title: Jurkat, sgCtrl_P258, stimulated, rep1, batch2, WCE

description: Stimulated Jurkats input control, sgCtrl_P258(non-targeting guide), second batch WCE used for TAL1 and H3K27me3 Ctrl_P258 sample normalization


title: Jurkat, sg70_P260, stimulated, rep2, batch2, WCE

status: Public on Feb 23 2023

type: SRA

city: Boston

first: Nauman

middle: Muhammad

last: Javed

state: MA

address: 450 BROOKLINE AVE

department: Cancer Biology

country: USA

institute: DANA-FARBER CANCER INSTITUTE INC

description: Stimulated Jurkats input control, sg70_P260(targeting guide), second batch WCE used for TAL1 and H3K27me3 Ctrl_P258 sample normalization

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.20. Alignment, filtering, peak calling and QC was performed using ENCODE ChIP-seq pipeline v. 2.1.6(https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters.
For GATA3, H3K27ac, BHLHE40 P258 (sgCtrl_P258, unedited)) WCE-P258-1 and WCE-P258-2 were used as input control. For GATA3, H3K27ac, BHLHE40 P260 (sg70_P260, unedited)) WCE-P260-1 and WCE-P260-2 were used as input control. For TAL1 P258, WCE-P258-1_batch2, WCE-P258-2_batch2 were used as input control samples. For TAL1 P260, WCE-P260-1_batch2, WCE-P260-2_batch2 were used as input control samples. For CtrlLV GATA3 and BHLHE40 ChIP, WCE-P258-1 and WCE-P258-2 were used as input control samples. No input controls were provided for H3K27ac/H3K27me3 processing
p-value bigWig files showing signal enrichment relative to input control were generated for merged filtered bams for each replicate using MACS2 bdgcmp -m FE and default parameters in the ENCODE pipeline
Assembly: hg38
Supplementary files format and content: Bigwigs contain enrichment p-value for merged replicates for each condition/treatment relative to the matched merged input controls generated using MACS2.
Supplementary files format and content: NarrowPeaks contain significant IDR peaks (0.05 cutoff) for BHLHE40 and GATA3 ChIP in Ctrl-LV (BHLHE40-WT) Jurkats, and pooled MACS2 raw peaks for H3K27ac ChIP

molecule: genomic DNA

organism: Homo sapiens

source_name: Jurkat

growth_protocol: Jurkat cells  were grown in 37C, 5%CO2 in complete RPM consisting of RPMI(GIBCO), 10% fetal bovine serum(FBS, heat inactivated, Peak Serum), 20 mM HEPES(GIBCO), 1% sodium pyruvate(GIBCO), 1% penicillin-streptomycin(GIBCO), 1% NEAA(GIBCO), at a maximum density of 2 x 10^6 cells. Cells were routinely tested for mycoplasma.

extract_protocol:
25 million cells per sample were pelleted and fixed using 1% formaldehyde and quenched with glycine. Pellets were washed with cold PBS+proteinase, resuspended in lysis buffer, and incubated on ice for 10 minutes. Sample was then diluted up to 1 ml in ChiP dilution buffer, sonicated using Covaris E220, and  incubated overnight with H3K27ac antibody(Active Motif, 39133), GATA3(CST-D13C9), or BHLHE40(Novus Biological NB100-1800) and incubated overnight.  Immunopreciitation was performed using protein G beads, and DNA fragments were purified using AMPure XP beads
Eluted fragments were then processed with DNA end-repair(Epicenter Biotech), Klenow a base adding(Klenow from NEB), adaptor ligation, PCR amplification, and purification using AMPure XP beads with final size of ~300 bp.

treatment_protocol: Jurkat cells were stimulated for 2 hours with 50 ng/ml PMA(Sigma-Aldrich) and 500 ng/ml ionomycin(Sigma,Aldrich). Lentivirus transduction was conducted using either  sgCtrl_P258(control guide RNA) or sg70_P260(RE4 base editing guide RNA) constructs. Cells were plated at a density of 2-5 x 10^5 cells and treated with lentiviral supernatant supplemented with 8 ug/ml polybrene, centrifuged at 2000g 32 C for 60 minutes, and incubated overnight at 37C 5%CO2. Cells were changed into complete RMPI the following day and puromycin selection was conducted using 5 ug/ml for 3 days.

tag: cell line

value: Jurkat

tag: cell type

value: T-ALL

tag: chip antibody

tag: genotype

tag: treatment

value: stimulated(PMA/ionomycin 5 hours)


title: Donor1_IL2_1 (ATAC-seq)

city: Philadelphia

first: Inyoung

last: Jung

state: PA

address: SPE, 9-304, 3400 Civic Center Blvd, Bldg. 421

institute: University of Pennsylvania

data_processing:
Cutadapt (https://github.com/marcelm/cutadapt/) was used to trim FASTQ files of adapter contamination. Reads were aligned to the hg19 reference genome using Bowtie2, retaining only properly aligned and paired reads from 10 and 1000 base pairs. Mitochondrial reads were then eliminated (https://github.com/jsh58/harvard/blob/master/removeChrom.py). Aligned reads were converted to BAM files and sorted with samtools, and Picard was used to remove PCR duplicates. BAM files were indexed using samtools to display tracks in the Integrative Genome Viewer (IGV). MACS2 was used to call peaks with an FDR q-value cutoff of 0.01. The R package Diffbind was used to remove ENCODE blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists), then to identify peaks differentially opened between the CAR-TCONV and -TRM populations.
Supplementary files format and content: narrowPeak files
Assembly: GRCh38

source_name: blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from healthy subjects via leukapheresis. Written informed consent for leukocyte collection was provided by study subjects according to the Declaration of Helsinki and the International Conference on Harmonization Guidelines for Good Clinical Practice. PBMCs were isolated from buffy coats and cryopreserved at 4 × 107 cells per vial. Cryopreserved PBMCs were thawed, and T-cell purification was carried out using the Pan T Cell Isolation Kit according to the manufacturer’s instructions (Miltenyi Biotec). For CAR-TCONV manufacturing, T-cells were activated with Cell Therapy Systems CD3/CD28 Dynabeads™ (Thermo Fisher Scientific) at a bead to cell ratio of 3:1 for three days in T-cell OpTmizer CTS SFM media (Gibco) supplemented with 5% human AB serum and 100U/mL human IL-2 (T-cell media). At 24-hours post-T-cell activation, T-cells were transduced with the lentiviral vectors (M5bbz CAR) at a multiplicity of infection (MOI) of 3. T-cell media was added to cultures every two days, and on day nine, CAR T-cells were cryopreserved in T-cell media supplemented with 20% human AB serum and 10% dimethyl sulfoxide. For CAR-TRM production, T-cell culture media was supplemented with 2ng/mL of TGFβ (R&D Systems or Cell Signaling Technology) in addition to IL-2, and the CAR T-cell engineering process was carried out.

extract_protocol: Anti-mesothelin M5 CAR-TCONV and CAR-TRM cells were harvested after nine days of in vitro expansion. CD8+ CAR T-cells were magnetically isolated using anti-mesothelin-coated beads (ACROBiosystems) and anti-CD8 microbeads (Miltenyi Biotec). After elimination of dead cells, 100,000 CD8+ CAR T-cells were cryopreserved. Library preparation was performed by Novogene as follows: a reaction mixture consisting of Tn5 transposase and equimolar adapter1 and adapter 2 was added to nuclei pellets and incubated at 37°C for thirty minutes. The library was enriched using PCR, and purification of final libraries was carried out using AMPure beads (Beckman Coulter). Paired-end sequencing (150bp reads) was conducted on a NovaSeq 6000 instrument.

tag: tissue

value: blood

tag: cell subtype

value: T-cell

tag: individual

tag: biological replication

value: Normal donor 1_rep1


title: HCASMCs, PAI-039, replicate 3

city: Columbia

first: Trupti

last: Joshi

state: Missouri

address: 103 Math Science Building

department: Department of Biomedical Informatics, Biostatistics and Medical Epidemiology (BBME)

institute: University of Missouri-Columbia

description: no additional information

library_source: transcriptomic

data_processing:
Trimmed fastq files were mapped to the reference genome GRCh38.p12 using hisat2
Cufflink was used to calculate the FPKM
Cuffdiff was used to identify the differentially expressed genes
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

source_name: HCASMCs

growth_protocol: HCASMCs were grown in Medium 231

extract_protocol:
Total cellular RNA was isolated using a commercially available kit (Cat. #74104, Qiagen), following manufacturer's instructions. Messenger RNA was isolated by oligo(dT) coupling.
The libraries were sequenced with an Illumina NextSeq SE75 machine using paired-end sequencing.

treatment_protocol: When approprate confluency was reached, cells were treated with either PAI-039 or vehicle control in a serum-poor medium (DMEM:F12 containing 0.2% FBS)

tag: Sex

value: Female

value: HCASMCs

tag: age

value: 32 year old


title: Jurkat, sgCtrl_P258, stimulated, rep2, batch2, WCE


title: Jurkat, Ctrl_LV, stimulated, rep1, H3K27ac

description:
Stimulated Jurkats H3K27ac, Ctrl_LV (control lentivirus)
CtrlLV_H3K27Ac.pval.signal.bigwig
CtrlLV_H3K27ac.pooled.narrowPeak.gz

value: H3K27ac (Active Motif 39133)


title: Donor1_TGFb_1 (ATAC-seq)

value: TGFb


title: HCASMCs, PAI-039, replicate 2

description: no additional information


title: HCASMCs, PAI-039, replicate 1

description: no additional information


title: Jurkat, Ctrl_LV, stimulated, rep2, BHLHE40

description:
Stimulated Jurkats BHLHE40, Ctrl_LV (control lentivirus)
CtrlLV_BHLHE40.pval.signal.bigwig
CtrlLV_BHLHE40.idr0.05.narrowPeak.gz

value: BHLHE40 ( Novus Biological, NB100-1800)


title: cMyBP-C-/- ECT 4 [s20020806E7]

city: Madison

first: Willem

middle: Jacobus

last: DE LANGE

state: Wisconsin

address: Room 8553, 1111 Highland Av

department: Pediatrics

institute: University of Wisconsin-Madison

data_processing:
Paired-end 150bp sequencing was performed, using standard SBS chemistry on an Illumina NovaSeq6000 sequencer.
Images were analyzed using bcl2fastq v2.20.0.422.
all samples passed appropriate quality control and we obtained a minimum of 7 x 10^7 reads per sample.
Assembly: GCA_000001405.25
Supplementary files format and content: Tab-delimited text file include RPKM values for each Sample

source_name: Engineered Cardiac

growth_protocol: ECTs were fed 2-3 days with fibrin ECT media (60.3% high-glucose DMEM; 20% F12 nutrient supplement; 1 mg/mL gentamicin; 8.75% FBS; 6.25% horse serum; 1% HEPES; 1x nonessential amino acid cocktail; 3 mM sodium pyruvate; 0.004% (wt/vol) NaHCO3; 1 µg/mL insulin; 400 µM tranexamic acid and 17.5 µg/mL aprotinin)

extract_protocol:
Total RNA was extracted from day-14 ECTs using the Direct-zol™ RNA MiniPrep kit (Zymo Research). Purity and integrity via the NanoDrop One Spectrophotometer and Agilent 2100 Bioanalyzer, respectively.
RNA libraries were prepared from samples that met the TruSeq® Stranded Total RNA Sample Preparation Guide (15031048 E) input guidelines using the Illumina® TruSeq® Stranded Total (Gold) RNA Sample Preparation kit (Illumina Inc., San Diego, California, USA). For each library preparation, cytoplasmic ribosomal RNA was removed using biotinylated target-specific oligos combined with paramagnetic beads tagged with streptavidin. Following purification, the reduced RNA was fragmented using divalent cations under elevated temperature. Fragmented RNA was copied into first stranded cDNA using SuperScript II Reverse Transcriptase (Invitrogen, Carlsbad, California, USA) and random primers. Second strand cDNA was synthesized using a modified dNTP mix (dTTP replaced with dUTP), DNA Polymerase I, and RNase H. Double-stranded cDNA was cleaned up with AMPure XP Beads (1X) (Agencourt, Beckman Coulter). The cDNA products were incubated with Klenow DNA Polymerase to add a single ‘A’ nucleotide to the 3’ end of the blunt DNA fragments. Unique dual indexes (UDI) were ligated to the DNA fragments and cleaned up with two rounds of AMPure XP beads (0.8X). Adapter ligated DNA was amplified by PCR and cleaned up with AMPure XP beads (0.8X).  Final libraries were assessed for size and quantity using an Agilent DNA1000 chip and Qubit® dsDNA HS Assay Kit (Invitrogen, Carlsbad, California, USA), respectively. Libraries were standardized to 2nM.

value: Engineered Cardiac

value: iPSC-drived cardiomyocyte and cardiac fibroblast

value: cMyBP-C-/-

value: Male


title: cMyBP-C-/- ECT 1 [s20020801E7]


title: cMyBP-C-/- ECT 3 [s20020805E7]


title: cMyBP-C-/- ECT 2 [s20020802E7]


title: HCASMCs, control, replicate 3

description: no additional information

value: Vehicle Control


title: Scr rep3

type: RNA

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

country: Israel

institute: Sheba Medical Center at Tel HaShomer

description: Gene expression data from HDLEC trasfected with  scrambled contro

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human PrimeView GeneChip  . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000

data_processing: RMA

label: biotin

source_name: HDLEC primary cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HDLECs were purchased from PromoCell and cultured in EGM-2, which consists of EBM-2 (Lonza) and 20% FBS (Lonza). Cells were grown in culture flasks with 0.1% gelatin (Sigma) at 37 °C, 5% CO2

extract_protocol: Total RNA  (three independent experiments) was isolated using Trizol (Invitrogen).

treatment_protocol: HDLECs transfected with let-7i versus scrambled control

value: HDLECs

tag: transfected with

value: HDLEC transfected with scrambled control


title: Jurkat, sgCtrl_P258, stimulated, rep2, TAL1

description:
Stimulated Jurkats TAL1, Ctrl_LV (control lentivirus)
TAL1_p258.pval.bigwig

value: Jurkat

value: T-ALL

value: TAL1 (Santa Cruz Biotechnology, # SC-393287)

value: stimulated(PMA/ionomycin 5 hours)


title: IgG_T0

type: genomic

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

description: IgG Treated

hyb_protocol: hybing was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

scan_protocol: scanning was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

data_processing: The raw intensity data extracted from the CEL files were normalized with cyclic loess normalization and log transformed. This data was later used to calculate the drop in expression between and initial and final time points for each replicates. The details of differential expression calculations are explained in the manuscript.

label: T0 Timepoint

source_name: Breast Cancer ex vivo cells

label_protocol: labeling was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

growth_protocol: ex vivo cells were collected as describled in the manuscript Zawily et al.

extract_protocol: genomic DNA was extracted as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

treatment_protocol: ex vivo cell were treated with IgG or anti-EphA2 as described in the manuscript Zawily et al.


title: IgG_T14_Rep2

description: IgG Treated

label: T14 Timepoint Replicate 2


title: IgG_T14_Rep1

description: IgG Treated

label: T14 Timepoint Replicate 1


title: EphA2_T14_Rep2

description: Anti-EphA2 Treated


title: EphA2_T14_Rep1

description: Anti-EphA2 Treated


title: cMyBP-C+/- ECT 4 [s2002081E7]

value: cMyBP-C+/-


title: Scr rep2


title: EphA2_T0

description: Anti-EphA2 Treated


title: HCASMCs, control, replicate 2

description: no additional information

value: Female

value: HCASMCs


title: Scr rep1


title: HCASMCs, control, replicate 1

description: no additional information

value: 32 year old


title: cMyBP-C+/- ECT 1 [s20020807E7]


title: Input of K562

city: Copenhagen N

first: Chunarum

last: Choudhary

state: --- Select a state ---

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: University of Copenhagen

description:
Input of K562.
none

data_processing:
Read alignment was performed using BWA with default parameters. Low mapping quality read (MAPQ 10) and duplicated reads were removed using samtools. The DAC Blacklisted Regions were also omitted from the bam file using bedtools. Peaks were called using Lanceotron with default model and filtered if the input subtracted peak height < 8rpm.
For H3K27ac ChIP-seq samples, the data in this data series are merged with the GSE146324 data sets and analyzed.
Assembly: mm10, hg19
Supplementary files format and content: bigWig

growth_protocol: E14Tg2A Rosa26-Cre Oct4-IRES-Puro mouse ESCs were cultured in custom-made (C.C.Pro GmbH, Oberdorla) N2B27 medium consisting of 1:1 mix of DMEM/F12 and Neurobasal medium, but lacking Arginine and Lysine. Prior to use, the media was supplemented with 640 µM L-Arginine, 550 µM L-Lysine, 100 µM 2-mercaptoethanol, 150 µM sodium pyruvate, 0.5x B27 supplement (Thermo Fisher Scientific), 0.5x N2 supplement (Thermo Fisher Scientific), 1% penicillin/streptomycin, and cell type-specific growth factors or inhibitors. For mESCs the medium was supplemented with 1000 units/ml leukemia inhibitory factor (LIF) (Merck Millipore), 1 µM PD0325901, and 3 µM CT-99021 (custom-made by ABCR GmbH, Karlsruhe). mESCs were passaged regularly (every 2 to 4 days) with Accutase (PAA) or TrypLE (Thermo Fisher Scientific), and were occasionally selected for Oct4 expression with 1µg/ml puromycin (Sigma). K562 cells were cultured in RPMI-1640 media supplemented with 10% FBS, and 1% penicillin/streptomycin. All cells were cultured at 5% CO2, 37 oC.

extract_protocol:
Cells were cross-linked for 10 min at room temperature with 1% formaldehyde solution with gentle agitation and quenched with 0.125 M glycine. Cross-linked cells were washed once with PBS, added swelling buffer (10 mM Tris-HCl pH8.0, 1.5 mM MgCl2, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 minutes. After centrifugation, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) containing proteinase inhibitor cocktail (Roche), and then were sonicated by using a BioRuptor sonicator (Diagenode). After centrifugation, solubilized chromatin was recovered and incubated with 5 µg of antibody bound to protein A/G magnetic beads (Pierce). After overnight incubation at 4ºC, the magnetic beads were washed with RIPA buffer twice, RIPA high salt buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) and TE buffer. The bound materials were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1% SDS) overnight at 65ºC and treated with RNaseA for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA was purified with a PCR purification kit (Qiagen).
ChIP-seq libraries were prepared by using the NEBNext Ultra II DNA prep kit (NEB E7645) following the manufacturer's instruction and sequenced on a Next-Seq 500 Sequencer (Illumina).

treatment_protocol: A-485 (10uM) or NVP2 (10uM) were treated for indicated time. For control samples, 0.1 % DMSO was added.

value: wild type


title: cMyBP-C+/- ECT 2 [s20020809E7]


title: Dorsal Forebrain Organoid

city: Vancouver

first: STEMCELL

last: Technologies

state: BC

address: 1618 Station st

department: RND

institute: STEMCELL Technologies

description: scRNA-seq data for 4 Dorsal Forebrain Organoids

library_source: transcriptomic single cell

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
The Antobody Capture barcodes were provided to Cell Ranger via the --feature-ref flag in order to demultiplexed the replicates (as described in https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis)
Further processing and demultiplexing was done with Seurat v4.1.1.
Assembly: hg19
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

source_name: CNS

extract_protocol:
Organoids were transferred to individual sterile tubes and rinsed with PBS. To each organoid, 500 µL of dissociation solution (250 U/mL papain plus 2000 U/mL DNase I in Hanks’ Balanced Salt Solution [HBSS]) was added. Organoids were incubated at 37°C for 30 minutes on an orbital shaker (Infors HT Celltron) set at 90 rpm. After incubation, a 1 mL pipettor was used to triturate each organoid 5 - 10 times. The cell suspension was incubated at 37°C for an additional 10 minutes on an orbital shaker set at 90 rpm. The cell suspension was triturated an additional 5 - 10 times. The dissociation reaction was quenched by adding 2 mL of ovomucoid protease inhibitor solution (10 mg/mL ovomucoid protease inhibitor in HBSS). Cells were centrifuged at 300 x g for 5 minutes and resuspended in HBSS followed by a cell count using AO/DAPI staining and analysis on NucleoCounter® NC-200™ (Chemometec). The cell suspension was passed through a 37 µm strainer to remove any additional aggregates. One million cells were labeled using TotalSeq™-B anti-human oligo-tagged antibody (Biolegend) using a concentration of 1 µg/mL for 30 minutes at room temperature. Cells were rinsed twice with sterile PBS and mixed in equal proportions to obtain > 2500 cells per organoid.
Library was prepared using Chromium Single Cell 3ʹ v1 protocol with Feature Barcoding technology (10x Genomics) following surface protein staining with TotalSeq™–B (BioLegend)

value: CNS

value: Neurons, Neural Progenitors, Glial Cells


title: Ventral Forebrain Organoid

description: scRNA-seq data for 4 Ventral Forebrain Organoids


title: Cerebral Organoid

description: scRNA-seq data for 4 Cerebral Organoids


title: H2BK20ac ChIP in K562 cell line rep2

description:
H2BK20ac ChIP-seq in K562, Control.
K562_Ctrl_TC0_H2BK20ac.ab177430.CST34156_CC16.CC20.n2.smooth.bw
K562_Ctrl_TC0_H2BK20ac.ab177430.CST34156_CC16.CC20_peak.bed

value: H2BK20ac (Cell Signaling, CST34156)


title: cMyBP-C+/- ECT 3 [s20020811E7]

value: Engineered Cardiac

value: iPSC-drived cardiomyocyte and cardiac fibroblast


title: BMMCs_HdcGC_KO_ATAC-seq_rep2

city: Denver

first: HUA

last: HUANG

state: Colorado

address: 1400 Jackson street, K511

department: Immunology and Genomic Medicine

institute: National Jewish Health

data_processing:
Raw sequencing reads (2 biological replicates for each group) were adaptor trimmed by Trimmomatic and the quality of sequenced data was analyzed by FastQC.
The trimmed reads were aligned to the mm10 reference genome using Bowtie2 with -very-sensitive and -x 2000 parameters.
The read alignments were filtered using SAMtools (version 1.7) to remove mitochondrial genome and PCR duplicates.
Peaks were identified by MACS2 with the q-value cut-off of 0.05
Supplementary files format and content: mm10
Supplementary files format and content: Tdf and bedgraph files for each sample

organism: Mus musculus

source_name: Bone-marrow

growth_protocol: Bone marrow-derived mast cells (BMMCs) were cultured from bone marrow cells of BALB/c mice in Iscove’s DMEM (10016CV, CorningTM cellgroTM, Manassas, VA) plus 10% FBS,100 units/mL penicillin, 100 μg/mL streptomycin, and 2 mM b-mercaptoethanol in the presence of 20 ng/mL IL-3 for four weeks. Over 99% of BMMCs were mast cells had a mast cell phenotype by FACS analysis (FcεRIα+ c-Kit+).

extract_protocol:
Briefly, 50,000 BMMCs were spin down and washed with cold PBS once. Then the cells were resuspended in 50 uL cold ATAC-RSB-lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin) and incubated for 3 minutes. The lysis buffer was immediately washed out with 1 mL ATAC-RSB buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1% Tween-20). The cell pellet was resuspended in 50 ul transposition mixture (25 uL 2X TD buffer, 2.5 uL transposase (Illumina, FC-121-1030), 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O) and incubated at 37 C for 30 minutes. The reaction was stopped by adding 2.5 uL of 0.5M EDTA pH 8 and transposed DNA was purified using Qiagen MiniElute PCR purification kit (Qiagen).
Purified DNA was amplified using the following condition: 72℃ for 5 min, 98 ℃ for 30 s, and 7 cycles: 98 ℃ for 10 s, 63 ℃ for 30 s, 72 ℃ for 1 min. The amplified libraries were cleaned up, size-selected, and the quality and quantity of libraries were assessed on an Agilent Technologies 2100 Bioanalyzer.

value: Bone-marrow

tag: strain

value: Balb/cJ

value: mast cell

value: Hdc GCbox -/-


title: H3K27ac ChIP in K562 cell line rep1

description:
H3K27ac ChIP-seq in K562, Control.
K562_Ctrl_TC0_H3K27ac.ab4729_CC10.n2.smooth.bw
K562_Ctrl_TC0_H3K27ac_CC10_peak.bed

value: H3K27ac (abcam, ab4729)


title: H2BK20ac ChIP in K562 cell line rep1

value: H2BK20ac (abcam, ab177430)


title: cMyBP-C+/+ ECT 3 [s20020815E7]

value: cMyBP-C+/+

value: Male


title: let 7i rep3

description: Gene expression data from HDLEC trasfected with let7i

value: HDLECs

value: HDLEC transfected with  let7i


title: BMMCs_HdcGC_KO_ATAC-seq_rep3


title: BMMCs_HdcGC_KO_ATAC-seq_rep1


title: cMyBP-C+/+ ECT 2 [s20020814E7]


title: BMMCs_HdcGC_WT_ATAC-seq_rep3

value: wide type


title: RNA NKG2A+ CD8+ T cell 02

city: Bundang-gu, Seongnam-si

first: Seong Jin

last: Choi

state: Gyeonggi-do

address: Dolma-ro, 172

department: Internal Medicine

country: South Korea

institute: Seoul National University Bundang Hospital

data_processing:
For RNA sequencing, single-end reads with 75 base pairs were aligned to the human reference genome using STAR (v 2.7.2)
For TCR sequencing, paired-end reads with 300 base pairs were aligned using MiXCR (v 3.0.3)
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files include read counts for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: txt files include clonal information for each Sample …

source_name: PBMC

extract_protocol:
Naïve, memory, NKG2A+, and KIR+ CD8+ T cells were isolated using a FACSAria II cell sorter (BD Biosciences).
RNA-seq libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) and sequenced on an Illumina NextSeq 500 for RNA sequencing. The TCR library was prepared using the SMARTer® Human TCR a/b Profiling Kit (Takara Bio, USA) and sequenced on an Illumina MiSeq

tag: disease

value: healthy

tag: clonotypes

value: NKG2A+ CD8+


title: cMyBP-C+/+ ECT 1 [s20020813E7]


title: RNA KIR+ CD8+ T cell 02

value: KIR+ CD8+


title: let 7i rep1


title: RNA KIR+ CD8+ T cell 01


title: RNA NKG2A+ CD8+ T cell 01


title: RNA KIR+ CD8+ T cell 03


title: BMMCs_HdcGC_WT_ATAC-seq_rep2


title: let 7i rep2


title: TC341 Treg TCR_subset

first: James

last: Garifallou

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia

description:
FACS sorted live cells (CD4+CD25hiCXCR5-PD1lo)
mRNA

data_processing:
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell V(D)J Reagent Kit (v1.1) per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled, and sequenced on an Illumina NovaSeq sequencer in a paired-end, single indexing run. Sequencing for each gene expression library targeted 20,000 mean reads per cell and each V(D)J library targeted 5,000 read pairs per cell. Data was then processed using the Cellranger multi pipeline (10x genomics, v5.0) for demultiplexing and alignment of sequencing reads to the GRCh38 transcriptome (10x Genomics v.3.0.0) and creation of feature-barcode matrices based on cell-associated cell barcodes across each paired gene-expression-VDJ library. Data was aggregated using the cellranger aggr pipeline (10x Genomics, v.5.0). Secondary analysis was performed using the Seurat package (v4.1, Hao et al, 2021) within the R computing environment. Data was filtered to only include cells expressing 200-4000 genes and having mitochondrial content consisting of less than 20 percent of the genes expressed. The filtered dataset was normalized, scaled, and clustered using the standard PCA based on the top 2000 variable genes. Finally, clustering and UMAP were performed on the dataset.
The immune profiling V(D)J data was added to the dataset by cell barcode to the gene expression data. Shared clonotypes were defined as clonotypes that were shared across at least two different Tcell populations in at least two different cells from each Tcell population and had the same TCR-alpha and TCR-beta chains, where both chains were defined by an amino acid sequence (neither chain was defined as NA).
Assembly: GRCh38
Supplementary files format and content: Processed data files for each sample consist of a barcode ID file, feature ID file, and count matrix file as produced from the Cellranger Pipeline (10x Genomics). An additional processed data file set includes the resulting filtered_contig_annotations.csv file for each library which contains the "annotations of each high-confidence cellular contig" (10x Genomics).
Library strategy: V(D)J-seq

source_name: Tonsil 341

extract_protocol:
Fresh tonsils were obtained as discarded surgical waste from de-identified immune- competent children undergoing tonsillectomy to address airway obstruction or recurrent tonsillitis. These studies were approved by The Children’s Hospital of Philadelphia Institutional Review Board as non-human subject research. The mean age was (x) and x % were male. A single cell suspension of tonsillar mononuclear cells (MNCs) was created by mechanical disruption (tonsils were minced and pressed through a 70-micron cell screen) followed by Ficoll-Paque PLUS density gradient centrifugation (GE Healthcare Life Sciences). CD19-positive cells were removed (StemCell) and CD4+ T cells were enriched with magnetic beads (Biolegend) prior to sorting Tfh cells (CD4+CD25-CXCR5hiPD1hi), CD25hiTfh cells (CD4+CD25hiCXCR5hiPD1hi), Tfr cells (CD4+CD25hiCXCR5+PD1int), and Treg (CD4+CD25hiCXCR5-PD1-) on a BD FACSAriaTM (BD Bioscience). Dead cells were excluded using LIVE/DEAD stain (Thermo Fisher Scientific).
CITE-Seq study was also developed on viable sorted Tfr cells from the 4-year-old donor. For the CITE-Seq sample preparation, Tfr cells were resuspended at 20 × 10^6 cells/ml in CITE-seq staining buffer (BioLegend) and incubated with Human TruStain FcX Fc Blocking reagent for 10 min at 4°C to block nonspecific antibody binding. Following Fc blocking, cells were incubated with a pool of 139 antibodies conjugated to an antibody-derived tag (ADT), inclusive of seven isotype controls (TotalSeq-C Human Universal Cocktail, anti-human GITR (108-17) and anti-human CD130 (2E1B02); BioLegend) for 30 min at 4°C. After incubation, cells were washed three times with 3.5 ml of staining buffer to remove antibody excess. Cells were passed through a 40-μm filter to remove any cell clumps and resuspended in 10% FBS RPMI media at 1 × 10^6 cells/ml for 10× Genomics 5’ single-cell RNA-seq.
Next-generation sequencing libraries were prepared using the 10× Genomics Chromium Single Cell 5’ Library and Gel Bead kit v1 with Feature Barcoding Technology for Cell Surface Protein, per manufacturer’s “Chromium Single Cell V(D)J Reagent Kits” protocol. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled, and sequenced on the Illumina NovaSeq 6000 sequencer (v1.5 chemistry) in a paired-end, single indexing run.

tag: disease state

value: male

value: tonsil

value: Treg cells


title: RNA Memory CD8+ T cell 02

value: Memory CD8+


title: RNA Memory CD8+ T cell 01


title: BMMCs_HdcGC_WT_ATAC-seq_rep1

value: Bone-marrow

value: Balb/cJ


title: cMyBP-C+/+ ECT 4 [s20020816E7]

value: Engineered Cardiac

value: iPSC-drived cardiomyocyte and cardiac fibroblast


title: RNA Naïve CD8+ T cell 03

value: Naïve CD8+


title: TC341 Treg 5GEX_subset

data_processing:
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell V(D)J Reagent Kit (v1.1) per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled, and sequenced on an Illumina NovaSeq sequencer in a paired-end, single indexing run. Sequencing for each gene expression library targeted 20,000 mean reads per cell and each V(D)J library targeted 5,000 read pairs per cell. Data was then processed using the Cellranger multi pipeline (10x genomics, v5.0) for demultiplexing and alignment of sequencing reads to the GRCh38 transcriptome (10x Genomics v.3.0.0) and creation of feature-barcode matrices based on cell-associated cell barcodes across each paired gene-expression-VDJ library. Data was aggregated using the cellranger aggr pipeline (10x Genomics, v.5.0). Secondary analysis was performed using the Seurat package (v4.1, Hao et al, 2021) within the R computing environment. Data was filtered to only include cells expressing 200-4000 genes and having mitochondrial content consisting of less than 20 percent of the genes expressed. The filtered dataset was normalized, scaled, and clustered using the standard PCA based on the top 2000 variable genes. Finally, clustering and UMAP were performed on the dataset.
The immune profiling V(D)J data was added to the dataset by cell barcode to the gene expression data. Shared clonotypes were defined as clonotypes that were shared across at least two different Tcell populations in at least two different cells from each Tcell population and had the same TCR-alpha and TCR-beta chains, where both chains were defined by an amino acid sequence (neither chain was defined as NA).
Assembly: GRCh38
Supplementary files format and content: Processed data files for each sample consist of a barcode ID file, feature ID file, and count matrix file as produced from the Cellranger Pipeline (10x Genomics). An additional processed data file set includes the resulting filtered_contig_annotations.csv file for each library which contains the "annotations of each high-confidence cellular contig" (10x Genomics).


title: RNA Naïve CD8+ T cell 02


title: BMMCs_HdcGC_KO_H3K27ac_rep3

data_processing:
The adaptor sequences in raw reads (two biological replicates for each group) were trimmed using Trimmomatic (version 0.33) (Bolger et al., 2014) and the quality of trimmed sequence data was analyzed by FastQC (version 0.11.9).
The trimmed reads were aligned to the mm10 reference genome using Bowtie2 (version 2.3.5.1) (Langmead and Salzberg, 2012).
Peak calling was performed using MACS2 (version 2.1.2) with default parameters (Zhang et al., 2008).
Supplementary files format and content: mm10
Supplementary files format and content: Tdf and bedgraph files for each sample
Library strategy: CUT&Tag

extract_protocol:
BMMCs (1 × 105) were treated with concanavalin A-coated beads (Bangs Laboratories, BP531) and incubated with rabbit anti-H3K27ac antibody (Abcam, ab4729) at 4 ℃ overnight. The cells were then incubated with guinea pig anti-rabbit antibody (Antibodies online, ABIN101961) at room temperature for 30 minutes. The cells were washed and incubated with pA-Tn5 adapter complex (Diagenode, C01070001) at room temperature for 1 hour on a rotator. The cell pellet was resuspended in 300 ml tagmentation buffer and incubated at 37 ℃ for 1 hour. The reaction was stopped by adding 10 μL 0.5M EDTA, 3 μL 10% SDS, and 2.5 μL 20 mg/mL Proteinase K, and cells were digested at 37 ℃ overnight. Then, DNA was extracted using phenol chloroform and diluted in 25 ml TE buffer with 1/400 RNAse A.
The tagmented DNA was enriched by PCR amplification using Universal i5 primer and uniquely barcoded i7 primers under the following conditions: 72 °C for 5 min, and 13 cycles: 98 °C for 30 sec, 98 °C for 10 sec, 63 °C for 10 sec, 72°C for 1 min and hold at 8 ℃. The PCR products were cleaned up and size-selected using Ampure XP beads (Beckman Coulter, A63880). The quality and quantity of libraries were analyzed with the Agilent TapeStation 4200 system.
H3K27ac CUT&Tag-seq

value: mast cell

value: Hdc GCbox -/-


title: RNA NKG2A+ CD8+ T cell 03


title: RNA Naïve CD8+ T cell 01


title: TC341 Tfr TCR_subset

description:
FACS sorted live cells (CD4+CD25hiCXCR5+PD1int)
mRNA

value: Tfr cells


title: TC341 Tfr 5GEX_subset


title: BMMCs_HdcGC_KO_H3K27ac_rep1


title: TC341 CD25hiTfh TCR_subset

description:
FACS sorted live cells (CD4+CD25hiCXCR5+PD1hi)
mRNA

value: CD25hiTfh cells


title: BMMCs_WT_H3K27ac_rep5

value: wide type


title: RNA Memory CD8+ T cell 03

value: healthy


title: IMP_4

city: Fort Collins

first: Ahmed

last: Gad

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Sequence reads were mapped to Equus caballus reference genome (EquCab3.0) Bowtie2 (2.2.2)
Mapped reads were used for annotation against equine mature and precursor miRNAs listed in the mirBase database (release 22)
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization) and presented as TMM-adjusted Counts Per Million (CPM)
The differential expression analysis was done using the DESeq2 statistical software package
Assembly: EquCab3.0
Supplementary files format and content: xlsx file include CPM values for each sample

organism: Equus caballus

source_name: Follicular fluid

extract_protocol:
For EV isolation, 2 ml of pre-centrifuged follicular samples were subjected to an ultracentrifugation procedure at 120,000 xg for 70 min at 4 OC using the Beckman SWTi55 rotor. The EVs pellet was washed with sterile PBS and then centrifuged again at 120,000 ×g for 70 min. Finally, EVs were resuspended in 500 µL of PBS and stored in −80 °C until further characterization and analysis.
Small-RNA libraries were prepared for next-generation sequencing (NGS) using a TruSeq Small RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: Follicular fluid

value: Extracellular Vesicles

tag: follicular stage

value: Impending ovulation

tag: follicle diameter

value: follicles with signs of imminent ovulation


title: IMP_2

tag: cell type


title: BMMCs_WT_H3K27ac_rep6


title: BMMCs_WT_H3K27ac_rep4


title: TC341 CD25hiTfh 5GEX_subset

value: male

value: tonsil


title: IMP_1


title: TC341_Tfh_TCR_subset

description:
FACS sorted live cells (CD4+CD25-CXCR5+PD1hi)
mRNA

value: Tfh cells


title: BMMCs_WT_H3K27ac_rep3

value: Bone-marrow

value: Balb/cJ


title: TC341 Tfr ADT_subset

description:
FACS sorted live cells (CD4+CD25hiCXCR5+PD1int)
protein (ADT)

library_source: other

data_processing:
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell V(D)J Reagent Kit (v1.1) per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled, and sequenced on an Illumina NovaSeq sequencer in a paired-end, single indexing run. Sequencing for each gene expression library targeted 20,000 mean reads per cell and each V(D)J library targeted 5,000 read pairs per cell. Data was then processed using the Cellranger multi pipeline (10x genomics, v5.0) for demultiplexing and alignment of sequencing reads to the GRCh38 transcriptome (10x Genomics v.3.0.0) and creation of feature-barcode matrices based on cell-associated cell barcodes across each paired gene-expression-VDJ library. Data was aggregated using the cellranger aggr pipeline (10x Genomics, v.5.0). Secondary analysis was performed using the Seurat package (v4.1, Hao et al, 2021) within the R computing environment. Data was filtered to only include cells expressing 200-4000 genes and having mitochondrial content consisting of less than 20 percent of the genes expressed. The filtered dataset was normalized, scaled, and clustered using the standard PCA based on the top 2000 variable genes. Finally, clustering and UMAP were performed on the dataset.
The immune profiling V(D)J data was added to the dataset by cell barcode to the gene expression data. Shared clonotypes were defined as clonotypes that were shared across at least two different Tcell populations in at least two different cells from each Tcell population and had the same TCR-alpha and TCR-beta chains, where both chains were defined by an amino acid sequence (neither chain was defined as NA).
Assembly: GRCh38
Supplementary files format and content: Processed data files for each sample consist of a barcode ID file, feature ID file, and count matrix file as produced from the Cellranger Pipeline (10x Genomics). An additional processed data file set includes the resulting filtered_contig_annotations.csv file for each library which contains the "annotations of each high-confidence cellular contig" (10x Genomics).
Library strategy: CITE-seq

molecule: protein

tag: antibody

value: TotalSeq-C Human Universal Cocktail, anti-human GITR (108-17) and anti-human CD130 (2E1B02)


title: TC341 Tfh 5GEX_subset


title: PreOV_4

value: Preovulatory


title: PreOV_3


title: BMMCs_WT_H3K27ac_rep2

value: mast cell

tag: genotype


title: BMMCs_HdcGC_KO_H3K27ac_rep2

value: Hdc GCbox -/-

tag: treatment


title: TC174 Treg TCR_subset

source_name: Tonsil 174

tag: tissue

value: Treg cells


title: IMP_3


title: CEM CNTR [L31]

city: pADOVA

first: Loredana

last: Urso

address: gattamelata 64

department: DISCOG

country: Italy

institute: Università degli studi di Padova

data_processing:
RNA reads preprocessing was performed by using fastp v0.20.0
Mapping to the human genome reference using STAR v2.7.0
Alignments were then elaborated by RSEM v1.3.3 to estimate gene abundances
DeSeq2 library (Love et al., 2014) was applied to normalize raw counts as in  (Anders and Huber, 2010), and to filter away irrelevant/not detected sequences
Assembly: Homo sapiens GRCh38 Ensembl v99
Supplementary files format and content: tab-delimited text files for raw and normalized counts

growth_protocol: Cell lines were cultured in RPMI 1640 medium (Euroclone) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 units/mL penicillin, and 20 units/mL streptomycin.

extract_protocol:
To extract the total RNA, we used a Trizol reagent according to the manufacturer's instructions. Then, we used the total RNA to construct of the sequencing libraries.
Illumina Stranded mRNA Prep

treatment_protocol: Jurkat, TALL-1 and CEM cells lines were treated with 10 μM everolimus or drug vehicle after for 24 hours. Then we collected cells and extracted the RNA to perform the RNASEq analysis.

value: blood

tag: cell line

value: CEM

value: T lymphocytes

value: p53 mut, NOTCH mut PTEN-

value: control


title: CEM EVE [L32]

value: everolimus 10mM


title: TC174 Treg 5GEX_subset

value: healthy


title: BMMCs_WT_H3K27ac_rep1

value: wide type


title: Muscle_HF+SFC+ALA_24h

city: Fujisawa

first: Naho

last: Kitamura

state: Kanagawa

department: Graduate School of Media and Governance

country: Japan

institute: Keio University

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45˚C on GeneChip Mouse Genome 430 2.0 Array. GeneChip array was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: GeneChip array was scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis was calculated by Microarray Suite version 5.0 (MAS5.0) with Thermo Fisher Scientific default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Gastrocnemius muscle of mice fed a HF+SFC+ALA diet after 24h fasting

label_protocol: Biotinylated cRNA was synthesized by GeneChip 3' IVT PLUS Reagent Kit Thermo Fisher Scientific) from 100 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield was checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNeasy Fibrous Tissue Mini Kit (Qiagen, Hilden, Germany) was used to extract skeletal muscle total RNA. Total RNA was extracted from the tissue cryopreserved with liquid nitrogen according to the kit’s instructions.

tag: gender

value: male

value: Gastrocnemius

tag: food

value: D12492+0.023% (w/w)  sodium ferrous citrate (SFC) and 0.2% (w/w) 5-aminolevulinic acid phosphate (ALA)

value: 21 months

tag: fasting period


title: Muscle_HF_24h

source_name: Gastrocnemius muscle of mice fed a HF diet after 24h fasting

tag: age


title: Muscle_Control_24h

source_name: Gastrocnemius muscle of mice fed a Control diet after 24h fasting


title: Muscle_HF+SFC+ALA

source_name: Gastrocnemius muscle of mice fed a HF+SFC+ALA diet after 4h fasting

value: 4 h


title: Muscle_Control

source_name: Gastrocnemius muscle of mice fed a Control diet after 4h fasting


title: CEM EVE [L30]


title: PreOV_1

value: Follicular fluid

value: Extracellular Vesicles

value: Preovulatory


title: PreOV_2


title: Muscle_HF

source_name: Gastrocnemius muscle of mice fed a HF diet after 4h fasting


title: TC174_Tfr_TCR_subset

tag: Sex

value: tonsil

value: Tfr cells


title: CEM CNTR [L29]

source_name: blood

value: blood

value: CEM


title: CEM EVE [L28]

value: T lymphocytes

value: p53 mut, NOTCH mut PTEN-


title: PostDEV_4

value: Postdeviation


title: TC174 Tfr 5GEX_subset

value: healthy


title: TC174_CD25hiTfh_TCR_subset

value: CD25hiTfh cells


title: PostDEV_3


title: CEM CNTR [L27]

value: control


title: PostDEV_2


title: TALL1 EVE [L26]

value: p53 mut, NOTCH wt, PTEN +

value: everolimus 10mM


title: PostDEV_1


title: TC174_Tfh_TCR_subset

value: male

value: Tfh cells


title: Day 10, replicate A, scRNAseq

city: Portland

first: H.

middle: Scott

last: Stadler

state: OR

address: 3101 SW Sam Jackson Park Rd

department: Research Center

institute: Shriners Children's Portland

description:
10x Genomics
Sample E

data_processing:
The raw scRNAseq data was processed following the 10X Genomics pipeline with Cell Ranger (version 6.1.2) software  to remove low-quality reads.
The remaining reads were aligned to the GRCm38 murine reference genome using STAR.
Gene count matrices were generated as described by Du et al., 2020.
Gene count matrices were imported into the R package Seurat (version 4.1.0) for all downstream analyses as described by Stuart et al., 2019.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: embryonic distal forelimb mesenchyme

extract_protocol:
Two independent DID cultures were processed as separate replicates for scRNAseq analysis of Day 2, 7 and 10 timepoints following the cell dissociation protocols as described by the manufacturer (10X Genomics).
Libraries were made with the 10x Genomics 3' Gene Expression, GEX V3.1 chromium kit. Library was performed according to the manufacter’s instructions.

value: embryonic cells

value: embryonic distal forelimb mesenchyme

tag: strain

tag: developmental stage


title: Day 10, replicate B, scRNAseq

description:
10x Genomics
Sample F


title: Day 7, replicate A, scRNAseq

description:
10x Genomics
Sample C


title: Day 2, replicate B, scRNAseq

description:
10x Genomics
Sample B


title: TALL1 CNTR [L25]


title: Day 7, replicate B, scRNAseq

description:
10x Genomics
Sample D


title: DEV_4

value: Follicular fluid

value: Extracellular Vesicles

value: Deviation


title: TALL1 EVE [L24]

value: blood


title: TC174 Tfh_5GEX subset

value: tonsil


title: Day 2, replicate A, scRNAseq

description:
10x Genomics
Sample A


title: DEV_3


title: 2R

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2200 Bonisteel Blvd

department: Biomedical Engineering

institute: University of Michigan

description:
10x Genomics Visium
merged_D7_D14.RDS
Integrated_Merged_spGEX_SeuratObj_v3.RDS
Mus_ST_list_label_transfer_1201.RDS

data_processing:
Manual alignment of spatial barcodes to tissue location was performed using 10x Genomics Loupe Browser version 6
De-multiplexing, genome alignment (mm10-2020-A or CanFam3.1.97), and count matrix generation was performed using 10x Genomics Space Ranger version 1.3.0
Count matrices were imported into R using Seurat v4. Data normalization was performed using SCTransform, followed by principal component analysis (top 30 dimensions), FindNeighbors, FindClusters, and RunUMAP with default conditions.
Mouse datasets were integrated with annotated scRNA-Seq matrices publically available at GSE163376
Assembly: mm10-2020-A and CanFam3.1.97
Supplementary files format and content: Process data files are provided as (1) a list of Seurat Objects for each sample and (2) a single Seurat Object with all of the samples from the given species merged.
Library strategy: Spatial transcriptomics

source_name: Skeletal Muscle

extract_protocol:
Tissues were simultaneously flash frozen and OCT embedded according to 10x Genomics demonstrated protocol CG000240
Libraries were prepared according to manufacturer's protocol (10x Genomics demonstrated protocol CG000239). Briefly, 10um tissue sections were placed onto capture areas of visium slides and stained with hematoxylin and eosin, imaged, then permeabilized for 18 minutes (murine) or 24 minutes (canine). cDNAs were synthesized and amplified, followed by library construction.

value: Skeletal Muscle

tag: days post_injury

tag: slide serial_number

value: Female


title: 2L


title: DEV_2

tag: follicular stage


title: TALL1 CNTR [L23]

value: T lymphocytes


title: TALL1 EVE [L22]


title: TC174 CD25hiTfh_5GEX_subset

tag: disease state

value: healthy


title: EC-K63-KO (bio rep 3)

city: Hamburg

first: Matthias

last: Rath

address: Am Kaiserkai 1

department: Institute of Molecular Medicine

country: Germany

institute: MSH Medical School Hamburg

description:
Sample 18 (Group F)
EC_WTvsEC_CCM1KO_Differential_expression_analysis_table
iPSC_CCM1KOvsEC_CCM1KO_Differential_expression_analysis_table

data_processing:
Read trimming was performed with Trimmomatic v.0.36
Mapping to GRCh37 was performed with STAR aligner v.2.5.2b.
Unique gene hit counts were extracted with featureCounts from the Subread package v.1.5.2.
Assembly: GRCh37
Supplementary files format and content: comma-separated values files include normalized counts, log2 fold changes, and (adjusted) p-values for differentially expressed genes

growth_protocol: iPSCs were maintained on growth factor reduced matrigel (Corning) in E8 Flex medium (Thermo Fisher)

extract_protocol:
The Direct-zol RNA MiniPrep Plus Kit (Zymo Research) was used for purification of extracted RNA.
RNA-seq library preparation via polyA selection

treatment_protocol: iPSCs were differentiated to early mesoderm progenitor cells and endothelial cells using the STEMdiff Endothelial Differentiation Kit (STEMCELL)

tag: cell type

value: iPSC derived endothelial cells

value: CCM1 KO

value: endothelial cell differentiation


title: EC-K48-KO (bio rep 2)

description:
Sample 17 (Group F)
EC_WTvsEC_CCM1KO_Differential_expression_analysis_table
iPSC_CCM1KOvsEC_CCM1KO_Differential_expression_analysis_table


title: EC-K22-KO (bio rep 1)

description:
Sample 16 (Group F)
EC_WTvsEC_CCM1KO_Differential_expression_analysis_table
iPSC_CCM1KOvsEC_CCM1KO_Differential_expression_analysis_table


title: Mecp2_KO_H3K27me3_CST_rep_3

city: Houston

first: Sameer

middle: Subhash

last: Bajikar

state: TX

address: 1250 Moursund St

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Adapter sequences were removed from sequence reads using Trimmomatic version 0.36 (2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25) from the Truseq3.PE.fa adapter library and kseq
Confirmation of adapter removal and read quality was performed with fastqc (v0.11.8)
Alignment was performed with bowtie2-2.3.4.1 (--dovetail --phred33) to both mm10 (GRCm38 GCA_000001635.2) and the spike-in Ecoli K12 Genomes (GCF_000005845.2_ASM584v2)
Bedtools (v2.29.1) was used to process BAM files to BED files, remove blacklist (mm9 blacklist lifted over to mm10 and combined with mm10 blacklist downloaded with CUT&RUNTools (Zhu et al., 2019) and to generate bedgraphs
Each sample was normalized to internal Ecoli spike-in utilizing spike_in_calibration.sh as described previously (Meers et al., 2019)
Assembly: mm10 and E. coli
Supplementary files format and content: E. coli spike in normalized bigwig tracks
Library strategy: CUT&RUN

source_name: hippocampus

extract_protocol:
Nuclei were purified from wild-type, MECP2-TG1, or Mecp2-knockout hippocampi according to Mo et al. Purified nuclei were bound to concavalin A beads and incubated with the indicated antibody. Next, nuclei were incubated with pAG-MNase to cleave around antibody-bound DNA regions. Release fragments were collected and used for library prep.
CUT&RUN libraries were prepared using NEB Next II DNA Ultra Kit (NEB #E7645S) with NEB Illumina Unique Combinatorial Dual Index Kit (NEB # E6442S). 25 uL CUT&RUN fragments were used to prepare libraries for MeCP2 and IgG samples, 6 ng of input was used for H3K27me3 samples. Libraries were amplified for 14 cycles and fragments. Post amplified libraries were selected for ~300bp in length using SPRI beads from Beckman Coulter. Libraries size distributions were measured using Agilent TapeStation HS DNA 1000 (Agilent #5067) and concentrations were determined using the KAPA library quantification kit (Roche #07960140001).

value: hippocampus

tag: chip antibody

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb, Cell Signaling Technology, #9733

value: Mecp2-knockout (BirdA allele)


title: Mecp2_KO_H3K27me3_CST_rep_2

tag: genotype

value: male


title: EC-K53-WT (bio rep 3)

description:
Sample 15 (Group E)
EC_WTvsEC_CCM1KO_Differential_expression_analysis_table
iPSC_WTvsEC_WT_Differential_expression_analysis_table

value: WT

tag: treatment


title: TALL1 CNTR [L21]

tag: tissue

value: p53 mut, NOTCH wt, PTEN +

value: control


title: Mecp2_KO_H3K27me3_CST_rep_1


title: PreDEV_4

value: Follicular fluid

value: Extracellular Vesicles

value: Predeviation

tag: follicle diameter


title: PreDEV_3


title: EC-K37-WT (bio rep 2)

description:
Sample 14 (Group E)
EC_WTvsEC_CCM1KO_Differential_expression_analysis_table
iPSC_WTvsEC_WT_Differential_expression_analysis_table

tag: cell line


title: MECP2_TG1_H3K27me3_CST_rep_3

value: MECP2 transgenic (MECP2-TG1)


title: EC-K15-WT (bio rep 1)

description:
Sample 13 (Group E)
EC_WTvsEC_CCM1KO_Differential_expression_analysis_table
iPSC_WTvsEC_WT_Differential_expression_analysis_table


title: Jurkat CNTR [L19]

value: blood

value: Jurkat

value: p53 mut, NOTCH mut, PTEN -


title: Jurkat EVE [L18]

value: T lymphocytes

value: everolimus 10mM


title: MECP2_TG1_H3K27me3_CST_rep_2


title: PreDEV_2


title: eMPC-K63-KO (bio rep 3)

description:
Sample 12 (Group D)
eMPC_WTvseMPC_CCM1KO_Differential_expression_analysis_table

value: iPSC derived early mesoderm progenitor cells

value: CCM1 KO

value: early mesoderm progenitor cell differentiation


title: PreDEV_1


title: MECP2_TG1_H3K27me3_CST_rep_1

value: hippocampus

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb, Cell Signaling Technology, #9733


title: Jurkat CNTR [L17]


title: eMPC-K48-KO (bio rep 2)

description:
Sample 11 (Group D)
eMPC_WTvseMPC_CCM1KO_Differential_expression_analysis_table


title: Jurkat EVE [L16]


title: DEV_1

value: Deviation


title: Wild_type_H3K27me3_CST_rep_6

value: wild-type

value: male


title: Jurkat EVE [L20]


title: Jurkat CNTR [L15]

value: control


title: eMPC-K22-KO (bio rep 1)

description:
Sample 10 (Group D)
eMPC_WTvseMPC_CCM1KO_Differential_expression_analysis_table


title: eMPC-K53-WT (bio rep 3)

description:
Sample 9 (Group C)
eMPC_WTvseMPC_CCM1KO_Differential_expression_analysis_table

value: WT


title: Wild_type_H3K27me3_CST_rep_4


title: Donor_2_GMT_Day_6_GT22

city: Buenos Aires

first: Fernando

last: Erra Diaz

address: Paraguay 2155 , 11th floor

department: Immunology

country: Argentina

institute: Universidad de Buenos Aires - The Jackson Laboratory

data_processing:
RNA-seq libraries were prepared with KAPA mRNA Hyperprep kit (Roche) according to manufacturer’s instruction. First, poly A RNA was isolated from 300ng total RNA using oligo-dT magnetic beads. Purified RNA was then fragmented at 85C for 6 mins, targeting fragments range 250-300bp. Fragmented RNA is reverse transcribed with an incubation of 25C for 10mins, 42C for 15mins and an inactivation step at 70C for 15mins. This was followed by second strand synthesis and A-tailing at 16C for 30mins and 62C for 10 min. A-tailed, double stranded cDNA fragments were ligated with illumina unique dual indexed adapters (Illumina). Adapter-ligated DNA was purified using Ampure XP beads. This is followed by 10 cycles of PCR amplification. The final library was cleaned up using AMpure XP beads. Quantification of libraries were performed using real-time qPCR (Thermo Fisher). Sequencing was performed on Illumina NovaSeq platform generating paired end reads of 150bp.
Fastq files were processed into BAMs using STAR with hg38_assembly reference and ncbiRefSeq.gtf from UCSC genome browser data files
Assembly: hg38_assembly reference
Supplementary files format and content: .txt files contain raw counts matrix , Deseq2 normalized count matrix and Metadata file

source_name: FACS sorted CD1a+ CD16- MoDCs obtained in the presence of GM-CSF (50ng/ml) + the mTORC1 inhibitor Temsirolimus (50nM)

extract_protocol: Total RNA from cells were isolated using QIAGEN RNeasy Mini Kit according to the manufacturer’s instructions.

value: Perypheral blood monocytes

value: MoDC

tag: donor


title: Donor_2_GMIL4_Day_6_GT22

source_name: FACS sorted CD1a+ CD16- MoDCs obtained in the presence of GM-CSF (50ng/ml) + the IL-4 (30ng/ml)


title: Wild_type_H3K27me3_CST_rep_3


title: AZ-521 cells, 10μM platycodon D treatment for 48h 2

city: Hangzhou

first: Guangzhao

last: Pan

address: Dongfang street

department: Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences

country: China

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Stomach

growth_protocol: AZ-521 gastric cancer cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS), 1% Sodium Pyruvate, 1% MEM Non-Essential Amino Acids, and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
The total RNA was isolated from cells using TRIzol reagent according to the manufacturer's instructions (Sigma).
The TruSeq stranded mRNA sample preparation kit (Illumina Inc., USA) was adopted to prepare the RNA libraries by using the 250 ng of RNA, subsequently, the RNA libraries were sequenced by a HiSeq platform (Illumina, San Diego, CA, USA) on a 150-bp paired-end run. The differentially expressed genes were screen by a p-value cut-off for false discovery rate (FDR) of 0.05 and a minimum 2-fold change in expression.

treatment_protocol: The AZ-521 cell lines were incubated with 10 μM PD or DMSO for 48 h. Then the samples were harvested, and total RNA was isolated from cells using TRIzol reagent (Sigma)

value: Stomach

value: Gastric cancer cell

value: 10uM platycodon D treatment for 48h


title: eMPC-K15-WT (bio rep 1)

description:
Sample 7 (Group C)
eMPC_WTvseMPC_CCM1KO_Differential_expression_analysis_table


title: DKO_H2AZ1

city: Debrecen

first: Gabor

last: Szabo

address: Egyetem ter 1

department: Biophysics and Cell Biology

country: Hungary

institute: University of Debrecen

hyb_protocol: 0.6 micro-g of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 micro-L containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 micro-L of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to G. gallus (Chicken) Oligo Microarray v2 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 micro-m, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

organism: Gallus gallus

source_name: Chicken DT40 cell line double knock out +H2A.Z1

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 micro-g Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).


title: DKO_H2AZ1deltaC

source_name: Chicken DT40 cell line double knock out +H2A.Z1ΔC


title: WT_DT40

source_name: Chicken DT40 cell line wild type

value: wild type


title: AZ-521 cells, 10μM platycodon D treatment for 48h 1

institute: Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences


title: Wild_type_H3K27me3_CST_rep_2


title: Wild_type_H3K27me3_CST_rep_1


title: iPSC-K63-KO (bio rep 3)

description:
Sample 6 (Group B)
iPSC_WTvsiPSC_CCM1KO_Differential_expression_analysis_table
iPSC_CCM1KOvsEC_CCM1KO_Differential_expression_analysis_table

value: induced pluripotent stem cells


title: AZ-521 cells, DMSO treatment for 48h 3

value: DMSO treatment for 48h


title: Wild_type_H3K27me3_CST_rep_5


title: iPSC-K48-KO (bio rep 2)

description:
Sample 5 (Group B)
iPSC_WTvsiPSC_CCM1KO_Differential_expression_analysis_table
iPSC_CCM1KOvsEC_CCM1KO_Differential_expression_analysis_table

value: CCM1 KO


title: iPSC-K22-KO (bio rep 1)

description:
Sample 4 (Group B)
iPSC_WTvsiPSC_CCM1KO_Differential_expression_analysis_table
iPSC_CCM1KOvsEC_CCM1KO_Differential_expression_analysis_table


title: Donor_3_GMGW_8h_GT22

source_name: Human monocytes cultured for 8h in the presence of GM-CSF (50ng/ml) + the PPARg inhibitor GW9662 (10uM)


title: Mecp2_KO_MeCP2_CST_rep_2

value: MeCP2 (D4F3) XP Rabbit mAB, Cell Signaling Technology, #3456

value: Mecp2-knockout (BirdA allele)


title: iPSC-K53-WT (bio rep 3)

description:
Sample 3 (Group A)
iPSC_WTvsiPSC_CCM1KO_Differential_expression_analysis_table
iPSC_WTvsEC_WT_Differential_expression_analysis_table


title: eMPC-K37-WT (bio rep 2)

description:
Sample 8 (Group C)
eMPC_WTvseMPC_CCM1KO_Differential_expression_analysis_table

value: iPSC derived early mesoderm progenitor cells

value: early mesoderm progenitor cell differentiation


title: AZ-521 cells, DMSO treatment for 48h 2


title: Donor_4_GMGW_Day_6_GT22

source_name: FACS sorted CD1a+ CD16- MoDCs obtained in the presence of GM-CSF (50ng/ml) + the PPARg inhibitor GW9662 (10uM)


title: AZ-521 cells, DMSO treatment for 48h 1


title: AZ-521 cells, 10μM platycodon D treatment for 48h 3


title: Donor_2_GMTGW_Day_6_GT22

source_name: FACS sorted CD1a+ CD16- MoDCs obtained in the presence of GM-CSF (50ng/ml) + the mTORC1 inhibitor Temsirolimus (50nM) + the PPARg inhibitor GW9662 (10uM)


title: Donor_5_GMT_8h_GT22

source_name: Human monocytes cultured for 8h in the presence of GM-CSF (50ng/ml) + the mTORC1 inhibitor Temsirolimus (50nM)


title: iPSC-K37-WT (bio rep 2)

description:
Sample 2 (Group A)
iPSC_WTvsiPSC_CCM1KO_Differential_expression_analysis_table
iPSC_WTvsEC_WT_Differential_expression_analysis_table


title: Mecp2_KO_MeCP2_CST_rep_3

value: hippocampus


title: MECP2_TG1_MeCP2_CST_rep_3

value: MECP2 transgenic (MECP2-TG1)

value: male


title: Donor_2_GMT_8h_GT22


title: HCT116_DMSO

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: File include Count and  FPKM values for each sample

growth_protocol: The human gastric cancer cell line AGS and colon cancer cell line HCT116 were purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The two gastric cancer cell lines were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The human cell lines  were grown as usual in 6-well plates. After 24 hours of cell adherent growth, DMSO and 100 nM 5-Aza-CdR were added to the culture medium respectively. After 48 hours of treatment, the cells were digested for next studies.

value: colon cancer cell

value: DMSO


title: HCT116_5-Aza-CdR


title: Donor_5_GMGW_8h_GT22

value: Perypheral blood monocytes

value: MoDC


title: iPSC-K15-WT (bio rep 1)

description:
Sample 1 (Group A)
iPSC_WTvsiPSC_CCM1KO_Differential_expression_analysis_table
iPSC_WTvsEC_WT_Differential_expression_analysis_table

value: WT


title: Donor_4_GM_8h_GT22

source_name: Human monocytes cultured for 8h in the presence of GM-CSF (50ng/ml)


title: MECP2_TG1_MeCP2_CST_rep_2


title: AGS_5-Aza-CdR

source_name: AGS

value: AGS

value: gastric cancer cell


title: MECP2_TG1_MeCP2_CST_rep_1


title: Donor_2_GMGW_Day_6_GT22


title: siKi_3

city: Wuhan

first: Miaomiao

last: Liu

state: Hubei

address: 237 Luoyu Road, Hongshan District, Wuhan, China

institute: Wuhan University

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
The alternative splicing events (***-AS) and regulated alternative splicing events (***-RAS) between ***-OE and control samples were defined and quantified using the SUVA pipeline described previously . The frequency and proportion of reads of SUVA AS events (pSAR) were calculated.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample

source_name: SCC-9 cells

growth_protocol: SCC-9 cells were cultured in a 1:1 mixture of DMEM and Ham’s F12 medium containing 10% FBS, 400 ng/mL hydrocortisone, and 1% antibiotic-antimycotic in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using TRIzol reagent and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RNase-free RQ1 DNase (Promega Corp.) and its quality and quantity were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (Bio-Rad Laboratories, Inc.). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 6000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).

treatment_protocol: SCC-9 cells were seeded into 12 well plates and transfected by 10 nM siRNA on Day 0. siNC was used as a control. Cells were passed and transfected again on Day 2.SCC-9 cells were transfected by Lipofectamine 3000 Reagent (Invitrogen, USA).

value: SCC-9 cells

value: siRNA transfection


title: AGS_DMSO


title: siKi_2


title: Donor_4_GMT_Day_6_GT22


title: SGC7901_miR-34a_mimics

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (1.26.0).
Assembly: GRCh38
Supplementary files format and content: File include Count and  FPKM values for each sample

source_name: SGC7901 cell line

growth_protocol: The human gastric cancer cell line AGS and SGC7901 were purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The two gastric cancer cell lines were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: SiRNA was used to establish GC cell lines with knockdown of FGD5-AS1 and ZEB1 expression. GC cells were transfected with NC siRNAs and the miR-34a-mimics (final concentration, 50 nM) by Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. At 48 h post-transfection, cells were harvested for RNA sequencing.

value: SGC7901 cell line


title: siKi_1


title: Mecp2_KO_MeCP2_CST_rep_1

value: MeCP2 (D4F3) XP Rabbit mAB, Cell Signaling Technology, #3456


title: Donor_5_GM_8h_GT22


title: Wild_type_MeCP2_CST_rep_5

value: wild-type


title: Donor_2_GMTGW_8h_GT22

source_name: Human monocytes cultured for 8h in the presence of GM-CSF (50ng/ml) + the mTORC1 inhibitor Temsirolimus (50nM) and the PPARg inhibitor GW9662 (10uM)

value: Monocyte


title: SGC7901_miR-34a_negativecontrol

value: negative control siRNA


title: NS_3


title: Wild_type_MeCP2_CST_rep_4

value: hippocampus


title: Donor_3_GM_8h_GT22


title: NS_2


title: AGS_miR-34a_mimics

source_name: AGS cell line

value: AGS cell line


title: AGS_miR-34a_negativecontrol


title: NS_1


title: SGC7901_ZEB1_KD

value: ZEB1 Knockdown


title: Donor_5_GMIL4_Day_6_GT22


title: Wild_type_MeCP2_CST_rep_2

source_name: hippocampus

value: male


title: Wild_type_MeCP2_CST_rep_1


title: Donor_4_GMTGW_Day_6_GT22


title: SGC7901_ZEB1_negativecontrol

value: Negative Control


title: Wild_type_MeCP2_CST_rep_6


title: Mecp2_KO_IgG_rep_3

value: Normal Rabbit IgG, Millipore, #12-370

value: Mecp2-knockout (BirdA allele)


title: AGS_ZEB1_KD


title: AGS_ZEB1_negativecontrol


title: Mecp2_KO_IgG_rep_2


title: Donor_4_GMT_8h_GT22

value: Perypheral blood monocytes


title: SGC7901_shFGD5-AS1-2


title: 2L6_rep2

city: Santa Cruz

first: Jonathan

middle: David

last: Magasin

state: CA

address: 1156 High Street

department: Ocean Sciences

institute: UC Santa Cruz

description: Gene expression 6h after sunrise, day 2

hyb_protocol: The hybridization of cDNA samples (1.0 μg of ds-cDNA) to the microarray was done at the Roy J. Carver Center for Genomics Facility (University of Iowa, Iowa city, Iowa, USA) according to the Agilent Technology protocol for arrays.

scan_protocol: All microarray slides were scanned by the Roy J. Carver Center for Genomics Facility (University of Iowa, Iowa city, Iowa, USA) using an Agilent SureScan G2600D Microarray Scanner and the 1-color gene expression scanning protocol GE1_1200_Jun14. Agilent Feature Extraction software version 11.5.1.1 was used.

data_processing: Microarray data were prepared using the MicroTOOLs R package (https://www.jzehrlab.com/microtools) with the UCYN-A microarray platform description (GPL32341).  Microarray quality was assessed using the arrayQualityMetrics R pacakge. Background correction was performed using the LIMMA backgroundCorrect function which uses a normal-exponential convolutional model for background noise (Ritchie et al. 2007; Silver et al. 2009. Then array intensities were normalized by quantiles (Bolstad et al. 2003) using the affyPLM function normalize.ExpressionSet.quantiles.  Sample matrices in this GEO series are the background-corrected, quantile-normalized probe intensities.  Our publication describes additional processing required for gene-level analysis.

source_name: seawater, 12pm, replicate 1

label_protocol: The labeling of cDNA samples (1.0 μg of ds-cDNA) to the microarray was done at the Roy J. Carver Center for Genomics Facility (University of Iowa, Iowa city, Iowa, USA) according to the Agilent Technology protocol for arrays.

extract_protocol: Environmental RNA containing transcripts from UCYN-A cells was extracted using the Ambion RiboPure Bacteria Kit (Ambion, ThermoFisher) and treated with the Turbo-DNA-free DNase Kit (Ambion, ThermoFisher) following the procedure described in Muñoz-Marín et al., 2019.  RNA purity, concentration and quality were determined using a NanoDrop 1000 (Thermo Scientific, Waltham, MA, USA) and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 Nano Kit (Agilent Technologies). Only samples with RNA Integrity Number >7.0 and ratios of A260/A230 and A260/A280 ≥1.8 were processed further.  Double-stranded (ds) cDNA was synthesized and amplified following the procedure described in Muñoz-Marín et al., 2019.  The amplified cDNA was purified with the GenElute PCR Clean-Up Kit (Sigma-Aldrich), and the quality and quantity of ds-cDNA was determined with NanoDrop 1000 and a 2100 Bioanalyzer using the Agilent DNA 7500 Kit (Agilent Technologies). Four hundred ng of total RNA yielded on average 12 µg of ds-cDNA.

tag: organism synonym

value: UCYN-A

tag: environment

value: seawater

tag: time

value: 6h after sunrise, day 2


title: Wild_type_MeCP2_CST_rep_3

tag: age

tag: strain

tag: Sex


title: Mecp2_KO_IgG_rep_1


title: Donor_5_GMGW_Day_6_GT22


title: MECP2_TG1_IgG_rep_3

value: MECP2 transgenic (MECP2-TG1)


title: Donor_3_GMT_8h_GT22


title: MECP2_TG1_IgG_rep_2


title: SGC7901_shFGD5-AS1-1

value: SGC7901 cell line

value: gastric cancer cell


title: Donor_4_GMIL4_8h_GT22

source_name: Human monocytes cultured for 8h in the presence of GM-CSF (50ng/ml) + IL-4 (30ng/ml)


title: MECP2_TG1_IgG_rep_1


title: SGC7901_negativecontrol_rep2

value: negative control shRNA


title: SGC7901_negativecontrol_rep1


title: Donor_3_GMIL4_8h_GT22

value: Monocyte


title: Donor_5_GMIL4_8h_GT22


title: Donor_4_GMIL4_Day_6_GT22

source_name: FACS sorted CD1a+ CD16- MoDCs obtained in the presence of GM-CSF (50ng/ml) + the IL-4 (30ng/ml)


title: Wild_type_Rb_IgG_rep_6

value: wild-type


title: Donor_5_GMTGW_Day_6_GT22


title: MSDC_lung

city: Rochester

first: Bibo

last: Zhu

state: MN

address: 200 1st ST SW

department: Pulmonary and Critical Care Medicine

institute: Mayo Clinic

data_processing:
Paired-end sequencing was performed using an DNBSEQ-G400 in rapid-run mode.
CellRanger software package (10x Genomics) were used to align and quantify sequencing data.
All scRNA-seq analyses were performed in R using the package Seurat (version 3.0; Butler, 2018)
To analyze the cell cycle signature from the dataset, we used Seurat to calculate a cell cycle score for each cell based on expression across a list of reported core gene set including 43 G1/S and 54 G2/M markers. Scaled residual expression obtained from Seurat modeling the relationship between gene expression and the cell cycle scores, that was used for dimensionality reduction and clustering.
UMAP dimensional reduction was performed to visualize data in 2D space. DEGs between clusters were determined using a Wilcoxon rank sum test.
Genome_build: mm10
Supplementary_files_format_and_content: h5

source_name: lung

extract_protocol:
DMSO- or MSDC-0602K- treated lung cells were loaded on the Chromium Controller (10x Genomics).
Single-cell libraries were prepared using the Chromium Single Cell 3’ Reagent kit (10x Genomics)

treatment_protocol: Lung cells were from Influenza virus infected-WT mice administrated with DMSO or MSDC-0602K.

value: Lung

value: Influenza A/PR8/34 (4 d.p.i.)

value: MSDC


title: Wild_type_Rb_IgG_rep_5

value: hippocampus

value: male


title: DMSO_lung

value: DMSO


title: 2L3_rep1

description: Gene expression 3h after sunrise, day 2

source_name: seawater, 9am, replicate 1

value: 3h after sunrise, day 2


title: 2L6_rep1

description: Gene expression 6h after sunrise, day 2


title: D9_rep2

description: Gene expression 9h after sunset

source_name: seawater, 3am, replicate 2

value: 9h after sunset


title: 2D12_rep2

description: Gene expression at sunrise, start of day 2

source_name: seawater, 6am, replicate 2

value: UCYN-A

value: at sunrise, start of day 2


title: 2D12_rep1

source_name: seawater, 6am, replicate 1

value: seawater


title: D9_rep1

description: Gene expression 9h after sunset

source_name: seawater, 3am, replicate 1


title: D6_rep1

description: Gene expression 6h after sunset

source_name: seawater, 12am, replicate 1

value: 6h after sunset


title: Wild_type_Rb_IgG_rep_4

value: Normal Rabbit IgG, Millipore, #12-370


title: Donor_2_GMGW_8h_GT22

source_name: Human monocytes cultured for 8h in the presence of GM-CSF (50ng/ml) + the PPARg inhibitor GW9662 (10uM)

value: Perypheral blood monocytes


title: db_MSDC_3

data_processing:
Paired-end libraries were sequenced on an DNBSEQ-G400  following BGI’s standard protocol. Base-calling was performed using RTA software (version 2.5.2). Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using RNA-seq spliced read mapper Tophat2 (v2.1.1).
Pre- and post-alignment quality controls, gene level raw read count and normalized read count (i.e. FPKM) were performed using RSeQC package (v2.3.6) with NCBI mouse RefSeq gene model.
Differential expression for each gene between various groups was identified by Cuffdiff. For functional analysis, GSEA was used to identify enriched gene sets, from the hallmark and C5 databases of MSigDB, having up-regulated and down-regulated genes, using a weighted enrichment statistic and a log2 ratio metric for ranking genes.
Genome_build: mm10
Supplementary_files_format_and_content: csv file include counts for each Sample

extract_protocol:
Total RNA was extracted from Trizol reagent with Chloroform and RNA quality was determined (RIN>7) via Agilent Bioanalyzer
Libraries were prepared according to BGI in-house kit instructions accompanying the RNA Sample Kit.
cDNA synthesis, end-repair, A-base addition, and ligation of the indexed adapters were performed. The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA).

treatment_protocol: Lung tissues were mechanically homogenized in Trizol

value: db/db

value: lung

tag: infection

value: Influenza A/PR8/34 (5 d.p.i.)


title: db_MSDC_2


title: Donor_5_GMT_Day_6_GT22

source_name: FACS sorted CD1a+ CD16- MoDCs obtained in the presence of GM-CSF (50ng/ml) + the mTORC1 inhibitor Temsirolimus (50nM)

value: Monocyte


title: db_MSDC_1


title: Wild_type_Rb_IgG_rep_2

value: wild-type


title: Wild_type_Rb_IgG_rep_3


title: Donor_5_GMTGW_8h_GT22


title: Donor_4_GMGW_8h_GT22


title: db_DMSO_3


title: L12_rep2

description: Gene expression at sunset

source_name: seawater, 6pm, replicate 2

value: at sunset


title: Donor_4_GMTGW_8h_GT22


title: 1203R

description:
10x Genomics Visium
Mus_ST_list_label_transfer.RDS
merged_filtered_599L_599R_600L_600R_1197L_1203L_1203R_1202L.RDS

source_name: Skeletal Muscle

value: Skeletal Muscle

tag: days post_injury

tag: slide serial_number

value: Male


title: Wild_type_Rb_IgG_rep_1

value: hippocampus

value: male


title: db_DMSO_2

value: DMSO


title: D3_rep1

description: Gene expression 3h after sunset

source_name: seawater, 9pm, replicate 1

value: UCYN-A

value: 3h after sunset


title: Donor_3_GMTGW_8h_GT22

source_name: Human monocytes cultured for 8h in the presence of GM-CSF (50ng/ml) + the mTORC1 inhibitor Temsirolimus (50nM) and the PPARg inhibitor GW9662 (10uM)

tag: cell type


title: L6_rep2

description: Gene expression 6h after sunrise

source_name: seawater, 12pm, replicate 2

value: seawater

value: 6h after sunrise


title: Donor_2_GMIL4_8h_GT22


title: db_DMSO_1


title: 600L

value: Female


title: L12_rep1

description: Gene expression at sunset

source_name: seawater, 6pm, replicate 1


title: M4-3

value: Influenza A/PR8/34 (4 d.p.i.)


title: L9_rep1

description: Gene expression 9h after sunrise

source_name: seawater, 3pm, replicate 1

value: 9h after sunrise


title: L9_rep2

description: Gene expression 9h after sunrise

source_name: seawater, 3pm, replicate 2


title: CO8-DA-treated pea roots, 24 h 3

city: Pushkin

first: Polina

last: Kozyulina

address: Podbelsky chausse 3

country: Russia

institute: ARRIAM

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39 with default parameters
Trimmed sequence reads were mapped to Pisum_sativum_v1a (GCA_900700895.2) using bowtie2 v2.4.4 (parameters --very-sensitive)
Read count extraction and normalization were performed using RSEM v1.3.1
Assembly: Pisum_sativum_v1a (GCA_900700895.2)
Supplementary files format and content: tab-delimited text files include estimated counts for each Sample

organism: Lathyrus oleraceus

source_name: roots

growth_protocol: Four to five-day-old pea seedlings of cultivar Frisson were used for treatment with elicitors

extract_protocol:
Extraction of RNA from the roots was done using the PuroZOL RNA isolation reagent (BioRad Laboratories, California, USA). DNA was eliminated using DNAse digestion (Thermo Fisher Scientific, USA). RNA quality and quantity were determined by Nanodrop (Implen GmbH, Munich, Germany).
The RNA sequencing libraries were prepared following the guidelines for NEBNext mRNA magnetic isolation module purification kit (E7490) (https://www.neb-online.de/en/art/E7490) and NEBNext Ultra II directional RNA library prep kit for Illumina (E7760) (https://www.neb-online.de/en/art/E7770S) (New England Biolabs, USA). The quality of RNA was estimated using Bioanalyzer 2100 (Agilent Technologies, California, USA) prior to sequencing. The NEBNext Multiplex Oligos primer set for Illumina (Index Primers Set 2) (E7500S) (New England Biolabs, USA) was used for preparation. At all stages, the material was cleaned using AMPure XP beads (Beckman Coulter, USA).

treatment_protocol:
Deacetylated COs with main degree of polymerization around eight (CO8-DA): Mn = 1089, Mw = 1514, Ip = 1.39, CDS = 93% in Cl-form were used for treatment.
Four- to five-day-old seedlings of cv. Frisson were placed on the supporting foil surface in glass jars with 0.5x Jensen’s medium (control) (van Brussel et al., 1982) or 0.5x Jensen’s medium with CO8-DA (10-5 M) and incubated for 24 h. After treatment, the roots of pea seedlings were harvested for RNA extraction and gene expression analysis and immediately frozen at −80 °C.

tag: cultivar

value: Frisson

value: roots

value: WT


title: CO8-DA-treated pea roots, 24 h 2

tag: genotype


title: M4-2

source_name: lung

tag: treatment

value: lung


title: 599R

tag: tissue


title: Donor_2_GM_8h_GT22

source_name: Human monocytes cultured for 8h in the presence of GM-CSF (50ng/ml)

value: Perypheral blood monocytes

value: Monocyte


title: M4-1


title: D4-2


title: 1203L

value: Skeletal Muscle

value: PBS

value: Male


title: 1197L


title: d10_gplc

city: Boston

first: Nora

middle: E

last: Renthal

state: MA

address: 3 Blackfan Circle

department: Endocrinology

institute: Boston Children's Hospital

data_processing:
Reads were mapped to mouse genome GRCm38 using STAR Aligner and gene-based readcounts were generated using featureCounts.
Differential gene expression was performed in edgeR after library size normalization. CPM values were compared.
Assembly: GRCm38
Supplementary files format and content: .xlsx spreadsheet containing CPM values

growth_protocol: Growth plate like chondrocyte (GPLC) cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 100 U/mL Penicillin/ 100mg/mL Streptomycin,  50 ug/mL Ascorbic acid, and 1X Insulin/Transferrin/Selenium in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from sorted cells using QIAGEN Rneasy Plus Mini Kit and concentrations were quantified using NanoDrop.
Libraries were prepared by the Harvard Medical School's Biopolymers Facility via KAPA HyperPrep with Ribo-Erase Library Prep

value: Day 10


title: D4-3

value: DMSO


title: d3_gplc

source_name: Growth plate like chondrocyte (GPLC) cells

value: Day 3


title: 600R


title: d1_gplc

value: Growth plate like chondrocyte (GPLC) cells

value: Day 1


title: L3_rep1

description: Gene expression 3h after sunrise

source_name: seawater, 9am, replicate 1

value: UCYN-A

value: seawater

value: 3h after sunrise


title: L6_rep1

description: Gene expression 6h after sunrise

source_name: seawater, 12pm, replicate 1

value: 6h after sunrise


title: Pea roots, control, 24 h 2

value: Frisson

value: roots

value: control


title: Pea roots, control, 24 h 3

value: WT


title: 599L

value: Female


title: D4-1

value: lung

value: Influenza A/PR8/34 (4 d.p.i.)


title: 1202L

value: Skeletal Muscle

value: Male


title: Pea roots, control, 24 h 1


title: d5_gplc

value: Day 5


title: CO8-DA-treated pea roots, 24 h 1


title: 896.00.1

status: Public on Feb 22 2023

city: Braunschweig

first: Prof. Hamid

last: Hossain

state: Lower Saxony

address: Celler Str. 38

department: Microbiology

institute: Klinikum Braunschweig

hyb_protocol: Purified cRNA were fragmented in fragmentation buffer (40 mM Tris-acetate pH 7.9, 100 mM KOAc, 31.5 mM MgOAc) at 94gr.C for 20 minutes. For hybridization on CodeLink bioarrays, 10 ug of fragmented cRNA in 260 ul of hybridization solution was added to each bioarray via the Flex Chamber port and incubated for 18 hours in a Minitron shaker incubator (Infors AG, Germany) at 37gr.C, 300 rpm. cRNA of each sample was hybridized in duplicate or triplicate (technical replicates). Bioarrays were processed in parallel using the CodeLink Shaker Kit and CodeLink Parallel Processing Kit (Amersham Biosciences).

scan_protocol: Bioarrays were scanned using the GenePix 4000 B scanner and the GenePix Pro 4.0 Software (Axon Instruments, Arlington, USA).

data_processing: Spot signals of CodeLink Bioarrays were quantified using the CodeLink System Software (Batch Submission (V2.2.27) and the Codelink Expression Analysis (V2.2.25), GE Healthcare, Germany).

source_name: Umbilical artery

label_protocol: Total RNA were subjected to cDNA synthesis using a poly-A binding primer containing the T7-polymerase promoter (CodeLink Expression Assay Kit). Double-stranded DNA fragments were purified using the QIAquickTM PCR Purification Kit (Qiagen, Germany). For target labeling, the cDNA was in-vitro transcribed (IVT) by partially substituting UTP with bio-16-UTP in the reaction mixture. Labeled cRNA was purified using the RNeasy Mini Kit (Qiagen, Germany). The eluted cRNA was quantified with the NanoDrop (NanoDrop Technologies) and quality was assesed with the Agilent 2100 bioanalyser (Agilent Technologies GmbH).

growth_protocol: Cord blood from preterm infants was sampled from an indwelling umbilical artery catheter at birth.

extract_protocol: RNA isolation according to the manufacturer’s recommendations (PreAnalytiX). Total RNA was quantified with Nanodrop (NanoDrop Technologies, Rockland DE, USA) and the quality of RNA was assessed using the Agilent 2100 Bioanalyzer Bioanalyzer (Agilent Technologies GmbH, Boeblingen, Germany).

treatment_protocol: 250-300 µl of whole umbilical cord blood was transferred to 750-900 µl of the PAXgene Blood RNA System (PreAnalytiX, Heidelberg, Germany).

tag: disease state

value: Mild BPD

value: Cord blood in PAXgene Blood RNA System

tag: gestational age (weeks)

tag: birth weight (g)

tag: gender (0=male; 1=female)


title: 896.00.2


title: 1091.00.1

value: Moderate/severe BPD


title: 1133.00.2


title: 1150.00.1


title: 1150.00.2


title: 896.00.4


title: 816.00.2


title: 816.00.3


title: 1091.00.2


title: 1157.00.2


title: 751.00.3


title: 1157.00.1


title: 751.00.1


title: 816.00.1


title: 1140.00.3


title: 751.00.2


title: 1140.00.2


title: 1004.00.2


title: 1133.00.1


title: 1004.00.1


title: 1004.00.3


title: 1091.00.3


title: 912.00.3

value: No BPD


title: 1140.00.1


title: 1149.00.2


title: 1087.00.3


title: 1149.00.1


title: 912.00.1


title: 912.00.2


title: 1081.00.1


title: 1080.00.2


title: 1082.00.1


title: 1086.00.1


title: 1081.00.2


title: 1087.00.2


title: 1081.00.3


title: 1087.00.1


title: 1080.00.1


title: 1073.00.2


title: 1069.00.2


title: 1069.00.1


title: 1038.00.3


title: 1074.00.3


title: 1074.00.1


title: 1074.00.2


title: 1069.00.3


title: 1038.00.2


title: 1073.00.1


title: 1038.00.1


title: 1082.00.3


title: 1005.00.2


title: 1006.00.3


title: 1006.00.2


title: 1086.00.2


title: 1080.00.3


title: 1006.00.1


title: 1082.00.2


title: 1073.00.4


title: 1005.00.3


title: CITE-seq Meis1-flox/VE-Cre replicate 2

city: Vancouver

first: Aly

last: Karsan

state: British Columbia

institute: Canada's Michael Smith Genome Sciences Centre

data_processing:
library strategy: CITE-seq
Illumina RTA software used for basecalling.
Cellranger count was ran using cellranger version 3.0.2 and cellranger mm10 reference
Genome_build: mm10
Supplementary_files_format_and_content: Features_count_matrix.csv.gz contains a matrix where rows are genes or ADT, columns are cells (with cell information in the cell_annotation_matrix.csv), and values are counts for the given gene in the given cell. cell_annotation_matrix.csv contains a data frame with annotations (i.e. cell barcode, cell type, genotype, etc.) for each cell

source_name: E10.5 AGM

extract_protocol:
Embryos were dissected at E10.5 and AGM were processed for flow cytometry. Cells were stained with CD31-BV605 and the following CITE-seq antibodies at a final concentration of 0.2 ug/100 µL: TotalSeq™-A0012 anti-mouse CD117 (BioLegend #105843), TotalSeq™-A0443 anti-mouse CD41 (BioLegend #133937), TotalSeq™-A0110 anti-mouse CD43 (BioLegend #143211), TotalSeq™-A0157 anti-mouse CD45.2 (BioLegend #109853), TotalSeq™-A0191 anti-mouse/rat/human CD27 (BioLegend #124235), and TotalSeq™-A0073 anti-mouse/human CD44 (BioLegend #103045). Cells from 2-5 embryos were pooled for any given samples based on genotype
Libraries were prepared using the 10X Chromium Single Cell 3’ Reagent v3 chemistry kit as per the standard protocol from 10X Genomics (Pleasanton, California)

tag: developmental stage


title: CITE-seq Meis1-flox/VE-Cre replicate 3


title: 1005.00.1


title: CITE-seq Meis1-flox/VE-Cre replicate 1


title: Tfh1-Spleen_No_GVHD

city: Duarte

first: wei

last: chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

data_processing:
Reads were aligned to mouse TRA and TRB reference (NG_007044.1 and NG_006980.1) using miXCR v2.1 with default settings.
Clone assembly and extraction were also done using miXCR v2.1 with default settings
Assembly: mouse mm10
Supplementary files format and content: text delimited text files containing the TRA and TRB clones
Library strategy: TCR-CDR3 sequencing

source_name: No GVHD

extract_protocol:
mRNAs from Tfh cells were extracted with “Qiagen miRNeasy Micro Kit”.
TCR-CDR3 libraries were prepared using Takara Smarter Mouse TCR a/b Profiling kit following manufacturer's recommendations

value: CD4+T cells subsets

value: Spleen


title: CD69+ Trh_cells_Liver_cGVHD

source_name: cGVHD

value: Liver


title: CD69+ Trh_cells_Lung_cGVHD

value: Lung


title: Tph_cells_PBL_cGVHD

value: Blood


title: CITE-seq WT replicate 5