title: fetal cord tissue, S0196

tag: pre-pregnancy bmi (kg/m^2)


title: WT113M-Wild-type virus rep2

status: Public on Sep 15 2020

type: SRA

city: san francisco

first: Tammy

middle: T

last: Chang

state: ca

address: 513 parnassus

department: surgery

country: USA

institute: UCSF

library_source: transcriptomic

data_processing:
" Real Time Analysis 3 " software was used for base calling.
Using ng_qc software, raw reads were filtered to remove reads that contain adapters or low quality data.  Reads with uncertain nucleotides that reflect more than 10% were filtered out.  In addition, low quality nucleotides (base quality < 20) that made up more than 50% of the reads were removed.
High-quality reads were imported into STAR2.5 for alignment into BAM files.
BAM files were imported into the RNA-Seq analysis pipeline at Novogene Inc. (Davis, CA).
FPKM counts were calculated by HTSeq v0.6.1. Then filtering the 5 types of counts:__no_feature,__ambiguous,__too_low_aQual,__not_aligned,__alignment_not_unique.
Genome_build: mm10
Supplementary_files_format_and_content: Excel table with raw gene counts and FPKM values for every gene in every sample.

molecule: total RNA

organism: Mus musculus

source_name: Fibrotic Liver

growth_protocol: Liver epithelial-specific FAK-deficient mice (FAKfl/fl;Alb-Cre+) and littermate controls (FAKfl/fl;Alb-Cre-) were generated by breeding FVB FAKfl/fl mice (gift from Hilary E. Beggs), in which the FAK gene was flanked by loxP sites, with Alb-Cre mice (gift from Derek LeRoith) that carry the Cre recombinase under the albumin promoter. Hepatocyte-specific FAK deletion was induced by tail vein injection of FAKfl/fl mice with 2.5x1011 AAV8-TBG-Cre (gift from James M. Wilson; Addgene viral prep # 107787-AAV8; http://n2t.net/addgene:107787; RRID:Addgene_107787; Addgene, Watertown, MA).  Littermates controls were injected with 2.5x1011 viral particles/mouse of control viral vector that did not express Cre recombinase (AAV8-TBG-Null).

extract_protocol:
Livers were removed, preserved in RNALater for at least 24 hours, and then RNA was harvested using Qiagen RNeasy Plus mini kit.
Sequencing libraries were generated by NEBNext Ultra directional RNA library prep kit (Illumina, San Diego, CA) with 1 ug of total RNA using standard Illumina protocols.

treatment_protocol: Gradual cholestatic injury was induced by providing mice with 0.1% w/w DDC diet (TestDiet, St. Louis, MO) ad libitum for 4-8 weeks.

tag: tissue

value: Liver

tag: strain

value: FVB

tag: genotype generation

value: AAV8-TBG-Null virus injection

tag: genotype

value: FAKfl/fl;Alb-Cre-


title: H3K4me1_ChIPseq_sonic_pSIN_HEAAUTX

city: New York

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

library_source: genomic

data_processing:
Low quality reads from each FASTQ file were filtered using the ShortRead R Bioconductor package, and filtered FASTQ files were aligned to the hg19 reference genome obtained from UCSC using the Rsubread R Bioconductor package. Bigwig files showing signal coverage over the genome were generated with the GenomicAlignments and rtracklayer R Bioconductor packages. Peak calling was done with macs2 using default settings, with the exception of using the ‘--broad’ flag for the histone H3K27ac, H3K27me3, and H3K4me1 ChIP sequencing experiments.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files normalized to read depth.
Supplementary_files_format_and_content: Peak files are macs2 output peak files.

molecule: genomic DNA

organism: Homo sapiens

source_name: UMUC1 bladder cancer cells

growth_protocol: Cells were maintained in Eagle’s Minimum Essential Medium (MEM, Corning, 10-009-CV), with 10% fetal bovine serum (Sigma-Aldrich) and then were harvested three days after being plated.

extract_protocol:
Three days after plating, UMUC1 cells were harvested from 15 cm tissue culture plates at ~75% confluency. For each histone ChIP, ~ 1x10e7 cells were harvested which yielded ~25 µg of chromatin DNA for immunoprecipitation after going through this protocol. For cell harvest, media was aspirated, cells were washed once in PBS, and then they were fixed directly on the plate with 1% paraformaldehyde in PBS for 5 minutes at room temperature with gentle shaking. Glycine, at a final concentration of 125 mM, was added directly to the plate, and the plate was incubated for 5 minutes at room temperature with gentle shaking. Cells were then put on ice, washed once with cold PBS, scraped off of the plate, and the fixed cells from each cell line (empty vector, wild-type UTX, and HEAA UTX) were pelleted. To get a soluble chromatin extract, cells were then washed in a series of buffers, LB1, LB2, and LB3 as specified below. Each cell line was resuspended in 1 mL LB1 buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x protease inhibitor (Sigma, 11836170001)) and incubated while rotating at 4°C for 10 min. Samples were then centrifuged and resuspended in 1 mL LB2 buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x protease inhibitor), and then were incubated while rotating at 4°C for 10 min. Samples were then centrifuged and resuspended in 1 mL LB3 buffer (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100, 1x protease inhibitor). The lysates were then passed through a 27-gauge needle three times, sonicated for 14 minutes using a Covaris E220 ultra-sonicator at peak power 140 W, duty factor 5%, and cycles per burst 200, then centrifuged for 10 minutes at 20,000xG at 4°C and the supernatants were collected. 20 µL of each lysate was kept to measure DNA concentration, while the remainder was flash frozen and stored at -80°C. The 20 µL sample was added to 200 µL ChIP elution buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA, 200 mM NaCl), incubated overnight at 65°C, treated with RNaseA for 1 hour at 37°C, then Proteinase K for 1 hour at 55°C, and the DNA was purified using the Qiagen PCR purification kit (28104) and lastly quantified with a Nanodrop. These quantifications were then used to dilute 25 µg of chromatin into 1 mL total of LB3, and 5% (50 µL) of each sample was set aside as an input sample. Then 75 µL of protein A Dynabeads that had been washed 3X with PBS + 0.01% Tween-20 and pre-bound with either 10 µL H3K27ac (Active Motif, 39133), 10 µL H3K4me1 (Abcam, ab8895), or 20 µL H3K27me3 (Cell Signaling Tech, 9733) antibody were added to each chromatin lysate and this mixture was incubated rotating overnight at 4°C. The beads were sequentially washed on a magnet two times each with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl pH 8.0), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl pH 8.0), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl pH 8.0) and once with TE buffer (1 mM EDTA; 10 mM Tris-HCl pH 8.0). After the TE wash the beads were spun down (not separated on the magnet), and 210 µL ChIP elution buffer was added to the beads and input samples. The samples were then incubated for 30 min at 65°C on a shaking heat block at 800 rpm. After centrifugation the eluate (supernatant) was reverse cross-linked by incubating overnight at 65°C. The eluate was then treated with RNaseA for 1 hr at 37°C then with Proteinase K for 1 hr at 55°C and DNA was recovered using the Qiagen PCR purification kit. Libraries were then prepared from this DNA using the Illumina TruSeq protocol and sequenced on a NextSeq500 sequencer.
Illumina TruSeq

tag: cell line

tag: cell type

value: bladder cancer

value: stably expressing pSIN-puro H1146A/E1148A-mutant UTX

tag: chip antibody

value: Histone H3 K4 mono-methylation


title: fetal cord tissue, S0195

type: genomic

city: Singapore

first: Jonathan

middle: Yinhao

last: Huang

state: « choose one »

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
GenomeStudio; R/Rstudio
green (RAW_ID_Grn.idat) and red (RAW_ID_Red.idat) channels provided
[value definition]  chip position, DNA extraction, and bisulfite conversion batch, and celltype-adjusted residuals provided

label: Cy3, Cy5

source_name: cord tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Prior to purification, 250 mg crushed cord tissue was enzymatically digested with hyaluronidase (~2.7U in 250 µl PBS) for 30 minutes at 37 C, mixed with 250 µl TNES lysis buffer, transferred to gentleMACS M Tubes (Miltenyi 130-093-236) for 1-minute homogenization followed by overnight treatment with 200 µg Proteinase K at 55 C. QIASymphony SP was used for automated purification of (buffy coat/cord tissue) DNA in combination with QIASymphony DSP DNA Midi Kit (Qiagen #937255) and DNA was bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).

value: fetal cord tissue

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)


title: H3K4me1_ChIPseq_sonic_pSIN_WTUTX

value: stably expressing pSIN-puro wild type UTX


title: fetal cord tissue, S0193


title: FAKWT278-Wild-type bred rep1

source_name: Liver

value: FVB FAKfl/fl mice bred with Alb-Cre mice


title: KO119M-Knock-out  virus rep3

value: AAV8-TBG-Cre virus injection


title: fetal cord tissue, S0192


title: WT112M-Wild-type virus rep1


title: H3K27me3_ChIPseq_sonic_pSIN_HEAAUTX

value: Histone H3 K27 tri-methylation


title: fetal cord tissue, S0199


title: seco.ij5

city: Stanford

first: Michael

middle: Warren

last: Guernsey

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University School of Medicine

description:
seco-fol-ij5_S5
processed data file: p_retropinna_est_counts.txt

data_processing:
Adapter sequences and low quality bases were trimmed using trim_galore v 0.3.3
A transcriptome reference was built using CDS fasta files from the P. retropinna (PRJNA555005) and P. turrubarensis (PRJNA555006 f) genomes using the Kallisto index function (Bray et. al 2016)
Sequences were alligned to transcriptome reference using Kallisto quant function (Bray et. al 2016)
resultin est_counts were used for subsequent analyses
Genome_build: P. retropinna version 1 (PRJNA555005) and P. turrubarensis version 1 (PRJNA555006 f)
Supplementary_files_format_and_content: Tab-delimited file containing est_counts for each gene/transcript

organism: Poeciliopsis retropinna

source_name: Seco_P. retropinna_maternal follicle

extract_protocol:
Pregnant ovaries were dissected in the field (Costa Rica) and placed in RNAlater and kept on ice, follicles were dissected from late stage (I/J Haynes 1995) embryos and pooled in TriZol and kept at -80C until extraction with direct-Zol RNA miniprep kit
NEBNext Ultra II Drirectional RNA Library Prep Kit for Illumina for use with rRNA depleted RNA. Briefly, 100ng of each RNA sample was fragmented for 7 minutes, primed using random primers, then cDNA synthesis was performed, samples were end-prepped, and NEBNext adapters were ligated to the resulting cDNA. All samples were enriched adapter-ligated DNA using a 7-cycle PCR where each sample was given a unique index primer. Samples were then purified with Ampure XP beads, library quality was assessed with Bioanalyzer and Qubit

tag: Stage

value: pregnant, late stage (I/J Haynes 1995)

tag: river

value: Seco

value: maternal follicle


title: seco.ij4

description:
seco-fol-ij4_S2
processed data file: p_retropinna_est_counts.txt


title: fetal cord tissue, S0198


title: fetal cord tissue, S0191


title: KO972M-Knock-out bred rep3

value: FAKfl/fl;Alb-Cre+


title: fetal cord tissue, S0194


title: KO56M-Knock-out bred rep2


title: fetal cord tissue, S0190


title: seco.ij3

description:
seco-fol-ij3_S1
processed data file: p_retropinna_est_counts.txt


title: sucio.ij5

description:
sucio-fol-ij5_S1
processed data file: p_retropinna_est_counts.txt

source_name: Sucio_P. retropinna_maternal follicle

value: Sucio


title: KO87M-Knock-out bred rep1

value: Liver


title: fetal cord tissue, S0189


title: sucio.ij4

description:
sucio-fol-ij4_S2
processed data file: p_retropinna_est_counts.txt


title: WT973M-Wild-type bred rep3

value: FVB


title: WT58M-Wild-type bred rep2


title: H3K27me3_ChIPseq_sonic_pSIN_WTUTX


title: sucio.ij3

description:
sucio-fol-ij3_S7
processed data file: p_retropinna_est_counts.txt


title: H3K27ac_ChIPseq_sonic_pSIN_HEAAUTX_2

value: Histone H3 K27 acetylation


title: H3K27ac_ChIPseq_sonic_pSIN_WTUTX_2


title: fetal cord tissue, S0187


title: pg.ij5

description:
pgrande-fol-ij5_S6
processed data file: p_retropinna_est_counts.txt

source_name: Potrero Grande_P. retropinna_maternal follicle

value: Potrero Grande


title: fetal cord tissue, S0185


title: WT73M-Wild-type bred rep1

value: FAKfl/fl;Alb-Cre-


title: H3K27ac_ChIPseq_sonic_pSIN_HEAAUTX_1

value: bladder cancer

value: stably expressing pSIN-puro H1146A/E1148A-mutant UTX


title: pg.ij3

description:
portgr-fol-ij3_S4
processed data file: p_retropinna_est_counts.txt


title: pg.ij2

description:
portgr-fol-ij2_S3
processed data file: p_retropinna_est_counts.txt


title: H3K27ac_ChIPseq_sonic_pSIN_WTUTX_1


title: fetal cord tissue, S0183

value: fetal cord tissue


title: D5_rep2

city: Oxford

first: Erinke

last: van Grinsven

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

description:
PolyA RNA
WT_D5_0hr_2
processed data file: Hoxb8_raw_counts.xlsx

data_processing:
Paired-end reads were mapped to the mm10 genome using STAR with the options: “—runMode alignReads –outFilterMismatchNmax 2.”
Uniquely mapped read pairs were counted over annotated genes using featureCounts with the options: “-T 18 -s 2 -Q 255.”
Differential expression was analysed with DESeq2.
Variance stabilised (VST) counts for all DESeq2 differentially expressed genes, likelihood ratio test, false discovery rates (FDRs) < 0.01, were used for dimensionality reduction and heatmaps.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Hoxb8_raw_counts.xlsx: Excel file includes raw read counts.

source_name: ER-Hoxb8 neutrophils

growth_protocol: ER-Hoxb8 progenitor cells were routinely cultured in RMPI-1640 medium supplemented with 10% FCS, 30 mM β-mercaptoethanol, 1% supernatant from stem cell factor (SCF)-producing CHO cells and 1 μM β-estradiol. Differentiation was induced by estrogen removal and culture in medium containing 1% SCF supernatant. The progenitor cells were differentiated into neutrophils by culturing with complete RPMI 1640 medium supplemented with 30 mM b-mercaptoethanol, 4% SCF containing supernatant and 20 ng/mL G-CSF in 5% CO2 tissue culture incubator at 37°C.

extract_protocol:
Total RNA of 1x10e6 Hoxb8 neutrophils of different maturation stages were extracted using RNeasy mini kit (Qiagen) according to the manufacturer’s instruction.
Poly-A selected mRNA libraries were prepared for Illumina HiSeq4000.

value: ER-Hoxb8 neutrophils

tag: number of days of in vitro differentiation

tag: replicate


title: H3K4me1_ChIPseq_sonic_pSIN_EV

value: stably expressing pSIN-puro empty vector

value: Histone H3 K4 mono-methylation


title: D3_rep2

description:
PolyA RNA
WT_D3_0hr_2
processed data file: Hoxb8_raw_counts.xlsx


title: ceibo.ij1

description:
ceibo-fol-ij1_S5
processed data file: p_retropinna_est_counts.txt

source_name: Ceibo_P. retropinna_maternal follicle

value: Ceibo


title: input_ChIPseq_mnase_pSIN_HEAAUTX

extract_protocol:
Three days after plating, UMUC1 cells were harvested from 15cm tissue culture plates at ~75% confluency. For each UTX or MLL4 ChIP, ~3x10e7 cells were harvested which yielded ~75 µg of chromatin DNA for immunoprecipitation after going through this protocol. The cells were then fixed as described for the histone modification ChIPs described above. The fixed cells for each sample were resuspended in 20 mL of PBS with 0.5% NP-40 and 1x protease inhibitors, then incubated on ice for 10 minutes and pelleted. Each pellet of fixed cells was divided into two tubes, so there were ~1.5x10e7 cells per tube, and these cell pellets were snap frozen. After thawing the cells, each tube of cells was then resuspended in 600 µL of room temperature micrococcal nuclease (MNase) reaction buffer (50 mM HEPES pH 7.5, 2 mM CaCl2, 0.2% NP-40). Before fragmenting the ChIP samples, the specific lot of MNase (Worthington, LS004798) was tested and a specific amount of MNase (~3-5uL) was determined in order to obtain fragments primarily 300-900 base pairs in length. The 600 µL of resuspended cells were then divided into three tubes of 200 µL and each tube of cells was treated with MNase for 3 minutes at 37°C. The reactions were stopped by adding 20 µL of 0.5M EDTA pH 8.0 and putting the samples on ice. The cells were centrifuged at 13,000xG for 1 minute and the supernatant was removed. The two tubes of cells for each sample were combined and these cells were resuspended in 200uL SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1, 1x protease inhibitors). Then 800 µL of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl, 1x protease inhibitors) was added to each sample, which was then sonicated for 5 minutes using the Bioruptor sonicator. The sample was centrifuged at 20,000xG for 10 minutes at 4°C and the supernatant was transferred to a new tube. Then 20 µL was removed to measure the amount of DNA as described above, and the rest was snap frozen and stored at -80°C. After quantifying the DNA concentration for each sample, 75 µg of chromatin was diluted into 2 mL total of ChIP dilution buffer, and 5% (100 µL) of each sample was set aside as an input sample. Then 75 µL of protein A Dynabeads that had been washed 3X with PBS + 0.01% Tween-20 and pre-bound with 20 µL UTX (Cell Signaling, 33510) or MLL4 (Sigma, HPA035977) antibody were added to each chromatin lysate and this mixture was incubated rotating overnight at 4°C. The beads were then sequentially washed on a magnet two times each with low salt buffer, high salt buffer, LiCl buffer and once with TE buffer (see histone modification ChIP section for buffer compositions). After the TE wash the beads were spun down (not separated on the magnet), and resuspended in 200 µL elution buffer (1% SDS, 0.1 M NaHCO3). 100 µL elution buffer was also added to each 100 µL input sample. Samples were incubated at 65°C for 30 minutes while shaking at 800 rpm. Then 8 µL of 5M NaCl was added to each sample before reverse crosslinking overnight at 65°C. The eluate was then treated with RNaseA for 1 hr at 37°C then with Proteinase K for 1 hr at 55°C and DNA was recovered using the Qiagen PCR purification kit. Libraries were prepared using the NEBNext Ultra II DNA Library Prep kit, and then sequenced on a NextSeq500 sequencer.
NEBNext Ultra II DNA


title: fetal cord tissue, S0182


title: fetal cord tissue, S0181


title: D3_rep1

description:
PolyA RNA
WT_D3_0hr_1
processed data file: Hoxb8_raw_counts.xlsx


title: ceibo.2017

description:
ceibo-fol-2017_S8
processed data file: p_retropinna_est_counts.txt

value: pregnant, late stage (I/J Haynes 1995)


title: D1_rep2

description:
PolyA RNA
WT_D1_0hr_2
processed data file: Hoxb8_raw_counts.xlsx


title: fetal cord tissue, S0177


title: input_ChIPseq_mnase_pSIN_WTUTX

value: stably expressing pSIN-puro wild type UTX


title: H3K27ac_ChIPseq_sonic_pSIN_EV_2


title: control_R2

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Department of Biological DNA Modification, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

description: control sample were used to generate final coverage file (ie. 5caCG_coverage.txt)

data_processing:
Select reads with length >= 80 nt
Select reads with 5' adapter and trim 3' adapter from the remaining reads
Align reads to a mouse genome (mm10 build), minimum mapping quality 30
Remove PCR duplicates (used an in house script)
Calculate coverage per CG (used an in house script)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include coverage per CG

source_name: Embryonic stem cells

growth_protocol: Cells were cultured in feeder-free gelatin-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco) supplemented with 15% FBS (Gibco), 2 mM l-glutamine (Gibco), 0.1 mM 2-mercaptoethanol (Gibco),  0.1 mM nonessential amino acids (Gibco), 1,000 units/ml LIF (Millipore, ESG1106) and 1 × pen/strep (Gibco). The cell culture was passaged every 2–3 d using 0.05% Trypsin-EDTA (GIBCO). For serum-2i conditions, medium was supplemented with 3 μM CHIR99021 (Sigma) and 1 μM PD0325901 (Sigma).

extract_protocol:
Standard DNA phenol-chloroform extraction
In sheared DNA 5hmC and unmodified CGs were blocked by glycosylation and methylation, respectively. Then, eM.SssI-directed decarboxylation and labeling reaction with Ado-6-azide cofactor was performed. DNA ends were prepared and adaptors ligated as in Staševskij, 2017. Alkyne-bearing oligodeoxyribonucleotide with biotin was attached to the azide moiety and modified DNA then was enriched using streptavidin-coupled magnetic beads. All enriched DNA was used for priming reaction, amplified, size-selected as in Staševskij, 2017 and subjected to Ion Proton sequencing.

tag: modification


title: input_ChIPseq_mnase_pSIN_EV


title: D1_rep1

description:
PolyA RNA
WT_D1_0hr_1
processed data file: Hoxb8_raw_counts.xlsx


title: fetal cord tissue, S0175

tag: pre-pregnancy bmi (kg/m^2)


title: fetal cord tissue, S0184

tag: tissue


title: MLL4_ChIPseq_mnase_pSIN_HEAAUTX


title: control_R1


title: D5_rep1

description:
PolyA RNA
WT_D5_0hr_1
processed data file: Hoxb8_raw_counts.xlsx


title: fetal cord tissue, S0173


title: serum2i_Tdg_R2


title: fetal cord tissue, S0172


title: D0_rep1

description:
PolyA RNA
WT_D0_0hr_1
processed data file: Hoxb8_raw_counts.xlsx


title: MLL4_ChIPseq_mnase_pSIN_WTUTX


title: ceibo.ij2

description:
ceibo-fol-ij2_S6
processed data file: p_retropinna_est_counts.txt

value: maternal follicle


title: MLL4_ChIPseq_mnase_pSIN_EV


title: serum2i_Tdg_R1


title: fetal cord tissue, S0170


title: fetal cord tissue, S0171


title: serum_Tdg_R2


title: UTX_ChIPseq_mnase_pSIN_HEAAUTX_1

value: UTX


title: UTX_ChIPseq_mnase_pSIN_WTUTX_1


title: serum_Tdg_R1


title: fetal cord tissue, S0169


title: D0_rep2

description:
PolyA RNA
WT_D0_0hr_2
processed data file: Hoxb8_raw_counts.xlsx


title: fetal cord tissue, S0168


title: C24pif4-101_27C_ZT0_7DAS

city: Ratchathewi

first: Varodom

last: Charoensawan

state: Bangkok

address: 272 Rama 6 road

department: Biochemistry

country: Thailand

institute: Mahidol University

data_processing:
Quality control by FastQC v.0.11.5
Discarding the low quaility reads and adapters  by Trimmomatics 0.36
Reads mapping to the reference genome (TAIR10) by HiSat2 with parameters set -k 1 and --no-mixed
Removal of duplicated reads by Picard (MarkDuplicates)
Selection of 0-2 mismatches aligned reads by Picard (FilterSamRead)
Transcripts quantification of FPKM and TPM by StringTie 1.3.5 and RAW by Htseq 0.6.1p1
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file includes raw count values for each Sample.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: C24xCol and C24xpif4-101 seeds were sterilized and stratified on ½ MS (Murashige and Skoog) media with 0.8% agar for 3 days at 4°C under dark condition and were allowed to germinate at control temperature (22˚C)  in 8/16 light/dark cycle at 170 mmol m-2 s-1 for 1 day

extract_protocol:
The seedlings from each experiment were pooled (~30 mg) and were subjected to total RNA extraction by using MagMAX-96 Total RNA Isolation kit (Ambion, AM1830).
Library preparation was  prepared by  1 mg of high integrity of total RNA (RIN>8) using TruSeq Stranded mRNA library preparation kit and TruSeq RNA Library Preparation Kit v2 (Illumina, RS-122-2101 and RS-122-2001)

treatment_protocol: The seedling of C24xCol and C24xpif4-101  were cultured at 22˚C  and 27˚C

tag: ecotype

tag: temp

tag: timepoint

tag: das

value: whole seedling


title: C24Col_27C_ZT0_7DAS


title: C24pif4-101_22C_ZT0_4DAS


title: serum2i_wt_R1


title: fetal cord tissue, S0166


title: RNAseq_fullMedia_pBabe_S249CFGFR3_pCDH_WTUTX_3

description:
S249C_UTX_Rep3
raw_counts_allsamples_FGFR3_UTX_UMUC1.csv

data_processing:
Transcript abundance was computed from FASTQ files using Salmon (v0.8) and the GENCODE reference transcript sequences (release 27), transcript counts were imported into R with the tximport R Bioconductor package, and differential gene expression was determined with the DESeq2 R Bioconductor package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Counts tables contain the raw counts quantified by Salmon and DESeq2.

growth_protocol: Cells were maintained in Eagle’s Minimum Essential Medium (MEM, Corning, 10-009-CV), with 10% fetal bovine serum (Sigma-Aldrich) and then were harvested three days after being plated in this same media composition.

extract_protocol:
NEBNext Ultra II RNA
RNA was purified using the Qiagen RNeasy kit.

tag: cell line

tag: cell type

tag: genotype

value: stably expressing pBabe-puro gateway S249C FGFR3 and pCDH-blasticidin wild type UTX


title: RNAseq_fullMedia_pBabe_S249CFGFR3_pCDH_WTUTX_2

description:
S249C_UTX_Rep2
raw_counts_allsamples_FGFR3_UTX_UMUC1.csv


title: serum_wt_R2


title: RNAseq_fullMedia_pBabe_S249CFGFR3_pCDH_WTUTX_1

description:
S249C_UTX_Rep1
raw_counts_allsamples_FGFR3_UTX_UMUC1.csv


title: fetal cord tissue, S0164

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)


title: C24Col_22C_ZT0_7DAS


title: serum_wt_R1


title: C24Col_27C_ZT0_4DAS


title: C24pif4-101_22C_ZT0_7DAS


title: fetal cord tissue, S0163

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)


title: RNAseq_fullMedia_pBabe_S249CFGFR3_pCDH_EV_3

description:
S249C_EV_Rep3
raw_counts_allsamples_FGFR3_UTX_UMUC1.csv

value: stably expressing pBabe-puro gateway S249C FGFR3 and pCDH-blasticidin empty vector


title: UTX_ChIPseq_mnase_pSIN_EV_1

tag: chip antibody


title: fetal cord tissue, S0161


title: serum2i_wt_R2


title: C24pif4-101_27C_ZT0_4DAS


title: C24Col_22C_ZT0_4DAS


title: fetal cord tissue, S0160


title: RNAseq_fullMedia_pBabe_S249CFGFR3_pCDH_EV_1

description:
S249C_EV_Rep1
raw_counts_allsamples_FGFR3_UTX_UMUC1.csv


title: RNAseq_fullMedia_pBabe_WTFGFR3_pCDH_WTUTX_3

description:
WTFGFR3_UTX_Rep3
raw_counts_allsamples_FGFR3_UTX_UMUC1.csv

value: stably expressing pBabe-puro gateway wild type FGFR3 and pCDH-blasticidin wild type UTX


title: RNAseq_fullMedia_pBabe_WTFGFR3_pCDH_WTUTX_2

description:
WTFGFR3_UTX_Rep2
raw_counts_allsamples_FGFR3_UTX_UMUC1.csv


title: fetal cord tissue, S0157


title: fetal cord tissue, S0156


title: T5c7379

type: RNA

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

hyb_protocol: Cy3-labeled cRNA (1.65 μg; specific activity of >9.0 pmol Cy3/μg of cRNA) was fragmented at 60 °C for 30 min in a reaction volume of 55 μl containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent, following the manufacturer's instructions. On completion of the fragmentation reaction, 55 μl of 2× GEx Hybridization buffer HI-RPM was added to the fragmentation mixture, and mixtures were hybridized to Agilent Whole-Human Genome Oligo Microarrays (G4845A) for 17 h at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 min at 37 °C with GE Wash buffer 2 (Agilent Technologies) and then dried

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using the one-color scan setting for 1 × 44 k array slides (scan area of 61 × 21.6 mm; scan resolution of 5 μm; dye channel set to green; green PMT set to 100%).

data_processing: Scanned images were analyzed with Feature Extraction Software 12.0.0.7 (Agilent Technologies) using default parameters (protocol GE1_1200_Jun14 and Grid:  026652_D_F_20150330 ) to obtain background-subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Signal intensities were normalized using quantile normalization for GE .

label_protocol: Cy3-labeled cRNA was prepared from 1 μg of RNA using One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) (Agilent Technologies) according to the manufacturer's instructions, and RNeasy column purification was performed (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared from biopsies using TRIzol (Life Technologies) following the manufacturer's instructions.

value: muscle

tag: gender

value: female

tag: age

value: 46 years

tag: mutation


title: RNAseq_fullMedia_pBabe_WTFGFR3_pCDH_WTUTX_1

description:
WTFGFR3_UTX_Rep1
raw_counts_allsamples_FGFR3_UTX_UMUC1.csv

value: bladder cancer


title: fetal cord tissue, S0155

value: fetal cord tissue

tag: pre-pregnancy bmi (kg/m^2)


title: RNAseq_fullMedia_pBabe_S249CFGFR3_pCDH_EV_2

description:
S249C_EV_Rep2
raw_counts_allsamples_FGFR3_UTX_UMUC1.csv


title: RNAseq_fullMedia_pBabe_WTFGFR3_pCDH_EV_3

description:
WTFGFR3_EV_Rep3
raw_counts_allsamples_FGFR3_UTX_UMUC1.csv

value: stably expressing pBabe-puro gateway wild type FGFR3 and pCDH-blasticidin empty vector


title: fetal cord tissue, S0154

tag: tissue


title: fetal cord tissue, S0158


title: fetal cord tissue, S0152


title: RNAseq_fullMedia_pBabe_WTFGFR3_pCDH_EV_2

description:
WTFGFR3_EV_Rep2
raw_counts_allsamples_FGFR3_UTX_UMUC1.csv


title: RNAseq_fullMedia_pBabe_WTFGFR3_pCDH_EV_1

description:
WTFGFR3_EV_Rep1
raw_counts_allsamples_FGFR3_UTX_UMUC1.csv


title: fetal cord tissue, S0151


title: T5b7379


title: RNAseq_sphereMedia_pSIN_HEAAUTX_3

description:
HA_sphere_Rep3
raw_counts_allsamples_full_vs_sphere_UMUC1.csv

growth_protocol: Cells were maintained in Eagle’s Minimum Essential Medium (MEM, Corning, 10-009-CV), with 10% fetal bovine serum (Sigma-Aldrich) and then were harvested three days after being plated in serum free MEM media with 1X B27 supplement without vitamin A (Life Technologies, 12587-010), human-FGF2 (bFGF) (20 ng/ml) (Shenandoah Biotech), and human-EGF (20 ng/ml) (Shenandoah).

extract_protocol:
Illumina TruSeq
RNA was purified using the Qiagen RNeasy kit.

value: stably expressing pSIN-puro H1146A/E1148A-mutant UTX


title: T5a7379


title: humanMelanocytes_UV60s_rep2

city: Greifswald

first: Anke

last: Schmidt

state: MV

address: Felix-Hausdorff-Str. 2

department: Plasma Life Science

country: Germany

institute: INP Greifswald

description: melanocytes used were isolated from human foreskin of a 5 years old male caucasian

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl 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 8x60k custom-design human Microarrays (design-ID: 06247)  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 37Â°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 using one color scan setting for 8x60k array slides (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Further data processing was performed with Agilent GeneSpring Software. Normalization: Thresholded to 1, shifted to 75.0 percentile, baseline to median of all samples. Statistics: oneway ANOVA, asymptotic p-value computation, Benjamini-Hochberg correction, standard p-value cut-off: 0.05.

source_name: human melanocyte

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (bio&sell, Feucht, Germany). Dye incorporation and cRNA yield were checked with the NanoDrop2000c Spectrophotometer.

growth_protocol: Primary human melanocytes were seeded at a density of 40,000 cells / well (12-well-format) in CnT-40 melanocyte specific medium (CELLnTEC advanced cell systems AG, Bern, Switzerland) 24 h before treatment.

extract_protocol: RNA was prepared using the RNA Mini Kit (bio&sell, Feucht, Germany) following manufacturer´s recommendations.

treatment_protocol: 5.5 ml CnT-40 melanocyte medium were treated for 60 s by the plasma device kINPen MED at a distance of 13 mm. 1 ml of freshly treated medium was directly transferred to the cells and incubated at 37 °C and 5 %CO2 for 2 h. For UV-irradiation, the cell culture medium was removed and the melanocytes were irradiated by 2 UVB-lamps (each 9 W at a distance of 21,7 cm) for 60 s before being cultivated for 2 h. Untreated control melanocytes were incubated in the same way.

value: skin

value: melanocytes

value: male

tag: treatment

value: UV


title: H3K27me3_ChIPseq_sonic_pSIN_EV

value: stably expressing pSIN-puro empty vector

value: Histone H3 K27 tri-methylation


title: T4d2638

value: 12 years


title: fetal cord tissue, S0150


title: RNAseq_sphereMedia_pSIN_HEAAUTX_2

description:
HA_sphere_Rep2
raw_counts_allsamples_full_vs_sphere_UMUC1.csv


title: humanMelanocytes_UV60s_rep3


title: fetal cord tissue, S0149


title: humanMelanocytes_ptl60s_rep5

value: ptl


title: humanMelanocytes_UV60s_rep1


title: humanMelanocytes_UV60s_rep4


title: T4b2638


title: RNAseq_sphereMedia_pSIN_HEAAUTX_1

description:
HA_sphere_Rep1
raw_counts_allsamples_full_vs_sphere_UMUC1.csv


title: RNAseq_sphereMedia_pSIN_WTUTX_3

description:
WT_sphere_Rep3
raw_counts_allsamples_full_vs_sphere_UMUC1.csv

value: stably expressing pSIN-puro wild type UTX


title: fetal cord tissue, S0148


title: fetal cord tissue, S0146


title: T4a2638


title: humanMelanocytes_ptl60s_rep6


title: T4c2638


title: RNAseq_sphereMedia_pSIN_WTUTX_2

description:
WT_sphere_Rep2
raw_counts_allsamples_full_vs_sphere_UMUC1.csv


title: humanMelanocytes_ptl60s_rep4


title: humanMelanocytes_ptl60s_rep3


title: T3d4449

value: 32 years


title: T3c4449

value: muscle


title: T3b4449

value: female


title: humanMelanocytes_ptl60s_rep1


title: humanMelanocytes_control_rep5

value: control


title: fetal cord tissue, S0144


title: T3a4449


title: RNAseq_sphereMedia_pSIN_EV_3

description:
EV_sphere_Rep3
raw_counts_allsamples_full_vs_sphere_UMUC1.csv

value: bladder cancer


title: RNAseq_sphereMedia_pSIN_WTUTX_1

description:
WT_sphere_Rep1
raw_counts_allsamples_full_vs_sphere_UMUC1.csv


title: T2c7322

value: 6 years


title: humanMelanocytes_ptl60s_rep2


title: fetal cord tissue, S0143

value: fetal cord tissue


title: T2b7322


title: humanMelanocytes_control_rep3


title: humanMelanocytes_control_rep4


title: fetal cord tissue, S0145


title: RNAseq_sphereMedia_pSIN_EV_2

description:
EV_sphere_Rep2
raw_counts_allsamples_full_vs_sphere_UMUC1.csv


title: fetal cord tissue, S0142


title: fetal cord tissue, S0188


title: humanMelanocytes_control_rep2


title: Rattus_MXZ(TBI)

city: Tianjin

first: Ru

middle: Si

last: Qin

address: No.10 Poyang Lake Road, Tuanbo new town, Jinghai District, Tianjin

country: China

institute: Tianjin University of Traditional Chinese Medicine

description: Gene expression data of brainstem

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Rattus norvegicus

source_name: Rattus brainstem

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

growth_protocol: At 1h after modeling (n=5), the rats were sacrificed by dislocation, and the brainstem and TBI-damaged cortex tissues were isolated and immediately frozen in liquid nitrogen (-195.79˚C) and then transferred to a refrigerator at -80°C until they were used for experiments.

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

treatment_protocol: The brainstem tissue were collected for further total RNA extraction.

value: Rattus brainstem of modeling

value: TBI


title: humanMelanocytes_control_rep1

value: skin

value: melanocytes


title: RNAseq_sphereMedia_pSIN_EV_1

description:
EV_sphere_Rep1
raw_counts_allsamples_full_vs_sphere_UMUC1.csv


title: T2a7322


title: T1c3369

value: male

value: 7 years


title: fetal cord tissue, S0141


title: RNAseq_fullMedia_pSIN_HEAAUTX_3

description:
HA_full_Rep3
raw_counts_allsamples_full_vs_sphere_UMUC1.csv

value: stably expressing pSIN-puro H1146A/E1148A-mutant UTX


title: H3K27ac_ChIPseq_sonic_pSIN_EV_1

value: stably expressing pSIN-puro empty vector

value: Histone H3 K27 acetylation


title: T1b3369


title: Rattus_JXZ(Hand Acu)

description: Gene expression data of brainstem

value: Hand Acu


title: fetal cord tissue, S0140


title: Rattus_JSSZ(Sham)

description: Gene expression data of brainstem

value: Sham


title: RNAseq_fullMedia_pSIN_HEAAUTX_2

description:
HA_full_Rep2
raw_counts_allsamples_full_vs_sphere_UMUC1.csv


title: T1a3369

value: muscle


title: fetal cord tissue, S0138


title: RNAseq_fullMedia_pSIN_WTUTX_3

description:
WT_full_Rep3
raw_counts_allsamples_full_vs_sphere_UMUC1.csv

value: stably expressing pSIN-puro wild type UTX


title: fetal cord tissue, S0139


title: Spl GC 3

city: London

first: Victor

last: Tybulewicz

address: 1 Midland Road

institute: Francis Crick Institute

data_processing:
Cutadapt v1.9.1 (Martin, 2011) was used to trim adapter sequences from reads with the following options: -a AGATCGGAAGAGC –A AGATCGGAAGAGC -e 0.1 –minimum length 30 –q 20,20.
Gene-level expected counts were calculated with RSEM v1.2.31 (Li and Dewey, 2011), using STAR v2.5.1b (Dobin et al., 2013) to align reads against the GRCm38 genome assembly with Ensembl release 86 transcript annotations.
Count data were rounded to integers and normalized for differences in sample library size using the standard median ratio method in DESeq2 (Anders and Huber, 2010).
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized log2 counts in tab-delimited text format. Gene ids are represented by Ensembl v86 identifiers.

source_name: splenic germinal center B cells

extract_protocol:
Single cell suspensions from spleen and bone marrow were depleted of erythrocytes using ACK lysis buffer and stained with a live/dead marker and the respective antibodies in PBS. Three replicates of each cell population (1,000 cells each) were sorted directly into TRIzol (Thermo Fisher). RNA was purified using the RNeasy Plus Micro kit (QIAgen) according to the manufacturer’s instructions.
Un-stranded, non-rRNA, non-polyA+ selected libraries were prepared using the SMARTer Ultra Low Input RNA kit for Sequencing v3 (Clontech Laboratories).
RNA sequencing: The libraries were sequenced on the Illumina HiSeq 2000 platform as 50 bp paired-end runs

treatment_protocol: FO B cells were isolated from C57BL/6J mice that had not been deliberately immunised. GC and MBC were isolated from C57BL/6J mice immunised with 50µg NP-CGG in alum 10d (GC) or 35 d (MBC) earlier. PB and PC were isolated from C57BL/6J-Blimp1GFP mice immunized with 50µg NP-CGG in alum 35 d earlier. All mice were aged 8-17 weeks.

tag: strain

tag: Sex

value: female

tag: organ

value: spleen

tag: surface markers used for sorting

tag: days after immunization

tag: immunization agent

value: NP-CGG in alum


title: fetal cord tissue, S0132

value: fetal cord tissue

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)


title: T2334

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality bases removed, with resulting reads that were less than 25bp removed. Reads were then mapped to mm10 whole genome using TopHat v2.0.14, utilising bowtie2 v2.2.5, with parameter --library-type fr-firststrand.
Number of reads aligned to each gene in the mm10 genome were quantified using HTSeq v0.6.1, using the following paratmers: --stranded=reverse -a 3, and the mm10 GTF file from ENSEMBL.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw number of counts aligned to every gene, each sample in an individual file

source_name: Mammary gland

extract_protocol:
Right thoracic mammary gland fat pads were excised intact, snap frozen in liquid nitrogen, and RNA was harvested using the mirVANA RNA Isolation Kit. Illumina TruSeq RNA Sample Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina TruSeq RNA Sample Prep Kit v2 following standard Illumina protocols

value: Mammary gland

value: post natal day 130

tag: treatment group


title: T2234


title: fetal cord tissue, S0131

tag: maternal age at delivery (years)

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)


title: fetal cord tissue, S0136

tag: child sex (male = 0; female = 1)


title: Spl GC 2


title: Spl GC 1


title: RNAseq_fullMedia_pSIN_WTUTX_1

description:
WT_full_Rep1
raw_counts_allsamples_full_vs_sphere_UMUC1.csv

tag: cell line

tag: cell type

value: bladder cancer

tag: genotype


title: RNAseq_fullMedia_pSIN_WTUTX_2

description:
WT_full_Rep2
raw_counts_allsamples_full_vs_sphere_UMUC1.csv


title: T2224

tag: age


title: fetal cord tissue, S0130

tag: tissue

tag: pre-pregnancy bmi (kg/m^2)


title: RNAseq_fullMedia_pSIN_EV_3

description:
EV_full_Rep3
raw_counts_allsamples_full_vs_sphere_UMUC1.csv


title: C4c8463

tag: gender

value: 47 years

tag: mutation


title: RNAseq_fullMedia_pSIN_EV_2

description:
EV_full_Rep2
raw_counts_allsamples_full_vs_sphere_UMUC1.csv


title: fetal cord tissue, S0129


title: RNAseq_fullMedia_pSIN_HEAAUTX_1

description:
HA_full_Rep1
raw_counts_allsamples_full_vs_sphere_UMUC1.csv


title: C4b8463


title: T2214

tag: strain


title: T2314


title: C2d6578

value: 5 years


title: C2a6578


title: C2c6578


title: C4a8463


title: C1d7875

value: male

value: 4,5 years


title: C2b6578


title: fetal cord tissue, S0128


title: T1324


title: fetal cord tissue, S0127


title: C1c7875


title: Optate 3 [G3_Treatment_S6]

city: Indianapolis

middle: Denning

last: Davis

state: Indiana

address: 1044 West Walnut Street R4-472

department: Pediatrics

institute: Indiana University

data_processing:
Basecalling with NextSeq Control Software 4.0.1.41/RTA 2.11.3
FASTQ files were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters “-s 2 –Q 10”
Genome_build: UCSC hg38
Supplementary_files_format_and_content: A tab-separated text file containing gene annotation information and RAW unfiltered read counts for each sample

molecule: polyA RNA

source_name: primary human airway epithelial cells_Optate

growth_protocol: 1 X 10^5 cells (second passage) were plated and allowed to adhere to the culture plate overnight. These cells underwent 48 hours of treatment (or control) and then underwent RNA extraction; both treatment and extraction are described below.

extract_protocol:
Cells were lysed and RNA was extracted using the Qiagen RNeasy Plus Mini Kit per manufacturers protocol (Qiagen, USA, Cat No. 74134).
KAPA mRNA Hyperprep Kit (KK8581).

treatment_protocol: Cells were exposd to 100 uM Optate in culture media (or PBS for the control group). Media and treatment were changed every 24 hours for a total of 48 hours.

value: primary human airway epithelial cells

tag: treatment

value: Optate for 48 hrs

tag: molecule type

value: polyA-enriched RNA


title: T1314


title: Optate 1 [G1_Treatment_S4]


title: Optate 2 [G2_Treatment_S5]


title: RNAseq_fullMedia_pSIN_EV_1

description:
EV_full_Rep1
raw_counts_allsamples_full_vs_sphere_UMUC1.csv

value: stably expressing pSIN-puro empty vector


title: fetal cord tissue, S0126


title: T1234


title: fetal cord tissue, S0124


title: fetal cord tissue, S0123


title: Control 3 [P3_Control_S3]

source_name: primary human airway epithelial cells_control

value: control


title: T1224


title: C1b7875

value: muscle


title: T1334


title: Control 2 [P2_Control_S2]


title: C1a7875


title: fetal cord tissue, S0122


title: fetal cord tissue, S0121


title: Input_control

city: Buffalo

first: Soo-Kyung

last: Lee

address: 109 Cooke Hall

department: Department of Biological Sciences

institute: University at Buffalo, The State University of New York

description: Chromatin DNA was isolated from E14.5 mouse brains, sonicated and then subjected to a high throughput sequencing.

data_processing:
For RNAseq, sequence reads were trimmed for TruSeq adaptor sequence by cutadapt v1.14, and then mapped to mm10 whole genome using STAR v2.6.0. Raw read counts were calculated using a featureCounts in subread v1.6.2. In short, exons from all isoforms of a gene were merged to create one meta-transcript.
For ChIPseq, Reads were aligned to the mm10 reference genome using bowtie2 with default settings. Duplicated reads were removed from alignments using Picard (v.2.8.3-7). Peak calling was performed using MACS2 (v. 2.1.1)70 with the following parameters: ‘-q 0.05 -g mm’ setting a q-value threshold of 0.05 except for Suz12 replicate 2 to have a comparable number of peaks with replicate 1 by relaxing a q-value threshold to 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: count_matrix, chipseq_peak_bed_file

source_name: Brains

growth_protocol: OPCs were cultured in DMEM-Sato base growth medium with the addtion of PDGF and NT-3. For OPC differentiation, T3 was added while PDGF was removed in the medium.

extract_protocol:
For RNAseq, total RNA was extracted using TRIzol regeat based on the manual instructions. For ChIPseq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies.
For RNA>100ng, the libraries were prepared using RNA-seq Stranded Library kit (Illumina TruSeq with PolyA selection). For RNA<100ng, we used Clontech SMARTer RNA kit to construct RNAseq Library. For ChIPseq, Libraries were prepared according to Illumina's instructions

tag: Stage

tag: stain

value: ICR/Ha

value: brain


title: BM PC 3

description: Sample 18

data_processing:
Cutadapt v1.9.1 (Martin, 2011) was used to trim adapter sequences from reads with the following options: -a AGATCGGAAGAGC –A AGATCGGAAGAGC -e 0.1 –minimum length 30 –q 20,20.
Gene-level expected counts were calculated with RSEM v1.2.31 (Li and Dewey, 2011), using STAR v2.5.1b (Dobin et al., 2013) to align reads against the GRCm38 genome assembly with Ensembl release 86 transcript annotations.
Count data were rounded to integers and normalized for differences in sample library size using the standard median ratio method in DESeq2 (Anders and Huber, 2010).
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized log2 counts in tab-delimited text format.  Gene ids are represented by Ensembl v86 identifiers.

source_name: bone marrow plasma cells

extract_protocol:
Single cell suspensions from spleen and bone marrow were depleted of erythrocytes using ACK lysis buffer and stained with a live/dead marker and the respective antibodies in PBS. Three replicates of each cell population (1,000 cells each) were sorted directly into TRIzol (Thermo Fisher). RNA was purified using the RNeasy Plus Micro kit (QIAgen) according to the manufacturer's instructions.
Un-stranded, non-rRNA, non-polyA+ selected libraries were prepared using the SMARTer Ultra Low Input RNA kit for Sequencing v3 (Clontech Laboratories).
RNA sequencing: The libraries were sequenced on the Illumina HiSeq 2000 platform as 50 bp paired-end runs

tag: Sex

value: female

tag: organ

value: bone marrow

tag: surface markers used for sorting

tag: days after immunization

tag: immunization agent

value: NP-CGG in alum


title: 4348

city: Goyang

first: Ho-Shin

last: Gwak

address: 323 Ilsan-ro

department: Department of Cancer Control

country: South Korea

institute: National Cancer Center Graduate School of Cancer Science and Policy

description:
exosomal RNA
953_Read_Count

data_processing:
The raw sequence reads are filtered based on quality using FastQC v0.11.7.
The adapter sequences are also trimmed off adapter sequences, primers, poly-A tails and other types of unwanted sequence using Cutadapt 1.16.
The reads were aligned to the 45S pre-rRNA and mitochondrial rRNA of hg19 reference genome and have them removed.
mature miRNA Quantification procedure. 1) mature miRNA sequences of relevant species are aligned to precursor miRNA sequences from miRBase v21 (bowtie option : -f -v 0 -a  --best --strata --norc). 2) unique clustered reads are aligned to precursor sequence (bowtie option : -f -v 1 -a --best --strata --norc). Bowtie aligner is used in the mapping  steps. 3) overlapping mature miRNA regions between two mapping results were determined. Afterwards, the read count of mature miRNAs are extracted from the overlapping regions in  the miRDeep2 Quantifier module. If a read is mapped to multiple mature miRNAs, the read counts are assigned equally to the abundance level of each mature miRNA.
Genome_build: hg19 by Bowtie and STAR, miRBase v21 by miRDeep2
Supplementary_files_format_and_content: Matrix table with raw gene counts for mature miRNA

source_name: cerebrospinal fluid

extract_protocol:
CSF exosome was precipitated using Exo2DTM for RNA assay (EXOSOME plus, Suwon, South Korea) according to the manufacture’s protocol (Kim, et al. 2017). 2 ml of CSF were added to Exo2DTM reagent B following mixing by inverting, and incubated at room temperature for 30 min. The supernatant was discarded and the exosome containing pellet was resuspended in 100 ul of PBS to further RNA isolation.  Total RNA was extracted from the CSF exosome fraction using a microRNA purification kit (Norgen Biotek corp., Thorold, Canada) according to the manufacture’s protocol. Briefly, samples were mixed with lysis buffer, and the lysate was added to absolute ethanol. The lysate was applied up to the column and centrifuged at 8,000 rpm for 1 min. The column was washed with wash solution and centrifuged at 14,000 rpm for 1 min. Finally, the column was applied to 20 ul of elution solution and centrifuged at 14,000 rpm for 2 min, and the flow-through was stored at –80 ℃ for storage.
The samples were quantified and qualified with Bioanalyzer Pico 6000 Chip (Agilent Technologies, Santa Clara, CA). The 10 ng of total RNA was provided to the cDNA library generation using SMARTer smRNA-Seq kit (Illumina Inc., San Diego, CA). The cDNA library was subjected to sequencing using Truseq SBS Kit and HiSeq 2500 System (Illumina Inc., San Diego, CA)

value: cerebrospinal fluid

tag: disease

value: medulloblastoma with leptomeningeal metastasis


title: 4344

description:
exosomal RNA
971_Read_Count


title: Control 1 [P1_Control_S1]

tag: cell type


title: 2246

description:
exosomal RNA
re-2246_Read_Count

tag: age

value: medullublastoma


title: fetal cord tissue, S0119

source_name: cord tissue

extract_protocol: Prior to purification, 250 mg crushed cord tissue was enzymatically digested with hyaluronidase (~2.7U in 250 µl PBS) for 30 minutes at 37 C, mixed with 250 µl TNES lysis buffer, transferred to gentleMACS M Tubes (Miltenyi 130-093-236) for 1-minute homogenization followed by overnight treatment with 200 µg Proteinase K at 55 C. QIASymphony SP was used for automated purification of (buffy coat/cord tissue) DNA in combination with QIASymphony DSP DNA Midi Kit (Qiagen #937255) and DNA was bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).

tag: tissue

value: fetal cord tissue

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)


title: 4231

description:
exosomal RNA
4231Exo-Exoplus_Read_Count

tag: gender


title: BM PC 2

description: Sample 17

tag: strain


title: BM PC 1

description: Sample 16


title: EED-ChIPseq

description: Eed antibodies were used to immunoprecipitate chromatin DNA in p3 spinal cords, which contain oligodendrocyte precursors and differentiating oligodendrocytes.

source_name: spinal cords

tag: Stage

value: spinal cords

tag: antibodies

value: Eed (Cell signal Technology #3737)


title: 4343

description:
exosomal RNA
939_Read_Count

value: male


title: Spl PC 3

description: Sample 15

source_name: splenic plasma cells

tag: Sex

value: spleen


title: Suz12-ChIPseq-1

description: Suz12 antibodies were used to immunoprecipitate chromatin DNA in p3 spinal cords, which contain oligodendrocyte precursors and differentiating oligodendrocytes.

tag: stain

value: Suz12 (Millipore #17-663)


title: Spl PC 2

description: Sample 14

tag: organ

tag: surface markers used for sorting


title: 2247

description:
exosomal RNA
re-2247_Read_Count


title: Suz12-ChIPseq-2


title: 4356

description:
exosomal RNA
779_Read_Count


title: 4347

description:
exosomal RNA
912_Read_Count


title: Spl PC 1

description: Sample 13

tag: days after immunization

tag: immunization agent


title: fetal cord tissue, S0116

tag: pre-pregnancy bmi (kg/m^2)


title: fetal cord tissue, S0115


title: Spl PB 3

description: Sample 12

source_name: splenic plasmablasts


title: Spl PB 2

description: Sample 11


title: 4361

description:
exosomal RNA
673_Read_Count

tag: age

tag: disease


title: 4355

description:
exosomal RNA
670_Read_Count

tag: tissue


title: rnaseq_ol_eed_ctr_rep2

description:
rnaseq_raw_counts.txt
Oligodendrocyte precursor cells (OPCs) were isolated from P6 EED cKO or control brains and then differentiated to immature oligodendrocytes (iOLs) in vitro for 2 days.  Transcriptomes from iOLs were then subjected to high throughput sequencing.

source_name: Day 2 differentiating oligodendrocytes

value: Brain

tag: genotype/variation

value: EED cKO


title: rnaseq_ol_eed_cko_rep2


title: fetal cord tissue, S0111

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)


title: rnaseq_ol_eed_cko_rep1


title: fetal cord tissue, S0117

tag: child sex (male = 0; female = 1)


title: fetal cord tissue, S0112


title: 4346

description:
exosomal RNA
624_Read_Count

tag: gender


title: 4358

description:
exosomal RNA
585_Read_Count


title: fetal cord tissue, S0114


title: Spl NP+ IgM+ MBC 3

description: Sample 9

source_name: splenic IgM+ memory B cells

tag: strain


title: rnaseq_ol_eed_ctr_rep1

tag: Stage


title: fetal cord tissue, S0110


title: 4359

description:
exosomal RNA
584_Read_Count


title: rnaseq_opc_eed_cko_rep3

description:
rnaseq_raw_counts.txt
Oligodendrocyte precursor cells (OPCs) were isolated from P6-7 EED cKO or control brains.  Transcriptomes from OPCs were then subjected to high throughput sequencing.

source_name: Oligodendrocyte precursor cells

tag: stain


title: 4370

description:
exosomal RNA
570_Read_Count


title: rnaseq_opc_eed_ctr_rep2


title: rnaseq_opc_eed_cko_rep2


title: fetal cord tissue, S0108


title: 4352

description:
exosomal RNA
566_Read_Count


title: Spl NP+ IgM+ MBC 1

description: Sample 7

tag: Sex

tag: organ


title: fetal cord tissue, S0109


title: Spl NP+ IgG1+ MBC 3

description: Sample 6

source_name: splenic IgG1+ memory B cells

tag: surface markers used for sorting

tag: days after immunization


title: 4351

description:
exosomal RNA
565_Read_Count


title: fetal cord tissue, S0106

tag: pre-pregnancy bmi (kg/m^2)


title: fetal cord tissue, S0107


title: Spl PB 1

description: Sample 10

tag: immunization agent


title: fetal cord tissue, S0105


title: rnaseq_opc_eed_ctr_rep1


title: Spl NP+ IgG1+ MBC 1

description: Sample 4


title: fetal cord tissue, S0104


title: Spl NP+ IgG1+ MBC 2

description: Sample 5


title: 595MOG19

city: Charlottesville

first: David

middle: Michael

last: Johanson

state: VA

address: 200 Jeanette Lancaster Way

department: Department of Neuroscience

institute: UVa School of Medicine

data_processing:
Demultiplexed FASTQ files were processed with the Dada2 v1.12.1 function "filterAndTrim": truncLen = c(300,250), maxN = 0, maxEE = c(10,10), truncQ = 2, rm.phix = TRUE, compress = TRUE, multithread = TRUE
Error learning with Dada2 v1.12.1 "learnErrors" for R1 and R2 reads: multithread = TRUE, Dereplication with "derepFastq": verbose = TRUE
Amplicon Sequence Variant Identification with  Dada2 v1.12.1 "dada" from learned error rates and dereplicated FASTQ reads: multithread = TRUE
Read pair merging with  Dada2 v1.12.1 "mergePairs": verbose = TRUE
Chimera identification and removal with  Dada2 v1.12.1 "removeBimeraDenovo": nethod = "consensus", multithread = TRUE, verbose = TRUE
Taxonomy assignment with  Dada2 v1.12.1 "assignTaxonomy": multithread = TRUE
Genome_build: Taxonomy was assigned manually with input from the following 16S reference databases: Silva v132, Greengenes v13_8_set_97, GTDB bac-arc_ssu_r86, and RefSeq RDB16S v2_May2018
Supplementary_files_format_and_content: comma separated files (.csv) containing: 1. ASV abundances per sample, 2. Taxonomy of each ASV, and 3. Sample parameter data and Identification

source_name: MOG+CFA_19d_mouse fecal matter

growth_protocol: Female C57BL/6 mice were maintained on a 12 hours light/dark cycle with lights on at 7am and provided with standard food and water ad libitum. Mice were housed at 2-3 per cage and experimental treatment was assigned randomly to each cage.

extract_protocol:
Fecal samples were collected from live mice restrained with a tail scruff. DNA for 16S amplification was extracted with a phenol-chloroform method: Fecal pellets were placed in 2 mL tubes containing 200 μL silica-zirconia beads (0.1 mm). The tubes were filled with 750 μL extraction buffer, 200 μL 20% SDS and 750 μL phenol-chloroform-isoamyl alcohol (25:24:1). After disruption, the aqueous phase was separated by centrifugation and cleaned up with two washes of chloroform-isoamyl alcohol (24:1). The DNA was precipitated and resuspended in 10 mM Tris solution.
The V3-V4 region of the 16S rRNA gene was amplified for 25 cycles using specific primers with adapter overhangs as per the Illumina library preparation guide (Forward Primer: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG, Reverse Primer: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC). Following purification of the PCR products, individual indexes were added to the amplicons by PCR. The amplicons were purified, pooled in equal quantities, and then sequenced on the Illumina MiSeq platform.
V3-V4 16S-seq

treatment_protocol: Each group recieved different treatments: naïve mice recieved no treatment, EAE (MOG+CFA) mice were immunized subcutaneously with 50 μg of myelin oligodendrocyte glycoprotein peptide 35–55 (MOG35–55) (CSBIO #CS0681) emulsified at a 1:1 ratio in Complete Freud’s Adjuvant (Sigma Aldrich #F5881). On days 0 and 2, 250 ng of pertussis toxin (List Biologicals #180) was administered intraperitoneally. CFA imce recieved only the equivalent dose of Complete Freud’s Adjuvant.

tag: body weight (grams)

tag: eae clinical score

tag: immunization

value: MOG+CFA

tag: day (relative to immunization)

tag: molecule subtype

value: 16S Amplicon


title: 4353

description:
exosomal RNA
4353-611_Read_Count

tag: tissue

tag: age

tag: disease


title: 4284

description:
exosomal RNA
4284_Read_Count

tag: gender


title: 4283

description:
exosomal RNA
4283_Read_Count


title: 595MOG29

source_name: MOG+CFA_29d_mouse fecal matter

tag: strain


title: fetal cord tissue, S0103

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)


title: Spl FO 1

description: Sample 1

source_name: splenic follicular B cells

tag: Sex

tag: organ

tag: surface markers used for sorting

tag: days after immunization


title: 4319

description:
exosomal RNA
4319_Read_Count


title: 595MOG14

source_name: MOG+CFA_14d_mouse fecal matter

tag: body weight (grams)

tag: eae clinical score


title: Spl FO 2

description: Sample 2

tag: immunization agent


title: Spl FO 3

description: Sample 3


title: fetal cord tissue, S0102

tag: pre-pregnancy bmi (kg/m^2)


title: 594MOG29

tag: immunization

tag: day (relative to immunization)

tag: molecule subtype


title: rnaseq_opc_eed_cko_rep1

tag: Stage

tag: stain

tag: tissue

tag: genotype/variation


title: fetal cord tissue, S0100

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)


title: 4277

description:
exosomal RNA
4277_Read_Count

tag: gender

tag: age

tag: disease


title: fetal cord tissue, S0101

tag: child sex (male = 0; female = 1)


title: sample4

city: Philadelphia

first: James

last: Garifallou

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia

data_processing:
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v3  per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled,  and sequenced on an Illumina NovaSeq sequencer in a paired-end, single indexing run. Sequencing for each library  targeted 25,000 mean reads per cell. Data was then processed using the Cellranger pipeline (10x genomics, v.3.0.2) for demultiplexing and  alignment of sequencing reads to the GRCh38 transcriptome and creation of feature-barcode matrices. Individual  single cell RNAseq libraries were aggregated using the cellranger aggr pipeline. Libraries were normalized for  sequencing depth across all libraries during aggregation. Secondary analysis on the aggregated feature barcode matrix  was performed using the Seurat package (v.3.0) within the R computing environment. Briefly, cells expressing less  than 200 or more than 2500 genes were excluded from further analysis. Additionally, cells expressing >5%  mitochondrial genes were excluded from the dataset.
Genome_build: hg19

source_name: Memory T cells from peripheral blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from five healthy donors. Tmemory T cells (CD45RA-CD4+) were sorted from PBMCs.

extract_protocol:
Dataset consists of a total of five single-cell datasets generated using the 10x Genomics Chromium platform. Prior to GEM generation, the sample’s concentration (cells/ul) and viability (%) were determined by staining the cells with trypan blue and by manually counting using an inverted microscope. Next-generation sequencing libraries were prepared following the 10X Single Cell v3 protocol without modification. Sample quality was evaluated using Agilent’s Bioanalyzer High Sensitivity reagent kit following cDNA amplification and library construction. The completed libraries were quantified using the Kapa Library Quantification Kit and the Life Technologies Viia7 Real-time PCR instrument. Libraries were sequenced in a paired-end, single-indexed format on the Illumina NovaSeq. Cells were sequenced to target a depth of at least 25,000 reads per cell.
scRNA-seq

treatment_protocol: Memory T cells were activated with PMA/Ion/GP for four hours.


title: 4270

description:
exosomal RNA
4270_Read_Count


title: sample3


title: fetal cord tissue, S0099

data_processing:
GenomeStudio; R/Rstudio
green (RAW_ID_Grn.idat) and red (RAW_ID_Red.idat) channels provided
[value definition]  chip position, DNA extraction, and bisulfite conversion batch, and celltype-adjusted residuals provided


title: fetal cord tissue, S0098


title: 594MOG19

tag: strain

tag: body weight (grams)

tag: eae clinical score


title: 593MOG29

tag: immunization


title: 4258

description:
exosomal RNA
4258_Read_Count


title: 593MOG14

tag: day (relative to immunization)


title: sample1


title: 4253

description:
exosomal RNA
4253_Read_Count


title: fetal cord tissue, S0096

tag: pre-pregnancy bmi (kg/m^2)


title: 4249

description:
exosomal RNA
4249_Read_Count


title: fetal cord tissue, S0097


title: sample5


title: 591MOG19

tag: molecule subtype


title: D78R5D01: Monocyte_R5D_01nM_biorep3

city: Dundee

first: Ignacio

last: Moraga

address: Dow Street

institute: University of Dundee

description: CD14 positive monocytes isolated by positive selection from human buffy coat. Cells rested for two days in M-CSF media. Cells then stimulated with R5A11D 0.1 nM for 24 hours

data_processing:
Primary data analysis for quality control, mapping to reference genome and quantification was conducted by Novogene as follows. Quality control: Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Genome_build: Mapping to reference genome: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. Quantification: HTSeq was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, (Reads Per Kilobase of exon model per Million mapped reads), considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels.
Supplementary_files_format_and_content: ENSG gene ID, stimulated value (RKPM), unstimulated value (RKPM), log2fold change(stimulated/unstimulated), p-value, p adjust, significance (yes/no), gene_name, gene_description

source_name: Human, monocyte

growth_protocol: See SAMPLES, description

extract_protocol:
Rneasy Mini Kit, Quiagen Cat#74104
Sequencing libraries were generated using NEBNext® UltraTM RNALibrary Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First StrandSynthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp inlength, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The platform used was Novoseq6000 (GPL27804)

treatment_protocol: See SAMPLES, characteristic: stimulation

value: monocyte

tag: stimulation

value: 24hr R5A11D 0.1nM treatment


title: 4281

description:
exosomal RNA
4281_Read_Count

tag: tissue

value: female


title: D78WTD01: Monocyte_WTD_01nM_biorep3

description: CD14 positive monocytes isolated by positive selection from human buffy coat. Cells rested for two days in M-CSF media. Cells then stimulated with WTD 0.1 nM for 24 hours

value: 24hrWTD 0.1nM treatment


title: fetal cord tissue, S0095


title: 591MOG14


title: D78R5M50: Monocyte_R5M_50nM_biorep2

description: CD14 positive monocytes isolated by positive selection from human buffy coat. Cells rested for two days in M-CSF media. Cells then stimulated with R5A11M 50 nM for 24 hours

value: 24hr R5A11M 50nM treatment


title: 4238

description:
exosomal RNA
4238_Read_Count

value: cerebrospinal fluid

value: medulloblastoma with leptomeningeal metastasis


title: fetal cord tissue, S0094

value: fetal cord tissue


title: 593MOG19


title: 4237

description:
exosomal RNA
4237-846_Read_Count

value: medullublastoma


title: 589MOG29


title: fetal cord tissue, S0093


title: 4233

description:
exosomal RNA
4233_Read_Count


title: sample2


title: D78WTM50: Monocyte_WTM_50nM_biorep3

description: CD14 positive monocytes isolated by positive selection from human buffy coat. Cells rested for two days in M-CSF media. Cells then stimulated with WTM 50 nM for 24 hours

value: 24hr WTM 50nM treatment


title: 589MOG19


title: 589MOG14


title: D78R5D50: Monocyte_R5D_50nM_biorep3

description: CD14 positive monocytes isolated by positive selection from human buffy coat. Cells rested for two days in M-CSF media. Cells then stimulated with R5A11D 50 nM for 24 hours

value: 24hr R5A11D 50nM treatment


title: D78WTD50: Monocyte_WTD_50nM_biorep3

description: CD14 positive monocytes isolated by positive selection from human buffy coat. Cells rested for two days in M-CSF media. Cells then stimulated with WTD 50 nM for 24 hours

value: 24hr WTD 50nM treatment


title: 591MOG29


title: fetal cord tissue, S0091


title: fetal cord tissue, S0090


title: D78US: Monocyte_Control_biorep3

description: CD14 positive monocytes isolated by positive selection from human buffy coat. Cells rested for two days in M-CSF media. Cells then left for a further 24 hours as control population

value: 24hr no IL-10 treatment


title: 588MOG29


title: 4218

description:
exosomal RNA
4218_Read_Count


title: fetal cord tissue, S0089


title: fetal cord tissue, S0088


title: D59R5D01: Monocyte_R5D_01nM_biorep2


title: 4200

description:
exosomal RNA
4200_Read_Count


title: 588MOG14


title: 588MOG19


title: 4189

description:
exosomal RNA
4189_Read_Count


title: D59WTD01: Monocyte_WTD_01nM_biorep2


title: fetal cord tissue, S0087


title: 4169

description:
exosomal RNA
4169_Read_Count

value: male


title: fetal cord tissue, S0085


title: D59R5M50: Monocyte_R5M_50nM_biorep2


title: 4225

description:
exosomal RNA
4225_Read_Count


title: 563control29

source_name: Naïve_29d_mouse fecal matter

value: Naïve


title: 4219

description:
exosomal RNA
4219_Read_Count


title: D59WTM50: Monocyte_WTM_50nM_biorep2


title: fetal cord tissue, S0084


title: 4168

description:
exosomal RNA
4168_Read_Count


title: 563control19

source_name: Naïve_19d_mouse fecal matter


title: 563control8

source_name: Naïve_8d_mouse fecal matter


title: 4152

description:
exosomal RNA
4152_Read_Count

source_name: cerebrospinal fluid


title: D59R5D50: Monocyte_R5D_50nM_biorep2


title: fetal cord tissue, S0083

source_name: cord tissue


title: 4092

description:
exosomal RNA
4092_Read_Count


title: 563control14

source_name: Naïve_14d_mouse fecal matter


title: D59WTD50: Monocyte_WTD_50nM_biorep2


title: 562control8


title: fetal cord tissue, S0082


title: D59US: Monocyte_Control_biorep3


title: 563control-2

source_name: Naïve_-2d_mouse fecal matter


title: 4080

description:
exosomal RNA
4080_Read_Count


title: D52R5D01: Monocyte_R5D_01nM_biorep1


title: fetal cord tissue, S0080


title: D52WTD01: Monocyte_WTD_01nM_biorep1


title: fetal cord tissue, S0081


title: 562control29


title: D52R5M50: Monocyte_R5M_50nM_biorep1


title: fetal cord tissue, S0078


title: D52WTM50: Monocyte_WTM_50nM_biorep1


title: 562control14


title: fetal cord tissue, S0076


title: 4068

description:
exosomal RNA
4068_Read_Count


title: 562control-2


title: D52R5D50: Monocyte_R5D_50nM_biorep1


title: 562control19


title: fetal cord tissue, S0077


title: 4066

description:
exosomal RNA
4066_Read_Count


title: 4093

description:
exosomal RNA
4093_Read_Count


title: D52WTD50: Monocyte_WTD_50nM_biorep1


title: 2763

description:
exosomal RNA
2763_Read_Count


title: fetal cord tissue, S0075


title: 4060

description:
exosomal RNA
4060_Read_Count


title: fetal cord tissue, S0074


title: D52US: Monocyte_Control_biorep1


title: fetal cord tissue, S0073


title: 561control8


title: D36R5D01: CD8_R5D_01nM_biorep3

description: CD8 T cells isolated by positive selection from human buffy coats. Cells activated for three days with anti-CD3 and IL-2 and expanded for a further three days with IL-2. Activation done in the presence of R5A11D

source_name: Human, CD8 cell

value: CD8 cell

value: activated in presence of R5A11D 0.1 nM


title: 2597

description:
exosomal RNA
2597_Read_Count


title: D36WTD01: CD8_WTD_01nM_biorep3

description: CD8 T cells isolated by positive selection from human buffy coats. Cells activated for three days with anti-CD3 and IL-2 and expanded for a further three days with IL-2. Activation done in the presence of WTD

value: activated in presence of WTD 0.1 nM


title: fetal cord tissue, S0071


title: 4061

description:
exosomal RNA
4061_Read_Count


title: 2587

description:
exosomal RNA
2587_Read_Count


title: D36R5M50: CD8_R5M_50nM_biorep2

description: CD8 T cells isolated by positive selection from human buffy coats. Cells activated for three days with anti-CD3 and IL-2 and expanded for a further three days with IL-2. Activation done in the presence of R5A11M.

value: activated in presence of R5A11M 50 nM


title: 561control14

value: 16S Amplicon


title: 561control-2


title: 2596

description:
exosomal RNA
2596_Read_Count


title: fetal cord tissue, S0070


title: D36WTM50: CD8_WTM_50nM_biorep3

description: CD8 T cells isolated by positive selection from human buffy coats. Cells activated for three days with anti-CD3 and IL-2 and expanded for a further three days with IL-2. Activation done in the presence WTM

value: activated in presence of WTM 50 nM


title: fetal cord tissue, S0068


title: 2586

description:
exosomal RNA
2586_Read_Count

value: female


title: 560control8


title: 2251

description:
exosomal RNA
2251_Read_Count

value: cerebrospinal fluid


title: 561control29


title: fetal cord tissue, S0067


title: 560control29


title: D36R5D50: CD8_R5D_50nM_biorep3

description: CD8 T cells isolated by positive selection from human buffy coats. Cells activated for three days with anti-CD3 and IL-2 and expanded for a further three days with IL-2. Activation done in the presence R5A11D

value: activated in presence of R5A11D 50 nM


title: 2634

description:
exosomal RNA
2634_Read_Count

value: medulloblastoma with leptomeningeal metastasis


title: fetal cord tissue, S0072

value: fetal cord tissue


title: 2243

description:
exosomal RNA
2243_Read_Count

value: medullublastoma


title: D36US: CD8_Control_biorep3

description: CD8 T cells isolated by positive selection from human buffy coats. Cells activated for three days with anti-CD3 and IL-2 and expanded for a further three days with IL-2.

value: activated in the absence of IL-10


title: D36WTD50: CD8_WTD_50nM_biorep3

value: activated in presence of WTD 50 nM


title: fetal cord tissue, S0065


title: 2242

description:
exosomal RNA
2242_Read_Count


title: 561control19


title: 560control-2


title: fetal cord tissue, S0064


title: fetal cord tissue, S0063


title: Spl NP+ IgM+ MBC 2

description: Sample 8

source_name: splenic IgM+ memory B cells

tag: Sex

tag: organ

value: spleen

tag: surface markers used for sorting

tag: days after immunization

tag: immunization agent

value: NP-CGG in alum


title: D93R5M50: CD8_R5M_50nM_biorep2


title: 559control29

value: Naïve


title: D93R5D01: CD8_R5D_01nM_biorep2

value: CD8 cell


title: 2218

description:
exosomal RNA
2218_Read_Count

tag: gender

value: male

tag: age


title: 559control8


title: 560control19


title: D93WTD01: CD8_WTD_01nM_biorep2

value: activated in presence of WTD 0.1 nM


title: 4368

description:
exosomal RNA
1068_Read_Count

tag: disease


title: 4369

description:
exosomal RNA
1055_Read_Count


title: fetal cord tissue, S0060

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)


title: 4345

description:
exosomal RNA
1025_Read_Count


title: 559control19

tag: strain

tag: body weight (grams)

tag: eae clinical score

tag: immunization

tag: day (relative to immunization)


title: 4349

description:
exosomal RNA
1019_Read_Count

tag: tissue


title: 560control14

tag: molecule subtype


title: D93WTM50: CD8_WTM_50nM_biorep2

tag: stimulation


title: fetal cord tissue, S0059

tag: pre-pregnancy bmi (kg/m^2)


title: 559control14


title: fetal cord tissue, S0066


title: D93R5D50: CD8_R5D_50nM_biorep2


title: 559control-2


title: D93WTD50: CD8_WTD_50nM_biorep2


title: fetal cord tissue, S0057


title: D93US: CD8_Control_biorep3


title: tur5

description:
p-turb-fol-ij5_S7
processed data file: P_turrubarensis_est_counts.txt

data_processing:
Adapter sequences and low quality bases were trimmed using trim_galore v 0.3.3
A transcriptome reference was built using CDS fasta files from the P. retropinna (PRJNA555005) and P. turrubarensis (PRJNA555006 f) genomes using the Kallisto index function (Bray et. al 2016)
Sequences were alligned to transcriptome reference using Kallisto quant function (Bray et. al 2016)
resultin est_counts were used for subsequent analyses
Genome_build: P. retropinna version 1 (PRJNA555005) and P. turrubarensis version 1 (PRJNA555006 f)
Supplementary_files_format_and_content: Tab-delimited file containing est_counts for each gene/transcript

organism: Poeciliopsis turrubarensis

source_name: P. turrubarensis_maternal follicle

extract_protocol:
Pregnant ovaries were dissected in the field (Costa Rica) and placed in RNAlater and kept on ice, follicles were dissected from late stage (I/J Haynes 1995) embryos and pooled in TriZol and kept at -80C until extraction with direct-Zol RNA miniprep kit
NEBNext Ultra II Drirectional RNA Library Prep Kit for Illumina for use with rRNA depleted RNA. Briefly, 100ng of each RNA sample was fragmented for 7 minutes, primed using random primers, then cDNA synthesis was performed, samples were end-prepped, and NEBNext adapters were ligated to the resulting cDNA. All samples were enriched adapter-ligated DNA using a 7-cycle PCR where each sample was given a unique index primer. Samples were then purified with Ampure XP beads, library quality was assessed with Bioanalyzer and Qubit

tag: Stage

value: pregnant, late stage (I/J Haynes 1995)

tag: river

value: maternal follicle


title: fetal cord tissue, S0056


title: 558control29

value: 16S Amplicon


title: fetal cord tissue, S0061


title: fetal cord tissue, S0055


title: fetal cord tissue, S0054


title: tur4

description:
p-turb-fol-ij4_S4
processed data file: P_turrubarensis_est_counts.txt


title: D85R5D01: CD8_R5D_01nM_biorep1

value: activated in presence of R5A11D 0.1 nM


title: 558control19


title: D85WTD01: CD8_WTD_01nM_biorep1


title: D85R5M50: CD8_R5M_50nM_biorep1

value: activated in presence of R5A11M 50 nM


title: tur3

description:
p-turb-fol-ij3_S3
processed data file: P_turrubarensis_est_counts.txt


title: D85WTM50: CD8_WTM_50nM_biorep1

value: activated in presence of WTM 50 nM


title: fetal cord tissue, S0052


title: 558control14


title: 557MOG8

source_name: MOG+CFA_8d_mouse fecal matter

value: MOG+CFA


title: D85R5D50: CD8_R5D_50nM_biorep1

value: activated in presence of R5A11D 50 nM


title: 558control-2


title: 557MOG-2

source_name: MOG+CFA_-2d_mouse fecal matter


title: D85WTD50: CD8_WTD_50nM_biorep1


title: 558control8


title: fetal cord tissue, S0050

value: fetal cord tissue


title: fetal cord tissue, S0051


title: D85US: CD8_Control_biorep1

value: activated in the absence of IL-10


title: fetal cord tissue, S0048


title: 556MOG-2


title: fetal cord tissue, S0053


title: fetal cord tissue, S0046


title: 555MOG8


title: 555MOG-2


title: fetal cord tissue, S0044


title: wt cells, serum-starved + 1 hour 100 ng/ml EGF, biological rep 1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from wt

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Hela cells stably transfected with pIRES-hrGFPII-IRF2BP1 wt

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Polyclonal Hela cells stably expressing an siRNA-resistant, untagged IRF2BP1 wildtype (wt) or IRF2BP1 K579R (KR) were grown in DMEM containing 10% FBS, 2 mM L-glutamine and 1 mM sodium pyruvate medium (full serum) at 37°C and 10% CO2.

extract_protocol: RNA samples were purified using Nucleospin RNA Plus kit (Machery-Nagel).

treatment_protocol: Cells were treated with siRNA against IRF2BP1 for 72 hours. After 56 hours, cells were either serum-starved for 16 hours (no_FBS), serum-starved for 15 hours and treated for 1 hour with 100 ng/ml EGF (EGF), or not serum-starved at all (full_serum).

tag: cell line

value: Hela

tag: genotype

value: wt

tag: treatment

value: EGF


title: KR cells, serum-starved + 1 hour 100 ng/ml EGF, biological rep 1

description: Gene expression data from KR

source_name: Hela cells stably transfected with pIRES-hrGFPII-IRF2BP1 K579R

value: KR


title: 553MOG8


title: KR cells, serum-starved, biological rep 1

description: Gene expression data from KR

value: no-FBS


title: 553MOG-2


title: 556MOG8


title: wt cells, full growth medium, biological rep 1

description: Gene expression data from wt

value: full-serum


title: 551MOG8


title: fetal cord tissue, S0043

last: Huang

address: 30 Medical Drive

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)


title: fetal cord tissue, S0041

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)


title: 551MOG-2

tag: strain

tag: body weight (grams)


title: KR cells, serum-starved + 1 hour 100 ng/ml EGF, biological rep 2

description: Gene expression data from KR


title: fetal cord tissue, S0040


title: fetal cord tissue, S0045


title: KR cells, full growth medium, biological rep 1

description: Gene expression data from KR


title: wt cells, serum-starved, biological rep 1

description: Gene expression data from wt


title: N2 replicate 2 Input

city: Klosterneuburg

first: Thanh

middle: TK

last: Vuong-Brender

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria

data_processing:
ChIP-seq processing pipeline using Bowtie2 mapping and MACS2 peak calling integrated in nucleome processing and analysis toolkit (https://github.com/tjs23/nuc_tools), we use fragment size = 300 bp and a cutoff p-value of 1E-5.
Genome_build: WS255_WBcel235
Supplementary_files_format_and_content: broadPeak and narrowPeak .bed files generated by MACS2

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Mix-staged worms are grown in liquid culture

extract_protocol:
Worms were snap-frozen in liquid N2, hand ground, fixed in formaldehyde and sonicated. CAMT-1::GFP pulldown was performed using Abcam anti-GFP antibodies and the DNA were de-crosslinked overnight at 65 degree Celcius.
Libraries were prepared following the protocol from NEBNext Ultra II DNA Library Prep Kit for Illumina.

value: Non

value: WT

tag: antibody


title: N2 replicate 1 Input


title: KR cells, full growth medium, biological rep 2

description: Gene expression data from KR


title: fetal cord tissue, S0038

city: Singapore

first: Jonathan

institute: Singapore Institute for Clinical Sciences


title: 550MOG8

tag: eae clinical score

tag: immunization

tag: day (relative to immunization)


title: wt cells, serum-starved + 1 hour 100 ng/ml EGF, biological rep 2

description: Gene expression data from wt


title: KR cells, serum-starved, biological rep 2

description: Gene expression data from KR


title: 548CFA8

source_name: CFA_8d_mouse fecal matter

value: CFA

tag: molecule subtype


title: 550MOG-2

value: 16S Amplicon


title: wt cells, full growth medium, biological rep 2

description: Gene expression data from wt


title: wt cells, serum-starved, biological rep 2

description: Gene expression data from wt


title: camt-1::gfp; egl-19(n2368) replicate 2 Input

value: GFP


title: KR cells, full growth medium, biological rep 3

description: Gene expression data from KR


title: camt-1::gfp; egl-19(n2368) replicate 1 Input


title: fetal cord tissue, S0039

tag: tissue

tag: pre-pregnancy bmi (kg/m^2)


title: camt-1::gfp; egl-19(n582) replicate 2 Input


title: fetal cord tissue, S0037


title: fetal cord tissue, S0036


title: camt-1::gfp replicate 1 Input


title: fetal cord tissue, S0035


title: 548CFA29

source_name: CFA_29d_mouse fecal matter


title: fetal cord tissue, S0033


title: camt-1::gfp; egl-19(n582) replicate 1 Input


title: camt-1::gfp  replicate 2 Input


title: fetal cord tissue, S0034


title: N2 replicate 2 pulldown

value: Abcam Anti-GFP ab290


title: 548CFA19

source_name: CFA_19d_mouse fecal matter


title: KR cells, serum-starved + 1 hour 100 ng/ml EGF, biological rep 3

description: Gene expression data from KR


title: 548CFA14

source_name: CFA_14d_mouse fecal matter


title: wt cells, full growth medium, biological rep 3

description: Gene expression data from wt


title: wt cells, serum-starved, biological rep 3

description: Gene expression data from wt


title: LSEC_late_3

description: CD31+ CD146+ Lyve1+ Retinoid-

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: liver endothelium derived from tumor bearing liver

growth_protocol: Primary liver endothelial cells were isolated by a collagenase digest, gradient centrifugation and magnetic labeling. Magnetically enriched Ecs were used for FACS and dead live staining. RNA was extracted directly after the cell sorting procedure.

extract_protocol: PicoPure extraction kit (Life technologies) according to the manufacturer*s instructions.

tag: cell type

value: total LSEC

value: TG

tag: timepoint

value: Late


title: wt cells, serum-starved + 1 hour 100 ng/ml EGF, biological rep 3

description: Gene expression data from wt

tag: cell line

tag: genotype


title: 548CFA-2

source_name: CFA_-2d_mouse fecal matter


title: N2 replicate 1 pulldown

tag: treatment


title: fetal cord tissue, S0032

source_name: cord tissue

value: fetal cord tissue

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)


title: fetal cord tissue, S0030

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)


title: fetal cord tissue, S0029


title: 547CFA29

tag: strain

tag: body weight (grams)


title: camt-1::gfp; egl-19(n2368) replicate 1 pulldown

tag: antibody


title: camt-1::gfp; egl-19(n2368) replicate 2 pulldown


title: fetal cord tissue, S0028


title: 547CFA19

tag: eae clinical score

tag: immunization


title: KR cells, serum-starved, biological rep 3

description: Gene expression data from KR


title: LSEC_late_2

description: CD31+ CD146+ Lyve1+ Retinoid-


title: 547CFA8

tag: day (relative to immunization)

tag: molecule subtype


title: camt-1::gfp; egl-19(n582) replicate 2 pulldown


title: fetal cord tissue, S0024

tag: tissue

tag: pre-pregnancy bmi (kg/m^2)


title: 547CFA14


title: LSEC_late_1

description: CD31+ CD146+ Lyve1+ Retinoid-

tag: cell type

tag: timepoint


title: LSEC_early4

description: CD31+ CD146+ Lyve1+ Retinoid-

source_name: liver endothelium derived from preneoplastic liver

tag: genotype

value: Early


title: fetal cord tissue, S0027


title: LSEC_early_3

description: CD31+ CD146+ Lyve1+ Retinoid-


title: 547CFA-2


title: camt-1::gfp; egl-19(n582) replicate 1 pulldown

tag: treatment


title: 546CFA29


title: 546CFA8


title: camt-1::gfp  replicate 2 pulldown


title: camt-1::gfp replicate 1 pulldown


title: LSEC_early_1

description: CD31+ CD146+ Lyve1+ Retinoid-


title: fetal cord tissue, S0022

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)


title: LSEC_early_2

description: CD31+ CD146+ Lyve1+ Retinoid-


title: LSEC_wt_3

description: CD31+ CD146+ Lyve1+ Retinoid-

source_name: liver endothelium derived from wt liver

value: Ctrl


title: fetal cord tissue, S0023

tag: maternal age at delivery (years)


title: 546CFA-2


title: fetal cord tissue, S0021

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)


title: SVEC_HGF6h_3

description: SVEC4-10 were serum staved for 3h and then further cultivated in fresh starvation medium with/without HGF supplementation

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: SVEC4-10 6h 20 ng/ml HGF

growth_protocol: SVEC4-10 were purchased from ATCC and cultivated according to the manufacturer's recommendations.

extract_protocol: RNA was extracted using NucleoSpin RNA II kit (Macherey Nagel) according to the manufacturer's instructions.

treatment_protocol: For HGF stimulation, SVEC4-10 were serum starved for 3h prior to supplementation of fresh starvation medium with/without HGF supplementation.

tag: cell line

value: endothelial cells


title: 545CFA8

tag: strain


title: fetal cord tissue, S0020

tag: child sex (male = 0; female = 1)


title: CEC_late_4

description: CD31+ CD146+ Lyve1- Retinoid-

value: CEC


title: fetal cord tissue, S0015


title: fetal cord tissue, S0016


title: fetal cord tissue, S0017


title: SVEC_HGF3h_4

source_name: SVEC4-10 3h 20 ng/ml HGF


title: LSEC_wt_2

description: CD31+ CD146+ Lyve1+ Retinoid-


title: 545CFA19

tag: body weight (grams)


title: 545CFA29

tag: eae clinical score


title: 546CFA19

tag: immunization


title: genomic DNA from crab-eating macaque brain; control-2

city: Kumamoto

first: Kazuya

last: Iwamoto

address: 1-1-1 Honjo, Chuo-ku

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto University

description: normal crab-eating macaque brain sample (control sample cont-2)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina MethylationEPIC kit Beadchip using standard manufacturer's protocols (Illumina).

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

data_processing: BeadStudio software

label: Cy5 and Cy3

organism: Macaca fascicularis

source_name: crab-eating macaque metylation EPIC cont-2

extract_protocol: Genomic DNA was extracted and purified from brain tissue samples using AllPrep DNA/RNA Mini Kit (QIAGEN) according to standard instructions

treatment_protocol: Crab-eating macaques were orally administered saline for about one month (28 days). Samples from macaque brains were collected at 5 days after administration.

tag: gender

value: Male

value: control


title: SVEC_HGF6h_2


title: fetal cord tissue, S0014


title: genomic DNA from crab-eating macaque brain; control-1

description: normal crab-eating macaque brain sample (control sample cont-1)

source_name: crab-eating macaque metylation EPIC cont-1


title: 545CFA14

tag: day (relative to immunization)

tag: molecule subtype


title: genomic DNA from crab-eating macaque brain; control-5

description: normal crab-eating macaque brain sample (control sample cont-5)

source_name: crab-eating macaque metylation EPIC cont-5

value: Female


title: genomic DNA from crab-eating macaque brain; control-4

description: normal crab-eating macaque brain sample (control sample cont-4)

source_name: crab-eating macaque metylation EPIC cont-4


title: CEC_late_2

description: CD31+ CD146+ Lyve1- Retinoid-


title: genomic DNA from crab-eating macaque brain; control-3

description: normal crab-eating macaque brain sample (control sample cont-3)

source_name: crab-eating macaque metylation EPIC cont-3


title: SVEC_HGF3h_1


title: CEC_late_1

description: CD31+ CD146+ Lyve1- Retinoid-


title: SVEC_HGF6h_1


title: CEC_late_3

description: CD31+ CD146+ Lyve1- Retinoid-


title: SVEC_HGF3h_2


title: fetal cord tissue, S0012

tag: tissue

tag: pre-pregnancy bmi (kg/m^2)


title: fetal cord tissue, S0013


title: 545CFA-2


title: fetal cord tissue, S0009


title: SVEC_HGF3h_3

tag: cell type

tag: timepoint


title: 544CFA29


title: CEC_early_1

description: CD31+ CD146+ Lyve1- Retinoid-

tag: genotype


title: SVEC_ctrl_1

value: ctrl


title: 544CFA8


title: CEC_early_3

description: CD31+ CD146+ Lyve1- Retinoid-


title: SVEC_ctrl_3


title: CEC_early_2

description: CD31+ CD146+ Lyve1- Retinoid-


title: 544CFA19


title: fetal cord tissue, S0010

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)


title: CEC_wt_2

description: CD31+ CD146+ Lyve1- Retinoid-

value: WT


title: 544CFA-2

value: CFA


title: Macrophage_wt_2

description: Retinoid- CD146- CD11b+ F4/80+

source_name: wildtype liver

growth_protocol: Macrophages were isolated by a collagenase digest, a gradient centrifugation and magnetic labeling. Magnetically enriched macrophages were further FACS purified using CD11b, F4/80, CD146 and live/dead cell discrimination. RNA was immediately extracted once the cell sorting procedure was complete.

extract_protocol: PicoPuro extraction kit (Life technologies) according to the manufacturer's instructions.

value: wildtype liver

value: macrophage


title: CEC_wt_3

description: CD31+ CD146+ Lyve1- Retinoid-


title: 544CFA14

value: 16S Amplicon


title: fetal cord tissue, S0008

tag: maternal age at delivery (years)


title: SVEC_ctrl_2


title: Macrophage_wt_4

description: Retinoid- CD146- CD11b+ F4/80+


title: Macrophage_wt_3

description: Retinoid- CD146- CD11b+ F4/80+


title: LSEC_wt_1

description: CD31+ CD146+ Lyve1+ Retinoid-

value: total LSEC


title: Macrophage_wt_1

description: Retinoid- CD146- CD11b+ F4/80+


title: fetal cord tissue, S0007

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)


title: CEC_wt_1

description: CD31+ CD146+ Lyve1- Retinoid-


title: 543CFA8

source_name: CFA_8d_mouse fecal matter


title: fetal cord tissue, S0003


title: fetal cord tissue, S0011


title: Macrophage_tg_3

description: Retinoid- CD146- CD11b+ F4/80+

source_name: tumor bearing liver

value: tumor bearing liver


title: fetal cord tissue, S0005


title: 543CFA-2


title: 543CFA14


title: fetal cord tissue, S0004


title: 543CFA29

source_name: CFA_29d_mouse fecal matter


title: Macrophage_tg_2

description: Retinoid- CD146- CD11b+ F4/80+


title: Hep_wt_2

description:
primary isolated hepatocytes
WT

growth_protocol: Primary hepatocytes were isolated through a perfusion with EGTA and collagenase buffer. Primary hepatocytes were cultivated for 4 hours. Medium change was performed to remove non-adherent cells. Cells were cultivated for another 20 hours and after this RNA extraction performed. Only samples with a RIN higher than 7 were used for expression profiling analysis.

extract_protocol: RNA was extracted using the Nucleo Spin RNA II kit (Macherey Nagel) according to the manufacturer's instructions.

value: liver


title: 543CFA19

source_name: CFA_19d_mouse fecal matter