIP-seq peaks were called with MACS2 using uniquely mapped ChIP and input sequence alignments.
---------------
RNA-Seq
Base calling was performed with Torrent Suite v4.0.1
Tophat2 (v2.0.10) was used to perform spliced alignment to the reference transcriptome and genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz) using default options with the following additional parameters: -g 3, --library-type fr-firststrand.
Unaligned sequences were subsequently remapped using TMAP (v3.0.1) with the following options: -o 1, map4.
Successful alignments were merged back into the Tophat2 SAM file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was calculated and differential expression testing between replicate groups was performed with Cuffdiff2 using default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited genelist of FPKM output from CuffDiff2
Supplementary_files_format_and_content: excel file of peaks called from MACS2 for both wildtype and mutant ChIPseq

source_name: 14.5DPC fetal liver

extract_protocol:
Fetal Livers were homogenized and washed in PBS. Trizol reagent was used to extract total RNA.
Total RNA was treated with GLOBINclear kit for mouse (ThermoFisher Scientific; AM1981). mRNA was then purified from treated RNA using DynaBeads mRNA Direct purification Kit (Thermofisher Scientific, #61012).  Ion Total RNA-Seq Kit v2 (ThermoFisher Scientific;  #4479789) was used to prepare libraries for sequencing on the Ion Proton™ System.

tag: developmental stage

value: Fetal Liver


title: KLF1 -/- mRNAseq rep 3


title: ILC2_anti-GATA3_2


title: KLF1 -/- mRNAseq rep 1


title: KLF1 D45/- mRNAseq rep 3


title: ILC2_Input


title: KLF1 D45/- mRNAseq rep 1


title: KLF1 +/- mRNAseq rep 3


title: MC, IgE/Ag, rep4

city: Toulouse

first: Eric

last: Espinosa

state: France

address: IRSD  INSERM U1220 105 Avenue de Casselardit

department: IMMUNOLOGY

country: France

institute: INSERM

data_processing:
FastQ files were generated via llumina bcl2fastq2 (version 2.20.0.422). Cutadapt 4.0 (Galaxy Version 4.0+galaxy1) was used to trim the reads (minimum length=20 and quality cutoff=10). Reads were next mapped to the human (hg38) Galaxy buit-in reference genome with RNA STAR (Galaxy Version 2.7.10b+galaxy3 and default parameters) using Ensembl GRCh38.p13 (v106) annotation file
Mapped reads were counted using the featureCounts function of Rsubread (v2.12.3) package
Assembly: GRCh38.p13 (v106)
Supplementary files format and content: tab delimited text file  includes normalized count matrix using Deseq2 for each sample

source_name: Mast cell

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from buffy coats (Etablissement Français du Sang). CD34+ precursors cells were isolated from PBMCs (EasySep™ Human CD34 Positive Selection Kit, STEMCELL Technologies). CD34+ cells were grown under serum-free conditions using StemSpanTM medium (STEMCELL Technologies) supplemented with recombinant human IL-6 (50 ng/mL; Peprotech), human IL-3 (10 ng/mL; Peprotech) and 3% supernatant of CHO transfectants secreting murine SCF (a gift from Dr. P. Dubreuil, Marseille, France, 3% correspond to ~50 ng/mL SCF) for one week. Cells were grown in IMDM Glutamax I, sodium pyruvate, 2-mercaptoethanol, 0.5% BSA, Insulin-transferrin selenium, Penicillin/Streptomycin (100 U/mL / 100 µg/mL) (all from Invitrogen), IL-6 (50 ng/mL) and 3% supernatant of CHO transfectants secreting murine SCF for 8 weeks and tested phenotypically (Tryptase+, CD117+, FceRI+) and functionally (b-hexosaminidase release in response to FceRI crosslinking) before use for experiments.

extract_protocol:
RNA was extracted using miRNeasy Mini Kit (Qiagen)
Libraries were prepared using 1 µg of high-quality total RNA. TruSeq stranded mRNA Library prep kit (Illumina) and Truseq RNA Unique Dual Indexed Adapters (Illumina) are used according to the manufacturer protocol. Size selection was performed using AMPure XP beads (Beckman Coulter). Library size and quality were confirmed on Fragment analyzer (Agilent). Libraries were quantified by qPCR using the KAPA quantification kit for Illumina platforms (KAPA Biosystems, Roche). Samples were pooled in equimolar fashion. The libraries were sequenced on a NextSeq 550 (Illumina) in pair end sequencing 2 × 75 bp with dual indexes (i7 and i5, 8bp).

treatment_protocol: 750000 MCs were either FACS-sorted after 24h of coculture with resting or anti-CD3/28 coated beads-activated effector/memory CD4+ T cells or stimulated for 4 hours with 10 ng/mL of IL-33 (Peprotech) or with 100 ng/mL of DNP-BSA (thermo-fischer scientific).

value: Mast cell

value: Primary mast cell line

value: 100 ng/mL DNP-BSA on IgE sensitized MC for 4hours


title: MC, anti-CD3/28 Beads stimulated CD4+ Teff cells, rep4

value: coculture with CD4+ effector/memory T cells plus anti-CD3/28 coatted beads(1 bead :10 T cell) for 24h


title: MC, IL-33, rep3

value: 10 ng/mL rhIL-33 for 4 hours


title: KLF1 +/- mRNAseq rep 1


title: ILC2_anti-Mef2d_2


title: KLF1 +/- mRNAseq rep 2


title: MC, Unstimulated, rep4


title: MC, resting CD4+ Teff cells, rep4

value: coculture with unstimulated CD4+ effector/memory T cells for 24h


title: MC, anti-CD3/28 Beads stimulated CD4+ Teff cells, rep3


title: MC, IgE/Ag, rep3


title: ILC2_anti-GATA3_1


title: MC, Unstimulated, rep3


title: KLF1 D45/- mRNAseq rep 2


title: MC, resting CD4+ Teff cells, rep3


title: MC, IL-33, rep2


title: ILC2_anti-Mef2d_3


title: MC, IL-33, rep4


title: MC, anti-CD3/28 Beads stimulated CD4+ Teff cells, rep2


title: MC, resting CD4+ Teff cells, rep2


title: MC, Unstimulated, rep2


title: MC, IL-33, rep1


title: MC, IgE/Ag, rep1


title: MC, anti-CD3/28 Beads stimulated CD4+ Teff cells, rep1


title: MC, Unstimulated, rep1


title: MC, IgE/Ag, rep2


title: Patient 48_SCC31

type: RNA

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

country: Italy

institute: Azienda USL- IRCCS di Reggio Emilia

hyb_protocol: RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol. Each reporter probe provided by the manufacturer was labeled with a propierty flourescent barcode system specific for each transcript.

scan_protocol: Scaning was conducted using the NanoString Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files. The data were normalized using 3 HK genes (CNOT4, FCF1, ZC3H14). Raw values are the number of copies of each molecular barcode representative of a specific transcript.
Mean count of negative controls plus two standard deviations was subtracted from each gene count to eliminate negative background. Then normalization on synthetic positive controls was conducted by multiplying the count of each gene for a correction factor. This factor was calculated for each sample as the ratio between the quadratic mean of positive controls counts and the mean of quadratic means in all samples. In order to performed CodeSet Content normalization on housekeeping genes, three reference genes were selected among the forty available in the panel based on the lowest coefficients of variation (CV= ratio between mean counts and standard deviations across all samples). Finally, CodeSet Content normalization was performed by multiplying genes counts for a further correction factor calculated on reference genes as described for positive technical controls. After completion of normalization processes, counts were log2 transformed.

label: Molecular barcode on reporter probe

source_name: Cutaneous Squamous Cell Carcinoma

label_protocol: RNA was not labeled, but it was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: Formalin-fixed, paraffin-embedded (FFPE) tumor diagnostic biopsies of Cutaneous Squamous Cell Carcinoma were reviewed by three different pathologists. For RNA purification, five 5um FFPE slides were cut for each tumor. Total RNA was extracted by Maxwell® RSC RNA FFPE kit (Promega). RNA quantity and quality were assessed by NanoDrop2000 (Thermo Fisher Scientific). For samples that reached the quality standards (A260/A280 ≥ 1.7 and A260/A230 ≥ 1.8), we evaluated the expression profile of 773 genes by NanoString using the nCounter PanCancer Progression Panel (NanoString Technologies).

treatment_protocol: Diagnostic biopsies from Cutaneous Squamous Cell Carcinoma patients

tag: gender

value: M

tag: age

tag: metastasis

value: yes

tag: sample group

value: SCC


title: MC, resting CD4+ Teff cells, rep1


title: Patient 46_SCC29


title: Patient 45_SCC28


title: Patient 44_SCC25

value: F


title: Patient 47_SCC30


title: Patient 43_SCC15


title: Patient 42_CT31

value: no

value: CT


title: Patient 41_CT30


title: Patient 40_CT29


title: Patient 39_CT28


title: BIDC091

type: genomic

city: Calgary

middle: Isabel

last: Hernandez Cordero

state: Alberta

address: 303 13th Avenue SW, unit 1004

country: Canada

institute: Heart Lung Innovation Centre

description: Bronchoalveolar lavage sample

hyb_protocol: bisulphite converted DNA and DNA methylation by  Illumina MethylationEPIC BeadChipv1 microarray

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

data_processing: detection p cutoff 1xe-10, Sample cutoff 0.05, Probe cutoff 0.05, background correction, BMIQ normalization and batch correction

label: Cy5 and Cy3

source_name: Bronchoalveolar lavage cells

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from uffy coat and purify using Qiagen DNeasy Kit according to standard instructions

tag: Sex


title: Patient 38_CT25


title: BIDC089

description: Bronchoalveolar lavage sample


title: BIDC069

description: Bronchoalveolar lavage sample


title: BIDC067

description: Bronchoalveolar lavage sample


title: BIDC079

description: Bronchoalveolar lavage sample


title: BIDC078

description: Bronchoalveolar lavage sample


title: BIDC084

description: Bronchoalveolar lavage sample


title: BIDC049

description: Bronchoalveolar lavage sample


title: BIDC053

description: Bronchoalveolar lavage sample


title: Patient 36_SCC8


title: BIDC082

description: Bronchoalveolar lavage sample


title: BIDC070

description: Bronchoalveolar lavage sample


title: BIDC072

description: Bronchoalveolar lavage sample


title: BIDC068

description: Bronchoalveolar lavage sample


title: BIDC083

description: Bronchoalveolar lavage sample


title: Patient 35_SCC7


title: BIDC062

description: Bronchoalveolar lavage sample


title: BIDC063

description: Bronchoalveolar lavage sample


title: Patient 34_SCC6


title: BIDC059

description: Bronchoalveolar lavage sample


title: BIDC060

description: Bronchoalveolar lavage sample


title: Patient 33_SCC22


title: BEC0176

description: Bronchoalveolar lavage sample


title: BIDC050

description: Bronchoalveolar lavage sample


title: Patient 37_CT15


title: Patient 32_SCC21


title: BIDC046

description: Bronchoalveolar lavage sample


title: BIDC061

description: Bronchoalveolar lavage sample


title: Patient 31_CT9


title: BIDC065

description: Bronchoalveolar lavage sample


title: BEC0178

description: Bronchoalveolar lavage sample


title: BIDC044

description: Bronchoalveolar lavage sample


title: Patient 30_CT8


title: BIDC051

description: Bronchoalveolar lavage sample


title: Patient 27_CT22


title: BEC0182

description: Bronchoalveolar lavage sample


title: BIDC043

description: Bronchoalveolar lavage sample


title: A152_vCTB

city: Nutley

first: Benjamin

last: Tycko

state: New Jersey

address: 111 Ideation Way

department: Epigenetics

institute: Hackensack Meridian Health Center for Discovery and Innovation (HMH-CDI)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina infinium MethylationEPIC using standard Illumina protocol

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

data_processing:
Illumina's GenomeStudio methylation module (v1.9.0).
normalized Average Beta
non_normalized.txt = Unmethylated and methylated signal intensities

source_name: Genomic DNA from vCTB

label_protocol: Standard Illumina Infinium HD Protocol

extract_protocol: Placental tissue was dissected manually then dispersed by 3 rounds of incubation  (20 min, 37°C) with collagenase/trypsin/nuclease. After pelleting and red cell lysis, cells were  labeled with PE-anti-HLA-G (EVT) or PE-anti-Integrin ß4 (CTB, vCTB) antibodies. After reoval of  unbound antibody, labeled cell mixtures were incubated with an anti-PE antibody coupled to  immunomagnetic beads. After removal of unconjugated beads, EVT, CTB or vCTB were isolated  on an automated cell separator (AutoMACS) using a double-column, positive selection protocol.  Purified cell fractions were extracted in Qiazol and stored (RNA) or frozen directly (DNA) at -  80°C.

value: Placenta

value: Villous cytotrophoblast


title: Patient 29_CT7


title: A147_vCTB


title: Patient 25_CT19


title: Patient 24_SCC9


title: Patient 28_CT6


title: A158_vCTB


title: A139_vCTB


title: A158_CTB

source_name: Genomic DNA from CTB

value: Cytotrophoblast


title: Patient 23_SCC20


title: Patient 22_SCC19


title: A152_CTB


title: Patient 26_CT21


title: A139_CTB


title: Patient 21_SCC18


title: Patient 20_SCC16


title: A152_EVT

source_name: Genomic DNA from EVT

value: Extravillous trophoblast


title: A147_CTB


title: BEC0170

description: Bronchoalveolar lavage sample


title: Patient 19_SCC13


title: Patient 18_SCC12


title: Patient 17_CT20


title: A147_EVT


title: Patient 16_CT16


title: A139_EVT


title: BEC0174

description: Bronchoalveolar lavage sample


title: Patient 15_CT13


title: Patient 13_CT11


title: Patient 14_CT12


title: Patient 11_SCC3


title: Patient 10_SCC2


title: Patient 9_SCC1


title: Patient 8_SCC14


title: PITG_18417_ME

type: protein

city: Riverside

first: Howard

last: Judelson

state: CA

address: Genomics Building

department: Microbiology and Plant Pathology

institute: University of California-Riverside

hyb_protocol: We used either 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate or proteins purified from E.coli. After a 2-h incubation at 37°C, 12.5 ul of the mix was added to 137.5 ul of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Alexa 647-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 uM resolution.  Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low).  The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used.   Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing:
We provide several scores for each 8-mer in each experiment. Median - median kmer intensity; Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots.  Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.
Median intensity for the 8mer sequence

label: Alexa 647

molecule: protein

organism: Phytophthora infestans

source_name: DBD IVT protein ME design

label_protocol: We used Alexa 647-labeled anti-GST antibody to detect the GST-tagged DNA binding proteins.

extract_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned into pTH6838 or pTH7069, a modified T7-driven GST expression vector. For in vitro transcription_translation (IVT), we used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate to produce the proteins. For protein produced in E. coli, soluble proteins were purified using nickel resin and eluted in phosphate buffered saline (PBS) containing 10 to 20% glycerol. Proteins in inclusion bodies were fist solubilized in 2 M urea in PBS and refolding in 0.5 M arginine containing 10 to 20% glycerol.

tag: dbd

tag: platform

value: ME


title: A158_EVT


title: Patient 7_SCC10


title: BEC0156

description: Bronchoalveolar lavage sample


title: PITG_19851_ME


title: Patient 6_CT5


title: PITG_19851_HK

source_name: DBD IVT protein HK design

value: HK


title: PITG_17894_HK


title: PITG_17894_ME


title: BEC0145

description: Bronchoalveolar lavage sample


title: PITG_18417_HK


title: PITG_16038_ME


title: PITG_12840_ME


title: Patient 5_CT3


title: BEC0147

description: Bronchoalveolar lavage sample


title: BEC0140

description: Bronchoalveolar lavage sample


title: BEC0139

description: Bronchoalveolar lavage sample


title: BEC0135

description: Bronchoalveolar lavage sample


title: PITG_09816_ME

source_name: DBD Purified protein ME design


title: Patient 12_SCC5


title: PITG_08960_HK


title: Patient 3_CT1


title: Donor 3 H413-CM moMO

city: Madrid

first: Pedro

middle: Antonio

last: Reche

state: Comunidad de Madrid

address: Pza Ramon y Cajal, s/n

department: Immunology & O2, Faculty of Medicine

institute: Complutense University of Madrid

data_processing:
Data were processed according to BGI standard protocols.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes FPKM, TPM, read counts and normalized read counts for each sample.

source_name: Macrophages

growth_protocol: H413 cells (1x106 cells) were cultured in a 10 cm cell culture plates with RPMI 1640 medium supplemented with 10 % FBS, 2 mM glutamine, 100 U/ml penicillin (complete RPMI) for 2 days. Cells were grown at 37°C and 5% CO2. Next, the conditioned growth media (H413-CM) was harvested and filtered with a 0.1 μm filter (Merck KGaA).

extract_protocol:
Total RNA from monocytes was isolated using the PureLink™ RNA Mini Kit (Invitrogen) following manufacturer’s instructions. In brief, monocytes were lysed and nucleic acids were loaded into RNA binding columns. Columns were washed, and total RNA was eluted.
RNA samples were sent to BGI China. RNA libraries for RNAseq were constructed using DNBSEQ high-throughput platform. Sequencing libraries were constructed from ≥ 500 ng of total RNA.

treatment_protocol: Monocytes were cultured for 5 days in complete RPMI or in H413-CM cells at 37°C and 5% CO2.

tag: individual

value: Donor 3

value: Macrophages


title: Donor 2 NT moMO

value: Donor 2

value: RPMI


title: Donor 3 NT moMO


title: Donor 1 H413-CM moMO

value: Donor 1


title: BEC0138

description: Bronchoalveolar lavage sample


title: PITG_12840_HK


title: PITG_07057_HK

value: HLH


title: PITG_02733_ME


title: Patient 2_CT14

value: M


title: PITG_08960_ME


title: Donor 2 H413-CM moMO


title: PITG_02733_HK

source_name: DBD Purified protein HK design


title: Donor 1 NT moMO


title: human_placenta_rep104

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

data_processing:
Transcript abundances were estimated using the quantification program Kallisto v0.42.5 with a human GRCh38 reference (Ensembl version 93). Length scaled counts were condensed to Ensembl Gene IDs using the Bioconductor TXImport package.
Assembly: GRCh38
Supplementary files format and content: abundance.tsv as tab delimited file containing transcript abundances in transcripts per million.

source_name: placenta

extract_protocol:
Tissue was collected from non-pathological placentas from pregnant individuals who delivered at the Magee Womens Hospital in Pittsburgh, PA. Inclusion criteria included singleton pregnancies with signed informed consent and gestational age >37 weeks. Exclusion criteria included pregnancy complications including, fetal growth restriction (FGR), chromosomal abnormalities, preeclampsia, gestational diabetes, chorioamnionitis, antepartum hemorrhage, and a previous history of preterm birth. Placental biopsies (5 mm3) were sharply dissected within 30-40 minutes after delivery from a region of the placenta midway between the cord insertion and the placental margin between the chorionic and basal plates, and free of any macroscopic lesions, as we previously detailed (80). Tissue biopsies were placed in RNAlater for 48 h in 4°C, then stored in -80°C until processed for RNA sequencing. Directional RNA-seq was performed by the Genomics, Epigenomics and Sequencing Core (GES Core) at the University of Cincinnati. Approximately 50 mg tissue was homogenized in 0.8 ml Lysis/Binding Buffer from mirVana miRNA Isolation Kit (Thermo Fisher, Grand Island, NY) by using FastPrep-24 5G homogenizer (MP Biomedicals, Solon, OH). Total RNA extraction was conducted according to manufacturer’s protocol. RNA quality was examined on an Agilent 2100 Bioanalyzer (Santa Clara CA).
Ribosomal RNA was depleted using the Ribo-Zero Gold kit (Illumina, San Diego, CA) with 1 µg of total RNA as input for the SMARTer Apollo NGS library prep system (Takara, Mountain View, CA). The library for RNA-seq was prepared by using NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs, Ipswich, MA), and the sequencing was run on an Illumina HighSeq2000 with paired end reads, 101bp read length, and at 50 million read depth.

value: placenta

tag: ga weeks

tag: type

tag: delivery method

tag: birthweight

tag: fetal sex

value: Female

tag: maternal race_group

value: White


title: PITG_16038_HK


title: human_placenta_rep103

tag: tissue

tag: treatment


title: human_placenta_rep102

value: Other


title: BEC0114

description: Bronchoalveolar lavage sample

value: F


title: BEC0146

description: Bronchoalveolar lavage sample


title: human_placenta_rep101

value: Male


title: PITG_02328_ME


title: BEC0116

description: Bronchoalveolar lavage sample


title: PITG_09816_HK


title: Patient 4_CT2

value: no

value: CT


title: PITG_07057_ME

value: ME


title: human_placenta_rep100


title: PITG_02328_HK

value: HK


title: human_placenta_rep99


title: BEC0120

description: Bronchoalveolar lavage sample


title: human_placenta_rep98

value: Spontaneous


title: human_placenta_rep97

value: Vaginal

value: Black


title: human_placenta_rep96


title: human_placenta_rep95


title: PITG_00016_ME


title: PITG_00016_HK


title: PITG_00015_ME


title: human_placenta_rep93


title: human_placenta_rep94


title: PITG_01302_HK


title: human_placenta_rep91


title: human_placenta_rep92


title: human_placenta_rep90


title: human_placenta_rep89


title: PITG_18326_ME


title: PITG_00015_HK


title: human_placenta_rep88


title: PITG_22459_ME


title: human_placenta_rep86


title: PITG_22459_HK


title: human_placenta_rep85


title: PITG_17750_HK


title: PITG_18326_HK


title: Patient 1_CT10


title: human_placenta_rep84

value: Induced


title: PITG_17861_ME

value: BrkDBD


title: PITG_15175_ME


title: human_placenta_rep83


title: PITG_14515_ME


title: human_placenta_rep82


title: human_placenta_rep81


title: human_placenta_rep80


title: human_placenta_rep79


title: PITG_10815_ME


title: PITG_01302_ME


title: PITG_14515_HK


title: PITG_10815_HK


title: PITG_15175_HK


title: PITG_10769_ME


title: PITG_10769_HK


title: PITG_10768_HK


title: PITG_10557_ME

value: Unknown


title: PITG_10768_ME


title: PITG_10557_HK


title: PITG_17750_ME


title: PITG_10525_ME


title: human_placenta_rep75


title: human_placenta_rep73


title: human_placenta_rep76


title: PITG_10525_HK


title: human_placenta_rep69


title: PITG_17861_HK


title: human_placenta_rep71


title: human_placenta_rep70


title: human_placenta_rep74


title: human_placenta_rep72


title: human_placenta_rep67


title: human_placenta_rep68


title: human_placenta_rep77


title: human_placenta_rep66


title: human_placenta_rep65


title: human_placenta_rep87


title: PITG_08199_ME


title: PITG_08159_ME


title: human_placenta_rep64


title: PITG_08199_HK


title: PITG_07059_ME


title: PITG_06416_ME


title: PITG_07059_HK


title: PITG_06416_HK


title: PITG_05353_ME


title: human_placenta_rep62


title: human_placenta_rep63


title: PITG_05353_HK


title: human_placenta_rep61


title: human_placenta_rep60


title: human_placenta_rep58


title: human_placenta_rep59


title: PITG_04694_ME


title: PITG_04694_HK


title: human_placenta_rep57


title: human_placenta_rep56


title: PITG_08159_HK


title: human_placenta_rep55


title: human_placenta_rep54


title: PITG_03306_HK


title: PITG_01306_HK


title: PITG_03306_ME


title: PITG_01306_ME


title: PITG_01305_ME


title: human_placenta_rep53


title: human_placenta_rep51


title: human_placenta_rep52


title: human_placenta_rep50


title: PITG_01305_HK


title: human_placenta_rep47


title: human_placenta_rep48


title: PITG_03223_HK


title: PITG_03223_ME


title: human_placenta_rep49


title: human_placenta_rep46


title: PITG_19177_HK


title: human_placenta_rep45


title: PITG_19177_ME


title: human_placenta_rep43


title: human_placenta_rep44


title: PITG_16183_ME


title: PITG_16183_HK


title: PITG_15534_HK


title: PITG_12760_ME

value: HLH


title: PITG_12296_HK


title: human_placenta_rep42

value: placenta


title: PITG_12296_ME


title: PITG_15534_ME


title: PITG_09280_ME


title: PITG_12760_HK


title: PITG_09280_HK


title: human_placenta_rep40

value: Female


title: human_placenta_rep39

value: White


title: human_placenta_rep38


title: human_placenta_rep41


title: PITG_09279_HK


title: human_placenta_rep37


title: human_placenta_rep35


title: PITG_02480_ME


title: human_placenta_rep34


title: human_placenta_rep32


title: human_placenta_rep31


title: PITG_09279_ME


title: PITG_01135_HK

value: Homeobox


title: human_placenta_rep36


title: PITG_02480_HK


title: PITG_23160_ME


title: PITG_01080_ME


title: PITG_01135_ME


title: human_placenta_rep33


title: PITG_01080_HK


title: human_placenta_rep30


title: human_placenta_rep29


title: human_placenta_rep27


title: human_placenta_rep26


title: human_placenta_rep78


title: PITG_23160_HK


title: PITG_19220_HK


title: human_placenta_rep24


title: PITG_19220_ME


title: PITG_17673_ME


title: PITG_17673_HK


title: PITG_15721_HK


title: human_placenta_rep28


title: human_placenta_rep23


title: human_placenta_rep20


title: human_placenta_rep21


title: PITG_12584_HK


title: human_placenta_rep19


title: PITG_11783_ME


title: PITG_12584_ME


title: PITG_11783_HK


title: human_placenta_rep22


title: human_placenta_rep25


title: human_placenta_rep18


title: PITG_15721_ME


title: human_placenta_rep16


title: human_placenta_rep17


title: PITG_10442_ME

value: CSD


title: PITG_10442_HK


title: human_placenta_rep14

value: Male


title: PITG_04908_ME


title: PITG_04902_ME


title: PITG_04902_HK


title: human_placenta_rep12


title: human_placenta_rep11


title: human_placenta_rep10


title: human_placenta_rep9


title: human_placenta_rep8


title: PITG_01387_HK


title: human_placenta_rep7


title: PITG_06748_HK


title: PITG_01387_ME


title: PITG_01056_ME


title: PITG_06748_ME


title: PITG_00988_ME


title: human_placenta_rep13


title: human_placenta_rep6


title: human_placenta_rep5


title: human_placenta_rep3


title: PITG_08807_ME


title: human_placenta_rep15


title: human_placenta_rep2


title: PITG_04908_HK


title: PITG_08755_HK


title: human_placenta_rep4


title: human_placenta_rep1


title: MNs 1-C9ORF72(G4C2)nD35_rep2 [M4 C9ORF72-1 D35]

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

data_processing:
RNA-Seq data analysis was performed by Genosplice (www.genosplice.com)
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2018_1 were also provide

source_name: iPSC-derived motor neurons

growth_protocol: iPSC clones were dissociated within StemPro™ Accutase™ (ThermoFisher Scientific) and 2.105 cells/ml were suspended into a Neuronal Basic Medium (NBM) composed of 1:1 DMEM/F-12/Neurobasal™, N2 and B27™ supplement minus vitamin A, L-Ascorbic acid (0.01 μM), supplemented with SB431542 (20µM), LDN-193189 (0.2µM) and CHIR99021 (3µM). Embryonic Bodies (EBs) were formed within one day, and 2 days later the NBM was supplemented with retinoic acid (0.1µM) and SAG smoothened ligand (0.5µM NY) until day 14. CHIR99021 was removed at day 2, while SB431542 and LDN-193189 were removed at day 4.  BDNF, GDNF (10ng/mL) were added from day 7. At day 9, DAPT (10µM) was added and EBs were dissociated the next day with Trypsin-EDTA (pMNs=D10). Dissociated single cells were seeded onto coverslips coated either with PEI (solution (2mg/ml) or Polyornithine (100μg/ml), and Laminin (20µg/ml). Between day 14 and day 17, cells were incubated in NBM with DAPT, BDNF and GNDF. From day 18 (yMNs = D17) and until the end of each experiment (mMNs = D35), DAPT was removed from NBM, while CNTF and IGF1 were added (10ng/mL).

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro kit (Qiagen).RNA concentrations were determined with High Sensitivity RNA ScreenTape on TapeStation (Agilent).
Kapa mRNA prep from ROCHE

tag: control or als

value: ALS

tag: time in days (d)

tag: iPSc clone name


title: MNs TARDBP1-1G348C D35_rep1 [M1 TARDBP1 D35]


title: MNs SOD2-1N139D D35_rep1 [M2 SOD1-2 D35]


title: MNs SOD2-1N139D D35_rep2 [M6 SOD1-2 D35]


title: PITG_01056_HK


title: PITG_08807_HK


title: MNs SOD1-1N139D D35_rep2 [M6 SOD1-1 D35]


title: PITG_13587_ME


title: PITG_13587_HK


title: PITG_05989_HK


title: PITG_05990_HK


title: PITG_01388_ME


title: PITG_00988_HK


title: PITG_05989_ME


title: MNs SOD1-1N139D D35_rep1 [M5 SOD1-1 D35]


title: PITG_13133_ME


title: PITG_05990_ME


title: MNs 1-C9ORF72(G4C2)nD35_rep1 [M2 C9ORF72-1 D35]


title: MNs 2-C9ORF72(G4C2)nD35_rep2 [M3 C9ORF72-2 D35]


title: MNs TARDBP1-1G348C D35_rep2 [M2 TARDBP1 D35]


title: PITG_12841_ME


title: PITG_12841_HK


title: MNs 2-C9ORF72(G4C2)nD35_rep1 [M2 C9ORF72-2 D35]


title: PITG_00215_ME


title: PITG_06978_ME


title: PITG_06978_HK


title: PITG_08755_ME


title: PITG_01388_HK


title: PITG_13133_HK


title: MNs Ctrl69-2 D35_rep2 [M2 Ctrl69_2 D35]

value: control


title: MNs Ctrl69-2 D35_rep1 [M1 Ctrl69_2 D35]


title: MNs Ctrl69-1 D35_rep1 [M2 Ctrl69_1 D35]


title: MNs Ctrl33 D35_rep2 [M3 Ctrl33 D35]


title: MNs 2-C9ORF72(G4C2)nD17_rep2 [M3 C9ORF72-2 D17]


title: MNs Ctrl69-2 D35_rep3 [M4 Ctrl69_2 D35]


title: MNs 2-C9ORF72(G4C2)nD17_rep1 [M2 C9ORF72-2 D17]


title: PITG_05545_ME

value: ME


title: MNs 1-C9ORF72(G4C2)nD17_rep2 [M4 C9ORF72-1 D17]


title: PITG_08236_HK

value: HK


title: PITG_05545_HK


title: MNs 1-C9ORF72(G4C2)nD17_rep1 [M2 C9ORF72-1 D17]


title: PITG_04701_HK


title: MNs TARDBP1-1G348C D17_rep1 [M1 TARDBP1 D17]


title: MNs TARDBP1-1G348C D17_rep3 [M3 TARDBP1 D17]


title: PITG_00215_HK


title: MNs Ctrl33 D35_rep1 [M2 Ctrl33 D35]


title: MNs TARDBP1-1G348C D17_rep2 [M2 TARDBP1 D17]


title: MNs SOD2-1N139D D17_rep1 [M2 SOD1-2 D17]


title: MNs SOD2-1N139D D17_rep2 [M5 SOD1-2 D17]


title: kidney sample 127

city: Taipei

first: Szu-Yuan

last: Li

address: No. 201, Sec. 2, Shih-Pai Road

country: Taiwan

institute: Taipei Veterans General Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37 whole genome using STAR v2.7.2b
Reads number were calculated using RSEM v1.3.1.
Assembly: GRCh37
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: Kidney (tubular interstital tissue(remove glomeruli))

extract_protocol:
The human kidney tissue specimens were promptly submerged into RNALater (Sigma) and kept in -80℃ to preserve the integrity of RNA. Manual microdissection techniques were employed to carefully isolate the glomerular and tubular compartments from the tissue. Subsequently, the dissected tubular tissues underwent homogenization, and RNA was purified using the RNeasy Mini Kit (Qiagen) along with DNase treatment (Qiagen).
RNA libraries were prepared for sequencing using standard NEBNext protocols


title: kidney sample 126

value: Kidney (tubular interstital tissue(remove glomeruli))


title: kidney sample 125


title: MNs SOD1-1N139D D17_rep1 [M5 SOD1-1 D17]


title: kidney sample 124


title: MNs SOD1-ISO2 D17_rep1 [M6 SOD1-ISO2 D17]


title: MNs SOD1-1N139D D17_rep2 [M6 SOD1-1 D17]


title: PITG_04701_ME


title: kidney sample 123


title: kidney sample 122


title: PITG_11760_HK


title: PITG_11760_ME


title: PITG_08236_ME


title: PITG_20387_ME


title: PITG_19429_HK


title: PITG_20387_HK


title: kidney sample 120


title: kidney sample 119


title: kidney sample 121


title: MNs Ctrl69-1 D17_rep1 [M2 Ctrl69_1 D17]


title: kidney sample 117


title: MNs Ctrl69-2 D17_rep2 [M2 Ctrl69_2 D17]


title: MNs SOD1-ISO1 D17_rep1 [M6 SOD1-ISO1 D17]


title: kidney sample 115


title: MNs Ctrl69-2 D17_rep3 [M4 Ctrl69_2 D17]


title: MNs Ctrl69-2 D17_rep1 [M1 Ctrl69_2 D17]


title: MNs Ctrl69-1 D17_rep2 [M5 Ctrl69_1 D17]


title: MNs 1-C9ORF72(G4C2)nD10_rep1 [M2 C9ORF72-1 D10]


title: kidney sample 112


title: kidney sample 118


title: MNs Ctrl33 D17_rep2 [M3 Ctrl33 D17]


title: kidney sample 113


title: kidney sample 116


title: MNs TARDBP1-1G348C_rep4 [M9 TARDBP1 D10]


title: kidney sample 114


title: PITG_19429_ME


title: kidney sample 111


title: MNs TARDBP1-1G348C D10_rep3 [M8 TARDBP1 D10]


title: kidney sample 110


title: kidney sample 109


title: kidney sample 108


title: MNs SOD1-2N139D D10_rep2 [M5 SOD1-2 D10]


title: MNs TARDBP1-1G348C D10_rep1 [M2 TARDBP1 D10]


title: MNs Ctrl33 D17_rep1 [M2 Ctrl33 D17]


title: MNs 1-C9ORF72(G4C2)nD10_rep2 [M4 C9ORF72-1 D10]


title: kidney sample 106


title: MNs SOD1-1N139D D10_rep4 [M9 SOD1-1 D10]


title: kidney sample 107


title: MNs SOD1-1N139D D10_rep2 [M6 SOD1-1 D10]


title: MNs TARDBP1-ISO2 D10_rep2 [M9 TARDBP1-ISO2 D10]


title: kidney sample 102


title: kidney sample 100


title: kidney sample 105


title: kidney sample 104


title: MNs TARDBP1-ISO1 D10_rep1 [M8 TARDBP1-ISO1 D10]


title: MNs TARDBP1-ISO1 D10_rep2 [M9 TARDBP1-ISO1 D10]


title: MNs SOD1-1N139D D10_rep1 [M5 SOD1-1 D10]


title: MNs TARDBP1-ISO2 D10_rep1 [M8 TARDBP1-ISO2 D10]


title: kidney sample 103


title: MNs SOD1-ISO2 D10_rep1 [M6 SOD1-ISO2 D10]


title: MNs SOD1-1N139D D10_rep3 [M7 SOD1-1 D10]


title: kidney sample 99


title: kidney sample 97


title: kidney sample 101


title: MNs TARDBP1-1G348C D10_rep2 [M3 TARDBP1 D10]


title: kidney sample 98


title: MNs SOD1-ISO1 D10_rep3 [M9 SOD1-ISO1 D10]


title: kidney sample 96


title: MNs SOD1-ISO1 D10_rep2 [M7 SOD1-ISO1 D10]


title: MNs SOD1-ISO1 D10_rep1 [M6 SOD1-ISO1 D10]


title: MNs SOD1-2N139D D10_rep1 [M2 SOD1-2 D10]


title: MNs Ctrl69-2 D10_rep2 [M4 Ctrl69-2 D10]


title: kidney sample 93


title: kidney sample 94


title: MNs Ctrl69-2 D10_rep1 [M2 Ctrl69-2 D10]


title: kidney sample 92


title: MNs Ctrl69-1 D10_rep2 [M5 Ctrl69-1 D10]


title: MNs Ctrl69-1 D10_rep1 [M2 Ctrl69-1 D10]


title: kidney sample 90


title: kidney sample 91


title: MNs Ctrl40 D10_rep2 [M8 Ctrl40 D10]


title: MNs Ctrl40 D10_rep1 [M7 Ctrl40 D10]


title: kidney sample 88


title: MNs Ctrl33 D10_rep2 [M3 Ctrl33 D10]


title: kidney sample 89


title: kidney sample 87


title: kidney sample 85


title: MNs Ctrl33 D10_rep1 [M2 Ctrl33 D10]


title: HEKa cells, AREG_MPS-3 [DK22001_67_15]

city: shimogyo-ku

first: Ryo

last: Hirase

address: chudoji, awatacho

country: Japan

institute: Maruho

data_processing:
Low quality reads and adapters were removed using fastp (v0.12.4). Reads were aligned to the RefSeq GRCh38.p14 human genome assembly using STAR (v2.7.6a). Expression levels in transcripts per million (TPM) for each sample were calculated with RSEM (v1.3.3).
Assembly: GRCh38.p14
Supplementary files format and content: tsv file including raw counts for each sample
Supplementary files format and content: tsv file including TPM counts for each sample

source_name: HEKa

growth_protocol: HEKa cells were maintained in Humedia KG2 in humidified atmosphere with 5% CO2 at 37C, 3D cultured keratinocytes were maintained in attached growth media in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Maxwell® RSC simplyRNA Cells Kit (Promega).
RNA libraries for RNA-seq were prepared using mRNA magnetic isolation module (New England Biolabs), followed by NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol:
HEKa were incubated with or without MPS, recombinant human amphiregulin, human amphiregulin antibody in HuMedia-KB2 for 24 hrs at 37 C.
3D-cultured keratinocytes were incubated with or without MPS in attached growth media for 24 hrs in humidified atmosphere with 5% CO2 at 37C.

tag: cell line

value: HEKa

tag: cell type

value: Primary keratinocytes

tag: genotype

value: WT

value: MPS 30 µg/mL, AREG 100 ng/mL

tag: time


title: kidney sample 84


title: kidney sample 86


title: HEKa cells, AREG_MPS-1 [DK22001_67_13]


title: kidney sample 82


title: kidney sample 83


title: HEKa cells, AREG_MPS-2 [DK22001_67_14]


title: kidney sample 95


title: kidney sample 81


title: HEKa cells, MPS-2-3 [DK22001_67_12]

value: MPS 30 µg/mL


title: HEKa cells, MPS-2-1 [DK22001_67_10]


title: HEKa cells, MPS-2-2 [DK22001_67_11]


title: kidney sample 80


title: HEKa cells, AREG-3 [DK22001_67_09]

value: AREG 300 ng/mL


title: kidney sample 79


title: kidney sample 78


title: MNs Ctrl40 D10_rep3 [M9 Ctrl40 D10]


title: HEKa cells, AREG-2 [DK22001_67_08]


title: kidney sample 77


title: HEKa cells, AREG-1 [DK22001_67_07]


title: kidney sample 76


title: kidney sample 75


title: HEKa cells, AREG antibody-2 [DK22001_67_05]

value: AREG antibody 50 µg/mL


title: HEKa cells, AREG antibody-1 [DK22001_67_04]


title: kidney sample 73


title: HEKa cells, Control-2_3 [DK22001_67_03]

value: untreated control


title: kidney sample 72


title: kidney sample 74


title: HEKa cells, Control-2_2 [DK22001_67_02]


title: HEKa cells, Control-2_1 [DK22001_67_01]


title: kidney sample 71


title: kidney sample 70


title: 3D-cultured keratinocytes, MPS_100-3 [DK21001_58_24]

source_name: 3D cultured keratinocytes

value: 3D cultured keratinocytes

value: MPS 100 µg/mL


title: kidney sample 69


title: kidney sample 68


title: kidney sample 67


title: 3D-cultured keratinocytes, MPS_100-2 [DK21001_58_23]


title: kidney sample 65


title: kidney sample 66


title: 3D-cultured keratinocytes, MPS_10-1 [DK21001_58_19]

value: MPS 10 µg/mL


title: kidney sample 64


title: 3D-cultured keratinocytes, MPS_1-3 [DK21001_58_18]

value: MPS 1 µg/mL


title: 3D-cultured keratinocytes, MPS_100-1 [DK21001_58_22]


title: HEKa cells, AREG antibody-3 [DK22001_67_06]


title: 3D-cultured keratinocytes, MPS_10-2 [DK21001_58_20]


title: 3D-cultured keratinocytes, MPS_1-2 [DK21001_58_17]


title: kidney sample 63


title: 3D-cultured keratinocytes, MPS_1-1 [DK21001_58_16]


title: 3D-cultured keratinocytes, Control-3 [DK21001_58_15]


title: kidney sample 60


title: kidney sample 62


title: kidney sample 59


title: HEKa cells, MPS-3 [DK21001_58_06]


title: kidney sample 57


title: 3D-cultured keratinocytes, Control-2 [DK21001_58_14]


title: kidney sample 58


title: HEKa cells, MPS-2 [DK21001_58_05]


title: 3D-cultured keratinocytes, MPS_10-3 [DK21001_58_21]


title: kidney sample 55


title: kidney sample 54


title: HEKa cells, MPS-1 [DK21001_58_04]


title: HEKa cells, Control-3 [DK21001_58_03]


title: HEKa cells, Control-2 [DK21001_58_02]


title: kidney sample 53


title: HEKa cells, Control-1 [DK21001_58_01]


title: MCF7-ER cells, 10 nM Estradiol, 24hrs, biorep 4

city: Edmonton

first: Judith

last: Hugh

address: 87 ave and 114 st

department: Laboratory Medicine and Pathology

institute: University of Alberta

description:
NextSeq 500/550 High Output Kit 2x75 cycles
ER10_24hr_4

data_processing:
Paired-end reads were aligned to hg38 using RNA STAR and counted with FeatureCounts
Assembly: hg38
Supplementary files format and content: FeatureCounts, txt file

source_name: cell line

growth_protocol: MCF7_EM and MCF7-ER cells were maintained in selection media containing 10% Tet-system approved FBS, 10 µg/ml bovine insulin, 500 µg/ml G418 and 1µg/ml puromycin

extract_protocol:
Total RNA was extracted from MCF7-EM and MCF7-ER cells treated with vehicle control or 10 nM E2 for 24 hours using the NucleoSpin RNA extraction kit, which included a DNase digestion step to remove potential contaminating DNA (Macherey-Negel).
cDNA libraries were made from 1 µg total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420) and indexed for sequencing using NEBNext Multiplex Oligos for Illumina.

treatment_protocol: For all experiments the cells were first rinsed with PBS then adapted in phenol red-free MEM containing 10% charcoal-stripped FBS, 10 µg/ml bovine insulin, 500 µg/ml G418 and 1µg/ml puromycin for three days. On day four the adaptation media was removed, and the MCF7-EM and MCF7-ER cells were induced with 0.5 µg/ml doxycycline for 24 hours. After this incubation, the doxycycline media was removed, and the cells were treated with adaptation media containing either 10 nM E2 dissolved in 100% ethanol or vehicle control (100% ethanol) for the times indicated.

value: cell line

value: Mammary epithelial cell

value: ESR1 transfected

value: 10 nM Estradiol 24hrs


title: kidney sample 52

value: Kidney (tubular interstital tissue(remove glomeruli))


title: kidney sample 51


title: MCF7-ER cells, 10 nM Estradiol, 24hrs, biorep 3

description:
NextSeq 500/550 High Output Kit 2x75 cycles
ER10_24hr_3


title: kidney sample 50


title: kidney sample 48


title: MCF7-ER cells, 10 nM Estradiol, 24hrs, biorep 2

description:
NextSeq 500/550 High Output Kit 2x75 cycles
ER10_24hr_2


title: kidney sample 61


title: kidney sample 49


title: MCF7-ER cells, ethanol control, 24hrs, biorep 4

description:
NextSeq 500/550 High Output Kit 2x75 cycles
ER0_24hr_4

value: Ethanol 24hrs


title: kidney sample 47


title: 3D-cultured keratinocytes, Control-1 [DK21001_58_13]

value: Primary keratinocytes


title: kidney sample 46


title: MCF7-ER cells, 10 nM Estradiol, 24hrs, biorep 1

description:
NextSeq 500/550 High Output Kit 2x75 cycles
ER10_24hr_1


title: kidney sample 56


title: MCF7-ER cells, ethanol control, 24hrs, biorep 3

description:
NextSeq 500/550 High Output Kit 2x75 cycles
ER0_24hr_3


title: kidney sample 45


title: MCF7-ER cells, ethanol control, 24hrs, biorep 1

description:
NextSeq 500/550 High Output Kit 2x75 cycles
ER0_24hr_1


title: MCF7-EM cells, 10 nM Estradiol, 24hrs, biorep 3

description:
NextSeq 500/550 High Output Kit 2x75 cycles
EM10_24hr_3

value: Mock transfected


title: kidney sample 43


title: kidney sample 44


title: kidney sample 42


title: MCF7-EM cells, 10 nM Estradiol, 24hrs, biorep 4

description:
NextSeq 500/550 High Output Kit 2x75 cycles
EM10_24hr_4


title: MCF7-ER cells, ethanol control, 24hrs, biorep 2

description:
NextSeq 500/550 High Output Kit 2x75 cycles
ER0_24hr_2


title: MCF7-EM cells, 10 nM Estradiol, 24hrs, biorep 2

description:
NextSeq 500/550 High Output Kit 2x75 cycles
EM10_24hr_2


title: kidney sample 40


title: MCF7-EM cells, ethanol control, 24hrs, biorep4

description:
NextSeq 500/550 High Output Kit 2x75 cycles
EM0_24hr_4


title: kidney sample 39


title: MCF7-EM cells, ethanol control, 24hrs, biorep3

description:
NextSeq 500/550 High Output Kit 2x75 cycles
EM0_24hr_3


title: kidney sample 38


title: kidney sample 41


title: MCF7-EM cells, ethanol control, 24hrs, biorep2

description:
NextSeq 500/550 High Output Kit 2x75 cycles
EM0_24hr_2


title: kidney sample 37


title: MCF7-EM cells, ethanol control, 24hrs, biorep1

description:
NextSeq 500/550 High Output Kit 2x75 cycles
EM0_24hr_1


title: kidney sample 36


title: kidney sample 35


title: K562_NuclearWashNorRNADepletion_rep3

first: Robert

last: Ietswaart

state: MA

address: 700 Main Street

institute: Cellforma, Inc

description: Nuclear Wash RNA, without rRNA depletion. Column 2C_NW_NRRD_S19 in processed data files

library_source: other

data_processing:
Read trimming with cutadapt v2.5 (see Churchman lab github for complete steps)
Alignment with STAR v2.7.0a (see Churchman lab github for complete steps)
Read count quantification using featureCounts v1.6.2 (see Churchman lab github for complete steps)
Assembly: hg38
Supplementary files format and content: tab-delimited text file with counts of reads mapped to gene
Supplementary files format and content: tab-delimited text file with counts of reads mapped to exons

molecule: other

extract_protocol:
RNA was extracted from subcellular fractions with Trizol LS according to the manufacturer's protocol. Synthetic yeast RNA spike-ins were added.
RNA libraries for RNA-seq were prepared using the SMARTer Stranded Total RNA HI Mammalian kit (Takara 634873) with 1 µg of RNA as input according to the manufacturer's protocol. For Nuclear Wash RNA without rRNA depletion (NW_NRRD) samples, the rRNA depletion step was omitted from the manufacturer's protocol.


title: K562_NuclearWashNorRNADepletion_rep1

description: Nuclear Wash RNA, without rRNA depletion. Column 1B_NW_NRRD_S17 in processed data files


title: K562_NuclearWashNorRNADepletion_rep2

description: Nuclear Wash RNA, without rRNA depletion. Column 2B_NW_NRRD_S18 in processed data files


title: kidney sample 34


title: kidney sample 33


title: kidney sample 32


title: K562_NuclearWash_rep4

description: Nuclear Wash RNA, rRNA depleted. Column 2C_NW_S15 in processed data files


title: kidney sample 31


title: K562_Cytoplasm_rep4

description: Column 2C_C_S14 in processed data files

molecule: cytoplasmic RNA


title: MCF7-EM cells, 10 nM Estradiol, 24hrs, biorep 1

description:
NextSeq 500/550 High Output Kit 2x75 cycles
EM10_24hr_1


title: kidney sample 30


title: kidney sample 28


title: kidney sample 29


title: K562_WholeCell_rep4

description: Column 2C_WC_S13 in processed data files


title: K562_NuclearWash_rep3

description: Nuclear Wash RNA, rRNA depleted. Column 2B_NW_S11 in processed data files


title: K562_Nucleus_rep3

description: Column 2B_N_S12 in processed data files

molecule: nuclear RNA


title: kidney sample 27


title: kidney sample 26


title: K562_Nucleus_rep2

description: Column 1B_N_S8 in processed data files


title: K562_NuclearWash_rep2

description: Nuclear Wash RNA, rRNA depleted. Column 1B_NW_S7 in processed data files


title: kidney sample 25


title: K562_WholeCell_rep3

description: Column 2B_WC_S9 in processed data files


title: kidney sample 24


title: kidney sample 23


title: kidney sample 22


title: K562_Nucleus_rep4

description: Column 2C_N_S16 in processed data files


title: K562_Cytoplasm_rep3

description: Column 2B_C_S10 in processed data files


title: kidney sample 21


title: K562_WholeCell_rep2

description: Column 1B_WC_S5 in processed data files


title: K562_Nucleus_rep1

description: Column 1A_N_S4 in processed data files


title: K562_NuclearWash_rep1

description: Nuclear Wash RNA, rRNA depleted. Column 1A_NW_S3 in processed data files


title: kidney sample 19


title: K562_Cytoplasm_rep1

description: Column 1A_C_S2 in processed data files


title: kidney sample 18


title: K562_WholeCell_rep1

description: Column 1A_WC_S1 in processed data files


title: kidney sample 16


title: kidney sample 15


title: SHI-1 5uM 3 niclosamide and 0.3uM disulfiram / 1uM copper 16 hours

city: London

first: Owen

last: Williams

address: 30 Guilford Street

department: Cancer section

institute: UCL GOS ICH

data_processing:
All tools in the analysis were invoked through the Galaxy Project for NGS analysis, as follows:
Fastq was demultiplexed and generated using Illumina bcl2fastq v2.19 before pre-processing (trimmomatic) to remove adapter read-through and poor quality sequences.
Pre-processed data were then aligned to the genome (UCSC hg38) with Bowtie 2 and deduplicated using Picard.
Reads-per-transcript were counted by FeatureCounts, before differential expresson analysis by SARTools, a DESeq2 wrapper.
Assembly: hg38
Supplementary files format and content: Reads-per-transcript (tab-delimited text file)

source_name: SHI-1 cells, MLL-AF6 positive

growth_protocol: SHI-1 cells (Acute Myeloid Leukemia cell line) (DSMZ, Braunschweig, Germany) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 100 units/ml penicillin and 100 ug/ml streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted with RNeasy Plus Mini Kit according to manufacturers instructions
Indexed RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA v2 protocols

treatment_protocol: SHI-1 cells were treated with DMSO, 0.3uM disulfiram / 1uM copper, 5uM niclosamide or combined drugs for 16 hours, from three independent experiments

value: SHI-1 cells, MLL-AF6 positive

value: Acute Myeloid Leukemia

value: 5uM niclosamide and 0.3uM disulfiram / 1uM copper 16 hours


title: SHI-1 5uM 1 niclosamide and 0.3uM disulfiram / 1uM copper 16 hours


title: SHI-1 5uM 2 niclosamide and 0.3uM disulfiram / 1uM copper 16 hours


title: SHI-1 5uM 3 niclosamide 16 hours

value: 5uM niclosamide 16 hours


title: SHI-1 5uM 2 niclosamide 16 hours


title: K562_Cytoplasm_rep2

description: Column 1B_C_S6 in processed data files


title: SHI-1 5uM 1 niclosamide 16 hours


title: kidney sample 14


title: kidney sample 13


title: SHI-1 0.3uM 3 disulfiram / 1uM copper 16 hours

value: 0.3uM disulfiram / 1uM copper 16 hours


title: K562_cytoplasm_60min_rep2

city: Boston

first: Brendan

middle: Michael

last: Smalec

address: 77 Avenue Louis Pasteur, Rm 356

department: Genetics

institute: Harvard Medical School

hyb_protocol: Unlabeled (unbound) RNA was hybridized with gene-specific probes at 67°C for at least 16 hours.

scan_protocol: Samples were loaded onto a nCounter Sprint Cartridge (NanoStrings) and analyzed on a nCounter SPRINT Profiler (NanoStrings)

data_processing: raw values are used as the final data set.

source_name: K562 cells

extract_protocol: RNA was extracted from subcellular fractions with Trizol LS according to the manufacturer's protocol. RNA was biotinylated with MTSEA biotin-XX and unlabeled RNA was quantified after depletion of 4sU-labeled RNA by binding to uMACS streptavidin beads.

tag: 4su pulse

tag: molecule subtype

value: Cytoplasm RNA


title: kidney sample 20


title: kidney sample 12


title: SHI-1 DMSO 1 16 hours

value: DMSO 16 hours


title: SHI-1 DMSO 2 16 hours


title: kidney sample 11


title: SHI-1 DMSO 3 16 hours


title: K562_cytoplasm_0min_rep2


title: kidney sample 17


title: A158_vCTB

city: Maplewood

first: Nick

last: Illsley

address: Richmond Ave

institute: Placental Research Group LLC

data_processing:
Quality control on raw FASTQ files was performed using FastQC v0.11.8 and reads were mapped to the UCSC hg38 genome build with STAR v2.7.4a using the following parameters: --runMode alignReads --outSAMtype BAM Unsorted --readFilesCommand zcat --genomeLoad LoadAndKeep --clip3pAdapterSeq AGATCGGAAGAGC --clip3pAdapterMMp 1 –-outFilterScoreMinOverLread 0.3 –-outFilterMatchNminOverLread 0.3. Feature counts were generated using SAMtools v1.10 in combination with HTSeq v0.11.2 with the iGenomes (Illumina) Homo sapiens reference file. Reads were subjected to adapter trimming using Trimmomatic v0.39.
Assembly: UCSC hg38
Supplementary files format and content: tab-delimited text file includes feature count values for each sample
Supplementary files format and content: Excel file includes feature count values for each sample

source_name: Placenta

extract_protocol:
Following trypsin/collagenase digestion, cells were purified by immunomagnetic separation using anti-HLA-G (EVT) or anti-integrin ß4 (CTB, vCTB).
RNA was extracted using the miRNeasy Micro kit (Qiagen) according to the manufacturer’s instructions. Genomic DNA was enzymatically digested by DNase I treatment and total RNA was captured by column purification.
Ribosome-depleted RNA was used to make cDNA libraries using NEBNext Ultra II RNA Library preparation kit for Illumina and NEBNext Multiplex Oligos for Illumina as per manufacturer’s protocol (New England Biolabs, Ipswich, MA)

value: Placenta

value: Villous cytotrophoblast


title: A154_vCTB


title: K562_nuclear_120min_rep2

value: Nuclear RNA


title: SHI-1 0.3uM 1 disulfiram / 1uM copper 16 hours


title: A147_vCTB


title: kidney sample 9


title: K562_cytoplasm_15min_rep2


title: kidney sample 10


title: A158_CTB

value: Cytotrophoblast


title: K562_nuclear_30min_rep2


title: K562_nuclear_60min_rep2


title: K562_cytoplasm_120min_rep2


title: SHI-1 0.3uM 2 disulfiram / 1uM copper 16 hours


title: A154_CTB


title: kidney sample 8


title: K562_cytoplasm_30min_rep2


title: A152_CTB


title: A151_CTB


title: kidney sample 7


title: A147_CTB


title: K562_nuclear_15min_rep2


title: kidney sample 6


title: A122_CTB


title: A139_CTB


title: A117_CTB


title: A116_CTB


title: kidney sample 4


title: K562_total_120min_rep2

value: Total RNA


title: K562_total_60min_rep2


title: A139_vCTB


title: A152_EVT

value: Extravillous trophoblast


title: K562_total_30min_rep2


title: A154_EVT


title: kidney sample 2

value: Kidney (tubular interstital tissue(remove glomeruli))


title: A147_EVT


title: A139_EVT


title: A116_EVT


title: kidney sample 1


title: K562_total_0min_rep2


title: A122_EVT


title: kidney sample 5


title: K562_cytoplasm_120min_rep1


title: K562_nuclear_0min_rep2


title: U87 A98 rep2

city: Glendale

first: Pamela

middle: A

last: Marshall

state: AZ

address: 4701 W Thunderbird Rd

institute: Arizona State University

data_processing:
Alignment was performed with STAR RNA-seq aligner
MultiQC was used to summarize the quality of the alignment files,
Assembly of aligned RNA-seq reads into transcripts representing gene loci was performed by StringTie
Default STAR parameters were used to align sample fastq data to the human reference genome from Ensembl4, using the build Ensembl_GRCh38_102. All alignment files generated by STAR, in BAM file format,
Assembly: human reference genome from Ensembl, using the build Ensembl_GRCh38_102.

growth_protocol: The cells were maintained in DMEM (HyClone, Cytiva Life Sciences) supplemented with 10% fetal bovine serum, 100 µg/mL streptomycin, 100 U/mL penicillin (Invitrogen, Carlsbad, CA) at 37 degrees Celsius, and 5% CO2 until they were ready to be plated, dosed with test compounds, and subsequently utilized for extraction of total cellular RNA.

extract_protocol:
The cells were subjected to a single 24-hour treatment of 10-7 M rexinoid, treated with RNAlater, and then subjected to RNA extraction and ribodepletion.
Total RNA was ribo depleted using KAPA’s RNA HyperPrep Kit with RiboErase (HMR) (Roche #KK8561), sheared to approximately 400 bp using heat and magnesium. Once RNA was sheared using random priming first strand synthesis was carried out then combined with second strand synthesis and A-tailing to convert RNA to cDNA. Illumina-compatible adapters with unique indexes (IDT #00989130v2) were then ligated onto each sample individually. The adapter ligated molecules were then cleaned using AMPure beads (Agencourt Bioscience/Beckman Coulter, A63883), and amplified with KAPA’s HIFI enzyme (KK2502). Each library was then analyzed for fragment size on Agilent’s Tapestation 4200 and quantified by qPCR (KAPA #KK4835) on Thermo Fisher Scientific’s Quantstudio 5 before multiplex pooling and sequencing on a 2x150 flow cell on Illumina’s NovaSeq6000 Platform at the University of Colorado Anschutz School of Medicine Genomics.

treatment_protocol: 1 X 10-7 rexinoid for 24 h or ethanol as negative control

value: glial cells

tag: genetic modification


title: Totalmix 1 in 75K rep4

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using bcl2fastq v2.20.0.422.
FASTQ files were aligned to the Human Surrogate+ Tox Panel (S1500+) v2.0 probes reference sequences using STAR 2.7.8a.
The qCount function from QuasR was used to extract feature counts specified in a GTF file (provided by BioSpyder) from the aligned reads.
Normalization was performed with DESeq2 R package v1.30.1
Log2 fold change shrinkage was performed using the ashr method.
Potential false positive DEGs were removed using filtering criteria defined in the Omics Data Analysis Frameworks for Regulatory application
Assembly: Genome_build: Biospyder S1500 Gene Set
Supplementary files format and content: Comma-delimited text file with genes by counts matrix

source_name: KGN

growth_protocol: KGN cells were maintained in DMEM/F12 medium supplemented with 10% charcoal-stripped fetal bovine serun (FBS) and 0.5% penicillin/streptomycin at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
No RNA extraction was done. Cells were directly lysed with 1X TempO-Seq lysis buffer and TempO-Seq libraries were constructed directly from cell lysates according to the TempO-Seq Assay User Guide (Version 2.1)
TempO-Seq (Templated Oligo assay with Sequencing readout)

treatment_protocol: Cells were exposed for 48 h to vehicle control (0.5% dimethyl sulfoxide; DMSO) or various concentrations of the mixture (ranging from 1 in 1 million to 1 in 30K dilutions).

value: KGN

value: Human ovarian granulosa cells

value: Totalmix 1 in 75K


title: U87 A98 rep3


title: A158_EVT


title: K562_cytoplasm_60min_rep1


title: Totalmix 1 in 75K rep3


title: U87 A80 rep3


title: kidney sample 3


title: Totalmix 1 in 75K rep2


title: Totalmix 1 in 75K rep1


title: U87 A98 rep1


title: K562_total_15min_rep2


title: A151_EVT


title: K562_cytoplasm_15min_rep1


title: A117_EVT


title: Totalmix 1 in 60K rep4

value: Totalmix 1 in 60K


title: K562_cytoplasm_0min_rep1


title: Totalmix 1 in 60K rep5


title: Totalmix 1 in 60K rep3


title: Totalmix 1 in 60K rep1


title: U87 A80 rep1


title: Totalmix 1 in 60K rep2


title: U87 A80 rep2


title: Totalmix 1 in 75K rep5


title: K562_nuclear_120min_rep1


title: Totalmix 1 in 30K rep5

value: Totalmix 1 in 30K


title: U87 A41 rep3


title: Totalmix 1 in 30K rep4


title: Totalmix 1 in 30K rep3


title: U87 A41 rep2


title: K562_cytoplasm_30min_rep1


title: Totalmix 1 in 30K rep1


title: Totalmix 1 in 30K rep2


title: U87 A41 rep1


title: K562_nuclear_30min_rep1


title: Totalmix 1 in 300K rep5

value: Totalmix 1 in 300K


title: Totalmix 1 in 300K rep4


title: U87 A34 rep3


title: Totalmix 1 in 300K rep2


title: K562_nuclear_15min_rep1


title: Totalmix 1 in 300K rep3


title: K562_total_120min_rep1


title: Totalmix 1 in 1M rep5

value: Totalmix 1 in 1M


title: Totalmix 1 in 300K rep1


title: Totalmix 1 in 1M rep3


title: Totalmix 1 in 1M rep4


title: U87 A34 rep1


title: Totalmix 1 in 1M rep2


title: K562_nuclear_60min_rep1


title: U87 A34 rep2


title: U87 Bexarotene rep2

value: Bexarotene


title: K562_total_30min_rep1


title: Totalmix 1 in 100K rep5

value: Totalmix 1 in 100K


title: Totalmix 1 in 1M rep1


title: K562_total_15min_rep1


title: Totalmix 1 in 100K rep4


title: U87 Bexarotene rep1


title: K562_total_0min_rep1


title: Bacteria, No Flow, rep3

city: Princeton

first: Ashwin

last: Ramachandran

address: Department of Molecular Biology, Department of Mechanical and Aerospace Engineering

institute: Princeton University

description: See column Ra2 for counts per million

data_processing:
RNA-Seq analysis was performed by SeqCenter (Pennsylvania). Quality control and adapter trimming was performed with bcl-convert. Read mapping was performed with HISAT2. Read quantification was performed using Subread’s featureCounts functionality. Raw, quantified read counts loaded into R were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm. Subsequent values were then converted to counts per million (CPM).
Assembly: Pseudomonas aeruginosa PAO1 (RefSeq: GCF_000006765.1)
Supplementary files format and content: tab-delimited text file contains counts per million (CPM) for all samples as a single matrix table

source_name: Planktonic bacteria

extract_protocol:
Total RNA was extracted from fixed cells using the Qiagen RNeasy Mini kit with the following modifications to the protocol. Fixed cells were spun down at 6000 ×g for 5 min and resuspended in an 80 µL volume containing 30 mM Tris-HCL (pH 8.0), 2 mM EDTA, and 0.1% Triton-X 100, and 20 mg/mL lysozyme. Lysis was performed at 37C for 20 min, followed by Proteinase K digestion at 65C for 1 h. In addition, on-column DNase digestion was performed during RNA extraction as per the Qiagen RNeasy protocol.
Libraries were prepared by SeqCenter (Pennsylvania) using llumina Stranded Total RNA library preparation and RiboZero Plus rRNA depletion

tag: strain

value: Planktonic bacteria

value: WT

value: No Flow


title: Totalmix 1 in 100K rep2


title: Totalmix 1 in 100K rep1


title: U87 Ethanol rep3

value: Ethanol


title: Pos Control HUMAN UNIVERSAL rep4

value: Pos Control HUMAN UNIVERSAL


title: Bacteria, Flow, rep3

description: See column Rc1 for counts per million

value: Flow


title: Totalmix 1 in 100K rep3


title: U87 Ethanol rep2


title: U87 Bexarotene rep3


title: K562_nuclear_0min_rep1

value: Nuclear RNA


title: Pos Control HUMAN BRAIN rep4

value: Pos Control HUMAN BRAIN


title: Pos Control HUMAN UNIVERSAL rep1

value: KGN


title: Pos Control HUMAN UNIVERSAL rep3

value: Human ovarian granulosa cells


title: Pos Control HUMAN UNIVERSAL rep2


title: Pos Control HUMAN BRAIN rep3


title: WI-38 TGFB1- MET 1

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

data_processing:
Demutliplexing and FASTQ extraction was performed using bcl2fastq v2.20.0.422.
Primary processing of FASTQ data including quality control, filtering, trimming,alignment of reads and counting of gene-sprecific genes was done using nf-core RNA-seq pipeline v3.7
Analysis of differentially expressed genes was performed using DESeq2.
Assembly: Assembly: HG38
Supplementary files format and content: Supplementary files format and content: Supplementary files format and content: RNA-seq read counts per gene (csv)

source_name: lung

growth_protocol: WI-38 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit combined with the Qiacube Connect.
according to the manufacturer’s instructions

value: lung

value: fibroblast

value: differentition myofibroblast/lipofibroblast (TGFb1 2ng/ml 4days; Metformin 5mM 4days)


title: Pos Control HUMAN BRAIN rep2


title: s73

city: Shanghai

first: yong

last: Jiang

address: No.168, Changhai Road, Yangpu District

department: Department of Burn Surgery

country: China

institute: Changhai Hospital, The People's Liberation Army Naval Medical University

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

source_name: circRNA expression data from controls patients' peripheral plasma

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.).

treatment_protocol: plasma from  patients' peripheral blood.

value: peripheral plasma

tag: age

tag: gender

value: Female

tag: condition

value: healthy control


title: Pos Control HUMAN BRAIN rep1


title: WI-38 TGFB1- MET 2


title: Neg Control LYIS BUFFER rep2

value: Neg Control LYIS BUFFER


title: Neg Control LYIS BUFFER rep4


title: Neg Control LYIS BUFFER rep1


title: WI-38 TGFB1- 1

value: differentition myofibroblast/lipofibroblast (TGFb1 2ng/ml 4days; vehicle 4 days)


title: 0.5% DMSO rep8

value: 0.5% DMSO


title: 0.5% DMSO rep10


title: U87 Ethanol rep1

value: glial cells


title: WI-38 TGFB1 2

value: WT

value: differentition myofibroblast/lipofibroblast (TGFb1 2ng/ml 4days)


title: WI-38 TGFB1 1


title: s67

value: Male


title: 0.5% DMSO rep6


title: WI-38 MET 3

value: differentition myofibroblast/lipofibroblast (Metformin 5mM 4days)


title: 0.5% DMSO rep5


title: 0.5% DMSO rep7


title: 0.5% DMSO rep9


title: WI-38 TGFB1- 2


title: s49


title: Neg Control LYIS BUFFER rep3


title: WI-38 MET 2


title: 0.5% DMSO rep4


title: s71


title: 0.5% DMSO rep2


title: 0.5% DMSO rep3


title: s41


title: s65

source_name: circRNA expression data from inhalation injury patients' peripheral plasma

value: inhalation injury


title: s77


title: 0.5% DMSO rep1

value: KGN


title: WI-38 MET 1


title: s57


title: s27


title: Lateral septum, control , 12 weeks, rep 3

first: Lixuan

last: Huang

address: 227 South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes FPKM values for each Sample
Supplementary files format and content: Tab-delimited text file includes counts for each Sample

source_name: Lateral septum

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
RNA libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Lateral septum

value: Control

value: 12 weeks


title: Coll_T5_Replicate2_scRNAseq

city: Utrecht

first: Peter

last: Haughton

address: Heidelberglaan 100

department: Pathology

country: Netherlands

institute: UMCU

library_source: transcriptomic single cell

data_processing:
Single cell RNA sequence data was de-multiplexed to FASTQ and aligned to the human reference genome (GRCh38 (hg38))
The single cell RNA-seq dataset was processed, explored and visualised using Cellenics® community instance (https://scp.biomage.net/) hosted by Biomage (https://biomage.net/). Briefly, cells with low quality reads, as determined by both high ERCC spike-in percentage and transcript number, and high mitochondrial reads (>5%) were removed, and mRNA expression data were normalized. To integrate data, “Harmony” was applied.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: HNSCC patient derived organoid

extract_protocol:
HNSCC PDO matrices were digested and single cells were isolated using tyrpsin. Cells were FACS sorted into 384-well plates (Muraro et al, 2016).
Preparation of single-cell libraries was performed using the CEL-Seq2 protocol (Muraro et al. 2016; Hashimshony et al., 2016)

value: HNSCC patient derived organoid

value: Collagen


title: s23

value: peripheral plasma


title: Lateral septum, control , 12 weeks, rep 2


title: BME_T5_Replicate2_scRNAseq

value: BME


title: WI-38 control 2

value: lung

value: fibroblast

value: differentition myofibroblast/lipofibroblast (vehicle 4days)


title: Coll_T5_Replicate1_scRNAseq


title: Lateral septum, control , 12 weeks, rep 1


title: BME_T5_Replicate1_scRNAseq


title: Coll_T4_Replicate2_scRNAseq


title: WI-38 control 1


title: Lateral septum, olanzapine trated, 12 weeks, rep 3

value: Olanzapine


title: Coll_T4_Replicate1_scRNAseq


title: BME_T4_Replicate2_scRNAseq


title: Lateral septum, olanzapine trated, 12 weeks, rep 2

value: WT


title: BME_T4_Replicate1_scRNAseq


title: GBM3, Patient3, Region4

city: Tianjin

first: xuejiao

last: lv

state: Tianjin

address: No.22 Qixiangtai Rd

institute: Tianjin Medical University

description:
GBM3-R4_D
Fresh frozen Spatial transcriptome sequencing

data_processing:
*library strategy: Spatial Transcriptomics
Raw sequencing data were processed using the 10 × Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to hg38 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding gene were quantified using Space Ranger's default settings
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_oimage.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png:low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots

source_name: WHO Grade IV GBM

extract_protocol:
For ST sequencing, 16 fresh tissue samples were extracted via surgery from 3 glioblastoma patients. The GBM tumor specimens were promptly frozen in liquid nitrogen and embedded in OCT compound. The frozen tissue specimens were then cryo-sectioned at a thickness of 10 µm and were mounted on pre-treated glass slides and incubated at 37°C for 1 minute , followed by fixation in methanol for 30 min at -20°C and washing in phosphate buffered saline. The current ST protocol was applied to all sections, resulting in both conventional hematoxylin and eosin (H&E) images that were amenable to annotation by pathologists, as well as gene expression profiles for each microarray spot.
Spatial Transcriptomome sequencing libraries were prepared with 10 × Genomics Visium Spatial Gene Expression Slides & Reagent Kit according to manufacturer's construction

value: WHO Grade IV GBM

tag: subject id


title: Dsg3.low_rep2

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Raw sequencing reads were trimmed using Cutadapt with TTGTGGAAAGGACGAAACACCG as an adapter input with compulsory 22 overlap and allowing 2 indels or mismatches to remove the bases upstream of the sgRNA coding sequence including the variable stagger.
Trimmed reads were aligned allowing for no mismatch with the human Brunello library using the count command of the MAGeCK software.
Resulting read count tables were analyzed using the test command of MAGeCK by comparing the two biological replicates of Dsg3low over Dsg3high or vice versa.
Hits were identified within the highest ranked genes that had a positive false discovery rate (FDR) < 0.2.
Assembly: Brunello library (Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol 34, 184-191, doi:10.1038/nbt.3437 (2016))
Supplementary files format and content: sgRNA_counts.tsv; tab seperated count table for each sgRNA and sample

source_name: human keratinocyte line (HaCaT)

growth_protocol: Brunello library transduced HaCat were selected for 3 days with puromycin dihydrochloride and afterwards were expanded for 2-3 weeks while maintaining a coverage of 600 cells/sgRNA. HaCaT were  cultured  in a  humidified  atmosphere  of  5%  CO2  and  37°C  in Dulbecco’s Modified Eagle Medium (DMEM) containing 1.8 mM Ca2+ and complemented with 10% fetal bovine serum, 50 U/ml penicillin, 50 μg/ml streptomycin and 4 mM L-glutamine.

extract_protocol:
Genomic DNA was isolated from 50 x 10^6 cells prior to sorting and from 1.5 – 3 x 10^6 cells after cell sorting using the Blood & Cell Culture DNA Kit with QIAGEN Genomic-tip 500/G or 20/G, respectively.
Genomic stretches containing the sgRNA sequence were amplified using forward primers introducing a stagger of 0-8 bases and reverse primers introducing an 8 base index. For pre-sort samples 8 and for sorted samples 2-3 parallel reactions with 10 ug gDNA each were performed using Ex Taq Polymerase.

value: human keratinocyte line (HaCaT)

tag: sotring strategy

tag: technical replicate

tag: cellular input


title: non.sorted_rep2_Dsg3


title: GBM3, Patient3, Region3

description:
GBM3-R3_C
Fresh frozen Spatial transcriptome sequencing

tag: tissue


title: Dsg3.high_rep2


title: Lateral septum, olanzapine trated, 12 weeks, rep 1

tag: treatment


title: Dsg3.low_rep1

tag: cell line


title: MOZ-TIF2 LSK, input, Rep B, ChIP

first: Mitzi

middle: I

last: Kuroda

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital/Harvard Medical School

data_processing:
Reads were aligned to both the mouse mm10 or Drosophila dm6 genome using bowtie 2.5.1. Duplicate reads were removed with samtools 1.14 using the markdup command
Aligned mouse bam files were normalized to Counts per Million (CPM) and input reads were subtracted from IP reads using deepTools bamCompare
To normalize to Drosophila spike-in DNA, we first reversed the CPM normalization of mouse reads by scaling to the original number of uniquely aligned mouse IP reads in each samples using deepTools bigwigCompare with the –scaleFactors setting. Next, a scaling factor for each sample was calculated based on Orlando et al, 2014 using the number of S2 reads that uniquely aligned to the Drosophila genome. Mouse reads were then normalized to their appropriate scaling factor using deepTools bigwigCompare with the –scaleFactors setting to generate bigwig files that were normalized to both the input and spike-in control
Processed input files were normalized to Counts mer Million (CPM)
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Lin- Sca1+ cKit+ (LSK)

growth_protocol: MOZ-TIF2 LSK cells were cultured at 37oC in IMDM media (Gibco) supplemented with 1% Pen/Strep, 20% Fetal Bovine Serum, 0.001% 2-Mercaptoethanol (BME), 6 ng/ml murine IL3, 10 ng/ml murine IL6, and 20 ng/ul murine SCF (Peprotech)

extract_protocol:
Cells were fixed in 1% formaldehyde with 5% S2 cells added as an exogenous spike-in control for 8 minutes at room temperature. Chromatin was sheared using a QSonica Probe Sonicator for 16 cycles with 15 seconds on and 45 seconds off with an amplitude of 40%.
Sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (NEB Cat #E7645S).

treatment_protocol: Cells were treated with DMSO for 1 hour

tag: cell type

value: Lin- Sca1+ cKit+ (LSK)

value: DMSO

tag: antibody

value: none; input


title: non.sorted_rep1


title: WI-38 control 3

tag: genotype


title: MOZ-TIF2 LSK, input, Rep A, ChIP


title: GBM3, Patient3, Region2

description:
GBM3-R2_B
Fresh frozen Spatial transcriptome sequencing


title: CDH-Poor_5

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University

data_processing:
CLC Genomics Workbench version 9.5.3 program
Sequence reads were trimmed and mapped to the miRbase 21 database allowing up to two base mismatches.
Assembly: miRbase 21
Supplementary files format and content: txt files of raw read counts of each samples

source_name: AF-EV

extract_protocol:
Amniotic fluid was collected during cesarean delivery, and we confirmed that no blood contamination or meconium stained amniotic fluid was observed. The samples were centrifuged at 3,000 rpm for 10 min at 4℃, and the supernatant was collected and stored. Then, small EVs were collected from approximately 1 mL of each amniotic fluid sample by the ultracentrifuge method. Briefly, the samples were centrifuged at 10,000 × g for 40 min at 4°C (Kubota 3520), and the supernatant was filtered using a 0.22 µm filter (Millex-GV 33 mm, Millipore). Subseqently. the supernatant was ultracentrifuged at 110,000 × g for 70 min at 4°C using an TLA55 rotor (Beckman Coulter Inc., USA). The pellet was washed with PBS, ultracentrifuged with the same conditions, and resuspended in PBS to extract small EVs. Finally, total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA). Then, PCR products were separated by electrophoresis (120 V, 60 min), and DNA fragments corresponding to 140–160 bp (the length of small non-coding RNA plus the adaptors) were recovered.

tag: Sex

value: male

value: AF-EV

tag: disease state

value: CDH with poor prognosis


title: GBM3, Patient3, Region1

description:
GBM3-R1_A
Fresh frozen Spatial transcriptome sequencing


title: CDH-Poor_4


title: GBM2, Patient2, Region4

description:
GBM2-R4_D
Fresh frozen Spatial transcriptome sequencing


title: CDH-Poor_3

value: female


title: MOZ-TIF2 LSK, H3K23ac, Rep B, ChIP


title: CDH-Poor_1


title: MOZ-TIF2 LSK, H3K23ac, Rep A, ChIP


title: CDH-Good_16

value: CDH with good prognosis


title: GBM2, Patient2, Region2

description:
GBM2-R2_B
Fresh frozen Spatial transcriptome sequencing


title: GBM2, Patient2, Region3

description:
GBM2-R3_C
Fresh frozen Spatial transcriptome sequencing


title: CDH-Good_15


title: MOZ-TIF2, mouse #2553, WM-1119 1 uM 1 hour, rep 3

description: MOZ-TIF2 2553 WM-1119 rep 3 mRNA

data_processing:
Reads were aligned to the mm10 genome using the STAR alignment tool
BigWig files were generated using Deeptools BamCoverage 3.5.0  and normalized using 1x genome coverage
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: MOZ-TIF2 and MLL-AF9 LSK cells were cultured at 37oC in IMDM media (Gibco) supplemented with 1% Pen/Strep, 20% Fetal Bovine Serum, 0.001% 2-Mercaptoethanol (BME), 6 ng/ml murine IL3, 10 ng/ml murine IL6, and 20 ng/ul murine SCF (Peprotech)

extract_protocol:
mRNA was extracted using the Monarch Total RNA Miniprep Kit (NEB). Ribosomal RNA was removed using PolyA enrichment (NEB)
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs E7760).

treatment_protocol: Cells were treated with DMSO or 1 uM WM-1119 for 1 hour

value: 1 uM WM-1119 1 hour


title: GBM2, Patient2, Region1

description:
GBM2-R1_A
Fresh frozen Spatial transcriptome sequencing


title: Dsg3.high_rep1


title: CDH-Good_14