title: F1_Control1_nmbu_sncRNA_1

value: 5.5 hpf (50 percent  epiboly)

value: AB

tag: genotype

value: wild type


title: B_GF_DM_2

status: Public on Feb 09 2021

type: SRA

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description:
4-week-old male mouse
GGCCAC

library_source: transcriptomic

data_processing:
Library strategy: tRNA-seq
Remove de-multiplexing, adapters, primers, and low-quality sequences for the raw sequencing data
Mapping using Geneious prime (version 2019.2.3) with appropriate parameters
Modification-related analyses based on the mutation fractions of main methylations at the Watson–Crick face of each tRNA
Counting of the following statistical values: (a) mapped tRNA reads; (b) mapped paired-end tRNA reads
Calculation of the mapped tRNA molecules ((including full-length tRNA molecules and partial tRNA fragments)
Calculation of the fragments per kilobase per million (FPKM) values of tRNAs
Expression-related analyses based on the FPKM values in the tRNA isodecoder/isoacceptor/isotype level
Genome_build: Construction of reference cytosolic (GtRNAdb, https://gtrnadb.ucsc.edu/genomes/eukaryota/Mmusc10/) and mitochondrial tRNA datasets of Mus musculus (GenBank accession no. NC005089)
Supplementary_files_format_and_content: Tab-delimited text files include the RPKM values of each sample;  Microsoft Excel (.xls) files include the sequencing read counts and mapping results of each sample, and include the list of all the used tRNA genes in the two datasets

molecule: total RNA

organism: Mus musculus

source_name: Brain tissue

growth_protocol: SPF mice were housed under specific pathogen free conditions and the mice had been tested free of designated pathogens. GF mice were housed in tightly controlled and monitored isolators to prevent contamination. GF mice are microbiologically sterile and no living organisms can be cultured from them

extract_protocol:
Experiments were carried out according to previously published protocols for DM-tRNA-seq (Zheng et al. Nat Methods. 2015;12:835–7). Dissected tissues were homogenized with glass beads using tissue homogenizer and total RNAs of them were isolated using TRIzol reagent (Ambion) following the manufacturer's protocol. RNA samples were dissolved in RNase-free water, and the concentration and purity of total RNAs were spectrophotometrically measured at 260 nm using a NanoDrop 2000 (Thermo Scientific). Total RNAs were firstly deacylated with Tris-HCl (pH = 9.0) at 37°C for 30 mins and then gel purified using 10% urea denaturing gel as standard procedures. The tRNA bands from each sample were cut off under the UV shadowing, and isolated total tRNAs (approximately 3 μg, 60 pmol) were dissolved in RNase-free water. About 1.5 μg total tRNA from each sample was treated with a 3× molar ratio of wild-type AlkB (180 pmol) and a 4× molar ratio of D135S mutant (240 pmol) to remove Watson–Crick face methylations on tRNAs that can impede the processivity of reverse transcription while another 1.5 μg total tRNA extracted from the same sample was untreated. Afterward, we performed reverse transcription of 150 ng of demethylase-treated (+DM) and untreated (−DM) tRNA with a thermophilic reverse transcriptase (TGIRT, InGex). We purified and eluded cDNAs on a 10% urea denaturing gel by using linear acrylamide (AM9520, Thermo Scientific) as the carrier. The purified cDNAs were circularized with CircLigase II (Epicentre) at 60°C overnight following the manufacturer's protocol and then extracted with phenol-chloroform-isoamyl alcohol (25: 24: 1) followed by ethanol precipitation
For library construction, the circularized cDNAs were amplified with Phusion-HF (NEB) by PCR amplification of 12 cycles using Illumina multiplex (5'–AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC–3') and barcode (5'–CAAGCAGAAGACGGCATACGAGAT [Index] GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT–3'). The PCR products were purified with AMPure XP beads (Beckman Coulter) and sequenced on an Illumina HiSeq system

treatment_protocol: Four tissues (brain, intestine, kidney, and liver) were dissected from the 4-week-old male C57BL/6 SPF and GF mice and freshly frozen on dry ice and stored at −80°C

tag: strain

tag: gender

value: Male

tag: tissue

value: Brain

tag: mouse

value: GF

tag: treatment

value: Demethylase-treated

tag: replicate

tag: sequenced molecule

value: Total tRNA


title: NSC-H3.3wt-1

type: RNA

city: Heidelberg

first: Daniel

last: Haag

state: Baden-Wuerttemberg

address: INF 580

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Cernter (DKFZ)

hyb_protocol: 3’ target hybridization was performed for cartridge arrays on a GeneChip Fluidics Station 450 (Affymetrix) using a GeneChip Hybridization, Wash and Stain Kit (Affymetrix) following the manufacturer’s protocols.

scan_protocol: Arrays were scanned on the GeneChip Scanner 3000 (GCS3000) controlled by the AGCC 4.0  standard processing workflow for  GeneChip cartridges (Affymetrix).

data_processing: Raw data was processed by the internal analysis pipeline of Genomics and Proteomics Core Facility of the German Cancer Research center (DKFZ)

label: biotin

organism: Homo sapiens

source_name: human iPSC-derived NSC

label_protocol: PolyA RNA was reverse transcribed into double-stranded cDNA for generation of biotin-labeled cRNA by in vitro transcription and production of fragmented labeled cRNA for hybridization using the GeneChip 3’ IVT Plus Reagent Kit Assay following the manufacturer’s protocol.

growth_protocol: iPSCs were grown on matrigel in mTeSR1 medium, iPSC-derived neural stem cells were grown on matrigel in NeuroCult NS-A Human Proliferation medium including FGF, EGF, and hLIF.

extract_protocol: Total RNA  was extracted using the Rneasy Mini Kit from Qiagen following the manufacturer's standard protocol and included on-column Dnase I digest.

treatment_protocol: iPSC and NSCs were infected with lentivirus expressing either Cre-GFP or Flp-GFP to induce the H3.3-K27M mutation or maintain the wildtype allele, respectively.

tag: cell type

value: human iPSC-derived NSC

tag: timepoint

value: 10 days after lentiviral infection


title: WT_PA2_E095_5

city: Kansas City

first: Irina

last: Pushel

state: MO

country: USA

institute: Stowers Institute for Medical Research

data_processing:
Reads were demultiplexed allowing up to one mismatch using Illumina bcl2fastq2 v2.18
Reads were aligned to mm10 (Ensembl91) GTF using Tophat 2.1.1 with parameters --no-novel-juncs -g 1.
Reads were counted using the summarizeOverlaps method from the GenomicAlignments v1.8.4 in R 3.3.2.
Data were filtered to remove genes with low counts (total CPM <= 2).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of counts per million reads (CPM) for each gene in each sample.

molecule: polyA RNA

source_name: embryo pharyngeal arch

extract_protocol:
Pharyngeal arches 1 and 2 were manually dissected from embryos in ice-cold PBS and flash frozen in liquid nitrogen. RNA was extracted using TRIzol and purified using the Zymo Research Direct-zol mini-prep kit (Cat#R2052).
Libraries were prepared using the Takara Clontech SMART-seq v4 ultra low input RNA kit (Cat#634891) to generate cDNA, and Illumina Nextera XT Library prep kit (Cat#FC-131-1096) and Illumina Nextera XT Index kit (Cat#FC-131-2001) for library construction according to standard protocols.

value: CBA/Ca/J x C57BL/10

value: pharyngeal arch 2

value: wildtype

tag: developmental stage


title: F1-Gamma1_nmbu_sncRNA_1

city: Oslo

first: Leonardo

middle: Martin

last: Martin

address: Ullevålsveien 72

department: Basic Sicences and Aquatic medicine

country: Norway

institute: Norwegian University of Life Sciences

data_processing:
Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7
Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt
Length filtered reads were mapped, classified into genomic features, and counted using Unitas (v1.5.2) under default settings
miRNAs were quantified with miRDeep2 v0.0.5  using the built-in script quantifier.pl
piRNA clusters were predicted using proTRAC (v4.2.4) under default values
Genome_build: GRCz10
Supplementary_files_format_and_content: matrix of raw read counts (abundances) as comma separated values

organism: Danio rerio

source_name: Whole embryo

extract_protocol:
Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads (Roche Diagnostics, Germany), and total RNA was isolated using Trizol following the instructions of manufacturer (Thermo Fisher Scientific, USA).
sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®,( New England Biolabs® inc, USA) from each sample 1 μg of total RNA was used as input material.

tag: develomental stage

tag: group

value: F1 from exposed parents


title: I_SPF_UT_1

description:
4-week-old male mouse
CGTGAT

source_name: Intestine tissue

value: Intestine

value: SPF

value: Untreated


title: WT_PA1_E105_2

value: pharyngeal arch 1


title: B_GF_UT_3

description:
4-week-old male mouse
GTAGCC


title: WT_PA2_E105_1


title: 697_EBF1_ChIPSeq

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the HG19 human genome assembly using bowtie version 1.12 with with parameters "-n 2 -m 1 -l 36 --best". RNA-seq reads were alined to the HG19 human genome sequence using TopHat with the default parameters.
Potential PCR duplicates in ChIP-seq reads were removed using samtools rmdup command.
Tiled data files (TDF) were generated by igvtools with parameters "-z 5 -w 10 -e 200" for ChIP-seq.
Genome_build: HG19
Supplementary_files_format_and_content: Tiled data files (TDF) for gene track visualization; tab-delimited text files include MACS peak calling output.

molecule: genomic DNA

source_name: pre-B leukemic 697 cells

growth_protocol: The human pre-B leukemia 697 cell line was grown in RPMI1640 (Sigma) supplemented with 10% fetal bovine serum at 37 °C.

extract_protocol:
Chromatin lysates were prepared by sonication and protein-DNA complexes were isolated with indicated antibodies followed by purification with PCR purification kit (Qiagen).
Multiplexing libraries were prepared for sequencing using Illumina standard protocol.

treatment_protocol: The cells were treated with indicated shRNAs before RNA extraction or without treatment for ChIP-seq analysis.

tag: cell line

value: pre-B leukemic cell line 697

value: parental 697

tag: chip antibody

value: anti-EBF1 (Epitomics, #3197-1)


title: iPSC-H3.3K27M-1

source_name: human iPSC line C6-a

value: human iPSC line C6-a

value: 6 days after lentiviral infection


title: B_SPF_DM_3

description:
4-week-old male mouse
GCTACC

value: Male

value: Brain

value: Demethylase-treated


title: Pediatric Patient 36

city: Richmond

first: Maren

middle: Lydia

last: Smith

state: Virginia

address: 1217 E Marshall St

department: Pharmacology and Toxicology

institute: Virginia Commonwealth University

data_processing:
Illumina software used for basecalling.
Sequence reads were mapped to GRC38.91 using STAR v2.6.
Count data was generated from STAR produced BAM files using HTSeq v0.61p1.
Count data was corrected for batch effects using ComBat (Johnson et al. PMID: 16632515) and transformed to positive whole numbers.
Genome_build: GRC38.91
Supplementary_files_format_and_content: Tab-deliminted text files countaining count values for each sample after batch correction by ComBat and transformation to positive, whole numbers.

source_name: whole blood

extract_protocol:
Whole blood (2 mL) was collected from study participants in Tempus Blood RNA tubes at the time of diagnosis or flareup. RNA was extracted from blood using the Tempus Spin RNA Isolation Kit (Thermo Fisher), and polyA enrichment was conducted using the NEBNEXT Poly(A) mRNA magnetic isolation kit (New England BioSciences).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole blood

tag: disease state

value: ANCA-associated vasculitis

tag: rna-cluster

value: cluster 2

tag: anca status

value: MPO


title: Pediatric Patient 39


title: WT_PA1_E095_3

tag: strain

value: CBA/Ca/J x C57BL/10

tag: genotype

value: wildtype


title: WT_PA1_E095_5

tag: tissue


title: PGC_BS-seq [MPGC1]

city: Nottingham

first: Fei

last: Sang

address: QMC

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

data_processing:
Basecalls by Illumine Software Suite
Raw PE reads were trimmed against adaptor sequences by scythe (v0.981), and quality-trimmed by sickle (v1.33) using default settings.
Trimmed reads from single cell sequencing then were directionally aligned to Sus scrofa v11.1 by hisat2 (v2.1.0) with --know-splicestie-infile. Uniquely and correctly mapped reads were extracted for the downstream analysis.
htseq-count was used to count the number of reads aligned to each gene (Sus scrofa v11.1 ensembl annotation build 91).  Gene expression level was calculated and normalised by Transcripts Per Kilobase Million (TPM).
Trimmed reads from bisulfite sequencing were aligned and analyzed by Bismark pipeline
Genome_build: sus scrofa v11.1
Supplementary_files_format_and_content: tab-delimited text files for raw read counts and tpms of each gene, as well as rpms; methylation levels

organism: Sus scrofa

source_name: Pig cells

growth_protocol:
embryos were obtained from artificially inseminated pigs
BS-seq: The Sda/GM2-positive (PGCs) and -negative (Somatic) cells collected by FACS were lysed with lysis buffer (0.1% SDS, 50 ng/ml carrier RNA (QIAGEN) and 1 mg/ml proteinase K (Zymo Research) in DNase-free water) for 60 min at 37°C

extract_protocol:
scRNA-seq: Single cells were collected manually into lysis buffer following the SMARTSEQ. 2 protocol published by Picelli et al., 2014 (Nat. Protocols 9, 171-181)
BS-seq: PBAT libraries were prepared as described by Tang et al. (2015)
scRNA-seq: Libraries were constructed using Nextera XT DNA Library Preparation Kit (Illumina), as used Picelli et al., 2014..
BS-seq: Libraries were subjected to paired-read 150bp sequencing on HiSeq 4000 sequencing system (Illumina)

tag: breed

value: Generic pig

tag: Sex

value: PGC


title: Somatic Cell_BS-seq [FSOMA]

value: Female

value: Somatic Cell


title: Pediatric Patient 38

value: outlier 1

value: NEG


title: WT_PA1_E095_4

value: pharyngeal arch 1


title: iPSC-H3.3wt-1

value: human iPSC line C6-a

value: 6 days after lentiviral infection


title: PGC_BS-seq [FPGC2]


title: Somatic Cell_BS-seq [MSOMA]

value: Male


title: WT_PA1_E095_2


title: B_SPF_DM_2

description:
4-week-old male mouse
CCACTC

tag: gender

value: Brain

tag: mouse

value: SPF

tag: treatment

value: Demethylase-treated

tag: replicate

value: Total tRNA


title: B_SPF_DM_1

description:
4-week-old male mouse
CGTACG

tag: sequenced molecule


title: Pediatric Patient 37

value: whole blood

value: ANCA-associated vasculitis

value: cluster 1

value: Not Done


title: B_SPF_UT_1

description:
4-week-old male mouse
TACAAG

value: Untreated


title: WT_PA2_E095_3

value: CBA/Ca/J x C57BL/10

value: pharyngeal arch 2

value: wildtype

tag: developmental stage


title: PGC_BS-seq [MPGC2]

value: Generic pig

tag: cell type

value: PGC


title: Pediatric Patient 34

value: cluster 2

value: BOTH


title: Pediatric Patient 35


title: B_SPF_UT_3

description:
4-week-old male mouse
GGAACT

value: Male


title: S23

city: Shanghai

first: Bing

last: Liu

address: No. 280, South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
the RNA-seq use Illumina PE150 (paired-end 150nt) sequencing
Raw data (raw reads) of FASTQ format were firstly processed by removing low-quality reads.
Clean reads for each sample were first mapped to mm10 whole genome with the software HISAT2 (Kim D et al., 2015).Reads alignment results were transferred to the program Cufflinks (http://cole-trapnell-lab.github.io/cufflinks) for transcript assembly.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Lung

extract_protocol:
Lungs were removed and flash frozen on liquid nitrogen. RNA was harvested using Trizol reagent and the integrity and quantity were finally measured using RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

tag: age

value: 6-8 weeks

tag: time point

value: treated with sleep deprivation for 10 hours


title: PGC_BS-seq [FPGC1]

value: Female


title: S24


title: Pediatric Patient 33

value: whole blood

tag: disease state

value: MPO


title: WT_PA2_E095_1


title: Pediatric Patient 31

value: ANCA-associated vasculitis

tag: rna-cluster

value: cluster 1


title: B_SPF_UT_2

description:
4-week-old male mouse
TTGACT

value: Brain

value: SPF

value: Untreated

value: Total tRNA


title: WT_PA2_E095_2

value: CBA/Ca/J x C57BL/10

value: pharyngeal arch 2

value: wildtype


title: WT_PA1_E095_1

value: pharyngeal arch 1


title: Pediatric Patient 32

tag: anca status


title: S22

tag: strain


title: S18_595_c

city: Xi'an

first: Li

middle: hui

last: chen

address: No.169 Changlexi Road

department: Biochemistry and Molecular Biology

institute: Fourth Military Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The consistently altered miRNAs in HCC patients from TCGA database then underwent Kaplan-Meier survival analysis.
We employed bioinformatics algorithms (TargetScan and StarBase) and extracellular database (https://www.proteinatlas.org/) to predict the targets of miR-144 and miR-451a
Genome_build: mirBase Release 22.1
Supplementary_files_format_and_content: read count

source_name: HCC

growth_protocol: The HCC and adjacent NH tissues were isolated from 7 HCC patients and RNA was extracted from the paired samples.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HCC

value: liver


title: WT_PA1_E090_5

tag: genotype


title: S21

tag: tissue

value: lung

value: 6-8 weeks


title: S19_651_c


title: S18_595_b

source_name: adjacent NH tissues

value: adjacent NH tissues


title: WT_PA2_E090_4


title: S20

value: treated with sleep deprivation for 10 hours


title: S19_651_b


title: S19


title: WT_PA2_E090_5


title: WT_PA1_E090_3


title: S19_632_c


title: S18


title: WT_PA2_E090_2


title: Hippocampal neurons_S6_sh_rep2

city: Kodaira

first: Hitomi

last: Matsuno

state: Tokyo

address: 4-1-1 Ogawa-Higashi

department: Department of Mental Disorder Research

country: Japan

institute: NCNP National Institute of Neuroscience

description: Gene expression of SIRT6 knockdwon (replicate2)

hyb_protocol: Cy3-labeled cRNA were hybridized to Sureprint G3 Rat Gene Expression V2  8X60K Microarray (Agilent Technologies) following to the manufacturer's protocol.

scan_protocol: Slides were scanned using Agilent SureScan G4900DA (Agilent technologies).

data_processing: The scanned images were analyzed with Feature Extraction software (version 11.5.1.1, Agilent Technologies). Data normalization and data processing were performed using GeneSpring software. Raw data was thresholded to 1.0, normalized with 75th percentile shift.

organism: Rattus norvegicus

source_name: Hippocampal neurons

label_protocol: Cy3 labeled cRNA was prepared from 100 ng total RNA using One color RNA spike-in kit and Low Input Quick Amp Labeling Kit according to the protocol from Agilent Technologies. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). cRNA quality was assessed using NanoDrop 1000 (Thermo Fisher Scientific) and (2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Neurons were cultured in NeurobasalA media (Invitrogen) supplemented with B27 (Invitrogen) and Glutamax (Invitrogen).

extract_protocol: Total RNA was extracted using RNA easy mini kit (Qiagen) according to the manufacturer's protocol. RNA quality was assessed using NanoDrop 1000 (Thermo Fisher Scientific) and 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: 3DIV hippocampal neurons were infected with lenti viral vectors expressing shRNAs at 6 multiplicity of infection (MOI), and incubated for 7 days.

value: Wistar

value: postnatal day 0-1

tag: days in vitro

value: 10 DIV

tag: shRNA

value: rat SIRT6 shRNA


title: Hippocampal neurons_S6_sh_rep4

description: Gene expression of SIRT6 knockdwon (replicate4)


title: Hippocampal neurons_S6_sh_rep1

description: Gene expression of SIRT6 knockdwon (replicate1)


title: S17


title: Hippocampal neurons_S6_sh_rep3

description: Gene expression of SIRT6 knockdwon (replicate3)


title: S19_632_b


title: Hippocampal neurons_SC_sh_rep3

description: Gene expression of control neurons (replicate3)

value: scrambled control shRNA


title: WT_PA1_E090_2


title: Hippocampal neurons_SC_sh_rep2

description: Gene expression of control neurons (replicate2)


title: S16


title: DMSO_1

first: xia

last: jing

address: 1678 Dongfang Road

institute: Shanghai Children’s Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2 with parameters -l 15 -q 0.2 -n 0.05
Sequenced reads were mapped to GRCh38 whole genome using HISAT2 v2.0.4 with parameters --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
The gene expression level (FPKM) was calculated according to the RSEM
Genome_build: GCF_000001405.38_GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: celllines

extract_protocol:
Total cellular RNA was isolated using the TRIzol reagent.
RNA libraries were prepared for sequencing using standard BGISEQ protocols

treatment_protocol: REH cells were seeded at a density of 1× 106 cells/ml and treated with 200nm SNS_032 or DMSO for 24h.

tag: cell line

value: REH cells

tag: agent

value: DMSO treated


title: PXGL-cR.H9_rep2

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

institute: Cerevance ltd

data_processing:
STAR alignment
HTseq-count
Genome_build: hg38
Supplementary_files_format_and_content: counts.txt (raw reads count text format)

source_name: naïve pluripotent sem cells

extract_protocol:
Cell lysate and RNA  are prepared using Trizol/Chloroform
Sequencing libraries are prepared using TruSeq RNA Sample Prep Kit( Illumina), following ribosomal RNA depletion using Ribozero(Illumina)

tag: treatment

value: PXGL


title: S18_552_c


title: WT_PA1_E090_4

value: CBA/Ca/J x C57BL/10


title: S15


title: Hippocampal neurons_SC_sh_rep4

description: Gene expression of control neurons (replicate4)


title: WT_PA1_E090_1

value: wildtype


title: S14


title: Hippocampal neurons_SC_sh_rep1

description: Gene expression of control neurons (replicate1)


title: WT_PA2_E090_1

value: pharyngeal arch 2


title: PXGL-HNES1_rep2


title: LK.zrsr2_ko.3

city: Seattle

first: Jacob

middle: Tyler

last: Polaski

state: Washington

address: 1100 Fairview Ave. N.

department: Public Health Sciences/Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Method of Zrsr2 deletion: LoxP sites flanking Zrsr2 exon 4 and an Frt-flanked neomycin selection cassette.
processed data file: Mx1_Cre_Zrsr2_cKO_Psi_values.xlsx

data_processing:
Gene annotations from UCSC knownGene track, Ensembl71, and MISO v2.0 were merged.
RNA-seq reads were mapped to the transcriptome with RSEM v1.2.4, modified to invoke Bowtie v1.0.0 with the ‘-v 2’ option.
Remaining unaligned reads were mapped to the genome as well as a database of possible splice junctions, consisting of all possible combinations of 5' and 3' splice sites annotated for each gene, using TopHat v2.0.8b.
Isoform ratios were quantified with MISO v2.0.
Psi (percent spliced in) values for all intron retention (ri) events were determined for individual samples: LK.zrsr2_wt.1, LK.zrsr2_wt.2, LK.zrsr2_wt.3, LK.zrsr2_ko.1, LK.zrsr2_ko.2, and LK.zrsr2_ko3.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Mx1_Cre_Zrsr2_cKO_Psi_values.xlsx: Excel file contains isoform ratio measurements (Psi) for splicing events (retained intron, ri) with a minimum of 20 supporting reads.

source_name: Hematopoietic stem/progenitor cells (DAPI- lineage-negative c-Kit+ cells)

extract_protocol:
RNA was extracted using RNeasy columns (Qiagen) per manufacturer’s instructions.
RNA was Poly(A)-selected, and unstranded Illumina libraries were prepared with the standard TruSeq protocol. To select for fragments <400 bp, 0.5× AMPure XP beads were added to the library followed by 1× AMPure XP beads to select for fragments >100 bp. These fragments were then amplified by PCR (15 cycles) and separated by gel electrophoresis (2% agarose).

treatment_protocol: The Zrsr2 allele was deleted by targeting exon 4. Two LoxP sites flanking exon 4 and an Frt-flanked neomycin selection cassette were inserted in the downstream intron.

tag: genotype/variation


title: S18_541_b


title: S12

value: untreated


title: S18_552_b

value: liver


title: PXGL-cR.H9_rep1


title: PXGL-HNES1_rep1


title: S11

value: lung


title: S18_530_c

value: HCC


title: S18_541_c


title: S13

value: 6-8 weeks


title: PDA8301-D5-HNES1_rep2

source_name: stem cell derivative

tag: time

value: Day 5


title: PDA8301-D5-cR.H9_rep2


title: LK.zrsr2_ko.2

value: Hematopoietic stem/progenitor cells (DAPI- lineage-negative c-Kit+ cells)


title: LK.zrsr2_ko.1


title: S9


title: PDA8301-D5-cR.H9_rep1


title: S18_530_b

value: adjacent NH tissues


title: S18_511_b


title: S18_511_c


title: S10


title: S8


title: S18_499_c


title: PDA8301-D3-cR.H9_rep1

value: Day 3


title: PDA8301-D3-cR.H9_rep2


title: LK.zrsr2_wt.2


title: S7


title: LK.zrsr2_wt.3


title: S6


title: PDA8301-D5-HNES1_rep1


title: S18_499_b


title: IgG ChIP - HA tagged Hoxa13 huh7 cells

city: Basel

first: Salvatore

last: Piscuoglio

address: Schönbeinstrasse 40

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Reads were aligned using BWA
Peaks were called against input using MACS2
Genome_build: GRCh38
Supplementary_files_format_and_content: MACS2 peaks called against input for Hoxa13 and HA ChIP from each cell line

source_name: huh7 cells

growth_protocol: HCC-derived cell lines (HepG2 and Huh-7) were maintained in a 5% CO2-humidified atmosphere at 37°C and cultured in DMEM supplemented with 10% FBS, 1% Pen/Strep (Bio-Concept) and 1% MEM-NEAA (MEM non-essential amino acids, ThermoFisher Scientific). Both cell lines were confirmed negative for mycoplasma infection using the PCR-based Universal Mycoplasma Detection kit (American Type Culture Collection, Manassas, VA) as previously described(51). Cells were stably transfected using the jetPRIME transfection reagent (Polyplus) following the manufacturer’s instructions.

extract_protocol:
 Briefly,  cells from four 100 cm Petri dishes at 70-80% confluence were crosslinked in 1% formaldehyde for 10 min with continuous shaking. Crosslinking was stopped by addition of 0.15 M glycine while continuing shaking. After collecting cells by scraping, pellets were washed 3x with cold PBS. Nuclei were isolated and lysed and the obtained chromatin was sonicated in fragments of approximately 200 bp using the Bioraptor instrument. Number of cycles and settings for sonication were previously described(53).  At the same time, antibodies used for immunoprecipitation were coupled with magnetic protein G beads (Invitrogen 100-03D) by incubating 75 μl of protein G beads with 10 μg of anti-HOXA13 antibody (anti human HOXA13 abcam, #ab106503), anti-HA tag antibody (abcam anti-HA tag ChIP grade  #ab9110)  or 10 μg of mouse IgG (Santa Cruz Biotechnology, #sc-2025) as a negative control for 1h at room temperature with constant rotation. At the end of the sonication process, an aliquot of chromatin was kept as input control for each sample and an equal amount of sonicated chromatin was incubated with magnetic beads-antibody previously coupled at 4°C overnight while rotating. After incubation, samples were washed several times and then eluted according to the protocol described by Blecher-Gonen et al.(52).
 All the samples including the input were processed for RNase and Proteinase K treatment, followed by overnight reverse cross-linking at 65°C with continuous shaking. DNA purification followed using Agencourt AMPure XP (A63880 Beckman Coulter). Library construction was performed using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® preparation kit according to the standard protocol. Massively parallel sequencing was performed on an Illumina NextSeq 550 according to manufacturer’s instructions. 50 million reads per sample were obtained.

value: huh7 cells

value: HCC cell line

tag: antibody

value: IgG


title: PDA8301-D3-HNES1_rep1


title: S18_495_c


title: PDA8301-D2-cR.H9_rep2

value: Day 2


title: S4


title: PDA8301-D3-HNES1_rep2


title: Input - HA tagged Hoxa13 huh7 cells

tag: cell type

value: Input


title: LK.zrsr2_wt.1


title: S5

tag: age


title: S18_495_b


title: PDA8301-D2-cR.H9_rep1


title: HepG2 cells - Input DNA

city: Beijing

first: Lin

last: He

address: Xueyuan Road 38

institute: Peking University

data_processing:
Raw data were preprocessed by using fastp version0.19.6
Filtered reads were aligned to the genome (GRCh37, hg19) assembly using Bowtie2.
Peaks were called using MACS version2.
Genome_build: GRCh37, hg19
Supplementary_files_format_and_content: bigwig files were generated using deepTools; Scores represent reads density.
Supplementary_files_format_and_content: peak xls files containing the specific binding region of the protein.

source_name: HepG2 cells

growth_protocol: HepG2 cells were maintained according to the ATCC’s recommendation.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
NG5-associated DNAs were amplified using non-biased conditions, labeled, and sequenced with HiSeq 2500 (Berry Genomics, Beijing).

treatment_protocol: Untreated

tag: tissue source

value: Liver

tag: chip antibody


title: S3

tag: time point


title: HA tagged Hoxa13 ChIP - HA tagged Hoxa13 huh7 cells

value: HA


title: Input - huh7 cells


title: IgG ChIP - huh7 cells


title: HepG2 cells - ING5

value: ING5 (Proteintech, 10665-1-AP)


title: PDA8301-D2-HNES1_rep2


title: PDA8301-D2-HNES1_rep1


title: S2

value: untreated


title: Hoxa13 ChIP - huh7 cells


title: PDA8301-D1-cR.H9_rep2

value: Day 1


title: a2KO_PA2

data_processing:
Reads were demultiplexed using cellranger v3.0.0 mkfastq.
Reads were aligned to mm10, filtered, and barcodes and UMIs counted using the cellranger v3.0.0 count pipeline with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of counts for each gene (row) in each cell (column) in a given sample.

source_name: embryo pharyngeal arch

extract_protocol:
Pharyngeal arches 1 and 2 were manually dissected from 6 wildtype and 5 Hoxa2-/- embryos in ice-cold PBS. Individual PAs were pooled to produce a total of four samples (WT PA1, WT PA2, a2KO PA1, and a2KO PA2). Pooled samples were dissociated in 0.25% Trypsin + EDTA with manual disruption by pipetting to a single-cell suspension. The reaction was stopped with fetal bovine serum and samples were washed in DPBS. The samples were then loaded on a 10X Chromium Single Cell Controller to capture single cells.
Libraries were prepared using the Chromium Single Cell 3' Reagents Kit v3 (Cat# CG000183 Rev A).

value: CBA/Ca/J x C57BL/10

value: pharyngeal arch 2

tag: developmental stage


title: PDA8301-D1-cR.H9_rep1


title: Input - HA tagged Hoxa13 HepG2 cells

value: HepG2 cells


title: HA tagged Hoxa13 ChIP - HA tagged Hoxa13 HepG2 cells


title: WT_PA2

tag: strain

value: wildtype


title: WT_PA1

value: pharyngeal arch 1

tag: genotype


title: PD-D5-cR.H9_rep1

value: Day 5


title: IgG ChIP - HepG2 cells


title: Input - HepG2 cells


title: PD-D5-HNES1_rep2


title: 11-BM_low

city: Seoul

first: sungjin

last: pyo

address: Hanyang University, 222 Wangshimni-ro, Seongdong-Gu

department: Dept. of Life Science

country: South Korea

institute: Hanyang University

description: mdsc.stranded.rCount.txt

data_processing:
NovaSeq 6000 System software was used for base-calling.
Low quality reads were detected using FastQC and trimmed using Sickle.
Filtered reads were aligned to mm10 using STAR aligner.
Gene expression levels were quantified using featureCounts.
See Materials and Methods for details.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: mdsc.stranded.rCount.txt

source_name: 20-week-old sanroque mice (C57BL/6)

growth_protocol: The Roquin(san/+) mice were intercrossed to generate homozygous Roquin(san/san). Female sanroque mice and their WT littermates were used at approximately 20 wks of age unless indicated.

extract_protocol:
Total RNA was extracted from CD11+Gr-1hi and CD11+Gr-1lo cells from the spleens and BM of approximately 20-wk-old sanroque mice.
cDNA libraries were prepared using a TruSeq Stranded mRNA LT Sample Prep kit (Illumina) and sequenced on a NovaSeq 6000 platform using 101 bp paired-read strategy.

value: sanroque

value: 20 weeks

tag: Sex

value: Female

tag: tissue

value: Bone marrow

value: M-MDSC (CD11+Gr-1low)


title: 12-BM_low

description: mdsc.stranded.rCount.txt


title: PDA8301-D1-HNES1_rep2


title: E14Soma_scRNA-seq [AK-ER7]

source_name: Pig embryo

tag: breed

value: Generic pig


title: E14Soma_scRNA-seq [AK-ER6]


title: PD-D5-cR.H9_rep2

tag: cell line


title: 10-BM_hi

description: mdsc.stranded.rCount.txt

value: G-MDSC (CD11+Gr-1hi )


title: PD-D5-HNES1_rep1


title: Hoxa13 ChIP - HepG2 cells

value: HCC cell line


title: E14Soma_scRNA-seq [AK-ER8]


title: 8-San_low

description: mdsc.stranded.rCount.txt

value: Spleen


title: S1

value: lung

value: 6-8 weeks

value: untreated


title: PD-D3-cR.H9_rep1

value: Day 3


title: E14Soma_scRNA-seq [AJ-ER14]


title: PDA8301-D1-HNES1_rep1

value: Day 1


title: 9-BM_hi

description: mdsc.stranded.rCount.txt


title: PD-D3-cR.H9_rep2


title: a2KO_PA1

value: CBA/Ca/J x C57BL/10


title: 7-San_low

description: mdsc.stranded.rCount.txt


title: E14Soma_scRNA-seq [AJ-ER11]


title: PD-D3-HNES1_rep2


title: 6-San_hi

description: mdsc.stranded.rCount.txt


title: E14Soma_scRNA-seq [AJ-ER10]


title: PD-D3-HNES1_rep1


title: 5-San_hi

description: mdsc.stranded.rCount.txt


title: Maoa knock out TILs

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

description:
KO-Tumor
raw_counts.txt.gz
barcode-2

data_processing:
Libraries were sequenced on an Illumina Novaseq 6000 System, using a Novaseq 6000 S2 Reagent Kit (100 cycles; 20012862, Illumina).
fastq files were generated using Cellranger mkfastq (version 3.0.2). The raw reads were mapped to human reference genome (refdata-cellranger-mm10-3.0.0) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: tumor infiltrating cells

extract_protocol:
B16-OVA tumors were harvested from Maoa WT and Maoa KO mice to prepare TII suspensions (10 tumors were combined for each group). TII suspensions were then sorted using a FACSAria II flow cytometer to purify immune cells (gated as DAPI-CD45.2+ cells). Sorted TIIs were immediately delivered to the Technology Center for Genomics & Bioinformatics (TCGB) facility at UCLA for library construction and sequencing. Cells were stained with trypan blue (Thermo Fisher Scientific, T10282) and counted using a Cell Countess II automated cell counter (Thermo Fisher Scientific).
10,000 TIIs from each experimental group were loaded on the Chromium platform (10X Genomics) and libraries were constructed using a Chromium Single Cell 3’ library & Gel Bead Kit V2 (10X Genomics, PN-120237) according to the manufacturer’s instructions.

value: Maoa knock out

value: tumor infiltrating cells


title: PD-D2-cR.H9_rep2

value: Day 2


title: E14Soma_scRNA-seq [AJ30]


title: PAX-SH-095-pre-methy

type: genomic

first: Wenbo

last: Guo

state: Beijing

address: Haidian

institute: Tsinghua University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol.   Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol.

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

data_processing: Arrays were imported and quality control. Methylation score of each CpG is represented as AVG_beta value.

label: Cy3 and Cy5

source_name: PDX model of pancreatic cancer patient PAX-SH-095 before gemcitabine treatment

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified using Qiagen DNeasy Kit according to standard instructions.

tag: patient id

value: patient-derived xenograft


title: E14Soma_scRNA-seq [AJ18]


title: IgG ChIP - HA tagged Hoxa13 HepG2 cells

value: HepG2 cells

value: IgG


title: E14Soma_scRNA-seq [AK79]


title: PAX-SH-091-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-091 before gemcitabine treatment


title: PD-D2-HNES1_rep1

tag: treatment


title: E14Soma_scRNA-seq [AK5]


title: E14Soma_scRNA-seq [AK39]


title: E14Soma_scRNA-seq [AJ106]


title: wild type TILs

description:
WT-Tumor
raw_counts.txt.gz
barcode-1

value: wild type


title: PD-D2-HNES1_rep2


title: PD-D1-HNES1_rep2


title: E14Soma_scRNA-seq [AJ26]

value: Generic pig


title: E14Soma_scRNA-seq [AJ10]


title: PD-D1-HNES1_rep1


title: PAX-SH-138-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-138 before gemcitabine treatment


title: PD-D2-cR.H9_rep1


title: PD-D1-cR.H9_rep1


title: PAX-SH-116-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-116 before gemcitabine treatment


title: PAX-BJ-019-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-019 before gemcitabine treatment


title: PAX-BJ-153-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-153 before gemcitabine treatment


title: N2B27-D5-cR.H9_rep2

value: Day 5


title: PD-D1-cR.H9_rep2


title: PAX-SH-108-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-108 before gemcitabine treatment


title: N2B27-D5-cR.H9_rep1


title: E14Soma_scRNA-seq [AJ8]


title: E14Soma_scRNA-seq [AK84]


title: N2B27-D5-HNES1_rep2


title: PAX-BJ-004-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-004 before gemcitabine treatment


title: N2B27-D5-HNES1_rep1


title: E14Soma_scRNA-seq [AK70]


title: PAX-SH-075-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-075 before gemcitabine treatment


title: ref6_r1

city: London

first: Charlie

last: Keyzor

address: Imperial College, Kensington

department: Department of Life Sciences

institute: Imperial College London

data_processing:
Read alignment to the TAIR10 genome performed by Bowtie2 with the following flags: -q --phred64 --sensitive -- dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Quantification of gene expression by FPKM was calcuated with RSEM
Genome_build: TAIR10
Supplementary_files_format_and_content: gene expression matrix listing the gene expression in FPKM for each gene. For each gene the table also details the transcripts associated with the gene, the gene length, and the expected counts.

organism: Arabidopsis thaliana

source_name: Inflorescence

growth_protocol: Plants were grown in soil in a controlled climate growth chamber under long day conditions.

extract_protocol:
Phenol-chloroform RNA extraction
1) Oligo (dT) magnetic beads are used to select mRNA with polyA tail, or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library.

tag: ecotype/background

value: stage 9-13 buds of the primary inflorescence


title: E14Soma_scRNA-seq [AK77]


title: PAX-BJ-179-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-179 before gemcitabine treatment


title: N2B27-D3-cR.H9_rep1

source_name: stem cell derivative

tag: time


title: PAX-SH-054-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-054 before gemcitabine treatment


title: E14Soma_scRNA-seq [AK38]


title: E14Soma_scRNA-seq [AK14]


title: PAX-BJ-165-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-165 before gemcitabine treatment


title: N2B27-D3-HNES1_rep2


title: PAX-BJ-181-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-181 before gemcitabine treatment


title: jmj13_r1


title: E14Soma_scRNA-seq [AK4]

source_name: Pig embryo


title: N2B27-D3-HNES1_rep1


title: elf6_r2


title: ref6_r2


title: N2B27-D3-cR.H9_rep2


title: E14Soma_scRNA-seq [AJ103]


title: E14Soma_scRNA-seq [AK78]


title: RNaseH treated sample_MCF-7

city: Espoo

first: Sini

last: Rautio

address: Konemiehentie 2

country: Finland

institute: Aalto University

data_processing:
Library strategy: DREAM-seq
Sequence reads were mapped with Bowtie2  (version 2.2.9) to the hg38 genome together with spike-in RNAs and synthetic R-loops. Only uniquely mapped reads were considered for further analysis. Duplicated reads were removed using Picard tool (version 1.77) and rRNA reads using split_bam.py script in RSeQC package (version 2.6.4).
bigWig files were created by homer
See detailed data processing steps in the article
Genome_build: hg38
Supplementary_files_format_and_content: bigWigs file contain normalized count per million values for reverse and forward strands separately.

source_name: MCF-7 cell line

extract_protocol:
10^6 cells were washed twice with PBS1X, and incubated with 380uL of HLB buffer to strip the cytoplasmic membrane. Cells were incubated for 10 minutes with occasional flicking, then briefly vortexed, and spun at 1000G/4C/3 minutes. Nuclei were then washed three times with 1mL of HLB buffer, with spinning at 300G/4C/3 minutes. 4mL of TE low EDTA were added and 12.5uL of Proteinase K (20mG/mL). Then, 104uL of SDS 20% were added and the tubes were flipped a few times to allow homogenization. An overnight digestion at 37C allowed a complete lysis of the nuclei and subsequent release of genomic DNA. The next day, a Phenol-Chloroform extraction was performed with phase-lock tubes (5-prime). DNA was dried for 5 minutes at room temperature, resuspended in Tris-HCl 10mM pH8.0, and set to a concentration of 111.11nG/uL. Aliquots were flash-frozen in liquid nitrogen, and stored at -80C. 2.2uL of turbo DNA free buffer 10x were added to 2uG of nucleic acids in 18uL of Tris-HCl 10mM pH8.0. The reaction was spiked with 20pG of spike-in controls in 0.5uL (pool of 3ssRNAs and 1 DNA:RNA hybrid). The reaction was further divided in two x 10uL: tube “-“, and tube “+”. In tube -, DNA was incubated with 0.5uL of H2O, and in tube + with 0.5uL of RNaseH (2u/uL, ThermoFisher), at 37C. After 45 minutes, another 0.5uL of H2O or RNase H were added, and a second incubation of 45 minutes at 37C was performed. 11.25uL of Turbo DNA free buffer 1x containing 1.25uL of DNase mix were added, followed by an incubation at 37C for 45 minutes. Another 1.25uL of DNase Mix was added and the mixture incubated at 37C for 45 minutes. In order to inactivate the DNase, 0.2 volume of inactivation reagent was added and incubated for 5 minutes at room temperature, with occasional vortexings. The mixture was spun at maximum speed for 2 minutes at room temperature, and the supernatant was harvested, and heated at 65C for 10 minutes, then placed on ice. Finally, RNA was purified using RNA clean and concentrator (Zymo), eluted in 2x8uL of H2O, and used for subsequent sequencing experiment.
RNAs were speedvac’d to have a total of 9uL, then 1 uL of fragmentation buffer (ThermoFisher) was added, and the mixture incubated at 70C for 2.30’. Next, 1uL of stop solution + 40uL of TT buffer were quickly added and RNA fragments were purified with RNA clean and concentrator (Zymo), and eluted in 2x6uL of H2O. RNA was quantified with Qubit 2.0 (ThermoFisher) and solution was speedvac’d to a total of 5uL. Approximatively 30nG were used for library, using the TruSeq Stranded mRNA Sample Preparation kit from Illumina, starting with incubation of RFP on page 20 (catalog #15031047, RevE), and following the manufacturer’s instructions, with the exception of the amplification step. For PCR amplification, KAPA HiFi Hotstart real-time kit was used (Kapa Biosystems). Briefly, 20uL of purified dsDNA was incubated with 5uL of PCR primer cocktail (ref 15031748, Illumina), and 25uL of 2x Master Mix from KAPA HiFi (Kapa Biosystems). Standards were also added. DNA was amplified following these conditions: 98C/45 seconds, (98C/15 seconds, 60C/30 seconds, 72C/40 seconds) x real-time. A final amplification of 72C for 2 minutes was performed, and library was purified using AMPure XP beads from Agencourt. DNA was eluted in a LoBind tube (Eppendorf) in 15uL of Tris-HCl 10mM pH8.0, and 0.05% tween was added. Library was quantified using Qubit 2.0 (ThermoFisher) and fragment sizes by Bioanalyzer (Agilent). Library was sequenced on a HiSeq instrument (Illumina).

value: RnaseH


title: PAX-BJ-014-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-014 before gemcitabine treatment


title: Mock treated sample_MCF-7

value: Mock


title: elf6_r1


title: E14Soma_scRNA-seq [AJ76]


title: jmj13_r2


title: N2B27-D2-cR.H9_rep2


title: PAX-BJ-008-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-008 before gemcitabine treatment


title: N2B27-D2-cR.H9_rep1


title: Col0_r2

value: wildtype


title: PAX-BJ-175-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-175 before gemcitabine treatment


title: Bilateral nuclues of the solitary tract single neurons [WR08]

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

description: Neurons idenfied with Rbfox3 flourescent stain, nuclei confirmed with DAPI flourescent signal collected using Laser Capture microdissection

data_processing:
Target gene signals normalized to median expression of each sample across all genes followed by centering the delta CT values across all samples within a gene.
Matrix normalized worksheet reports normalized signal (against median gene expression).

label: EvaGreen

source_name: RVLM

label_protocol: qPCR reactions were performed using a combination of 96.96 and 192.24 BioMark™ Dynamic IFC Arrays (Fluidigm®, South San Francisco, CA) enabling quantitative measurement of multiple mRNAs and samples under identical reaction conditions (Spurgeon et al. 2008). Each run consisted of 30 amplification cycles (15s at 95°C, 5s at 70°C, 60s at 60°C). Ct values were calculated by the Real-Time PCR Analysis Software (Fluidigm). Intron-spanning PCR primers for every assay were designed and tested for proper targeted amplification before use on a BioMark array.

extract_protocol: Laser capture microdissection was used to obtain precise regional samples from NTS.

treatment_protocol: The 25 uL injection consisted of a 1:1 ratio of anti-miR-376a and anti-miR-135a Locked Nucleic  303 Acid (LNA, Exiqon, 41,42 ) 10 uM solution in artificial cerebrospinal fluid, this condition was  304 considered AM-Combo. A negative control antisense oligonucleotide LNA (a sequence that  305 does not align to any known microRNA or mRNA transcript), called “Scrambled”. No surgery  306 and sham surgery conditions were also assayed. Sham surgeries included cannulas that were  307 inserted and an empty needle was placed for the duration of the corresponding injection time  308 were also performed.

value: Wistar Kyoto (WKY) Rat

tag: animal id

value: WKY

tag: cell count


title: N2B27-D2-HNES1_rep1


title: PAX-BJ-172-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-172 before gemcitabine treatment


title: Bilateral nuclues of the solitary tract single neurons [WR07]


title: N2B27-D2-HNES1_rep2


title: Bilateral nuclues of the solitary tract single neurons [WR06]


title: PAX-BJ-168-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-168 before gemcitabine treatment


title: PAX-BJ-030-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-030 before gemcitabine treatment


title: E14Soma_scRNA-seq [AJ25]

tag: cell type


title: E14Soma_scRNA-seq [AJ60]


title: E14Soma_scRNA-seq [AK83]


title: E14Soma_scRNA-seq [AK76]


title: PAX-BJ-158-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-158 before gemcitabine treatment


title: E14Soma_scRNA-seq [AK69]


title: E14Soma_scRNA-seq [AK37]


title: PAX-BJ-035-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-035 before gemcitabine treatment


title: N2B27-D1-HNES1_rep2

value: Day 1


title: N2B27-D1-cR.H9_rep1


title: A8301-D3-cR.H9_rep2

value: Day 3


title: E14Soma_scRNA-seq [AJ16]


title: Bilateral nuclues of the solitary tract single neurons [WR01]


title: Bilateral nuclues of the solitary tract single neurons [WN17]

source_name: NTS


title: Bilateral nuclues of the solitary tract single neurons [WR05]


title: N2B27-D1-cR.H9_rep2


title: Bilateral nuclues of the solitary tract single neurons [WN16]


title: PAX-SH-130-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-130 before gemcitabine treatment


title: Bilateral nuclues of the solitary tract single neurons [WN15]


title: PAX-SH-129-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-129 before gemcitabine treatment


title: A8301-D3-HNES1_rep1

source_name: stem cell derivative


title: Bilateral nuclues of the solitary tract single neurons [WR02]


title: PAX-BJ-167-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-167 before gemcitabine treatment


title: Bilateral nuclues of the solitary tract single neurons [WR03]


title: N2B27-D1-HNES1_rep1


title: Col0_r1

source_name: Inflorescence


title: E14Soma_scRNA-seq [AJ1]

source_name: Pig embryo


title: Bilateral nuclues of the solitary tract single neurons [WN13]


title: E14Soma_scRNA-seq [AK12]


title: E14Soma_scRNA-seq [AJ57]


title: E14Soma_scRNA-seq [AJ6]


title: A8301-D3-cR.H9_rep1


title: PAX-BJ-020-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-020 before gemcitabine treatment


title: A8301-D2-HNES1_rep2


title: E14Soma_scRNA-seq [AJ100]


title: A8301-D3-HNES1_rep2


title: E14Soma_scRNA-seq [AJ75]


title: Bilateral nuclues of the solitary tract single neurons [WN14]


title: PAX-BJ-026-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-026 before gemcitabine treatment


title: A8301-D1-cR.H9_rep2


title: A8301-D2-cR.H9_rep2


title: PAX-SH-115-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-115 before gemcitabine treatment


title: A8301-D2-cR.H9_rep1


title: A8301-D1-cR.H9_rep1


title: E14Soma_scRNA-seq [AK11]


title: PAX-SH-128-pre-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-128 before gemcitabine treatment


title: Bilateral nuclues of the solitary tract single neurons [WN12]


title: E14Soma_scRNA-seq [AJ99]


title: Bilateral nuclues of the solitary tract single neurons [WN11]


title: E14Soma_scRNA-seq [AK75]


title: Bilateral nuclues of the solitary tract single neurons [WN10]


title: Bilateral nuclues of the solitary tract single neurons [WN07]


title: Bilateral nuclues of the solitary tract single neurons [WN08]


title: A8301-D1-HNES1_rep2


title: A8301-D1-HNES1_rep1


title: E14Soma_scRNA-seq [AJ33]


title: TXX_3

first: Lihua

last: Ding

address: 27th Taiping Rd, Haidian District

institute: Beijing Institute of Biotechnology

data_processing:
Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Hisat2 v2.0.5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MDA-MB-231 cells

extract_protocol:
Total RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MDA-MB-231 cells

value: Breast cancer tissue

value: Treated with TXX-1-10


title: E14Soma_scRNA-seq [AK66]

data_processing:
Basecalls by Illumine Software Suite
Raw PE reads were trimmed against adaptor sequences by scythe (v0.981), and quality-trimmed by sickle (v1.33) using default settings.
Trimmed reads from single cell sequencing then were directionally aligned to Sus scrofa v11.1 by hisat2 (v2.1.0) with --know-splicestie-infile. Uniquely and correctly mapped reads were extracted for the downstream analysis.
htseq-count was used to count the number of reads aligned to each gene (Sus scrofa v11.1 ensembl annotation build 91).  Gene expression level was calculated and normalised by Transcripts Per Kilobase Million (TPM).
Trimmed reads from bisulfite sequencing were aligned and analyzed by Bismark pipeline
Genome_build: sus scrofa v11.1
Supplementary_files_format_and_content: tab-delimited text files for raw read counts and tpms of each gene, as well as rpms; methylation levels

extract_protocol:
scRNA-seq: Single cells were collected manually into lysis buffer following the SMARTSEQ. 2 protocol published by Picelli et al., 2014 (Nat. Protocols 9, 171-181)
BS-seq: PBAT libraries were prepared as described by Tang et al. (2015)
scRNA-seq: Libraries were constructed using Nextera XT DNA Library Preparation Kit (Illumina), as used Picelli et al., 2014..
BS-seq: Libraries were subjected to paired-read 150bp sequencing on HiSeq 4000 sequencing system (Illumina)


title: Postnatal Peripheral Blood_TD141 [methylation]

city: Tokyo

first: Kohei

last: Kashima

address: 7-3-1 Hongo Bunkyo-ku

department: Pediatrics

institute: The University of Tokyo Hospital

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: background correction and dye-bias equalization (Noob) was performed using minfi package (v. 1.20.2), and furthermore, beta-mixture quantile normalization (BMIQ) was performed using ChAMP package(v. 2.6.0).

label: Cy3, Cy5

source_name: PBMC

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Qiagen AllPrep kit.

treatment_protocol: Mononuclear cells were separated by gradient centrifugation using Ficoll-Hypaque from cord blood and postnatal peripheral blood samples within 24 h of the sample collection.

tag: gender

value: male

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

value: Yes

tag: gestational age

tag: birthweight sdscore

tag: parity

value: primipara

tag: delivery

value: Cesarean

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

value: No

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Bilateral nuclues of the solitary tract single neurons [WN05]

tag: strain

tag: animal id

tag: cell count


title: Bilateral nuclues of the solitary tract single neurons [WN06]


title: Bilateral nuclues of the solitary tract single neurons [WN03]


title: E14Soma_scRNA-seq [AJ23]

first: Fei

last: Sang

address: QMC

institute: University of Nottingham

tag: breed

value: Generic pig

tag: cell type


title: TXX_2

tag: cell line

tag: treatment


title: Bilateral nuclues of the solitary tract single neurons [WN09]


title: SR_3

value: Treated with Rimonabant


title: E14Soma_scRNA-seq [AJ13]


title: Bilateral nuclues of the solitary tract single neurons [WN04]


title: E14Soma_scRNA-seq [AJ72]


title: TXX_1


title: Bilateral nuclues of the solitary tract single neurons [WN02]


title: Postnatal Peripheral Blood_TD114 [methylation]

tag: gender

value: female

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

value: Vaginal

tag: maternal age

tag: maternal bmi


title: E14Soma_scRNA-seq [AJ5]

tag: breed

tag: cell type


title: SR_2

tag: cell line

tag: treatment


title: E14Soma_scRNA-seq [AK81]


title: Postnatal Peripheral Blood_TD120 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Postnatal Peripheral Blood_TD126 [methylation]

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi


title: Bilateral nuclues of the solitary tract single neurons [WN01]

tag: strain

tag: animal id

tag: cell count


title: SR_1

tag: cell line

tag: cell type

tag: treatment


title: E14Soma_scRNA-seq [AK74]

tag: breed


title: Bilateral nuclues of the solitary tract single neurons [SR08]

source_name: RVLM

value: Spontaneously Hypertensive Rat (SHR)

value: SHR


title: Con_3

value: Treated with DMSO


title: Bilateral nuclues of the solitary tract single neurons [SR07]


title: Con_2


title: E14Soma_scRNA-seq [AK50]


title: Postnatal Peripheral Blood_TD108 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Postnatal Peripheral Blood_TD125 [methylation]

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

value: parous

tag: delivery

tag: maternal age

tag: maternal bmi


title: Bilateral nuclues of the solitary tract single neurons [SR05]

tag: strain

tag: animal id

tag: cell count


title: E14Soma_scRNA-seq [AK29]

tag: breed

tag: cell type


title: E14Soma_scRNA-seq [AJ109]


title: Bilateral nuclues of the solitary tract single neurons [SR06]


title: E14Soma_scRNA-seq [AJ97]


title: Postnatal Peripheral Blood_TD143 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation


title: E14Soma_scRNA-seq [AK10]


title: Bilateral nuclues of the solitary tract single neurons [SR03]

tag: strain

tag: animal id

tag: cell count


title: Con_1

tag: cell line

tag: cell type

tag: treatment


title: A8301-D2-HNES1_rep1

tag: time

value: Day 2


title: Bilateral nuclues of the solitary tract single neurons [SR01]


title: E14Soma_scRNA-seq [AJ12]

tag: breed


title: Bilateral nuclues of the solitary tract single neurons [SR04]


title: Postnatal Peripheral Blood_TD112 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: preeclampsia

tag: placenta previa


title: E14Soma_scRNA-seq [AJ3]

tag: breed

tag: cell type


title: E14Soma_scRNA-seq [AJ55]


title: E14Soma_scRNA-seq [AJ69]


title: Bilateral nuclues of the solitary tract single neurons [SN14]

tag: strain

tag: animal id

tag: cell count


title: E14Soma_scRNA-seq [AJ22]


title: E14Soma_scRNA-seq [AK80]


title: Bilateral nuclues of the solitary tract single neurons [SN13]


title: Postnatal Peripheral Blood_TD105 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation


title: Bilateral nuclues of the solitary tract single neurons [SN12]

tag: strain


title: Bilateral nuclues of the solitary tract single neurons [SN16]

tag: animal id


title: Bilateral nuclues of the solitary tract single neurons [SN15]

tag: cell count


title: E14Soma_scRNA-seq [AK7]

tag: breed

tag: cell type


title: E14Soma_scRNA-seq [AJ108]


title: E14Soma_scRNA-seq [AK49]


title: Postnatal Peripheral Blood_TD104 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: preeclampsia

tag: placenta previa


title: Postnatal Peripheral Blood_TD106 [methylation]

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation


title: Postnatal Peripheral Blood_TD109 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity


title: E14Soma_scRNA-seq [AJ96]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract single neurons [SN11]

tag: strain

tag: animal id

tag: cell count


title: Postnatal Peripheral Blood_TD101 [methylation]

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: preeclampsia

tag: placenta previa


title: E14Soma_scRNA-seq [AK28]

tag: breed

tag: cell type


title: E14Soma_scRNA-seq [AJ2]


title: E14Soma_scRNA-seq [AK8]


title: Bilateral nuclues of the solitary tract single neurons [SN09]

tag: strain

tag: animal id

tag: cell count


title: Postnatal Peripheral Blood_TD099 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: chorioamnionitis

tag: idiopathic prom without inflammation


title: E14Soma_scRNA-seq [AJ20]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract single neurons [SN08]

tag: strain

tag: animal id

tag: cell count


title: Postnatal Peripheral Blood_TD088 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated mono

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: preeclampsia

tag: placenta previa


title: Postnatal Peripheral Blood_TD103 [methylation]

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: chorioamnionitis

tag: idiopathic prom without inflammation


title: Bilateral nuclues of the solitary tract single neurons [SN07]

tag: strain

tag: animal id

tag: cell count


title: Postnatal Peripheral Blood_TD100 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated mono

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus


title: Postnatal Peripheral Blood_TD089 [methylation]

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: chorioamnionitis

tag: preeclampsia

tag: placenta previa


title: Bilateral nuclues of the solitary tract single neurons [SN10]

tag: strain

tag: animal id

tag: cell count


title: E14Soma_scRNA-seq [AK44]

tag: breed

tag: cell type


title: Postnatal Peripheral Blood_TD073 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated mono

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: idiopathic prom without inflammation


title: Bilateral nuclues of the solitary tract single neurons [SN05]

tag: strain

tag: animal id

tag: cell count


title: Postnatal Peripheral Blood_TD077 [methylation]

tag: gender

tag: estimated cd8t

tag: estimated gran

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: chorioamnionitis

tag: preeclampsia

tag: placenta previa


title: Postnatal Peripheral Blood_TD072 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated mono

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus


title: Postnatal Peripheral Blood_TD085 [methylation]

tag: gender

tag: estimated cd8t

tag: estimated gran

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: idiopathic prom without inflammation


title: Postnatal Peripheral Blood_TD078 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated mono

tag: parity

tag: delivery

tag: chorioamnionitis

tag: preeclampsia

tag: placenta previa


title: Bilateral nuclues of the solitary tract single neurons [SN02]

tag: strain

tag: animal id

tag: cell count


title: Postnatal Peripheral Blood_TD115 [methylation]

tag: gender

tag: estimated cd8t

tag: estimated gran

tag: estimated nk

tag: estimated nrbc

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus


title: E14Soma_scRNA-seq [AJ95]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SSh27]

description: Sections anatomically confirmed with DAPI and NeuN flourescent signal collected using Laser Capture microdissection

source_name: Rat brain NTS

tag: strain

value: Spontaneously Hypertensive (SHR) Rat

tag: treatment

value: Sham


title: Bilateral nuclues of the solitary tract single neurons [SN04]

tag: animal id

tag: cell count


title: E14Soma_scRNA-seq [AK73]


title: E14Soma_scRNA-seq [AJ19]


title: E14Soma_scRNA-seq [AJ29]


title: Bilateral nuclues of the solitary tract sections [SSh26]


title: Postnatal Peripheral Blood_TD076 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated mono

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Postnatal Peripheral Blood_TD071 [methylation]

tag: estimated gran

tag: estimated nk

tag: estimated nrbc

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus


title: E14Soma_scRNA-seq [AJ65]

tag: breed

tag: cell type


title: Postnatal Peripheral Blood_TD058 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated mono

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery


title: Bilateral nuclues of the solitary tract single neurons [SN03]

tag: strain

tag: animal id

tag: cell count


title: E14Soma_scRNA-seq [AK72]


title: Bilateral nuclues of the solitary tract sections [SSh25]

tag: treatment


title: Bilateral nuclues of the solitary tract single neurons [SR02]


title: Postnatal Peripheral Blood_TD067 [methylation]

tag: estimated gran

tag: estimated nk

tag: estimated nrbc

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: E14Soma_scRNA-seq [FP1]

tag: breed

tag: cell type


title: E14Soma_scRNA-seq [FS5]


title: Postnatal Peripheral Blood_TD060 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated mono

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery


title: Bilateral nuclues of the solitary tract sections [SSh21]

tag: strain

tag: animal id

tag: treatment


title: Postnatal Peripheral Blood_TD055 [methylation]

tag: estimated gran

tag: estimated nk

tag: estimated nrbc

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: E14Soma_scRNA-seq [FS4]

tag: breed

tag: cell type


title: Postnatal Peripheral Blood_TD059 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated mono

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery


title: Postnatal Peripheral Blood_TD057 [methylation]

tag: estimated gran

tag: estimated nk

tag: estimated nrbc

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis


title: E14Soma_scRNA-seq [AJ15]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SSh19]

tag: strain

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [SSh18]


title: Postnatal Peripheral Blood_TD054 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated mono

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Bilateral nuclues of the solitary tract single neurons [SN01]

tag: strain

tag: cell count


title: Bilateral nuclues of the solitary tract sections [SSh24]

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [SSh23]


title: E14Soma_scRNA-seq [FS3]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SSh22]


title: Postnatal Peripheral Blood_TD062 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated gran

tag: estimated nk

tag: estimated nrbc

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis


title: Postnatal Peripheral Blood_TD048 [methylation]

tag: estimated cd8t

tag: estimated mono

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Postnatal Peripheral Blood_TD050 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated gran

tag: estimated nk

tag: estimated nrbc

tag: maternal age

tag: maternal bmi


title: Bilateral nuclues of the solitary tract sections [SSh16]

tag: strain

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract single neurons [SN06]

tag: cell count


title: E14Soma_scRNA-seq [FS29]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SSh15]


title: Bilateral nuclues of the solitary tract sections [SSh20]


title: Bilateral nuclues of the solitary tract sections [SSh14]


title: E14Soma_scRNA-seq [FS10]


title: E14Soma_scRNA-seq [FP8]


title: E14Soma_scRNA-seq [FS28]


title: Postnatal Peripheral Blood_TD047 [methylation]

tag: estimated cd8t

tag: estimated mono

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: E14Soma_scRNA-seq [FP7]

tag: breed


title: Bilateral nuclues of the solitary tract sections [SSh17]

tag: strain

tag: animal id

tag: treatment


title: E14Soma_scRNA-seq [FP37]

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SSh11]


title: E14Soma_scRNA-seq [FS23]


title: E31PGC_scRNA-seq [GM18]


title: E14Soma_scRNA-seq [FP10]


title: Postnatal Peripheral Blood_TD043 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: maternal age

tag: maternal bmi

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [SSh09]

tag: strain

tag: animal id


title: Bilateral nuclues of the solitary tract sections [SSh13]

tag: treatment


title: Bilateral nuclues of the solitary tract sections [SSh12]


title: E31PGC_scRNA-seq [GM28]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SSh07]


title: Postnatal Peripheral Blood_TD030 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: birthweight sdscore

tag: parity

tag: delivery

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Postnatal Peripheral Blood_TD022 [methylation]

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: maternal age

tag: maternal bmi

tag: placenta previa


title: E14Soma_scRNA-seq [FS6]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SSh10]

tag: strain

tag: animal id

tag: treatment


title: Postnatal Peripheral Blood_TD023 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: birthweight sdscore

tag: parity

tag: delivery

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: E31PGC_scRNA-seq [GF26]

tag: breed

tag: cell type


title: E31PGC_scRNA-seq [GM31]


title: E31PGC_scRNA-seq [GF14]


title: Bilateral nuclues of the solitary tract sections [SSh08]

tag: strain

tag: animal id

tag: treatment


title: Postnatal Peripheral Blood_TD003 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: maternal age

tag: maternal bmi

tag: placenta previa


title: Postnatal Peripheral Blood_TD008 [methylation]

tag: birthweight sdscore

tag: parity

tag: delivery

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Bilateral nuclues of the solitary tract sections [SSh06]

tag: strain

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [SSh05]


title: E31PGC_scRNA-seq [GM15]

tag: breed

tag: cell type


title: Cord Blood_TD142 [methylation]

source_name: CBMC

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: maternal age

tag: maternal bmi

tag: placenta previa


title: E31PGC_scRNA-seq [GM17]


title: Cord Blood_TD133 [methylation]

tag: birthweight sdscore

tag: parity

tag: delivery

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Bilateral nuclues of the solitary tract sections [SSh04]

tag: strain

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [SSh02]


title: E31PGC_scRNA-seq [GF13]

tag: breed

tag: cell type


title: E14Soma_scRNA-seq [FS12]


title: Bilateral nuclues of the solitary tract sections [SSh01]


title: Bilateral nuclues of the solitary tract sections [SSc15]

value: Scrambled


title: Postnatal Peripheral Blood_TD040 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: maternal age

tag: maternal bmi

tag: placenta previa


title: E31PGC_scRNA-seq [GM14]


title: Postnatal Peripheral Blood_TD018 [methylation]

tag: birthweight sdscore

tag: parity

tag: delivery

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: E31PGC_scRNA-seq [GF23]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SSc14]

tag: strain

tag: animal id

tag: treatment


title: Cord Blood_TD141 [methylation]

tag: gender

value: male

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: maternal age

tag: maternal bmi

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [SSc13]

tag: strain


title: E31PGC_scRNA-seq [GF15]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SSc12]

tag: animal id

tag: treatment


title: E31PGC_scRNA-seq [GM13]


title: E31PGC_scRNA-seq [GM25]


title: E31PGC_scRNA-seq [GF12]


title: Bilateral nuclues of the solitary tract sections [SSc11]


title: Postnatal Peripheral Blood_TD012 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: birthweight sdscore

tag: parity

tag: delivery

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

value: Yes


title: E31PGC_scRNA-seq [GM3]

tag: breed

tag: cell type


title: Cord Blood_TD147 [methylation]

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: maternal age

tag: maternal bmi

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [SSc10]

tag: strain

tag: animal id

tag: treatment


title: Postnatal Peripheral Blood_TD013 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: birthweight sdscore

tag: parity

tag: delivery

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Bilateral nuclues of the solitary tract sections [SSc09]

tag: strain


title: E31PGC_scRNA-seq [GM21]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SSc08]

tag: animal id

tag: treatment


title: E31PGC_scRNA-seq [GM2]


title: Cord Blood_TD146 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

value: primipara

tag: maternal age

tag: maternal bmi

tag: placenta previa


title: Cord Blood_TD145 [methylation]

tag: birthweight sdscore

tag: parity

tag: delivery

value: Cesarean

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Bilateral nuclues of the solitary tract sections [SSc07]

tag: strain

tag: animal id

tag: treatment


title: E31PGC_scRNA-seq [GF17]

tag: breed

tag: cell type


title: E31PGC_scRNA-seq [GM1]


title: Cord Blood_TD143 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: maternal age

tag: maternal bmi

value: No

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [SSc06]

tag: strain

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [SSc05]


title: Cord Blood_TD144 [methylation]

tag: gender

tag: birthweight sdscore

tag: parity

tag: delivery

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: E31PGC_scRNA-seq [GM22]

tag: breed

value: Generic pig

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SSc03]

tag: strain


title: E14PGC_scRNA-seq [AJ53]


title: E31PGC_scRNA-seq [GM24]


title: Bilateral nuclues of the solitary tract sections [SSc02]

tag: animal id


title: Cord Blood_TD138 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: maternal age

tag: maternal bmi

tag: placenta previa


title: E14PGC_scRNA-seq [AJ44]

tag: breed


title: Cord Blood_TD139 [methylation]

tag: gender

tag: birthweight sdscore

tag: parity

tag: delivery

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: E14PGC_scRNA-seq [AJ42]

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SSc01]

tag: strain

tag: animal id

tag: treatment


title: Cord Blood_TD126 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: maternal age

tag: maternal bmi

tag: placenta previa


title: E31PGC_scRNA-seq [GF24]

tag: breed

tag: cell type


title: Cord Blood_TD132 [methylation]

tag: gender

tag: birthweight sdscore

tag: parity

tag: delivery

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Bilateral nuclues of the solitary tract sections [SSh03]

tag: strain

tag: animal id

tag: treatment


title: Cord Blood_TD140 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: maternal age

tag: maternal bmi

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [SC17]

value: Cocktail


title: E14PGC_scRNA-seq [AJ7]

tag: breed

tag: cell type


title: E14PGC_scRNA-seq [AK1]


title: Cord Blood_TD105 [methylation]

tag: gender

tag: birthweight sdscore

tag: parity

tag: delivery

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: E14PGC_scRNA-seq [AJ40]


title: Bilateral nuclues of the solitary tract sections [SC16]

tag: strain

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [SSc04]


title: Cord Blood_TD120 [methylation]

value: female

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: maternal age

tag: maternal bmi

tag: placenta previa


title: Cord Blood_TD106 [methylation]

tag: gender

tag: birthweight sdscore

tag: parity

tag: delivery

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Cord Blood_TD115 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?


title: E14PGC_scRNA-seq [AJ24]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SC14]

tag: strain

tag: animal id

tag: treatment


title: Cord Blood_TD125 [methylation]

tag: gender

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: placenta previa


title: Cord Blood_TD108 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Bilateral nuclues of the solitary tract sections [SC13]

tag: strain

tag: animal id

tag: treatment


title: Cord Blood_TD099 [methylation]

tag: gender

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus


title: Cord Blood_TD134 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

value: Vaginal

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: placenta previa


title: Cord Blood_TD107 [methylation]

tag: gender

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: preeclampsia


title: Bilateral nuclues of the solitary tract sections [SC15]

tag: strain

tag: animal id

tag: treatment


title: Cord Blood_TD124 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus


title: Cord Blood_TD112 [methylation]

tag: gender

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: placenta previa


title: Cord Blood_TD123 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: preeclampsia


title: E14PGC_scRNA-seq [AK82]

tag: breed

tag: cell type


title: E14PGC_scRNA-seq [AK31]


title: Bilateral nuclues of the solitary tract sections [SC12]

tag: strain

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [SC11]


title: Cord Blood_TD119 [methylation]

tag: gender

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis


title: Bilateral nuclues of the solitary tract sections [SC10]

tag: strain


title: E14PGC_scRNA-seq [AJ56]

tag: breed

tag: cell type


title: E14PGC_scRNA-seq [AJ110]


title: Bilateral nuclues of the solitary tract sections [SC09]

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [SC08]


title: Cord Blood_TD101 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Cord Blood_TD110 [methylation]

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis


title: E14PGC_scRNA-seq [AK26]

tag: breed

tag: cell type


title: E14PGC_scRNA-seq [AJ46]


title: Bilateral nuclues of the solitary tract sections [SC07]

tag: strain

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [SC06]


title: Bilateral nuclues of the solitary tract sections [SC05]


title: Bilateral nuclues of the solitary tract sections [SC04]


title: E14PGC_scRNA-seq [AK71]


title: E14PGC_scRNA-seq [AJ17]


title: E14PGC_scRNA-seq [AK9]


title: Cord Blood_TD116 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Cord Blood_TD103 [methylation]

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis


title: Bilateral nuclues of the solitary tract sections [SC03]

tag: strain

tag: animal id

tag: treatment


title: E11EPI_scRNA-seq [D9]

tag: breed

tag: cell type


title: Cord Blood_TD114 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: E11EPI_scRNA-seq [F23]


title: Bilateral nuclues of the solitary tract sections [SC02]

tag: strain

tag: animal id

tag: treatment


title: Cord Blood_TD097 [methylation]

tag: gender

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis


title: Cord Blood_TD118 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: idiopathic prom without inflammation

tag: preeclampsia


title: E11EPI_scRNA-seq [F15]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [SC01]

tag: strain

tag: animal id

tag: treatment


title: Cord Blood_TD113 [methylation]

tag: gender

tag: batch

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: placenta previa


title: E11EPI_scRNA-seq [F32]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [WSh07]

tag: strain

value: Wistar Kyoto (WKY) Rat

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [WSh08]


title: E11EPI_scRNA-seq [F31]


title: E11EPI_scRNA-seq [F22]


title: Bilateral nuclues of the solitary tract sections [WSh06]


title: E14PGC_scRNA-seq [AJ31]


title: E11EPI_scRNA-seq [F14]


title: Bilateral nuclues of the solitary tract sections [WSh05]


title: E11EPI_scRNA-seq [F30]


title: Cord Blood_TD111 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: idiopathic prom without inflammation

tag: preeclampsia


title: E11EPI_scRNA-seq [D24]

tag: breed

tag: cell type


title: Cord Blood_TD092 [methylation]

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: placenta previa


title: E11EPI_scRNA-seq [F21]


title: Bilateral nuclues of the solitary tract sections [WSh03]

tag: strain

tag: animal id

tag: treatment


title: E11EPI_scRNA-seq [F13]


title: Bilateral nuclues of the solitary tract sections [WSh01]


title: Cord Blood_TD089 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Bilateral nuclues of the solitary tract sections [WSh04]

tag: strain