title: OE33

value: OE33 (RRID:CVCL_0471)


title: JH_EsoAd1

status: Public on Jun 01 2022

type: SRA

city: Cambridge

first: David

last: Shorthouse

address: Hutchison/MRC Research Centre

country: United Kingdom

institute: MRC Cancer Unit

library_source: transcriptomic

data_processing:
Quality control of raw sequencing reads was performed using FastQC v0.11.7.
Reads were aligned to GRCh37 using STAR v2.6.1d.
Read counts were generated within R 3.6.1 summarizeOverlaps. Reads are pooled from 3 lanes
Genome_build: GRCh37
Supplementary_files_format_and_content: comma delimited file containing read counts for every gene in every sample
Supplementary_files_format_and_content: tab delimited file for each sample containing FPKM values for each gene

molecule: total RNA

organism: Homo sapiens

source_name: Gastric cardia adenocarcinoma

growth_protocol: Human oesophageal cancer cell lines; OACP4 C (RRID: CVCL_1843), OE19 (RRID: CVCL_1622), FLO-1 (RRID: CVCL_2045), SK-GT-4 (RRID: CVCL_2195), ESO-26 (RRID: CVCL_2035), OE33 (RRID: CVCL_0471), ESO-51 (RRID: CVCL_2036), OAC,5.1 C (RRID: CVCL_1842), JH-EsoAd1 (RRID: CVCL_8098) were  preserved in a cell culture incubator set at 5% CO2, 37°C and subcultured to 80% confluency according to supplier instructions.

extract_protocol:
Cell pellets were homogenised using QIAshredder columns (Qiagen, 79656) and total RNA was purified using the RNeasy Mini Kit (Qiagen, 74106) as per manufacturer instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Oesophageal Adenocarcinoma

tag: cell line

value: JH-EsoAd1 (RRID:CVCL_8098)


title: TNF 3

city: Beijing

first: Dan

last: Wu

address: No. 16, Nei Nanxiao Street, Dongzhimen, Dongcheng District

country: China

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

description: gene_fpkm_all_samples.txt;transcript_fpkm_all_samples.txt

data_processing:
Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.
Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers.
This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H.
These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters.
The products are then purified and enriched with PCR to create the final cDNA library.
Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).
Supplementary_files_format_and_content: Expression value of genes and transcripts

organism: Mus musculus

source_name: murine macrophage-like cell line

growth_protocol: The murine macrophage-like cell line (RAW264.7) was obtained from Cell Resource Center, IBMS, CAMS/PUMC (Beijing, China) and cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum and antibiotics (100 U/mL penicillin and 100 U/mL streptomycin) at 37 °C in a humidified atmosphere containing 95% O2 and 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated using an RNeasy mini kit (Qiagen, Germany) according to the manufacturer’s protocol. RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The quantity of total RNA in the samples was measured using a Qubit®3.0 Fluorometer (Thermo Fisher Scientific, USA) and NanoDrop One (Wilmington, DE, USA).
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). The sequencing work was undertaken by Beijing Zhimei Yinuo Biotechnology Co., Ltd (Beijing, China).

value: macrophage

tag: treatment

value: treated with TNF-α for 24 hours

tag: strain

value: BALB/c


title: MDMs_RNAseq_LDHD-rep1

city: Oxford

first: Ping

last: Zhang

address: Roosevelt Drive

department: Wellcome Centre for Human Genetics

institute: University of Oxford

description: MDMs_LDHD_rep123456_RPKM.bw; MDMs_LDHD_rep123456_RPKM_FR.bedgraph.gz.tbi;  MDMs_LDHD_rep123456_RPKM_FR.bedgraph.gz

data_processing:
RNA Sequencing reads were trimmed using Trim Galore (version 0.6.2), and mapped to human genome assembly hg38 using the HISAT2 (version 2.1.0).  The aligned Binary-sequence Alignment Format (BAM) files were used to determine the transcript counts through featureCounts (version 1.6.2) and GENCODE annotations (release 31). For gene differential expression analysis, the raw read counts were used as input into the R package DESeq2 (version 1.28.1) for pair-wise comparisons. For differential exon usage analysis, a featureCounts readable GTF file for exonic regions was generated through (https://github.com/vivekbhr/Subread_to_DEXSeq). The number of reads overlapping with each exonic region was counted by featureCounts with parameters -p -f -O -s 2 -t exonic_part. The exonic regions with read counts ≥ 10 in at least 30% of samples were used as input into the R package DEXSeq (version 1.32.0). The strandedness of the RNA-seq reads was extracted using Samtools, and the normalized bidirectional bedgrapgh files were generated using Bedtools and Bedops. The RPKM (Reads Per Kilobase per Million mapped reads) normalized bigwig files were generated using the bamCoverage function of deepTools (version 3.3.1).
Differential analyses for chromatin accessibility (ATAC) and histone modifications (H3K27ac and H3K4me3) were processed via an in-house pipeline. Briefly, sequencing reads were aligned to human genome assembly hg38 using bowtie2. The resulting BAM files were filtered to remove non-uniquely mapped reads, non-properly paired reads, reads mapped to mitochondrial chromosome, duplicate reads and reads with a mapping quality score less than 30 using Picard (version 2.0.1) and Samtools (version 1.9). Peaks were called using MACS2 (version 2.1.0) with the appropriate input dataset (paired non-ChIP data were used as controls for histone modifications). ATAC peaks were called using parameters --nomodel --shift -100 --extsize 200, and H3K27ac and H3K4me3 peaks were called using --bw 200. Peaks that overlay the ENCODE Blacklist and with p value > 1e-08 were filtered out. Peaks called in at least 30% of samples were defined as recurrent, and merged as a list of coordinates to count the number of overlapping reads in each condition using htseq-count (version 0.6.1). Finally, the reads were normalized using DESeq2 and then pair-wise comparisons were performed to determine the differential (fold change >2, FDR < 0.05) ATACs and histone modifications per condition. Potential batch effect or technical variable was examined by principal component analysis and was included as a covariate in DESeq2 design formula. The normalized bigwig files showing the average sequencing depth across samples with same treatment were generated using wiggletools and wigToBigWig.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig; bedgraph

source_name: MDMs

growth_protocol: Peripheral blood samples were obtained from healthy volunteers and PBMC isolated by Ficoll-Paque centrifugation. Monocytes (CD14+), T-cells (CD4+ and CD8+) and B-cells (CD19+) were separated from peripheral blood mononuclear cells (PBMCs) by positive selection with magnetic MicroBeads (Miltenyi Biotec). The isolated CD14 monocytes were differentiated into macrophages (MDMs) by culturing cells for 6 days in RPMI-1640 (Sigma) supplemented with 20% FBS (Sigma), L-glutamine (Sigma), sodium pyruvate (Sigma), non-essential amino acids (Sigma) and 20 ng/mL M-CSF (Gibco). Induced pluripotent stem cell (iPSC) line (SFC840-03-03) was reprogramed from dermal fibroblasts from a healthy donor recruited by the Oxford Parkinson’s Disease Centre, and cultured with feeder-free TeSR-E8 media (STEMCELL) on tissue culture plates coated with Matrigel (Corning). iPSCs were then transferred into AggreWell plate (STEMCELL) with E8 media (Gbico) supplemented with 50ng/mL BMP4 (ThermoFisher), 50 ng/mL VEGF (ThermoFisher) and 20 ng/mL SCF (Miltenyi) for four days to generate Embryoid Bodies (EBs) which were then used for generation of macrophage precursor in XVIVO-15 media (Lonza) supplemented with 25 ng/mL IL-3 (Gibco), GlutaMax, 2-mercaptoethanol and 100 ng/mL M-CSF.

extract_protocol: RNA-seq library was prepared using a standardised rRNA depletion and dUTP protocol (NEB) followed by sequencing on either a HiSeq4000 or NextSeq500 platform.(Illumina) at the Oxford Genomics Centre (Wellcome Centre for Human Genetics, Oxford, UK). Omni-ATAC-seq and ChIP for histone modifications were amplified for optimized cycles and were subjected to sequencing using a HiSeq4000 platform (Illumina).

treatment_protocol: Cells were treated with 20 ng/ml LPS for 6 hours (HD) or 2 ng/ml LPS for 16 hours and subsequent 20 ng/ml LPS challenge for 6 hours (LDHD).

value: monocyte-derived macrophage


title: OAC_5.1_C

value: OAC,5.1 C (RRID:CVCL_1842)


title: TNF 1


title: Con 1

value: untreated


title: Con 3


title: Control LCM Astrocytes_2

type: RNA

city: SHEFFIELD

first: Rachel

last: Waller

state: South Yorkshire

address: SITraN, 385A Glossop Road

department: Neuroscience

institute: The University of Sheffield

description: Gene expression data from control astrocytes

hyb_protocol: Approximately 5.5 μg amplified cDNA was fragmented, labelled and hybridised to Affymetrix Clariom S Array chips for 16 h at 45 °C in a rotating oven at 60 rpm

scan_protocol: Using the Fluidics Station 400, and Gene Chip Operating System, the hybridisation cocktail was removed, and a series of stringency washing steps followed to remove any unbound DNA, before each microarray was stained. Each microarray chip was scanned using the GeneChip 3000 scanner to determine the fluorescence intensity of hybridised transcripts.

data_processing: Transcription Analysis Console (TAC) was used for quality control and analysis of the data, the .CEL files were imported into TAC version 4.0.1 (Applied Biosystems, USA) and normalised to the median of all genes, prior to statistical analysis, to identify differentially expressed genes (DEGs). Transcripts were defined as being significantly differentially expressed if they showed a p-value of < 0.05 (unpaired t-test). DEGs were classified according to their biological function using the Database for Annotation Visualisation and Integrated Discovery (DAVID)  using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to identify specific pathways while Functional Annotation Clustering (FAC) was used to cluster together functionally similar genes. In the case of a significant result, the p value was adjusted for multiple testing using the Bonferroni correction method and considered significant if p < 0.05

label: Biotin

source_name: Laser capture miscrodissected astrocytes from human control brain tissue

label_protocol: Target labelled mRNA was prepared following the GeneChip WT Pico amplification protocol (Affymetrix). RNA amplification was achieved using low-cycle PCR followed by amplification using T7 in vitro transcription. The cRNA was converted to biotinylated sense-strand DNA hybridisation targets.

growth_protocol: All samples were snap frozen and stored at -80°C

extract_protocol: Total RNA was extracted from each isolated group of cells using the PicoPure RNA isolation kit

treatment_protocol: Toluidine blue histologically stained pyramidal neurons, glial fibrillary acidic protein-positive (GFAP+)- astrocytes and collagen IV-positive (Coll-IV+)- endothelial cells were isolated from each human case (PSD, PSND and Control) using a PixCell II laser capture microdissection (LCM) system. Toluidine blue histologically stained pyramidal neurons were isolated from each mouse case (BCAS and SHAM) using a PixCell II laser capture microdissection (LCM) system.

tag: gender

value: F

tag: condition

value: Control


title: MDMs_RNAseq_HD-rep4

description: MDMs_HD_rep123456_RPKM.bw; MDMs_HD_rep123456_RPKM_FR.bedgraph.gz.tbi;  MDMs_HD_rep123456_RPKM_FR.bedgraph.gz


title: SG231_monolayer_3

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

data_processing:
base calling with bcl2fastq 2.20.0.422
read cleaning with fastp (v0.20.0): fastp -A -q 30 -u 50 -l 70 -y -w 20 -i raw/r1_raw -I raw/r2_raw -o pre/r1_prep -O pre/r2_prep -h pre/log.html -j /dev/null
read mapping with salmon (v0.14.1): salmon quant -p 22 --numGibbsSamples 500 -i genome -l A -1 r1_prep -2 r2_prep --validateMappings -o mapped
data collection: R (v3.6.3) Bioconductor tximport (v1.14.2)
analysis package: R Bioconductor DESeq2 (v2_1.26.0)
Genome_build: Homo sapiens GRCh38.p13
Supplementary_files_format_and_content: transcript and gene abundance tables both as R saved file and tab-separated txt file

source_name: SG231 cell line

growth_protocol: The cells were grown for 10 days in anchoring-independent conditions with selective serum-free Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium supplemented with 1X B27 supplement minus vitamin A , human recombinant epidermal growth factor (hrEGF) (20 ng/ml), and bFGF (20 ng/ml).

extract_protocol:
Total RNA was isolated from cells using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. Depletion of mammalian and mitochondrial rRNA was performed with the RiboGone – Mammalian kit according to manufacturer's instructions
Paired-end RNA libraries were prepared for sequencing using standard Illumina protocols

value: cholangiocarcinoma

tag: growth type

value: monolayer

tag: replicate


title: Sample 3_HN878

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

country: USA

institute: University of Chicago

data_processing:
Sample preprocessing was done using the count command of CellRanger.
We excluded cells that featured: (i) a high fraction of mitochondrial RNA reads, (ii) a low percentage of protein-coding genes or (iii) a number of UMIs that was too low iv) a complexity ratio (log(nGenes) / log(nUMIs)) that was too low.
we filtered out genes detected in less than five cells in all conditions
We used the function computeSumFactors, from the R package scran (Lun et al., 2016) to normalize the data
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

growth_protocol: C57BL/6J (B6) and Ifnar-/- mice on the B6 background were purchased from The Jackson Laboratory (Bar Harbor, ME). All mice were maintained in the animal facility at Washington University in St. Louis and bred in house. Experimental mice were age and sex matched and infected between the ages of 6 and 8 weeks. All mice were maintained and used in accordance with the approved Washington University in St. Louis Institutional Animal Care and Use Committee guidelines.

extract_protocol:
BM was harvested from both femurs and tibiae and lysed for RBCs. BM cells were then stained with LIVE/DEAD fixable viability dye (Thermofisher), followed by staining with appropriate fluorochrome-labeled specific antibodies.
Single-cell GEMs were generated using a Chromium Controller instrument (10x Genomics).
Cell suspensions were loaded at 1,000 cells/μl to capture 10,000 cells/lane. The 10x Chromium Controller generated GEM droplets, where each cell was labeled with a specific barcode, and each transcript was labeled with a unique molecular identifier (UMI) during reverse transcription. The barcoded cDNA was isolated and removed from the BSL-3 space for library generation. The cDNA underwent 11 cycles of amplification, followed by fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR as per the manufacturer’s instructions. Libraries were sequenced on a NovaSeq S4 (200 cycles) flow cell, targeting 50,000 read pairs/cell.

treatment_protocol: Mtb strain HN878 was obtained from BEI resources (Manassas, VA) under National Institutes of Health contract AI-75320. Independent rifampicin resistant Mtb HN878 colonies (biological replicates) were selected from rifampicin (2 μg/ml) containing 7H11 agar plates (Ford et al., 2013). The sequences of rpoB were confirmed by Sanger sequencing (Genewiz), and Mtb stocks were created for further experimentation. All Mtb strains were cultured in Proskauer Beck medium supplemented with 0.05% Tween 80 and frozen at −80°C while in mid-log phase. Mice were aerosol infected with low doses (~100 CFU) of indicated Mtb strains in sterile PBS using a Glass-col nebulizer (Khader et al., 2007).  30 days after treatment, animals were sacrificed, and their BM extracted.

value: PBS HN878 aerosol

value: LKS+ Hematopoietic stem cells


title: ESO-26

value: ESO-26 (RRID:CVCL_2035)


title: Con 2


title: MDMs_RNAseq_HD-rep1


title: Control LCM Astrocytes_4


title: FLO-1

value: FLO-1 (RRID:CVCL_2045)


title: MDMs_RNAseq_HD-rep2


title: MTCHC01_monolayer_3

source_name: MTCHC01 cell line


title: OACP4_C

value: OACP4 C (RRID:CVCL_1843)


title: Sample 2_H445Y

value: MTB rpoB-H445Y aerosol


title: Control LCM Astrocytes_3

value: M


title: MTCHC01_spheroid_3

value: spheroid


title: HUCCT1_spheroid_2

source_name: HUCCT1 cell line


title: SK-GT-4

value: Oesophageal Adenocarcinoma

value: SK-GT-4 (RRID:CVCL_2195)


title: OE19

value: OE19 (RRID:CVCL_1622)


title: Sample 1_CTL

source_name: CTL

value: PBS aerosol


title: Control LCM Astrocytes_1


title: PSD LCM Astrocytes_2

description: Gene expression data from PSD astrocytes

source_name: Laser capture miscrodissected astrocytes from human PSD brain tissue

value: PSD


title: PSD LCM Astrocytes_3

value: F


title: PSND LCM Astrocytes_2

description: Gene expression data from PSND astrocytes

source_name: Laser capture miscrodissected astrocytes from human PSND brain tissue

value: PSND


title: HEK293T_KCNQ3_overexpression_4

description:
HEK293T cells overexpressing KCNQ3
KCNQ3_OE_4

data_processing:
Raw reads were trimmed and clipped for quality control using cutadapt v 2.8, command: cutadapt -m 10 -q 20 -j 8
Quality was checked using FastQC v0.11.5
Alignment to GRCh38.p13 was performed using hisat2 v 2.1.0 and samtools v 1.9
Reads were quantified using stringtie v2.1.0 to create transcript level reads
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab delimited file containing read counts for every transcript in every sample
Supplementary_files_format_and_content: tab delimited file containing TPM for every transcript in every sample

source_name: Kidney

growth_protocol: HEK 293T/17 cells (ATCC CRL-11268) were grown in standard culture conditions: DMEM high glucose (ThermoFisher Scientific 41966029) containing 10% fetal bovine serum (ThermoFisher Scientific 10500064) and 1x penicillin/streptomycin (ThermoFisher Scientific 15070063). Cultures were grown at 37°C and 5% C02.

extract_protocol:
48 hours post-transfection samples were harvested and RNA extracted using the RNeasy Plus Mini Kit (Qiagen 74134).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected using FuGene HD Transfection Reagent (Promega, E2311) with a human KCNQ3 open reading frame tagged construct (Origene RG234832). Transfection was carried out following manufacturers recommendations with the 3:1 ratio of transfection reagent to DNA.

value: Human Embryonic Kidney cell line HEK293T

tag: genotype

value: KCNQ3 Overexpression


title: FB-18-F2: GBM Tumor - IFN-a-DHFR - Rep3

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
10x CellRagner software was used to generate input (sparse) matrix files
Genome_build: mm10
Supplementary_files_format_and_content: Gene-by-cell sparse matrix files of UMI counts

molecule: polyA RNA

source_name: Brain

extract_protocol:
Tumors were isolated and dissociated with Tumor dissociation Kit (Miltenyi Biotec). After debris removal procedure (Debris Removal Solution, Miltenyi Biotec) donor-derived CD45+ cells were sorted.
Single-cell RNA-Seq libraries were generated using a microfluidics-based approach on Chromium Controller (10X Genomics) using the Chromium Single Cell 3’ Reagent Kit v2.0 according to the manufacturers’ instructions. Briefly, sorted single cells were suspended in 0.4% BSA-PBS, at a concentration ranging from 1000 to 2000 cells/µL. 8,700 cells were added to each channel in order to achieve a recovery rate of 5,000 cells per sample. Cells were partitioned in Gel Beads in Emulsion (GEMs) and lysed, followed by RNA barcoding, reverse transcription and PCR amplification (13 cycles).

tag: treatment group

value: IFN-a-DHFR gene therapy treated

tag: tumor

value: Glioblastoma


title: MTCHC01_spheroid_2

value: cholangiocarcinoma


title: Siha_Ctl_I

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

data_processing:
Reads were aligned and mapped to reference genome using STAR
Peaks from bigwig files were visualized using IGV
TPM values were calculated using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cervical cancer cell line

growth_protocol: 293T cells were grown inDulbecco modified Eagle medium (Life Technologies, Grand Island,N.Y.) supplemented with 10% fetal calf serum(FCS) (Hyclone). Human cervical carcinoma cell lines HeLa(HPV18-positive), SiHa(HPV16-positive), CaSKi (HPV16-positive), were obtained from the American Type Culture Collection (Manassas, VA). Two independently-derived primary human foreskin keratinocyte lines (designated as 10HFK and 11HFK)were cultured in KGM medium (KGMTMKeratinocyte Growth Medium BulletKitTM, Lonza,). NTERT1 cell line (TERT immortalized keratinocytes) was kindly provided by Dr. James Rheinwald and has been described previously(Ref). The human immortalized keratinocyte cell line, HaCaT, were maintained in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum . HNCC cells SCC1, SCC10B, SCC11 and HCC38 were obtained (from Dr. Thomas Carey, University of Michigan, Ann Arbor, MI) and HPV+ve HNCC cell lines, UPCI:SCC090, UPCI:SCC152, and UPCI:SCC154, were obtained from S. Gollin, University of Pittsburgh Cancer Institute.These cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum. Cells were grown at 37°C in a humidified atmosphere with 5% CO2in alpha-MEM supplementedwith 10% FCS. Mycoplasmacontamination was examined by DAPI staining/fluorescence microscopy.

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA.
RNA libraries were prepared for sequecing using standard Illumina protocols

treatment_protocol: SiHacells were  transfected with Control siRNA and siRNA against ECD, PRPF8 orDDX39A,cells  were  collected  using  Trizol  reagent  and  RNA  was  isolated. RNA  was  analyzed  by UNMC genome facility for BIOANALYZERforpurity and then subjected to sequencing. Beginning with 800 ng of total RNA from each sample, RNAseq libraries were generated using the TruSeq Stranded RNA Library preparation kit (Illumina) per manufacturers recommended protocol. Libraries were multiplexed  together  and subjected  to  75 bp paired  end  sequencing  on  an  Illumina  NextSeq  500 instrument to generate approximately 25 M pairs of reads per sample. FASTq files were provided to the Bioinformatics and Systems Biology Core for further analysis.

value: SiHa


title: FB-17-E3: GBM Tumor - IFN-a-DHFR - Rep2


title: MTCHC01_monolayer_1

value: monolayer


title: HEK293T_KCNQ3_overexpression_3

description:
HEK293T cells overexpressing KCNQ3
KCNQ3_OE_3


title: FB-12-F1: GBM Tumor - IFN-a-DHFR - Rep1


title: HEK293T_KCNQ3_overexpression_2

description:
HEK293T cells overexpressing KCNQ3
KCNQ3_OE_2


title: FB-11-C0: GBM Tumor - IFN-a - Rep3

value: IFN-a gene therapy treated


title: MTCHC01_spheroid_1


title: PSD LCM Astrocytes_1

value: M


title: HUCCT1_spheroid_1

value: spheroid


title: HEK293T_KCNQ3_overexpression_1

description:
HEK293T cells overexpressing KCNQ3
KCNQ3_OE_1


title: HEK293T_control_4

description:
Normal HEK293T cells
Control4

value: control


title: PSND LCM Astrocytes_1


title: DSS_D4_D

city: Boston

first: Ilya

last: Korsunsky

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

data_processing:
Reads mapped with Kallisto
Genome_build: GRCm 38, Gencode M25
Supplementary_files_format_and_content: Matrix of gene counts

source_name: Cd45-Epcam-Cd31-Pdpn+Pdgfra+ dissociated gut cells

extract_protocol:
Animal experiments were carried out under the relevant Home Office license at the University of Oxford (PPL: P508FFA1F). Female 7-week–old C57BL/6J mice were obtained from The Jackson Laboratory and housed in ventilated cages with 12-hour light cycles under specific pathogen-free conditions (SPF). They received food and water ad libitum. For induction of colitis, 2.5% w/v dextran sulfate sodium (DSS; MP Biomedicals) was supplemented in drinking water and given to mice for six consecutive days, with renewal on day three. After the treatment was ceased, mice returned to receiving standard water for the remaining time. Mice were monitored every day for alterations in body weight and clinical disease scores, until euthanised with carbon dioxide. Colons were resected, cleaned and washed in RPMI1640 supplemented with 5% fetal calf serum (FCS), 1% Penicillin-Streptomycin and 5mM EDTA for two total washes of 30 minutes and 20 minutes respectively at 37C to remove bulk epithelium. This was followed by tissue digestion using 100 g /ml Liberase TL and 40 g/ml DNAse for 3 x 1-hour cycles to dissociate all tissue into single-cell suspension. These were then stained with relevant reagents and antibodies (below) and FACS sorted (BD FACSAria III and BD FACSDiva 8.0.1) for live fibroblasts on CD45 -ve, EpCAM -ve, CD31 -ve, Podoplanin +ve, Pdgfra +ve cells at the time points described.
Cells were directly sorted into RNA lysis buffer and RNA was isolated using Zymo Quick RNA 96 kits as per the manufacturer’s instructions. Libraries were prepared using NEBNext ultra-low input RNA library prep with 1ng of RNA per sample and sequenced on a NovaSeq6000 (150 paired-end).
cDNA and library generation per manufacturer protocol.

tag: diease

value: DSS induced colitis

tag: day

tag: cage

value: D


title: Input_10

first: Zhongfei

last: Ma

address: 5, DongDan SanTiao, Dongcheng district

department: Department of Immunology

institute: Chinese Academy of Medical Sciences

library_source: genomic

data_processing:
Illumina CASAVA 1.8 software was used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse genome (GRCm38/mm10) using BWA mem v 0.7.12.
MACS2 version 2.1.0 peak finding algorithm was used to indentify regions of IP enrichment over background.
MEME and DREME were used to detect the sequence motif and Tomtom software was performed to annotate the motifs.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include peaks and annotation for each sample

molecule: genomic DNA

source_name: RAW 264.7 cells

extract_protocol:
ChIP was done using SimpleChIP Enzymatic Chromatin IP Kit (CST, 9003) following manufacturer’s protocol.
Library was constructed by Novogene China Co. Ltd. Briefly, DNA fragments were undergone end repair. Adenylation of 3’ ends of DNA fragments. Adaptor with hairpin loop structure were ligated to prepare for hybridization. Following purification, PCR was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cells were treated with LPS (100 ng/ml) for 0, 4h and 10h.

value: murine macrophage cells

value: treated with 100 ng/ml LPS for 10 h

tag: chip antibody


title: FB-6-D1: GBM Tumor - IFN-a - Rep2


title: HEK293T_control_3

description:
Normal HEK293T cells
Control3


title: Input_4

value: treated with 100 ng/ml LPS for 4 h


title: FB-16-B1: GBM Tumor - Control - Rep3

value: Control


title: HEK293T_control_2

description:
Normal HEK293T cells
Control2

value: Human Embryonic Kidney cell line HEK293T


title: PC9 siControl 96h  biological rep3

city: Hamamatsu

first: Kazuo

last: Tsuchiya

department: Tumor pathology

country: Japan

institute: Hamamatsu University School of Medicine

hyb_protocol: 100 μL of the hybridization solution was prepared using 73 μL Hybridization Master Mix and 2.3 μg Fragmented and Labeled cDNA. The array was incubated using the Gene Chip TM Hybridization Oven 645 at 45 ° C for 16 hours (60 rpm) according to the protocol included with the kit.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Raw data were processed to perform gene-level normalization using Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA) by Affymetrix Expression Console Software (Thermo Fisher Scientific). Annotation version was clariom_s_human.r1.na36.hg38.a1.

label: biotin

source_name: PC9 siControl 96h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: Cells were maintained in a 5% CO2 and 95% air incubator at 37℃.

extract_protocol: Total RNA was extracted using RNeasy Plus Mini Kit (#74136, Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Cells were cultured for 24 hours prior to transfection and transfected with 15 nM of final concentrations of siRNAs. Total RNA were extracted from ALKBH5 knockdown PC9 cells at 96 h after transfection.

value: lung adenocarcinoma cell line

tag: genotype/variation


title: Input_0

value: untreated


title: FB-10-A4: GBM Tumor - Control - Rep2

value: Glioblastoma


title: PC9 siControl 96h  biological rep2


title: PSND LCM Neurons_1

description: Gene expression data from PSND neurons

source_name: Laser capture miscrodissected neurons from human PSND brain tissue

value: F

value: PSND


title: ChIP_10

value: hnRNP UL1 (Proteintech, 10578-1-AP)


title: PC9 siALKBH5#3 96h biological rep3

source_name: PC9 siALKBH5#3 96h

value: ALKBH5 knockdown


title: FB-4-B3: GBM Tumor - Control - Rep1


title: PC9 siControl 96h  biological rep1


title: ChIP_4


title: PC9 siALKBH5#3 96h biological rep2


title: ChIP_0


title: SiEs05_T_TCR

city: La Jolla

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Division of Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

description:
SiEs05_T_TCR
eschweiler_tcr_data.txt.gz

data_processing:
mkfastq (Cell Ranger 3.1.0) was used to generate FASTQ files with default parameters
count (Cell Ranger 3.1.0) was used to generate the filtered UMI matrix with default parameters
vdj (Cell Ranger 3.1.0) was used to generate the filtered TCR annotation tables with default parameters
Seurat (3.0) was used to filter, normalize and scale the UMI matrix
Genome_build: hg19
Supplementary_files_format_and_content: eschweiler_umi_data.txt.gz UMI count data matrix for 8772 cells
Supplementary_files_format_and_content: eschweiler_annotation.txt.gz meta data for 8772 cells
Supplementary_files_format_and_content: eschweiler_tcr_data.txt.gz TCR data for 2378 FOXP3 cluster cells

source_name: TCR of Tumor-infiltrating T cells

extract_protocol:
T cells were isolated from cryopreserved tumor tissue using a combination of enzymatic and mechanical dissociation
Libraries were prepared according to standard 10x SOP for gene expression-seqencing and TCR sequencing
RNA-seq, TCR-seq

tag: sample type

value: Tumor TCR


title: SiEs05_LN_TCR

description:
SiEs05_LN_TCR
eschweiler_tcr_data.txt.gz

value: methasthatic tumor infiltrated LN


title: WT_Bm rep2

city: Shanghai

first: Peng

last: Ding

address: No.600, Yishan Road

department: Orthopaedics

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

data_processing:
The Cell Ranger software pipeline  provided by 10x Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner..
the unique molecular identifier (UMI) count matrix using the R package Seurat(version 2.3.4)
Library size normalization was performed with NormalizeData function in Seurat to obtain the normalized count. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and the results were logtransformed.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz (cell barcode file), features.tsv.gz (gene file), matrix.mtx.gz (gene-barcode file)

source_name: Bone marrow mononuclear cells

extract_protocol:
Femur and tibia were dissected and bone marrow were flushed, then cells were layered on Ficoll-paque (GE Healthcare) and centrifuged. Cells at the interface were collected and washed twice with ice-cold PBS.For the quality check and counting of single cell suspension, the cell survival rate is generally above 80%. The cells that have passed the test are washed and resuspended to prepare a suitable cell concentration of 700~1200 cells/ul for 10x Genomics ChromiumTM.
Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were all performed as per the manufacturer’s protocol.

tag: cell type

value: Bone marrow mononuclear cells

value: wildtype


title: FB-5-C1: GBM Tumor - IFN-a - Rep1

value: IFN-a gene therapy treated


title: PC9 siALKBH5#3 96h biological rep1

tag: cell line


title: WT_Bm rep1


title: TLR9-KO_Bm rep2


title: 002_SiEs05_LN_Gex

description:
002_SiEs05_LN_Gex_B8
eschweiler_umi_data.txt.gz

source_name: Tumor-infiltrating T cells


title: WT3

first: Youbo

state: China

address: Xueyuan Road No. 38

institute: Peking University

data_processing:
The raw data obtained by sequencing Illumina Hiseq was filtered and the clean reads obtained were compared to the reference sequence by HISAT(D, 2015).
Based on the comparison results, new transcript prediction, differential splicing gene detection, SNP and Indel detection, and fusion gene detection were performed
The Quantitative analysis of known genes and new genes were analyzed for differential expression according to the amount of genes expressed in different sample groups
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

source_name: Liver

extract_protocol:
Liver tissue samples were homogenized, and total RNA was extracted using the Qiagen miRNeasy mini kit.
cDNA libraries were constructed using an Illumina TruSeq RNA LS Sample Preparation kit v2 (Illumina, San Diego, CA, USA). Final individual cDNA libraries were assessed for fragment size and quality with the 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA) and sequencing libraries were quantified with the ABI StepOnePlus Real-Time PCR System

tag: age

value: 22 weeks


title: 001_SiEs05_T_Gex

description:
001_SiEs05_T_Gex_A8
eschweiler_umi_data.txt.gz

value: Tumor T cells


title: WT2

tag: strain


title: heart  AngII+PGE1 rep3

first: Yejiao

last: Shen

address: 241 West Huaihai Road

institute: Shanghai Jiaotong University affiliated chest hospital

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Genome_build: mm9
Supplementary_files_format_and_content: form files include information of genes expressed by all samples

source_name: heart

extract_protocol:
Total RNA was extracted from the heart tissues in the mice treated with saline, AngII, and AngII + PGE1 using Trizol (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s instructions.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

tag: tissue

value: heart

tag: treatment

value: AngII + PGE1


title: TLR9-KO_Bm rep1


title: HEK293T_control_1

description:
Normal HEK293T cells
Control1

value: Human Embryonic Kidney cell line HEK293T

value: control


title: PC9 siALKBH5#1 96h biological rep2

source_name: PC9 siALKBH5#1 96h

value: lung adenocarcinoma cell line


title: HC2-spheres2_WT-mouse_06_male [HC2_WT06]

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

country: Germany

institute: Goethe University Frankfurt

description:
HC2_WT_06
NSph prepared from adult mice

data_processing:
Starting with demultiplexed fastq.gz files, the fastqc program FASTQC (Version 0.11.5-cegat) was applied to assess sample quality
The alignment was performed with SeqMan NGen 15 (Lasergene) using the reference genome mm10 provided from UCSC (GRCm38.P3) as template, a minimum read length of 35 bp and automatic adapter trimming.
Results were displayed with ArrayStar 16 (Lasergene) including the amount of mapped reads, target length, source length and position, strand, genes and gene IDs, annotated according to the mm10 assembly
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Alternative DEseq2 normalization yielded comparable results.
Normalized data were further analyzed with ArrayStar (Lasergene 16). Because of gender differences of donor mice, genes located on the Y-chromosome were excluded. Genes were filtered for at least 8 valid samples in total to exclude low expression genes. Single missing values were set to an auto-calulated minimum or imputed from the normal distribution. Data were log2 transformed and results displayed as scatter plots and as Volcano plots, the latter showing the log2 difference i.e. fold change (positive for upregulated genes and negative for downregulated genes) versus the –log10 of the ttest P value. The P value was set at 0.05 and adjusted according to Benjamini Hochberg. Hierarchical clustering was employed to assess gene expression patterns using Euclidean distance metrics. Gene set enrichment analyses (GSEA) (http://www.gsea-msigdb.org) were used to further assess functional implications of up- or downregulated genes and to obtain a gene ranking and heat map of the leading edge 50 up- and downregulated genes.
Genome_build: mm10
Supplementary_files_format_and_content: linear RPKM normalized counts for each sample for all genes, target length and coordinates, and gene name
Supplementary_files_format_and_content: linear RPKM normalized counts of filtered valid genes with gene IDs
Supplementary_files_format_and_content: gene IDs of all genes

growth_protocol: Primary neurosphere cultures were prepared from adult C57BL/6 mice (8-12 weeks old). Tissue from the hippocampus or SVZ was enzymatically dissociated by incubation in Leibowitz L-15 medium, containing 0.8 mg/ml papain and 0.5 mM EDTA (dissociation medium, pre-activated at 37°C for 30 min) at 37°C for 30 min. After centrifugation for 3 min at 300 g, the supernatant was removed, and the tissue was resuspended in ovomucoid inhibitor. Cells were triturated with a fire-polished Pasteur pipette, collected by centrifugation for 3 min at 300 g, resuspended in DMEM/F-12 medium containing 1 mM HEPES, 10 μg/ml penicillin, 10 μg/ml streptomycin, 1 x B27 supplement and 20 ng/ml EGF and FGF (NSC medium) and plated in T75 flasks. Cells were incubated at 37°C and 5% CO2. For RNAseq analysis neurospheres of the HC were grown for 5d, of SVZ for 3d in vitro.

extract_protocol:
RNA from neurospheres was harvested using Trizol reagent. llumina TruSeq RNA Sample Prep Kit (TruSeq Stranded Total RNA with Ribo-Zero (Illumina) was used with 0.5 µg of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina's instructions. The SureSelectXT Mouse All Exon enrichment kits (Agilent) were used. Sequencing of 2x 100 bp was done on NovaSeq6000 with a sequencing depth of 50 Mio reads per sample
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Neurospheres were untreated

tag: strain background

tag: donor mouse sex

value: male

value: wildtye control

value: 5d (culture day)

value: hippocampus

value: neurospheres


title: KO3

tag: genotype


title: PC9 siALKBH5#1 96h biological rep1

value: ALKBH5 knockdown


title: heart  AngII rep3

value: AngII


title: PC9 siALKBH5#1 96h biological rep3


title: HC2-spheres2_WT-mouse_05_male [HC2_WT05]

description:
HC2_WT_05
NSph prepared from adult mice


title: KO1


title: KO2


title: heart  AngII rep2


title: HC2-spheres2_WT-mouse_02_male [HC2_WT02]

description:
HC2_WT_02
NSph prepared from adult mice


title: HC2-spheres2_WT-mouse_03_male [HC2_WT03]

description:
HC2_WT_03
NSph prepared from adult mice


title: heart  AngII+PGE1 rep2


title: heart saline rep3

value: saline


title: D10 Blastema [D1]

city: Dallas

first: Robert

middle: J

last: Tower

address: 5323 Harry Hines Blvd

institute: UTSW

description:
mRNA
D1
This Sample includes a pool of 2 young digits and 2 aged digits.

data_processing:
SpaceRanger
Seurat
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: matrix.h5 files
Supplementary_files_format_and_content: *_spatial.tar: Tar archives include aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, and tissue_positions_list.csv files.
Supplementary_files_format_and_content: Digit_cropping_and_ID.txt: Each reaction had 2 young digits and 2 aged digits arranged in a 2x2 grid. This file describes the position of each digit used for analysis and what group it falls into.

source_name: Young and Aged mouse digits 10 days after amputation

extract_protocol:
Enzymatic permeabilization (manufacturer's protocol).
10X Visium Spatial Gene Expression (manufacturer's protocol).

treatment_protocol: Digits amputated at 6 months (young) or 18 months (aged). Distal 1/3 of the P3 phalangeal element amputated.

value: Digit

tag: time point

value: 10 days post amputation


title: WT1

value: 22 weeks


title: heart  AngII+PGE1 rep1


title: HC-spheres1_WT-mouse_03_female [HC_WT03]

description:
HC_WT03
NSph prepared from adult mice

value: female


title: heart saline rep2

value: heart


title: heart saline rep1


title: D10 Blastema [B1]

description:
mRNA
B1
This Sample includes a pool of 2 young digits and 2 aged digits.


title: D10 Blastema [C1]

description:
mRNA
C1
This Sample includes a pool of 2 young digits and 2 aged digits.


title: SVZ-spheres1_WT-mouse_06_male [SVZ_WT03]

description:
SVZ_WT03
NSph prepared from adult mice

value: 3d (culture day)

value: subventricular zone


title: HC-spheres1_WT-mouse_01_female [HC_WT01]

description:
HC_WT01
NSph prepared from adult mice


title: FAL11238

city: Pokfulam

first: Rita

middle: Lok Hay

last: Yim

address: Room 311, 3rd Floor, Professorial Block, Queen Mary Hospital,

department: Department of Medicine

country: Hong Kong

institute: Hong Kong University

data_processing:
base calling using guppy (v4.0.5)
minimap2 (v2.17)
eventalign (v0.13.2)
xpore (v0.5.3)
Genome_build: GrCh38
Supplementary_files_format_and_content: diffmod.table (differental methylated table for P39-AZA-S (i.e.FAL11238) vs P39-AZA-R (i.e.FAL15992))

source_name: Bone Marrow Cell Line

growth_protocol: RPMI-1640 GlutaMAX supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
Qiagen RNAeasy mini kit
Direct RNA sequencing kit (SQK-RNA002)
RNA reverse transcribed was purified and directly loaded into flow cell (FLO-MIN106D) for sequencing.

treatment_protocol: Parental P39 sensitive to HMA were treated with 1µM of AZA or DEC for 48 hours, namely P39-AZA-S, P39-DEC-S. To establish derivative cell lines resistant to AZA or DEC, both cell lines were continuously exposed to AZA or DEC starting at a concentration of 5nM. P39 resistant to at least 10µM of AZA or DEC was established as P39-AZA-R and P39-DEC-R

value: AZA, 48 hours

tag: phenotype

value: HMA sensitive


title: AD_4

city: Guangzhou

first: Lan

last: Yang

state: Guangdong

address: 1838 North Guangzhou Street

department: Department of Plastic and Aesthetic Surgery

institute: Nanfang Hospital of Southern Medical University

description: ceRNA expression in PBMCs from AD patient.

hyb_protocol: Each slide was hybridized with 1.65 μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent Technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent Technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent Technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent Technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: PBMCs, AD, replicate 4

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent Technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Freshly drawn peripheral blood from healthy volunteers and AD patients was subjected to ceRNA microarray analysis.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit (Cat#217004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).

tag: diagnosis

value: Atopic dermatitus

value: peripheral blood mononuclear cells (PBMCs)

tag: gender

value: 7 y


title: 007-12(miR-26a-L.m infection 5h-3)

city: ChongQing

first: Jiangbei

last: Yuan

state: Please select

address: School of Pharmaceutical Sciences,Huxi Campus, Chongqing University

institute: Chongqing University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

source_name: miR-26a-overexpressing Raw 264.7 cells

extract_protocol:
The cells were stored in liquid nitrogen immediately after mature and then transferred to the -80℃ freezer. Total RNA was extracted from the frozen cells using the TIANamp DNA/RNA Isolation Kit (TIANGEN), including additional treatment with RNase-free DNase I (Ambion) for 30 minutes at 37℃ to remove contaminating DNA.18-30nt RNA segments were separated and recovered by PAGE gel. The steps which followed were the same as for generating the mRNA sequencing library from the addition of poly-A. The miRNA DNBs were loaded into the patterned nanoarrays and single-end reads of 50 bp were read through on the BGISEQ-500 platform at Beijing Genomics Institute (BGI; Shenzhen, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: miR-26a-overexpressing Raw 264.7 cells

tag: infection time

value: L.m infection 5h


title: FAL15992

value: AZA, continuously exposed

value: HMA resistant


title: D10 Blastema [A1]

description:
mRNA
A1
This Sample includes a pool of 2 young digits and 2 aged digits.


title: HC-spheres1_WT-mouse_02_female [HC_WT02]

description:
HC_WT02
NSph prepared from adult mice

value: wildtye control

value: 5d (culture day)

value: hippocampus

value: neurospheres


title: adapted T9-1 fumarate-only 2

city: Wuhan

first: Pier-Luc

last: Tremblay

state: Hubei

address: 122 Luoshi Road

department: School of Chemistry, Chemical Engineering and Life Science

institute: Wuhan University of Technology

data_processing:
Quality-scored basecalling was performed with the Illumina HiSeq Control software
Sequenced reads were mapped on the reference G. sulfurreducens PCA genome with Bowtie 2
Transcripts per million (TPM) were calculated with RSEM
FDR-adjusted p-values (q-values) were calculated with DeSeq2
Genome_build: NC_002939.5
Supplementary_files_format_and_content: Tab-delimited text files including gene, annotation, raw count for each replicate, TPM for each replicate, TPM mean,  log2 fold change, p-value and q-value

organism: Geobacter sulfurreducens PCA

source_name: Bacterial culture

growth_protocol: G. sulfurreducens wild type and T9-1 were grown anaerobically under a N2:CO2 (80:20) atmosphere to mid-log in NB medium at 30 ℃. G. sulfurreducens wild type was grown with both acetate and fumarate while G. sulfurreducens T9-1 was grown with fumarate only. Both strains were grown in triplicate in 10 ml volume.

extract_protocol:
Total RNA was extracted from G. sulfurreducens strains with the TRIzol reagent from ThermoFisher Scientific
The library was constructed with the Illumina TruSeq Stranded Total RNA Library Prep Kit

value: fumarate-only adapted

tag: number of transfer on fumarate-only

tag: growth phase

value: mid-log


title: heart  AngII rep1

value: heart

value: AngII


title: HC2-spheres2_EGFL7-mouse_08_male [HC2_EGFL7_08]

description:
HC2_EGFL7_08
NSph prepared from adult mice

value: male

value: knockout


title: SVZ-spheres1_WT-mouse_05_male [SVZ_WT02]

description:
SVZ_WT02
NSph prepared from adult mice

value: 3d (culture day)

value: subventricular zone


title: 007-10(miR-26a-L.m infection 5h-1)


title: GV stage oocytes, TdrkhIP_2

city: Mainz

first: David

last: Rosenkranz

address: Anselm-Franz-von-Bentzel-Weg 7

department: Institute of Anthropology

institute: Johannes Gutenberg-University Mainz

description: small RNAs

data_processing:
FASTQ to FASTA conversion (NGS TOOLBOX)
adapter trimming (NGS TOOLBOX)
size filtering 18-36nt (NGS TOOLBOX)
collapsing (NGS TOOLBOX)
filtering of low complexity reads (NGS TOOLBOX)
mapping with SeqWrap (custom Perl script that uses SeqMap to find best alignments with up to 1 internal mismatch and up to 2 non-template 3' bases)
sequence annotation with unitas v.1.5.3
Genome_build: bosTau7
Supplementary_files_format_and_content: Tab-delimited table (plain text file) containing sequences of mapped small RNAs, abundance and annotation (small RNA class)

organism: Bos taurus

source_name: GV stage oocytes

extract_protocol:
TRIZOL, ThermoFisher
NEXTflex Small RNA-Seq Kit V3
small RNA sequencing, NextSeq 500 75bp single-end

tag: developmental stage

value: GV stage

value: oocytes

tag: ip antibody

value: anti-Tdrkh (Proteintech, Catalog# 13528-1-AP, Lot# 00024452)


title: GV stage oocytes, TdrkhIP_1

description: small RNAs

tag: cell type


title: AD_2

source_name: PBMCs, AD, replicate 2

value: Atopic dermatitus

value: peripheral blood mononuclear cells (PBMCs)

value: female

tag: age


title: Normal_4

description: ceRNA expression in PBMCs from healthy control.

source_name: PBMCs, healthy control, replicate 4

value: Healthy


title: HC2-spheres2_EGFL7-mouse_07_male [HC2_EGFL7_07]

description:
HC2_EGFL7_07
NSph prepared from adult mice

value: 5d (culture day)

value: hippocampus


title: Normal_3

source_name: PBMCs, healthy control, replicate 3


title: GV stage oocytes, Input_2

description: small RNAs


title: AD_3

source_name: PBMCs, AD, replicate 3


title: SVZ-spheres1_WT-mouse_04_male [SVZ_WT01]

description:
SVZ_WT01
NSph prepared from adult mice

value: wildtye control

value: neurospheres


title: 007-11(miR-26a-L.m infection 5h-2)

value: miR-26a-overexpressing Raw 264.7 cells

value: L.m infection 5h


title: wild type acetate-fumarate 2

tag: strain

value: wild type

value: mid-log


title: Normal_2

source_name: PBMCs, healthy control, replicate 2

tag: tissue


title: 007-8(WT-L.m infection 5h-2)

source_name: NC-plasmid-transfected Raw 264.7 cells

value: NC-plasmid-transfected Raw 264.7 cells


title: Normal_1

source_name: PBMCs, healthy control, replicate 1


title: adapted T9-1 fumarate-only 1

value: fumarate-only adapted


title: TNF 2

city: Beijing

first: Dan

last: Wu

address: No. 16, Nei Nanxiao Street, Dongzhimen, Dongcheng District

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

description: gene_fpkm_all_samples.txt;transcript_fpkm_all_samples.txt

data_processing:
Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.
Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers.
This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H.
These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters.
The products are then purified and enriched with PCR to create the final cDNA library.
Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).
Supplementary_files_format_and_content: Expression value of genes and transcripts

source_name: murine macrophage-like cell line

extract_protocol:
Total RNA was isolated using an RNeasy mini kit (Qiagen, Germany) according to the manufacturer’s protocol. RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The quantity of total RNA in the samples was measured using a Qubit®3.0 Fluorometer (Thermo Fisher Scientific, USA) and NanoDrop One (Wilmington, DE, USA).
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). The sequencing work was undertaken by Beijing Zhimei Yinuo Biotechnology Co., Ltd (Beijing, China).

value: macrophage

tag: treatment

value: treated with TNF-α for 24 hours

value: BALB/c


title: HC2-spheres2_EGFL7-mouse_04_male [HC2_EGFL7_04]

description:
HC2_EGFL7_04
NSph prepared from adult mice

tag: strain background

value: male

value: knockout


title: GV stage oocytes, Input_1

description: small RNAs

value: GV stage

value: oocytes


title: adapted T9-1 fumarate-only 3


title: wild type acetate-fumarate 3


title: HC2-spheres2_EGFL7-mouse_01_male [HC2_EGFL7_01]

description:
HC2_EGFL7_01
NSph prepared from adult mice

tag: donor mouse sex

value: 5d (culture day)


title: 007-6(miR-26a-No infection-3)

value: No infection


title: 007-9(WT-L.m infection 5h-3)


title: wild type acetate-fumarate 1


title: 007-5(miR-26a-No infection-2)


title: AD_1

source_name: PBMCs, AD, replicate 1

value: Atopic dermatitus

value: peripheral blood mononuclear cells (PBMCs)

value: female


title: 007-7(WT-L.m infection 5h-1)

value: L.m infection 5h


title: HC-spheres1_EGFL7-mouse_01_male [HC_EGFL7_01]

description:
HC_EGFL7_01
NSph prepared from adult mice

tag: genotype

value: hippocampus

value: neurospheres


title: MouseEHBD_48hours_Sham

city: Ann Arbor

first: Nureen Hanisah

last: Mohamad Zaki

state: Michigan

address: 109 Zina Pitcher Pl, RM2438

department: Internal Medicine, GI

institute: University of Michigan

description:
Razumilava_Razumilava_1pNCRC_20190502_P220190410.txt_3
Sham_48hr

data_processing:
Data was normalized to control genes with relatively invariant cycle threshold values. Genomic DNA was undetectable and there was no inhibition of the reverse transcription step.
Normalized values to an average of 5 housekeeping genes {Actb, B2m, Gapdh, Gusb, Hsp90ab1)

label: SYBR green

source_name: whole EHBD

label_protocol: According to Qiagen RT² Profiler™ PCR Array Mouse Growth Factors PAMM-041Z manufacturer protocol

growth_protocol: [1. whole EHBD] Mice were fed with 5L0D diet. [2. cell culture] Organoid and neofibroblasts were cultured in 50% L-WRN conditioned media, 1X penicillin–streptomycin, 1X GlutaMAX, 10 mM 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid, 1X Fungizone, 1X gentamicin, 1X B27, and 1X N2 in advanced Dulbecco’s modified Eagle’s medium/F12. FGF10 and EGF were withdrawn from the culture media after 3 days of seeding.

extract_protocol: [1. whole EHBD] Whole tissue was isolated into RNAlater, homogenized with a bead mill homogenizer, and processed with Qiagen Rneasy micro kit according to manufacturer protocol. [2. cell culture] Whole EHBD tissue was isolated and dissociated in accutase followed by filtration for size and grown in selective media and matrigel. Total RNA is isolated at either passage 3 or 5 using Trizol, followed by Qiagen RNeasy mini kit according to manufacturer protocol. Complementary DNA (cDNA) from all samples were generated from 500 ng total RNA using the iScript cDNA synthesis kit according to manufacturer protocol.

treatment_protocol: [1. whole EHBD] Mice were treated as shams or ligated at the distal end of the EHBD for 12/24/48 hour timepoints prior to sacrifice. [2.cell culture] No treatment

value: wildtype

tag: Sex

value: Male

tag: passage

tag: age at sacrifice

value: 2.7 mos

tag: agent

value: Sham

tag: time point


title: 007-3(WT-No infection-3)

value: NC-plasmid-transfected Raw 264.7 cells

tag: infection time


title: TPN-1

first: Lu

last: Jiang

address: 1665 Kongjiang Rd

institute: Xinhua hospital affiliated to Shanghai Jiao Tong Unvertsity schoool of medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rat  (Rnor 6.0) whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Gene expression levels were estimated using Cufflinks software by FPKM value.
Supplementary_files_format_and_content: All_gene_fpkm.txt  (tab-delimited text file includes FPKM values for each sample)

organism: Rattus norvegicus

source_name: liver

extract_protocol:
Total RNA from liver was extracted using TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control rats received 0.9% saline, TPN rats received total parenteral nutrition for 7 days

value: Sprague-Dawley

value: 4 weeks old

tag: disease state

value: PNALD

value: liver


title: TPN-3


title: MouseEHBD_48hours_BDL

description:
Razumilava_Razumilava_1pNCRC_20190502_P220190410.txt_4
BDL_48hr

value: Female

value: 3.3 mos

value: BDL


title: MouseEHBD_24hours_Ligation

description:
Razumilava_Razumilava_1pNCRC_20190502_P220190410.txt_2
BDL_24hr

value: 8.2 mos


title: 007-2(WT-No infection-2)

value: No infection


title: SVZ-spheres1_EGFL7-mouse_05_male [SVZ_EGFL7_02]

description:
SVZ_EGFL7_02
NSph prepared from adult mice

value: male

value: knockout

value: 3d (culture day)

value: subventricular zone


title: Control1

value: normal


title: 007-1(WT-No infection-1)


title: SVZ-spheres1_EGFL7-mouse_06_male [SVZ_EGFL7_03]

description:
SVZ_EGFL7_03
NSph prepared from adult mice

value: neurospheres


title: HC-spheres1_EGFL7-mouse_03_male [HC_EGFL7_03]

description:
HC_EGFL7_03
NSph prepared from adult mice

value: 5d (culture day)

value: hippocampus


title: TPN-2

value: Sprague-Dawley


title: HC-spheres1_EGFL7-mouse_02_male [HC_EGFL7_02]

description:
HC_EGFL7_02
NSph prepared from adult mice


title: Control3

value: 4 weeks old


title: 007-4(miR-26a-No infection-1)

value: miR-26a-overexpressing Raw 264.7 cells


title: Control2

value: liver


title: MouseEHBD_12hours_Sham

description:
Razumilava_Razumilava_11aNCRC_20190502_P120190410.txt_1
Sham_12hr

value: wildtype

value: Female

value: 2.4 mos

value: Sham


title: SVZ-spheres1_EGFL7-mouse_04_male [SVZ_EGFL7_01]

description:
SVZ_EGFL7_01
NSph prepared from adult mice


title: MouseEHBD_24hours_Sham

description:
Razumilava_Razumilava_11aNCRC_20190502_P120190410.txt_3
Sham_24hr

value: Male

value: 8.2 mos


title: MouseEHBD_12hours_Ligation

description:
Razumilava_Razumilava_11aNCRC_20190502_P120190410.txt_2
BDL_12hr

value: 3.7 mos

value: BDL


title: 4w Achilles tendon - DicerKO_whole

status: Public on May 31 2022

city: Hiroshima

first: Shigeru

last: Miyaki

state: Hiroshima

address: 1-2-3, kasumi Minami-ku

department: Medical Center for Translational and Clinical Research

institute: Hiroshima University

data_processing:
Adaptor sequences were removed from sequenced reads, and the trimmed reads were mapped to the GRCm38-mm10 assembly of the mouse genome with Tophat and bowtie2.
Raw read counts were then assigned to genes using HTSeq.
Differential gene expression was analyzed with the R Bioconductor DESeq2 package using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Achilles tendon

extract_protocol:
Achilles tendon from 4-week-old mice was harvested, total RNA was extracted by ISOGEN and Zymo Direct-zol RNA microprep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Achilles tendon

value: 4 week

value: ScxCre/+ Knock In:Dicer f/f

tag: sample

tag: molecule subtype

value: Total RNA


title: 4w Achilles tendon - Cont_whole

value: Dicer f/f


title: 4w Achilles tendon - Cont_small

value: Small RNA


title: REFPB,  scRNAseq

city: London

first: Luca

last: Biasco

address: 30 Guilford St, Holborn

institute: UCL

description:
10x Genomics
BL6mouse, reference, PB

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Peripheral Blood

extract_protocol:
After transcardial perfusion, the brains of one male and female mice from IV and ICV groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspension was stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). GFP- positve and GFP-negative fractions of microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACS- sorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology).
For the generation of single cell transcriptomes, 5x103 target cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 Sequencing System (Illumina) using NextSeq 500/550 High Output v2.5 (150 cycles) Kit (Illumina).

tag: cell type

value: White Blood Cells

value: Peripheral Blood

value: 8-12 weeks


title: IV, 2female, GFPneg

description: 10x Genomics

source_name: Brain

value: Microglia

value: Brain

tag: age

value: female

tag: gfp status

value: GFPneg

value: IV


title: IV, 27male, GFPneg

description: 10x Genomics

tag: tissue

tag: strain

value: male


title: ICV, 4female, GFPpos

description: 10x Genomics

value: GFPpos

tag: treatment

value: ICV


title: ICV, 19male, GFPpos

description: 10x Genomics


title: REFMicroglia, scRNAseq

description:
10x Genomics
BL6mouse, reference, Brain


title: ICV, 19male, GFPneg

description: 10x Genomics


title: ICV, 4female, GFPneg

description: 10x Genomics


title: 3013_v4_BLD

city: New Haven

first: Jun

last: Zhao

state: CT

address: 300 George Street

department: Pathology/Immunology

institute: Yale University

data_processing:
Raw sequencing reads were processed with cellranger v3.0.2 to generate the gene-barcode count matrix.
Count matrices from different samples were normalized, integrated and analyzed by Seurat v3.
Assembly: hg38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated by Ficoll gradient with Sepmate. CSF cells were isolated by centrifuging whole CSF
Libraries were prepared using the 10X 3' V2 kit

tag: disease status

value: Uninfected control

value: Blood

value: Peripheral blood mononuclear cells

tag: ID


title: REFNeurons, scRNAseq

description:
10x Genomics
BL6mouse, reference, Brain

value: Neurons


title: 3013_v4_CSF

source_name: cerebrospinal fluid cells

value: CSF

value: cerebrospinal fluid cells


title: 1044_V5_BLD

value: HIV

value: ART


title: 4w Achilles tendon - ScxHT_whole

value: Achilles tendon

value: 4 week

tag: genotype

value: ScxCre/+ Knock In:Dicer +/+

value: Total RNA


title: IV, 27male, GFPpos

description: 10x Genomics

value: Microglia

value: Brain

tag: Sex


title: REFAstrocytes, scRNAseq

description:
10x Genomics
BL6mouse, reference, Brain

value: Astrocytes

value: 8-12 weeks


title: 3031-base_CSF


title: IV, 2female, GFPpos

description: 10x Genomics

value: female

value: GFPpos

value: IV


title: 3031-base_BLD

value: Uninfected control

value: Blood

value: Peripheral blood mononuclear cells


title: 1044_V5_CSF

value: CSF

value: cerebrospinal fluid cells


title: 3029_base_BLD


title: 1073_base_CSF

value: HIV

value: ART


title: 3009_V3_BLD


title: 4w Achilles tendon - ScxHT_small

value: Achilles tendon

value: 4 week

value: Small RNA


title: 1072_base_BLD


title: 3029_base_CSF


title: 4w Achilles tendon - DicerKO_small

value: ScxCre/+ Knock In:Dicer f/f


title: 1071_base_BLD


title: 1070_base_BLD


title: Tle4_P7_R2 (ATAC-seq)

city: Cambridge

first: Paola

last: Arlotta

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: FinalIDR_ArlottaLab_P7_Tle4_macs2.regionPeak

data_processing:
Reads were aligned to the mm9 reference using Bowtie2
Aligned reads were filtered for duplicates using Picard
performed peak calling for each sample group using the IDR framework in combination with the macs2 peak caller, with two independent biological replicates in each group
We then performed differential peak enrichment analysis across all pairwise group comparisons
Assembly: mm9
Supplementary files format and content: tab-delimited text file include peak calling

source_name: somatosensory cortex and motor cortex

growth_protocol: Experiments using mice were conducted under protocols approved by the Harvard University Institutional Animal Care and Use Committee and followed the guidelines set forth in the National Institute of Health Guide for the Care and Use of Laboratory Animals.

extract_protocol:
To prepare nuclei, around 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge.
Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition the sample was purified using a Qiagen MinElute kit. Then, amplified library fragments were made by using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2, using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ∼30 nM in 20 μL. Libraries were amplified for a total of 10–12 cycles.

treatment_protocol:
4-Hydroxytamoxifen (4-OHT; Sigma) dissolved in corn oil was administered to pregnant mice at 1 mg 4-OHT/10g body weight.
Cortex was dissected in cold dissociation medium (20 mm glucose, 0.8 mm kynurenic acid, 0.05 mmAPV, 50 U/ml penicillin–0.05 mg/ml streptomycin, 0.09mNa2SO4, 0.03mK2SO4, and 0.014m MgCl2). The cortex was enzymatically digested in dissociation medium containing 0.16 gm/l l-cysteine and 12 U/ml papain at 37°C for 30 min. Papain digestion was then blocked with dissociation medium containing 10 mg/ml ovomucoid (Sigma, St. Louis, MO) and 10 mg/ml bovine serum albumin (BSA) at room temperature. Neurons were mechanically dissociated to create a single cell suspension by gentle trituration in iced OptiMem (Life Technologies, Gaithersburg, MD) containing 20 mm glucose and both 0.4 mmkynurenic acid and 0.025 mm APV to protect against glutamate-induced neurotoxicity. Td-tomato labeled projection neurrons were purified from the cortical cell suspension by fluorescence-activated cell sorting (FACS) using a FACSVantage flow cytometer.

value: somatosensory cortex and motor cortex

value: 4-HydroxyTamoxifen injection


title: Cux2_P48_R2 (ATAC-seq)

description: FinalIDR_ArlottaLab_P48_v2_macs2.regionPeak


title: Tle4_P48_R2 (ATAC-seq)

description: FinalIDR_ArlottaLab_P48_Tle4_macs2.regionPeak


title: Tle4_P3_R2 (ATAC-seq)

description: FinalIDR_ArlottaLab_P3_Tle4_macs2.regionPeak


title: 1073_base_BLD


title: 1037_V4_BLD


title: Cux2_P7_R2 (ATAC-seq)

description: FinalIDR_ArlottaLab_P7_v2_macs2.regionPeak


title: 1070_base_CSF


title: 3009_V3_CSF


title: 1037_v4_CSF


title: Cux2_P1_R2 (ATAC-seq)

description: FinalIDR_ArlottaLab_P1_v2_macs2.regionPeak


title: 1071_base_CSF


title: Cux2_P21_R2 (ATAC-seq)

description: FinalIDR_ArlottaLab_P21_v2_macs2.regionPeak


title: 1072_base_CSF


title: Cux2_P3_R2 (ATAC-seq)

description: FinalIDR_ArlottaLab_P3_v2_macs2.regionPeak


title: Tle4_E18_5_R1 (ATAC-seq)

description: FinalIDR_ArlottaLab_E18_5_Tle4_macs2.regionPeak


title: Tle4_P21_R2 (ATAC-seq)

description: FinalIDR_ArlottaLab_P21_Tle4_macs2.regionPeak


title: Cux2_P7_R1 (ATAC-seq)


title: Cux2_E18_5_R2 (ATAC-seq)

description: FinalIDR_ArlottaLab_E18_5_v2_macs2.regionPeak


title: Tle4_P3_R1 (ATAC-seq)


title: Cux2_P3_R1 (ATAC-seq)


title: Tle4_P1_R2 (ATAC-seq)

description: FinalIDR_ArlottaLab_P1_Tle4_macs2.regionPeak


title: Tle4_P48_R1 (ATAC-seq)


title: Cux2_P48_R1 (ATAC-seq)


title: Cux2_P21_R1 (ATAC-seq)


title: CE30

type: genomic

city: Valencia

first: Hortensia

last: Ferrero

state: Valencia

address: Avenida Fernando Abril Martorell 106, Torre A

department: Reproductive Medicine

country: Spain

institute: Instituto de Investigación Sanitaria La Fe / Fundación IVI

hyb_protocol: Not provided

scan_protocol: Epigenomic studies were performed with the Infinium MethylationEPIC BeadChips 850K array (Illumina, USA) used for the analysis of over 850,000 CpG sites (dinucleotides that are the main target for methylation) (66). 4 μl of tissue bisulfite-DNA was processed following the Illumina Infinium HD Methylation Assay Protocol. The methylation score for each CpG was represented as a beta value according to the fluorescent intensity ratio. Beta values may take any value between 0 (non-methylated) and 1 (completely methylated).

data_processing:
The raw data (IDAT files) were normalized using functional normalization as implemented in the R-package minfi (version 1.22.1).
Every beta value in the EPIC array is accompanied by a detection p-value which represents the confidence of a given beta value. Probes and sample filtering involved a two-step process in which unreliable betas with high detection p value > 0.01 and  CpGs associated with SNPs were removed. After the filtering, the remaining 861483 CpGs were considered valid for the study. A Wilcoxon test for paired samples was performed for each CpG beta. Pvalues were adjusted by using False Discovery Rate and Holm correction.
Methyl_RAW.csv: Matrix table with beta values for every CpG and every sample

label: Cy3, Cy5

source_name: Uterine myometrium

label_protocol: Not provided

extract_protocol: Genomic DNA (gDNA) was extracted from UL and MM frozen tissues (n=31) using QIAamp DNA Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. 500 ng of purified DNA were randomly distributed on a 96-well plate and processed using the EZ-96 DNA Methylation kit (Zymo Research Corp., CA, USA) following the manufacturer’s recommendations for Infinium assays.

tag: gender

value: Uterine myometrium

tag: group

value: Caucasian women

tag: patient

value: Patient 30

tag: bmi


title: CE28

value: female

value: Patient 28


title: Cux2_P1_R1 (ATAC-seq)


title: Pool.P7.rep1.mm10

library_source: genomic single cell

data_processing:
Mouse and marmoset libraries were first downsampled to similar overall complexity in terms of reads/cell across all conditions
Cleaned data was processed with the scasat83 pipeline using macs2 as peak caller
Only cells with at least 1,000 reads and 300 peaks from the master list overlapping with at least one read, but not more than 15,000 reads and 8,000 peaks were retained for analysis
matrix was processed using R implementing a custom processing pipeline based on the strategy outlined in Cusanovich et al. 2018 and refined by Andrew Hill, following the log-LSI workflow
Assembly: mm10, calJac3
Supplementary files format and content: gene-cell matrix with raw counts (RDS format) and tab-delimited text file with cell metadata

growth_protocol: Experiments using animal were conducted under protocols approved by the Harvard University and MIT Institutional Animal Care and Use Committee and followed the guidelines set forth in the National Institute of Health Guide for the Care and Use of Laboratory Animals.

extract_protocol:
To prepare nuclei, around 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge.
For mouse: Briefly, cells were fixed with 0.1% formaldehyde and incubated at room temperature for 5 min. The fixation was stopped by adding glycine to the final concentration of 125 mM. The sample was incubated at room temperature for 5 min and washed in PBS. The cell concentration was counted, and approximately 1600-2000 cells per well were distributed into each well of a 96-well plate. Cells were transposed with 96 uniquely barcoded Tn5 at 37°C for 30 min with shaking at 300 rpm. The reaction was stopped by adding 0.5 M EDTA and incubated at 37°C for 15 min. All the cells were then pooled and MgCl2 was added to the pooled sample to quench EDTA. The sample was re-distributed onto another 96-well plate with 20 cells in each well by FACS sorting. Reverse crosslinking buffer and barcode PCR primers were added to each sample. The plate was incubated at 55°C for 16 hours for reverse crosslinking. Tween 20 was then added to quench SDS before PCR amplification. The PCR reaction was carried out at the following conditions: 72°C for 5 min (extension), 98°C for 5 min, and then thermocycling at 98°C for 10 s, 70°C for 30 s and 72°C for 1 min for 12-15 cycles. Libraries were pooled and purified using Qiagen MinElute PCR purification column. The libraries were quantified using KAPA library quantification kit. Libraries were sequenced on the Next-seq platform (Illumina) using a 150-cycle kit (Read 1: 47 cycles, Index 1: 36 cycles, Index 2: 36 cycles, Read 2: 47 cycles). For marmoset: Somatosensory and motor cortex from wild-type animals was dissected and dissociated with the Worthington Papain Dissociation System (Worthington Biochemical Corporation), and live cells were isolated by FACS sorting as DAPI-negative, Vybrant DyeCycle Ruby (Thermo Fisher)-positive events. Libraries were prepared using the 10x Genomics Chromium Single Cell ATAC kit (10x Genomics).

treatment_protocol:
non
Cortex was dissected in cold dissociation medium (20 mm glucose, 0.8 mm kynurenic acid, 0.05 mmAPV, 50 U/ml penicillin–0.05 mg/ml streptomycin, 0.09mNa2SO4, 0.03mK2SO4, and 0.014m MgCl2). The cortex was enzymatically digested in dissociation medium containing 0.16 gm/l l-cysteine and 12 U/ml papain at 37°C for 30 min. Papain digestion was then blocked with dissociation medium containing 10 mg/ml ovomucoid (Sigma, St. Louis, MO) and 10 mg/ml bovine serum albumin (BSA) at room temperature. Neurons were mechanically dissociated to create a single cell suspension by gentle trituration in iced OptiMem (Life Technologies, Gaithersburg, MD) containing 20 mm glucose and both 0.4 mmkynurenic acid and 0.025 mm APV to protect against glutamate-induced neurotoxicity. Td-tomato labeled projection neurrons were purified from the cortical cell suspension by fluorescence-activated cell sorting (FACS) using a FACSVantage flow cytometer.

value: Wild type


title: Pool.P21.rep1.mm10


title: Pool.P1.rep2.mm10


title: CE27

value: Patient 27


title: Tle4_E18_5_R2 (ATAC-seq)


title: Pool.P21.rep2.mm10


title: P21.10.17.rep2.mm10


title: Tle4_P21_R1 (ATAC-seq)


title: CE31

value: Patient 31


title: CE25

value: Patient 25


title: Tle4_P7_R1 (ATAC-seq)


title: Tle4_P1_R1 (ATAC-seq)


title: CE23

value: Patient 23


title: P21.10.17.rep1.mm10


title: CE21

value: Patient 21


title: Cux2_E18_5_R1 (ATAC-seq)


title: CE19

value: Patient 19


title: Pool.P1.rep1.mm10


title: P1.10.18.rep2.mm10


title: CE17

value: Patient 17


title: CE24

value: Patient 24


title: Pool.P7.rep2.mm10


title: Mouse_WT_P21_5_22_18

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
filtered the dataset to retain only cells with at least 1000 genes, a mitochondrial read fraction below 10%, and not more than 6000 genes or 15000 UMIs
performed cell clustering and subtype identification separately for each time point P1, P7 and P21
Assembly: mm10
Supplementary files format and content: gene-cell matrix with raw counts (RDS format) and tab-delimited text file with cell metadata

extract_protocol:
Live cells were isolated by FACS sorting as DAPI-negative, Vybrant DyeCycle Ruby (Thermo Fisher)-positive events.
Libraries were prepared using the 10x Genomics Chromium Single Cell 3' kit v2 (10x Genomics) according to the manufacturer’s protocol.

treatment_protocol:
Non
Cortex was dissected in cold dissociation medium (20 mm glucose, 0.8 mm kynurenic acid, 0.05 mmAPV, 50 U/ml penicillin–0.05 mg/ml streptomycin, 0.09mNa2SO4, 0.03mK2SO4, and 0.014m MgCl2). The cortex was enzymatically digested in dissociation medium containing 0.16 gm/l l-cysteine and 12 U/ml papain at 37°C for 30 min. Papain digestion was then blocked with dissociation medium containing 10 mg/ml ovomucoid (Sigma, St. Louis, MO) and 10 mg/ml bovine serum albumin (BSA) at room temperature. Neurons were mechanically dissociated to create a single cell suspension by gentle trituration in iced OptiMem (Life Technologies, Gaithersburg, MD) containing 20 mm glucose and both 0.4 mmkynurenic acid and 0.025 mm APV to protect against glutamate-induced neurotoxicity. Td-tomato labeled projection neurrons were purified from the cortical cell suspension by fluorescence-activated cell sorting (FACS) using a FACSVantage flow cytometer.


title: P1.10.18.rep1.mm10


title: P7.10.19.rep1.mm10


title: CE20

value: Patient 20


title: CE22

value: Patient 22


title: CE29

value: Patient 29


title: Mouse_WT_P21_5_16_18

value: somatosensory cortex and motor cortex


title: CE13

value: Uterine myometrium

value: Caucasian women

value: Patient 13


title: CE16

value: female

value: Patient 16


title: P7.10.19.rep2.mm10

value: Wild type


title: CE15

value: Patient 15


title: CE8

value: Patient 8


title: CE9

value: Patient 9


title: CE26

value: Patient 26


title: CE12

value: Patient 12


title: CE18

value: Patient 18


title: CE10

value: Patient 10


title: CE5

value: Patient 5


title: CE4

value: Patient 4


title: CE14

value: Patient 14


title: CE11

value: Patient 11


title: Mouse_WT_P1_4_15_18

value: somatosensory cortex and motor cortex


title: Mouse_WT_P21_5_1_18


title: CE1

value: Uterine myometrium

value: Caucasian women

value: Patient 1


title: ME31

source_name: Uterine leiomyoma

value: female

value: Uterine leiomyoma

value: Patient 31


title: Mouse_WT_P1_5_2_18

value: Wild type


title: CE6

value: Patient 6


title: CE2

value: Patient 2


title: ME30

value: Patient 30


title: Mouse_WT_2_P7_4_17_18


title: ME17

value: Patient 17


title: ME16

value: Patient 16


title: CE7

value: Patient 7


title: ME20

value: Patient 20


title: ME22

value: Patient 22


title: ME21

value: Patient 21


title: ME27

value: Patient 27


title: ME24

value: Patient 24


title: ME13

value: Caucasian women

value: Patient 13


title: ME23

value: female

value: Patient 23


title: ME18

value: Uterine leiomyoma

value: Patient 18


title: ME29

value: Patient 29


title: CE3

value: Uterine myometrium

value: Patient 3


title: Mouse_WT_1_P7_4_17_18

value: somatosensory cortex and motor cortex

value: Wild type


title: ME11

value: Patient 11


title: ME28

value: Patient 28


title: ME25

value: Patient 25


title: Mouse_WT_P1_5_4_18


title: ME10

value: Patient 10


title: ME14

value: Patient 14


title: ME9

value: Patient 9


title: ME26

value: Caucasian women

value: Patient 26


title: ME7

value: female

value: Patient 7


title: ME19

value: Uterine leiomyoma

value: Patient 19


title: ME8

value: Patient 8


title: ME4

value: Patient 4


title: ME5

value: Patient 5


title: ME3

value: Patient 3


title: ME6

value: Patient 6


title: Cux2_P21_R2

data_processing:
Raw reads were trimmed, removing 8bp from the 5’ and 25 bp from the 3’ end.
Reads were aligned to the mm9 reference genome using Tophat2
Subsequently, differential gene expression analysis and FPKM quantification was performed for all pairwise comparisons
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
To prepare nuclei, around 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge.
Pools of 5,000-10,000 cortical pyramidal neurons were sorted directly into TRIzol-LS buffer (Invitrogen) and RNA was extracted according to the manufacturer’s protocol. 10 ng total RNA was used for library preparation using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) and the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s protocols.

value: somatosensory cortex and motor cortex

value: 4-HydroxyTamoxifen injection


title: ME12

value: Patient 12


title: Cux2_P7_R2


title: ME1

value: Patient 1


title: Tle4_P7_R2


title: ME15

value: Patient 15


title: Cux2_P1_R2


title: Cux2_P3_R2


title: Cux2_P21_R1


title: Tle4_E18_5_R2


title: Cux2_P48_R2


title: Tle4_P3_R2


title: Cux2_P7_R1


title: Cux2_E18_5_R2


title: Cux2_P1_R1


title: ME2

value: Patient 2


title: Cux2_E18_5_R1


title: Tle4_P1_R2


title: Tle4_P48_R1


title: Tle4_P48_R2


title: Cux2_P3_R1


title: Tle4_E18_5_R1


title: Tle4_P1_R1


title: Tle4_P21_R2


title: Tle4_P7_R1


title: Cux2_P48_R1


title: Tle4_P21_R1


title: Cortical_shPum2_Rep1 [JE01003]

city: Martinsried

first: Michael

last: Kiebler

address: Großhaderner Str. 9

department: BioMedical Center

institute: Ludwig-Maximilians University Munich

description: Replicate 1

data_processing:
Reads in fastq format were aligned to a database of rat miRNAs and quantified considering the UMIs using the QIAseq miRNA Library Kit - Primary Quantification analysis tool from QIAgen GeneGlobe
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: plain text files containing smallRNA counts collapsed by UMIs

source_name: Primary cortical neurons

growth_protocol: Rat (Sprague Dawley) cortical cultures, E17 cortices were trypsinized and dissociated, the cell suspension sequentially filtered through 100-, 70-, and 40-μm cell strainers and then plated at a density of 100,000 cells/cm2 on poly-L-lysine coated 60 mm dishes. Medium exchange (50%) was performed every 3 days.

extract_protocol:
Total RNA was batch-isolated using the miRNeasy Mini kit (Qiagen) according to manufacturer's protocols. Only RNA with an RNA integrity number (RIN) 9.5, determined on a Bioanalyzer 2100 (Agilent), was subjected to library preparation.
Sequencing libraries were prepared using the QIAgen smallRNA Library Prep Kit with Unique Molecular Identifiers (UMIs) according to manufacturer's protocols.

treatment_protocol: Cortical neurons were transduced with lentiviral suspension expressing shNTC (control), shStau2 or shPum2 at 10 days in vitro (DIV). At 14 DIV, neurons were washed twice with warm HBSS, lysed in QIAzol (Qiagen) and frozen at -80°C until batch RNA isolation.

value: Sprague Dawley

value: E17 derived primary cortical neurons

value: shRNA against Pum2


title: Cortical_shStau2_Rep1 [JE01002]

description: Replicate 1

value: shRNA against Stau2


title: Cortical_shStau2_Rep3 [JE01008]

description: Replicate 3


title: Cortical_shNTC_Rep4 [JE01010]

description: Replicate 4

value: non-targeting control


title: Cortical_shNTC_Rep3 [JE01007]

description: Replicate 3


title: Tle4_P3_R1


title: Cortical_shPum2_Rep4 [JE01012]

description: Replicate 4


title: Cortical_shStau2_Rep4 [JE01011]

description: Replicate 4


title: Cortical_shStau2_Rep2 [JE01005]

description: Replicate 2


title: Cortical_shPum2_Rep3 [JE01009]

description: Replicate 3


title: Cortical_shNTC_Rep2 [JE01004]

description: Replicate 2


title: Heterogenous NLB (Wnt1-tdT negative) [sample-5]

city: Boston

first: Rhian

last: Stavely

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

institute: Massachusetts General Hospital

description: The muscularis of the small bowel was digested in collagenase-dispase solution to generate primary single-cell suspensions. Cells were cultured for 10 days in neuroproliferation medium to generate heterogenous spheroids before neural crest-derived cells were purified by FACS of Wnt1-tdT expressing cells. The Wnt1-tdT negative non-neural crest-derived population was collected for RNA isolation.

data_processing:
The sequencing libraries were multiplexed and clustered on one lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Paired End (PE) configuration.
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).  Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Quality control and adapter trimming of fastq files was performed using Fastp .
Reads were aligned to mouse reference genome (mm10) using HISAT.
Reads were quantified by FeatureCounts and data was normalised to counts per million (CPM)
Assembly: Mm10
Supplementary files format and content: Processed data contains count output in CPM

source_name: Cultured Cells

growth_protocol: Wnt1-Cre mice were crossed with R26R-tdT reporter mice to obtain Wnt1-Cre;tdTomato (Wnt1-tdT) mice in which all neural crest-derived cells are fluorescently labelled. Primary cells were isolated from the smooth muscle and myenteric plexus (SMMP) layer small bowel or posterior subcutaneous fat pads by enzymatic digestion in collagenase XI (1 mg ml-1) - dispase(250 µg ml-1) solution. Neural crest-derived cells were either purified by FACS and cultured to generate neurospheres (Method 1, M1), or cultured as heterogenous spheroids (neurosphere-like body, NLB) for 10 days and then purified by FACS to generate ‘Secondary’ neurospheres (Method 2, M2). Cells were cultured in neuroproliferation media containing Neurocult Mouse Proliferation Supplement (10%, StemCell Technologies), basic fibroblast growth factor (20 ng/mL, StemCell Technologies), epidermal growth factor (20 ng/mL, StemCell Technologies), heparin (0.0002%, StemCell Technologies) and penicillin and streptomycin (1%, Life Technologies, Thermo Fisher Scientific, Waltham, MA) in Neurocult Mouse Basal Medium (StemCell Technologies) for the duration of the culture period.

extract_protocol:
Samples were pooled equally from three 1-month old Wnt1-tdT mice (2 female and 1 male) and total RNA was extracted from ~50,000 cells per group following the Trizol Reagent User Guide.
SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments.

value: Small Bowel

tag: neural crest-derived

value: Non Neural crest-derived


title: Primary Wnt1-tdT cells (small bowel) [sample-3]

description: The muscularis of the small bowel was digested in collagenase-dispase solution to generate primary single-cell suspensions. Neural crest-derived cells were purified by FACS of Wnt1-tdT expressing cells before RNA isolation.

source_name: Primary Cells

value: Neural crest-derived


title: Heterogenous NLB (Wnt1-tdT positive) [sample-6]

description: The muscularis of the small bowel was digested in collagenase-dispase solution to generate primary single-cell suspensions. Cells were cultured for 10 days in neuroproliferation medium to generate heterogenous spheroids before neural crest-derived cells were purified by FACS of Wnt1-tdT expressing cells. The Wnt1-tdT positive neural crest-derived population was collected for RNA isolation.


title: Primary Wnt1-tdT cells (Adipose)  [sample-1]

description: The subcutaneous adipose tissue was digested in collagenase-dispase solution to generate primary single-cell suspensions. Neural crest-derived cells were purified by FACS of Wnt1-tdT expressing cells before RNA isolation.

value: Subcutaneous Adipose Tissue


title: Wnt1-tdT neurospheres (Adipose) [sample-2]

description: The subcutaneous adipose tissue was digested in collagenase-dispase solution to generate single-cell suspensions. Cells were cultured for 10 days in neuroproliferation medium to generate heterogenous spheroids before neural crest-derived cells were purified by FACS of Wnt1-tdT expressing cells. Purified neural crest-derived cells were cultured for a further 10 days to generate neurospheres prior to RNA isolation.


title: HC14

last: McCluskey

address: Guy's Hospital

institute: King's College London

data_processing:
Sequencing output files were demultiplexed and coverted to fastq files using Cell Ranger v3.0.2 (10X genomics).
Cell Ranger was used to align demultiplexed reads to the reference genome, perform filtering, barcode counting, UMI counting and estimate the number of cells.
Data analaysis was performed in R using Seurat v3.
Genome_build: Ensembl release 86 and GRCh38.p7
Supplementary_files_format_and_content: For each sample there are three associated files: tab-seperated values file containing barcdoes, tab-separated file containing annotated genes (features), matrix file containing UMI counts and indices for the barcode and gene tsv files

extract_protocol:
PBMCs were isolated from the whole blood of either PPP patients or healthy controls and then cryopreserved until sequencing
Libraries were prepared using the Chromium 10X Single Cell 3'  reagent Kits v2 according to the manufacturer's instructions

value: Peripheral blood mononuclear cells

tag: disease state

value: Healthy control


title: Cortical_shNTC_Rep1 [JE01001]

description: Replicate 1


title: Wnt1-tdT neurosphere M2 (small bowel) [sample-7]

description: The muscularis of the small bowel was digested in collagenase-dispase solution to generate primary single-cell suspensions. Cells were cultured for 10 days in neuroproliferation medium to generate heterogenous spheroids before neural crest-derived cells were purified by FACS of Wnt1-tdT expressing cells. Purified neural crest-derived cells were cultured for a further 10 days to generate neurospheres prior to RNA isolation.


title: HC11


title: Cortical_shPum2_Rep2 [JE01006]

description: Replicate 2


title: HC13


title: Wnt1-tdT neurospheres M1 (small bowel) [sample-4]

description: The muscularis of the small bowel was digested in collagenase-dispase solution to generate primary single-cell suspensions. Neural crest-derived cells were purified by FACS of Wnt1-tdT expressing cells. Purified neural crest-derived cells were cultured for 10 days to generate neurospheres prior to RNA isolation.


title: PPP07

value: Palmoplantar pustulosis


title: HC10


title: PPP06


title: PPP08


title: PPP04


title: PPP05


title: PPP02