title: ALVACComp_P851_post2nd_48h


title: ALVACComp_P836_post1st_48h

status: Public on Aug 13 2021

type: RNA

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

country: Canada

institute: RPM Bioinfo Solutions

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

molecule: total RNA

organism: Macaca mulatta

source_name: post-1st immunization_48 hours

label_protocol: Isolated mRNA was amplified and biotinylated using the TargetAmpTM 2-Round Biotin-aRNA Amplification Kit 3.0 for microarray studies

growth_protocol: Not applicable. Cells were isolated directly from PBMCs

extract_protocol: RNA was extracted from PBMC using TRIzol and phenol-chloroform extraction

treatment_protocol: Not applicable. Cells were taken directly from blood

tag: subject

tag: vaccination number

value: post-1st immunization

tag: vaccination time

value: Week 0

tag: time after immunization

value: 48 hours

tag: immunogen

tag: cell type

value: PBMC

tag: tissue

value: blood


title: ALVACComp_P863_prevax

value: pre-vaccination

value: Day 0

value: pre


title: ALVACComp_P836_post2nd_72h

source_name: post-2nd immunization_72 hours

value: post-2nd immunization

value: Week 12

value: 72 hours


title: ALVACComp_P851_post1st_16h

source_name: post-1st immunization_16 hours

value: 16 hours


title: ALVACComp_P836_post3rd_24h

source_name: post-3rd immunization_24 hours

value: post-3rd immunization

value: Week 4

value: 24 hours


title: MCC_H441_rep2

type: SRA

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

description: Micrococcal nuclease digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

library_source: genomic

data_processing:
Library strategy: Micro Capture-C (MCC)
The raw fastq file is processed to reconstruct a single read from the paired end sequencing. This is then mapped to the 800bp sequence surrounding the capture oligonucleotide using the non-stringent aligner BLAT. This allows the reads to be cut into ‘slices’ depending on whether they align to the sequence around the capture site. This strategy allows ligation junctions in the read to be determined with base pair accuracy. The resulting fastq file is aligned to the genome using bowtie and replicates for each cell type merged.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: NCI-H441 Lung Epithelia

growth_protocol:
NCI-H441 cells (ATCC HTB-174) were grown in RPMI 1640 medium (Gibco) supplemented with 10% non-heat inactivated FBS (Sigma) and 1% Penicillin-Streptomycin (Gibco), cells were given fresh media every two days and passaged by light trypsination twice weekly
Cells were resuspended in aliquots of 1 x 107 in 10 ml media with 10% FCS in a 15-ml conical centrifuge tube using an automated cell counter (CountessII, Thermo Fisher). Formaldehyde (37% (vol/vol)) was added to each aliquot to make a final concentration of 2% (vol/vol) and the cells were incubated on a roller mixer for 10 minutes at room temperature. The crosslinking reaction was quenched with cold 1 M glycine to a final concentration 130 mM and the sample was centrifuged (5 min at 220 g). The supernatant was discarded and the cell pellet was washed with 10 ml cold Phosphate Buffered Saline (PBS) and reconstituted in 1 ml PBS. An automated cell count on was performed on 10 ml of the cell suspension to reconfirm the cell number. Digitonin (Sigma D-141) was prepared fresh for each experiment (0.5% in dimethylsulfoxide (DMSO) (wt/vol)). Each batch of digitonin was tested for its ability to permeabilise cells at a concentration of 0.005% (wt/vol). 10 ml digitonin was added to make a final concentration of 0.005% (wt/vol). For standard nuclear preparation, the pellet was resuspended in 5ml cold lysis buffer (TRIS-HCl pH 8 10 mM, NaCl 10 mM, Igepal NP-40 (Sigma I8896) 0.2%, cOmplete proteinase inhibitor cocktail (PIC) (Roche 4693116001) (x1 tablet / 50 ml)) and incubated on ice for 20 min. The nuclei were centrifuged (300 g, 5 min) and resuspended in 1ml lysis buffer.

extract_protocol:
Qiagen DNeasy blood and tissue kit
7-10 µg of each 3C library was sonicated to a mean fragment size of 200 bp using a Covaris S220 Focussed Ultrasonicator (1-3 cycles of 60s: duty cycle 10%; intensity 5; cycles per burst 200). The library size was assessed using an Agilent TapeStation (DNA 1000) and an Ampure XP (Beckman Coulter) bead clean-up was performed once the sample had been adequately sonicated. To maximise library complexity three aliquots, each containing 2 µg sonicated 3C library, were processed in parallel for each sample to add sequencing adaptors. NEB Ultra II reagents were used following the standard protocol with the following modifications: first, additional adapter was added into the ligation reactions (7.5 µl rather than 2.5 µl); no size selection was performed (Ampure XP bead clean ups were always performed with a sample:bead ratio of 1:1.8) and the final PCR to add indices was amplified in triplicate from each aliquot using the Herculase II PCR kit (Agilent) to maximise DNA yield. All parallel library preparations and PCR reactions were pooled for each reaction.

tag: cell line

value: Epithelial cell


title: BAL1

city: Rochester

first: Irfan

last: Rahman

state: NY

address: 601 elmwood ave

department: Environmental Medicine

country: USA

institute: University of Rochester Medical Center

library_source: transcriptomic

data_processing:
The raw sequence reads analyzed by the team of bioinformaticians at Norgen using their advanced analysis pipeline for the processing of raw counts and alignment to endogenous genome and annotated transcriptome
The miRNA data from various batches normalized using trimmed mean of M-values (TMM) normalization method
EdgeR statistical software package used for DE analysis. The DE was considered significant if log fold change of ≥ 1 or ≤ -1 at p- value and FDR of ≤ 0.05 was reported for the miRNA target.
GO analyses and KEGG analyses performed on the data
Genome_build: hg18
Supplementary_files_format_and_content: .txt files for DE analysed files and significantly varied files
Supplementary_files_format_and_content: .txt files for TMM

source_name: BALF

extract_protocol:
BALF exosome isolation using Plasma/Serum Exosome Purification and RNA Isolation Midi Kit from Norgen Biotek. Lung tissue exosome isolated using optimized protocol described by Dooner et al (2018). RNA isolation using Exosomal RNA isolation kit (for BALF) from Norgen and miRNeasy Mini Kit (for lung tissues)from Qiagen.
The library preparation was performed using the standard library preparation workflow of Norgen using Norgen Biotek Small RNA Library Prep Kit

tag: group

value: Non-smoker


title: S90_grade1

city: Norwich

first: Darrell

last: Green

address: Earlham Road

department: Norwich Medical School

institute: University of East Anglia

description: Small RNA seq

data_processing:
The original fastq files were converted to fasta format and reads without Ns were kept for further analysis
The 3' adapter and HD signatures [Sorefan et al. 2012] were trimmed and the files were converted from redundant to non-redundant format
The reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al. 2008]
The reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
The abundances of the reads were normalized using the RPM method [Mortazavi et al. 2008]
The differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20
Genome_build: GRCh38
Supplementary_files_format_and_content: *csv: Comma-separated text files include sequences and raw abundances.

source_name: blood spot

extract_protocol:
Fingerstick samples were used for RNA extraction before construction of small RNA libraries
Illumina compatible method with HD adapters

tag: disease state

value: grade 1 chondrosarcoma


title: S93_clearCell

description: Small RNA seq

value: Clear cell


title: MCC_H441_rep1


title: S114_chondroblastic

description: Small RNA seq

value: Chondroblastic


title: ALVACComp_P464_post1st_16h

value: post-1st immunization

value: Week 0

value: PBMC


title: ALVACComp_P863_post2nd_16h

source_name: post-2nd immunization_16 hours

value: blood


title: MCC_HUDEP2_rep3

source_name: Human Umbilical Cord Blood-Derived Erythroid Progenitor

growth_protocol:
Human Umbilical Derived Erythroid Progenitor line 2 cells (HUDEP-2; Kurita, PLoS One 2013) were maintained at 0.7-1.5x106 cells ml-1 in HUDEP expansion media and changed into fresh media containing 2x doxycycline (DOX) every two days.
Cells were resuspended in aliquots of 1 x 107 in 10 ml media with 10% FCS in a 15-ml conical centrifuge tube using an automated cell counter (CountessII, Thermo Fisher). Formaldehyde (37% (vol/vol)) was added to each aliquot to make a final concentration of 2% (vol/vol) and the cells were incubated on a roller mixer for 10 minutes at room temperature. The crosslinking reaction was quenched with cold 1 M glycine to a final concentration 130 mM and the sample was centrifuged (5 min at 220 g). The supernatant was discarded and the cell pellet was washed with 10 ml cold Phosphate Buffered Saline (PBS) and reconstituted in 1 ml PBS. An automated cell count on was performed on 10 ml of the cell suspension to reconfirm the cell number. Digitonin (Sigma D-141) was prepared fresh for each experiment (0.5% in dimethylsulfoxide (DMSO) (wt/vol)). Each batch of digitonin was tested for its ability to permeabilise cells at a concentration of 0.005% (wt/vol). 10 ml digitonin was added to make a final concentration of 0.005% (wt/vol). For standard nuclear preparation, the pellet was resuspended in 5ml cold lysis buffer (TRIS-HCl pH 8 10 mM, NaCl 10 mM, Igepal NP-40 (Sigma I8896) 0.2%, cOmplete proteinase inhibitor cocktail (PIC) (Roche 4693116001) (x1 tablet / 50 ml)) and incubated on ice for 20 min. The nuclei were centrifuged (300 g, 5 min) and resuspended in 1ml lysis buffer.

value: Erythroid cell


title: ALVACComp_P464_post3rd_24h


title: ALVACComp_P464_post1st_48h

value: 48 hours


title: MCC_HUDEP2_rep2


title: S122_Paget

description: Small RNA seq

value: Paget disease


title: MCC_HUDEP2_rep1


title: MCC_HUVEC_rep3

source_name: Human Umbilical Vein endothelial Cell

growth_protocol:
Primary neonatal Human Umbilical Vein Endothelial Cells (HUVEC; Lonza, Gibco, PromoCell) were expanded in endothelial cell growth medium (Sigma) up to five passages following the manufacturer’s protocol. For passaging, HUVECs were grown to 60% confluence, washed with HBSS at room temperature and sub-cultured following light trypsination using Trypsin-EDTA (Sigma) at room temperature with trypsin inhibitor (Sigma) added upon rounding of the cells to achieve gentle release from the flask. HUVECs were fixed in RPMI supplemented with 10 % FBS
Cells were resuspended in aliquots of 1 x 107 in 10 ml media with 10% FCS in a 15-ml conical centrifuge tube using an automated cell counter (CountessII, Thermo Fisher). Formaldehyde (37% (vol/vol)) was added to each aliquot to make a final concentration of 2% (vol/vol) and the cells were incubated on a roller mixer for 10 minutes at room temperature. The crosslinking reaction was quenched with cold 1 M glycine to a final concentration 130 mM and the sample was centrifuged (5 min at 220 g). The supernatant was discarded and the cell pellet was washed with 10 ml cold Phosphate Buffered Saline (PBS) and reconstituted in 1 ml PBS. An automated cell count on was performed on 10 ml of the cell suspension to reconfirm the cell number. Digitonin (Sigma D-141) was prepared fresh for each experiment (0.5% in dimethylsulfoxide (DMSO) (wt/vol)). Each batch of digitonin was tested for its ability to permeabilise cells at a concentration of 0.005% (wt/vol). 10 ml digitonin was added to make a final concentration of 0.005% (wt/vol). For standard nuclear preparation, the pellet was resuspended in 5ml cold lysis buffer (TRIS-HCl pH 8 10 mM, NaCl 10 mM, Igepal NP-40 (Sigma I8896) 0.2%, cOmplete proteinase inhibitor cocktail (PIC) (Roche 4693116001) (x1 tablet / 50 ml)) and incubated on ice for 20 min. The nuclei were centrifuged (300 g, 5 min) and resuspended in 1ml lysis buffer.

value: HUVEC

value: Endothelial cell


title: S107_normal

description: Small RNA seq

value: normal patient


title: MCC_HUVEC_rep2


title: S78_normal

description: Small RNA seq


title: ALVACComp_P836_post2nd_24h

source_name: post-2nd immunization_24 hours

value: post-2nd immunization

value: Week 12


title: ALVACComp_P862_post3rd_16h

source_name: post-3rd immunization_16 hours

value: post-3rd immunization

value: Week 4

value: 16 hours


title: ALVACComp_P841_post2nd_48h

source_name: post-2nd immunization_48 hours


title: ALVACComp_P863_post1st_72h

source_name: post-1st immunization_72 hours

value: 72 hours


title: ALVACComp_P464_post3rd_48h

source_name: post-3rd immunization_48 hours


title: ALVACComp_P841_post2nd_72h


title: MCC_HUVEC_rep1


title: MCC_IMR90_rep5

source_name: IMR-90 Lung Fibroblast

growth_protocol:
IMR-90 lung fibroblasts (ATCC CCL-186) were cultured in Eagle’s Minimal Essential Medium supplemented with 10% FBS, 1 mM sodium pyruvate (Gibco), 1x MEM Non-Essential Amino Acids (Gibco) and Penicillin-Streptomycin (100 U/mL each) Cell were sub-cultured every two-three days following light trypsination using 0.05% Trypsin-EDTA (Gibco)
Cells were resuspended in aliquots of 1 x 107 in 10 ml media with 10% FCS in a 15-ml conical centrifuge tube using an automated cell counter (CountessII, Thermo Fisher). Formaldehyde (37% (vol/vol)) was added to each aliquot to make a final concentration of 2% (vol/vol) and the cells were incubated on a roller mixer for 10 minutes at room temperature. The crosslinking reaction was quenched with cold 1 M glycine to a final concentration 130 mM and the sample was centrifuged (5 min at 220 g). The supernatant was discarded and the cell pellet was washed with 10 ml cold Phosphate Buffered Saline (PBS) and reconstituted in 1 ml PBS. An automated cell count on was performed on 10 ml of the cell suspension to reconfirm the cell number. Digitonin (Sigma D-141) was prepared fresh for each experiment (0.5% in dimethylsulfoxide (DMSO) (wt/vol)). Each batch of digitonin was tested for its ability to permeabilise cells at a concentration of 0.005% (wt/vol). 10 ml digitonin was added to make a final concentration of 0.005% (wt/vol). For standard nuclear preparation, the pellet was resuspended in 5ml cold lysis buffer (TRIS-HCl pH 8 10 mM, NaCl 10 mM, Igepal NP-40 (Sigma I8896) 0.2%, cOmplete proteinase inhibitor cocktail (PIC) (Roche 4693116001) (x1 tablet / 50 ml)) and incubated on ice for 20 min. The nuclei were centrifuged (300 g, 5 min) and resuspended in 1ml lysis buffer.

value: Fibroblast cell


title: MCC_IMR90_rep4


title: S73_normal

description: Small RNA seq


title: S77_Paget

description: Small RNA seq


title: S72_normal

description: Small RNA seq


title: S71_normal

description: Small RNA seq


title: ALVACComp_P863_post2nd_24h

value: 24 hours


title: ALVACComp_P836_post1st_16h

value: post-1st immunization

value: Week 0


title: MCC_IMR90_rep3


title: MCC_IMR90_rep2


title: S70_normal

description: Small RNA seq

value: blood


title: S69_normal

description: Small RNA seq


title: S52_normal

description: Small RNA seq


title: MCC_IMR90_rep1


title: H441_ATAC_rep4

description: Genome-wide library of tagmented fragments

data_processing:
Mapping : bowtie2 -x $hg38 -1 ${read1} -2 ${read2} | samtools view -b > ${name}.unsorted.bam
Sorting: samtools sort -o ${name}.srt.bam ${name}.unsorted.bam
Removing duplicates: samtools rmdup
Generating bigwig tracks: deeptools
Genome_build: hg38
Supplementary_files_format_and_content: bigWig: bamCoverage --bam ${name}.bam -o ${name}.bw --binSize 10 --normalizeUsing RPKM --minMappingQuality 1

growth_protocol: NCI-H441 cells (ATCC HTB-174) were grown in RPMI 1640 medium (Gibco) supplemented with 10% non-heat inactivated FBS (Sigma) and 1% Penicillin-Streptomycin (Gibco), cells were given fresh media every two days and passaged by light trypsination twice weekly

extract_protocol:
ATAC-seq was performed as published (Buenrostro et al., 2013). 10,000-50,000 cells were used per biological replicate where possible; if cells numbered less than 10,000 an optimised low cell number protocol was used. Cells were spun at 500g for 10 min, then lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl 3 mM MgCl2, 0.1% IGEPAL CA-630). Transposition was then performed with Tn5 transposase (Nextera, Illumina) for 30 min at 37ÅãC following the reaction volumes as published. DNA was purified using the Qiagen MinElute kit following the manufacturer’s instructions, then eluted in 20μl of elution buffer; samples could be stored at this point at -20ÅãC. Libraries were amplified and barcoded using the NEBNext 2xMastermix kit with custom primers as published (Buenrostro et al., 2013). ATAC-seq library profiles were visualized using the D1000 tape on the Agilent Tapestation to ensure correct tagmentation. Libraries were quantified using the universal library quantification kit (KAPA Biosystems) prior to massively parallel sequencing using a standard Illumina protocol (NextSeq High Output v2 75 cycle sequencing kit). The low cell number protocol uses proportionally less lysis buffer and Tn5 transposase (Corces et al., 2017). After spinning at 500g for 10 min and removing the supernatant, cells were permeabilised and tagmented with Dig-transposition buffer (25 μL 2x TD buffer [Illumina], 2.5 μL Tn5 Transposase, 0.5 μL 1% digitonin and 22 μL H2O) for 30 min. After the transposition step, samples were processed as per larger cell numbers.
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).

value: Epithelial cell


title: H441_ATAC_rep3


title: H441_ATAC_rep2


title: Mexico Man

description:
sRNA
Small RNA-seq
osteoblast
osteoclast

data_processing:
The original fastq files were converted to fasta format and reads without Ns were kept for further analysis.
The 3' adapter and HD signatures [Sorefan et al. 2012] were trimmed and the files were converted from redundant to non-redundant format.
The reads were mapped to the reference genome, allowing 0 mis-matches and 0 gaps using PatMaN [Pruffer et al. 2008].
The reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRBase, release 21.
Genome_build: GRCh38
Supplementary_files_format_and_content: S133_MexicoMan.csv: Comma-separated text file includes sequences and expression levels (raw counts).

source_name: bone tissue

extract_protocol:
Bone tissue was homogenised in liquid nitrogen before RNA extraction using the miRCURY RNA isolation kit (Exiqon). Small RNA libraries were constructed using HD adapters and commercially available reagents.
Small RNA libraries prepared as described in Xu et al. 2015.

value: femur

tag: age

value: 5000 years


title: S113_chondroblastic_osteosarcoma

description: Small RNA-seq

data_processing:
The original fastq files were converted to fasta format and reads without Ns were kept for further analysis.
The 3' adapter and HD signatures [Sorefan et al. 2012] were trimmed and the files were converted from redundant to non-redundant format.
The reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al. 2008].
The reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRBase, release 21.
The abundances of the reads were normalized using the RPM method [Mortazavi et al. 2008].
The differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20.
Genome_build: GRCh38
Supplementary_files_format_and_content: *csv: Comma-separated text files include sequences and raw abundances.

source_name: malignant osteosarcoma

extract_protocol:
Resected tissue was used for RNA extraction before small RNA library construction.
Illumina compatible method using HD adapters.

value: chondroblastic osteosarcoma

value: osteosarcoma


title: C. elegans daf2nr-4

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
Sequencing pairs were aligned to the C. elegans genome WBcel235 (ce11) and Ensembl transcriptome (release 95) by using STAR (v.2.7.0e). Aligned pairs on genes or transcripts were quantified by using RSEM (v.1.3.1). Detailed parameters of alignment and quantification were calculated by following guidelines of ENCODE long RNA-Seq processing pipeline.
Genome_build: WBcel235 (ce11)
Supplementary_files_format_and_content: txt files with read counts were generated by using RSEM (v.1.3.1)

organism: Caenorhabditis elegans

source_name: Whole body

growth_protocol: Worms were grown on NGM plates as previously described in 'Maintenance of C. elegans (Stiernagle T, WormBook, 2006)'.

extract_protocol:
RNA extraction was performed as previously described (Park et al., Sci Adv, 2020). Total RNA in the animals was extracted using RNAiso plus (Takara, Seta, Kyoto, Japan).
Libraries were constructed with TruSeq mRNA LT Sample Prep Kit (Illumina, CA, USA) by Macrogen Inc. (Seoul, South Korea) following the manufacture’s instruction.

treatment_protocol: daf-2(e1370), daf-2(e1370); daf-18(yh1), and daf-2(e1370); daf-18(nr2037) mutant animals were synchronized by using an embryo bleaching method, and synchronized larvae were fed with OP50 E. coli until the worms reached young adult stage. Worms were harvested with M9 buffer, washed to remove remaining bacteria.

tag: strain

tag: genotype

tag: devlopment stage

value: Day 0 adult


title: H441_ATAC_rep1


title: C. elegans daf2nr-2


title: DD/CM/ID 59

type: genomic

city: Jeddah

first: Sajjad

last: Karim

state: Makka

address: Sulemania, CEGMR-80216

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

description: Developmental delay and Dysmorphic features, VSD, Intellectual Disability

hyb_protocol: Probe mixture of Cy3-labelled sample DNA, Cy5-labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 52 μl of Agilent 10X Blocking Agent and 260 μl of Agilent 2X Hybridization Buffer (Part/Cat No of human reference DNA Male and Female: 5190-3796 and 5190-3797, Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 seconds and incubated at 37C for 30 minutes. The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Arrays were washed according to the manufacturer’s recommendation and air dried.

scan_protocol: Arrays were scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc).

data_processing: Data were processed using Agilent’s Feature Extraction software protocol for array-CGH data. To analyze genomic imbalance tumour samples (2 arrays each) the processed R signal and processed G signal columns from the Agilent Feature Extraction-generated a-CGH .txt files were imported into PGS. The tumour-specific signal across all probes was normalized as a ratio to baseline using Normalise to Baseline Tool in PGS, where baseline data corresponded to the normal human DNA. The data was then log2 transformed using the PGS Normalization and Scaling Tool. In order to detect regions of genomic gain and loss we applied the Genomic Segmentation tool with segmentation parameters set at: min. probes: 10, p-value threshold: 0.01, and signal to noise: 0.1. Region report was set at values bellow -.5/+.5 (log2) and p-value threshold of 0.05 for 2/2 (replicate) arrays in individual analysis or at 40% cut-off in cumulative analysis (i.e. 4/10 tumour samples). Regions of significant gain or loss were annotated to the corresponding genes present on the Affymetrix Gene 1.0 Array using the HuGene-1_0-st-v1.na24.hg18.transcript.csv file. Visualizations and VENN analysis were performed in PGS.

source_name: Peripheral Blood

label_protocol: Labelling was performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, DNA was labelled with 1.5 - 3 mM Cy3-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA).

growth_protocol: Not Applicable

extract_protocol: DNA was extracted after harvesting the cells by Trypsin (Invitrogen) followed by phenol-chloroform extraction and subsequent precipitation in 100% ethanol. DNA precipitate was washed with 70% ethanol then eluted in DNAse free water.

treatment_protocol: Not Applicable

value: 5 years

tag: gender

value: Female

tag: phenotype

value: Peripheral Blood

source_name: Agilent Euro reference DNA

tag: sample type

value: reference sample


title: C. elegans daf2nr-1


title: BOEC_ATAC_rep4

source_name: BOEC

growth_protocol: Blood outgrowth endothelial cells (BOECs) were isolated as previously described. Briefly 20-40 mL of fresh blood was diluted 1:1 with PBS, layered over histopaque (Sigma) and centrifuged for 15 min at 500 rcf, brake off. Peripheral blood mononuclear cells were washed with PBS then resuspended in EGM-2 Bullet kit growth media (Lonza) supplemented with 10% heat inactivated FBS. Cells were cultured for 21-28 days in collagen coated flasks until BOEC colonies formed. BOEC colonies were passaged by light trypsinisation. BOEC cells were passaged twice before any experimentation to ensure endothelial cell purity, which was also confirmed by FACS and immunofluorescence. BOEC cells were fixed in growth medium.

value: BOEC

value: Endothelial cell


title: DD/CM/ID 58

description: Developmental delay and Delayed Speech, Microcephaly, Brain Atrophy, Seizures

value: 5.6 years


title: DD/CM/ID 61

description: Developmental delay and Autism

value: 6 years

value: Male

value: Developmental delay and Autism


title: DD/CM/ID 63

description: Developmental delay and Skeletal and cardiac abnormalities, Marfan Syndrome


title: DD/CM/ID 62

description: Developmental delay and Developmental Delay


title: DD/CM/ID 55

description: Developmental delay and No Speech, Intellectual Disability, ADHD,Epilepsy


title: C. elegans daf2yh1-4


title: BOEC_ATAC_rep2


title: DD/CM/ID 54

description: Developmental delay and Hypotonia, Microcephaly

value: 7 months


title: DD/CM/ID 60

description: Developmental delay and Delayed Speech

value: Developmental delay and Delayed Speech


title: DD/CM/ID 53

description: Developmental delay and Delayed Speech, Microcephaly

value: 5.9 years


title: BOEC_ATAC_rep3


title: DD/CM/ID 57

description: Developmental delay and Delayed Speech, Floppy baby syndrome.

value: 2.5 years


title: DD/CM/ID 50

description: Developmental delay and Not Walking, No speech

value: 2 years


title: C. elegans daf2yh1-3


title: DD/CM/ID 56

description: Developmental delay and Dysmorphic, Hyperactive, Intellectual Disability, ADHD, Small Ears, Seizures

value: 12 years


title: DD/CM/ID 51

description: Developmental delay and No Walking, Delayed Speech, Seizures

value: 3 years


title: DD/CM/ID 49

description: Developmental delay and Intellectual Disability, Delayed Speech, Delayed Walking

value: 8 years


title: BOEC_ATAC_rep1


title: IMR90_H3K4me1

description: Genome-wide library of Immunoprecipitated fragments

growth_protocol:
IMR-90 lung fibroblasts (ATCC CCL-186) were cultured in Eagle’s Minimal Essential Medium supplemented with 10% FBS, 1 mM sodium pyruvate (Gibco), 1x MEM Non-Essential Amino Acids (Gibco) and Penicillin-Streptomycin (100 U/mL each) Cell were sub-cultured every two-three days following light trypsination using 0.05% Trypsin-EDTA (Gibco)
For ChIP, single cell suspensions of 106 cells mL-1 in growth media were generated after light trypsin treatment. Cells were fixed by addition of 1% formaldehyde for 10 min at room temperature, which was quenched by addition of glycine at a final concentration of 125 mM. Fixed cells were washed with PBS and snap frozen. Cell lysis and immunoprecipitation was carried out using ChIP Assay Kit (Merk Millipore) on 5x 106 cells by overnight incubation with 1 µL polyclonal antibody.

extract_protocol:
DNA was isolated by phenol- chloroform isoamylalcohol extraction and ethanol precipitation
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

value: Fibroblast cell

tag: antibody

value: 0.3 µg ab8895 (AbCam)


title: C. elegans daf2yh1-2

value: Day 0 adult


title: DD/CM/ID 42

description: Developmental delay and Congenital heart disease, DiGeorge Syndrome

value: 3 months

value: Peripheral Blood

value: reference sample


title: DD/CM/ID 52

description: Developmental delay and Floppy, Dysmorphic, Left Axial Polydactyly


title: DD/CM/ID 38

value: Female

value: Developmental delay and Developmental Delay


title: C. elegans daf2yh1-1


title: C. elegans daf2-4


title: DD/CM/ID 46

description: Developmental delay and Microcephaly, Intellectual Disability, Dysmorphic

value: 4.5 years

value: Male


title: DD/CM/ID 41

description: Developmental delay and GH Deficiency

value: 8 months

value: Developmental delay and GH Deficiency


title: DD/CM/ID 40

description: Developmental delay and Dysmorphic feature

value: 4.7 years


title: DD/CM/ID 48

description: Developmental delay and Bilateral disease, Talipes, Microcephaly

value: 6 years


title: DD/CM/ID 36

description: Developmental delay and Short Stature

value: 1.5 years

value: Developmental delay and Short Stature


title: DD/CM/ID 39

description: Developmental delay and Delayed Speech, Dysmorphic Feature, Mental Disability

value: 3.6 years


title: DD/CM/ID 37

description: Developmental delay and Congenital Heart Disease

value: 10 months


title: DD/CM/ID 47

description: Developmental delay and Dysmorphic features, Delayed Speech,

value: 16 years


title: DD/CM/ID 44

description: Developmental delay and Hirschsprung Disease, Dilated Lat. Ventricle


title: C. elegans daf2-3

value: Day 0 adult


title: DD/CM/ID 43

description: Developmental delay and Congenital Heart Disease, ASD, PWS

value: 1.7 years


title: DD/CM/ID 45

description: Developmental delay and Hypospadias, Undescended Testis, VSD, Dysmorphic features

value: 9.5 years

value: Peripheral Blood


title: IMR90_Input

value: Fibroblast cell


title: IMR90_H3K27ac

value: 0.3 µg ab4729 (AbCam)


title: C. elegans daf2-2


title: BOEC Input

growth_protocol:
Blood outgrowth endothelial cells (BOECs) were isolated as previously described. Briefly 20-40 mL of fresh blood was diluted 1:1 with PBS, layered over histopaque (Sigma) and centrifuged for 15 min at 500 rcf, brake off. Peripheral blood mononuclear cells were washed with PBS then resuspended in EGM-2 Bullet kit growth media (Lonza) supplemented with 10% heat inactivated FBS. Cells were cultured for 21-28 days in collagen coated flasks until BOEC colonies formed. BOEC colonies were passaged by light trypsinisation. BOEC cells were passaged twice before any experimentation to ensure endothelial cell purity, which was also confirmed by FACS and immunofluorescence. BOEC cells were fixed in growth medium.
For ChIP, single cell suspensions of 106 cells mL-1 in growth media were generated after light trypsin treatment. Cells were fixed by addition of 1% formaldehyde for 10 min at room temperature, which was quenched by addition of glycine at a final concentration of 125 mM. Fixed cells were washed with PBS and snap frozen. Cell lysis and immunoprecipitation was carried out using ChIP Assay Kit (Merk Millipore) on 5x 106 cells by overnight incubation with 1 µL polyclonal antibody.

value: BOEC

value: Endothelial cell


title: DD/CM/ID 34

description: Developmental delay and Ambiguous Genitalia, Dysmorphic

value: 29 days

value: Female

value: reference sample


title: DD/CM/ID 35

description: Developmental delay and Fragile X syndrome

value: 6 years

value: Male


title: DD/CM/ID 33

description: Developmental delay and Hypotonia

value: 6 months

value: Developmental delay and Hypotonia


title: C. elegans daf2-1


title: HPAFII/tet-MUC1shRNA dox 3

city: Boston

first: Yoshihiro

last: Morimoto

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).

source_name: HPAFII

growth_protocol: HPAF-II cells were cultured in Eagle’s Minimum Essential Medium (ATCC) supplemented with 10% fetal bovine serum (FBS). AsPC-1 cells were cultured in RPMI 1640 medium (Corning, NY, USA) supplemented with 10% FBS and 2 mM glutamine.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline.

value: pancreatic adenocarcinoma

tag: treatment

value: puromycin resistance

tag: tag

value: 500 ng/ml doxycycline


title: H441_Input

growth_protocol:
NCI-H441 cells (ATCC HTB-174) were grown in RPMI 1640 medium (Gibco) supplemented with 10% non-heat inactivated FBS (Sigma) and 1% Penicillin-Streptomycin (Gibco), cells were given fresh media every two days and passaged by light trypsination twice weekly
For ChIP, single cell suspensions of 106 cells mL-1 in growth media were generated after light trypsin treatment. Cells were fixed by addition of 1% formaldehyde for 10 min at room temperature, which was quenched by addition of glycine at a final concentration of 125 mM. Fixed cells were washed with PBS and snap frozen. Cell lysis and immunoprecipitation was carried out using ChIP Assay Kit (Merk Millipore) on 5x 106 cells by overnight incubation with 1 µL polyclonal antibody.

value: Epithelial cell


title: H441_CEBPB


title: DD/CM/ID 28

description: Developmental delay and Intellectual Disability, Delayed Speech,

value: 8 years


title: HPAFII/tet-MUC1shRNA dox 1


title: HPAFII/tet-MUC1shRNA dox 2


title: DD/CM/ID 32

description: Developmental delay and Dysmorphic feature, Low-set Ears, Closed VSD

value: 1 month

value: Peripheral Blood


title: DD/CM/ID 29

description: Developmental delay and Delayed Walking, Unstable, Muscle Wasting

value: 4 years


title: HPAFII/tet-MUC1shRNA cont3

value: 0.1% DMSO as the vehicle control


title: H441_H3K27ac

description: Genome-wide library of Immunoprecipitated fragments

value: 0.3 µg ab4729 (AbCam)


title: DD/CM/ID 30

value: Developmental delay and Congenital Heart Disease


title: DD/CM/ID 31

description: Developmental delay and Delayed Speech, Delayed Walking, Hypotonia,

value: 3.4 years

value: Female


title: DD/CM/ID 27

value: 4.7 years

value: Developmental delay and Dysmorphic feature

value: reference sample


title: HUVEC_CEBPB

source_name: HUVEC

growth_protocol:
Primary neonatal Human Umbilical Vein Endothelial Cells (HUVEC; Lonza, Gibco, PromoCell) were expanded in endothelial cell growth medium (Sigma) up to five passages following the manufacturer’s protocol. For passaging, HUVECs were grown to 60% confluence, washed with HBSS at room temperature and sub-cultured following light trypsination using Trypsin-EDTA (Sigma) at room temperature with trypsin inhibitor (Sigma) added upon rounding of the cells to achieve gentle release from the flask. HUVECs were fixed in RPMI supplemented with 10 % FBS
For ChIP, single cell suspensions of 106 cells mL-1 in growth media were generated after light trypsin treatment. Cells were fixed by addition of 1% formaldehyde for 10 min at room temperature, which was quenched by addition of glycine at a final concentration of 125 mM. Fixed cells were washed with PBS and snap frozen. Cell lysis and immunoprecipitation was carried out using ChIP Assay Kit (Merk Millipore) on 5x 106 cells by overnight incubation with 1 µL polyclonal antibody.

value: HUVEC

value: Endothelial cell


title: DD/CM/ID 26

description: Developmental delay and Delayed Speech, Dysmorphic feature

value: 2 years

value: Male


title: PBMC sample from subject HC-9 at time point 0

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

data_processing:
Processing and analysis of bulk B cell receptor sequences was carried out using tools from the Immcantation framework as done previously (44). Preprocessing was a performed using pRESTO. Briefly, sequences with a phred score below 20 were removed and only those that  contained constant region and template switch sequences were preserved. UMI sequences were then grouped, and consensus sequences were constructed for each group and assembled into V(D)J sequences in a two-step process involving an analysis of overlapping sequences (<8 nucleotides) or alignment against the IMGT (the international ImMunoGeneTics information system®) IGHV reference (IMGT/GENE-DB v3.1.19; retrieved December 1, 2019) if no significant overlap was found. Isotypes were assigned by local alignment of the 3' end of the V(D)J sequence to constant region sequences. Duplicate sequences were removed and only V(D)J sequences reconstructed from more than 1 amplicon were preserved.
V(D)J germline genes were assigned to reconstructed V(D)J sequences using IgBLAST v.1.14.0 and also using the December 1, 2019 version of the IMGT gene database (45). V(D)J sequences with IGH associated V and J genes were then selected for further analysis and non-functional sequences were removed. Germline sequences were reconstructed for each V(D)J sequence with D segment and N/P regions masked (with Ns) using the CreateGermlines.py function within Change-O v1.0.0(46). VH gene nucleotides up to IMGT position 312 were translated from both the aligned sequence and germline reconstructed V(D)J sequence using BioPython v1.75. To quantify the frequency of N-X-S/T glycosylation motifs, matches to the regular expression pattern "N[^P][S,T]" were quantified for each  translated sequence, including for translated CDR and FWR fragments of the VH gene sequence (defined by IMGT coordinates) (4). N-X-S/T glycosylation motifs in the CDR3 and FWR4 regions were similarly quantified separately and included for CDR and FWR distribution analyses.
Genome_build: IMGT (the international ImMunoGeneTics information system®) IGHV reference (IMGT/GENE-DB v3.1.19
Supplementary_files_format_and_content: AIRR-C, a tab-delimited file format (.tsv) that defines the required and optional annotations for rearranged adaptive immune receptor sequences.

extract_protocol:
RNA was isolated from frozen peripheral blood mononuclear cells using the RNAeasy Mini kit (Qiagen) per manufacturer’s instructions.
Bulk libraries were prepared from RNA using reagents from New England Biolabs as part of the NEBNext® Immune Sequencing Kit. cDNA was reverse-transcribed by a template-switch reaction to add a 17-nucleotide unique molecular identifier (UMI) to the 5' end with streptavidin magnetic bead purification. This was then followed by two rounds of PCR; the first round enriched for immunoglobulin sequences using IGHA, IGHD, IGHE, IGHG, and IGHM-specific 3' primers and added a 5' index primer. Libraries were purified with AMPure XP beads (Beckman) after which another round of PCR added Illumina P5 Adaptor sequences to each amplicon. The number of PCR cycles were selected based on real-time quantitative PCR to avoid the plateau phase. Libraries were then purified again with AMPure  XP beads. Libraries were pooled in equimolar libraries and sequenced by 325 cycles for read1 and 275 cycles for read 2 using paired-end sequencing with a 20% PhiX spike on the Illumina MiSeq platform according to manufacturer’s recommendations.

tag: study sample number

tag: Sex

tag: age at time of collection

tag: antibody status


title: HUVEC_H3K27ac

tag: cell line

tag: cell type


title: PBMC sample from subject HC-7 at time point 0

tag: tissue


title: HPAFII/tet-MUC1shRNA cont2

tag: disease state

value: pancreatic adenocarcinoma

value: puromycin resistance


title: PBMC sample from subject HC-8 at time point 0


title: PBMC sample from subject HC-6 at time point 0


title: AsPC1/tet-MUC1shRNA dox 3

value: 500 ng/ml doxycycline


title: BOEC_H3K27ac

value: BOEC


title: HPAFII/tet-MUC1shRNA cont1


title: DD/CM/ID 25

tag: age

value: 5 years

value: Developmental delay and Delayed Speech, Dysmorphic feature

value: Peripheral Blood


title: IMR90_CEBPB

value: Fibroblast cell


title: PBMC sample from subject HC-5 at time point 0


title: PBMC sample from subject HC-3 at time point 0


title: ESC_rep3

description: DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

data_processing:
Library strategy: Capture-C

Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie 2
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Genome_build: hg38
Supplementary_files_format_and_content: custom format (chr start stop interactions viewpoint)

source_name: WiCell

growth_protocol:
Human ESC line H1 (H1-hESC; WiCell) was grown on Matrigel (Corning) coated plates in mTeSR1 medium (StemCell technologies). Cells were harvested as a single cell suspension using Accutase (EDM Millipore); Fixation were carried out in mTeSR1 medium.
For erythroid cells, fresh blood was sourced either as 100 ml whole blood collected from three healthy donors (two males, one female) using EDTA Vacuettes (Becton Dickson) or 5 ml leukocyte cones (NHS Blood & Transport). Whole cell counts were performed on a Pentra ES60 (Horiba) for donor blood to ensure clinically healthy red blood cell counts. Blood was diluted with PBS and overlaid onto Histopaque-1077 (Sigma) and centrifuged for 30 min at 630 rcf (no brake). Peripheral Blood Mononuclear Cells (PBMCs) were washed in PBS and MACS buffer (PBS, 2 µM EDTA, 0.5% BSA) and stained with Human CD34 Microbead kit (Miltenyi Biotec) following the manufacturer’s instruction for 30 minutes (4 ºC) before being passed successively through two LS Columns (Miltenyi Biotec) with three MACs buffer washes. Counting of cells was performed on a Luna FL (Logos) after staining with acridine orange (AO) and propidium iodide (PI). CD34+ cells were either stored in freezing buffer (90% FBS, 10% DMSO) or resuspended in Phase I mediumfor a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 0.5-2.5x105 cells were resuspended on day 0 in Phase I media at 105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase II media at 3x105 cells ml-1. Cells were counted on day 9 and diluted to 3x105 cells ml-1 Phase II media. On day 11, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase III media at 106 cells ml-1. Cells were counted on days 13 and 15 and diluted to 106 cells ml-1 in Phase III media. Reproducibility between differentiations was confirmed morphologically with cytospins and immunologically with six FACS cell surface markers (CD34, CD36/Fatty acid translocase, CD71/Transferrin receptor, CD235a/Glycophorin A, CD49d/α-Integrin, CD233/Band). Human ESC line H1 (H1-hESC; WiCell) was grown on Matrigel (Corning) coated plates in mTeSR1 medium (StemCell technologies). Cells were harvested as a single cell suspension using Accutase (EDM Millipore); Fixation were carried out in mTeSR1 medium. Primary neonatal Human Umbilical Vein Endothelial Cells (HUVEC) were sourced from three suppliers to provide genetic diversity (Lonza, Gibco, PromoCell). HUVECs were expanded in endothelial cell growth medium (Sigma) up to five passages following the manufacturer’s protocol. Briefly, HUVECs were grown to 60% confluence, washed with HBSS at room temperature and sub-cultured following light trypsination using Trypsin-EDTA (Sigma) at room temperature and terminating the reaction with trypsin inhibitor (Sigma) upon rounding of the cells and gentle release from the flask. HUVECs were fixed in RPMI supplemented with 10 % FBS. CD4+T cells were enriched from whole blood (93–99% pure, RosetteSep Human CD4+T Cell Enrichment Cocktail,StemCell Technologies) and were plated at 250,000 cells per well in U-96 well plates (Greiner) and cultured in medium alone or stimulated with anti-CD3/CD28 T-activator beads (Dynabeads, Life Technologies) at a ratio of 0.3 beads per cell for four hours at 37°C in X-VIVO-15 (Lonza)+ 1% AB serum (Lonza) and penicillin/ streptomycin (Life Technologies). Non-activated or activated CD4+ T cells were pooled after 4 hours of culture and fixed in growth media.

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies)
5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a D1000 Tapestation (Agilent). DNA indexing was performed on 2µg of sheared DNA using NEB Ultra II DNA sample preparation reagent kits, using the modified protocol described in (Downes et al 2020). Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. 1 µg of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation (D1000). The resulting libraries were sequenced using Illumina Nextseq 500 (75 bp paired-end reads)

value: Unknown


title: ESC_rep2


title: PBMC sample from subject HC-2 at time point 0

value: Female


title: AsPC1/tet-MUC1shRNA dox 1


title: PBMC sample from subject HC-1 at time point 0


title: AsPC1/tet-MUC1shRNA dox 2


title: Mpbmi11l_H3K27me3_R2_L16

city: Uppsala

first: Shujing

last: Liu

state: Uppsala

address: Torgny Segerstedts Alle 20

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

description: 15 days old plants

data_processing:
ChIP-seq: Raw files (fastq, paired-end) were aligned to the Marchantia polymorpha MpTak1 v5.1 reference genome, using Bowtie2 with default parameters. Homer was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation. Bigwig files were outputted from “bamCoverage” function in deepTools (Ramírez et al., 2014) using Reads Per Kilobase Million (RPKM) as normalization parameter.
Genome_build: MpTak1v5.1
Supplementary_files_format_and_content: bigWig files contain the genomic coordinates and p value of each peak.

organism: Marchantia polymorpha

source_name: Thallus

growth_protocol: Plants were grown on vented 9 by 2.5 cm petri dishes containing Gamborg’s B5 medium solified with 1.4% plant agar, pH 5.5, under 16/8 h photoperiod at 22°C with light intensity at 60-70 umol m-2 s-1. Plate lids were taped to prevent loss of water.

extract_protocol:
300 mg 15d thalli of WT, Mpbmi1/1l, Mph2a;H2AK115R/K116R and Mph2a;H2AK119R mutants were harvested. ChIP was performed as described before (Villar and Köhler, 2010). The ChIP-seq experiments were done using two biological replicates per IP, per genotype.
The antibodies used were anti-H3 (07-690, Merck Millipore, Burlington, MA, USA), anti-H2Aub (#8240S, Cell signalling technology, Danvers, MA) and anti-H3K27me3 (07-449, Merck Millipore, Burlington, MA, USA).
Libraries were generated using the Ovation Ultralow Sytem V2 (NuGEN, Redwood city, CA, USA) according to manufacturer’s instructions, and 150 bp paired-end sequencing was performed on the HiseqX platform at Novogene (Hong Kong).

tag: ecotype

value: Upp

tag: genotype

tag: biological replicate

value: thallus


title: PBMC sample from subject HC-4 at time point 0


title: HUVEC_Input


title: DD/CM/ID 15

description: Developmental delay and Delayed Speech, Dysmorphic Features

value: 4 years

tag: gender

tag: phenotype

value: reference sample


title: DD/CM/ID 23

description: Developmental delay and Dysmorphic feature

tag: sample type


title: PBMC sample from subject AChR-12 at time point 0

value: AChR


title: DD/CM/ID 18

description: Developmental delay and Obesity, Congenital Heart Disease, Normal Milestones


title: Mpbmi11l_H3K27me3_R1_L16

description: 15 days old plants


title: AsPC1/tet-MUC1shRNA cont 2

tag: treatment

value: 0.1% DMSO as the vehicle control


title: DD/CM/ID 16

description: Developmental delay and Dysmorphic Feature, Intellectual Disability

value: 2 years

value: Male


title: DD/CM/ID 20

description: Developmental delay and Hypotonia, Cleft Lip, VSD, ASD, Pulmonary Stenosis.

value: 2.6 years


title: HUVEC_rep3

source_name: Umbilical Vein (PromoCell)

growth_protocol:
Primary neonatal Human Umbilical Vein Endothelial Cells (HUVEC) were sourced from three suppliers to provide genetic diversity (Lonza, Gibco, PromoCell). HUVECs were expanded in endothelial cell growth medium (Sigma) up to five passages following the manufacturer’s protocol. Briefly, HUVECs were grown to 60% confluence, washed with HBSS at room temperature and sub-cultured following light trypsination using Trypsin-EDTA (Sigma) at room temperature and terminating the reaction with trypsin inhibitor (Sigma) upon rounding of the cells and gentle release from the flask. HUVECs were fixed in RPMI supplemented with 10 % FBS.
For erythroid cells, fresh blood was sourced either as 100 ml whole blood collected from three healthy donors (two males, one female) using EDTA Vacuettes (Becton Dickson) or 5 ml leukocyte cones (NHS Blood & Transport). Whole cell counts were performed on a Pentra ES60 (Horiba) for donor blood to ensure clinically healthy red blood cell counts. Blood was diluted with PBS and overlaid onto Histopaque-1077 (Sigma) and centrifuged for 30 min at 630 rcf (no brake). Peripheral Blood Mononuclear Cells (PBMCs) were washed in PBS and MACS buffer (PBS, 2 µM EDTA, 0.5% BSA) and stained with Human CD34 Microbead kit (Miltenyi Biotec) following the manufacturer’s instruction for 30 minutes (4 ºC) before being passed successively through two LS Columns (Miltenyi Biotec) with three MACs buffer washes. Counting of cells was performed on a Luna FL (Logos) after staining with acridine orange (AO) and propidium iodide (PI). CD34+ cells were either stored in freezing buffer (90% FBS, 10% DMSO) or resuspended in Phase I mediumfor a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 0.5-2.5x105 cells were resuspended on day 0 in Phase I media at 105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase II media at 3x105 cells ml-1. Cells were counted on day 9 and diluted to 3x105 cells ml-1 Phase II media. On day 11, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase III media at 106 cells ml-1. Cells were counted on days 13 and 15 and diluted to 106 cells ml-1 in Phase III media. Reproducibility between differentiations was confirmed morphologically with cytospins and immunologically with six FACS cell surface markers (CD34, CD36/Fatty acid translocase, CD71/Transferrin receptor, CD235a/Glycophorin A, CD49d/α-Integrin, CD233/Band). Human ESC line H1 (H1-hESC; WiCell) was grown on Matrigel (Corning) coated plates in mTeSR1 medium (StemCell technologies). Cells were harvested as a single cell suspension using Accutase (EDM Millipore); Fixation were carried out in mTeSR1 medium. Primary neonatal Human Umbilical Vein Endothelial Cells (HUVEC) were sourced from three suppliers to provide genetic diversity (Lonza, Gibco, PromoCell). HUVECs were expanded in endothelial cell growth medium (Sigma) up to five passages following the manufacturer’s protocol. Briefly, HUVECs were grown to 60% confluence, washed with HBSS at room temperature and sub-cultured following light trypsination using Trypsin-EDTA (Sigma) at room temperature and terminating the reaction with trypsin inhibitor (Sigma) upon rounding of the cells and gentle release from the flask. HUVECs were fixed in RPMI supplemented with 10 % FBS. CD4+T cells were enriched from whole blood (93–99% pure, RosetteSep Human CD4+T Cell Enrichment Cocktail,StemCell Technologies) and were plated at 250,000 cells per well in U-96 well plates (Greiner) and cultured in medium alone or stimulated with anti-CD3/CD28 T-activator beads (Dynabeads, Life Technologies) at a ratio of 0.3 beads per cell for four hours at 37°C in X-VIVO-15 (Lonza)+ 1% AB serum (Lonza) and penicillin/ streptomycin (Life Technologies). Non-activated or activated CD4+ T cells were pooled after 4 hours of culture and fixed in growth media.

value: Endothelium


title: DD/CM/ID 19

description: Developmental delay and VSD, Failure to thrive

value: 1 years


title: AsPC1/tet-MUC1shRNA cont 3

value: pancreatic adenocarcinoma

value: puromycin resistance

tag: tag


title: H2AK119R_H3K27me3_R2_L16

description: 15 days old plants


title: HUVEC_rep1

source_name: Umbilical Vein (Lonza)


title: AsPC1/tet-MUC1shRNA cont 1


title: DD/CM/ID 21

value: 1.7 years

value: Developmental delay and Dysmorphic feature

value: Peripheral Blood


title: DD/CM/ID 14

description: Developmental delay and Congenital heart disease, Dysmorphic Feature

value: 1.8 years


title: PBMC sample from subject AChR-9 at time point 0

tag: study sample number


title: ESC_rep1

tag: Sex

value: Unknown


title: H2AK119R_H3K27me3__R1

description: 15 days old plants

value: Upp

value: thallus


title: DD/CM/ID 24

description: Developmental delay and Microcephaly, Dysmorphic, Brain Atrophy

value: 2.3 years

value: reference sample


title: H2AK115RK116R_H3K27me3_R1_L16

description: 15 days old plants


title: PBMC sample from subject AChR-5 at time point 0

value: Female

tag: age at time of collection

value: AChR


title: D5/D6 Natural human embryos

city: Pasadena

first: Victoria

last: Jorgensen

state: CA

address: 1200 E California Blvd.

department: Biology and Bioengineering

institute: California Institute of Technology

data_processing:
The single-cell sequencing library was prepared as per the manufacturer's instructions and sequenced on an Illumina Hiseq 4000 at a minimum coverage of 20,000 PE reads per cell (read 1: 28bp, i7: 8bp, read 2: 91bp).
Sample-specific LMO tags were separately amplified according to Ding et al. and sequenced at a read depth of 2,016 reads per cell. Sample demultiplexing was performed using an in-house demultiplexing pipeline that discovers sample-specific thresholds49, scores each cell as being positive or negative for a specific tag, and retains only singly-labeled cells.
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: tsv/mtx files for transcript counts per cell

source_name: Embryo

growth_protocol: All hEPSCs were maintained under 20% O2 and 5% CO2 at 37°C conditions on irradiated CF1 mouse embryonic fibroblasts (MEF) feeder cells.  hEPSCs were grown using ‘human Expanded Potential’ (hEP) medium (as described in Y Yang et al. 2017, Cell).     For generation of hEP-structures, hEPSCs were dissociated to single cells by incubation with Accutase (07920, Stem Cell Technologies) at 37°C for 3 min. Cells were collected and pelleted by centrifugation for 4 min at 1000 rpm and resuspended in hEP-LCDMYI medium (Y Yang et al. 2017, Cell). This cell suspension was pre-incubated at 37°C in an atmosphere of 5% CO2 on gelatinized tissue-culture-grade plates for 30 min to remove inactive MEFs. Post incubation on gelatin plates, cells were counted using a haemocytometer and a total of 7200 hEPSCs was added to 1mL of media composed of 50% IVF media (Continuous Single Culture-NX Complete (CSCM-NXC)) (90168, FUJIFILM), 25% hEP media, and 25% hTS media.  This media was also supplemented with CHIR99021 (2uM), Y27632 (5uM), BMP4 (20ng/mL), FGF2 (40ng/mL), and A83-01 (2uM). Cell suspensions were added dropwise to the Aggrewells.  All wells without cells were filled with 1mL PBS to humidify the local atmosphere to minimize evaporation. The AggreWell plate (24-well, 1200 Aggrewell format) was then centrifuged for 3 min at 100g, and placed at 37°C under hypoxic conditions (5% CO2 and 5% O2). After 48h, media was removed from wells and replaced with fresh culture media, although FGF2 concentration was lowered to 20ng/mL and A83-01 was omitted. Cells were left to grow for an additional 48-72h until proper morphology was observed, or switched to IVC1 for D6 structures.     The human embryos at the blastocyst stage were warmed using Embryo Thaw Media Kit following the manufacturer’s instructions (Fujifilm Irvine Scientific, Cat. No. 90124). The day before warming, Continuous Single Culture-NX Complete medium (Fujifilm Irvine Scientific, Catalog No: 90168) was equilibrated overnight at 37°C + 5% CO2. On the day of warming (day 1), the straw that contains the embryo was defrosted at room temperature for 30 sec and immersed in prewarmed (37°C) water for 1 min until ice melted. The embryo was then transferred into T-1 (5 min), T-2 (5 min), T-3 (10 min) solutions for slow warming and finally into Multipurpose Handling Medium (MHM, Fujifilm Irvine Scientific, Cat. No. 90163) for recovery. All these incubation steps were done using 4 well plates (Nunc) and 1 ml per solution. Warmed embryos were finally incubated in drops of preequilibrated Continuous Single Culture-NX Complete medium under mineral oil (9305, Irvine Scientific). Culture conditions are the following: 37°C 21% O2 and 5% CO2. Embryos were incubated for a total of 24h until used for further RNA-sequencing protocols.

tag: developmental stage


title: DD/CM/ID 17

description: Developmental delay and Hypotonia, Undescended Testis, Talipes, High Arched Palate

value: Male


title: PBMC sample from subject AChR-8 at time point 0

tag: antibody status


title: PBMC sample from subject AChR-11 at time point 0


title: H2AK115RK116R_H3K27me3_R2_L16

description: 15 days old plants


title: DD/CM/ID 12

description: Developmental delay and Intellectual Disability, Congenital Heart Disease.

value: 6.8 years


title: DD/CM/ID 13

description: Developmental delay and Central Hypotonia, Microcephaly

value: 3 years


title: DD/CM/ID 22

description: Developmental delay and Spinal Muscular Atrophy.

value: 2.6 years


title: CD4N_rep2

source_name: Peripheral blood

growth_protocol:
CD4+T cells were enriched from whole blood (93–99% pure, RosetteSep Human CD4+T Cell Enrichment Cocktail,StemCell Technologies) and were plated at 250,000 cells per well in U-96 well plates (Greiner) and cultured in medium alone or stimulated with anti-CD3/CD28 T-activator beads (Dynabeads, Life Technologies) at a ratio of 0.3 beads per cell for four hours at 37°C in X-VIVO-15 (Lonza)+ 1% AB serum (Lonza) and penicillin/ streptomycin (Life Technologies). Non-activated or activated CD4+ T cells were pooled after 4 hours of culture and fixed in growth media.
For erythroid cells, fresh blood was sourced either as 100 ml whole blood collected from three healthy donors (two males, one female) using EDTA Vacuettes (Becton Dickson) or 5 ml leukocyte cones (NHS Blood & Transport). Whole cell counts were performed on a Pentra ES60 (Horiba) for donor blood to ensure clinically healthy red blood cell counts. Blood was diluted with PBS and overlaid onto Histopaque-1077 (Sigma) and centrifuged for 30 min at 630 rcf (no brake). Peripheral Blood Mononuclear Cells (PBMCs) were washed in PBS and MACS buffer (PBS, 2 µM EDTA, 0.5% BSA) and stained with Human CD34 Microbead kit (Miltenyi Biotec) following the manufacturer’s instruction for 30 minutes (4 ºC) before being passed successively through two LS Columns (Miltenyi Biotec) with three MACs buffer washes. Counting of cells was performed on a Luna FL (Logos) after staining with acridine orange (AO) and propidium iodide (PI). CD34+ cells were either stored in freezing buffer (90% FBS, 10% DMSO) or resuspended in Phase I mediumfor a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 0.5-2.5x105 cells were resuspended on day 0 in Phase I media at 105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase II media at 3x105 cells ml-1. Cells were counted on day 9 and diluted to 3x105 cells ml-1 Phase II media. On day 11, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase III media at 106 cells ml-1. Cells were counted on days 13 and 15 and diluted to 106 cells ml-1 in Phase III media. Reproducibility between differentiations was confirmed morphologically with cytospins and immunologically with six FACS cell surface markers (CD34, CD36/Fatty acid translocase, CD71/Transferrin receptor, CD235a/Glycophorin A, CD49d/α-Integrin, CD233/Band). Human ESC line H1 (H1-hESC; WiCell) was grown on Matrigel (Corning) coated plates in mTeSR1 medium (StemCell technologies). Cells were harvested as a single cell suspension using Accutase (EDM Millipore); Fixation were carried out in mTeSR1 medium. Primary neonatal Human Umbilical Vein Endothelial Cells (HUVEC) were sourced from three suppliers to provide genetic diversity (Lonza, Gibco, PromoCell). HUVECs were expanded in endothelial cell growth medium (Sigma) up to five passages following the manufacturer’s protocol. Briefly, HUVECs were grown to 60% confluence, washed with HBSS at room temperature and sub-cultured following light trypsination using Trypsin-EDTA (Sigma) at room temperature and terminating the reaction with trypsin inhibitor (Sigma) upon rounding of the cells and gentle release from the flask. HUVECs were fixed in RPMI supplemented with 10 % FBS. CD4+T cells were enriched from whole blood (93–99% pure, RosetteSep Human CD4+T Cell Enrichment Cocktail,StemCell Technologies) and were plated at 250,000 cells per well in U-96 well plates (Greiner) and cultured in medium alone or stimulated with anti-CD3/CD28 T-activator beads (Dynabeads, Life Technologies) at a ratio of 0.3 beads per cell for four hours at 37°C in X-VIVO-15 (Lonza)+ 1% AB serum (Lonza) and penicillin/ streptomycin (Life Technologies). Non-activated or activated CD4+ T cells were pooled after 4 hours of culture and fixed in growth media.

tag: cell type

value: CD4 T-cell

tag: stimulated

value: No


title: Mpbmi11l_H2Aub_R2

description: 15 days old plants

tag: tissue


title: CD4N_rep1


title: CD14_rep2

growth_protocol:
Whole blood was collected into EDTA tubes (BD vacutainer system) and peripheral blood mononuclear cells were obtained by density centrifugation (Ficoll Paque). CD14 cell isolation was carried out by positive selection (Miltenyi) according to the manufacturer’s instructions.
For erythroid cells, fresh blood was sourced either as 100 ml whole blood collected from three healthy donors (two males, one female) using EDTA Vacuettes (Becton Dickson) or 5 ml leukocyte cones (NHS Blood & Transport). Whole cell counts were performed on a Pentra ES60 (Horiba) for donor blood to ensure clinically healthy red blood cell counts. Blood was diluted with PBS and overlaid onto Histopaque-1077 (Sigma) and centrifuged for 30 min at 630 rcf (no brake). Peripheral Blood Mononuclear Cells (PBMCs) were washed in PBS and MACS buffer (PBS, 2 µM EDTA, 0.5% BSA) and stained with Human CD34 Microbead kit (Miltenyi Biotec) following the manufacturer’s instruction for 30 minutes (4 ºC) before being passed successively through two LS Columns (Miltenyi Biotec) with three MACs buffer washes. Counting of cells was performed on a Luna FL (Logos) after staining with acridine orange (AO) and propidium iodide (PI). CD34+ cells were either stored in freezing buffer (90% FBS, 10% DMSO) or resuspended in Phase I mediumfor a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 0.5-2.5x105 cells were resuspended on day 0 in Phase I media at 105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase II media at 3x105 cells ml-1. Cells were counted on day 9 and diluted to 3x105 cells ml-1 Phase II media. On day 11, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase III media at 106 cells ml-1. Cells were counted on days 13 and 15 and diluted to 106 cells ml-1 in Phase III media. Reproducibility between differentiations was confirmed morphologically with cytospins and immunologically with six FACS cell surface markers (CD34, CD36/Fatty acid translocase, CD71/Transferrin receptor, CD235a/Glycophorin A, CD49d/α-Integrin, CD233/Band). Human ESC line H1 (H1-hESC; WiCell) was grown on Matrigel (Corning) coated plates in mTeSR1 medium (StemCell technologies). Cells were harvested as a single cell suspension using Accutase (EDM Millipore); Fixation were carried out in mTeSR1 medium. Primary neonatal Human Umbilical Vein Endothelial Cells (HUVEC) were sourced from three suppliers to provide genetic diversity (Lonza, Gibco, PromoCell). HUVECs were expanded in endothelial cell growth medium (Sigma) up to five passages following the manufacturer’s protocol. Briefly, HUVECs were grown to 60% confluence, washed with HBSS at room temperature and sub-cultured following light trypsination using Trypsin-EDTA (Sigma) at room temperature and terminating the reaction with trypsin inhibitor (Sigma) upon rounding of the cells and gentle release from the flask. HUVECs were fixed in RPMI supplemented with 10 % FBS. CD4+T cells were enriched from whole blood (93–99% pure, RosetteSep Human CD4+T Cell Enrichment Cocktail,StemCell Technologies) and were plated at 250,000 cells per well in U-96 well plates (Greiner) and cultured in medium alone or stimulated with anti-CD3/CD28 T-activator beads (Dynabeads, Life Technologies) at a ratio of 0.3 beads per cell for four hours at 37°C in X-VIVO-15 (Lonza)+ 1% AB serum (Lonza) and penicillin/ streptomycin (Life Technologies). Non-activated or activated CD4+ T cells were pooled after 4 hours of culture and fixed in growth media.

value: CD14 Monocytes


title: PBMC sample from subject AChR-6 at time point 0


title: CD4A_rep3

value: Yes


title: CD14_rep3


title: Upp5_H3K27me3_R2_L16

description: 15 days old plants

value: WT


title: PBMC sample from subject AChR-1 at 4 months since first sample collection

value: Peripheral Blood


title: CD4N_rep3

value: Unknown


title: H2AK119R_H2Aub__R1

description: 15 days old plants

value: Upp


title: PBMC sample from subject AChR-4 at time point 0


title: PBMC sample from subject MuSK-3 at 25 months since first sample collection

value: MuSK


title: PBMC sample from subject MuSK-3 at 10 months since first sample collection


title: Mpbmi11l_H2Aub_R1

description: 15 days old plants

value: thallus


title: CD4A_rep1


title: PBMC sample from subject AChR-3 at time point 0


title: hEPSCs, D5 hEP-structures, D6 hEP-structures (multiplexed samples)

source_name: Embryonic stem cells (ESCs)

extract_protocol: The single-cell sequencing library was prepared as per the manufacturer's instructions and sequenced on an Illumina Hiseq 4000 at a minimum coverage of 20,000 PE reads per cell (read 1: 28bp, i7: 8bp, read 2: 91bp).

tag: cell line


title: Ery_rep3

source_name: CD34 Culture

growth_protocol:
For erythroid cells, fresh blood was sourced either as 100 ml whole blood collected from three healthy donors (two males, one female) using EDTA Vacuettes (Becton Dickson) or 5 ml leukocyte cones (NHS Blood & Transport). Whole cell counts were performed on a Pentra ES60 (Horiba) for donor blood to ensure clinically healthy red blood cell counts. Blood was diluted with PBS and overlaid onto Histopaque-1077 (Sigma) and centrifuged for 30 min at 630 rcf (no brake). Peripheral Blood Mononuclear Cells (PBMCs) were washed in PBS and MACS buffer (PBS, 2 µM EDTA, 0.5% BSA) and stained with Human CD34 Microbead kit (Miltenyi Biotec) following the manufacturer’s instruction for 30 minutes (4 ºC) before being passed successively through two LS Columns (Miltenyi Biotec) with three MACs buffer washes. Counting of cells was performed on a Luna FL (Logos) after staining with acridine orange (AO) and propidium iodide (PI). CD34+ cells were either stored in freezing buffer (90% FBS, 10% DMSO) or resuspended in Phase I mediumfor a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 0.5-2.5x105 cells were resuspended on day 0 in Phase I media at 105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase II media at 3x105 cells ml-1. Cells were counted on day 9 and diluted to 3x105 cells ml-1 Phase II media. On day 11, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase III media at 106 cells ml-1. Cells were counted on days 13 and 15 and diluted to 106 cells ml-1 in Phase III media. Reproducibility between differentiations was confirmed morphologically with cytospins and immunologically with six FACS cell surface markers (CD34, CD36/Fatty acid translocase, CD71/Transferrin receptor, CD235a/Glycophorin A, CD49d/α-Integrin, CD233/Band).
For erythroid cells, fresh blood was sourced either as 100 ml whole blood collected from three healthy donors (two males, one female) using EDTA Vacuettes (Becton Dickson) or 5 ml leukocyte cones (NHS Blood & Transport). Whole cell counts were performed on a Pentra ES60 (Horiba) for donor blood to ensure clinically healthy red blood cell counts. Blood was diluted with PBS and overlaid onto Histopaque-1077 (Sigma) and centrifuged for 30 min at 630 rcf (no brake). Peripheral Blood Mononuclear Cells (PBMCs) were washed in PBS and MACS buffer (PBS, 2 µM EDTA, 0.5% BSA) and stained with Human CD34 Microbead kit (Miltenyi Biotec) following the manufacturer’s instruction for 30 minutes (4 ºC) before being passed successively through two LS Columns (Miltenyi Biotec) with three MACs buffer washes. Counting of cells was performed on a Luna FL (Logos) after staining with acridine orange (AO) and propidium iodide (PI). CD34+ cells were either stored in freezing buffer (90% FBS, 10% DMSO) or resuspended in Phase I mediumfor a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 0.5-2.5x105 cells were resuspended on day 0 in Phase I media at 105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase II media at 3x105 cells ml-1. Cells were counted on day 9 and diluted to 3x105 cells ml-1 Phase II media. On day 11, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase III media at 106 cells ml-1. Cells were counted on days 13 and 15 and diluted to 106 cells ml-1 in Phase III media. Reproducibility between differentiations was confirmed morphologically with cytospins and immunologically with six FACS cell surface markers (CD34, CD36/Fatty acid translocase, CD71/Transferrin receptor, CD235a/Glycophorin A, CD49d/α-Integrin, CD233/Band). Human ESC line H1 (H1-hESC; WiCell) was grown on Matrigel (Corning) coated plates in mTeSR1 medium (StemCell technologies). Cells were harvested as a single cell suspension using Accutase (EDM Millipore); Fixation were carried out in mTeSR1 medium. Primary neonatal Human Umbilical Vein Endothelial Cells (HUVEC) were sourced from three suppliers to provide genetic diversity (Lonza, Gibco, PromoCell). HUVECs were expanded in endothelial cell growth medium (Sigma) up to five passages following the manufacturer’s protocol. Briefly, HUVECs were grown to 60% confluence, washed with HBSS at room temperature and sub-cultured following light trypsination using Trypsin-EDTA (Sigma) at room temperature and terminating the reaction with trypsin inhibitor (Sigma) upon rounding of the cells and gentle release from the flask. HUVECs were fixed in RPMI supplemented with 10 % FBS. CD4+T cells were enriched from whole blood (93–99% pure, RosetteSep Human CD4+T Cell Enrichment Cocktail,StemCell Technologies) and were plated at 250,000 cells per well in U-96 well plates (Greiner) and cultured in medium alone or stimulated with anti-CD3/CD28 T-activator beads (Dynabeads, Life Technologies) at a ratio of 0.3 beads per cell for four hours at 37°C in X-VIVO-15 (Lonza)+ 1% AB serum (Lonza) and penicillin/ streptomycin (Life Technologies). Non-activated or activated CD4+ T cells were pooled after 4 hours of culture and fixed in growth media.

value: Erythroid

tag: day of differentiation

value: Day 13


title: H2AK115RK116R_H2Aub_R1

description: 15 days old plants

tag: ecotype

tag: genotype


title: Upp5_H3K27me3_R1_L16

description: 15 days old plants

tag: biological replicate


title: CD4A_rep2


title: H2AK119R_H2Aub_R2

description: 15 days old plants


title: PBMC sample from subject AChR-2 at time point 0

value: AChR


title: Ery_rep1

value: Female


title: Upp5_H2Aub_R2

description: 15 days old plants


title: Upp5_H2Aub_R1

description: 15 days old plants


title: PBMC sample from subject MuSK-3 at 1 month since first sample collection


title: Ery_rep2

value: Male


title: H2AK115RK116R_H2Aub_R2

description: 15 days old plants


title: TS147_TLE3_KD

city: Manchester

first: Tim

middle: C

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

institute: Cancer Research UK

data_processing:
Reads were aligned to the human genome (hg38) using BWA-MEM v0.7.15 (5). Read duplicates were removed using Picard v2.1.0. Reads were further filtered using Bedtools v2.25.0 to keep only paired reads that mapped to standard chromosomes and to remove reads with a mapping quality of less than 10. Reads mapped to blacklisted regions defined by ENCODE were then removed using Bedtools (http://mitra.stanford.edu/kundaje).
Genome_build: GRCh38

source_name: Fujioka cells

growth_protocol: Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).

extract_protocol:
10^8 cells were used for each precipitation using the method described by Lee et al. (2006). Briefly, cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature before the reaction was quenched with 0.125M glycine. Cell pellets were washed twice with PBS and nuclear lysates sonicated for 6 cycles using a Bioruptor® Pico (Diagenode, Liege, Belgium). 10μg of antibody bound to 100μl of magnetic beads (Dynabeads Protein G, Invitrogen, Carlsbad, CA) was added to each sample and immunoprecipitation performed overnight on a rotator at 4°C and 20rpm. After five washes with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl), chromatin IP-bound fractions were extracted by incubating for 15 min at 65°C with elution buffer (50mM TrisHCl pH8, 10mM EDTA, 1% SDS). Crosslinking was then reversed by incubation at 65°C for 6 hours. RNaseA (1mg/ml) and proteinase K (20mg/ml) were added to eliminate RNA and protein from the samples. DNA was extracted using phenol:chloroform:isoamyl alcohol and precipitated by adding 2 volumes of ice-cold 100% ethanol, glycogen (20μg/μl), 200mM NaCl and freezing at -80°C for at least 1hr. Pellets were washed with 70% ethanol and eluted in 50μl 10mM TrisHCl pH8.0.
Libraries were prepared for sequencing using a Microplex Library Preparation Kit (Diagenode). 200-800bp fragments were selected using AMPure beads (Beckman Coulter, Brea, CA) and quantified by qPCR with a KAPA Library Quantification Kit (Kapa Biosystems, Basel, Switzerland). Sequencing was performed using a NextSeq desktop sequencing system (Illumina) with 75bp, paired-end high output generating 65-80M reads per sample.

value: Fujioka

tag: antibody

tag: agent

value: lentivirus targeting FOXC1


title: PBMC sample from subject MuSK-2 at 76 months since first sample collection


title: PBMC sample from subject MuSK-2 at time point 0


title: PBMC sample from subject MuSK-3 at time point 0


title: TS120_SMARCC2_NTC

treatment_protocol: Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).

value: non-targeting control (NTC)


title: TS147_TLE3_NTC


title: Epidermal_Equivalent_SSc_2 [3dSSc2]

city: Geneva

first: Barbara

last: Russo

address: Rue Michel Servet 1

department: DEPARTEMENT DE MEDECINE (DEMED)

country: Switzerland

institute: Centre Medical Universitaire

data_processing:
Sequencing: SR50 – libraries TruSeqHT mRNA stranded – Illumina HiSeq 4000 – run 238
The sequencing quality control was done with FastQC v.0.11.5.
The reads were mapped with STAR aligner v.2.5.3a to the UCSC human hg38 reference.
The transcriptome metrics were evaluated with the Picard tools v.1.141
The table of counts with the number of reads mapping to each gene feature of the UCSC human hg38 reference was prepared with HTSeq v0.9.1
Genome_build: HG38
Supplementary_files_format_and_content: normalized gene counts for every gene and every sample.txt

molecule: polyA RNA

extract_protocol:
miRNA isolarion kit from Qiagen (USA)
cDNA libraries were constructed by the Genomic platform of the University of Geneva using the Illumina TruSeq RNA stranded Kit according to the manufacturer's protocol

tag: subject status

value: systemic sclerosis (SSc)

value: keratinocytes

value: epidermal equivalent [EE)


title: H2AK119R_H3_R1

description: 15 days old plants


title: PBMC sample from subject MuSK-1 at 31 months since first sample collection


title: PBMC sample from subject MuSK-2 at 56 months since first sample collection


title: H2AK119R_H3_R2

description: 15 days old plants


title: Mpbmi11l_H3_R1

description: 15 days old plants


title: PBMC sample from subject MuSK-2 at 6 months since first sample collection


title: TS120_CEBPA_NTC

value: CEBPA


title: Upp5_H3_R2

description: 15 days old plants

value: WT


title: Peripheral_Blood_TCR

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

state: MA

address: 500 Main St

department: Koch Institute

institute: MIT

data_processing:
Library strategy: TCR-Seq
Paired TCR sequencing and read alignment was performed as described in Tu et al., Nat Immunol 2019. Briefly, whole-transcriptome amplification product for each sample was enriched for TCR transcripts using biotinylated probes for the human TRAC and TRBC regions and magnetic streptavidin beads. The enriched product was further amplified using human V-region primers and Nextera sequencing handles. Libraries were then sequenced on an Illumina MiSeq or Nextseq using 150 base pair single-end reads. CDR3 consensus sequences were aligned as outlined previously.
Supplementary_files_format_and_content: _processed.tsv: results of TCR sequencing by UMI

extract_protocol:
Cryopreserved PBMC from 8 of the 10 patients included in the tissue-resident single-cell analysis were thawed, and memory CD4+ T cells were isolated with the EasySep human memory CD4+ T cell enrichment kit (Stemcell Technologies, Vancouver, BC, Canada). T cells were cultured in AIM V medium (Gibco, Waltham, MA) for 6 hours at a density of 2 x 10e6 in 0.5 ml medium per well in 48-well plates, with human T-Activator CD3/CD28 beads (Thermo Fisher, Waltham, MA) in a 1:3 ratio of beads to T cells. After harvesting, the cells were labeled with BUV395-conjugated anti-CD3 (clone UCHT1), APC-Cy7-conjugated anti-CD4 (RPA-T4), PE-Cy7-conjugated anti-CD45RA (HI100), PerCP-Cy5.5-conjugated anti-CRTH2 (BM16) (all from BD Biosciences, San Jose, CA), eFluor450-conjugated anti-CD161 (HP-3G10), and Live/Dead Fixable Blue stain (L23105) (both from Thermo Fisher). Live CD3+CD4+CD45RA- CRTH2+CD161+, CRTH2+CD161-, and CRTH2-CD161- T cells were sorted with a FACSAria Fusion instrument (BD Biosciences).
Nextera

value: Peripheral blood

tag: diagnosis

value: Eosinophilic esophagitis (EoE)


title: TS120_RUNX1_KD


title: TS120_P300_NTC


title: H2AK115RK116R_H3_R1

description: 15 days old plants

value: Upp


title: Epidermal_Equivalent_SSc_1 [3dSSc1]


title: Upp5_H3_R1

description: 15 days old plants

value: thallus


title: PBMC sample from subject MuSK-1 at 39 months since first sample collection

tag: study sample number

value: MuSK

value: Peripheral Blood


title: TS120_CEBPA_KD


title: TS120_RUNX1_NTC


title: Epidermal_Equivalent_healty_donor 5 [HD3d5]

value: healthy donor (HD)


title: Epidermal_Equivalent_SSc_3 [3dSSc3]


title: Mpbmi11l_R2

description: 15 days old plants

data_processing:
RNA-seq: Untrimmed reads were mapped to the Marchantia polymorpha MpTak1 v5.1 reference genome (Montgomery et al., 2020) using STAR (v2.5.3.a, (Dobin et al., 2013)). Read numbers of mapping statistics are reported in Supplementary Table S2. Expression counts were generated using the R function summarizeOverlaps from the package HTSeq in union mode on exons from the reference transcriptome MpTak1v5.1_r1. Differential expression analyses were performed using the R package DESeq2 (v1.20.0, (Love et al., 2014)).
Genome_build: MpTak1v5.1
Supplementary_files_format_and_content: Tables with the values of the differential expression analysis for genes and TEs are presented in text files

extract_protocol:
50 mg 15d thalli of WT, Mpbmi1/1l, Mph2a;H2AK115R/K116R and Mph2a;H2AK119R mutants were used for RNA extraction. RNA was extracted using the MagMAX™ Plant RNA Isolation Kit (Thermo Fisher Scientific) in biological triplicates.
Libraries were generated using DNA-free RNA with the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina according to manufacturer’s instructions. Sequencing was performed on an Illumina HiSeqX in 150-bp pair-end mode at Novogene (Hong Kong).


title: TS120_HDAC1_NTC


title: Mpbmi11l_H3_R2

description: 15 days old plants


title: PBMC sample from subject MuSK-1 at 36 months since first sample collection

tag: Sex

value: Female


title: TS105_SPI1


title: Epidermal_Equivalent_healty_donor 4 [HD3d4]


title: Mpbmi11l_R3

description: 15 days old plants


title: H2AK119R_R3

description: 15 days old plants


title: H2AK119R_R2

description: 15 days old plants


title: H2AK119R_R1

description: 15 days old plants


title: TS120_P300_KD


title: H2AK115RK116R_H3_R2

description: 15 days old plants


title: TS53_ATAC_KD


title: Tissue_TCR_Lane2

source_name: Esophageal biopsy, duodenal biopsy

value: Esophageal biopsy, duodenal biopsy


title: SMN0013_S12: human spinal motor neurons in SOD1

city: Baltimore

first: Hojae

address: 733 north broadway

institute: Johns hopkins medicine

description: SOD1A4V ALS

data_processing:
The raw data was processed with the STAR aligner (version 2.5.2b). Reads were aligned to the Homo sapiens genome.
Sequenced reads were aligned to the mouse reference genome hg19
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab separated values of expression matrix; rows are genes; columns are cells

source_name: SOD1A4V HB9::GFP+

growth_protocol: human ES/iPS cells were cultured using hES media and seeding for differentiation. After seeding,  LDN193189, SB431542, Purmorphamine, Retinoic acid were used for spinal motor neuron differentiation and LDN193189, SB431542, CHIR, FGF8, Purmorphamine, SHH were used for ocular motor neurons.

extract_protocol:
Total RNA was extracted using miRNeasy mini kit (Qiagen) as per manufacturer’s instructions. RNA concentration and purity were assessed by Nanodrop (Thermo Fisher), and RNA integrity was assessed using the Agilent Bioanalyzer.
cDNA Libraries were prepared for mRNA-enriched sequencing using TruSeq Stranded mRNA kit (Illumina). This was followed by normalization to 6 nM and pooling of libraries, followed by single end 75 bp sequencing on the Illumina HighSeq 4000.

treatment_protocol: Each compounds were treated at culture day 11 with 4 different concentrations

value: human spinal motor neurons

value: amyotrophic lateral sclerosis (ALS)


title: SMN078_S11: human spinal motor neurons in C9ORF72

description: C9ORF72 ALS

source_name: C9ORF72 HB9::GFP+


title: Epidermal_Equivalent_healty_donor 3 [HD3d3]


title: Epidermal_Equivalent_healty_donor 2 [HD3d2]


title: SMN078_S9: human spinal motor neurons in C9ORF72

description: C9ORF72 ALS


title: TS120_SMARCC2_KD

value: Fujioka

value: lentivirus targeting FOXC1


title: TS49_ H3K4me2_ KD


title: PBMC sample from subject MuSK-1 at time point 0

source_name: Peripheral Blood

tag: age at time of collection


title: Tissue_TCR_Lane1


title: TS83_H3K4me1


title: Upp5_R3

description: 15 days old plants


title: OMN078_S5: human ocular motor neurons in C9ORF72

description: C9ORF72 ALS

source_name: C9ORF72 PHOX2B::GFP+

value: human ocular motor neurons


title: SMN0013_S8: human spinal motor neurons in SOD1

description: SOD1A4V ALS


title: TS154_03_BB171_FOXC1

source_name: Primary AML

treatment_protocol: Cyropreserved primary cells were thawed and immediately crosslinked for ChIP.

value: Primary AML

tag: chip antibody


title: OMN078_S3: human ocular motor neurons in C9ORF72

description: C9ORF72 ALS


title: TS49_ H3K27Ac_ KD


title: H2AK115RK116R_R3

description: 15 days old plants


title: Upp5_R1

description: 15 days old plants


title: Mpbmi11l_R1

description: 15 days old plants


title: SMN0013_S10: human spinal motor neurons in SOD1

description: SOD1A4V ALS


title: P475_CRTH2-CD161-

data_processing:
Reads were aligned to the hg38 reference genome and collapsed by cell barcode and unique molecular identifier, and tabulated as described in Macosko et al.
Cells with fewer than 900 unique genes detected and genes detected in fewer than 5 cells were filtered out
Genome_build: hg38
Supplementary_files_format_and_content: barcodes.tsv.gz: single-cell barcodes from sample. Genes.txv: gene names from sample. Matrix.mtx.gz: single-cell gene/cell counts matrix in 10x sparse format.

extract_protocol:
Cryopreserved PBMC from 8 of the 10 patients included in the tissue-resident single-cell analysis were thawed, and memory CD4+ T cells were isolated with the EasySep human memory CD4+ T cell enrichment kit (Stemcell Technologies, Vancouver, BC, Canada). T cells were cultured in AIM V medium (Gibco, Waltham, MA) for 6 hours at a density of 2 x 10e6 in 0.5 ml medium per well in 48-well plates, with human T-Activator CD3/CD28 beads (Thermo Fisher, Waltham, MA) in a 1:3 ratio of beads to T cells. After harvesting, the cells were labeled with BUV395-conjugated anti-CD3 (clone UCHT1), APC-Cy7-conjugated anti-CD4 (RPA-T4), PE-Cy7-conjugated anti-CD45RA (HI100), PerCP-Cy5.5-conjugated anti-CRTH2 (BM16) (all from BD Biosciences, San Jose, CA), eFluor450-conjugated anti-CD161 (HP-3G10), and Live/Dead Fixable Blue stain (L23105) (both from Thermo Fisher). Live CD3+CD4+CD45RA- CRTH2+CD161+, CRTH2+CD161-, and CRTH2-CD161- T cells were sorted with a FACSAria Fusion instrument (BD Biosciences).
Seq-Well

tag: patient

tag: sort fraction


title: OMN0013_S6: human ocular motor neurons in SOD1

description: SOD1A4V ALS

source_name: SOD1A4V PHOX2B::GFP+

tag: cell type


title: HUVEC_rep2

source_name: Umbilical Vein (Gibco)

value: Endothelium

value: Unknown


title: TS69_FOXC1


title: TS154_05_BB171_Input

value: none (input)


title: OMN078_S1: human ocular motor neurons in C9ORF72

description: C9ORF72 ALS

tag: tissue


title: Fa+Pg-H2O2-3

city: Loma Linda

first: Yuetan

last: Dou

address: 11021 Campus Street AH114

department: Microbiology and Molecular Genetics

institute: Loma Linda University

description: 0.25 mM of hydrogen peroxide stressed for 15 min

data_processing:
NextSeq 550 onboard basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings.
RNA-seq fastq files were trimmed with trimmomatic, aligned to F. alocis ATCC35896 genome, and reads were qunatified with cutfflinks. Gene differential expression was analyzed using cuffdiff with FPKM threshold of 1.
Genome_build: F. alocis ATCC35896
Supplementary_files_format_and_content: .csv file, with all gnes reads in one file

organism: Filifactor alocis

source_name: Coculture of F. alocis & P. gingivalis

growth_protocol: Anaerobic conditions (80% N2, 10% H2, 10%CO2)

extract_protocol:
Briefly, RNA were harvested by Qiagen RNA kit. ribosomal RNA was removed from 2 µg of total RNA by using RiboMinus Transcriptome Isolation Kit (Life Technologies, Carlsbad, CA).
The first- and the second- strand cDNA synthesis, the RNA-seq barcode ligation, and other steps of libraries construction were performed by using Nextflex RNA-Seq kit according to the protocol of manufacturer (Bioo Scientific, Austin, TX).

treatment_protocol: Treatment group treated by 0.25 mM of hydrogen peroxide

tag: strain

value: new oral pathogen F. alocis

tag: growing condition

value: anaerobic

tag: treatment

value: hydrogen peroxide stress


title: P475_CRTH2+CD161+

value: Eosinophilic esophagitis (EoE)

value: Peripheral blood


title: SMN078_S7: human spinal motor neurons in C9ORF72

description: C9ORF72 ALS


title: TS41_Fujioka _FOXC1 KD2

data_processing:
Reads were aligned to the human genome (GRCh38 and gene annotated with its corresponding GTF files (GENCODE GRCh38) using STAR version 2.4.2a with the settings --outFilterMultimapNmax 20 ,--outFilterType BySJout, --alignSJoverhangMin 8, --quantMode GeneCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig

growth_protocol: Fujioka cells were cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).

extract_protocol:
Total RNA was extracted from NTC or FOXC1 KD Fujioka cells using QIAshredder spin columns and an RNeasy Plus Micro Kit (Qiagen, Manchester, UK) and its quality confirmed using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: H2AK115RK116R_R1

description: 15 days old plants

source_name: Thallus

tag: ecotype

value: Upp

tag: genotype

tag: biological replicate

value: thallus


title: Epidermal_Equivalent_healty_donor 1 [HD3d1]

tag: subject status

value: healthy donor (HD)

value: keratinocytes

value: epidermal equivalent [EE)


title: TS49_ H3K4me2_ NTC

value: Fujioka

tag: antibody

tag: agent

value: non-targeting control (NTC)


title: P474_CRTH2+CD161-

tag: diagnosis


title: Fa+Pg-3

value: control


title: TS120_HDAC1_KD

value: lentivirus targeting FOXC1


title: P475_CRTH2+CD161-


title: Upp5_R2

description: 15 days old plants

value: WT


title: TS85_ FOXC1_BB475

value: Primary AML


title: P474_CRTH2+CD161+


title: TS49_ H3K27Ac_ NTCf


title: TS53_ATAC_NTC


title: TS154_04_BB171_RUNX1


title: P474_CRTH2-CD161-


title: OMN0013_S4: human ocular motor neurons in SOD1

description: SOD1A4V ALS

value: human ocular motor neurons

value: amyotrophic lateral sclerosis (ALS)


title: Fa+Pg-1

value: new oral pathogen F. alocis

value: anaerobic


title: Fa+Pg-H2O2-2

value: hydrogen peroxide stress


title: TS41_Fujioka _NTC2


title: TS41_Fujioka _NTC1


title: TS41_Fujioka _FOXC1 KD1


title: Fa+Pg-H2O2-1


title: d9_2

city: Qingdao

first: Wencheng

last: Wang

state: Shandong province

address: 700,Changcheng Road, Chengyang District

department: College of Horticulture

country: China

institute: Qingdao Agricultural University

data_processing:
Illumina software used for Base Calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Pyrus bretschneideri Rehd whole genome using HISAT.
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.
Genome_build: Pyrus bretschneideri Rehd genome
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

organism: Pyrus ussuriensis

source_name: adventitious roots

growth_protocol: The adventitious buds of Pyrus ussuriensis Maxim were preserved in Qingdao Agricultural University, and the roots were induced by the adventitious buds with consistent growth and subculture for 25 days.

extract_protocol:
The adventitious roots of the four developmental stages were sampled, flash frozen on Liquid nitrogen, and RNA was harvested using EASYspin reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The medium induced by adventitious roots of Pyrus ussuriensis Maxim was: 1/2 MS + 0.5 mg/L IBA + 30.0 g/L sucrose + 7.5 g agar, pH = 6.0.

value: adventitious roots

tag: development stage

value: Day 9


title: d9_1


title: P451_CRTH2-CD161-

value: Eosinophilic esophagitis (EoE)

value: Peripheral blood


title: 12-0732-MR

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

data_processing:
RNA-seq data was aligned to the hg38 reference genome using GSNAP (v.   ) with default options. Required a mapping quality scofe of ≥30 for each read. Quality control analysis of the aligned data was performed using program RNA-SeQC.
Transcripts were assembled using Cufflinks (v.  ). A gene was considered differentially expressed if the false discovery rate (FDR) -adjusted p-value is <0.05.
Genome_build: hg38

source_name: Macula Retina

extract_protocol:
Donor eyes were obtained from non-diabetic Caucasians at a death-to-preservation interval of <6h. Eyes were stored in RNA later before extraction of RNA. For each eye we dissected macula and periphery from retina and RPE/choroid/sclera resulting in 4 samples per eye. RNA was extracted using the ALLPrep DNA/RNA Mini Kit (Qiagen). All RNA had an RNA integrity number of ≥8.
Strand specific RNA library was prepared from 100 ng total RNA using the Encore Complete RNA-Seq library kit (Nugen Technologies, San Carlos, CA).
RNA-Seq on the Illumina HiSeq 2000.

tag: disease state

value: Normal


title: 12-0732-PR

source_name: Periphral Retina


title: d12_3

value: Day 12


title: d9_3


title: 12-0732-PRCS

source_name: Peripheral Choroid


title: d12_2


title: Fa+Pg-2