title: Single Dorsal root ganglion neuron_SNI 14d [S133]

description:
S133
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_4hr_PBS_CBP_rep2

status: Public on Feb 24 2021

type: SRA

city: New York

first: Richard

last: Koche

state: New York

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human assembly hg19 using bowtie2 (v2.2.2) with default parameters and duplicates were collapsed using Picard (v2.16).
To create density files, read overlap density was calculated with an extension of 200 bp, the signal was then normalized to sequencing depth and converted to BigWig using BEDTools.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files containing read densities normalized to sequencing depth.

molecule: genomic DNA

organism: Homo sapiens

source_name: MV411 cell line

growth_protocol: MV411 cells were cultured at 37°C in 5% CO2 humidified atmosphere in RPMI medium supplemented with 10% fetal bovine serum (FBS), antibiotics (100 U/mL penicillin, 100 mg/mL streptomycin), and L-glutamine (1%).

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: MV411 cells were resuspended to a concentration of 15 million cells/5 mL of working media. Peptide suspensions were made in PBS of CREBMIM and CRYBMIM peptides from lyophilized product. Peptide suspensions or PBS control were added directly to working media to a final concentration of 20 µM. Cells were incubated with peptide or control for 1h or 4h at 37°C and then resuspended in PBS.

tag: cell line

value: MV411 leukemia cell line

tag: treatment

value: PBS control

tag: time

value: 4 hr

tag: chip antibody

value: Cell Signaling  #7425 Anti-CBP, rabbit monoclonal, Clone D9B6, lot #1


title: MV411_4hr_CRYBMIM_MYB_rep3

value: CRYBMIM peptide

value: Abcam ab45150 Anti-v-Myb and c-Myb, rabbit monoclonal, Clone #EP769Y, lot # GR246427-10


title: MV411_4hr_CRYBMIM_MYB_rep2


title: Single Dorsal root ganglion neuron_SNI 14d [S131]

city: Shanghai

first: Kaikai

last: Wang

address: 393 Middle Huaxia Road

country: China

institute: ShanghaiTech University

description:
S131
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

library_source: transcriptomic

data_processing:
Basecalls were performed using bcl2fastq2-v2.19.1.403
Sequenced reads of 10x genomics were processed using Cell Ranger (version.2.1.0) with default parameters
Sequenced reads of Smart-seq2 were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit (version 0.0.13), then mapped to mm10 using hisat2 (version: 2.0.4), finally,  the reads counts were normalized to FPKM (Fragments Per Kilobase of exon per Megabase of library size)
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values, raw UNI counts for each single cell and cell information

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
For Smart-seq2, Total RNA was extracted with AMBION AM1560 kit; for 10x Genomics, The cellular suspensions were further processed with Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v2, 16 rxns PN-120237
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: SNI 14d

tag: tissue/cell type

value: Single Dorsal root ganglion neuron

tag: technology


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject0014

type: RNA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description:
Pre TW19610 Sub014
UPN119 cells stimulated with PRE Sub0014 plasma

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through Paired TTest function in Partek GS.

label: biotin

molecule: total RNA

source_name: UPN119 cells stimulated with pre-Lp299v supplementation plasma in men with stable CAD

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN119 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of plasma samples obtained prior to and immediately following 6 weeks of Lp299v supplementation from 19 men with stable CAD.  Cultures were prepared in Costar 24-well plates (Cellular Technology LTD) using 500,000 cells/well and in RPMI 1,640 medium supplemented with 100 U/ml penicillin and 100 ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN119 cells

value: stimulated with PRE Sub0014 plasma


title: Single Dorsal root ganglion neuron_SNI 14d [N957]

description:
N957
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_4hr_CRYBMIM_Input_rep1


title: MV411_4hr_CRYBMIM_CREB_rep3

value: EMD Millipore 17-600 Anti-CREB, rabbit monoclonal, Clone # NL904


title: Single Dorsal root ganglion neuron_SNI 14d [N894]

description:
N894
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_4hr_CRYBMIM_CREB_rep2


title: Single Dorsal root ganglion neuron_SNI 14d [N887]

description:
N887
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_4hr_CRYBMIM_CBP_rep3


title: MV411_4hr_CRYBMIM_CREB_rep1


title: Single Dorsal root ganglion neuron_SNI 14d [S160]

description:
S160
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N886]

description:
N886
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N888]

description:
N888
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N889]

description:
N889
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N883]

description:
N883
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_4hr_CRYBMIM_CBP_rep2


title: MV411_4hr_CRYBMIM_CBP_rep1


title: Single Dorsal root ganglion neuron_SNI 14d [N881]

description:
N881
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_1hr_PBS_MYB_rep2

value: 1 hr


title: MV411_1hr_PBS_MYB_rep1


title: MV411_1hr_PBS_MYB_rep3


title: Single Dorsal root ganglion neuron_SNI 14d [N88]

description:
N88
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N882]

description:
N882
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_1hr_PBS_CREB_rep3


title: MV411_1hr_PBS_Input_rep1


title: MV411_4hr_CRYBMIM_MYB_rep1


title: Single Dorsal root ganglion neuron_SNI 14d [N874]

description:
N874
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_1hr_PBS_CREB_rep2


title: Single Dorsal root ganglion neuron_SNI 14d [N878]

description:
N878
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N873]

description:
N873
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N892]

description:
N892
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N87]

description:
N87
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_1hr_PBS_CREB_rep1


title: MV411_1hr_PBS_CBP_rep3


title: MV411_1hr_PBS_CBP_rep2


title: Single Dorsal root ganglion neuron_SNI 14d [N865]

description:
N865
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N86]

description:
N86
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_1hr_CRYBMIM_MYB_rep3


title: Single Dorsal root ganglion neuron_SNI 14d [N82]

description:
N82
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N84]

description:
N84
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_1hr_PBS_CBP_rep1


title: Single Dorsal root ganglion neuron_SNI 14d [N80]

description:
N80
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_1hr_CRYBMIM_Input_rep1


title: MV411_1hr_CRYBMIM_MYB_rep2


title: Single Dorsal root ganglion neuron_SNI 14d [N77]

description:
N77
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N78]

description:
N78
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N79]

description:
N79
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_1hr_CRYBMIM_CREB_rep1


title: MV411_1hr_CRYBMIM_CREB_rep3


title: MV411_1hr_CRYBMIM_CBP_rep3


title: Single Dorsal root ganglion neuron_SNI 14d [N72]

description:
N72
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N75]

description:
N75
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_1hr_CRYBMIM_CREB_rep2


title: Single Dorsal root ganglion neuron_SNI 14d [N70]

description:
N70
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N69]

description:
N69
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_1hr_CRYBMIM_CBP_rep1


title: MV411_1hr_CRYBMIM_CBP_rep2


title: ChIP_RUNX1_PBS_rep3

value: Active Motif #39000 Anti-RUNX1, rabbit polyclonal


title: ChIP_RUNX1_PBS_rep2


title: Single Dorsal root ganglion neuron_SNI 14d [N68]

description:
N68
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: ChIP_RUNX1_PBS_rep1


title: Single Dorsal root ganglion neuron_SNI 14d [N800]

description:
N800
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N66]

description:
N66
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_1hr_CRYBMIM_MYB_rep1


title: ChIP_RUNX1_CRYBMIM_rep3


title: ChIP_RUNX1_CRYBMIM_rep2


title: Single Dorsal root ganglion neuron_SNI 14d [N64]

description:
N64
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: S12e_10_10

city: Leiden

first: Johannes

middle: Han

last: de Winde

address: Sylviusweg 72

department: Faculty of Science

country: Netherlands

institute: Leiden University

data_processing:
Paired-end sequence reads were generated using the Illumina MiSeq system. Initial quality assessment was based on data  passing the Illumina Chastity filtering. Subsequently, reads containing PhiX control signal were removed using an in-house  filtering protocol. In addition, reads containing (partial) adapters were clipped (up to a minimum read length of 50 bp).  The second quality assessment was based on the remaining reads using the FASTQC quality control tool version 0.11.5.
Tophat2 version 2.1.1 (Kim et al 2013) aligns RNA-seq reads to a reference genome using the ultra-high-throughput short read aligner Bowtie version 2.2.6 (Langmead et al. 2012).
Cufflink is used to test for differential expression and regulation in RNA-Seq samples. It assembles the aligned RNASeq  reads into a parsimonious set of transcripts. Cuffldiff then estimates the relative abundances of these  transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
Genome_build: CP009974 and (for wildtype S12 which contains megaplasmid) CP009975
Supplementary_files_format_and_content: tab-delimited text files (.fpkm_tracking) of FPKM values for each sample

organism: Pseudomonas putida S12

source_name: bacterial cell

growth_protocol: bacterial cells were grown from overnight culture (1:100 dilution) on liquid lysogeny broth for 2 hours (30 °C, 200rpm)

extract_protocol:
total RNA was extracted using TRIzol RNA Isolation Reagents (ThermoFisher) followed by column clean-up using NucleoSpin® RNA Plant and Fungi (Macherey-Nagel)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 0.1% v/v toluene was added to bacterial cell cultures (sample 10-18) at the beginning of growth

tag: genotype

value: ALE-derived plasmid-cured (strain 10)

tag: protocol

value: grown on LB media + 0.1percent v/v toluene

tag: growth phase

value: mid-log phase


title: S12e_10_22

value: ALE-derived plasmid-cured (strain 22)


title: ChIP_RUNX1_CRYBMIM_rep1

value: MV411 leukemia cell line


title: S12e_10_06

value: ALE-derived plasmid-cured (strain 06)


title: S12d_10_22

value: plasmid cured (strain 22)


title: Single Dorsal root ganglion neuron_SNI 14d [N63]

description:
N63
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: S12d_10_10

value: plasmid cured (strain 10)


title: ChIP_PU1_PBS_rep3

value: PBS control

value: Cell Signaling #2266 Anti-PU.1, rabbit polyclonal


title: S12_10_02

value: wildtype (replicate 2)


title: Single Dorsal root ganglion neuron_SNI 14d [N61]

description:
N61
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: SNI 14d

value: Single Dorsal root ganglion neuron


title: S12d_10_06

value: plasmid cured (strain 06)


title: S12_10_03

value: wildtype (replicate 3)


title: ChIP_PU1_PBS_rep2

value: 1 hr


title: ChIP_PU1_PBS_rep1


title: Single Dorsal root ganglion neuron_SNI 14d [N67]

description:
N67
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N60]

description:
N60
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: S12e_0_10

value: grown on LB media


title: S12_10_01

value: wildtype (replicate 1)


title: S12e_0_06


title: ChIP_PU1_CRYBMIM_rep3

value: CRYBMIM peptide


title: S12e_0_22

value: mid-log phase


title: Single Dorsal root ganglion neuron_SNI 14d [N65]

description:
N65
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N57]

description:
N57
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: S12d_0_10


title: S12d_0_22


title: ChIP_PU1_CRYBMIM_rep1


title: Single Dorsal root ganglion neuron_SNI 14d [N62]

description:
N62
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: S12_0_03


title: Single Dorsal root ganglion neuron_SNI 14d [N54]

description:
N54
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: S12_0_02


title: ChIP_LYL1_PBS_rep3

value: Santa Cruz sc-374164x Anti-LYL1, mouse monoclonal, Clone C-4


title: Single Dorsal root ganglion neuron_SNI 14d [N538]

description:
N538
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: S12_0_01


title: 21RNAwt.3

city: Potsdam

first: Juan Camilo

last: Moreno Beltran

state: Brandenburg

address: Am Muehlenberg 1

department: Molecular Physiology

country: Germany

institute: MPI for Molecular Plant Physiology

data_processing:
Integrated data analysis was performed by Lexogen (STAR aligner) where reads were mapped against the Nitab 4.5 reference genome and read-counts were determined.
Differential expression was computed using DESeq2 in R (Love et al., 2014).
Genome_build: Nitab 4.5 reference genome (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/edwards_et_al_2017/)
Supplementary_files_format_and_content: Default STAR output files (ASCII format, tab delimited): Gene identifier, Read count (unstranded RNA-seq), Read count (counts for the 1st read strand aligned with RNA), Read count (counts for the 2nd read strand aligned with RNA)

organism: Nicotiana tabacum

source_name: leaves

growth_protocol: Tobacco transgenic lines corresponding to the T4 generation of our previously published DcLCYB1-expressing lines were used in this work (Moreno et al., 2016). Tobacco (Nicotiana tabacum cultivar Xanthi NN) wild type and transgenic lines were raised from seeds germinated in Petri dishes containing MS medium supplemented with 30 g/L sucrose (Murashige and Skoog, 1962) and kanamycin (100 mg/mL).

extract_protocol:
Total RNA was extracted from frozen powder of tobacco leaves of 5-week-old T3 plants using the Nucleo Spin RNA extraction kit (Macherey-Nagel, Germany). Genomic DNA traces were eliminated by a 15 min DNase I treatment.
QuantSeq 3’ mRNA-Seq services were performed for the wild type and transgenic DcLCYB1 line L14, L15 and L16, at Lexogen GmbH (Vienna, Austria). 500 ng total RNA were used as input for generating sequencing-ready libraries using the QuantSeq FWD 3’ mRNA-Seq library preparation kit (Lexogen, Vienna, Austria; SKU 015). Libraries were characterized by microcapillary electrophoresis and fluorometry prior to pooling and sequencing.
A sequencing yield of 572,9M-demultiplexed reads was obtained from a single run on a NextSeq 500 device in SR75 HO mode

tag: cultivar

value: Xanthi NN

tag: transgenic line

value: wild type

tag: replicate


title: S12d_0_06


title: Single Dorsal root ganglion neuron_SNI 14d [N532]

description:
N532
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: ChIP_LYL1_PBS_rep1

value: MV411 leukemia cell line


title: Single Dorsal root ganglion neuron_SNI 14d [N520]

description:
N520
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 19RNAwt.1


title: 20RNAwt.2


title: 13RNA16.1

value: Dclcyb1 transgenic line L16


title: ChIP_LYL1_CRYBMIM_rep3


title: Single Dorsal root ganglion neuron_SNI 14d [N519]

description:
N519
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 14RNA16.2


title: 7RNA15.1

value: Dclcyb1 transgenic line L15


title: Single Dorsal root ganglion neuron_SNI 14d [N514]

description:
N514
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N56]

description:
N56
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 8RNA15.2


title: 15RNA16.3


title: ChIP_LYL1_CRYBMIM_rep2


title: ChIP_LYL1_CRYBMIM_rep1


title: 3RNA14.3

value: Dclcyb1 transgenic line L14


title: ChIP_LYL1_PBS_rep2

value: PBS control


title: ChIP_PU1_CRYBMIM_rep2

value: Cell Signaling #2266 Anti-PU.1, rabbit polyclonal


title: ChIP_JUN_PBS_rep2

value: Cell Signaling #9165 Anti-c-Jun, rabbit monoclonal, Clone 60A8


title: Single Dorsal root ganglion neuron_SNI 14d [N497]

description:
N497
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: SNI 14d

value: Single Dorsal root ganglion neuron


title: 1RNA14.1


title: 9RNA15.3


title: Single Dorsal root ganglion neuron_SNI 14d [N508]

description:
N508
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N494]

description:
N494
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: ChIP_JUN_PBS_rep1

value: 1 hr


title: 2RNA14.2


title: Single Dorsal root ganglion neuron_SNI 14d [N492]

description:
N492
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: ChIP_JUN_CRYBMIM_rep3


title: Single Dorsal root ganglion neuron_SNI 14d [N45]

description:
N45
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N44]

description:
N44
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: ChIP_JUN_CRYBMIM_rep2


title: Pt25

city: Portland

first: Vanderlene

last: Kung

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: OHSU

description: Total RNA analyzed with nCounter HOT and Fibrosis panels

hyb_protocol: nCounter default

scan_protocol: nCounter default

data_processing: nSolver defaults were used to filter based on default quality control measures.  Transcript counts outputted were normalized to kidney housekeeping genes, and imported into the R/Bioconductor package DESeq.

source_name: allograft kidney

label_protocol: nCounter default

extract_protocol: Total RNA was extracted from three consecutive 20 um-thick fresh cut ribbons of formalin-fixed, paraffin-embedde tissue using the RecoverAll Total Nucleic Acid Isolation kit (Invitrogen, Life Technologies, Carlsbad, CA).

tag: tissue

value: allograft kidney

tag: status after 5 years

value: Alive

tag: histology

value: CA TCMR

tag: age

tag: Sex

tag: Stage


title: Pt24


title: ChIP_JUN_CRYBMIM_rep1

tag: cell line

tag: treatment

value: CRYBMIM peptide

tag: time

tag: chip antibody


title: Single Dorsal root ganglion neuron_SNI 14d [N43]

description:
N43
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

tag: strain

tag: tissue/cell type

tag: technology


title: Pt22


title: Pt23


title: Pt21


title: Pt19


title: Pt20


title: Pt16


title: Pt17


title: Pt15


title: ChIP_CEBPa_PBS_rep1

value: Santa Cruz sc-166258X Anti-CEBPa, mouse monoclonal, Clone G-10


title: ChIP_JUN_PBS_rep3


title: ChIP_CEBPa_PBS_rep3


title: Single Dorsal root ganglion neuron_SNI 14d [N30]

description:
N30
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N36]

description:
N36
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N39]

description:
N39
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Pt14


title: Pt10


title: Pt12


title: ChIP_CEBPa_CRYBMIM_rep3


title: Pt13


title: Pt11


title: ChIP_CEBPa_CRYBMIM_rep2


title: Pt7


title: Single Dorsal root ganglion neuron_SNI 14d [N28]

description:
N28
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: ChIP_CEBPa_CRYBMIM_rep1


title: Pt8


title: ChIP_CEBPa_PBS_rep2


title: Pt6


title: Pt5


title: Pt18


title: Single Dorsal root ganglion neuron_SNI 14d [N179]

description:
N179
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 53: D13 0 4239

city: Foster City

first: Ricardo

last: Ramirez

state: CA

address: 333 Lakeside Drive

institute: Gilead Sciences, Inc.

data_processing:
Basecalls from Illumina samples were performed using CASAVA
Reads were aligned to human genome assembly hg19 using STAR 2.4
Reads per gene were quantified by RSEM
Genome_build: hg19
Supplementary_files_format_and_content: Read Counts matrix with samples as columns

source_name: Primary human hepatocytes

growth_protocol: Cryopreserved primary human hepatocytes (PHH) isolated from multiple donors were purchased from Thermo Fisher Scientific (HMCPTS; Donors Hu8181, Hu8130, Hu4239), After thawing, cells were recovered by centrifugation at 100g through cryopreserved hepatocyte recovery medium (Thermo Fisher Scientific; CM7500) and plated in collagen coated 96-well plates (Thermo Fisher Scientific; CM1096) at a density of 65,000 – 70,000 live cells per well. Cells were plated in William’s E medium (Thermo Fisher Scientific; A1217601) supplemented with 3.6 % hepatocyte thawing and plating supplement (Thermo Fisher Scientific, A15563), 5 % fetal bovine serum (Thermo Fisher Scientific; 16000-036), 1 µM dexamethasone (Thermo Fisher Scientific, A15563), and 0.2 % Torpedo antibiotic mix (Bioreclamation; Z990008). Approximately 12 – 14 hours after plating, plating medium was removed, and cells were switched into maintenance medium: William’s E medium supplemented with 4 % hepatocyte maintenance supplement (Thermo Fisher Scientific; AI15564), 2 % fetal bovine serum, 0.1 µM dexamethasone, 1.5 % DMSO (Sigma-Aldrich, St. Louis, MO; D8418), and 0.2 % Torpedo antibiotic mix. Approximately 24 hours after plating, PHH were infected with 6 µl of patient sera containing the HBV virus (041FY67821P; genotype A) in maintenance medium supplemented with 4 % PEG 8000. Infections were allowed to proceed for 20 – 24 hours before removing remaining extracellular virions by washing with maintenance medium three times.

extract_protocol:
RNA samples were converted into cDNA libraries using the Illumina TruSeq  Stranded mRNA sample preparation kit (Illumina # RS-122-2103).
Libraries were prepared for sequencing using the Ampliseq human transcriptome kit (Thermo) for sequencing on Ion Torrent

treatment_protocol: HBV-infected primary human hepatocytes were treated with the KDM5 inhibitor prodrug GS-5801 at 0, 0.03, 0.3, and 10 µM final concentration every three to four days for 13 days. GS-5801 was formulated in 100 % DMSO at a concentration of 10 mM.

tag: donor

tag: dose (um)

tag: hbv

tag: day


title: Single Dorsal root ganglion neuron_SNI 14d [N173]

description:
N173
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Pt4

tag: tissue


title: Single Dorsal root ganglion neuron_SNI 14d [N172]

description:
N172
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Pt9

tag: status after 5 years


title: 51: D13 0.3 4239


title: Pt1

tag: histology


title: Single Dorsal root ganglion neuron_SNI 14d [N171]

description:
N171
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: LW3_4THD50n2

city: Hospitalet de Llobregat (Barcelona)

first: Meritxell

last: Pons

address: Avinguda Gran Via, 199-203

country: Spain

institute: IDIBELL

description:
Skin Fibroblasts
Nanostring nCounter® Human Neuropathology Panel

hyb_protocol: All the steps were carried out in the ice and using the nCounter nanoString reagent for the Neuropathology panel. The master mix for the hybridization process was prepared by mixing hybridization buffer and reporter CodeSet. A dilution of 10μg/μl for each RNA to be analyzed was prepared and maintained in ice. For each sample, a tube was prepared with 5μl of RNA (10μg/μl) and 8μl of master mix. 2μl of Capture ProbeSet was added in each tube and the hybridization process was started using a PCR machine at 65ºC for at least 16 hours.

scan_protocol: nSolver™ Analysis Software, Advanced Analysis Modules

label_protocol: nCounter Human Neuropathology Panel: XT-CSO-HNROP1-12

growth_protocol: Human iPSC were routinely cultured in mTESR medium on matrigel coated plates. Directed differentiation of iPSC onto ventral dopaminergic neurons was carried out following a previously published protocol (Kriks, et al. Nature 480, 547-551; 2011), with minor modifications. Neurons were cultured for 50 days.

extract_protocol: Total RNA was extracted using Quiazol lysis reagent (Qiagen) and RNAeasy extraction kit (Qiagen) according to manufacturer's instructions.

tag: cell type

value: iPSC-derived dopaminergic neurons

tag: genotype

value: gene-edited isogenic lines with corrected LRRK2 mutation


title: Single Dorsal root ganglion neuron_SNI 14d [N170]

description:
N170
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N180]

description:
N180
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: LW3_4THD50n1

data_processing: nSolver™ Analysis Software, Advanced Analysis Modules


title: Single Dorsal root ganglion neuron_SNI 14d [N169]

description:
N169
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Pt3

tag: age

tag: Sex

tag: Stage


title: LL3_4THD50n3

value: LRRK2 G2019S


title: LW2_3THD50n4


title: LL3_4THD50n2


title: Single Dorsal root ganglion neuron_SNI 14d [N168]

description:
N168
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

tag: treatment


title: 48: D13 0.03 8130


title: 47: D13 0.3 8130


title: 52: D13 0.03 4239


title: MM_tumor_bort_high_2

city: Charlestown

first: Maolin

last: Ge

state: Massachusetts

address: 149 13th Street

department: MGH Cancer Center

institute: Harvard Medical School

data_processing:
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg38 whole genome using HISAT2.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample.

source_name: Multiple myeloma cell line MM1.S

growth_protocol: Cells were cultured in Gibco RPMI 1640 containing 10% FBS at 37°C with 5% CO2 and were maintained between a density of 5 × 10^5 cells/ml and 2 × 10^6 cells/ml.

extract_protocol:
Tissue blocks were lysed in TRIzol reagent (Sigma-Aldrich). The lysate was well mixed with chloroform and spun for 15 min at 13000 g at 4 °C. RNA in top aqueous phase was collected and mixed with propan-2-ol to precipitate total RNA.
RNA libraries were prepared for sequencing using MGIEasymRNA Library Prep Kit V2.

treatment_protocol: Induced drug-tolerant cells were generated by exposing parental cells to sublethal dose of bortezomib for at least 4 weeks. The remaining cells after the treatment were considered as ‘Tolerant’ cells and were collected for analysis. ‘Reversed’ cells were generated from bortezomib-tolerant cells by culturing without bortezomib for a minimum of 4 weeks.

value: Multiple myeloma

tag: cell line

value: Multiple myeloma cell line MM1.S

tag: drug treatment

value: Bortezomib


title: LL3_4THD50n1


title: Pt2


title: LL2_3THD50n1


title: LL2_3THD50n2


title: C1#1 TH D50 n2

source_name: Control

value: control


title: MM_tumor_bort_high_1


title: 46: D13 10 8130


title: MM_tumor_bort_SAHA_2

value: Bortezomib+SAHA


title: MM_tumor_bort_SAHA_1


title: C1#1 TH D50 n1


title: 50: D13 10 4239


title: 45: D13 0 8181


title: Single Dorsal root ganglion neuron_SNI 14d [N165]

description:
N165
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

tag: strain

tag: tissue/cell type


title: MM_tumor_rev_2


title: Single Dorsal root ganglion neuron_SNI 14d [N163]

description:
N163
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

tag: technology


title: 44: D13 0.03 8181

tag: donor

tag: dose (um)


title: MM_tumor_rev_1


title: MM_tumor_bort_low_2


title: MM_tumor_bort_low_1


title: Single Dorsal root ganglion neuron_SNI 14d [N166]

description:
N166
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N159]

description:
N159
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MM_tumor_ctrl_2


title: MM_tumor_ctrl_1


title: Single Dorsal root ganglion neuron_SNI 14d [N158]

description:
N158
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MM1.S_reversed


title: 42: D13 10 8181

tag: hbv

tag: day


title: Single Dorsal root ganglion neuron_SNI 14d [N157]

description:
N157
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MM1.S_parental

tag: tissue


title: 40: D10 0.03 8130


title: MM_patient_rev3

source_name: Multiple myeloma patient


title: MM_patient3


title: Single Dorsal root ganglion neuron_SNI 14d [N152]

description:
N152
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MM_patient_rev2


title: Single Dorsal root ganglion neuron_SNI 14d [N154]

description:
N154
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 39: D10 0.3 8130


title: MM_patient2


title: MM_patient_rev1


title: 38: D10 10 8130


title: Single Dorsal root ganglion neuron_SNI 14d [N149]

description:
N149
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MM_patient1


title: Single Dorsal root ganglion neuron_SNI 14d [N151]

description:
N151
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 37: D10 0 8181


title: 229_Wang_HiC_BWX3834_1mMIPTG_60min

city: Bloomington

first: Xindan

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

description: parS∆9 (loxP-spec-loxP), -94˚ parS (loxP no a.b.), yrvN (-122˚):: tetO120 cat, yvbJ::Pspank (optRBS) tsr-tetR-yfp erm

data_processing:
Library strategy: HiC-Seq
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.     For Staphylococcus aureus Hi-C, we mapped reads in each FASTQ file back to the genome of Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.     For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) or Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1)  independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) genomes was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1; NC_007795.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv: comma-separated values files of ChIP-seq results.
Supplementary_files_format_and_content: matrix.txt files: 10kb bins of B. subtilis genome; normalized Hi-C interaction scores
Supplementary_files_format_and_content: csv files: genome position; reads; number of reads at each genome position

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature. Staphylococcus aureus strains were derived from HG003 (Herbert et al 2010, PMID: 20212089). Cells were grown in tryptic soy broth (TSB) at specified temperature.

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC, or anti-His antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina HiSeq2500, Nextseq550, or MiSeq sequencing platforms. Illumina Truseq indexes were used.

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 60 min, fixed by 3% formaldehyde for 30min at room temperature

tag: protocol

value: CH, 37degree C, 1mM IPTG for 60 min

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), yrvN (-122degree)::tetO120 cat, yvbJ::Pspank (optRBS) tsr-tetR-yfp erm

tag: restriction enzyme

value: HindIII


title: 226_Wang_HiC_BWX3821

description: parS∆9 (loxP-spec-loxP), -94˚ parS (loxP no a.b.), -109˚ 12x XDS (loxP-spec-loxP)

treatment_protocol: Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37degree C

tag: genotype

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), -109degree 12x XDS (loxP-spec-loxP)


title: Single Dorsal root ganglion neuron_SNI 14d [N148]

description:
N148
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: SNI 14d

value: Single Dorsal root ganglion neuron


title: MM1.S_tolerant


title: 43: D13 0.3 8181


title: 224_Wang_HiC_BWX3391

description: parS∆9 no a.b., +153˚ parS (loxP-kan-loxP)

value: parSdelta9 no a.b., +153degree parS (loxP-kan-loxP)


title: 36: D10 0.03 8181


title: 223_Wang_HiC_BWX3389

description: parS∆9 no a.b., +117˚ parS (loxP-kan-loxP)

value: parSdelta9 no a.b., +117degree parS (loxP-kan-loxP)


title: 41: D10 0 8130


title: 225_Wang_HiC_BWX3799

description: parS∆9 (loxP-spec-loxP), -94˚ parS (loxP no a.b.), -109˚ 4x XDS (loxP-spec-loxP)

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), -109degree 4x XDS (loxP-spec-loxP)


title: 35: D10 0.3 8181


title: 222_Wang_HiC_BWX3227

description: parS∆9 no a.b., +91˚ parS (loxP-spec-loxP)

value: parSdelta9 no a.b., +91degree parS (loxP-spec-loxP)


title: Single Dorsal root ganglion neuron_SNI 14d [N146]

description:
N146
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 221_Wang_HiC_BWX3388

description: parS∆9 no a.b., +58˚ parS (loxP-kan-loxP)

value: parSdelta9 no a.b., +58degree parS (loxP-kan-loxP)


title: 34: D10 10 8181


title: L6_L4_I354: LN-elongation zone-R2

city: zheng zhou

first: xiaohuan

last: mu

address: zhengzhou long zi hu

institute: Henan Agricultural University

data_processing:
Raw reads were pre-processed to remove low quality regions and adapter sequences.
Clean reads from each sample were aligned to the maize reference genome (B73 RefGen_v3, http://www.maizegdb.org/assembly/) using TopHat2
Aligned reads from TopHat2 mapping were subjected to String Tie for DeNovo transcript assembly
The R package edgeR was used to identify the differentially expressed genes.The expression of each gene was normalized to fragments per kilobase of transcript per million reads (FPKM) to compare among different samples.
Genome_build: B73 RefGen_v3 (http://www.maizegdb.org/assembly/)
Supplementary_files_format_and_content: tab-delimited text files include tags,copy number and TPM

organism: Zea mays

source_name: supply 0.04mM nitrogen (LN)

growth_protocol: maize inbrid B73 grown in hydroculture.

extract_protocol:
The division and elongation zone of maize leaf 6 was harvested, flash frozen and stored at -80℃.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: line

value: maize inbred B73

value: elongation zone of leaf sixth


title: Single Dorsal root ganglion neuron_SNI 14d [N144]

description:
N144
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N145]

description:
N145
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 33: D3 0 4239


title: Single Dorsal root ganglion neuron_SNI 14d [N143]

description:
N143
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 32: D3 0.03 4239


title: L4_L4_I347: LN-elongation zone-R1


title: H6_L4_I355: HN-elongation zone-R2

source_name: supply 4mM nitrogen (HN)


title: L3_L4_I346: LN-division zone-R2

value: division zone of leaf sixth


title: L1_L4_I345: LN-division zone-R1


title: Single Dorsal root ganglion neuron_SNI 14d [N142]

description:
N142
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 31: D3 0.3 4239


title: H3_L4_I351: HN-division zone-R2


title: Single Dorsal root ganglion neuron_SNI 14d [N136]

description:
N136
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: H1_L4_I350: HN-division zone-R1


title: 30: D3 10 4239


title: 282_Wang_input_SaWX019

description: HG003 spa::Tn (erm), geh (40˚):: pWX725 (Ptet xerD-his6 cat) (100ng/ml aTc)

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.     For Staphylococcus aureus Hi-C, we mapped reads in each FASTQ file back to the genome of Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.     For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) or Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1)  independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) genomes was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1; NC_007795.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv: comma-separated values files of ChIP-seq results.
Supplementary_files_format_and_content: matrix.txt files: 10kb bins of B. subtilis genome; normalized Hi-C interaction scores
Supplementary_files_format_and_content: csv files: genome position; reads; number of reads at each genome position

organism: Staphylococcus aureus

source_name: Staphylococcus aureus HG003

treatment_protocol: Cells were growing in TSB medium at 37˚C with aTc at 100ng/ul final concentration, fixed by 3% formaldehyde for 30min at room temperature

value: TSB, 37degree C, 100ng/ul aTc

value: HG003 spa::Tn (erm), geh (40degree)::pWX725 (Ptet xerD-his6 cat) (100ng/ml aTc)

tag: antibody

value: none, input


title: Single Dorsal root ganglion neuron_SNI 14d [N134]

description:
N134
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 260_Wang_ChIPHis_SaWX019

value: ChIP using anti-His antibodies


title: Single Dorsal root ganglion neuron_SNI 14d [N127]

description:
N127
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 29: D3 0 8130


title: 28: D3 0.03 8130


title: 27: D3 0.3 8130


title: H4_L4_I352: HN-elongation zone-R1


title: Single Dorsal root ganglion neuron_SNI 14d [N125]

description:
N125
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Control replicate 1

city: Kweishan, Taoyuan

first: Shu Yuan

last: Yang

address: Wenhua 1st Rd, No. 259

country: Taiwan

institute: Chang Gung University

data_processing:
Reads mapped to Drosophila genome (dm6) with HISAT2
Expression counts tallied by htseq-count
Gene expression values calculated by Cufflinks
Differential gene expression determined with DESeq2 (FDR>0.05)
Genome_build: dm6
Supplementary_files_format_and_content: NCBI GEO DESeq2.xlsx (contains differential gene expression results as determined by DESeq2)

organism: Drosophila melanogaster

source_name: vas-GFP stage 17 embryonic gonads

extract_protocol:
RNA reagent (Bioman)
QuantSeq 3’ mRNA-seq Library Prep Kit, Lexogen

value: embryonic gonad

tag: developmental stage

value: stage 17

value: vas-GFP


title: Control replicate 2


title: 26: D3 10 8130


title: Phf7 mutant replicate 1

source_name: Phf7[DN18]; vasGFP stage 17 embryonic gonads

value: Phf7[DN18]; vasGFP


title: Phf7 mutant replicate 2


title: Single Dorsal root ganglion neuron_SNI 14d [N122]

description:
N122
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

tag: treatment

value: SNI 14d

value: Single Dorsal root ganglion neuron


title: Single Dorsal root ganglion neuron_SNI 14d [N123]

description:
N123
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 24: D3 0.03 8181


title: Single Dorsal root ganglion neuron_SNI 14d [N121]

description:
N121
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 23: D3 0.3 8181


title: Single Dorsal root ganglion neuron_SNI 14d [N119]

description:
N119
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N126]

description:
N126
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 22: D3 10 8181


title: Maternal_blood_TD_101

city: Davis

first: Janine

last: LaSalle

address: Medical Microbiology and Immunology

institute: UC Davis

description: nutrient metabolites: Y: yes, we have metabolites data for that sample; N: no, we don't have metabolites data for that sample.  Nutrient metabolites information is included in the paper supplementary tables. There are multiple metabolites and different samples have different metabolites, as detailed in the paper methods and supplementary tables.

hyb_protocol: Biotin-labeled cRNA was hybridized to Human Gene 2.0 array (Affymetrix) at the John's Hopkins Sequencing and Microarray core using the manufacturer's protocol

scan_protocol: Hybridized arrays were scanned at the John's Hopkins Sequencing and Microarray core. The manufacturer’s protocol was followed for all washing, staining and scanning procedures.

data_processing: Robust Multi-Chip Average (RMA) in oligo R package was used for data normalization using Affymetrix CEL files. For the quality control, we used oligo and ArrayQualityMetrics R packages. No samples were identified as outliers with principal component analysis, Kolmogorov-Smirnov test and distances to other arrays analysis. Probes were mapped to the transcripts and genes using pd.hugene.2.0.st R package on 36,459 probes.

label_protocol: Total RNA with RIN > 7 was converted cDNA and in vitro transcribed to biotin-labeled cRNA at the John's Hopkins Sequencing and Microarray core using the manufacturer's protocol (Affymetrix)

extract_protocol: Maternal peripheral blood was collected at study visits during all three trimesters of pregnancy in PAXgene Blood RNA tube with the RNA stabilization reagent (BD Biosciences) and stored frozen at -80°C. RNA was isolated using the PAXgene Blood RNA Kit (Qiagen) according to the manufacturer’s instructions. Total RNA was converted to cDNA and biotin labeled. Expression was measured using Human Gene 2.0 Affymetrix microarray chips by the John Hopkins Sequencing and Microarray core following by washing, staining and scanning procedures based on manufacture’s protocol.

tag: diagnosis

value: TD

tag: Sex

value: F

tag: study

value: MARBLES

tag: array batch

tag: nutrient metabolites

value: Y


title: Single Dorsal root ganglion neuron_SNI 14d [N117]

description:
N117
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

tag: strain

tag: tissue/cell type

tag: technology


title: Maternal_blood_TD_100

value: N


title: Maternal_blood_TD_102


title: Maternal_blood_TD_103

value: M


title: Maternal_blood_TD_99


title: Single Dorsal root ganglion neuron_SNI 14d [N115]

description:
N115
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Maternal_blood_TD_96


title: 25: D3 0 8181

tag: donor

tag: dose (um)

tag: hbv

tag: day


title: 20: D1 0.03 4239


title: Maternal_blood_TD_95


title: Maternal_blood_TD_98


title: 19: D1 0.3 4239


title: Maternal_blood_TD_93


title: 21: D1 0 4239


title: Single Dorsal root ganglion neuron_SNI 14d [N113]

description:
N113
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N112]

description:
N112
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 18: D1 10 4239


title: Single Dorsal root ganglion neuron_SNI 14d [N114]

description:
N114
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 17: D1 0 8130


title: Maternal_blood_TD_92


title: Maternal_blood_TD_90


title: 16: D1 0.03 8130


title: Maternal_blood_TD_88


title: 15: D1 0.3 8130


title: Single Dorsal root ganglion neuron_SNI 14d [N111]

description:
N111
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N109]

description:
N109
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Maternal_blood_TD_97


title: Maternal_blood_TD_89


title: Maternal_blood_TD_91


title: Maternal_blood_TD_94


title: Maternal_blood_TD_86


title: Maternal_blood_TD_87


title: Single Dorsal root ganglion neuron_SNI 14d [N108]

description:
N108
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Maternal_blood_TD_85


title: 14: D1 10 8130


title: Single Dorsal root ganglion neuron_SNI 14d [N105]

description:
N105
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Maternal_blood_TD_84


title: Maternal_blood_TD_82


title: Maternal_blood_TD_81


title: Maternal_blood_TD_79


title: Maternal_blood_TD_80


title: Maternal_blood_TD_78


title: Maternal_blood_TD_77


title: 13: D1 0 8181


title: Single Dorsal root ganglion neuron_SNI 14d [N104]

description:
N104
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N103]

description:
N103
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [N102]

description:
N102
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 11: D1 0.3 8181


title: Single Dorsal root ganglion neuron_SNI 14d [N101]

description:
N101
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 10: D1 10 8181


title: 9: D0 4239


title: Maternal_blood_TD_75


title: Maternal_blood_TD_83


title: 12: D1 0.03 8181


title: Maternal_blood_TD_76


title: Maternal_blood_TD_71


title: Maternal_blood_TD_69


title: Maternal_blood_TD_67


title: 6: D0 HBV- 4239


title: 7: D0 8181


title: Maternal_blood_TD_68


title: Maternal_blood_TD_73


title: Maternal_blood_TD_74


title: 5: D0 HBV- 8130


title: P21

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

source_name: Septic shock W/O cirrhosis

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol:
Whole blood from 7 patients with stable cirrhosis, 7 patients with acutely decompensated cirrhosis without ACLF and 17 patients with ACLF (8 related to sepsis and 9 unrelated to sepsis) was sampled into tempus tubes (Applied biosystems, Ambion). The same method was used to sample whole blood from 7 healthy subjects and from 8 patients with septic shock without cirrhosis that were used as comparators.RNA was then extracted using the PerfectPure RNA blood kit (3 PRIME) according to manufactuter instructions.
RNA was then extracted using the PerfectPure RNA blood kit (3 PRIME) according to manufactuter instructions: lysis, Dnase, column purification and elution

tag: cell type

value: whole blood

tag: stage of cirrhosis

value: No

tag: sepsis

value: Yes

tag: disease state

value: Patient with a septic shock but without cirrhosis


title: Maternal_blood_TD_66


title: Maternal_blood_TD_70


title: 8: D0 8130


title: 49: D13 0 8130


title: 4: D0 HBV- 8181


title: Maternal_blood_TD_65


title: P18


title: Maternal_blood_TD_62


title: Maternal_blood_TD_64


title: Maternal_blood_TD_61


title: Maternal_blood_TD_60


title: Maternal_blood_TD_59


title: Maternal_blood_TD_58


title: ST_U937_PBS-3

data_processing:
To generate a genome annotation, we combined the UCSC knownGen, Ensembl 71, and MISO v.2.0 annotations.
We mapped all reads to the merged genome annotation and obtained gene expression estimates using RSEM v.1.2.4 modified to invoke Bowtie v.1.0.0 through the ‘-v 2’ option.
We normalized all expression estimates via the trimmed mean of M values (TMM) method.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with read counts over all genes.

source_name: U937 cell line

growth_protocol: The indicated cells were cultured at 37°C in 5% CO2 humidified atmosphere in RPMI medium supplemented with 10% fetal bovine serum (FBS), antibiotics (100 U/mL penicillin, 100 mg/mL streptomycin), and L-glutamine (1%).

extract_protocol:
RNA was isolated by TRIzol extraction
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

treatment_protocol: The indicated cells were resuspended to a concentration of 15 million cells/5 mL of working media. Peptide suspensions were made in PBS of CREBMIM and CRYBMIM peptides from lyophilized product. Peptide suspensions or PBS control were added directly to working media to a final concentration of 20 mM. Cells were incubated with peptide or control for 1h or 4h at 37°C and then resuspended in PBS.

value: leukemia cell

tag: cell line

tag: treatment

value: PBS control

tag: time point


title: P16


title: ST_U937_PBS-2


title: Maternal_blood_TD_72

tag: diagnosis

tag: Sex

tag: study


title: P11


title: Maternal_blood_TD_63

tag: array batch

tag: nutrient metabolites


title: P10


title: P8


title: ST-U937_CRYBMIM-3

value: CRYBMIM peptide


title: Maternal_blood_TD_54


title: Maternal_blood_TD_56


title: P7


title: ST_U937_PBS-1


title: ST_U937_CRYBMIM-2


title: ST_U937_CRYBMIM-1


title: Maternal_blood_TD_53


title: Maternal_blood_TD_57


title: ST_OCIAML3_PBS-2

source_name: OCIAML3 cell line


title: Maternal_blood_TD_55


title: Maternal_blood_TD_49


title: Maternal_blood_TD_52


title: Maternal_blood_TD_47


title: Maternal_blood_TD_50


title: Maternal_blood_TD_48


title: Maternal_blood_TD_43


title: P112

source_name: ACLF unrelated to sepsis

value: ACLF

value: Patient with ACLF that is unrelated to sepsis


title: P109


title: P5


title: P104


title: Maternal_blood_TD_45


title: Maternal_blood_TD_46


title: Maternal_blood_TD_44


title: ST_OCIAML3_PBS-3


title: P32


title: ST_OCIAML3_CRYBMIM-2


title: P30


title: ST_OCIAML3_PBS-1


title: Maternal_blood_TD_42


title: ST_OCIAML3_CRYBMIM-1


title: Maternal_blood_TD_41


title: ST_OCIAML3_CRYBMIM-3


title: Maternal_blood_TD_39


title: ST_Kasumi1_PBS-2

source_name: Kasumi1 cell line


title: P17


title: Maternal_blood_TD_38


title: Maternal_blood_TD_40


title: Maternal_blood_TD_37


title: P15


title: ST_Kasumi1_PBS-1


title: Maternal_blood_TD_36


title: ST_Kasumi1_CRYBMIM-3


title: Maternal_blood_TD_35


title: ST_Kasumi1_PBS-3


title: P9


title: P14


title: P24

source_name: Sepsis-induced ACLF

value: Patient with ACLF that is related to sepsis


title: ST_Kasumi1_CRYBMIM-2


title: 414C2, day 56 of induction, biological replicate 2

city: Kyoto

first: Junya

last: Toguchida

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Application

description: 414C2 iPSC line, re-analysis of GSM4477821

hyb_protocol: Samples were hybridized to the arrays with the GeneChip Hybridization Wash and Stain Kit. The arrays were washed and stained on the GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned with the GeneChip Scanner 3000 7G.

data_processing: The GeneSpring GX 14.9 software was used for analysis. Data were normalized using the RMA-16 algorithm and the baseline was adjusted to the median of all samples.

source_name: 414C2 iPSC-derived cartilage pellet on day 56 of induction

label_protocol: Samples were fragmented and labeled with the GeneChip WT Terminal Labeling and Controls kit.

growth_protocol: iPSCs were differentiated into hypertrophic chondrocytes in 3D culture

extract_protocol: Cartilage pellets were frozen in liquid nitrogen and powderized before RNA extraction with the QIAGEN RNeasy Micro Kit. 50-100 ng of total RNA was used for reverse transcription and amplification with the Ambion WT Expression Kit.

tag: tissue

value: cartilage

tag: genotype

value: wild type


title: 414C2, day 56 of induction, biological replicate 3

description: 414C2 iPSC line, re-analysis of GSM4477823


title: 414C2, day 56 of induction, biological replicate 1

description: 414C2 iPSC line, re-analysis of GSM4477822


title: Maternal_blood_TD_34

description: nutrient metabolites: Y: yes, we have metabolites data for that sample; N: no, we don't have metabolites data for that sample.  Nutrient metabolites information is included in the paper supplementary tables. There are multiple metabolites and different samples have different metabolites, as detailed in the paper methods and supplementary tables.

value: TD

value: F


title: P12


title: ST_HL60_PBS-3

source_name: HL60 cell line


title: 414C2, day 28 of induction, biological replicate 2

description: 414C2 iPSC line

source_name: 414C2 iPSC-derived cartilage pellet on day 28 of induction


title: ST_Kasumi1_CRYBMIM-1


title: 414C2, day 28 of induction, biological replicate 3

description: 414C2 iPSC line


title: Maternal_blood_TD_32

value: MARBLES


title: Maternal_blood_TD_31

value: Y


title: ST_HL60_PBS-2


title: P4


title: 414C2, day 28 of induction, biological replicate 1

description: 414C2 iPSC line


title: ST_HL60_PBS-1


title: P6


title: ST_HL60_CRYBMIM-3


title: 414C2, day -1 sclerotome 2, biological replicate 2

description: 414C2 iPSC line

source_name: 414C2 iPSC-derived sclerotome on day -1 of induction

value: sclerotome


title: Maternal_blood_TD_29

value: M


title: 414C2, day -1 sclerotome 3, biological replicate 3

description: 414C2 iPSC line


title: P2

value: whole blood


title: P3

value: Yes


title: P1


title: P19


title: P117

source_name: Acute decompensation

value: Acute decompensation

value: No

value: Patient with acutely decompensated cirrhosis


title: ST_HL60_CRYBMIM-1

value: leukemia cell

value: CRYBMIM peptide


title: ST_HL60_CRYBMIM-2


title: 414C2, day -1 sclerotome 1, biological replicate 1

description: 414C2 iPSC line


title: Maternal_blood_TD_28


title: RNA_MV411_PBS_4C

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly hg19 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with un-normalized read counts over all genes.

source_name: MV411 cell line

treatment_protocol: MV411 cells were resuspended to a concentration of 15 million cells/5 mL of working media. Peptide suspensions were made in PBS of CREBMIM and CRYBMIM peptides from lyophilized product. Peptide suspensions or PBS control were added directly to working media to a final concentration of 20 mM. Cells were incubated with peptide or control for 1h or 4h at 37°C and then resuspended in PBS.

value: PBS control


title: LS049B

city: Munich

first: Ulrich

middle: M

last: Zissler

address: Biedersteiner Str. 29

department: Center of Allergy & Environment (ZAUM)

institute: Technical University of Munich & Helmholtz Center Munich

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Agilent.SingleColor.28004 microarray, Software GeneSpring 14.5; Threshold: 1.0, Logbase: 2; Normalization: Quantile; Baseline Transformation: None; Filtered on Expression (20.0-100.0); Filtered on Flags (Detected, Not Detected); T test unpaired , P<=:0.05, FC>=1.5

source_name: induced sputum

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 17 ng RNA using the One-Color Agilent Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, GER). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Induced sputum samples were processed and isolated cells were directly transferred into RNAcell protect reagent (Qiagen) and stored at -80°C until RNA extraction. Total RNA was extracted using RNeasy Mini Kit (Cat.-No. 74104, Qiagen, Hilden, Germany) with on-column DNase digestion (Cat.-No. 79254, DNase-Free DNase Set, Qiagen) for avoiding DNA contaminations {Zissler, 2016 #317}. RNA quantification was performed by ultraviolet–visible spectrophotometry (Nanodrop Technologies, Wilmington, DE, USA), for assessment of the RNA integrity by the RNA 6000 Nano Chip Kit with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

value: allergy

tag: season

value: off season

tag: ait treatment

value: SCIT


title: Maternal_blood_TD_26

value: TD


title: Maternal_blood_TD_27

value: F

value: N


title: Maternal_blood_TD_25

value: MARBLES

value: Y


title: RNA_MV411_PBS_4B


title: Maternal_blood_TD_24

value: M


title: Maternal_blood_TD_23


title: LS042B


title: P116

value: whole blood


title: P107


title: LS038B


title: RNA_MV411_PBS_4A


title: P103


title: RNA_MV411_PBS_1C


title: Maternal_blood_TD_51


title: LS037B


title: LS042

value: in season


title: LS049


title: P105

value: Acute decompensation


title: Maternal_blood_TD_22


title: RNA_MV411_PBS_1B


title: RNA_MV411_PBS_1A


title: LS038


title: RNA_MV411_CRYBMIM_4C


title: LS037


title: P25

value: No

value: Patient with stable cirrhosis


title: Maternal_blood_TD_21


title: Maternal_blood_TD_19


title: RNA_MV411_CRYBMIM_4B

value: leukemia cell


title: P29

value: Patient with acutely decompensated cirrhosis


title: Maternal_blood_TD_17


title: RNA_MV411_CRYBMIM_4A

value: CRYBMIM peptide


title: Maternal_blood_TD_20


title: LS017B

value: healthy

value: control


title: LS043B

value: off season


title: LS040B


title: P111

source_name: Stable decompensated cirrhosis

value: Stable decompensated cirrhosis


title: Maternal_blood_TD_16

value: TD


title: P101


title: Maternal_blood_TD_18

value: N


title: LS025B


title: P28


title: Maternal_blood_TD_14

value: F

value: MARBLES


title: RNA_MV411_CRYBMIM_1B


title: Maternal_blood_TD_15

value: Y


title: Maternal_blood_TD_33


title: LS017


title: RNA_MV411_CRYBMIM_1A


title: Maternal_blood_TD_30


title: P27

value: whole blood


title: P31


title: RNA_MV411_CRYBMIM_1C


title: LS043

value: in season


title: T8

source_name: Healthy subject

value: Healthy control


title: Maternal_blood_TD_13


title: RNA_MV411_CREBMIM_4B

value: CREBMIM peptide


title: Maternal_blood_TD_12

value: M


title: RNA_MV411_CREBMIM_4C

value: leukemia cell


title: Maternal_blood_TD_11


title: LS040


title: RNA_MV411_CREBMIM_4A


title: LS025


title: P26

value: No

value: Patient with stable cirrhosis


title: T7


title: RNA_MV411_CREBMIM_1C


title: RNA_MV411_CREBMIM_1B


title: LS050B

value: healthy


title: Maternal_blood_TD_9


title: Maternal_blood_TD_10


title: RNA_MV411_CREBMIM_1A


title: T4


title: T6


title: Cranial tissue, E9.5 KO (ATAC-seq)

city: Houston

first: Rachel

last: Keuls

state: TX

address: One Baylor Plaza, Alkek N1020

institute: Baylor College of Medicine

data_processing:
cell ranger align
Seurat
Signac
Supplementary_files_format_and_content: E9.5_KOvWT.rds (R object with both genotypes and combined mRNA and ATAC data overlaid)

source_name: Cranial tissue

extract_protocol:
10x ATAC v1
10x ATAC v1 single index

tag: age

value: miR-302 KO

value: cranial region


title: T5

tag: cell type


title: LS036B

value: allergy+asthma

value: off season

value: control


title: Cranial tissue, E9.5 WT (ATAC-seq)

value: WT


title: m34-unbound-input

city: Philadelphia

first: yinfei

last: tan

state: PA

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

data_processing:
fastq files was generated at the basespace cloud
fastq files was aligned to human genome using Bowtiew to generate bam files
MACS2 Peak calling
fetches nearest gene around the peaks
annotate genes
Genome_build: GRCh37
Supplementary_files_format_and_content: MACS2-called-peaks
Supplementary_files_format_and_content: nearest-genes-of-peaks
Supplementary_files_format_and_content: unique-gene-symbols

source_name: human mesothelioma cell line m34

growth_protocol: Human mesothelioma cell lines were maintained in RPMI with 10% FBS.

extract_protocol:
Cells were fixed with formadihyde, sonicated to 100-1000bp, and immunoprecipitated with active motif MBD2b/MBD3L1 recombinant proteins.
Illumina DNA library was prepared with NEB DNA ultra II kit

value: human mesothelioma cell line


title: ATACseq-iEpiSC-rp2

city: Guangzhou

first: dongwei

last: Li

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

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

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 with options --very-sensitive
Data were filterd using samtools -q  35 and awk '!x[$0]++'
peaks were called using run_dfilter15 with options -non-zero -bs=100 -ks=20 -lpval=3 -refine -std=5
Genome_build: mm10
Supplementary_files_format_and_content: wig file were generated with genomeCoverageBed and bedGraphToBigWig. Scores represent the number of fragments overlapping each genomic position.

source_name: induced EpiSC

growth_protocol: ESCs cells cells were cultured in N2B27+2i+LIF medium, EpiSCs were maintained in FN medium which comprised F12 / Neurobasal (1:1) with N2, B27, NEAA, GlutaMAX, BSA, 100 mM 2-mercaptoethanol, 20 ng/ml ActivinA and 20 ng/ml bFGF

extract_protocol:
A total of 50,000 cells were washed once with cold PBS and resuspended in 50ul lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free H2O) of Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina), and incubated at 37°C for 30min. DNA was isolated using a MinElute Kit (Qiagen).
ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described5, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with a Qiaquick PCR (Qiagen) column. Library concentration was measured using a KAPA Library Quantification kits (KK4824) according to the manufacturers instructions. Library integrity was checked by gel electrophoresis. Finally, the ATAC library was sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) (FC-404-2002, Illumina) according to the manufacturers instructions.

treatment_protocol: ESCs were digested to single cells and replanted in serum coated 6-well plate at a density of 1×104 per well. After 8 hours, the ESCs culture medium was removed, and cells were washed with DPBS twice carefully. FN medium plus XAV939 (2 μM) and IWR-1 (2.5 μM) was used to converse ESCs to iEpiSCs. FN+X/I medium were changed everyday, and EpiSC-like colonies were emerged at 4-5 days. iEpiSCs were cultured as EpiSCs

value: induced EpiSC


title: Maternal_blood_TD_8

value: TD

value: F

value: MARBLES

value: Y


title: LS010B


title: m34-MBD-ChIP


title: LS053B


title: Maternal_blood_TD_6

value: M


title: Maternal_blood_TD_7


title: LS053

value: in season


title: ATACseq-iEpiSC-rp1


title: Maternal_blood_TD_5


title: LS050


title: T2

value: whole blood

tag: stage of cirrhosis

value: No

value: Healthy control


title: m29-unbound-input

source_name: human mesothelioma cell line m29


title: m29-MBD-ChIP


title: ATACseq-iEpiSC-JunKO-rp2


title: ATACseq-iEpiSC-JunKO-rp1


title: T3

tag: sepsis


title: Maternal_blood_TD_4


title: LS036

tag: disease state


title: Maternal_blood_TD_3


title: LS010


title: m20-unbound-input

source_name: human mesothelioma cell line m20

tag: cell line


title: ATACseq-ESC-TO-Epi-D5-rp2

source_name: naïve to prime transition cells

value: naive to prime transition cells


title: LS046B

value: allergy


title: m12-unbound-input

source_name: human mesothelioma cell line m12


title: LS020B


title: LS019B


title: ATACseq-ESC-TO-Epi-D5-rp1


title: ATACseq-ESC-TO-Epi-D4-rp2


title: m12-MBD-ChIP


title: ATACseq-ESC-TO-Epi-D4-rp1


title: Maternal_blood_TD_2


title: Maternal_blood_TD_1


title: HeLa DRIP WT LS2B rep2

first: Frederic

last: Chedin

address: 1 Shields Avenue

department: MCB

data_processing:
Library strategy: DRIP-seq
Raw fastq reads were trimmed with fastq-mcf v2.4.4 and mapped with STAR v2.7. Mapped reads were duplicate-removed using samtools.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30)

source_name: HeLa cells

extract_protocol:
Standard illumina protocol.
DRIP-seq and DRIPc-seq were performed as described in Sanz et al, 2016. Briefly, for DRIP-seq, genomic DNA was extracted from HeLa and K562 cell lines and fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI. Monoclonal S9.6 antibody was used to enrich for RNA/DNA hybrid and RNA was removed using RNase H before being subjected to standard Illumina library construction protocol. For DRIPc-seq, enriched R-loop fragments were further subjected to DNase I treatment and the remaining RNA was subjected to second strand synthesis using dUTP instead of dTTP for strand-specific library construction. Illumina TruSeq Single adapter was ligated and the cDNA and amplified as per standard Illumina TruSeq Single end protocol.

treatment_protocol: DRIPc-seq samples were treated with or without RNase H

value: HeLa

value: cervical cancer cells

tag: treatment


title: ATACseq-ESC-TO-Epi-D3-rp3


title: m20-MBD-ChIP


title: ATACseq-ESC-TO-Epi-D3-rp2


title: Maternal_blood_NonTD_55

value: NonTD


title: K562 DRIPc WT LS42B

data_processing:
Library strategy: DRIPc-seq
Raw fastq reads were trimmed with fastq-mcf v2.4.4 and mapped with STAR v2.7. Mapped reads were duplicate-removed using samtools.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30)

source_name: K562 cells

value: bone marrow CML cells

value: control


title: HeLa DRIP WT LS2A rep1


title: Maternal_blood_NonTD_54


title: LS046


title: HeLa DRIP RNaseH LS2C

value: RNase H


title: Maternal_blood_NonTD_53


title: Maternal_blood_NonTD_52


title: LS020


title: ATACseq-ESC-TO-Epi-D2-rp3


title: ATACseq-ESC-TO-Epi-D2-rp4


title: Maternal_blood_NonTD_51


title: ATACseq-ESC-TO-Epi-D1-rp4


title: LS019


title: Maternal_blood_NonTD_50


title: LS018


title: Maternal_blood_NonTD_49


title: LS059B

value: allergy+asthma

value: off season

value: SCIT


title: LS041B


title: Maternal_blood_NonTD_47

value: MARBLES

value: Y


title: P118

value: Stable decompensated cirrhosis

value: Patient with stable cirrhosis


title: ATACseq-ESC-TO-Epi-D1-rp3


title: AGS/shGFP

city: Chia-Yi

first: Yu Ming

last: Chuang

address: 168 University Road,Min Hsiung

department: Department of Biomedical Science

institute: National Chung Cheng University

description: AGS cell infected with control vector by lentivirus.

data_processing:
Illumina HiSeq 2500 used for basecalling.
Alignment followed the standard pipeline
BAM files were analyzed according to standard PrEMeR-CG workflow
BAM files were also analyzed by EaSeq
Genome_build: hg19
Supplementary_files_format_and_content: Processed data was selected by 1.5 fold hypomethylation and included mean and sum about CpG probable methylation (cpm).

source_name: MBD enriched DNA from AGS/shGFP cell line

growth_protocol: AGS cells were maintained in RPMI-1640 medium supplemented with 10% FBS. Cells were incubated at 37C under a humidified atmosphere containing 5% CO2

extract_protocol: DNA was harvested by Genomic DNA Purification Kit, which followed with sonication and MBD-Biotin Protein enrichment.

treatment_protocol: AGS cells were either infected with lentivirus containing pLKO.1-puro-shGFP as control or pLKO.1-puro-shSTAT3 targeting the endogenous STAT3. Stable clones were selected using medium containing 2ug/ml Puromycin.

value: gastric cancer cell line

value: AGS


title: AGS/shSTAT3

description: AGS cell infected with knockdown STAT3 vector by lentivirus.

source_name: MBD enriched DNA from AGS/shSTAT3 cell line


title: RNA-seq_D5_MDDCs_R848

city: Dallas

first: Edward

last: Wakeland

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

data_processing:
Illumina bcl2fastq2.17.04 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, and mapped to hg19 whole genome using CLC-Bio Genomics Workbench
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC-Bio Genomics Workbench.
Genome_build: hg19

source_name: Human monocyte-derived dendritic cells

growth_protocol: Human monocytes were cultured in RPMI-1640 medium with 10% FBS, 2mM L-glutamine, 10mM HEPES, 1mM sodium pyruvate, 100U/ml penicillin, and 100 µg/mL streptomycin. To differentiate monocytes into macrophages or dendritic cells, recombinant human M-CSF (50ng/mL) or recombinant human GM-CSF (100ng/mL) and recombinant human IL-4 (50ng/mL) were used, respectively. The culture medium which contained fresh recombinant human M-CSF or recombinant human GM-CSF and recombinant human IL-4 was replaced every 2 days.

extract_protocol:
RNA was extracted using TRIzol reagent and RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.
RNA-seq libraries were prepared with the Illumina TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: Monocytes, MDMs or MDDCs were stimulated with Pam3CSK4 (1 μg/ml), LPS (10 ng/ml), R837 (10 μg/ml) or R848 (10 μg/ml) for 18 hours.

value: Human monocyte-derived dendritic cells

tag: donor

value: Donor 5


title: RNA-seq_D5_MDDCs_LPS


title: ATACseq-EpiSC-JunKO17-rp1

source_name: EpiSC

value: EpiSC


title: ATACseq-EpiSC-JunKO17-rp2


title: RNA-seq_D5_MDDCs_Pam3CSK4


title: ATACseq-EpiSC-JunKO16-rp2


title: LS018B

value: allergy


title: RNA-seq_D5_MDDCs_unstimulated

value: NT


title: Maternal_blood_NonTD_48

tag: diagnosis

value: NonTD

value: M


title: Maternal_blood_NonTD_45

tag: Sex


title: ATACseq-EpiSC-JunKO16-rp1


title: LS011B


title: LS059

value: in season


title: RNA-seq_D5_MDMs_R848

source_name: Human monocyte-derived macrophages

value: Human monocyte-derived macrophages


title: Maternal_blood_NonTD_44

tag: study


title: LS058B

source_name: induced sputum

value: allergy+asthma

value: off season


title: Nuclear small RNAs

city: shang hai

first: Qian

last: Zhang

address: xiangyin road 800

institute: Second military medical university

description: small RNA

data_processing:
Basecalls performed using CASAVA
small RNA-seq reads were aligned to the mm10 genome using Short Oligonucleotide Alignment Program (SOAP) .
RNAs were calculated as the log2 ratio using the normalized TPM (transcripts per million reads) value that was taken as abundance of each sRNA for a rigorous significance test to determine the expression difference of each sRNA from nuclear and cytoplasmic fractions.
The superior nucleus-localized sRNAs were picked out according to the criteria that abundance of each sRNA was over 20 and x>10y (x: abundance of sRNA from nuclear fraction; y: abundance of sRNAs from cytoplasm fraction)
Genome_build: mm10
Supplementary_files_format_and_content: expression text files

source_name: dendritic cells

growth_protocol: Bone marrow cells were cultured in RPMI 1640 (10% FBS) with GM-CSF+IL-4 for 7 days.

extract_protocol:
BMDC were swelled in RSB buffer containing Tris-HCl, NaCl, NP40 and MgCl2, and centrifuged. RNAs from cytoplasmic faction and pellet containing the nucleus were extarcted using mirVana™ miRNA Isolation Kit (Ambion, Waltham, MA, USA).
Libraries were prepared according to illumina small RNA librarying protocol.

treatment_protocol: LPS stimulation

tag: strain

tag: cell types

value: Bone marrow-derived dendritic cells

value: LPS


title: LS041

value: SCIT


title: Maternal_blood_NonTD_43

value: MARBLES

tag: array batch

tag: nutrient metabolites

value: Y


title: Cytoplasmic small RNAs

description: small RNA


title: LS058

tag: season


title: Maternal_blood_NonTD_46

value: F


title: cDC2 zfp366 KO CUT&Tag replicate 1

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Library strategy: CUT&Tag
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using Rsubread::align.
BAM files were sorted with Sambamba v0.6.6 (Tarasov et al., 2015). Duplicate reads were removed and reads were filtered to retain reads with template length between 10 and 300 bp.
Biological replicates were combined. For each cDC type, the HOMER pipeline used to call peaks in the wildtype samples with the corresponding knockout samples as the input.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: HOMER peak files, one for cDC1s and one for cDC2s.

source_name: Splenic conventional dendritic cells 2

extract_protocol:
Ampure XP beads
As described by Mezger et al., High-throughput chromatin accessibility profiling at single-cell resolution, Nature Communications 9, 3647 (2018).

treatment_protocol: cDC1/cDC2 isolated from the spleen using collagenase/dnase.

tag: genotype

tag: gender

value: Female

tag: biological replicates (mouse pool)


title: RNA-seq_D5_MDMs_R837

tag: cell type

value: Donor 5


title: cDC2 zfp366 KO CUT&Tag replicate 2


title: RNA-seq_D5_MDMs_LPS


title: cDC1 zfp366 KO CUT&Tag replicate 2

source_name: Splenic conventional dendritic cells 1


title: w20-hsh-day10-replicate-1

city: Boston

first: Satya

last: Kota

state: MA

address: 188 Longwood Ave

institute: Harvard School of Dental Medicine

description:
TRA00078371
78371L001

data_processing:
NOT PROVIDED; REQUESTED
Supplementary_files_format_and_content: gene_exp.diff is the resulting differential expression results(1.5 fold) for control shRNA vs. Elavl1 shRNA. This file is output by cuffdiff. A q-value cutoff of 0.05 was used to determine differentially expressed genes.

extract_protocol: Qiagen Rneasy

treatment_protocol: short hairpin RNA knockdown W20 MSCs were cultured in osteogenic differentiation medium for 10 days.

tag: cell line/type

value: W20 cells in osteogenic differentiation medium

tag: genotype/variation

value: Elavl1 shRNA


title: Maternal_blood_NonTD_42


title: w20-hsh-day10-replicate-2

description:
TRA00078372
78372L001


title: RNA-seq_D5_MDMs_Pam3CSK4


title: w20-lucsh-day10-replicate-2

description:
TRA00078370
78370L001

value: Luciferase shRNA


title: RNA-seq_D5_MDMs_unstimulated

value: NT


title: cDC1 zfp366 KO CUT&Tag replicate 1


title: cDC2 zfp366 WT CUT&Tag replicate 1


title: Maternal_blood_NonTD_41

value: NonTD


title: RNA-seq_D5_mono_R848

source_name: Human monocytes

value: Human monocytes


title: Maternal_blood_NonTD_40


title: Maternal_blood_NonTD_38

value: M


title: Maternal_blood_NonTD_39


title: LS011

tag: disease state

value: allergy+asthma

value: in season

tag: ait treatment


title: UND_VEH_C

city: Stuttgart

first: Cristiana

last: Lungu

state: BW

address: Allmandring 31

department: Institute of Cell Biology and Immunology

institute: University of Stuttgart

data_processing:
The FASTQ  files were mapped to the mouse mm9 genome using TopHat Gapped-read mapper for RNA-seq data with very-sensitive BOWTIE2 settings. The differential analysis was performed by using Cuffdiff with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: The provided mRNA-Seq analysis files present the differentially regulated genes between the indicated conditions in excel file format.

growth_protocol: Mouse calvarial osteoblasts were maintained in aMEM complete media with 10% FBS and 1% P/S

extract_protocol:
The total cell RNA was isolated with standard TRIzol extraction protocol
4 µg of total cell RNA was used for library preparation with NEXTflex Rapid Directional mRNA-Seq from Bioo Scientific and 500ng of total cell RNA was used for library preparation with TruSeq RNA Smaple Prep Kit-v2 following manufacturers' protocols.

treatment_protocol: For induction of RNF40 knockout, the cells were treated with 250nM of 4-hydroxytamoxifen or equivalent volume of vehicle (ethanol). For differentiation, cells were treated with 5 mM β-glycerophosphate and 0.2 mM ascorbate. For vitamin D studies, cells were treated for 7 days with 10nM calcitriol or equal volume of vehicle (DMSO).

tag: strain background

value: Mutant RNF40RosaCreERT2 mouse

value: Primary Calvarial Osteoblasts

tag: treatment

value: for 7 d with vehicle(ethanol)

tag: library prep kit

value: NEXTflex Rapid Directional mRNA-Seq Kit, Bioo Scientific


title: cDC1 zfp366 WT CUT&Tag replicate 3


title: cDC1 zfp366 WT CUT&Tag  replicate 2


title: UND_VEH_A


title: cDC1 zfp366 WT CUT&Tag replicate 1


title: RNA-seq_D5_mono_R837

tag: donor


title: RNA-seq_D5_mono_LPS


title: RNA-seq_D5_mono_Pam3CSK4


title: UND_TAM_C

value: for 7 d with 250nm 4-hydroxytamoxifen


title: cDC2 WT replicate 3

description: 2789 cDC2

data_processing:
Sequencing was undertaken on an Illumina NextSeq 500 to produce 86bp paired-end reads.
Read-pairs were aligned to the GRCm38/mm10 build of the Mus musculus genome using Rsubread::align.
Genewise counts were obtained using featureCounts with Rsubread's inbuilt mm10 annotation.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text giving Entrez Gene IDs, gene length (number of bases in union of all exons) and the number of read-pairs assigned to that read.

extract_protocol:
RNeasy Plus Mini kit (Qiagen).
TruSeq RNA Sample preparation kit (Illumina)

treatment_protocol: ex-vivo isolated splenic DCs (tissue digested with collagenase and DNAse)

tag: strain

tag: biological replicate (mouse pool)


title: Maternal_blood_NonTD_36

data_processing: Robust Multi-Chip Average (RMA) in oligo R package was used for data normalization using Affymetrix CEL files. For the quality control, we used oligo and ArrayQualityMetrics R packages. No samples were identified as outliers with principal component analysis, Kolmogorov-Smirnov test and distances to other arrays analysis. Probes were mapped to the transcripts and genes using pd.hugene.2.0.st R package on 36,459 probes.

tag: diagnosis

tag: Sex

tag: study

value: MARBLES

tag: array batch

value: Y


title: UND_TAM_B


title: RNA-seq_D5_mono_unstimulated

value: Donor 5


title: cDC1 WT replicate 3

description: 2789 cDC1

tag: genotype

tag: gender

value: Female


title: Maternal_blood_NonTD_37

tag: nutrient metabolites


title: w20-lucsh-day10-replicate-1

description:
TRA00078369
78369L001

tag: cell line/type

value: W20 cells in osteogenic differentiation medium


title: Maternal_blood_NonTD_34

value: F


title: Maternal_blood_NonTD_35


title: cDC2 WT replicate 2

description: 2456 cDC2


title: UND_TAM_A

tag: genotype/variation

tag: cell type


title: RNA-seq_D4_MDDCs_LPS

value: Human monocyte-derived dendritic cells

value: Donor 4


title: DIF_VEH_C

value: for 7 d with vehicle(ethanol) and then differentiated for additional 7 days with addition of 5 mM β-glycerophosphate and 0.2 mM ascorbate.


title: cDC1 WT replicate 2

description: 2456 cDC1


title: UND_VEH_B


title: Maternal_blood_NonTD_32

value: NonTD

value: M


title: RNA-seq_D4_MDDCs_Pam3CSK4


title: cDC2 WT replicate 1

description: 2012 cDC2


title: DIF_VEH_B


title: DIF_VEH_A


title: cDC1 WT replicate 1

description: 2012 cDC1


title: RNA-seq_D4_MDDCs_unstimulated

value: NT


title: DIF_TAM_C

value: Mutant RNF40RosaCreERT2 mouse

value: for 7 d with 250nm 4-hydroxytamoxifen, and then differentiated for additional 7 days with addition of 5 mM β-glycerophosphate and 0.2 mM ascorbate.


title: RNA-seq_D4_MDMs_R837

value: Human monocyte-derived macrophages


title: cDC2 zfp366 KO replicate 3

description: 1789 cDC2


title: DIF_TAM_B

value: Primary Calvarial Osteoblasts

value: NEXTflex Rapid Directional mRNA-Seq Kit, Bioo Scientific


title: cDC1 zfp366 KO replicate 3

description: 1789 cDC1


title: RNA-seq_D4_MDDCs_R848


title: DIF_TAM_A


title: cDC2 zfp366 KO replicate 2

description: 1456 cDC2


title: VEH_INPUT_B

data_processing:
The FASTQ files were mapped to the mouse reference genome (assembly mm9) using BOWTIE2 with very-sensitive presets in end-to-end mode. The resulting BAM files of ChIPs were deduplicated and MAPQ >2 filtered using Samtools. The corresponding BAM files of the replicates were merged within condition. The merged BAM files were normalized to 1x genomic content (RPGC) using the bamCoverage function of Deeptools.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig represent the normalized reads per genomic content (RPGC) values of ChIP-seq signal

extract_protocol:
The ChIP was performed with 20 min crosslinking in 1 % formaldehyde in PBS. 1µg antibody was used for immunoprecipitation. After reversing the cross-linking, the DNA was isolated by phenol-chloroform-isoamyl extraction.
Libraries were prepared with MicroPlex Library Preparation Kit following the manufacturer's instructions

value: for 7 d with vehicle(ethanol)

tag: molecule subtype

value: Genomic DNA


title: cDC1 zfp366 KO replicate 2

description: 1456 cDC1


title: VEH_INPUT_A

tag: strain background


title: cDC2 zfp366 KO replicate 1

description: 1012 cDC2


title: RNA-seq_D4_MDMs_R848

tag: treatment


title: Maternal_blood_NonTD_33

extract_protocol: Maternal peripheral blood was collected at study visits during all three trimesters of pregnancy in PAXgene Blood RNA tube with the RNA stabilization reagent (BD Biosciences) and stored frozen at -80°C. RNA was isolated using the PAXgene Blood RNA Kit (Qiagen) according to the manufacturer’s instructions. Total RNA was converted to cDNA and biotin labeled. Expression was measured using Human Gene 2.0 Affymetrix microarray chips by the John Hopkins Sequencing and Microarray core following by washing, staining and scanning procedures based on manufacture’s protocol.

value: MARBLES

value: Y


title: RNA-seq_D4_mono_R848

value: Human monocytes


title: DIF_VEH_INPUT_B

value: for 7 d with vehicle(ethanol) and then differentiated for additional 7 days with addition of 5 mM β-glycerophosphate and 0.2 mM ascorbate


title: cDC1 zfp366 KO replicate 1

description: 1012 cDC1

value: Female


title: RNA-seq_D4_MDMs_LPS

value: Donor 4


title: Maternal_blood_NonTD_31


title: Maternal_blood_NonTD_30


title: Ripk1 knocking down

first: Weiyi

last: Peng

state: Texas

address: 3517 Cullen Blvd, Room 3025

institute: University of Houston

data_processing:
The reads were mapped to mouse mm10+gencodevM14 using HiSAT2/2.1.0.
stringtie/1.3.0 were used to calculate the gene expressions. preDE.py was used to count the reads.
edgeR were used to do differential expression analysis
GSEA were applied to logFC ranked genes
Genome_build: mm10+gencodevM14
Supplementary_files_format_and_content: differential expression analysis results in Excel file

source_name: MC38/gp100 murine cancer cell line

extract_protocol:
Cell lines were washed and RNAs were harvested using Qiagen RNeasy Plus kit. 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

treatment_protocol: Non-treament

tag: cell line


title: RNA-seq_D4_mono_LPS

tag: donor


title: RNA-seq_D4_MDMs_Pam3CSK4


title: DIF_TAM_INPUT_B

value: for 7 d with 250nm 4-hydroxytamoxifen, and then differentiated for additional 7 days with addition of 5 mM β-glycerophosphate and 0.2 mM ascorbate


title: DIF_VEH_INPUT_A


title: Maternal_blood_NonTD_29

value: NonTD


title: RNA-seq_D4_MDMs_unstimulated


title: Maternal_blood_NonTD_27

value: M


title: Maternal_blood_NonTD_28

value: N


title: Prmt1 knocking down


title: DIF_TAM_INPUT_A

value: Mutant RNF40RosaCreERT2 mouse


title: RNA-seq_D4_mono_Pam3CSK4


title: DIF_VEH_RNAPII_B

tag: chip antibody

value: RNAPII (N-20), Santa Cruz sc-899

value: ChIP DNA


title: RNA-seq_D4_mono_R837


title: RNA-seq_D4_mono_unstimulated

value: NT


title: DIF_VEH_RNAPII_A

value: Primary Calvarial Osteoblasts


title: Maternal_blood_NonTD_25


title: RNA-seq_D3_MDDCs_LPS

value: Human monocyte-derived dendritic cells

value: Donor 3


title: Maternal_blood_NonTD_24

value: F

value: MARBLES


title: DIF_TAM_RNAPII_B


title: RNA-seq_D3_MDDCs_R848