title: MNase-seq,HBV cccDNA loaded with reconstituted nucleosomes,  In vitro Experiment1

description: MNase-seq


title: aMDM-Blood13

status: Public on Mar 03 2023

type: SRA

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description:
Monocytes from blood 13 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours.
D440T10

library_source: transcriptomic

data_processing:
Raw sequencing reads were aligned on the human hg38 reference genome using the STAR mapper [7] (2.5.3a), up to the generation of a raw count table per gene (Gencode annotation v26). Expressed genes (TPM>=1 in at least one sample) have then been selected for downstream analysis.The raw count table was then normalized using the TMM method from the edgeR R package [5] (v3,22,3), and the limma voom (v3.36.3) functions were applied to detect genes with differential expression between untreated and EGF samples. Genes with an adjusted pvalue < 0,05 were called significant.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Homo sapiens

source_name: monocyte-derived macrophages treated with IFN-gamma and LPS

growth_protocol: Peripheral blood samples were collected from healthy donors. Pan monocytes were sorted using microbeads (negative sorting) according to the manufacturer's instructions (Miltenyi Biotec, Somerville, MA, USA), cultured in RPMI 1640 with glutamine (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum.

extract_protocol:
RNA extracted using the RNeasy mini kit (QIAGEN)
RNA sequencing libraries were prepared from 1 µg total RNA using the Illumina TruSeq Stranded mRNA Library Preparation Kit, which allows strand specific sequencing to be performed. A first step of polyA selection using magnetic beads was performed to allow sequencing of polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing followed by ligation of TruSeq indexed adapters. PCR amplification was finally achieved to generate the final barcoded cDNA libraries. Sequencing was carried out on a NovaSeq 6000 instrument from Illumina based on a 2*100 cycle mode (paired-end reads, 100 bases).

treatment_protocol: Monocytes were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to generate their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) and co-treated with LCC-12 (10 μM) during 24 hours.

tag: individual

tag: tissue

value: blood

tag: cell type

value: pan monocyte

tag: treatment

value: Activated


title: RA0850_LN-AX-R [A0022_S185_L002]

city: Cambridge

first: Siddharth

last: Raju

state: Massachusetts

address: 415 Main Street

country: USA

institute: Broad Institute

description:
A0022_S185_L002
Rhesus monkey

data_processing:
Host transcriptomics data was processed using the umiRNAseq custom pipeline for Bulk RNA-seq Processing with UMI correction (https://github.com/broadinstitute/sabeti-host-txnomics-internal/blob/master/bulk-rna-seq/umiRNASeq.wdl).
Briefly, raw Fastq files were merged and tagged with their corresponding UMI barcode, then they were mapped using STAR to the Rhesus monkey (M. mulatta) reference genome and annotation (Mmul_10).
Resulting BAM files were filtered for multiple mapped reads, sorted and indexed using samtools. Then, PCR duplicates were removed by UMI-tools using the UMI barcodes of each transcript.
Furthermore, featureCounts were used to quantify expression from the aligned and processed RNA-Seq BAM files. Additionally, The BioMart R package was used to annotate the gene type, gene name, and gene function using the Ensembl M. mulatta database “mmulatta_gene_ensembl”.
Quality control over the sample was performed removing samples with low sequencing quality and mismatch sex assignment.
Assembly: Mmul_10
Supplementary files format and content: 20230121_counts_submission.txt: Tab-delimited format, raw counts.

organism: Macaca mulatta

source_name: Lymph node:LN-AX-R

extract_protocol:
Total RNA was extracted from tissue homogenates inactivated in TRIzol using the MagMAX MirVana total RNA kit (ThermoFisher) on a KingFisher FLEX instrument.
Ribosomal RNA was depleted using an RNase H-based method, RNA was then heat-fragmented, reverse transcription was performed, and strand-specific double-stranded cDNA was generated. xGen UDI-UMI (IDT) adapters were ligated and libraries were amplified.

value: Lymph node:LN-AX-R

tag: monkey id

value: infected with Ebola virus

tag: time


title: Bacillus subtilis 168, High Temperature control (37°C), rep3

city: Newcastle upon Tyne

first: David

last: Markham

address: Devonshire Building

department: ICOS

country: United Kingdom

institute: Newcastle University

data_processing:
Nextflow nf-core/rnaseq 3.8.1
Trimming and removal of unwanted sequences by the following tools in the workflow: UMI-tools,  Trim Galore 0.6.7, BBSplit, SortMeRNA
Alignment of reads performed by STAR 2.6.1d and quantified using Salmon 1.5.2
Additional FASTA file was included for alignment against ERCC spike-in controls, ERCC92
Assembly: eb2
Supplementary files format and content: tab-delimited text file containing a matrix of all gene-counts established by Salmon. Samples as columns, Features as rows.

organism: Bacillus subtilis

source_name: Bacillus subtilis

extract_protocol:
RNA was extracted using Total RNA Purification Kit (Norgen Biotek) according to maunfacturer's specifications for gram-positive bacteria
The rRNA depletion was performed using NEBNext rRNA Depletion Kit (Bacteria). RNA sequencing library preparation was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented according to manufacturer’s instruction. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).

tag: strain

value: strain 168

value: Bacillus subtilis

value: Control Temperature (37degreeC)


title: MNase-seq, HBV cccDNA, Empty, In vitro Experiment1

city: New York

first: Andres

last: Mansisidor

state: NY

address: 1230 York Ave Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: Rockefeller University

description: MNase-seq

library_source: genomic

data_processing:
UMI demultiplexing (custom script)
adapter trimming (custom script)
alignment to HBV genome (Bowtie2 v2.3.4.3)
nucleosome coverage mapping (nucleoATAC)
Bedgraphs from both RNA- and MNase-seq were plotted using Sushi package v1.30.0 in R v4.1.0
Assembly: NC_003977.2 (offset by 500 bp)
Supplementary files format and content: bedgraph files that include coverage of fragment centers (50 bp windows)

molecule: genomic DNA

organism: Hepatitis B virus

source_name: in vitro

extract_protocol:
In vivo MNase-seq was performed on purified nuclei at different timepoints after transfection with HBV cccDNA or on in vitro reconstituted chromatin.
For MNase-seq on in vitro reconstituted chromatin, titration of MNase was performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested chromatin arrays. Chromatinized DNA (100 ng) was digested using MNase (NEB) in 25 µL reactions with 2.5–25 units of enzymes that was incubated for 5 minutes at 37C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37C. The reaction was stopped by adding 20 mM EDTA and 1% SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index Barcodes or Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out using only 5 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). For MNase-seq on cell cultured samples, HEK293T cells were transfected with recombinant cccDNA 4 or 24-hours prior to harvest for MNase-seq. The nuclei of HEK293 cells were purified by incubating cells in Nuclei isolation buffer for 10 minutes (0.1% Igepal, 0.1% Triton X -100, 1 mM DTT in 1 X PBS), mechanically lysing with 10 strokes of loose (A) pestle Dounce homogenizer, and washing nuclei twice in 10 mL of Wash Buffer with Tween (10 mM Tris-HCl pH 7.5, 2.5 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Titration of MNase was similarly performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested genomic DNA. MNase (NEB) was added to 2 x 106 nuclei in 50 µL reaction volume with 250–2000 units of enzyme that was incubated for 5 minutes at 37 C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37 C. The reaction was stopped by adding 20 mM EDTA and 1 % SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). Libraries were then pooled and enriched for HBV-containing reads using custom-designed xGen Lockdown probes (Integrated DNA Technology) of 60 bp each tiling the entire HBV genome and oligo capture protocol was followed per manufacture’s protocol. Enriched libraries were subsequently amplified using 11 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and purified using Ampure XP beads.

value: in vitro

tag: genotype

value: not applicable

value: empty


title: naMDM-Blood13

description:
Monocytes from blood 13 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) during 6 days to induce their differentiation.
D440T09

source_name: monocyte-derived macrophages

value: Unactivated


title: naMDM-Blood14

description:
Monocytes from blood 14 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) during 6 days to induce their differentiation.
D440T13


title: Bacillus subtilis 168, High Temperature control (37°C), rep2


title: RA0850_Ovary [A0021_S15_L001]

description:
A0021_S15_L001
Rhesus monkey

source_name: Sex Organ:Testis

value: Sex Organ:Testis


title: NFO181-VeroE6-SARSCoV2-5L

city: Copenhagen

last: Fossat

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

description: Single-end 1 x 150bp

data_processing:
CLEAR-CLIP_Preprocessing: Removal of adaptors and  quality trimming using Trimmomatic with settings 'SLIDINGWINDOW:4:20'. Collapsing of PCR duplicates, read demultiplexing and barcode/index/linker removal was aided by the R package CLIPflexR v0.1.20.
CLEAR-CLIP_Singleton reads: Sequenced reads were aligned to hg38/chlSab2/SARS-CoV-2 reference genomes using Rbowtie2, through the CLIPflexR wrapper with default settings. BED files and bedgraphs were created using CLIPflexR, and normalized to RPM for downstream analyses and coverage plots. Peak calling of aligned reads was done using Homer through the CLIPflexR wrapper, and peaks where annotated using GenomicFeatures v1.38.2, GenomicRanges v1.38 and ChiPseeker v1.22.1. Prediction of miRNA seed sites from 7mer-m8 or 7mer-A1 seed matches was done using a combination of CLIPflexR and custom methods.
CLEAR-CLIP_Chimera reads: Reads that remained unmapped after singleton alignment, were treated as potential chimeras. Unmapped reads were thus reverse aligned to the sequences of mature microRNAs and forward aligned to possible target sequences in hg38/chlSab2/SARS-CoV-2 reference genomes using Rbowtie2 and CLIPflexR. Chimeras were analysed for differential miRNA abundance (infected vs. non-infected), using edgeR, to indirectly scan for putative viral miRNA sequestration, by analysing loss of cell-bound miRNAsusing the edgeR package. Relative abundances of miRNAs for non-infected cells, were calculated as the average fraction of the three non-infected samples for each cell line.
RNA-Seq: Demultiplexed files were lane-merged and aligned to the SARS-CoV-2 reference genome using STAR (v2.7.9a). RPKM normalized genome coverage was generated from BAM files using deeptools genomecov. Average coverage was plotted against colored backgrounds, according to SARS-CoV-2 annotation regions in R.
Assembly: Green monkey: chlSab2; Human: hg38; SARS-CoV-2: Strain DK-AHH1 (PMID: 33903110). For each mutant, strain DK-AHH1 was also used but modified to carry the corresponding engineered point mutations.
Supplementary files format and content: Table_S1.xlsx - Number of reads per sample for CLEAR-CLIP in VeroE6 cells
Supplementary files format and content: Table_S2.txt - Singleton reads for CLEAR-CLIP in VeroE6 cells
Supplementary files format and content: Table_S3.txt - Chimeric reads for CLEAR-CLIP in VeroE6 cells
Supplementary files format and content: Table_S4.xlsx - List of miRNAs binding SARS-CoV-2 RNA in VeroE6 cells
Supplementary files format and content: Table_S5.xlsx - Functional miRNAs expressed in VeroE6 cells
Supplementary files format and content: Table_S6.xlsx - Number of reads per sample for CLEAR-CLIP in A549hACE2 cells
Supplementary files format and content: Table_S7.txt - Singleton reads for CLEAR-CLIP in A549hACE2 cells
Supplementary files format and content: Table_S8.txt - Chimeric reads for CLEAR-CLIP in A549hACE2 cells
Supplementary files format and content: Table_S9.xlsx - List of miRNAs binding SARS-CoV-2 RNA in A549hACE2 cells
Supplementary files format and content: Table_S10.xlsx - Functional miRNAs expressed in A549hACE2 cells
Supplementary files format and content: Table_S11.xlsx - Differential expression of miRNAs in infected VeroE6 cells
Supplementary files format and content: Table_S12.xlsx - Differential expression of miRNAs in infected A549hACE2 cells
Supplementary files format and content: Table_S13.xlsx - Differential miRNA binding on cellular RNAs in infected VeroE6 cells
Supplementary files format and content: Table_S14.xlsx - Differential miRNA binding on cellular RNAs in infected A549hACE2 cells
Supplementary files format and content: Table S15.txt Differential gene expression in infected VeroE6 cells
Supplementary files format and content: Table S16.txt Differential gene expression in infected A549hACE2 cells (72 hpi)

organism: Chlorocebus sabaeus

source_name: Monkey kidney VeroE6 cells

growth_protocol: Cells were grown in standard conditions.

extract_protocol:
For CLEAR-CLIP, cells were washed twice with ice cold PBS, UV254 cross-linked or not, scrapped, collected, pelleted by centrifugation at 500 g for 5 min at 4C and snap frozen, before to be gently lysed and processed further as described in PMID: 26602609 with minor changes. For RNA-Seq, cells were washed twice with ice cold PBS, dissolved in ice-cold reagent and total RNA extracted using a RNA Clean & Concentrator-25 kit (Zymo Research Z1018) strictly following manufacturer instrcutions and adding a DNAse I step.
For CLEAR-CLIP, library was constructed following a custom-made protocol (see PMID: 26602609) and minor changes. For RNA-Seq, library was constructed strictly following the TruSeq Stranded Total RNA protocol from Illumina and using TruSeq RNA CD index plate (96 indexes, 96 samples).

treatment_protocol: Cells were infected or not with SARS-CoV-2 (Wild-type or engineered mutants) at MOI = 0.001 for 48 hours.

tag: infected

value: Yes

tag: sars-cov-2 genotype

value: Mutant 5L

tag: moi

tag: duration of infection

value: 48 hours

tag: experiment

value: CLEAR-CLIP

tag: cross-linked

tag: igg used for ip

value: anti-pan AGO

tag: molecule subtype

value: RNA obtained after CLEAR-CLIP


title: RA0850_Sex-Organ [A0026_S14_L001]

description:
A0026_S14_L001
Rhesus monkey

source_name: Sex Organ:Sex-Organ

value: Sex Organ:Sex-Organ


title: RA0850_Brain-Gr [A0020_S88_L002]

description:
A0020_S88_L002
Rhesus monkey


title: aMDM-Blood10

description:
Monocytes from blood 10 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours.
D440T06

value: blood

value: pan monocyte

value: Activated


title: Bacillus subtilis 168, High Temperature control (37°C), rep1

value: strain 168

value: Bacillus subtilis


title: aMDM-Blood14

description:
Monocytes from blood 14 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours.
D440T14


title: NFO181-VeroE6-SARSCoV2-4L

description: Single-end 1 x 150bp

value: Mutant 4L


title: Bacillus subtilis 168, Nutrient shift (Glucose to Malate), rep1

value: Nutrient shift (Glucose to Malate)


title: NFO181-VeroE6-SARSCoV2-6L

description: Single-end 1 x 150bp

value: Mutant 6L


title: Bacillus subtilis 168, High Temperature (51°C), rep3

value: High Temperature (51degreeC)


title: RA0850_Adrenal [A0018]

description:
A0018
Rhesus monkey

source_name: Adrenal Gland

value: Adrenal Gland

value: infected with Ebola virus


title: naMDM-Blood10

description:
Monocytes from blood 10 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) during 6 days to induce their differentiation.
D440T05

value: Unactivated


title: NFO181-VeroE6-SARSCoV2-3L

description: Single-end 1 x 150bp

value: Yes

value: Mutant 3L

value: 48 hours


title: Bacillus subtilis 168, High Temperature (51°C), rep2


title: RA0850_Kidney [A0016_S123_L002]

description:
A0016_S123_L002
Rhesus monkey

source_name: Kidney

value: Kidney


title: NFO181-VeroE6-SARSCoV2-2L

description: Single-end 1 x 150bp

value: Mutant 2L

value: CLEAR-CLIP

value: anti-pan AGO

value: RNA obtained after CLEAR-CLIP


title: aMDM+LCC-12-Blood9

description:
Monocytes from blood 9 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were treated with IFN-gamma (20 ng/mL), LPS (100 ng/mL) and LCC-12 (10 µM) during 24 hours.
D440T03

source_name: monocyte-derived macrophages treated with IFN-gamma, LPS and LCC-12

value: blood

value: pan monocyte


title: Bacillus subtilis 168, High Temperature (51°C), rep1

value: strain 168

value: Bacillus subtilis


title: RA0850_Spleen [A0015_S120_L002]

description:
A0015_S120_L002
Rhesus monkey

source_name: Spleen

value: Spleen


title: aMDM+LCC-12-Blood10

description:
Monocytes from blood 10 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were treated with IFN-gamma (20 ng/mL), LPS (100 ng/mL) and LCC-12 (10 µM) during 24 hours.
D440T07


title: aMDM-Blood9

description:
Monocytes from blood 9 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours.
D440T02

value: Activated


title: NFO181-VeroE6-SARSCoV2-1L

description: Single-end 1 x 150bp

value: Mutant 1L


title: Bacillus subtilis 168, No Ethanol, rep3

value: Without Ethanol


title: NFO181-VeroE6-SARSCoV2-5G

description: Single-end 1 x 150bp

value: Mutant 5G


title: Bacillus subtilis 168, No Ethanol, rep2


title: naMDM-Blood9

description:
Monocytes from blood 9 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) during 6 days to induce their differentiation.
D440T01

value: Unactivated


title: RA1803_Skin-Rash [A0013_S47_L001]

description:
A0013_S47_L001
Rhesus monkey

value: infected with Ebola virus


title: NFO181-VeroE6-SARSCoV2-3G

description: Single-end 1 x 150bp

value: Yes

value: Mutant 3G

value: 48 hours


title: RA1803_Sex-Organ [A0012_S16_L001]

description:
A0012_S16_L001
Rhesus monkey

value: Sex Organ:Sex-Organ


title: RA1082_LN-MES [A0010_S19_L001]

description:
A0010_S19_L001
Rhesus monkey

source_name: Lymph node:LN-MES

value: Lymph node:LN-MES


title: NFO181-VeroE6-SARSCoV2-WT

description: Single-end 1 x 150bp

value: Wild-type

value: CLEAR-CLIP

value: anti-pan AGO

value: RNA obtained after CLEAR-CLIP


title: aMDM-Blood4

description:
sample name in manuscript:
act. MDM
Monocytes from blood 4 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours.
D367T20

data_processing:
Raw sequencing reads were aligned on the human hg38 reference genome using the STAR mapper [7] (2.5.3a), up to the generation of a raw count table per gene (Gencode annotation v26). Expressed genes (TPM>=1 in at least one sample) have then been selected for downstream analysis.The raw count table was then normalized using the TMM method from the edgeR R package [5] (v3,22,3), and the limma voom (v3.36.3) functions were applied to detect genes with differential expression between untreated and EGF samples. Genes with an adjusted pvalue < 0,05  were called significant.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: activated monocyte-derived macrophages

treatment_protocol: Monocytes were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to generate their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours.

value: blood

value: pan monocyte


title: naMDM-Blood6

description:
sample name in manuscript:
MDM
Monocytes from blood 6 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) during 6 days to induce their differentiation.
D367T25


title: NFO147_H-VeroE6-XL-AGO

description:
Single-end 1 x 150bp
Table_S1.xlsx; Table_S2.txt.gz; Table_S3.txt.gz; Table_S9.xlsx; Table_S11.xlsx; Table_S13.xlsx

value: No


title: aMDM-Blood6

description:
sample name in manuscript:
act. MDM
Monocytes from blood 6 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours.
D367T26

value: Activated


title: RA1803_LN-AX-R [A0008_S140_L002]

description:
A0008_S140_L002
Rhesus monkey

value: Lymph node:LN-AX-R


title: Bacillus subtilis 168, Ethanol, rep2

value: strain 168

value: Bacillus subtilis

value: Ethanol


title: Bacillus subtilis 168, No Ethanol, rep1

value: Without Ethanol


title: Bacillus subtilis 168, Ethanol, rep3


title: NFO147_G-VeroE6-XL-AGO

value: Yes


title: Bacillus subtilis 168, Ethanol, rep1


title: NFO147_F-VeroE6-XL-AGO


title: aMDM-Blood3

description:
sample name in manuscript:
act. MDM
Monocytes from blood 3 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours.
D367T14


title: RA1803_Ovary [A0007_S17_L001]

description:
A0007_S17_L001
Rhesus monkey

source_name: Sex Organ:Ovary

value: Sex Organ:Ovary

value: infected with Ebola virus


title: A0014 [A0014]

description:
A0014
Rhesus monkey


title: Bacillus subtilis 168, No Diamide, rep3

value: Without Diamide


title: NFO147_E-VeroE6-SARSCoV2-XL-IgG

description:
Single-end 1 x 150bp
Table_S1.xlsx; Table_S2.txt.gz; Table_S3.txt.gz; Table_S11.xlsx; Table_S13.xlsx

value: Wild-type

value: 48 hours

value: Unspecific


title: naMDM-Blood3

description:
sample name in manuscript:
MDM
Monocytes from blood 3 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) during 6 days to induce their differentiation.
D367T13

value: Unactivated


title: Bacillus subtilis 168, No Diamide, rep2


title: aMDM-Blood2

description:
sample name in manuscript:
act. MDM
Monocytes from blood 2 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours.
D367T08

value: blood


title: NFO147_D-VeroE6-SARSCoV2-NoXL-AGO

value: CLEAR-CLIP

value: anti-pan AGO

value: RNA obtained after CLEAR-CLIP


title: RA1803_Brain-Gr [A0006_S89_L002]

description:
A0006_S89_L002
Rhesus monkey


title: Bacillus subtilis 168, No Diamide, rep1


title: RA1803_Liver-L [A0003]

description:
A0003
Rhesus monkey

source_name: Liver

value: Liver


title: NFO147_C-VeroE6-SARSCoV2-XL-AGO

description:
Single-end 1 x 150bp
Table_S1.xlsx; Table_S2.txt.gz; Table_S3.txt.gz; Table_S4.xlsx; Table_S11.xlsx; Table_S13.xlsx


title: naMDM-Blood2

description:
sample name in manuscript:
MDM
Monocytes from blood 2 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) during 6 days to induce their differentiation.
D367T07

value: pan monocyte


title: Bacillus subtilis 168, Diamide, rep3

value: strain 168

value: Bacillus subtilis

value: Diamide


title: RA1803_LN-ING-L [A0009_S139_L002]

description:
A0009_S139_L002
Rhesus monkey

source_name: Lymph node:LN-ING-L

value: Lymph node:LN-ING-L


title: naMDM-Blood4

description:
sample name in manuscript:
MDM
Monocytes from blood 4 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) during 6 days to induce their differentiation.
D367T19


title: RA1803_Kidney [A0002_S124_L002]

description:
A0002_S124_L002
Rhesus monkey

value: Kidney


title: Bacillus subtilis 168, Diamide, rep2


title: RA1803_Spleen [A0001_S121_L002]

description:
A0001_S121_L002
Rhesus monkey

value: Spleen

value: infected with Ebola virus


title: NFO147_B-VeroE6-SARSCoV2-XL-AGO

value: Yes

value: Wild-type


title: NFO147_A-VeroE6-SARSCoV2-XL-AGO

value: 48 hours


title: naMDM-Blood1

description:
sample name in manuscript:
MDM
Monocytes from blood 1 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) during 6 days to induce their differentiation.
D367T01

value: Unactivated


title: Bacillus subtilis 168, Diamide, rep1


title: Sting-/- DOX repeat2

status: Public on Mar 02 2023

city: Shanghai

first: Wei

last: Luo

address: Fenglin Road No.180

country: China

institute: Fudan University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2).by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5)  was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: heart

extract_protocol:
Total RNA was extracted from hearts or cells by using the commercial kit (Cat No. 74104, QIAGEN) according to the manufacturer’s instructions.
An RNA-seq library was made with the MGIEasy RNA Library Prep KIT (MGI, Shenzhen, China) according to the manufacturer’s instructions.

value: heart

value: Sting-/-

value: doxorubicin


title: WT DOX repeat2

value: WT


title: control siRNA DOX repeat1

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2).by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5)  was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: human cardiac microvascular endothelial cells

value: nc


title: Sting-/- DOX repeat1


title: control siRNA saline repeat1

value: human cardiac microvascular endothelial cells

value: saline


title: WT DOX repeat3


title: control siRNA DOX repeat3


title: control siRNA DOX repeat2


title: WT DOX repeat1


title: control siRNA saline repeat2


title: Sting-/- DOX repeat3


title: STING siRNA DOX repeat1

value: STING knockdown


title: WT saline repeat3


title: WT saline repeat1


title: LL_1,biol rep 1

city: Beijing

first: Baoli

last: Lin

address: No.7 Beinong Road, Shigezhuang Street

institute: College of Landscape Architecture, Beijing Agricultural College

data_processing:
The rawdata data measured by small RNA will be evaluated firstly, mainly for spurious filtering and preliminary judgment of the data.
Sequence reads were 1) Removelow quality tags 2) Removetagswith5'primer contaminants 3) Removetagswithout3'primer 4) Removetagswithoutinsertion 5) RemovetagswithpolyA 6) Removetagsshorterthan18nt 7) Summarizethelengthdistributionofthecleantags
We used the alignment software AASRA to align clean reads to the reference base and other small RNA databases, except for Rfam which was matched using cmsearch.
Assembly: without  reference genome
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Acer rubrum

source_name: LL is an Acer rubrum L. 'Autumn Blaze' cuttings leaf treated for fourteen days under 40% low light, 15°C/5°C day/night conditions.

growth_protocol: Before sampling, Acer rubrum L cuttings were grown in the ordinary greenhouse of the practical teaching base of the College of Landscape Architecture of Beijing Agricultural College (temperature 25°C~30°C, humidity 85%~95%)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) . 1.3 ug of total RNA was used for the construction of sequencing libraries.
The Small RNA Sample Pre Kit was used to construct the library, using the special structure of the 3' and 5' ends of Small RNA (complete phosphate group at the 5' end and hydroxyl group at the 3' end) , and using total RNA as the starting sample. After PCR amplification, the target DNA fragments were separated by PAGE gel electrophoresis, and the cDNA library was obtained by cutting and recycling.

treatment_protocol: Before sampling, the treatment conditions of Acer rubrum L blades were CC: 100% full light, and the day/night temperature was 30°C/20°C, respectively; LC: 100% full light, day/night temperature is 15°C/5°C, respectively; CL.: 40 % low light, day/night temperature is 30°C/20°C, respectively; LL: 40% low light, day/night temperature 15 °C/5 °C, after sampling, store the leaves in an ultra-low temperature freezer at -80 degrees Celsius and wait for RNA extraction.

value: leaf cells

value: Day 14

value: miRNA


title: aMDM-Blood1

description:
sample name in manuscript:
act. MDM
Monocytes from blood 1 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours.
D367T02

value: blood

value: pan monocyte

value: Activated


title: LL_3,biol rep 3


title: LL_2,biol rep 2


title: LC_2,biol rep 2

source_name: LC is Acer rubrum L. 'Autumn Blaze' cuttings leaves treated for fourteen days under 100% full light, 15°C/5°C day/night conditions.


title: LC_3,biol rep 3


title: LC_1,biol rep 1


title: Control_3,biol rep 3

source_name: Control is the untreated Acer rubrum L. 'Autumn Blaze' cuttings leaf mixing on day 0.

value: Day 0


title: Control_1,biol rep 1


title: Control_2,biol rep 2


title: STING siRNA DOX repeat2


title: CL_2, biol rep 2

source_name: CL is the leaves of Acer rubrum L. 'Autumn Blaze' cuttings treated for fourteen days under 40% low light, 30°C/20°C day/night conditions.


title: control siRNA saline repeat3


title: STING siRNA DOX repeat3


title: WT saline repeat2


title: CC_3, biol rep 3

source_name: CC is Acer rubrum L. 'Autumn Blaze' cuttings leaves treated for fourteen days under 100% full light, 30°C/20°C day/night conditions.


title: CC_1, biol rep 1


title: CC_2, biol rep 2


title: Testicular_control_scRNA-seq

first: Bo

middle: O

last: Zhou

address: 320 Yueyang Road

institute: State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS

data_processing:
Aligned reads and gene-barcode matrices were generated from FASTQ files including Read 1, Read 2 and i7 index using Cell Ranger (v.2.1.1) processing pipeline
Further analyses were performed with R package Seurat (v3.1). Genes expressed in fewer than three cells in a sample were excluded. Threshold of unique counts over 3500 or less than 200 was set to filter cell doublets.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every single cell

source_name: testis

extract_protocol:
Testicular cells were sorted by FACS after testis digestion and then subjected to 10x Genomics platform
Single cell library was generated using Chromium Single Cell 3’ Library Kit v2.

value: testis

tag: age


title: CL_3, biol rep 3


title: 7ss, replicate 2, scRNAseq

city: Bethesda

first: Laura

last: Kerosuo-Pahlberg

state: MD

address: 30 Convent Dr

institute: NIDCR

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger v6.1.1 pipeline using default settings.
Secondary analysis was performed using Seurat v4
Assembly: Custom GRCg6a chicken genome, that included extension to the 3’ UTR the gene definitions of the genes Nanog, Klf4, Runx2 and Ets1.
Supplementary files format and content: 10X Genomics Cell Ranger v6.1.1 standard output raw gene counts matrices.
Supplementary files format and content: 10X Genomics Cell Ranger v6.1.1 standard output filtered gene counts matrices.

organism: Gallus gallus

source_name: all tissue at midbrain axial level

extract_protocol: Library preparation was performed according to the manufacturer’s instructions for the 10× Chromium single-cell kit (10x Genomics). The libraries were then pooled and sequenced on two lanes of  NovaSeq 6000 sequencer (Illumina).

value: all tissue at midbrain axial level

value: 7 somite stage


title: SNK6-H3K27ac

city: Guangzhou

first: jinghong

last: Chen

address: Panyu

institute: SYSUCC

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by bowtie2 and STAR instruction
MACS2 were used for the binding profile
RSEM were used for counting
IGV and R were used for visualization
Genome_build: GRCh38
Supplementary_files_format_and_content: ChIP-seq samples: bigwig file for each sample
RNA-seq samples: TXT file contain counts for each sample

growth_protocol: HANK1 and SNT8 were cultured in Artemis medium-2 supplemented with 2% human plasma serum and 1% P/S. 100 IU/ml IL-2 was included into HANK1 growth media and 700 IU/ml IL-2 into SNT8, respectively. SNK6 and NK92 were maintained in RPMI1640 medium supplemented with 10% FBS, 10% horse serum, 1% P/S and 100 IU/ml IL-2. KHYG1 was grown in RPMI1640 medium supplemented with 10% FBS, 1% P/S and 100 IU/ml IL-2. MEC04 was cultured in RPMI1640 medium supplemented with 15% FBS, 1% P/S and 50 IU/ml IL-2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. RNA was harvested using Trizol reagent (Invitrogen).
ChIP-seq libraries were prepared according to NEB ChIP-Seq Library Prep Kit (E6240). RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: HANK1 was treated with DMSO, 0.25um tofacitinib or 0.125um ruxolitinib for 24h.

value: Natural Killer/T-cell lymphoma

tag: cell line

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: SNK6-H3K4me3

tag: tissue

value: H3K4me3 (Millipore, 07-473)


title: Testicular_Scf-cKO_scRNA-seq


title: 1ss, replicate 1, scRNAseq

description: 10x Genomics

value: 1 somite stage

value: WT

tag: treatment


title: SNK6-Input 2


title: 4ss, replicate 1, scRNAseq

description: 10x Genomics

value: 4 somite stage


title: 4ss, replicate 2, scRNAseq

description: 10x Genomics


title: HH5, replicate 2, scRNAseq

description: 10x Genomics

value: stage 5


title: 500 nM PTX 3

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

data_processing:
STAR (version 2.6.0c) was used to align sequence reads to human genome build hg38.
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
Variance-stabilizing-transformed (VST) expression values were computed using the DESeq2 R package (version 1.23.10).
Assembly: hg38
Supplementary files format and content: counts.txt: 60627 x 12 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 60627 x 12 matrix of variance-stabilizing-transformed (VST) expression values

molecule: polyA RNA

source_name: Human umbilical vascular endothelial cells

growth_protocol: Pooled human umbilical vascular endothelial cells (ECs) (Cat No. C2519AS) were obtained from Lonza and grown in EGM-2 media made from EBM-2 media supplemented with an EGM-2 BulletKit (Cat No. CC-3162; Lonza). Cells were incubated in a 37˚C humidified incubator with 5% CO2. ECs were grown in gelatin-coated plates. The culture plates were coated with 2% gelatin (Cat No. G1890; Sigma) and air dried for at least 1 hour before use.

extract_protocol:
Cells were harvested for RNA extraction following the RNeasy Mini Kit protocol (Cat No. 74104; Qiagen). RNA was eluted with 40 µL of RNase-free water. RNA concentration was measured with a spectrophotometer (BioDrop).
Libraries were prepared from isolated mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA) and NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs, USA).

treatment_protocol: Paclitaxel (PTX) (Cat No. P9600; LC Laboratories) was dissolved in DMSO (Cat No. D8418-250ML; Sigma). ECs were seeded in p60 plates and treated with DMSO or PTX at ~60% confluence for 24h.

tag: cell type

value: 500 nM paclitaxel


title: 500 nM PTX 2

value: Human umbilical vascular endothelial cells


title: HANK1-Input


title: SNK6-Input 1


title: 50 nM PTX 3

value: 50 nM paclitaxel


title: 50 nM PTX 2


title: Testicular_somatic_cells_scRNA-seq


title: 500 nM PTX 1


title: 1ss, replicate 2, scRNAseq

description: 10x Genomics


title: MEC04-H3K4me3


title: 7ss, replicate 1, scRNAseq

description: 10x Genomics


title: CL_1, biol rep 1

value: leaf cells

value: Day 14

value: miRNA


title: HH5, replicate 1, scRNAseq

description: 10x Genomics


title: 50 nM PTX 1


title: HANK1-H3K4me3


title: 5 nM PTX 3

value: 5 nM paclitaxel


title: MEC04-Input


title: MEC04-H3K27ac


title: 5 nM PTX 2


title: KHYG1-H3K4me3


title: KHYG1-H3K27ac


title: 5 nM PTX 1


title: DMSO 1

value: DMSO


title: DMSO 3


title: KHYG1-Input


title: 1567 (F508del CF patient of rapid progressive phenotye)

first: Feiya

last: Wang

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

data_processing:
The sample was processed using the standard cellranger pipeline
Reads were mapped to GRCh38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: the processed files are the standard output from the cellranger pipeline:

extract_protocol:
10X Chromium system
NextSeq2000

tag: culture

value: iPSC-derived airway epithelium, s/p D15CD47hi/CD26lo sort, 210DCYI media x

value: iPSC


title: 1564 (CF-repaired),

value: iPSC-airway epithelium through basal cell intermediate.  iPSC-D15CD47/CD26sort- NGFR sort x 2


title: DK-RW_121719_CF

source_name: iPSC

value: iPSCs- derived airway epithelium at D90 (D15 CD47hi/CD26lo; replated in 3DMG cultured in 210DCIY x 2 weeks, single-cell passaged and cultured in PNExPlus+dual smad media in 3D,  s/p 2 NGFR sorts, cultured at air-liquid interface at 2D)


title: 1565 (CF DF508homozygous)


title: 1566 (isogenic CFTR-repaired pair).


title: 3090_Cord_blood

type: RNA

city: Pune

first: Chittaranjan

middle: Sakerlal

last: Yajnik

state: Maharashtra

address: Sardar Moodliar Road, Rasta Peth

department: Diabetes Unit

country: India

institute: King Edward Memorial Hospital Research Centre, Pune

hyb_protocol: Agilent Human miRNA Microarray, Release 21.0, 8x60K.

scan_protocol: Agilent scanner (G2600D)

data_processing: 90th percentile normalization method

source_name: Cord blood plasma

label_protocol: miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, CA, USA) with a sample input of 10uL of total RNA.

extract_protocol: RNA was isolated from Adipocyte derived extracellular vesicles using TRIzol reagent (ThermoFisher Scientific, Waltham, MA USA) according to manufacturer’s instructions.

treatment_protocol: Maternal and cord blood plasma samples at delivery were treated with 10μL [611U/mL] Thrombin (System Biosciences, Palo Alto, CA, USA) per 0.5mL plasma.  Adipocyte derived extracellular vesicles (ADsEVs) were isolated from filtered plasma supernatants using ExoQuick exosome precipitation solution (System Biosciences, Palo Alto, CA, USA) according to manufacturer’s instructions. ADsEVs were positively selected with a fatty acid-binding protein antibody (FABP4) (0.5 mg/mL; Mouse IgG monoclonal antibody, Abgent cat. No AM2235b, Inc., San Diego, CA, USA) using a magnetic capture technique (EasySep™ Do-It-Yourself Positive Selection Kit II - StemCell Technologies, Vancouver, BC, Canada). After positive selection, the ADsEVs were resuspended in TRIzol™ Reagent (ThermoFisher Scientific, Waltham, MA, USA).

tag: neonatal adiposity classification

value: Adipose

tag: neonatal sum of skinfolds (mm)

tag: neonatal sex

value: Female

tag: materal age (years)

tag: materal vitamin b12 status

value: Below median

tag: materal folate status

tag: materal adiposity

tag: maternal gdm status

value: Normal glucose tolerant

tag: maternal vitamin b12 at diagnosis (pmol/l)

tag: maternal folate levels at diagnosis (nmol/l)

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: 3098_Cord_blood

value: Adipocyte derived extracellular vesicles

value: Male

value: Above median


title: 3097_Cord_blood


title: Vecad, replicate 1, scRNAseq

city: Charlottesville

first: Uma Devi

last: Paila

address: 1335 Lee St

institute: University of Virginia

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Seurat R package version 4 was used for downstream analysis
Assembly: mm10
Supplementary files format and content: filtered feature-barcode matrices from the Cell Ranger output for each replicate (tsv, feature and matrix files)

source_name: adult mouse brain cortex and SVZ (subventricular zone))

extract_protocol:
Primary ECs and NSPCs from mouse brain cortex and SVZ were FACS-isolated.Briefly, brain cortex and SVZ were harvested , minced into small pieces . Minced pieces were then subjected to enzymatic dissociation in collagenase/dispase  solution for 30 min at 37C . The digested tissues were triturated in 2% FBS in PBS supplemented with DNAse  with a P1000 pipette. Antibodies  were added to the resuspended cells  and incubated for 20 mins on ice protected from light. Post-immunostaining cells were washed with HBSS/BSA/glucose buffer. From SVZ CD45- cells, ECs (CD31+Glast- population) and NSPCs (Glast+CD31- population) were collected using a BD FACS Melody cell sorter in pre-filled FACS tubes with EC and NSC media respectively to cushion the cells. Post-FACS processing, cells were pelleted, snap frozen in liquid nitrogen and stored at -80 C for RNA isolation.
FACS-purified live single cell suspensions were used for single cell RNA library preparation and next-generation sequencing. Single cell RNA libraries were prepared using the 10X Genomics Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (PN-1000121) and Chromium Controller. Next-generation sequencing was performed using an Illumina NextSeq 2000 Sequencing System on the P3 flow cell with a 100 bp paired-end sequencing reagent kit. Two biological replicate samples for each condition were prepared, sequenced, and aligned using CellRanger v5.0.0 to the mm10 genome. Estimated cell number outputs for each sample were: Cx43fl/fl (1) = 1083; Cx43fl/fl (2) = 1076; Cx43GlastiKO (1) = 710; Cx43GlastiKO (2) = 1319; Cx43ECiKO (1) = 571; Cx43ECiKO (2) = 2674. Sequencing yielded a mean of ~70,000,000 reads/sample, ~78,000 reads/cell, and ~1,500 genes/cell.

value: EC and NSPC

tag: genotype

tag: age

value: 8-12 weeks old


title: 3083_Cord_blood

tag: tissue

value: Lean


title: 3081_Cord_blood


title: Vecad, replicate 2, scRNAseq

description: 10x Genomics

value: adult mouse brain cortex and SVZ (subventricular zone))


title: 3086_Cord_blood


title: 3078_Cord_blood


title: 3075_Cord_blood


title: Glast, replicate 2, scRNAseq

description: 10x Genomics


title: Glast, replicate 1, scRNAseq

description: 10x Genomics


title: HANK1-H3K27ac

value: Natural Killer/T-cell lymphoma

tag: cell line

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: 3063_Cord_blood


title: CT, replicate 1, scRNAseq

description: 10x Genomics

tag: cell type


title: DMSO 2

value: Human umbilical vascular endothelial cells

tag: treatment

value: DMSO


title: 3064_Cord_blood

tag: neonatal adiposity classification

tag: neonatal sum of skinfolds (mm)

value: Gestational diabetes


title: 3061_Cord_blood

tag: neonatal sex

tag: materal age (years)


title: 3059_Cord_blood

tag: materal vitamin b12 status

tag: materal folate status


title: Hif1aloxP/loxP Ub-Cre IMV-3

city: Aurora

first: Christine

last: Vohwinkel

state: COLORADO

institute: University of Colorado

description: IMV

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of four housekeeping genes: B2M, Gusb, ACTB, Hsp90ab1
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target ? Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., Ctrl/IMV) ratios.

label: SYBR Green

source_name: AT II cells isolated from lungs after mechanical ventilation

label_protocol: PCR were performed with Qiagen RT2 prolfer assay according to the manufacturer's instruction

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: Mice  were subjected to IMV (peak inspiratory pressure 45, PEEP 3, RR 80, FiO2 100%) or control ventilation  (peak inspiratory pressure 12, PEEP 3, RR 80, FiO2 100%) , duration of mechanical ventilation 4 hours. After that alveolar type II epithelial cells were isolated form lungs

tag: time

value: 4 hours


title: 3049_Cord_blood

tag: materal adiposity

tag: maternal gdm status

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: 3044_Cord_blood

tag: maternal folate levels at diagnosis (nmol/l)

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: 3038_Cord_blood

tag: tissue


title: Ub-Cre IMV-3

description: IMV


title: Ub-Cre IMV-4

description: IMV


title: CT, replicate 2, scRNAseq

description: 10x Genomics

tag: genotype

tag: age


title: 3025_Cord_blood


title: 3031_Cord_blood

value: Adipose


title: 10ss, replicate 3, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
10ss_4

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCg6a chiken genome using STAR v2.7.2a in  single-pass mode with the following parameters:  --outFilterMultimapNmax 20 –outFilterType BySJout --alignSJoverhangMin 3 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.01 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.7.2a built-in counting option --quantMode GeneCounts against a GRCg6a genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: GRCg6a.v98
Supplementary files format and content: Raw gene counts in tab-delimited txt format.
Supplementary files format and content: Filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: TMM-normalized annotated gene expression matrix in counts per million reads units, tab-delimited txt format.

source_name: midbrain level recently emigrated neural crest and dorsal neural tube

extract_protocol: Library preparation was performed according to the manufacturer’s instructions for the Illumina Nextera XT unstranded library kit. The libraries were then pooled and sequenced on tow separate runs on a NextSeq2000 sequencer (Illumina) on 55x55 paired-end mode.

tag: cell type

value: neural crest

value: WT


title: 3014_Cord_blood

value: Female

value: Below median

value: Normal glucose tolerant


title: 3036_Cord_blood

value: Adipocyte derived extracellular vesicles

value: Male

value: Above median


title: Ub-Cre Ctrl-3

description: Ctrl


title: Ub-Cre IMV-1

description: IMV


title: Ub-Cre Ctrl-2

description: Ctrl


title: 10ss, replicate 2, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
10ss_3

value: midbrain level recently emigrated neural crest and dorsal neural tube

tag: treatment


title: 3060_Cord_blood

tag: neonatal adiposity classification

value: Lean


title: 3054_Cord_blood

tag: neonatal sum of skinfolds (mm)


title: Hif1aloxP/loxP Ub-Cre IMV-1

description: IMV


title: Hif1aloxP/loxP Ub-Cre IMV-2

description: IMV


title: 3005_Cord_blood

tag: neonatal sex


title: 10ss, replicate 1, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
10ss_1


title: 9ss, replicate 4, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
9ss_4


title: 9ss, replicate 3, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
9ss_3


title: 3004_Cord_blood

tag: materal age (years)


title: Ub-Cre IMV-2

description: IMV


title: 9ss, replicate 2, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
9ss_2


title: 3008_Cord_blood

tag: materal vitamin b12 status


title: 2300_Cord_blood

tag: materal folate status


title: 9ss, replicate 1, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
9ss_1


title: 2295_Cord_blood


title: Ub-Cre Ctrl-1

description: Ctrl

tag: time


title: 2296_Cord_blood

tag: materal adiposity


title: 2298_Cord_blood

tag: maternal gdm status


title: 8ss, replicate 1, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
8ss_1


title: 8ss, replicate 3, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
8ss_3


title: 2294_Cord_blood

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: 7ss, replicate 4, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
7ss_4

source_name: midbrain level neural crest domain

value: midbrain level neural crest domain


title: 7ss, replicate 3, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
7ss_3


title: 7ss, replicate 2, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
7ss_2


title: 2286_Cord_blood

tag: maternal folate levels at diagnosis (nmol/l)


title: 2285_Cord_blood

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: 2287_Cord_blood

tag: tissue


title: 7ss, replicate 1, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
7ss_1

tag: genotype


title: 2284_Cord_blood


title: 2281_Cord_blood


title: 2283_Cord_blood


title: 6ss, replicate 2, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
6ss_2

tag: age


title: 6ss, replicate 3, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
6ss_3

tag: cell type


title: 6ss, replicate 1, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
6ss_1

tag: treatment


title: 5ss, replicate 4, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
5ss_4


title: 2278_Cord_blood

tag: neonatal adiposity classification


title: 2280_Cord_blood

tag: neonatal sum of skinfolds (mm)


title: 5ss, replicate 3, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
5ss_3


title: 8ss, replicate 2, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
8ss_2


title: 5ss, replicate 2, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
5ss_2


title: 4ss, replicate 4, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
4ss_4


title: 2266_Cord_blood

tag: neonatal sex


title: 2267_Cord_blood

tag: materal age (years)


title: 2269_Cord_blood

tag: materal vitamin b12 status


title: 2261_Cord_blood

tag: materal folate status


title: 4ss, replicate 2, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
4ss_2


title: 3006_Cord_blood


title: 2254_Cord_blood


title: 2259_Cord_blood


title: 2252_Cord_blood


title: 5ss, replicate 1, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
5ss_1


title: 3ss, replicate 4, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
3ss_4


title: 2260_Cord_blood


title: 3ss, replicate 3, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
3ss_3


title: 3ss, replicate 2, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
3ss_2


title: 2249_Cord_blood


title: 2244_Cord_blood


title: 2243_Cord_blood


title: 3ss, replicate 1, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
3ss_1


title: 2239_Cord_blood


title: 2235_Cord_blood


title: 2237_Cord_blood


title: 4ss, replicate 3, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
4ss_3


title: 2ss, replicate 2, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
2ss_2


title: 2234_Cord_blood


title: 4ss, replicate 1, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
4ss_1


title: 2ss, replicate 3, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
2ss_3


title: HH7, replicate 4, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
HH7_4


title: 2233_Cord_blood


title: 2ss, replicate 1, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
2ss_1


title: HH7, replicate 3, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
HH7_3


title: 2224_Cord_blood


title: HH7, replicate 1, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
HH7_1


title: 2226_Cord_blood


title: 2221_Cord_blood


title: HH7, replicate 2, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
HH7_2


title: HH6, replicate 3, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
HH6_3


title: 2220_Cord_blood


title: 2216_Cord_blood


title: HH6, replicate 1, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
HH6_1


title: HH6, replicate 2, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
HH6_2


title: 2211_Cord_blood


title: 2210_Cord_blood


title: HH5, replicate 4, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
HH5_4


title: 2207_Cord_blood


title: 2205_Cord_blood


title: 2ss, replicate 4, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
2ss_4


title: HH5, replicate 3, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
HH5_3


title: HH5, replicate 2, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
HH5_2


title: HH6, replicate 4, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
HH6_4


title: 2201_Cord_blood


title: HH5, replicate 1, bulk RNAseq

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
HH5_1


title: 2222_Cord_blood


title: 2202_Cord_blood


title: L2HG_NRF2_ChIP_2

city: Augusta

first: Xingguo

last: Zhu

state: Georgia

department: Cancer Center

institute: Augusta University

data_processing:
ChIP-seq reads were aligned to the Human (GRCh37/hg19) genome assembly using EasyAlign version 3.2 with the following configurations…
reads were mapped with Bowtie2 and analyzed by MACS2 for the peak calling

source_name: Day-12 cultured erythroid progenitors from SCD patient

extract_protocol: Peripheral blood mononuclear cells were isolated from sickle cell disease pateint and CD34+ cells were enriched by microbeads and cultured in a Fibach two-phase cultured system. On day 10 of culture, cells were either treated with PBS or cell permeable trifluoromethylbenzyl ester derivative of L2HG or PBS for 48 hours. On day-12 of culture, cells were crosslinked with 1% formaldehyde, sonicated, and immunoprecipitated with NRF2 antibody and subjected to library preparation using TruSeq ChIP Sample Preparation kit (Illumina) for the construction of sequencing libraries.

tag: antibody

value: 2-3 month


title: 2194_Cord_blood

tag: materal adiposity


title: PBS_NRF2_ChIP_2

value: PBS


title: PBS_NRF2_ChIP_1


title: L2HG_NRF2_ChIP_1


title: 2170_Cord_blood

tag: maternal gdm status


title: 2177_Cord_blood

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: 2191_Cord_blood

tag: maternal folate levels at diagnosis (nmol/l)


title: 2166_Cord_blood

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: 2165_Cord_blood

tag: tissue


title: 8Z-3

city: Debrecen

first: Melinda

last: Szilágyi-Bónizs

address: Egyetem tér 1

department: Human Genetics

country: Hungary

institute: University of Debrecen

data_processing:
Fastq data were generated by BaseSpace (Illumina)
Raw sequencing data (fastq) was aligned to human reference genome version GRCh38 using Novoalign algorithm and BAM files were generated
Downstream analysis was performed using StrandNGS software (Deseq) where the FPKM values were generated
Assembly: GRCh38 human reference genome
Supplementary files format and content: tab-delimited matrix text file that include the FPKM values for each Sample

growth_protocol: PEO1 cells were cultured in RPMI1640 medium supplemented with 10%FBS during plating. 24h later the medium was replaced to PRF-RPMI1640 supplemented with 5% DCC-FBS and cells were further incubated for 24h. Then cells were treated with 10 nM E2, 10 nM ZEA or 100 nM BPA. This time point was designated as 0h. The non-treated control samples were exposed to the same culturing procedure expect that these cells were not treated with any estrogens.

extract_protocol:
Total RNA including small RNAs was isolated by the miRNeasy Kit (Qiagen) according to the protocol provided by the manufacturer.
Library preparation was performed by the NEBNext Multiplex Small RNA Perp Set for Illumina (1-48) 96 rxn kit (New England BioLabs) according to the protocol provided by the manufacturer.

tag: cell line

value: ovarian cancer

value: ZEA treated


title: Human Skin MNPs, Naive, rep3, scRNAseq, CJ16_mRNA

city: Lebanon

first: Claudia

middle: V

last: Jakubzick

state: NH

address: 1 Medical Center Drive, Rm 626 W Borwell, PO#1250960

department: Microbiology and Immunology

institute: Dartmouth College

description: 10x Genomics

data_processing:
Raw sequencing reads were demultiplexed, mapped to the GRCh38 human reference genome, and gene expression matrices were generated using CellRanger v6.1 (10X Genomics). The following analyses were conducted in R 4.2 (R Core Team, 2014). Seurat package v4.3 was used for downstream data analyses (Hao et al, 2021), and figures were produced using the package ggplot2. Following a standard workflow, the gene expression matrix was filtered to discard cells with less than 200 genes, as well as genes that were expressed in less than three cells. Samples then underwent quality control to remove cells with either too many or too few expressed genes (average around 1,300 and 4,400) and cells with too many mtRNA (average around 10%), resulting in a total of 58,982 cells. Then, “SCTransform” was applied with the “glmGamPoi” method to normalize gene expression data (Stuart et al, 2019; Ahlmann-Eltze & Huber, 2021). After individual preparation, all the samples were merged into a combined Seurat object. Then scaled values of variable genes were then subject to principal component analysis for linear dimension reduction. A shared nearest neighbor network was created based on Euclidean distances between cells in multidimensional PC space (the first 50 PC were used) and a fixed number of neighbors per cell (50 neighbors). This was used to generate a two-dimensional Uniform Manifold Approximation and Projection (UMAP) for visualization as a harmonized atlas to dissect the cell populations from different treatment groups.
DEGs were calculated with “FindAllMarkers” function of Seurat in R 4.1 to study the different expression profiles in different cell types and up-regulated genes in different treatment groups (R Core Team, 2014; Hao et al, 2021). The “data” matrices of “SCT” assay were used, and the minimal log fold change was set to 0.25. Only genes that were detected in more than 25% of cells in either of the two populations were used to compute the DEGs with the Wilcoxon rank-sum test. Markers were identified as genes exhibiting significant up-regulation when compared against all other clusters and defined by having a Bonferroni-adjusted P-value < 0.05. The DEGs are ranked by the adjusted P-value to select the top DEGs for downstream analysis.
To identify cell types, “FindClusters” function with the Leiden algorithm with the various resolution from 0.5 to 2.0 in the Seurat package were used for clustering (Hao et al, 2021). “FindAllMarkers” function was then applied. The top DEGs of individual clusters were examined for well-studied marker genes across literature and the clusters were then annotated for the most likely identity. For re-clustered IMs subtypes, “FindClusters” was performed with different resolution until the right resolution is reached so that each cluster has unique gene expression pattern. For re-clustered IMs subtypes, “FindClusters” was performed with different resolution until the right resolution is reached so that each cluster has unique gene expression pattern. Eleven distinct cell types were identified, including IMs, langerhan cells, DC1, DC2, DC3, AXL+ SIGLEC6+ DCs, MMP12+ DCs, lymphocytes, basal cells, fibroblasts, and cycling cells.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Integrated SeuratObject in rds format contains all 3 samples and different assays of expression/detection matrixes (for both mRNA and protein; CITE-seq Ab: CD88, CD1c, CD1a, CD64, CD14, CD93, CD197, XCR1); The meta data in rds format for every cells, includes the sample source and cell types

source_name: Digested brest reduction skin

extract_protocol:
The surface layer of skin was obtained by gently peeling it with razor blades. The collected tissue was then minced and digested in HBSS medium containing a mixture of enzymes, including collagenase D, dispase, liberase, Miltenyi enzymes, and DNase I (Sigma-Aldrich) for 2 hours at 37°C on a shaker. The resulting cell suspension was filtered through a series of filtration from 300 um to 100 um. Cells were centrifugated at 300g for 5 min at 4°C and stained with fluorescent labeled antibodies. Stained single cell suspensions were enriched by MACS bead purification (Miltenyi, San Diego, CA) using anti-CD45 microbeads and then FACS sorted for mononuclear phagocytes using the FACS Aria Fusion (BD Biosciences). Sorted cells were centrifugated at 300g for 5 min at 4°C. Supernatants were aspirated, and pellets were resuspended with HBSS plus 0.5% BSA at an approximate concentration of 1.2 × 106 cells/ml. Cell quality and viability were assessed with a Cellometer K2 (Nexcelom Bioscience). All samples had viability >88%.
Single cells were then processed using the Chromium Next GEM Single Cell 3′ Platform (10X Genomics). Approximately 29,000 cells were loaded on each channel with an average recovery rate of 24,000 cells. Libraries were sequenced on NextSeq 500/550 (Illumina) with an average sequencing depth of 50,000 reads/cell.

value: Mononuclear Phagocytes

value: Digested brest reduction skin

tag: strain

value: Healthy individual

tag: age

value: 17 years old


title: Human Skin MNPs, Naive, rep1, scRNAseq, CJ14_Protein

description: 10x Genomics

library_source: other

data_processing:
Raw sequencing reads were demultiplexed, mapped to the GRCh38 human reference genome, and gene expression matrices were generated using CellRanger v6.1 (10X Genomics). The following analyses were conducted in R 4.2 (R Core Team, 2014). Seurat package v4.3 was used for downstream data analyses (Hao et al, 2021), and figures were produced using the package ggplot2. Following a standard workflow, the gene expression matrix was filtered to discard cells with less than 200 genes, as well as genes that were expressed in less than three cells. Samples then underwent quality control to remove cells with either too many or too few expressed genes (average around 1,300 and 4,400) and cells with too many mtRNA (average around 10%), resulting in a total of 58,982 cells. Then, “SCTransform” was applied with the “glmGamPoi” method to normalize gene expression data (Stuart et al, 2019; Ahlmann-Eltze & Huber, 2021). After individual preparation, all the samples were merged into a combined Seurat object. Then scaled values of variable genes were then subject to principal component analysis for linear dimension reduction. A shared nearest neighbor network was created based on Euclidean distances between cells in multidimensional PC space (the first 50 PC were used) and a fixed number of neighbors per cell (50 neighbors). This was used to generate a two-dimensional Uniform Manifold Approximation and Projection (UMAP) for visualization as a harmonized atlas to dissect the cell populations from different treatment groups.
DEGs were calculated with “FindAllMarkers” function of Seurat in R 4.1 to study the different expression profiles in different cell types and up-regulated genes in different treatment groups (R Core Team, 2014; Hao et al, 2021). The “data” matrices of “SCT” assay were used, and the minimal log fold change was set to 0.25. Only genes that were detected in more than 25% of cells in either of the two populations were used to compute the DEGs with the Wilcoxon rank-sum test. Markers were identified as genes exhibiting significant up-regulation when compared against all other clusters and defined by having a Bonferroni-adjusted P-value < 0.05. The DEGs are ranked by the adjusted P-value to select the top DEGs for downstream analysis.
To identify cell types, “FindClusters” function with the Leiden algorithm with the various resolution from 0.5 to 2.0 in the Seurat package were used for clustering (Hao et al, 2021). “FindAllMarkers” function was then applied. The top DEGs of individual clusters were examined for well-studied marker genes across literature and the clusters were then annotated for the most likely identity. For re-clustered IMs subtypes, “FindClusters” was performed with different resolution until the right resolution is reached so that each cluster has unique gene expression pattern. For re-clustered IMs subtypes, “FindClusters” was performed with different resolution until the right resolution is reached so that each cluster has unique gene expression pattern. Eleven distinct cell types were identified, including IMs, langerhan cells, DC1, DC2, DC3, AXL+ SIGLEC6+ DCs, MMP12+ DCs, lymphocytes, basal cells, fibroblasts, and cycling cells.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Integrated SeuratObject in rds format contains all 3 samples and different assays of expression/detection matrixes (for both mRNA and protein; CITE-seq Ab: CD88, CD1c, CD1a, CD64, CD14, CD93, CD197, XCR1); The meta data in rds format for every cells, includes the sample source and cell types
Library strategy: CITE-seq

molecule: protein

tag: cell type

value: 45 years old


title: Human Skin MNPs, Naive, rep2, scRNAseq, CJ15_mRNA

description: 10x Genomics

value: 24 years old


title: Human Skin MNPs, Naive, rep3, scRNAseq, CJ16_Protein

description: 10x Genomics


title: Human Skin MNPs, Naive, rep2, scRNAseq, CJ15_Protein

description: 10x Genomics


title: Human Skin MNPs, Naive, rep1, scRNAseq, CJ14_mRNA

description: 10x Genomics


title: 8Z-2

tag: treatment


title: 2149_Cord_blood

tag: neonatal adiposity classification

tag: neonatal sum of skinfolds (mm)

value: Below median

value: Normal glucose tolerant


title: 2150_Cord_blood

value: Adipocyte derived extracellular vesicles

tag: neonatal sex

value: Female

tag: materal age (years)


title: 2142_Cord_blood

value: Adipose

tag: materal vitamin b12 status

value: Above median

tag: materal folate status

value: Gestational diabetes


title: 2154_Cord_blood

value: Lean

tag: materal adiposity


title: 2141_Cord_blood

tag: maternal gdm status


title: 2144_Cord_blood

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: 8E-3

value: E2 treated


title: 8K-1

value: ovarian cancer

value: non treated control


title: 8K-2


title: 8E-2


title: 2130_Cord_blood

value: Male

tag: maternal folate levels at diagnosis (nmol/l)


title: 2129_Cord_blood

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: 2123_Cord_blood

tag: tissue


title: 2122_Cord_blood


title: 2151_Cord_blood


title: 2156_Cord_blood


title: 8B-3

tag: cell line

value: BPA treated


title: 2164_Cord_blood


title: 8Z-1

value: ZEA treated


title: HZ-3

data_processing:
Fastq data were generated by BaseSpace (Illumina)
Raw sequencing data (fastq) was aligned to human reference genome version GRCh38 using HISAT2 algorithm and BAM files were generated
Downstream analysis was performed using StrandNGS software (Deseq) where the FPKM values were generated
Assembly: GRCh38 human reference genome
Supplementary files format and content: tab-delimited matrix text file that include the FPKM values for each Sample

extract_protocol:
Total RNA was isolated with the Quick-RNA MiniPrep Kit (Zymo Research) according to the protocol provided by the manufacturer.
Library preparation was performed by the NEBNext Ultra II RNA Sample Prep kit (New England BioLabs) according to the protocol provided by the manufacturer.


title: HZ-2


title: 2117_Cord_blood


title: HZ-1


title: 2127_Cord_blood


title: HK-3


title: 2109_Cord_blood


title: 2110_Cord_blood


title: HK-2


title: HK-1


title: 2102_Cord_blood


title: 2105_Cord_blood


title: 8B-1


title: HE-2


title: 2101_Cord_blood


title: 2088_Cord_blood


title: HE-1


title: HE-3


title: HB-3


title: 2121_Cord_blood


title: 2112_Cord_blood


title: 2081_Cord_blood


title: 2080_Cord_blood


title: 2078_Cord_blood


title: HB-2


title: 2071_Cord_blood


title: HB-1


title: 2075_Cord_blood


title: 2103_Cord_blood


title: 2070_Cord_blood


title: SD21_DC_csRNAinput

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Sequencing reads were aligned to the human genome using STAR 2.7.1a.
Aligned reads were quantified, normalized, and aggregated using HOMER.
Assembly: hg38
Supplementary files format and content: initiation.txt: tab-delimited log-transformed transcription initiation values at specified genomic intervals
Library strategy: csRNA-seq

molecule: other

source_name: Peripheral blood leukocytes

extract_protocol:
Subject's peripheral blood was collected in potassium EDTA tubes (BD Vacutainer, REF 367861) and processed within 4 hours. Briefly, peripheral leukocytes were enriched by centrifugation followed by red blood cells lysis. Cell pellets were resuspended and lysed in Trizol (ThermoFisher Scientific) and stored in -80C until use. We extracted RNA per manufracture's recommended protocol for Trizol.  Precipitated RNA was desolved in RNAse-free ddH2O. RNA amount was determined using Nanodrop (ThermoFisher Scientific).
Small RNAs of ~20-60 nt were size selected form 2-15 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’ capped RNAs with 3’-OH. Monophosphorylated RNAs were selectively degraded by Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequent 5’dephosporylation by CIP (NEB) followed by decapping with RppH (NEB) augments Cap-specific 5’adapter ligation by T4 RNA ligase 1 (NEB). The 3’ adapter was ligated using truncated T4 RNA ligase 2 (NEB) without prior 3’ repair to select against degraded RNA fragments.

value: Peripheral blood leukocytes

tag: patient id

tag: patient outcome

value: Prolonged recovery

tag: timepoint

value: DC

tag: library type

value: csRNAinput

tag: library strategy

value: small RNA-seq


title: SD21_DC_csRNA

value: csRNA

value: capped short RNA-seq (csRNA-seq)


title: SD21_D7_csRNAinput


title: SD21_D7_csRNA


title: 2069_Cord_blood

value: Adipocyte derived extracellular vesicles

tag: neonatal adiposity classification

tag: neonatal sum of skinfolds (mm)

value: Below median

value: Normal glucose tolerant


title: 2056_Cord_blood

value: Adipose

tag: neonatal sex

value: Female

tag: materal age (years)

value: Above median

value: Gestational diabetes


title: 2066_Cord_blood

value: Lean

tag: materal vitamin b12 status

tag: materal folate status


title: SD21_D5_csRNAinput


title: SD21_D3_csRNA


title: SD21_D3_csRNAinput


title: SD21_D5_csRNA


title: SD20_DC_csRNAinput

value: Fatal


title: SD20_DC_csRNA


title: 2046_Cord_blood

tag: materal adiposity

tag: maternal gdm status


title: 2048_Cord_blood

tag: maternal vitamin b12 at diagnosis (pmol/l)

tag: maternal folate levels at diagnosis (nmol/l)


title: 2043_Cord_blood

tag: tissue

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: 2037_Cord_blood


title: SD20_D9_csRNAinput

tag: patient id


title: SD20_D9_csRNA

tag: patient outcome


title: SD20_D7_csRNAinput

tag: timepoint


title: 2035_Cord_blood


title: 2036_Cord_blood


title: 2034_Cord_blood

value: Male


title: SD20_D7_csRNA

value: Peripheral blood leukocytes

tag: library type


title: 2033_Cord_blood


title: SD20_D5_csRNA

tag: library strategy


title: 2044_Cord_blood

tag: neonatal adiposity classification


title: 2032_Cord_blood

tag: neonatal sum of skinfolds (mm)


title: SD20_D3_csRNA


title: SD20_D3_csRNAinput


title: SD20_D2_csRNAinput


title: 2030_Cord_blood

tag: neonatal sex


title: SD20_D2_csRNA


title: 2026_Cord_blood

tag: materal age (years)


title: SD20_D11_csRNAinput


title: SD20_D11_csRNA


title: 2023_Cord_blood

tag: materal vitamin b12 status


title: SD19_DC_csRNAinput

value: Prolonged recovery


title: SD20_D1_csRNAinput


title: SD20_D1_csRNA


title: SD20_D5_csRNAinput


title: 2020_Cord_blood

tag: materal folate status


title: 2015_Cord_blood

tag: materal adiposity


title: SD19_DC_csRNA

value: DC


title: 2012_Cord_blood

tag: maternal gdm status


title: 2011_Cord_blood

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: 2029_Cord_blood

tag: maternal folate levels at diagnosis (nmol/l)


title: 2008_Cord_blood

tag: tissue


title: 2014_Cord_blood

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: 2010_Cord_blood


title: SD19_D9_csRNA

tag: patient id


title: 2016_Cord_blood


title: SD19_D7_csRNAinput

tag: patient outcome

value: csRNAinput


title: SD19_D7_csRNA

tag: timepoint


title: 8K-3

tag: cell line

tag: cell type

value: ovarian cancer

tag: treatment

value: non treated control


title: SD19_D5_csRNAinput

tag: library type

tag: library strategy

value: small RNA-seq


title: 3097_Maternal_plasma

source_name: Maternal plasma

value: Adipocyte derived extracellular vesicles

tag: neonatal adiposity classification

tag: neonatal sum of skinfolds (mm)

tag: neonatal sex

tag: materal age (years)


title: 3090_Maternal_plasma

tag: materal vitamin b12 status

value: Below median

tag: materal folate status

tag: materal adiposity

tag: maternal gdm status


title: SD19_D3_csRNAinput

tag: tissue


title: SD19_D5_csRNA

tag: patient id

value: csRNA

value: capped short RNA-seq (csRNA-seq)


title: 3086_Maternal_plasma

value: Normal glucose tolerant

tag: maternal vitamin b12 at diagnosis (pmol/l)

tag: maternal folate levels at diagnosis (nmol/l)

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: SD19_D3_csRNA

tag: patient outcome

tag: timepoint


title: 3083_Maternal_plasma

value: Above median


title: SD19_D9_csRNAinput

tag: library type


title: SD19_D2_csRNAinput

tag: library strategy


title: 3081_Maternal_plasma

tag: neonatal adiposity classification

value: Adipose

value: Female


title: 3078_Maternal_plasma

tag: neonatal sum of skinfolds (mm)


title: 3098_Maternal_plasma

tag: neonatal sex


title: SD19_D2_csRNA


title: SD19_D11_csRNAinput


title: SD19_D11_csRNA


title: 3063_Maternal_plasma

tag: materal age (years)


title: 3064_Maternal_plasma

tag: materal vitamin b12 status

value: Gestational diabetes


title: SD19_D1_csRNAinput


title: SD18_DC_csRNAinput


title: SD19_D1_csRNA


title: 3075_Maternal_plasma

value: Lean

value: Male

tag: materal folate status


title: 3061_Maternal_plasma

tag: materal adiposity


title: SD18_DC_csRNA

value: Peripheral blood leukocytes

value: Prolonged recovery


title: SD18_D9_csRNAinput

value: csRNAinput


title: 3060_Maternal_plasma

tag: maternal gdm status


title: 3054_Maternal_plasma

tag: tissue


title: SD18_D9_csRNA

tag: patient id


title: 3044_Maternal_plasma

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: 3036_Maternal_plasma

tag: maternal folate levels at diagnosis (nmol/l)


title: SD18_D7_csRNAinput


title: 3038_Maternal_plasma

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: 3031_Maternal_plasma


title: SD18_D7_csRNA

tag: patient outcome


title: SD18_D5_csRNAinput

tag: timepoint


title: SD18_D5_csRNA

tag: library type


title: SD18_D3_csRNA

tag: library strategy


title: 3059_Maternal_plasma

tag: neonatal adiposity classification


title: 3049_Maternal_plasma

tag: neonatal sum of skinfolds (mm)


title: 3008_Maternal_plasma

tag: neonatal sex


title: SD18_D2_csRNA


title: SD18_D2_csRNAinput


title: SD18_D3_csRNAinput


title: 3025_Maternal_plasma

tag: materal age (years)


title: 3004_Maternal_plasma

tag: materal vitamin b12 status


title: 3005_Maternal_plasma

tag: materal folate status


title: 3006_Maternal_plasma

tag: materal adiposity


title: 2298_Maternal_plasma

tag: maternal gdm status


title: 3014_Maternal_plasma

tag: tissue


title: SD18_D11_csRNAinput

tag: patient id


title: 2300_Maternal_plasma

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: 8E-1

tag: cell line

tag: cell type

value: ovarian cancer

tag: treatment

value: E2 treated


title: SD18_D1_csRNAinput

tag: patient outcome

tag: timepoint

value: small RNA-seq


title: 2296_Maternal_plasma

value: Adipocyte derived extracellular vesicles

tag: maternal folate levels at diagnosis (nmol/l)

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: 8B-2

value: BPA treated


title: 2295_Maternal_plasma

tag: neonatal adiposity classification

tag: neonatal sum of skinfolds (mm)

value: Below median


title: 2294_Maternal_plasma

tag: neonatal sex

tag: materal age (years)


title: SD18_D1_csRNA

tag: library type

value: csRNA

tag: library strategy

value: capped short RNA-seq (csRNA-seq)


title: SD15_D5_csRNA

value: Fatal


title: SD15_D3_csRNAinput


title: 2286_Maternal_plasma

tag: materal vitamin b12 status

tag: materal folate status

tag: materal adiposity

value: Above median

tag: maternal gdm status


title: 2285_Maternal_plasma

tag: tissue

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: SD15_D2_csRNAinput

tag: patient id


title: SD15_D2_csRNA

tag: patient outcome


title: 2287_Maternal_plasma

value: Adipose

value: Female


title: SD15_D3_csRNA

tag: timepoint


title: 2284_Maternal_plasma

value: Gestational diabetes

tag: maternal folate levels at diagnosis (nmol/l)


title: 2283_Maternal_plasma

value: Lean

value: Male

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: SD14_DC_csRNAinput

value: Peripheral blood leukocytes

value: Fast recovery

value: DC


title: 2281_Maternal_plasma

tag: neonatal adiposity classification

value: Normal glucose tolerant


title: 2280_Maternal_plasma

tag: neonatal sum of skinfolds (mm)


title: SD15_D1_csRNA


title: SD14_DC_csRNA


title: SD13_DC_csRNAinput

value: csRNAinput

value: small RNA-seq


title: SD15_D5_csRNAinput


title: SD18_D11_csRNA

value: Prolonged recovery


title: SD13_DC_csRNA


title: SD13_D1_csRNA


title: 2278_Maternal_plasma

value: Adipocyte derived extracellular vesicles

tag: neonatal sex

value: Below median


title: SD13_D1_csRNAinput


title: 2260_Maternal_plasma

tag: materal age (years)


title: 2269_Maternal_plasma


title: 2267_Maternal_plasma


title: SD15_D1_csRNAinput

tag: library type


title: 2266_Maternal_plasma


title: 2259_Maternal_plasma


title: 2254_Maternal_plasma


title: SD11_DC_csRNA

value: csRNA

tag: library strategy

value: capped short RNA-seq (csRNA-seq)


title: SD11_D9_csRNA


title: SD11_D7_csRNAinput


title: 2252_Maternal_plasma

tag: materal vitamin b12 status

value: Above median


title: SD11_D9_csRNAinput


title: 2249_Maternal_plasma

value: Adipose

tag: materal folate status


title: 2244_Maternal_plasma

value: Female

tag: materal adiposity


title: 2243_Maternal_plasma

tag: maternal gdm status

value: Gestational diabetes


title: SD11_D5_csRNAinput

tag: tissue


title: 2261_Maternal_plasma

value: Lean

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: SD11_DC_csRNAinput

tag: patient id


title: 2239_Maternal_plasma

value: Male


title: 2237_Maternal_plasma


title: SD11_D3_csRNAinput

value: Peripheral blood leukocytes

tag: patient outcome


title: SD11_D3_csRNA

tag: timepoint


title: 2235_Maternal_plasma

tag: maternal folate levels at diagnosis (nmol/l)


title: 2234_Maternal_plasma

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: SD11_D11_csRNAinput


title: 2233_Maternal_plasma

tag: neonatal adiposity classification


title: SD11_D1_csRNA


title: 2226_Maternal_plasma

tag: neonatal sum of skinfolds (mm)


title: SD11_D11_csRNA


title: 2221_Maternal_plasma

tag: neonatal sex


title: SD09_DC_csRNAinput


title: SD09_DC_csRNA


title: SD11_D5_csRNA


title: 2220_Maternal_plasma

tag: materal age (years)


title: 2222_Maternal_plasma


title: SD09_D9_csRNAinput

tag: library type


title: SD11_D7_csRNA

tag: library strategy


title: 2210_Maternal_plasma

tag: materal vitamin b12 status


title: SD09_D7_csRNA


title: SD09_D9_csRNA


title: 2211_Maternal_plasma

tag: materal folate status


title: 2207_Maternal_plasma

tag: materal adiposity


title: 2224_Maternal_plasma

tag: maternal gdm status


title: SD11_D1_csRNAinput

tag: tissue


title: SD09_D5_csRNAinput


title: 2216_Maternal_plasma

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: 2205_Maternal_plasma


title: 2194_Maternal_plasma


title: 2202_Maternal_plasma


title: SD09_D11_csRNA

tag: patient id


title: SD09_D3_csRNAinput

tag: patient outcome


title: SD09_D3_csRNA

tag: timepoint


title: SD09_D5_csRNA


title: 2191_Maternal_plasma

tag: maternal folate levels at diagnosis (nmol/l)


title: 2201_Maternal_plasma

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: SD09_D11_csRNAinput


title: 2177_Maternal_plasma

tag: neonatal adiposity classification


title: SD09_D1_csRNA


title: SD08_DC_csRNAinput


title: 2170_Maternal_plasma

tag: neonatal sum of skinfolds (mm)


title: 2166_Maternal_plasma

tag: neonatal sex


title: SD09_D1_csRNAinput


title: SD09_D7_csRNAinput


title: 2164_Maternal_plasma

tag: materal age (years)


title: SD08_DC_csRNA

tag: library type


title: 2165_Maternal_plasma


title: SD08_D9_csRNAinput

tag: library strategy


title: 2156_Maternal_plasma

tag: materal vitamin b12 status


title: SD08_D7_csRNA


title: 2151_Maternal_plasma

tag: materal folate status


title: SD08_D9_csRNA


title: SD08_D7_csRNAinput


title: 2150_Maternal_plasma

tag: materal adiposity


title: 2154_Maternal_plasma

tag: maternal gdm status


title: SD08_D3_csRNA

tag: tissue


title: SD08_D5_csRNA


title: 2149_Maternal_plasma

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: 2144_Maternal_plasma


title: SD08_D3_csRNAinput

tag: patient id


title: 2142_Maternal_plasma


title: 2141_Maternal_plasma


title: SD08_D11_csRNA

tag: patient outcome


title: SD08_D1_csRNAinput

tag: timepoint


title: 2123_Maternal_plasma

tag: maternal folate levels at diagnosis (nmol/l)


title: 2130_Maternal_plasma

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: SD07_DC_csRNAinput


title: 2121_Maternal_plasma

tag: neonatal adiposity classification


title: SD08_D5_csRNAinput


title: SD07_DC_csRNA


title: 2122_Maternal_plasma

tag: neonatal sum of skinfolds (mm)


title: SD07_D9_csRNAinput


title: SD07_D9_csRNA


title: breast tissue, mRNA-derived cDNA, rep 3

city: Berkeley

first: Iain

middle: Christopher

last: Clark

address: 374 Stanley Hall

institute: University of California, Berkeley

description:
3' mRNA library: read1 file contains cell barcode and molecular index; read2 file contains transcript
poly A RNA

data_processing:
The processed matrices for gene expression and MULTIseq barcode were subsetted to cells classified to the patients described in the study.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Folder containing raw FASTQ files for gene expression (RNA) and MULTIseq barcode (HTO) matrices; Folder containing processed matrices for gene expression (RNA) and MULTIseq barcode (HTO)

source_name: Breast tissue

extract_protocol:
Fresh reduction mammoplasty tissue was processed according to Murrow et al (2022) doi: https://doi.org/10.1016/j.cels.2022.06.005
Libraries were prepared using 10X Chromium Next GEM Single Cell 3' Kit v3.1
Single-cell RNA-Seq with MULTIseq workflow

value: Breast tissue

tag: cell type

value: Multiple cell types

value: Transcript

tag: antibodies/tags


title: SD07_D7_csRNAinput

tag: library type

value: csRNAinput


title: SD07_D7_csRNA

tag: library strategy


title: 2117_Maternal_plasma

tag: neonatal sex

tag: materal age (years)

tag: materal vitamin b12 status

value: Normal glucose tolerant


title: SD08_D11_csRNAinput

value: Prolonged recovery

value: small RNA-seq


title: 2112_Maternal_plasma

value: Adipocyte derived extracellular vesicles

tag: materal folate status

value: Below median

tag: materal adiposity

tag: maternal gdm status


title: 2110_Maternal_plasma

tag: tissue

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: 2127_Maternal_plasma


title: SD08_D1_csRNA

tag: patient id

tag: patient outcome

tag: timepoint

value: csRNA

value: capped short RNA-seq (csRNA-seq)


title: 2109_Maternal_plasma

tag: neonatal adiposity classification

value: Adipose

value: Above median

tag: maternal folate levels at diagnosis (nmol/l)

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: breast tissue, mRNA-derived cDNA, rep 1

tag: cell type

tag: antibodies/tags


title: SD07_D5_csRNAinput

tag: library type

tag: library strategy


title: 2129_Maternal_plasma

tag: neonatal sum of skinfolds (mm)

tag: neonatal sex

value: Female

tag: materal age (years)

value: Gestational diabetes


title: SD07_D3_csRNAinput


title: SD07_D5_csRNA


title: bresat tissue, MULTIseq barcode-derived cDNA, rep 3

description:
Cell Barcode library: read1 file contains cell barcode and molecular index; read2 file contains MULTIseq barcode reads
MULTIseq-derived oligonucleotide (HTO)

value: MULTIseq barcode


title: SD07_D3_csRNA

value: Peripheral blood leukocytes


title: SD07_D1_csRNAinput


title: 2105_Maternal_plasma

value: Lean

tag: materal vitamin b12 status

tag: materal folate status

tag: materal adiposity


title: 2103_Maternal_plasma

tag: tissue

tag: maternal gdm status

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: breast tissue, MULTIseq barcode-derived cDNA, rep 2

value: Breast tissue

value: Multiple cell types


title: SD06_D5_csRNAinput

tag: patient id

tag: patient outcome

value: Fast recovery

tag: timepoint

value: csRNAinput


title: SD06_D5_csRNA


title: SD07_D1_csRNA

value: Prolonged recovery


title: breast tissue, mRNA-derived cDNA, rep 2

value: Transcript


title: SD06_D3_csRNAinput

value: small RNA-seq


title: SD20_DC_RNA

data_processing:
Sequencing reads were aligned to the human genome using STAR 2.7.3a.
Gene-level read counts were generated using STAR 2.7.3a.
Assembly: hg38
Supplementary files format and content: count_gene.txt: tab-delimited raw gene counts

extract_protocol:
Subject's peripheral blood was collected in potassium EDTA tubes (BD Vacutainer, REF 367861) and processed within 4 hours. Briefly, peripheral leukocytes were enriched by centrifugation followed by red blood cells lysis. Cell pellets were resuspended and lysed in Trizol (ThermoFisher Scientific) and stored in -80C until use. We extracted RNA per manufracture's recommended protocol for Trizol.  Precipitated RNA was desolved in RNAse-free ddH2O and treated with DNAse (AM1907, ThermoFisher Scientific) per manufracture's protocol. RNA amount was determined using Nanodrop (ThermoFisher Scientific).
RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: Fatal

value: DC


title: SD20_D9_RNA


title: breast tissue, MULTIseq barcode-derived cDNA, rep 1


title: SD06_D3_csRNA

value: csRNA

value: capped short RNA-seq (csRNA-seq)


title: SD06_D1_csRNA


title: 2088_Maternal_plasma

value: Adipocyte derived extracellular vesicles

tag: neonatal adiposity classification

value: Adipose

value: Male

value: Above median

value: Below median

value: Normal glucose tolerant

tag: maternal folate levels at diagnosis (nmol/l)

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: SD20_D7_RNA

value: Peripheral blood leukocytes


title: SD06_D1_csRNAinput

tag: library type


title: SD05_DC_csRNAinput

tag: library strategy


title: 2102_Maternal_plasma

tag: neonatal sum of skinfolds (mm)

value: Female

value: Gestational diabetes


title: SD05_DC_csRNA


title: SD05_D9_csRNAinput

value: csRNAinput


title: 2081_Maternal_plasma

tag: neonatal sex


title: SD05_D7_csRNAinput


title: 2078_Maternal_plasma

value: Lean

tag: materal age (years)


title: SD20_D5_RNA


title: SD20_D3_RNA


title: SD05_D9_csRNA


title: SD20_D2_RNA


title: SD05_D5_csRNAinput


title: SD05_D5_csRNA


title: SD05_D3_csRNAinput


title: SD20_D11_RNA


title: SD05_D3_csRNA


title: 2101_Maternal_plasma

tag: materal vitamin b12 status


title: 2080_Maternal_plasma

tag: materal folate status


title: 2071_Maternal_plasma

tag: materal adiposity


title: SD20_D1_RNA

tag: tissue


title: SD05_D11_csRNAinput


title: 2070_Maternal_plasma

tag: maternal gdm status


title: SD05_D11_csRNA


title: SD05_D1_csRNA


title: SD15_D5_RNA


title: SD04_DC_csRNAinput

value: Prolonged recovery


title: SD04_DC_csRNA


title: SD05_D1_csRNAinput

value: small RNA-seq


title: SD05_D7_csRNA

value: Fatal


title: 2056_Maternal_plasma

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: SD04_D9_csRNA

tag: patient id


title: SD15_D2_RNA

tag: patient outcome


title: 2066_Maternal_plasma


title: SD15_D3_RNA

tag: timepoint


title: 2075_Maternal_plasma

tag: neonatal adiposity classification


title: SD15_D1_RNA


title: 2048_Maternal_plasma

tag: maternal folate levels at diagnosis (nmol/l)


title: SD04_D7_csRNA


title: SD04_D5_csRNAinput


title: SD14_DC_RNA

value: Fast recovery

value: DC


title: 2046_Maternal_plasma

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: SD04_D3_csRNAinput

tag: library type


title: SD13_DC_RNA


title: SD04_D3_csRNA

value: csRNA

tag: library strategy

value: capped short RNA-seq (csRNA-seq)


title: SD04_D11_csRNAinput


title: SD04_D11_csRNA


title: 2069_Maternal_plasma

value: Adipocyte derived extracellular vesicles

tag: neonatal sum of skinfolds (mm)


title: 2043_Maternal_plasma

tag: neonatal sex


title: SD04_D9_csRNAinput


title: SD03_DC_csRNAinput


title: SD04_D7_csRNAinput


title: SD04_D1_csRNAinput


title: 2037_Maternal_plasma

value: Adipose

tag: materal age (years)


title: SD09_D9_RNA


title: SD09_DC_RNA


title: SD03_DC_csRNA


title: 2036_Maternal_plasma

tag: materal vitamin b12 status

value: Above median


title: SD03_D3_csRNAinput


title: SD04_D1_csRNA


title: 2044_Maternal_plasma

value: Male

tag: materal folate status

value: Below median


title: SD03_D3_csRNA

value: Peripheral blood leukocytes


title: SD09_D7_RNA


title: SD04_D5_csRNA


title: 2034_Maternal_plasma

tag: materal adiposity


title: SD09_D5_RNA

tag: tissue


title: SD03_D1_csRNA


title: SD03_D1_csRNAinput


title: 2035_Maternal_plasma

value: Female

tag: maternal gdm status

value: Normal glucose tolerant


title: SD13_D1_RNA


title: SD02_D7_csRNAinput

value: csRNAinput


title: SD02_D3_csRNAinput


title: SD09_D3_RNA


title: SD02_D7_csRNA


title: 2033_Maternal_plasma

tag: maternal vitamin b12 at diagnosis (pmol/l)


title: SD02_D3_csRNA

tag: patient id


title: SD02_D1_csRNAinput

tag: patient outcome


title: SD09_D11_RNA

tag: timepoint


title: SD02_D1_csRNA


title: SD09_D1_RNA


title: SD07_DC_RNA


title: SD01_DC_csRNA


title: SD01_DC_csRNAinput


title: SD01_D9_csRNAinput


title: SD01_D9_csRNA


title: 2030_Maternal_plasma

tag: neonatal adiposity classification

value: Lean

value: Gestational diabetes


title: SD01_D7_csRNAinput

value: Prolonged recovery

value: small RNA-seq


title: 2029_Maternal_plasma

tag: maternal folate levels at diagnosis (nmol/l)


title: SD07_D7_RNA


title: SD01_D7_csRNA


title: SD01_D5_csRNAinput


title: SD07_D5_RNA


title: 2032_Maternal_plasma

tag: maternal sub-scapular skin folds at diagnosis (mm)


title: 2023_Maternal_plasma


title: 2020_Maternal_plasma


title: SD01_D5_csRNA

tag: library type


title: 2016_Maternal_plasma


title: SD01_D3_csRNA

tag: library strategy


title: SD07_D1_RNA


title: SD01_D11_csRNAinput


title: SD01_D3_csRNAinput


title: SD01_D11_csRNA


title: 2015_Maternal_plasma

tag: neonatal sum of skinfolds (mm)


title: SD07_D9_RNA


title: SD01_D1_csRNAinput


title: SD06_D5_RNA

value: Fast recovery


title: 2026_Maternal_plasma

tag: neonatal sex


title: 2014_Maternal_plasma

tag: materal age (years)


title: SD01_D1_csRNA


title: SD06_D3_RNA


title: SD06_D1_RNA


title: 2011_Maternal_plasma

tag: materal vitamin b12 status


title: HC5_NA_csRNAinput

value: Healthy control


title: 2012_Maternal_plasma

tag: materal folate status


title: SD07_D3_RNA


title: HC7_NA_csRNA

value: csRNA


title: 2010_Maternal_plasma

tag: materal adiposity


title: SD05_DC_RNA

tag: tissue

value: Fatal

value: DC


title: HC2_NA_csRNAinput


title: HC5_NA_csRNA

value: capped short RNA-seq (csRNA-seq)


title: SD05_D9_RNA


title: HC1_NA_csRNA


title: SD05_D7_RNA


title: 2008_Maternal_plasma

value: Adipocyte derived extracellular vesicles

value: Adipose

value: Above median

tag: maternal gdm status


title: HC2_NA_csRNA

value: Peripheral blood leukocytes


title: HC7_NA_csRNAinput