title: Patient R2268 treated with placebo [R2268_prot]


title: Patient R2433 treated with azithromycine [R2433_prot]

status: Public on Aug 22 2022

type: SRA

city: Paris

first: David

last: Michonneau

address: 1 avenue Claude Vellefaux

department: Hematology and transplantation

country: France

institute: Assistance Publique des Hôpitaux de Paris

description:
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
filteredinbarcodes.csv.gz

library_source: other

data_processing:
library strategy: CITE-seq
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger v6.0 pipeline where ADT and mRNA sequences were concatenated and aligned using GRCh38 genome assembly as reference data. Individual outputs were concatenated without normalization with CellRanger aggr v6.0
Cell surface proteins were identified with specific oligonucleotide sequence (Format TotalSeqB, Biolegend): CD3_TotalSeqB, CD45RA_TotalSeqB, CCR4_TotalSeqB, CD4_TotalSeqB_SK3, CD4_TotalSeqB_RPAT4, CD8_TotalSeqB_SK1, CD8_TotalSeqB_RPAT8, CD25_TotalSeqB, PD1_TotalSeqB, CXCR3_TotalSeqB, CCR6_TotalSeqB, CXCR5_TotalSeqB, CCR7_TotalSeqB, CD161_TotalSeqB, CTLA4_TotalSeqB, CD95_TotalSeqB, HLA-DR_TotalSeqB, ICOS_TotalSeqB, CD39_TotalSeqB, CD27_TotalSeqB, KLRG1_TotalSeqB, CD28_TotalSeqB, CD38_TotalSeqB_HB7, CD38_TotalSeqB_HIT2, CD127_TotalSeqB, CD73_TotalSeqB, TCRVa72_TotalSeqB, CD56_TotalSeqB, CD19_TotalSeqB, CD11c_TotalSeqB, CD123_TotalSeqB, CD14_TotalSeqB, IgD_TotalSeqB, CD36_TotalSeqB, KID2DL1_TotalSeqB, NKp30_TotalSeqB, CD16_TotalSeqB, CD20_TotalSeqB, NKp46_TotalSeqB, IgM_TotalSeqB, CCR5_TotalSeqB, CD11b_TotalSeqB, NKG2D_TotalSeqB, CD24_TotalSeqB_ref1, CD24_TotalSeqB_ref2, 2B4_TotalSeqB. All sequences are available on https://www.biolegend.com/en-us/totalseq/barcode-lookup
Further processing was done with Seurat v4.0.0 (cell and gene filtering, normalization, clustering, differential gene expression analysis).
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

organism: Homo sapiens

source_name: Peripheric blood

extract_protocol:
Library was prepared using Chromium Single Cell 3ʹ version CG000317 rev B protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ version CG000317 rev B protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA and the antibody-derived tagged cDNAs. For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ version CG000317 rev B protocol (10x Genomics).
Libraries were equimolar pooled to obtain at least 20,000 read pairs per cell and 5,000 read pairs for feature barcode part after sequencing on Illumina Novaseq 6000 (100 cycles cartridge).

tag: tissue

value: Peripheric blood

tag: cell type

value: PBMC

tag: library type

value: ADT

tag: treatment

value: azithromycine


title: NCoR_WT_Day0 rep1

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr

department: CMM

country: USA

institute: University of California, San Diego

library_source: genomic

data_processing:
FASTQ files were mapped to the mm10 mouse reference genome with Bowtie2.  Peaks were called with HOMER (findPeaks) using parameters “-style factor -minDist 200 -size 200”.  After merging these peaks, correlations among replicates from the same cell subset/treatment were evaluated by correlation using tag counts.  The two most highly correlated samples were used for identifying the most robust peaks using the irreproducible discovery rate (IDR) method.  For this step, peaks were called with HOMER’s findPeaks, using parameters “-L 0 -C 0 -fdr 0.9 -minDist 200 -size 200”.  IDR peaks from different conditions involved in a comparison merged with HOMER’s mergePeaks and annotated with HOMER’s annotatePeaks.pl.  The raw tags of all samples which had reasonable correlation were quantified with HOMER (annotatePeaks.pl) using parameter “-noadj”.  Peaks which contained at least 4 tags in at least 1 sample were used to identify differentially bounded peaks (DBP) by DESeq2.  Peaks were categorized as distal peaks which are 2 kb away from known TSS and promotor peaks which are located within 2 kb region of known TSS sites.
ChIP peak single was normalized to the sequence depth.
Assembly: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: Bone marrow cell

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed in biological replicates as previously described (Heinz et al., 2018: Sakai et al., 2019) with modifications as follows.  For H3K27ac ChIP assays, cells were cross-linked with 1% (vol/vol) formaldehyde (Thermo Fisher Scientific) in PBS for 10 min at room temperature.  For NCoR1, HDAC3, PU.1, p65, Jdp2, Fosl2, PGC1b and FLAG-tag ChIP assays, cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG) (ProteoChem) in PBS for 30 min at room temperature, and then directly a second crosslinking was performed by the addition of 1% (vol/vol) formaldehyde in PBS for 10 min.  The crosslinking reaction was quenched by 0.125 M glycine (Thermo Fisher Scientific).  Cells were washed once with cold PBS and pelleted at 1,000 g for 5 min at 4°C.  Crosslinked cells were resuspended in ice-cold hypotonic buffer (10 mM HEPES-KOH (pH 7.9), 85 mM KCl, 1 mM EDTA, 1% NP-40, 1 mM PMSF (Sigma), 0.5 mM sodium butyrate (Sigma), 1X protease inhibitor cocktail (Sigma)), and centrifuged at 1,000 g for 5 min at 4°C to obtain a nuclear fraction.  Nuclear pellets were resuspended in 100 ml of either LB3 buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-laurosylsarcosine, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail for H3K27ac ChIP) or PIPA-NR buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% sodium deoxycholate, 0.1% SDS, 1% NP-40, 0.5 mM DTT, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail, for NCoR, HDAC3, PU.1, p65, Fosl2, PGC1b and FLAG-tag ChIP).  Chromatin DNA was sonicated in a 96 Place microTUBE Rack (Covaris) using a Covaris E220 for 12-18 cycles with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were centrifuged at 15,000 rpm for 10 min at 4°C, and the supernatant was used for immunoprecipitation.  LB3 lysate was diluted 1.1-fold with 10% Triton X-100.  1% of the lysate was kept as ChIP input.  The lysates were rotated with each antibody pre-bound to 20 ml of beads (10 ml of Dynabeads protein A (Invitrogen) + 10 ml of Dynabeads protein G (Invitrogen)) overnight at 4°C.  After the immunoprecipitation, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail), wash buffer III (10 mM Tris-HCl (pH 7.5), 250 mM LiCl, 1% Triton X-100, 0.7% sodium deoxycholate, 1 mM EDTA, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail) and twice with TET (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.2% Tween-20, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail), and then resuspended in 25 ml of TT (10mM Tris-HCl (pH 7.5), 0.05% Tween-20).
The immunoprecipitated chromatin samples were used for library preparation with NEBNext Ultra II Library kit (NEB) according to the manufacturer’s instructions.  DNA in 46.5 ml of NEB reactions was crosslinks reversed by adding 4 ml of 10% SDS, 4.5 ml of 5 M NaCl, 3 ml of 500 mM EDTA, 1 ml of 20 mg/ml proteinase K (NEB) and 20 ml of water by incubation for 1 hr at 55°C, and then 30 min at 65°C.  DNA was purified with 2 ml of SpeedBeads (GE Healthcare) in 20% PEG 8000/1.5 M NaCl (Final 12% PEG 8000), and eluted with 25 ml of TT.  The eluted DNA was amplified for 14 cycles in 50 ml of PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix and 0.5 mM each of primers Solexa 1GA and Solexa 1GB.  The amplified libraries were purified with 2 ml of SpeedBeads in 20% PEG 8000/2.5 M NaCl (Final 13% PEG 8000), eluted with 20 ml of TT, size selected using PAGE/TBE gel (Invitrogen) for 225-325 bp fragments by gel extraction, and single-end sequenced on HiSeq 4000.  ChIP input material (1% of sheared DNA) in 46.5 ml of TE was crosslinks reversed by adding 4 ml of 10% SDS, 4.5 ml of 5 M NaCl, 3 ml of 500 mM EDTA, 1 ml of 20 mg/ml proteinase K and 20 ml of water by incubation for 1 hr at 55°C, and then 30 min at 65°C.  The input DNA was purified with SpeedBeads as described above, and eluted with 25 ml of TT.  The eluted input DNA was prepared for libraries and amplified as described for ChIP samples.

tag: cell line

value: Bone marrow cell

tag: chip antibody

value: NCoR


title: Patient R2268 treated with placebo [R2268_geneexp]

library_source: transcriptomic

molecule: polyA RNA

value: mRNA

value: placebo


title: Patient R2122 treated with placebo [R2122_geneexp]


title: Primary_Ctrl_Day3_Input_ChIPseq

city: Marseille

first: Estelle

last: Duprez

address: 27 Boulevard Lei Roure

institute: CRCM

description: Spiked-ChIPseq with S2 drosophila chromatin

data_processing:
quality control 1 before mapping
Sequencing quality control was determined using the FastQC tool
quality control 2 before mapping
Reads with a Phred quality score less than 30 were filtered out
mapping
Reads were mapped to an "hybrid genome" combining Mus musculus (GRCm38/mm10) and Drosophila melanogaster (dm6) genomes using default parameters of Bowtie2 (v2.3.4.1) . Tags were sorted according to their genome of origin (mm10 or dm6).
quality after mapping
Duplicate tags were removed by samtools rmdup function and mapped tags were filtered using samtools view -F 4 for further analysis
down-sampling through spike-in correction
A scaling factor was calculated using dm6 mapped tags (Spike-in antibody-bound regions) and mm10 mapped tags were normalized according to this scaling factor (Spike-in correction)
Genome_build: mm10 + dm6
Supplementary_files_format_and_content: Normalized-mapped reads were converted into BigWig using the deepTools suite (v2.2.4)

source_name: PLZF/RARA transformed progenitor cells

extract_protocol:
PLZF/RARA transformed progenitors (late promyelocytes: Cd45.2+, C-Kit+, Gr1+, Cd34-, FcγR+) were purified using the FACS Aria III cell sorter (Beckman Dickinson). Cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Genomic DNA was purified using the i-Pure kit (Diagenode)
Libraries were generated using the MicroPlex Library Preparation Kit (Diagenode) following the manufacturer's instructions and analyzed on a 2100 Bioanalyzer system (Agilent) prior sequencing.

treatment_protocol: A cohort of 3-5 mice was treated with retinoic acid or corn oil supplemented with 10% of DMSO for 3 or 7 days.

value: Late promyelocytes

value: Leukemic bone marrow

value: Corn Oil 10% DMSO / Intraperitoneally injected


title: △T PC3ML + EV PIC 1

type: RNA

city: Norfolk

first: Allison

middle: Heath

last: Mathiesen

state: VA

address: 700 W Olney Rd, Department of Physiology

institute: Eastern Virginia Medical School

description: mRNA was detected using the NanoString PanCancer Progression Panel according to manufacturer instructions

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The NanoString RCC files were normalized in Rosalind and a threshold cutoff of 20 was applied for the normalized samples.

molecule: total RNA

source_name: PC3ML prostate cancer cell

label_protocol: not provided

growth_protocol: PC3ML were cultured in DMEM/F12 supplemented with 10% FBS and Pen/Strep until 70% confluent

extract_protocol: Following overnight incubation cells were collected and RNA isolated using the Direct-Zol miniprep kit (Zymo research corporation cat# R2072

treatment_protocol: Once cells reached 70% confluency they were treated with EV at 100,000 EV/cell and incubated overnight

value: PC3ML prostate cancer cell

value: HAMVEC EV PIC


title: △T PC3ML No EV 2

value: No Treatment


title: Patient R2433 treated with azithromycine [R2433_geneexp]


title: H3K27ac_NKO_Day4 rep1


title: NoTreatment_Replicat1_H3K4me3_ChIPseq

value: no treatment

tag: chip antibodies

value: H3K4me3 (Diagenode, 15410003) + Spike-in antibody (Active Motif, 61686)


title: Patient R2192 treated with azithromycine [R2192_prot]


title: WT PC3ML + EV PIC 3


title: Patient R1862 treated with azithromycine [R1862_geneexp]


title: △T PC3ML + EV C 3

value: HAMVEC EV C


title: Patient R3753 treated with placebo [R3753_geneexp]

value: Peripheric blood


title: △T PC3ML + EV C 1


title: NoTreatment_Replicat2_H3K4me1_ChIPseq

value: H3K4me1 (Abcam, ab8895) + Spike-in antibody (Active Motif, 61686)


title: NoTreatment_Replicat2_H3K27ac_ChIPseq

value: H3K27ac (Active Motif, 39133) + Spike-in antibody (Active Motif, 61686)


title: Patient R3732 treated with azithromycine [R3732_geneexp]

value: PBMC

value: azithromycine


title: △T PC3ML No EV 3


title: NoTreatment_Replicat2_Input_ChIPseq


title: H3K27ac_NKO_Day0 rep2

value: Bone marrow cell


title: H3K27ac_NKO_Day0 rep1


title: ATAC_WT_Day4_RGFP966 rep1

data_processing:
FASTQ files were mapped to the mm10 mouse reference genome with Bowtie2.  Peaks were called with HOMER (findPeaks) using parameters “-style factor -minDist 200 -size 200”.  After merging these peaks, correlations among replicates from the same cell subset/treatment were evaluated by correlation using tag counts.  The two most highly correlated samples were used for identifying the most robust peaks using the irreproducible discovery rate (IDR) method.  For this step, peaks were called with HOMER’s findPeaks, using parameters “-L 0 -C 0 -fdr 0.9 -minDist 200 -size 200”.  IDR peaks from different conditions involved in a comparison merged with HOMER’s mergePeaks and annotated with HOMER’s annotatePeaks.pl.  The raw tags of all samples which had reasonable correlation were quantified with HOMER (annotatePeaks.pl) using parameter “-noadj”.  Peaks which contained at least 4 tags in at least 1 sample were used to identify differentially bounded peaks (DBP) by DESeq2.  Peaks were categorized as distal peaks which are 2 kb away from known TSS and promotor peaks which are located within 2 kb region of known TSS sites.
ATAC peak quantification was normalized to the total tags in peaks.
Assembly: mm10

extract_protocol:
70000 cultured cells were washed once with PBS and once with cold lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40).  The cells were suspended in 50 µl of 1X Reaction Buffer (25 ul of Tagment DNA Buffer, 2.5 ul of Tagment DNA enzyme I, and 22.5 ul of water) (Nextera DNA Library Preparation Kit, Illumina).  Transposase reactions were carried out at 37°C for 30 min, and then DNA was purified using ChIP DNA Clean & Concentrator Kit (Zymo Research).
DNA was amplified using the Nextera primer Ad1 and a unique Ad2.n barcoding primer using NEBNext High-Fidelity 2X PCR Master Mix (NEB) for 7 cycles.  The amplified libraries were purified with 2 ul of SpeedBeads (GE Healthcare) in 20% PEG 8000/2.5 M NaCl (Final 13% PEG 8000), eluted with 15 ul of EB (Zymo Research), size selected using PAGE/TBE gel (Invitrogen) for 175-225 bp fragments by gel extraction, and single-end sequenced on HiSeq 4000 (Illumina).

tag: genotype

value: Wild type

value: Osteoclast differentiation

tag: time


title: Patient R2192 treated with azithromycine [R2192_geneexp]

value: mRNA


title: WT PC3ML + EV C 2


title: ATAC_WT_Day4 rep1


title: H3K27ac_WT_Day0 rep2


title: Mock-2-input-2

city: BeiJing

first: Kai

last: Li

address: Yi He Yuan Street No.5

department: School of Life Science

country: China

institute: Peking University

data_processing:
The index of the reference genome was built using BWA v0.7.12.
The pre-processed and clean reads were aligned to the reference genome using BWA-MEM v0.7.12 with the default parameters.
The exomePeak R package (version 2.16.0) was used for m6A peak calling in each anti-m6A immunoprecipitation group, with the corresponding input samples serving as a control (q-value: 0.05)
The m6A-enriched motifs of each group were identified by MEME, with 100-nt long peak summit-centered sense sequences as input sequence.
Weblogo 3.0 was used to analyze the sequence context of m6A regions.
Assembly: hg19
Supplementary files format and content: peak bw files

source_name: Huh7 cells

growth_protocol: DMEM, 15% fetal bovine serum(FBS, Gibco) and supplemented with 100 U/mL penicillin and 100 mg/mL streptomycin (Gibco). Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
RNA was harvested using TRIzol reagent (Thermo Fisher Scientific) . 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for MeRIP-seq were prepared using SMARTer® Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara) following manufacturer's protocols.

value: Huh7 cells

value: human hepatocarcinoma cell

value: WT

tag: infection

value: uninfected

value: Day 3


title: ATAC_WT_Day0 rep2


title: H3K27ac_WT_Day4 rep1


title: △T PC3ML No EV 1

value: PC3ML prostate cancer cell

value: No Treatment


title: OxLDL-PPARG KD_3

city: Seoul

first: Jae-Hoon

last: Choi

address: 222 Wangsimniro, Seongdong Gu

department: Department of Life Science

country: South Korea

institute: Hanyang University

description: OxLDL-PPARG KD_3

data_processing:
The RNA reads were aligned to the reference sequences (GRCh38) and quantified as transcript per million (TPM) using STAR (v2.7.8a) and RSEM (v1.3.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include TPM values

source_name: Aortic valve

growth_protocol: Human aortic valves from patients were collected into the cold sterile saline solution. After incubation with collagenase solution, aortic valvular endothelial cells were isolated from valve tissue according to the previous report (Gould & Butcher, J Vis Exp. 2010, doi: 10.3791/2158). Isolated cells were cultured with Endothelial Cell Growth Medium-2 (EGM-2) with BulletKit (Lonza), supplemented with 10% FBS in humidified CO2 Incubator (5% CO2, 37°C).

extract_protocol:
Total RNA was extracted from aortic valvular endothelial cells using the TRIzol Reagent (Invitrogen).
cDNA libraries for sequencing were constructed from total RNA, by using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer's protocol and sequenced using the Illumina NovaSeq 6000 system with 100nt paired-end reads.

treatment_protocol: Cells were transfected with siRNA targeting PPARG or negative control siRNA by electrophoresis using Neon Transfection System (Invitrogen). 48 hours after transfection, cells were treated with or without oxLDL (150µg/mL) for 24 hours.

value: Aortic valve

value: Valvular endothelial cell

tag: Sex

value: male

value: oxLDL

tag: transfection

value: siRNA targeting PPARG


title: Mock-1-IP-2


title: ATAC_WT_Day4 rep2


title: NoTreatment_Replicat1_H3K4me1_ChIPseq

value: Late promyelocytes

value: Leukemic bone marrow

value: no treatment

value: H3K4me1 (Abcam, ab8895) + Spike-in antibody (Active Motif, 61686)


title: H3K27ac_WT_Day0 rep1

value: Bone marrow cell


title: OxLDL-PPARG KD_1

description: OxLDL-PPARG KD_1


title: ATAC_WT_Day4_RGFP966 rep2

value: Wild type

value: Osteoclast differentiation


title: Patient R2155 treated with azithromycine [R2155_prot]

value: Peripheric blood

value: PBMC

value: ADT

value: azithromycine


title: NoTreatment_Replicat1_H3K27ac_ChIPseq

value: H3K27ac (Active Motif, 39133) + Spike-in antibody (Active Motif, 61686)


title: WT PC3ML No EV tx 3

value: PC3ML prostate cancer cell

value: No Treatment


title: OxLDL-NC_3

value: Aortic valve

value: Valvular endothelial cell

value: male

value: negative control siRNA


title: WT PC3ML + EV PIC 1

value: HAMVEC EV PIC


title: WT PC3ML + EV C 3

value: HAMVEC EV C


title: Patient R2155 treated with azithromycine [R2155_geneexp]

value: mRNA


title: NoTreatment_Replicat1_Input_ChIPseq

value: Late promyelocytes

value: Leukemic bone marrow

value: no treatment


title: ATAC_NWT_Day0 rep2

value: Bone marrow cell

value: NCoR1 flox/flox

value: Osteoclast differentiation


title: NoTreatment_Replicat1_H3K27me3_ChIPseq

value: H3K27me3 (Cell Signalling, C36B11) + Spike-in antibody (Active Motif, 61686)


title: OxLDL-NC_1

value: oxLDL


title: WT PC3ML + EV C 1

value: PC3ML prostate cancer cell


title: WT PC3ML + EV PIC 2


title: OxLDL-PPARG KD_2

description: OxLDL-PPARG KD_2

value: siRNA targeting PPARG


title: NT-PPARG KD_3

description: NT-PPARG KD_3

value: Aortic valve

value: Not treated


title: ATAC_WT_Day0 rep1

value: Wild type


title: ProRep_MS_Replicat1

description: Treated cells

data_processing:
quality control 1 before mapping:
Sequencing quality control was determined using the FastQC tool
quality control 2 before mapping:
Reads with a Phred quality score less than 30 were filtered out
mapping: Reads were mapped to mm10 genome using subread-align (v1.5.0) with default parameters
Gene expression was determined by counting mapped tags at gene levels using featureCounts
Assembly: mm10
Supplementary files format and content: Gene Count csv files; each file contains data for both replicates

growth_protocol: Cells were maintained at exponential growth in IMDM with 20% foetal calf serum, 1% penicillin streptomycin supplemented with Il-6 (20ng/ml), Il-3 (20ng/ml), GM-CSF (10ng/ml) and SCF 50ng/ml

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro kit (Qiagen)
cDNA was synthesized using a SMART-Seq v3 Ultra Low Input RNA kit for Sequencing (Clontech). ds-cDNA was fragmented using S220 Focused ultrasonicator (Covaris) and libraries were generated using a NEBNext Ultra DNA Library Prep kit (New England Biolabs).

treatment_protocol: Cells were  for 72 hours with GSK126 2.5µM or MS1943 2.5µM

value: Promyelocytes


title: SZ1901-2-IP-2

value: Huh7 cells

value: human hepatocarcinoma cell

value: WT

value: ZIKV

value: Day 3


title: Mock-2-IP-2

value: uninfected


title: Liver, female, FGF21, sample9

city: Davis

first: Karen

middle: K

last: Ryan

address: 1 Shields Ave

department: Neurobiology, Physiology and Behavior

institute: University of California Davis

data_processing:
The quality of raw reads was assessed using fastqc.
Ribosomal RNA content was determined by aligning the reads against a set of Mus musculus rRNA sequences using bowtie2 v.2.3.4.1.
Raw reads were processed and trimmed to remove phiX and adapter sequences, and to remove the first 11 bases from each read.
Tables of raw counts and counts-per-million (CPM) normalized counts were generated.
Assembly: Processed reads were aligned to GRCm38 primary genome assembly using GENCODE vM15 annotation, with STAR v.2.6.0c to generate counts per gene.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each Sample
Supplementary files format and content: tab-delimited text file includes normalized counts-per-million (cpm) values for each Sample
Supplementary files format and content: tab-delimited text file includes log2 normalized counts-per-million (cpm) values for each Sample

source_name: Liver

extract_protocol:
Total RNA was isolated from livers using RNeasy mini kit (Qiagen).
RNA libraries were prepared using the QuantSeq FWD kit (Lexogen) for multiplexed sequencing according to the recommendations of the manufacturer using both, the UDI-adapter and UMI Second-Strand Synthesis modules (Lexogen).

treatment_protocol:
C57B/6J male and female mice were put on 60% high-fat diet for approx. 10 weeks beginning at 10 weeks of age.
Mice were counterbalanced into vehicle or FGF21 treatment groups based on body weight, then given two injections of recombinant human FGF21 (0.1 mg/kg, i.p.) or saline vehicle: one dose right before onset of the dark cycle, and a second dose right after onset of the light cycle the following day.
Mice were euthanized two hours after the AM injection. Livers were collected, snap frozen in liquid nitrogen, and stored at -80c.

value: Liver

tag: strain

value: Female


title: WT PC3ML No EV tx 2

value: No Treatment


title: NT-PPARG KD_1

description: NT-PPARG KD_1

value: Valvular endothelial cell

value: male


title: Liver, female, FGF21, sample7


title: RNAseq_OB_rep1

city: Xi'an

first: Ruohan

last: Hao

state: Shaanxi

address: No.28 West Xianning Road

institute: Xi'an Jiaotong University

data_processing:
RNA-seq reads were aligned to hg19 using STAR (Dobin et al., 2013) with default parameters. The transcript and gene-based expression levels were quantified and normalized to transcript per million (TPM) using RSEM (Li et al., 2011).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited txt files contain gene expression values and expected counts evaluated by RSEM.

source_name: osteoblasts differentiated from mesenchymal stem cells

growth_protocol: Human umbilical cord derived MSCs were cultured at 37 °C, 5% CO2 in Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics (penicillin 100 U/ml, streptomycin 100 μg/ml)

extract_protocol:
Total RNA was extracted form samples using the TRIzol (Invitrogen) method. RNA concentration and purity were evaluated with a NanoDrop spectrophotometer (Thermo Fisher).
RNA-seq libraries were constructed under manufacturer’s instructions and were then sequenced on the Illumina HiSeq X Ten platform using the 150-bp pair-end sequencing strategy.

treatment_protocol: Cells were induced to osteogenic differentiation by culturing in DMEM supplemented with 10% FBS, 1% antibiotics, 10 mM glycerol-2-phosphate, 50 μM L-ascorbic acid, and 100 nM dexamethasone. Medium was replaced every 3 days.  Adipogenic differentiation was induced in hMSC cells cultured by alternately supplying treatment of solution A and B. Solution A: DMEM medium containing 10% FBS, 1% penicillin/streptomycin, 10mg/L insulin (Novo Nordisk), 1 umol/L dexamethasone, 0.5mmol/L IBMX (Sigma), 100 umol/L indometacin (Sigma). Solution B: DMEM medium containing 10% FBS, 1% penicillin/streptomycin, 10mg/L insulin. Cells were firstly cultured in solution A for 3 days and were additionally supplied with solution B for another day.

value: Osteoblast

tag: differentiation timepoint


title: SZ1901-2-input-2


title: Liver, female, FGF21, sample6


title: WT PC3ML No EV tx 1

value: PC3ML prostate cancer cell


title: NT-NC_3

value: Aortic valve

value: negative control siRNA


title: OxLDL-NC_2

value: oxLDL


title: ProRep_MS_Replicat2

description: Treated cells

value: Promyelocytes

value: Leukemic bone marrow


title: NT-NC_2

value: Not treated


title: NT-NC_1


title: SZ1901-1-IP-2

value: Huh7 cells

value: human hepatocarcinoma cell

value: WT


title: ProRep_NT_Replicat1

description: Untreated cells

value: DMSO


title: SZ1901-1-input-2

value: ZIKV

value: Day 3


title: RNAseq_AC_rep1

source_name: adipocytes differentiated from mesenchymal stem cells

value: Adipocyte


title: Mock-1-input-2

value: uninfected


title: Liver, female, saline, sample8

value: Liver

value: Female

value: Saline


title: RNAseq_hMSC_rep2

source_name: Human umbilical cord derived mesenchymal stem cells

value: hMSC

value: Undifferentiated


title: NT-PPARG KD_2

description: NT-PPARG KD_2

value: Aortic valve

value: Valvular endothelial cell

value: male

value: siRNA targeting PPARG


title: Liver, female, saline, sample10


title: ATAC_NWT_Day0 rep1

value: Bone marrow cell

value: NCoR1 flox/flox

value: Osteoclast differentiation


title: RNAseq_OB_rep2

value: Osteoblast


title: Undiff. hiPSC - Rep 3

city: Genova

first: Luca

last: Pandolfini

state: Genova

address: Via Enrico Melen 83, Building B

department: Center for Human Technologies

country: Italy

institute: Istituto Italiano di Tecnologia - I

data_processing:
Transcripts were pseudoaligned using Salmon  in mapping-based mode (with its default "--validateMappings" flag). A decoy-aware version of the Ensembl mouse transcriptome (mm10; refgenomes.databio.org) was used as a reference.
Assembly: mm10 (refgenomes.databio.org)
Supplementary files format and content: Salmon counts

source_name: Human induced pluripotent stem cells

growth_protocol: Starting from hiPSCs (ATCC DYS0100) cells were seeded onto Geltrex™ LDEV-Free Reduced Growth Factor Basement Membrane Matrix (ThermoFisher, A1413202) in Essential 8™ Medium (ThermoFisher A1517001) containing Essential 8™ Medium Supplement(ThermoFisher A1517-01), 100 U/ml Penicillin-streptomycin, and 2 μM Y-27632 (Cell Guidance Systems SM02-5). Less than 24 hours later, E8 containing Y-27632 was aspirated and fresh E8 media without Y-27632 was added. E8 media was changed daily for another 2 days. Cells were then subjected to neural induction (DIV 0) and incubated in WiBiTi media based in DMEM/F-12 containing containing 2mM Glutamine, 1 mM Sodium Pyruvate, 100 U/ml Penicillin-streptomycin, 1mM Non-essential amino acids, 0.05mM β-mercaptoethanol, 10 μM 53AH, 10 μM LDN193189 hydrochloride, 1 μM RepSox (SigmaAldrich R0158-5MG), N-2 Supplement 100X, and B-27 Supplement minus Vitamin A 50X. WiBiTi was changed daily until DIV 10 where cells were passaged and reseeded in N2B27 media containing Y-27632 at a density of 200,000 cells/cm2 on poly-l-ornithine and Laminin iMatrix-511silk E8 (511 human laminin, Amsbio AMS.892 021) coated plastic. Less than 24 hours later, N2B27 containing Y-27632 was aspirated and fresh WiBiTi media without Y-27632 was added. Cells were maintained in WiBiTi for another 4 days until DIV 15, where the media was changed to N2B27. The following day, DIV 16, cells were then cultured for an additional 6 days (DIV 21) in CH27 media, N2B27 media supplemented with 3 μM CHIR99021 (SigmaAldrich SML1046-5MG). At DIV 21 cells reach confluency and required another passage in CH27 media supplemented with Y-27632 and onto poly-l-ornithine/511 human laminin coated plastic at a density of 200,000 cells/cm2. Less than 24 hours later, CH27 containing Y-27632 was aspirated and fresh CH27 media without Y-27632 was added. Media was changed daily with fresh CH27 until DIV 28 wherein cells were passaged for longitudinally maintaining the huDG NSC niche, their final reseeding, frozen in N2B27 containing Y-27632 and 10% DMSO, fixed for immunocytodetection, or allowed to grow another 6 days in N2B27 media for qRT-PCR harvesting.     Starting from DIV 28, huDG NSCs were passaged and reseeded in N2B27 media containing Y-27632 at a density of 100,000 cells/cm2 on poly-l-ornithine/511 human laminin coated plastic. Less than 24 hours later, CH27 containing Y-27632 was aspirated and fresh CH27 media without Y-27632 was added. CH27 media was changed daily for 2 weeks from the reseeding date (DIV 42) whereupon cells were passaged again in an identical manner until DIV 200.

extract_protocol:
All in vitro samples used for transcriptomic assays were harvested by 5’, 37oC trypsinization after which was inactivated with inactivated Fetal Bovine Serum (Euroclone ECS0180L). Detached cells were homogeneously suspended in solution, collected in microcentrifuge tubes and pelleted at 200 g for 5’. After centrifugation, the supernatant was aspirated, and the cell pellet was disrupted and processed using NucleoSpin® RNA kit (Machery-Nagel, 740955.250). RNA concentration was measured using a NanoDrop™ Lite Spectrophotometer (ThermoFisher ND-LITE).
RNA-seq libraries were prepared with the SMART-Seq® HT PLUS Kit (Takara) as described in manufacturer's instructions

treatment_protocol: When ready to differentiate, either endogenously or by NOTCH inhibitor, DAPT, huDG NSCs were seeded onto poly-l-ornithine/purified mouse laminin coated plates. For immuncytodetection purposes, cells were seeded onto Eppendorf biofilm-bottom plates as they did not survive differentiation on Eppendorf glass-bottom plates without a layer of mESC-derived hippocampus neurons, derived using the protocol from Terrigno et al, 2018. Cells were also seeded in a density corresponding to their age and purpose i.e. for RNAseq, DIV 28 cells were plated at 200,000 cells/cm2 and DIV160 cells were plated at 400,000 cells/cm2. After passaging/thawing, cell suspensions were centrifuged at 200 g for 4 minutes and the cell pellet resuspended in CH27 supplemented with Y-27632. Less than 24 hours later, CH27 containing Y-27632 was aspirated and fresh CH27 media without Y-27632 was added. Media was changed daily with fresh CH27 until cells reached 90% confluency (after ~10 days) whereupon media was changed to Dentate Gyrus Differentiation (DGD) media, containing DMEM/F-12 2mM Glutamine, 1 mM Sodium Pyruvate, 100 U/ml Penicillin-streptomycin, 0.05mM β-mercaptoethanol, N-2 Supplement (100X) B-27 Supplement (50X) (with Vitamin A, ThermoFisher 125870-01), 20 ng/ml  Recombinant human BDNF (NBP2-52006, Novus Biologicals), and 0.5 mM Ascorbate (A92902, Sigma Aldrich). Experimental differentiation media included +3 μM CHIR99021 (DGDC), +12.5 μM DAPT (DGDD, Sigma Aldrich D5942-5MG), or both (DGDCD).

value: ATCC- DYS0100

tag: replicate


title: Liver, female, saline, sample7


title: HiC_OB_rep6

data_processing:
Hi-C reads from each replicate were aligned to hg19, filtered and paired following HiCUP pipeline (Wingett et al., 2015). Raw contact matrices were normalized using ICE normalization (Imakaev et al., 2012). Chromatin loops were identified by combining results from two computational strategies HOMER (Heinz et al., 2010) and HiCCUPS (Rao et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited txt files contain the coordinates of loop calls identified in each cell.

extract_protocol:
Cells were crosslinked with 1% formaldehyde solution for 10 min, and quenched by 0.2 M glycine.  Cells were then lysed, and chromatin was digested using MboI and prepared as previously described (Rao et al., 2014).
Hi-C libraries were constructed following Hi-C protocol. Libraries were sequenced on the Illumina X Ten system following the manufacturer's protocols.


title: Liver, female, saline, sample6


title: ProRep_GSK_Replicat1

description: Treated cells

value: Promyelocytes

value: Leukemic bone marrow


title: ProRep_GSK_Replicat2

description: Treated cells


title: Liver, female, FGF21, sample8


title: Liver, female, saline, sample5


title: ProRep_NT_Replicat2

description: Untreated cells

value: DMSO


title: csf1

city: Taoyuan

first: ChiHui

last: Tsao

address: No. 259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Hisat2 (v2.0.1) was used to index reference genome sequence, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
For each exon (or part of an exon) and each sample, we count how many reads map to this exon and how many reads map to any of the other exons of the same gene.To analysis DEU, we used Bioconductor package DEXSeq (V 1.21.1).
Assembly: GRCm39.104
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: brain

extract_protocol:
RNA was harvested using 1-Bromo-3-Chloropropane. 1 ug of total RNA was used for the construction of sequencing libraries.
VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina

value: brain

value: female

tag: conditions

value: chronic-stressed

tag: pooling sizes


title: csf3

tag: tissue


title: Liver, female, saline, sample9

value: Liver

value: Female

value: Saline


title: HiC_OB_rep3

tag: cell type


title: Liver, female, saline, sample4


title: csm4


title: Osteoclast_PGC1B_eclip_rep2

data_processing:
Clipper eCLIP processing pipeline was used for peakcalling.
Assembly: mm10

source_name: RAW 264.7 cell

extract_protocol:
20 million RAW264.7 cells per 15 cm tissue culture plates were cultured in RPMI 1640 containing 10% FBS, 1% penicillin/streptomycin+L-glutamine with 50 ng/ml RANKL for 4 days.
eCLIP assay was performed as previously described (Van Nostrand et al., 2016).

value: RAW 264.7 cell

value: WT

value: 4 days


title: RNAseq_AC_rep2

value: Adipocyte


title: Liver, female, FGF21, sample5


title: csm3

value: male


title: Liver, female, FGF21, sample3


title: Dentate Gyrus Differentiation DAPT - DIV50 - Rep 3

value: DAPT


title: Osteoclast_PGC1B_eclip_rep1

value: Bone marrow cell

value: Osteoclast differentiation


title: Undiff. hiPSC - Rep 2

value: ATCC- DYS0100


title: RNAseq_hMSC_rep1

value: hMSC

value: Undifferentiated


title: Undiff. hiPSC - Rep 1


title: HiC_AC_rep5


title: HiC_OB_rep5

value: Osteoblast


title: Dentate Gyrus Differentiation - DIV50 - Rep 3


title: HiC_OB_rep2


title: csf2

value: brain

value: female


title: HiC_OB_rep1


title: Dentate Gyrus Differentiation - DIV50 - Rep 2


title: HiC_OB_rep4


title: HiC_AC_rep4


title: HiC_AC_rep3


title: csf4

value: chronic-stressed


title: cbf3

value: non-stressed


title: Dentate Gyrus Differentiation - DIV50 - Rep 1


title: Liver, female, FGF21, sample4

value: Liver

value: Female


title: Liver, female, FGF21, sample2


title: Dentate Gyrus Differentiation DAPT - DIV50 - Rep 2


title: csm2


title: Liver, female, FGF21, sample1


title: HiC_AC_rep2


title: cbf4


title: HiC_AC_rep6


title: Dentate Gyrus Differentiation DAPT - DIV50 - Rep 1


title: HiC_AC_rep1


title: csm1


title: Liver, female, saline, sample3

value: Saline


title: Liver, female, saline, sample2


title: cbm4


title: Dentate Gyrus Differentiation CHIR99021 - DIV50 - Rep 3


title: Dentate Gyrus Differentiation CHIR99021 - DIV50 - Rep 2


title: Liver, female, saline, sample1


title: Liver, male, saline, sample10

value: Male


title: cbm2


title: cbf2


title: Dentate Gyrus Differentiation CHIR99021 - DIV50 - Rep 1


title: Liver, male, FGF21, sample8


title: Dentate Gyrus Differentiation - DIV28 - Rep 2


title: Dentate Gyrus Differentiation - DIV28 - Rep 1


title: Liver, male, FGF21, sample11


title: cbf1


title: HiC_hMSC_rep6

source_name: Human umbilical cord derived MSC


title: HiC_hMSC_rep3


title: Dentate Gyrus Differentiation CHIR99021+DAPT - DIV50 - Rep 3


title: Dentate Gyrus Differentiation CHIR99021+DAPT - DIV50 - Rep 1


title: Liver, male, saline, sample11


title: HiC_hMSC_rep5


title: Dentate Gyrus Differentiation CHIR99021 - DIV174 - Rep 3


title: Liver, male, FGF21, sample10


title: Dentate Gyrus Differentiation - DIV28 - Rep 3


title: E13.5 Dental mesenchymal bio rep1 [E13_M]

city: Guangzhou

first: Jiawen

last: Chen

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District, Guangzhou, Guangdong, China, 510515

institute: Southern Medical University

data_processing:
we aligned reads of all samples to the Mus musculus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/Mus musculus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: mm10
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: dental mesenchyme

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)

value: dental mesenchyme

value: dental mesenchymal cells

value: WT

tag: time point


title: E13.5 Dental mesenchymal bio rep3 [E13_M_3]


title: cbm1

value: male


title: HiC_hMSC_rep7


title: Dentate Gyrus Differentiation CHIR99021+DAPT - DIV50 - Rep 2

tag: treatment


title: Liver, male, FGF21, sample9


title: HiC_hMSC_rep4


title: E13.5 Dental mesenchymal bio rep2 [E13_M_2]


title: Liver, male, FGF21, sample7


title: Dentate Gyrus Differentiation CHIR99021 - DIV174 - Rep 1

tag: cell line


title: ChIP_OB_rep2_input

data_processing:
ChIP-seq reads were aligned to hg19 using Bowtie2 (Langmead et al., 2012) with default parameters. MACS2 (Zhang et al., 2008) was used to perform peak calling with the following parameters (-g hs -p 0.01 --nomodel --extsize 147 --keep-dup all).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files indicate ChIP-seq and ATAC-seq fragment density at each position in the genome for visualization in genome browser.

extract_protocol:
ChIP assay was performed using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology). Briefly, cells were crosslinked with 1% formaldehyde, then quenched with glycine solution. Nucleus were digested with Micrococcal Nuclease (2,000 gel units/μL), then deactivated with 0.5 M EDTA. They lysate was sonicated and immunoprecipitated with H3K4me1 and H3K27ac antibodies (Abcam), precleared with agarose beads. DNA protein complex was then precipitated with agarose beads, eluted from the beads, and reversely cross-linked by 5M NaCl and Proteinase K.
Libraries for ChIP-seq were prepared following Illumina protocols. Libraries were next sequenced on the Illumina HiSeq X Ten platform configured for 150-bp pair-end reads.

tag: antibody

value: input


title: cbm3


title: Liver, male, FGF21, sample6


title: Liver, male, saline, sample9


title: Dentate Gyrus Differentiation CHIR99021 - DIV174 - Rep 2

value: ATCC- DYS0100


title: HiC_hMSC_rep2

value: hMSC


title: E13.5 Dental epithelium bio rep2 [E13_E_2]

source_name: dental epithelium

value: dental epithelium

value: dental epithelial cells


title: ChIP_OB_rep1_input

value: Osteoblast


title: Liver, male, saline, sample8


title: HiC_hMSC_rep1

value: Undifferentiated


title: ChIP_OB_H3K4me1_rep1


title: Liver, male, saline, sample6


title: Dentate Gyrus Differentiation CHIR99021+DAPT - DIV174 - Rep 1


title: Dentate Gyrus Differentiation CHIR99021+DAPT - DIV174 - Rep 2


title: E11.5 Dental mesenchymal bio rep2 [E11_M_2]


title: Dentate Gyrus Differentiation CHIR99021+DAPT - DIV174 - Rep 3


title: ERRg-4_S24

city: Birmingham

first: Rita

middle: M

last: Cowell

state: AL

address: 2000 9th Avenue South

department: Neuroscience

institute: Southern Research

data_processing:
Basecalls performed using CASAVA
TrimGalore! version 0.6.7 was used to trim primer adapter contamination from raw FASTQ files using parameters: --paired --trim-n
Trimmed FASTQ files were then aligned with STAR version 2.7.9a using parameters: --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using HTSeq-count version 0.11.3 using parameters: -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Normalization and differential expression was done by DESeq2 following their default parameters in their vignette
Assembly: Gencode GRCh38 p13 Release 36
Supplementary files format and content: tab-delimited text file containing Ensmebl IDs and raw count values for each sample

source_name: SH-SY5Y Cell line

growth_protocol: DMEM Media FBS 10% P/S 1% grown in 10 cm plates until 80% confluent before treatment

extract_protocol:
Total RNA isolated with Trizol/Chloroform/Isopropanol/Ethanol then quantified with nanodrop
rRNA depletion method
Addition of directional library preparation module to retain strand information in RNA library preparation

treatment_protocol: Cells were transfected with .5 ul of either GFP or Flag-Esrrg Adenovirus for 24 hours and then RNA was isolated

value: Flag-ERRg transfection

value: neuronal progenitor


title: E11.5 Dental mesenchymal bio rep3 [E11_M_3]


title: ChIP_OB_H3K4me1_rep2


title: E13.5 Dental epithelium bio rep3 [E13_E]


title: Liver, male, saline, sample7

value: Liver


title: ERRg-3_S23


title: E11.5 Dental epithelium bio rep3 [E11_E]


title: GFP-4_S21

value: GFP Transfection


title: E13.5 Dental epithelium bio rep1 [E13_E_3]


title: E11.5 Dental epithelium bio rep2 [E11_E_2]


title: ChIP_AC_rep2_input

value: Adipocyte


title: ChIP_OB_H3K27ac_rep1


title: Liver, male, saline, sample 5

value: Male

value: Saline


title: Liver, male, FGF21, sample4


title: GFP-3_S20


title: ChIP_AC_H3K4me1_rep2


title: E11.5 Dental mesenchymal bio rep1 [E11_M]

value: dental mesenchyme

value: dental mesenchymal cells


title: ChIP_OB_H3K27ac_rep2


title: Liver, male, saline, sample4


title: Liver, male, saline, sample3


title: FLOX-4 midbrain

data_processing:
Basecalls performed using CASAVA
TrimGalore! version 0.6.6 was used to trim primer adapter contamination from raw FASTQ files using parameters: --paired --trim-n
Trimmed FASTQ files were then aligned with STAR version 2.7.9a using parameters: --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using HTSeq-count version 0.11.3 using parameters: -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Normalization and differential expression was done by DESeq2 following their default parameters in their vignette
Assembly: Gencode GRCm39 Release M26
Supplementary files format and content: tab-delimited text file containing Ensmebl IDs and raw count values for each sample

source_name: Midbrain

extract_protocol:
Brains were removed and midbrain were flash frozen on dry ice, and RNA was harvested using the BAC-TRAP method of RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All mice were injected with AAV:THCre

value: Midbrain

tag: age

value: 4 months

value: L10a;Esrrg Flox


title: Liver, male, FGF21, sample5


title: ERRg-2_S22


title: E11.5 Dental epithelium bio rep1 [E11_E_3]

tag: genotype

value: WT


title: Liver, male, saline, sample2


title: Liver, male, FGF21, sample3


title: FLOX-2 midbrain


title: ChIP_AC_H3K27ac_rep2


title: ChIP_AC_rep1_input

value: input


title: WT-4 midbrain

value: L10a;Esrrg WT


title: ChIP_AC_H3K4me1_rep1


title: 36N_prot

description: 10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

data_processing:
Alignment, filtering, barcode counting, UMI counting were performed with count function from 10x Genomics Cell Ranger (version 6.0) using GRCh38 genome assembly as reference data.
Cell surface proteins were identified with specific oligonucleotide sequence (Format TotalSeqB, Biolegend): CD3_TotalSeqB, CD45RA_TotalSeqB, CCR4_TotalSeqB, CD4_TotalSeqB, CD8_TotalSeqB, CD25_TotalSeqB, PD1_TotalSeqB, CXCR3_TotalSeqB, CCR6_TotalSeqB, CXCR5_TotalSeqB, CCR7_TotalSeqB, CD161_TotalSeqB, CTLA4_TotalSeqB, CD95_TotalSeqB, HLA-DR_TotalSeqB, ICOS_TotalSeqB, CD39_TotalSeqB, CD27_TotalSeq, KLRG1_TotalSeqB, CD28_TotalSeqB, CD38_TotalSeqB, CD127_TotalSeqB, CD73_TotalSeqB, TCRVa72_TotalSeqB. All sequences are available on https://www.biolegend.com/en-us/totalseq/barcode-lookup
Genome_build: refdata-cellranger-GRCh38-3.0.0
Supplementary_files_format_and_content: The cellranger pipeline outputs an HDF5 file containing per-molecule information for all molecules that contain a valid barcode, a valid UMI, and were assigned with high confidence to a gene or Feature Barcode. This HDF5 file contains data corresponding to the observed molecules, as well as data about the libraries and feature set(s) usedEach element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column). This file can be input into third-party packages and allows users to wrangle the barcode-feature matrix (e.g. to filter outlier cells, run dimensionality reduction, normalize gene expression).

source_name: Healthy donor number 36 treated by Unstimulated

growth_protocol: CD3+ cells were isolated from frozen PBMC (Miltenyi, cat.130-050-101) and resuspended at 1 million cells per mL in antibiotic free medium with RPMI-1640 (Gibco, cat. 61870036) supplemented with 10% human AB serum (Biowest, cat. S4190-100). Treatments (azithromycin 10 mg/L, SIGMA cat. PZ0007, reconstituted in DMSO) or control (dimethylsulfoxide, equal volume of azithromycin) were added to the medium, then 200000 cells were plated in 96 flat-bottom plate. After one day of culture, activation withwas performed with a 1:1 cell:Dynadeads Human T-activated CD3/CD28 ratio following manufacturer instructions (Gibco, cat. 11131D).

extract_protocol:
To perform single cell RNA sequencing after cDNA amplification, the concentration of each sample was measured using Tapestation 2200 (Agilent). To prepare the cDNA libraries for 10x Genomics Chromium controller, we used the single-cell 3′ v3.1 kit (Dual Index) with Feature Barcode technology for Cell Surface Protein, following manufacturer guidelines. QC libraries were performed using Tapestation 2200 (Agilent). The input number of cells was estimated at 10,000 cells/samples. FASTQ files were obtained with bcl2fastq (Illumina).
Libraries were equimolar pooled to obtain at least 20,000 read pairs per cell and 5,000 read pairs for feature barcode part after sequencing on Illumina Novaseq 6000 (100 cycles cartridge).

treatment_protocol: Two days following activation, sample were retrieved from the incubator and kept on ice. Following 10X Genomics Feature Barcoding recommendations, cells were washed, labeled with antibody with high affinity to a known Cell Surface Protein coupled to a Feature Barcode oligonucleotide that identifies the antibody for 30 minutes at 4°C. Cell suspensions were subjected to in Gel Bead Emulsion using Chromium 10x Genomics controller according to manufacturer guidelines. Chromium™ Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, cat. 1000268) and 3’ Feature Barcorde Kit (10X Genomics, cat. 1000262) were used to prepare reagents.

value: Sorted T cells from frozen PBMCs

tag: phenotype

value: healthy donor

tag: sample identifier

tag: activation

value: non-activated

value: control

tag: targeted sequence

value: Feature barcode oligonucleotides that identify cell surface proteins


title: Liver, male, saline, sample1

value: Liver

tag: strain

tag: Sex


title: Liver, male, FGF21, sample1


title: ChIP_AC_H3K27ac_rep1

value: Adipocyte

tag: differentiation timepoint


title: Liver, male, FGF21, sample2

value: Male


title: 23D_prot

source_name: Healthy donor number 23 treated by Control

value: activated


title: WT-3 midbrain


title: 36D_prot

source_name: Healthy donor number 36 treated by Control


title: ChIP_hMSC_H3K4me1_rep2

value: hMSC

value: Undifferentiated


title: 23N_prot

source_name: Healthy donor number 23 treated by Unstimulated


title: WT-2 midbrain

value: Midbrain


title: 23A_prot

source_name: Healthy donor number 23 treated by AZM

value: azithromycin


title: 39N_prot

source_name: Healthy donor number 39 treated by Unstimulated


title: ChIP_hMSC_H3K4me1_rep1


title: RNA-seq ICSI 2-cell stage embryos rep2

city: Kofu

first: Mizuki

last: Sakamoto

country: Japan

institute: University of Yamanashi

data_processing:
For RNA-seq analysis, adaptor and low-quality sequences were removed by fastp with the option '-l 50 -w 10'. Reads correspond to ribosomal RNA were discarded from the analysis by extracting reads unmapped to ribosomal DNA using Bowtie2.
Reads were aligned to the mouse genome (mm10) using STAR (version 2.7.4a)
Read counts were calculated by featureCounts (Rsubread version 2.4.3 package in R), and the expression of each gene annotated by GENCODE vM12 was quantified by calculating TPM (transcripts per million) using R.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file indicating TPM values (for RNA-seq)

source_name: Embryo

growth_protocol: ICSI-embryos were cultured in KSOM. ROSI-embryos were activated by culturing in Ca2+-free CZB medium containing 5 mM SrCl2 for 1-2 h, and subsequently, cultured in KSOM until collection.

extract_protocol:
Total RNA was extracted from embryos using ISOGEN II (NIPPON GENE, Tokyo, Japan) according to manufacturer’s instructions.
RNA-seq libraries were constructed by SMART-seq stranded kit with 1 ng of extracted total RNA according to manufacturer’s instruction.

tag: developmental stage

value: Embryo

value: ICSI 2-cell stage embryos


title: GFP-1_S19

value: GFP Transfection

value: neuronal progenitor


title: RNA-seq ICSI 2-cell stage embryos rep3


title: 39D_prot

source_name: Healthy donor number 39 treated by Control

value: Sorted T cells from frozen PBMCs


title: ChIP_hMSC_H3K27ac_rep2

source_name: Human umbilical cord derived mesenchymal stem cells


title: ChIP_hMSC_rep1_input

value: input


title: ChIP_hMSC_rep2_input


title: ChIP_hMSC_H3K27ac_rep1


title: 39A_prot

source_name: Healthy donor number 39 treated by AZM

value: healthy donor


title: Apoe-/-_WD_3

data_processing:
The RNA reads were aligned to the reference sequences (mm10) and quantified as transcript per million (TPM) using STAR (v2.7.8a) and RSEM (v1.3.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file include TPM values

source_name: whole aortic valve tissue

growth_protocol: For induction of aortic valve lesions of lipid accumulation by hypercholesterolemia, male Ldlr-/- and Apoe-/- mice (sacrificed at 14-week-old) were fed a western diet at 6-week-old for 8 weeks. For control, male 14-week-old C57BL/6J (WT), Ldlr-/-, and Apoe-/- mice fed a chow diet were used.

extract_protocol:
Mice were euthanized by carbon dioxide (CO2) inhalation, and aortic valves were collected into the cold Dulbecco's Phosphate Buffered Saline (DPBS). For each sample, isolated mouse aortic valves from 10 mice were pooled into RNAlater solution. After stabilization, RNA was extracted from aortic valves using the TRIzol Reagent.
Sequencing libraries were constructed using amplified cDNA according to TruSeq Stranded mRNA Sample Preparation Guide (Part #15031047 Rev. E, Illumina) for the HiSeq 4000 system (Illumina) and sequenced using the Illumina HiSeq 4000 system with 101-bp read length and paired-end reads, according to HiSeq 4000 System Guide (Document #15066496, Illumina).

value: whole aortic valve tissue

value: Apoe-/-

tag: diet

value: Western diet (WD)


title: ATAC_OB_rep2

data_processing:
Adaptors were trimmed from ATAC-seq reads sequences using custom python scripts. Pair-end reads were aligned to hg19 using Bowtie2. Reads mapping to the mitochondria and chromosome Y were removed. The qualified reads were subjected to MACS2 to call peaks for each sample with parameters (-q 0.05 --nomodel --shift -100 --extsize 200 --keep-dup all). Peaks mapped to the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) were filtered.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files indicate ChIP-seq and ATAC-seq fragment density at each position in the genome for visualization in genome browser.

source_name: osteoblasts differentiated from mesenchymal stem cells

extract_protocol:
Cells were lysed with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.03% Tween20), and centrifuged. the nuclei was resuspended with Tn5 transposase reaction mix (25 μl 2 × TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free water) (Illumina) at 37 °C for 30 min. DNA was purified using a Qiagen MinElute kit.
Libraries for ATAC-seq were prepared following Illumina protocols. Libraries were next sequenced on the Illumina HiSeq X Ten platform.

value: Osteoblast


title: Ldlr-/-_WD_1

tag: tissue

value: Ldlr-/-


title: RNA-seq ICSI 2-cell stage embryos rep1


title: RNA-seq ROSI 2-cell stage embryos rep1

value: ROSI 2-cell stage embryos


title: 36A_prot

source_name: Healthy donor number 36 treated by AZM

tag: cell type

value: activated

value: Feature barcode oligonucleotides that identify cell surface proteins


title: ATAC_OB_rep1


title: 32N_prot

source_name: Healthy donor number 32 treated by Unstimulated

value: non-activated

value: control


title: Ldlr-/-_WD_3


title: ATAC_AC_rep2

source_name: adipocytes differentiated from mesenchymal stem cells

value: Adipocyte


title: Ldlr-/-_WD_2


title: RNA-seq ROSI 2-cell stage embryos rep3

value: Embryo


title: RNA-seq ICSI zygotes rep3

value: zygotes

value: ICSI zygotes


title: Apoe-/-_chow_2

value: Normal chow diet (chow)


title: Apoe-/-_chow_1


title: 32D_prot

source_name: Healthy donor number 32 treated by Control

value: Sorted T cells from frozen PBMCs


title: 40N_prot

source_name: Healthy donor number 40 treated by Unstimulated

value: healthy donor


title: RNA-seq ROSI 2-cell stage embryos rep2


title: Apoe-/-_WD_1

value: whole aortic valve tissue


title: RNA-seq ICSI zygotes rep2


title: 40D_prot

source_name: Healthy donor number 40 treated by Control


title: ATAC_AC_rep1


title: Apoe-/-_chow_3

value: Apoe-/-


title: RNA-seq ICSI zygotes rep1


title: RNA-seq ROSI zygotes rep2

value: ROSI zygotes


title: 40A_prot

source_name: Healthy donor number 40 treated by AZM

value: azithromycin


title: Xenopus laevis Embryos, Flowthrough RNA, 9 hpf, Rep 4 [FL_9hpf_rep4]

city: Philadelphia

first: Matthew

middle: C

last: Good

state: PA

address: Room 1140, 421 Curie Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

data_processing:
Fastq files were aligned to transcripts annotated in Xenopus laevis genome build 9.2 (xenbase.org) using salmon v0.12.0 yeilding raw counts per transcript.
Raw counts quantified from salmon were normalized to library size using DESeq2.
Assembly: Xenopus laevis genome build 9.2  (xenbase.org)
Supplementary files format and content: DESeq2 normalized reads per transcript, comma separated values text file

organism: Xenopus laevis

growth_protocol: Xenopus laevis embryos were cultured in 0.1× Marc’s Modified Ringer’s (MMR) medium. All embryo experiments were performed at room temperature (22℃ ± 0.5 ℃)

extract_protocol:
Total RNAs were isolated using the RNeasy Mini Kit (Qiagen), following the instructions provided by the manufacturer. Nascent EU-RNAs were biotinylated using bisulfide biotin azide via click reaction and purified using streptavidin beads following the instructions provided by the Click-iTTM Nascent RNA Capture Kit (Thermo Fisher Scientific, Cat# C10365).
The cDNA libraries for 'All' (Total RNA), 'Bead' (Nascent transcripts), 'FL' (Flowthrough RNA) and 'Egg' (Maternal RNA) were prepared using the Universal RNA-seq with NuQuant® kit (NuGEN, Cat# 0364), following the manual provided by the manufacturer. Ribosomal RNAs were depleted using the custom designed AnyDeplete Probe Mix for Xenopus laevis provided by the kit.

treatment_protocol: Embryos at 1-cell stage were microinjected with 10 nl of 50 mM EU. The final concentration of EU is at ~ 0.5 mM. Embryos developed to blasula stages at 5-9 hpf were collected for RNA extraction.

value: Blastula

tag: time

value: 9 hpf

value: Wildtype

value: EU microinjected

tag: batch

value: Experiment 2


title: Ldlr-/-_chow_1

value: Ldlr-/-


title: RNA-seq ROSI zygotes rep1

tag: treatment


title: 35N_prot

source_name: Healthy donor number 35 treated by Unstimulated

value: non-activated

value: control

value: Feature barcode oligonucleotides that identify cell surface proteins


title: Xenopus laevis Embryos, Flowthrough RNA, 8 hpf, Rep 4 [FL_8hpf_rep4]

value: Embryo

value: 8 hpf


title: 32A_prot

source_name: Healthy donor number 32 treated by AZM

value: Sorted T cells from frozen PBMCs

value: activated


title: Apoe-/-_WD_2

value: whole aortic valve tissue

value: Western diet (WD)


title: Xenopus laevis Embryos, Flowthrough RNA, 8 hpf, Rep 3 [FL_8hpf_rep3]


title: ATAC-seq ICSI 2-cell stage embryos rep2

data_processing:
For ATAC-seq analysis, adaptor and low-quality sequences were removed by fastp (version 0.20.1) with option ‘-l 30 -w 10’.
Reads were aligned to the mouse genome (mm10) using Bowtie2 (version 2.4.3) with option ‘--no-mixed --no-discordant -X 2000’, and unmapped reads were discarded by Samtools (version 1.4.1) with option ‘-F 0x4’.
Reads from PCR duplicates were removed using picard MarkDuplicates (version 2.23.8)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig (for ATAC-seq)

extract_protocol:
Omni-ATAC seq was performed by following the methods as reported in the previous study (Corres et al., Nature Methods 2017).
For Omni ATAC-seq, DNA was isolated by MinElute PCR purification (Qiagen) after ATAC-reaction for 30 min at 37˚C . Twenty-two ul of eluted sample were stored  at -20˚C until subsequent PCR amplification. After 5 cycles pre-amplification, additional 9 cycles of  PCR were performed. Amplified DNA was purified by MinElute PCR purification.

value: ICR

value: ICSI 2-cell stage embryos


title: 35D_prot

source_name: Healthy donor number 35 treated by Control

value: healthy donor


title: Ldlr-/-_chow_2

value: Normal chow diet (chow)


title: C57BL/6J_chow_3

value: wild type


title: C57BL/6J_chow_2


title: 35A_prot

source_name: Healthy donor number 35 treated by AZM

value: azithromycin


title: Xenopus laevis Embryos, Flowthrough RNA, 9 hpf, Rep 3 [FL_9hpf_rep3]

source_name: Embryo

value: Blastula

value: 9 hpf

value: Wildtype

value: EU microinjected

value: Experiment 2


title: ATAC-seq ROSI 2-cell stage embryos rep1

value: Embryo

value: ROSI 2-cell stage embryos


title: ATAC-seq ICSI zygotes  rep2

value: zygotes

value: ICSI zygotes


title: C57BL/6J_chow_1

value: whole aortic valve tissue


title: ID_20_E4F

city: Los Angeles

first: Berislav

last: Zlokovic

address: 1501 San Pablo Street

department: Zilkha Neurogenetic Institute

institute: University of Southern California

data_processing:
To process fastq raw data, a customized pre-mRNA GRCm38 reference database was created, which includes human APOE transgene sequence. Alignment and gene quantification was then performed using Cellranger v3.1.0 with default parameters and 64 CPU threads for parallel processing. From aligned bam files, APOE3 and APOE4 genotypes were first examined. For downstream secondary analysis, gene count matrices from all the samples were combined before applying a cutoff of 500-7500 genes and percent of mitochondrial genes less than 5%.
Genome_build: GRCm38
Supplementary_files_format_and_content: Cellranger filtered h5 format gene count matrices

growth_protocol: Human APOE3 and APOE4 knock-in (KI)flox/flox mice, E3F and E4F, respectively, in which the human apoE coding region is surrounded by loxP sites, were generated and produced by the Cure Alzheimer’s Fund. All mice in the study were maintained on C57BL/6J background. Mice were housed in designated animal rooms at 23°C on a 12 h light/dark cycle with food and water available ad libitum.

extract_protocol:
Once the mice were ready to be sacrificed for tissue extraction, animals were anesthetized intraperitoneally and transcardially perfused. The brain was collected and the brainstem and cerebellum were removed. For isolation of nuclei, the right cortical mantle was separated from the right hemisphere after the removal of the hippocampus and the visible white matter, and subsequently flash frozen in liquid nitrogen. Flash frozen cortical mantles were homogenized in a Dounce homogenizer in Lysis Buffer. Single nuclei isolated from the mouse cortical mantles were loaded onto the Chromium platform from 10X Genomics for droplet-based library preparation. The Chromium 3’ Reagent Kits v3 was used to capture RNA molecules for amplification. Integrity and quality of the libraries were assessed using a BioAnalyzer (Agilent) at the Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at University of Southern California.
Single nuclei isolated from the young and aged mouse cortex were loaded onto the Chromium platform from 10X Genomics for droplet-based library preparation. The Chromium 3’ Reagent Kits v3 was used to capture RNA molecules for amplification. Further cDNA fragment sizes were analyzed before QC sequencing runs using an Illumina MiSeq sequencer to examine sample multiplexing and mapping rate to the reference mouse genome. Production sequencing runs were carried out on Illumina HiSeq platform to acquire more than 400 million read pairs per sample.

value: cortex

value: 2-3 month

tag: knock-in


title: 38D_prot

source_name: Healthy donor number 38 treated by Control

value: Sorted T cells from frozen PBMCs

value: activated

value: control

value: Feature barcode oligonucleotides that identify cell surface proteins


title: Xenopus laevis Embryos, Flowthrough RNA, 7 hpf, Rep 4 [FL_7hpf_rep4]

value: 7 hpf


title: 38N_prot

source_name: Healthy donor number 38 treated by Unstimulated

value: healthy donor

value: non-activated


title: Ldlr-/-_chow_3

value: Ldlr-/-

value: Normal chow diet (chow)


title: Xenopus laevis Embryos, Flowthrough RNA, 6 hpf, Rep 3 [FL_6hpf_rep3]

value: Blastula

value: 6 hpf

value: Wildtype

value: EU microinjected

value: Experiment 2


title: ATAC-seq ICSI 2-cell stage embryos rep1

value: ICR

value: Embryo

value: ICSI 2-cell stage embryos


title: 38A_prot

source_name: Healthy donor number 38 treated by AZM

value: Sorted T cells from frozen PBMCs

value: azithromycin


title: Xenopus laevis Embryos, Flowthrough RNA, 6 hpf, Rep 4 [FL_6hpf_rep4]


title: Xenopus laevis Embryos, Flowthrough RNA, 5 hpf, Rep 4 [FL_5hpf_rep4]

value: 5 hpf


title: Xenopus laevis Embryos, Flowthrough RNA, 7 hpf, Rep 3 [FL_7hpf_rep3]


title: ATAC-seq ROSI 2-cell stage embryos rep2

value: ROSI 2-cell stage embryos


title: 37N_prot

source_name: Healthy donor number 37 treated by Unstimulated

value: control

value: Feature barcode oligonucleotides that identify cell surface proteins


title: ATAC-seq ICSI zygotes rep1

value: zygotes

value: ICSI zygotes


title: ID_3_E3F

value: cortex

tag: age

value: 2-3 month


title: ATAC-seq ROSI zygotes rep1

value: ROSI zygotes


title: ID_E3F


title: ATAC-seq ROSI zygotes rep2


title: ID_21_E4F


title: 37D_prot

source_name: Healthy donor number 37 treated by Control

value: healthy donor

value: activated


title: 37A_prot

source_name: Healthy donor number 37 treated by AZM


title: Xenopus laevis Embryos, EU-RNA, 9 hpf, Rep 3 [Bead_9hpf_rep3]

value: Blastula

value: 9 hpf

tag: genotype

value: Wildtype

value: EU microinjected

value: Experiment 2


title: Dgcr8.KO.EpiLC3

city: Mishima

first: Yumiko

last: Saga

state: Shizuoka

address: 1111 Yata

department: Department of Gene Function and Phenomics

institute: National Institute of Genetics

description: EpiLC was induced from ESCs

data_processing:
For all libraries, Low-quality sequences, adapters were trimmed or removed using fastp (version 0.20.0) with the following options: "-G -3 -n 1 -l 80".
For preparation for mapping reads to the mouse reference genome, the Ensembl mouse reference genome (release-102, Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz) and the gene annotation GTF file (Mus_musculus.GRCm38.102.gtf.gz) were downloaded from the Ensembl ftp site (http://ftp.ensembl.org/). To increase mapping accuracy of splicing reads, splicing-site and exon information were extracted from the gene annotation GTF file using the Python scripts hisat2_extract_splice_sites.py and hisat2_extract_exons.py, respectively, from the HISAT2 (version 2.2.1) package. The HISAT2 index files of the reference genome were built including the extracted genomic information using "hisat2-build" command with options: "--ss" and "--exon". Clean reads were then mapped to the HISAT2 index files using the HISAT2 with default options.
The obtained SAM files were sorted by genomic coordinates and converted to BAM files using SAMtools (version 1.13) "sort" command with option: "-O BAM".
Raw read counts per gene were calculated using featureCounts (version 2.0.3) with options: "-s 2 -p --countReadPairs -B --primary -t exon -g gene_id -a Mus_musculus.GRCm38.102.gtf"
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: EpiLC Day2

growth_protocol: ES colonies were maintained in 2i-LIF medium (ESGRO Complete Basal medium (Millipore, Germany) supplemented with LIF (Wako, Japan), 0.4 μM MEK inhibitor PD0325901 and 3 μM GSK3 inhibitor CHIR99021, and Penicilin-Streptomycin (Invitrogen).

extract_protocol:
Cells were dissolved in Trizol reagent then RNA was extracted.
We used TruSeq Stranded mRNA (illumina, 20020595) and followed the accompanied protocol.

treatment_protocol: For EpiLC induction, the protocol provided by Hayashi et al., 2011 was used.

tag: strain background

value: Mixture of C57/BL6, CBA, ICR

value: Dgcr8 -/-

value: EpiLC Day2


title: Dgcr8.KO.EpiLC2

description: EpiLC was induced from ESCs


title: Xenopus laevis Embryos, EU-RNA, 9 hpf, Rep 4 [Bead_9hpf_rep4]

value: Embryo


title: Xenopus laevis Embryos, Flowthrough RNA, 5 hpf, Rep 3 [FL_5hpf_rep3]

value: 5 hpf


title: 30D_prot

source_name: Healthy donor number 30 treated by Control

value: Sorted T cells from frozen PBMCs

tag: phenotype

tag: sample identifier

value: control

value: Feature barcode oligonucleotides that identify cell surface proteins


title: ID_9_E3F

value: cortex

value: 2-3 month


title: ID_5_E3F


title: 30N_prot

source_name: Healthy donor number 30 treated by Unstimulated

value: healthy donor

tag: activation

value: non-activated

tag: targeted sequence


title: ID_25_E4F


title: Xenopus laevis Embryos, EU-RNA, 8 hpf, Rep 4 [Bead_8hpf_rep4]

value: Blastula

value: 8 hpf


title: Xenopus laevis Embryos, EU-RNA, 8 hpf, Rep 3 [Bead_8hpf_rep3]

value: Wildtype


title: ID_26_E4F


title: ApoE4-97-loxlox

value: 9-12 month


title: Xenopus laevis Embryos, EU-RNA, 7 hpf, Rep 3 [Bead_7hpf_rep3]

value: 7 hpf

value: EU microinjected

value: Experiment 2


title: 18N_prot

source_name: Healthy donor number 18 treated by Unstimulated


title: Dcp2.KO.EpiLC2

description: EpiLC was induced from ESCs

value: Mixture of C57/BL6, 129, ICR

value: EpiLC Day2


title: 18D_prot

source_name: Healthy donor number 18 treated by Control

value: activated


title: Dgcr8.KO.EpiLC1

description: EpiLC was induced from ESCs

value: Mixture of C57/BL6, CBA, ICR

value: Dgcr8 -/-


title: ApoE4-105-loxlox


title: Xenopus laevis Embryos, EU-RNA, 6 hpf, Rep 4 [Bead_6hpf_rep4]

value: Embryo

value: 6 hpf


title: 30A_prot

source_name: Healthy donor number 30 treated by AZM

value: Sorted T cells from frozen PBMCs

value: azithromycin

value: Feature barcode oligonucleotides that identify cell surface proteins


title: Xenopus laevis Embryos, EU-RNA, 6 hpf, Rep 3 [Bead_6hpf_rep3]

value: Blastula


title: ApoE3-90-loxlox

value: cortex


title: Dcp2.KO.EpiLC3

description: EpiLC was induced from ESCs


title: 18A_prot

source_name: Healthy donor number 18 treated by AZM

value: healthy donor


title: Xenopus laevis Embryos, EU-RNA, 7 hpf, Rep 4 [Bead_7hpf_rep4]

value: Wildtype


title: 36D_geneexp

source_name: Healthy donor number 36 treated by Control

value: control

value: Gene expression


title: Eif4enif1.KO.EpiLC3

description: EpiLC was induced from ESCs

value: Eif4enif1 -/-


title: ApoE3-93-loxlox

value: 9-12 month


title: ApoE4-96-loxlox


title: Dcp2.KO.EpiLC1

description: EpiLC was induced from ESCs

value: Mixture of C57/BL6, 129, ICR

value: EpiLC Day2


title: Xenopus laevis Embryos, EU-RNA, 5 hpf, Rep 4 [Bead_5hpf_rep4]

value: 5 hpf

value: EU microinjected

value: Experiment 2


title: Eif4enif1.KO.EpiLC1

description: EpiLC was induced from ESCs


title: 36N_geneexp

source_name: Healthy donor number 36 treated by Unstimulated

value: non-activated


title: Eif4enif1.KO.EpiLC2

description: EpiLC was induced from ESCs


title: ApoE4-104-loxlox


title: Ddx6.KO.EpiLC1

description: EpiLC was induced from ESCs

value: Mixture of C57/BL6, CBA, ICR


title: Ddx6.KO.EpiLC2

description: EpiLC was induced from ESCs


title: Xenopus laevis Embryos, Total RNA, 5 hpf, Rep 3 [All_5hpf_rep3]

value: Embryo


title: Xenopus laevis Embryos, Total RNA, Egg, Rep 2 [All_egg_rep2]

source_name: Egg

value: Egg


title: 23A_geneexp

source_name: Healthy donor number 23 treated by AZM

value: Sorted T cells from frozen PBMCs

value: activated

value: azithromycin


title: Xenopus laevis Embryos, Total RNA, Egg, Rep 1 [All_egg_rep1]

value: Wildtype


title: 39N_geneexp

source_name: Healthy donor number 39 treated by Unstimulated

value: healthy donor

value: control


title: WT.EpiLC2

description: EpiLC was induced from ESCs

value: WT


title: Xenopus laevis Embryos, Total RNA, 5 hpf, Rep 4 [All_5hpf_rep4]

source_name: Embryo

value: Blastula


title: P6 Endothelial Cells

city: Charlottesville

first: Nicholas

middle: W

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

data_processing:
Alignment of sequencing was performed in collaboration with WuXi NextCODE (Boston, MA and Shanghai, China)
Single cell RNA sequencing datasets were analyzed by Seurat v3.0 to filter out cells by high mitochondrial gene expression, low or high gene numbers, and contaminating cell types (Hbb.bt, Neurod1, Cd63)
P6 and P15 datasets were integrated by IntegrateData function using SCT normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Integrated_scRNAseq.xlsx : Excel file with integrated data of genes versus cells. P6_RetinalEC_counts.tsv.gz : Aligned counts of P6 Retinal Endothelial Cells. P15_RetinalEC_counts.tsv.gz : Aligned counts of P15 Retinal Endothelial Cells.

source_name: Retinal Tissue

extract_protocol:
Endothelial cells from P6 and P15 wild-type mice were isolated, and single cell suspensions of endothelial cells were selected through FACS of CD31+CD45- immunostaining
Single cell RNA sequencing was then performed by the Yale Center for Genomic Analysis, which used around 12,000 cells per sample through the 10x Genomics Drop-Seq platform to generate single cell barcoded cDNA libraries.
Next-generation sequencing of single cell barcoded cDNA libraries was performed in collaboration with WuXi NextCODE (Boston, MA and Shanghai, China)

tag: strain

value: Endothelial cell


title: Ddx6.KO.EpiLC3

description: EpiLC was induced from ESCs

value: EpiLC Day2


title: Xenopus laevis Embryos, Flowthrough RNA, 9 hpf, Rep 2 [FL_9hpf_rep2]

value: 9 hpf

value: Experiment 1


title: 23N_geneexp

city: Paris

first: David

last: Michonneau

institute: Assistance Publique des Hôpitaux de Paris

source_name: Healthy donor number 23 treated by Unstimulated

value: Gene expression


title: ApoE4-86-loxlox

value: cortex

value: 9-12 month


title: 36A_geneexp

source_name: Healthy donor number 36 treated by AZM


title: TKO3

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

description: Cells for single cell RNA-seq were harvested 7 months after tumor induction by Adeno-CMV-cre

data_processing:
Analyzed using 10X genomics analysis pipeline CellRanger for alignment and filtering.
We used a combination of Scanpy and Dropkick v1.2.6 (https://github.com/KenLauLab/dropkick) to label and filter out low-quality cells from each sample.
We hierarchically perform the filtering, following the recipe_dropkick function from the Dropkick package, We initially filter out cells with < 100 genes using scanpy.pp.filter_cells with min_genes = 100.
We normalize the data using scanpy.pp.normalize_total, which removes any biases due to varying total counts per cell. We used default arguments for this normalization (as described in the Scanpy API v 1.8), such that after normalization, each cell has a total count equal to the median of total counts for cells before normalization.
Next, numpy.log1p is used to log transform the data (+1, which keeps zeroes from being transformed to negative infinity). Finally, the log-transformed, normalized counts are then scaled using scapy.pp.scale, which rescales the data to unit variance and mean-centers each gene. We then use scanpy.tl.pca to compute a 50-component PCA embedding of the data, using all genes, and use scvelo.pp.neighbors and scvelo.tl.umap to generate a UMAP dimensionality reduction.
Assembly: mm10
Supplementary files format and content: Processed read counts as describe above.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
One tumor was dissected from the lung of a mouse, chopped and digested in 1ml of PBS containing 2mg/ml of Collagenase/Dispase (Roche) in a 37°C shaker for 45 minutes. Tumors were then cooled on ice, treated with 2.5μg/ml DNAse (Sigma) for 5 minutes and passed through a 40μm filter. Red blood cells were lysed and the sample was single cell-sorted by FACS.
Single cell capture and library generation was performed using the Chromium Single Cell Controller from 10x Genomics.

value: Lung

value: Mixed genetic background of C57BL/6, 129/SVJ and 129/SvOla

value: Rb-/-; Trp53-/-; Rbl2-/-; Rosa26membrane-Tomato or membrane-GFPI:IB40H:H


title: Dgcr8.KO.ESC3

source_name: ESC

value: Mixture of C57/BL6, CBA, ICR

value: Dgcr8 -/-

value: ESC


title: 32N_geneexp

address: 1 avenue Claude Vellefaux

source_name: Healthy donor number 32 treated by Unstimulated

value: Sorted T cells from frozen PBMCs

value: healthy donor

value: non-activated


title: Dgcr8.KO.ESC1


title: P15 Endothelial Cells


title: 32A_geneexp

source_name: Healthy donor number 32 treated by AZM

value: activated

value: azithromycin


title: 23D_geneexp

source_name: Healthy donor number 23 treated by Control

value: control


title: 39A_geneexp

source_name: Healthy donor number 39 treated by AZM


title: Xenopus laevis Embryos, Flowthrough RNA, 6 hpf, Rep 2 [FL_6hpf_rep2]

value: Embryo

value: Blastula

value: 6 hpf

value: Wildtype

value: EU microinjected


title: Dcp2.KO.ESC1

value: Mixture of C57/BL6, 129, ICR


title: Xenopus laevis Embryos, EU-RNA, 5 hpf, Rep 3 [Bead_5hpf_rep3]

value: 5 hpf

value: Experiment 2


title: WT.EpiLC1

description: EpiLC was induced from ESCs

source_name: EpiLC Day2

value: Mixture of C57/BL6, CBA, ICR

value: WT

value: EpiLC Day2


title: Eif4enif1.KO.ESC2

value: Eif4enif1 -/-

value: ESC


title: m3_popB_rna

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: Annotation file containing RPKM normalized read counts for all detected genes.

source_name: CD4 T cell

growth_protocol: Cells from spleen and lymph nodes were harvested from untreated mice

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

treatment_protocol: Cells were stained with antibodies and sorted by Fluorescence Activated Cell Sorting (FACS). Cells were not treated with any TCR stimuli

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPint Ly6C+

value: Tg(Nr4a1-EGFP)GY139Gsat transgene plus Foxp3tm1Flv targeted mutation on C57/BL6 background

tag: mouse


title: ApoE3-84-loxlox

value: cortex

value: 9-12 month


title: m3_popA_rna

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPlo Ly6C+


title: m3_popC_rna

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPint Ly6Cneg


title: 32D_geneexp

source_name: Healthy donor number 32 treated by Control

value: Sorted T cells from frozen PBMCs

value: healthy donor

value: activated

value: control

value: Gene expression


title: 40N_geneexp

source_name: Healthy donor number 40 treated by Unstimulated

value: non-activated


title: m3_popD_rna

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPhi Ly6Cneg


title: Eif4enif1.KO.ESC1

value: Mixture of C57/BL6, 129, ICR


title: Dcp2.KO.ESC3


title: m2_popA_rna


title: WT.EpiLC3

description: EpiLC was induced from ESCs

value: Mixture of C57/BL6, CBA, ICR

value: WT

value: EpiLC Day2


title: Ddx6.KO.ESC2

value: ESC


title: 35D_geneexp

source_name: Healthy donor number 35 treated by Control


title: Xenopus laevis Embryos, Flowthrough RNA, 8 hpf, Rep 2 [FL_8hpf_rep2]

value: Embryo

tag: developmental stage

value: Blastula

value: 8 hpf

value: Wildtype

value: EU microinjected

value: Experiment 1


title: m2_popD_rna

value: Tg(Nr4a1-EGFP)GY139Gsat transgene plus Foxp3tm1Flv targeted mutation on C57/BL6 background


title: Xenopus laevis Embryos, Flowthrough RNA, 8 hpf, Rep 1 [FL_8hpf_rep1]


title: m2_popC_rna

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPint Ly6Cneg


title: Xenopus laevis Embryos, Flowthrough RNA, 9 hpf, Rep 1 [FL_9hpf_rep1]

value: 9 hpf


title: Dgcr8.KO.ESC2

value: Dgcr8 -/-


title: Xenopus laevis Embryos, Flowthrough RNA, 6 hpf, Rep 1 [FL_6hpf_rep1]

value: 6 hpf


title: WT.ESC3


title: 39D_geneexp

source_name: Healthy donor number 39 treated by Control

value: Sorted T cells from frozen PBMCs

value: healthy donor

value: activated

value: control

value: Gene expression


title: Xenopus laevis Embryos, Flowthrough RNA, 7 hpf, Rep 1 [FL_7hpf_rep1]

value: 7 hpf


title: 38N_geneexp

source_name: Healthy donor number 38 treated by Unstimulated

value: non-activated


title: 40D_geneexp

source_name: Healthy donor number 40 treated by Control


title: m2_popB_rna

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPint Ly6C+


title: Xenopus laevis Embryos, Flowthrough RNA, 5 hpf, Rep 2 [FL_5hpf_rep2]

source_name: Embryo

value: Embryo

value: Blastula

value: 5 hpf


title: Xenopus laevis Embryos, EU-RNA, 8 hpf, Rep 2 [Bead_8hpf_rep2]

value: 8 hpf

value: Wildtype

value: EU microinjected

value: Experiment 1


title: WT10.ESC1

value: Mixture of C57/BL6, CBA, ICR

value: WT

value: ESC


title: Xenopus laevis Embryos, Flowthrough RNA, 7 hpf, Rep 2 [FL_7hpf_rep2]


title: 35N_geneexp

source_name: Healthy donor number 35 treated by Unstimulated

value: Sorted T cells from frozen PBMCs

value: healthy donor


title: Xenopus laevis Embryos, Flowthrough RNA, 5 hpf, Rep 1 [FL_5hpf_rep1]


title: Xenopus laevis Embryos, EU-RNA, 9 hpf, Rep 1 [Bead_9hpf_rep1]

value: 9 hpf


title: MPLGD15

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

data_processing:
The raw sequence files were first chekced for quality by FASTQC.
The quality control was performed using cutadpat
Bismark tool 'bismark_genome_preparation' was used to process reference genome that is suitable for WGBS read mapping.
Bowtie2 was used for read aligment to processd genome sequences
The bismark toll 'bismark_methylation_extractor' tool was used to generate the coverage files for methylations.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Bismark coverage files of genome positions (1-based genomic genomic coordinates) with percentage and count of methylated and unmthylated reads for each sample. The columns represent <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>.

source_name: Placenta

growth_protocol: Gestation day 15 of wildtype mice. The vaginal plug was observed was considered day 0.5 of gestation to detemine gestational age.

extract_protocol:
Freshly collected gestation day 15 placenta and fetal brain from littermate  wildtype mice were snap frozen in liquid nitrogen. Genomic DNA was isolated from frozen specimen using
Genomic DNA was extracted using Gentra Puregene Tissue Kit (catalog #158667, Qiagen) from placenta and fetal brain of day 15 fetuses of both sexes from the wildtype mice (total 4 samples). Equimolar amount of DNA from three biological replicates for these samples. The pooled DNA was used for bisulfite conversion and libraries were prepared by the University of Missouri DNA core using  NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

value: Placenta

tag: Sex

value: Male


title: 40A_geneexp

source_name: Healthy donor number 40 treated by AZM

value: activated

value: azithromycin

value: Gene expression


title: Xenopus laevis Embryos, EU-RNA, 7 hpf, Rep 2 [Bead_7hpf_rep2]

tag: tissue

value: Embryo

value: Blastula

value: 7 hpf


title: m1_popC_rna

tag: cell type

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPint Ly6Cneg

value: Tg(Nr4a1-EGFP)GY139Gsat transgene plus Foxp3tm1Flv targeted mutation on C57/BL6 background


title: m1_popD_rna

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPhi Ly6Cneg


title: Ddx6.KO.ESC1

source_name: ESC

value: Mixture of C57/BL6, CBA, ICR


title: m1_popB_rna

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPint Ly6C+


title: 35A_geneexp

source_name: Healthy donor number 35 treated by AZM


title: MBRGD15

source_name: Fetal brain

value: Fetal brain


title: m3_popD_atac

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie
For each sample peaks of accessibility were identified and annotated using MACS2
Assembly: mm10
Supplementary files format and content: Annotation file containing reads per peak per million (rppm) normalized read counts for all peaks with at least 1 read per million in all samples of at least 1 group.

extract_protocol: 10,000 cells were centrifuged for 10 minutes at 500xg, and tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1X TD buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μl Tn5 transposase, 0.1% Tween 20 and 0.02% Digitonin) and then incubated for 1 h at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).


title: m1_popA_rna

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPlo Ly6C+


title: m3_popC_atac


title: FPLGD15

value: Female


title: 37N_geneexp

source_name: Healthy donor number 37 treated by Unstimulated

value: Sorted T cells from frozen PBMCs

value: healthy donor

value: non-activated

value: control


title: Xenopus laevis Embryos, EU-RNA, 9 hpf, Rep 2 [Bead_9hpf_rep2]

tag: time

value: 9 hpf

value: Wildtype

value: EU microinjected

value: Experiment 1


title: 38A_geneexp

source_name: Healthy donor number 38 treated by AZM

value: activated

value: azithromycin

value: Gene expression


title: 38D_geneexp

source_name: Healthy donor number 38 treated by Control


title: m3_popB_atac

source_name: CD4 T cell

value: Tg(Nr4a1-EGFP)GY139Gsat transgene plus Foxp3tm1Flv targeted mutation on C57/BL6 background


title: FBRGD15


title: Xenopus laevis Embryos, EU-RNA, 7 hpf, Rep 1 [Bead_7hpf_rep1]

value: Embryo

value: Blastula

value: 7 hpf

tag: batch


title: 37D_geneexp

source_name: Healthy donor number 37 treated by Control

tag: treatment


title: Xenopus laevis Embryos, EU-RNA, 8 hpf, Rep 1 [Bead_8hpf_rep1]

value: 8 hpf


title: m3_popA_atac

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPlo Ly6C+


title: Xenopus laevis Embryos, EU-RNA, 6 hpf, Rep 2 [Bead_6hpf_rep2]

value: 6 hpf


title: 37A_geneexp

source_name: Healthy donor number 37 treated by AZM

value: Sorted T cells from frozen PBMCs

value: healthy donor


title: 30N_geneexp

source_name: Healthy donor number 30 treated by Unstimulated

value: non-activated

value: control


title: Xenopus laevis Embryos, EU-RNA, 6 hpf, Rep 1 [Bead_6hpf_rep1]

value: Wildtype


title: m2_popD_atac

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPhi Ly6Cneg


title: 18N_geneexp

source_name: Healthy donor number 18 treated by Unstimulated


title: m1_popD_atac


title: Xenopus laevis Embryos, EU-RNA, 5 hpf, Rep 2 [Bead_5hpf_rep2]

value: 5 hpf

value: EU microinjected

value: Experiment 1


title: 30D_geneexp

source_name: Healthy donor number 30 treated by Control

value: activated

value: Gene expression


title: Xenopus laevis Embryos, Total RNA, 9 hpf, Rep 2 [All_9hpf_rep2]

value: Embryo

value: 9 hpf


title: m2_popC_atac

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPint Ly6Cneg

value: Tg(Nr4a1-EGFP)GY139Gsat transgene plus Foxp3tm1Flv targeted mutation on C57/BL6 background


title: 30A_geneexp

source_name: Healthy donor number 30 treated by AZM

value: azithromycin


title: m1_popC_atac


title: m1_popA_atac

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPlo Ly6C+


title: m1_popB_atac

value: CD4+ Foxp3-RFPneg CD44lo Nur77-GFPint Ly6C+


title: BF_48h_samp 3_Co-18

city: Hannover

first: Carina

last: Mikolai

address: Carl-Neuberg-Str. 1

department: Department of Prosthetic Dentistry and Biomedical Materials Science

country: Germany

institute: Hannover Medical School

description: Gene expression of mucosa after biofilm exposure for 48h

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ by use of 1650ng of labelled cRNA for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’. Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)    Subsequently, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: Peri-implant mucosa + biofilm, 48 h, sample 3, experiment Co-18

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) using 500ng of total RNA as input and according to the manufacturer’s recommendations, except that reaction volumes were halved.

growth_protocol: Organotypic peri-implant mucosa construction: Human gingiva fibroblasts were embeeded in a collagen typer-I hydrogel and a HGF-colonized titanium disk was integrated. Immortalized human oral keratinocytes were seede on the top of the HGF-collagen and stimulated in order to epithelial differentitaion. The peri-implant mucosa models were cultivated at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol: RNA was isolated by using the RNeasy Mini Kit (Qiagen) with On-column DNase digestion according to the manufacturer’s protocol.

treatment_protocol: Peri-implant mucosa was exposed to multispecies biofilm for 24 or 48 h at 37 °C in a humidified 5% CO2 atmospehere. Untreated peri-implant mucosa models served as control.

value: organotypic oral mucosa

tag: time point

value: with biofilm


title: BF_48h_samp 4_Co-18

source_name: Peri-implant mucosa + biofilm, 48 h, sample 4, experiment Co-18


title: 18A_geneexp

source_name: Healthy donor number 18 treated by AZM

value: Sorted T cells from frozen PBMCs

value: healthy donor


title: 18D_geneexp

source_name: Healthy donor number 18 treated by Control

value: control


title: Xenopus laevis Embryos, Total RNA, 8 hpf, Rep 2 [All_8hpf_rep2]

source_name: Embryo

value: Blastula

value: 8 hpf

value: Wildtype


title: m2_popB_atac


title: THR-428

city: New York City

first: Coen

last: van Solingen

state: New York

address: 435 E30th street, Science Building 723T, Science Building 723T

department: Cardiology/Medicine

institute: NYU School of Medicine

data_processing:
Fastq qualtiy assessed via FastQC 0.11.7
Sample contamination assessed via fastqscreen v0.13.0
Fastq files trimmed via Trimmomatic v0.36
Fastq files aligned to the HG38 human genome via STAR v2.7.3a
Reads counted via featurecounts v1.6.3
Genome_build: hg38
Supplementary_files_format_and_content: Raw count table as a .txt file

source_name: whole blood

extract_protocol:
QIAsymphony PAXgene RNA isolation
Sequencing libraries were barcoded and prepared using the Clontech SMART-Seq HT with Nxt HT kit (Takara Bio USA) as per the manufacturer's instruction

value: whole blood

tag: cohort

value: Control

value: Female


title: Xenopus laevis Embryos, Total RNA, 9 hpf, Rep 1 [All_9hpf_rep1]

value: Embryo

value: 9 hpf

tag: genotype

value: EU microinjected

value: Experiment 1


title: Xenopus laevis Embryos, Total RNA, 8 hpf, Rep 1 [All_8hpf_rep1]


title: C_48h_samp 4_Co-18

description: Gene expression of mucosa without biofilm after 48h

source_name: Peri-implant mucosa control, 48 h, sample 3, experiment Co-18

value: without biofilm


title: THR-432

value: Male


title: C_48h_sam 2_Co-17

description: Gene expression of mucosa without biofilm for 48h

source_name: Peri-implant mucosa control, 48 h, sample 2, experiment Co-17

value: organotypic oral mucosa


title: Xenopus laevis Embryos, Total RNA, 7 hpf, Rep 1 [All_7hpf_rep1]

value: 7 hpf


title: C_48h_samp3_Co-18

source_name: Peri-implant mucosa control, 48 h, sample 4, experiment Co-18


title: mammary gland tissue, age 30M, 18 months CYP19A1 transgene induction, biol rep 3 [4107AROM18M30M_S8]

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

institute: Dankook University

data_processing:
Sequencing quality was checked using FastQC (version 0.11.9; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Contaminated adaptor and/or row quality portions of sequenced reads were trimmed using Trim Galore (version 0.6.5; https://github.com/FelixKrueger/TrimGalore).
Trimmed reads were aligned to the reference mouse genome (mm10), using STAR (version 2.7.9a) (Dobin et al. Bioinformatics 2013).
Batch effect was normalized using RUVSeq (version 1.26.0) with the RUVg method (Risso et al. Nat Biotech. 2014).
Normalized expression levels were estimated by means of transcripts per million (TPM) using RSEM (version 1.3.1) (Li and Dewey, BMC Bioinformatics 2011)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: mammary gland

extract_protocol:
Thoracic (second) mammary glands were flash frozen in liquid nitrogen and stored at -80℃ until processing. Glands were thawed in Invitrogen Trizol reagent (ThermoFisher Scientific) and homogenized using a Qiagen Tissuruptor and Qiashredder (Qiagen). RNA was then isolated using Direct Zol RNA miniprep kit (Zymo Research), quantified on a Qubit 2.0 or 4.0 Fluorometer (Qiagen) and analyzed for RNA integrity using the Agilent 2100 Bioanalyzer.
Indexed, single-index sequencing libraries prepared from total RNA (1 microgram/sample) using the Illumina TruSeq Stranded Total RNA Library Preparation Human/Mouse/Rat Kit (rRNA depletion and random-primed cDNA synthesis)
Sequencing using the Illumina NextSeq 550, SE 75 bp read length; minimum reads ≥50M per sample

value: mammary gland

tag: age

value: 18 months CYP19A1 transgene induction


title: Xenopus laevis Embryos, EU-RNA, 5 hpf, Rep 1 [Bead_5hpf_rep1]

value: 5 hpf


title: BF_24h_samp 4_Co-11

description: Gene expression of mucosa after biofilm exposure for 24h

source_name: Peri-implant mucosa + biofilm, 24 h, sample 4, experiment Co-11

value: with biofilm


title: C_48h_samp 1_Co-11

source_name: Peri-implant mucosa control, 48 h, sample 1, experiment Co-11


title: BF_48h_samp 1_Co-11

source_name: Peri-implant mucosa + biofilm, 48 h, sample 1, experiment Co-11


title: C_24h_samp 4_Co-11

description: Gene expression of mucosa without biofilm after 24h

source_name: Peri-implant mucosa control, 24 h, sample 4, experiment Co-11


title: THR-417


title: mammary gland tissue, age 30M, 18 months CYP19A1 transgene induction, biol rep 2 [4171AROM18M30M_S8]


title: Xenopus laevis Embryos, Total RNA, 6 hpf, Rep 1 [All_6hpf_rep1]

value: Blastula

value: 6 hpf


title: mammary gland tissue, age 30M, 18 months CYP19A1 transgene induction, biol rep 1 [4182AROM18M30M_S8]


title: Xenopus laevis Embryos, Total RNA, 7 hpf, Rep 2 [All_7hpf_rep2]

value: Wildtype


title: THR-399

value: whole blood

value: Control


title: THR-415