title: SA2

city: Akita

first: Yosuke

last: Okamoto

address: 1-1-1 Hondo

institute: Akita University Graduate School of Medicine

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Rat GE microarray 8x60K v2 (G4853B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent) and 1 minute at room temperature with acetonitrile then dried immediately by nitrogen blower.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol: GE1-1100_Jul11 and Grid: 074036_D_F_20150914) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: Sinoauricular node, replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low-Imput QuickAmp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using QIAGEN RNeasy mini columns (QIAGEN, Venlo, Netherland) following the manufacturer's instructions.  The protocol includes cell lysis and DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Left atrium (LA) adjacent to the pulmonary vein (PV), a mass of left ventricle (LV), and free-wall of the right ventricle (RV) was separated from freshly isolated rat heart. Sinoatrial node reigion was isolated separately from two rats.During tissue isolation, the external solution was perfused at a rate of 10 ml/min on ice. The composition of the external solution (mM) was: NaCl 136.9, KCl 5.4, NaH2PO4 0.33, HEPES 5.0, MgCl 0.5 and glucose 5.5 (pH 7.4 with NaOH).

value: Sinoauricular node


title: SA4

status: Public on Jun 22 2022

type: RNA

department: Cell Physiology

country: Japan

molecule: total RNA

source_name: Sinoauricular node, replicate4

tag: tissue


title: SA1

source_name: Sinoauricular node, replicate1


title: SA3

source_name: Sinoauricular node, replicate3


title: RV3

source_name: Right ventricle, replicate3

value: Right ventricle


title: RV2

source_name: Right ventricle, replicate2


title: WT heart 3dpa expt. 4

type: SRA

city: Pittsburgh

first: Michael

last: Tsang

state: PA

address: 3501 Fifth Ave. BST3-5062

department: Cell Biology

country: USA

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
fastq files were analyzed using CLC genomics workbench 20.0
sequence reads were mapped onto Danio rerio GRC.z11
EDGE test was performed using CLC genomics workbench
Assembly: Danio rerio GRC.z11
Supplementary files format and content: Zuppo_3dpa_vs._uninj.xlsx
Supplementary files format and content: Zuppo_WT_vs_foxm1mut_3dpa.xlsx

organism: Danio rerio

source_name: Heart

growth_protocol: Zebrafish adult at 6-1year of age

extract_protocol:
Adutls hearts were injured through ventricular resection and allowed to recover until 3 days post amputation.
Ventricles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit (Cat# 74004).

value: Heart

tag: genotype

value: AB*


title: Micorwell-seq datasets of Xenopus_lung_COL123

city: Hangzhou

first: Haide

last: Chen

address: 866 Yuhangtang road

country: China

institute: Zhejiang University

data_processing:
Base call files were performed with Illumina bcl2fastq.
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. We took a dark reaction for R1, where R1 measured 24bp and R2 measured 150bp. The cell barcode is at position 1-18 of R1, and the UMI barcode is at position 19-24 of R1.
scRNA-seq reads were aligned to the Xenopus laevis J-strain 9.2 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Assembly: Xenopus laevis J-strain 9.2
Supplementary files format and content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.

molecule: polyA RNA

organism: Xenopus laevis

extract_protocol:
Tissues or whole-body single-cell dissociation and lysate
Library preparations were performed with the Microwell-seq protocol

tag: strain

value: wild-type

tag: age

value: one year elder

value: lung


title: WT heart 3dpa expt. 2


title: Progeria‐AG03257‐P7‐R3

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: Tennessee

address: 1311 Cumberland Avenue

department: Department of Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

library_source: genomic

data_processing:
Sequenced reads were mapped to the hg19 genome using bowtie2
Filtering was carried out using the dekkerlab-cMapping pipeline available on github https://github.com/dekkerlab/cMapping
Iterative correction was performed using method described by Imakaev et al.
Assembly: hg19
Supplementary files format and content: Each .tar.gz file contains the iteratively corrected and raw matrix.gz files for 40 kb, 100 kb, 250 kb, and 2.5 Mb in their respective directories.  Bin size indicated as “C-40000” for example.  All matrices are for individual chromosomes except for the 2.5 Mb bin size

molecule: genomic DNA

organism: Homo sapiens

source_name: Skin fibroblast (Coriell: https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=AG03257&Product=CC)

growth_protocol: Fibroblast lines were grown to confluency prior to crosslinking.

extract_protocol:
Briefly, 5-20 million cells were fixed with 1% formaldehyde, suspended in cell lysis buffer for permeabilization, and homogenized by douncing.  Samples were then digested overnight with HindIII or DpnII (as indicated per sample).  Ends were filled in with biotin and ligated.  Then, crosslinking was reversed.
Biotinylated DNA was pulled down using streptavidin coated magnetic beads and prepared for multiplex sequencing on an Illumina platform using the NEBNext Ultra II kit (NEB). All end preparation, adaptor ligation, and PCR amplification steps were carried out on bead bound DNA libraries.

tag: enzyme

value: Arima combination

tag: condition

value: WT

tag: media

tag: passage

value: Passage 7

tag: hi-c protocol

value: Arima Kit


title: Progeria‐AG03257‐P7‐R1

value: DpnII

value: Golloshi et al., 2018


title: Progeria‐168‐DpnII‐P16‐R1

source_name: Skin fibroblast (HGADFN168, Progeria Research Foundation)

value: Passage 16


title: Micorwell-seq datasets of Xenopus_lung_COL121


title: Progeria‐167‐DpnII‐P19‐R1

source_name: Skin fibroblast (HGADFN167, Progeria Research Foundation)

value: HGPS (2036C>T, GLY608GLY)

value: Passage 19


title: Micorwell-seq datasets of Xenopus_liver_COL128

value: liver


title: WT heart 3dpa expt. 1


title: PV3

source_name: Pulmonary vein, replicate3

value: Pulmonary vein


title: RV1

source_name: Right ventricle, replicate1

value: Right ventricle


title: PV4

source_name: Pulmonary vein, replicate4


title: dusp6 mutant heart uninjured expt. 1

value: Heart

value: dusp6 pt30a/pt30a


title: Micorwell-seq datasets of Xenopus_liver_COL117

value: wild-type


title: Micorwell-seq datasets of Xenopus_heart_COL127

value: one year elder

value: heart


title: WT heart uninjured expt. 1

value: AB*


title: Dusp6 mutant heart 3dpa expt. 1


title: PV1

source_name: Pulmonary vein, replicate1


title: PV2

source_name: Pulmonary vein, replicate2


title: NG11572

data_processing:
The fastq reads were first processed for adapter and quality trimming using the BBDuk. Following that, the reads were aligned to the reference genome hg19 using STAR aligner. Finally, the mapped reads were sorted based on genomic coordinates and feature count was performed with HTSeq-Counts.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw gene count values for each sample.

source_name: Skin Fibroblast

extract_protocol:
Ten micrograms of purified RNA from several progeria cell lines were acquired from the Coriell Institute (Camden, NJ).
RNA-seq library construction and analysis was carried out by Genewiz using Illumina PolyA selection (South Plainfield, NJ).

tag: Sex

value: F

value: Skin Fibroblast

value: 2 yr

tag: cell line

value: HGPS

tag: biomaterial provider


title: NG10677

value: M

value: 4 yr


title: Micorwell-seq datasets of Xenopus_heart_COL126


title: NG11513

value: 8 yr

value: HGPS (2036C>T, GLY608GLY)


title: NG10578

value: 17 yr


title: Micorwell-seq datasets of Xenopus_eye_COL122

value: eye


title: PA2

source_name: Pulmonary artery, replicate2

value: Pulmonary artery


title: Micorwell-seq datasets of Xenopus_brain_COL127

value: brain


title: 12 week HFD group liver, biological replicate 2

city: Shanghai

first: Weize

last: Zhu

address: Zhangjiangzhen

institute: Shanghai University of Traditional Chinese Medicine

description: Transcriptomics Array in  mice liver under high fat diet, replicate 2

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

organism: Mus musculus

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: mice were fed with either chow diet, high fat diet or chow diet with 30% sucrose in drinking water (high sucrose diet) for continued 12 weeks.

extract_protocol: The liver total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: liver

tag: gender

value: male

value: HFD


title: PA1

source_name: Pulmonary artery, replicate1


title: PA4

source_name: Pulmonary artery, replicate4


title: Micorwell-seq datasets of Xenopus_brain_COL124

value: wild-type

value: one year elder


title: LV3

source_name: Left ventricle, replicate3

value: Left ventricle


title: NG07493

value: F

value: Skin Fibroblast


title: NG06917

value: 3 yr


title: NG08466

value: HGPS


title: NG03198

value: 10 yr


title: 12 week HFD group liver, biological replicate 1

description: Transcriptomics Array in  mice liver under high fat diet, replicate 1


title: Micorwell-seq datasets of Xenopus_brain_COL66


title: LV4

source_name: Left ventricle, replicate4


title: Micorwell-seq datasets of Xenopus_brain_COL65


title: Micorwell-seq datasets of Xenopus_bone marrow_COL125

source_name: Xenopus_bone marrow_sample1

value: bone marrow


title: NG01178

value: M

value: 20 yr


title: NA01972

value: 14 yr

value: HGPS (2036C>T, GLY608GLY)


title: 12 week HFD group liver, biological replicate 3

description: Transcriptomics Array in  mice liver under high fat diet, replicate 3


title: PA3

source_name: Pulmonary artery, replicate3

value: Pulmonary artery


title: Micorwell-seq datasets of Xenopus_bone marrow_COL124


title: AgRP_HTO

status: Public on Jun 21 2022

city: Dallas

first: Li

last: Li

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

library_source: other

data_processing:
Unique molecular identifier (UMI) counts were obtained by aligning FASTQ files to the mouse reference genome (mm10) using Cell Ranger software (version 6.0.0) from 10x Genomics.
Assembly: mm10
Supplementary files format and content: Matrix table with UMI counts

molecule: protein

source_name: NPC antibodies

extract_protocol:
The snRNA-seq protocol was adapted from others’ (Gaublomme et al., 2019; Stoeckius et al., 2018). Fifteen mouse hypothalami were dissected and stored at -80°C.
10x GenomicsTM single-cell 3’ v3 assay

value: 4 weeks

value: wildtype

value: NPC antibodies

tag: cell type

value: AgRP-Cre; Sun1-GFP


title: 12 week HSD group liver, biological replicate 2

description: Transcriptomics Array in  mice liver under high sucrose diet, replicate 2

value: liver

value: male

value: HSD


title: LV2

source_name: Left ventricle, replicate2

value: Left ventricle


title: AgRP_Gex

source_name: hypothalamus

value: hypothalamus


title: LA4

source_name: Left atrium, replicate4

value: Left atrium


title: 12 week HSD group liver, biological replicate 1

description: Transcriptomics Array in  mice liver under high sucrose diet, replicate 1


title: MX1308-C5JC1ACXX-2-GGTAGA

city: Vancouver

first: Wan

middle: L

last: Lam

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Research Centre

data_processing:
Raw fastq files were processed by the miRMaster platform (April 2018, miRBase v21), using its default settings. Briefly, sequence reads undergo adapter trimming, quality filtering, and read collapsing, before being aligned to the hg38 assembly.
Predicted novel miRNA precursor sequences were retained only if miRMaster classified them as ‘novel’, i.e. if they did not partially or fully overlap with a miRBase entry or annotated miRNA.
Reads from the 5p and 3p miRNAs of each predicted novel miRNA precursor were summed together.
Genome_build: hg38
Supplementary_files_format_and_content: novel_miRs files: Chromosome, Strand (+ or -), Start (nucleotide position of the start of the putative miRNA precursor), Stop (nucleotide position of the end of the putative miRNA precursor), mirna_5p_sequence (sequence of the precursor's corresponding 5p miRNA), mirna_3p_sequence (sequence of the precursor's corresponding 3p miRNA), RPM (total expression of the precursor's 5p and 3p miRNAs, normalized to reads-per-million); known_miRs files: precursor, miRNA, RPM (expression of miRNA, normalized to reads-per-million); supplementary file: Reference (for known-miRs, has the format precursor|mature miRNA; for novel-miRs, has the format chromosome|strand|start|stop), Subtype (known-miR or novel-miR), subsequent columns denote reads-per-million expression in each individual sample.

source_name: fetal liver

extract_protocol:
Samples were derived from elective terminations for medical reasons during the second trimester of gestation (17–24 weeks), and were chromosomally normal (46XX / 46XY). Total RNA was isolated from frozen tissue using TRIzol (Life Technologies, Carlsbad, CA, USA).
Library construction and sequencing were performed as previously described in  [TCGA: Comprehensive molecular portraits of human breast tumours. Nature 2012, 490(7418):61-70].


title: LV1

source_name: Left ventricle, replicate1


title: LA3

source_name: Left atrium, replicate3


title: MX1307-C5JC4ACXX-7-CGCGGC


title: MX1305-C5JC4ACXX-5-TTCTCG


title: MX1308-C5JC1ACXX-2-GCTGTA


title: 12 week Con group liver, biological replicate 3

description: Transcriptomics Array in  mice liver under chow diet, replicate 3

value: control


title: MX1305-C5JC4ACXX-5-CATGGG


title: LA1

source_name: Left atrium, replicate1


title: 12 week HSD group liver, biological replicate 3

description: Transcriptomics Array in  mice liver under high sucrose diet, replicate 3


title: LA2

source_name: Left atrium, replicate2


title: 12 week Con group liver, biological replicate 1

description: Transcriptomics Array in  mice liver under chow diet, replicate 1


title: MX1306-C5JC4ACXX-6-GGTTTC


title: MX1304-C5JC4ACXX-4-TGAGTG


title: MX1303-C5JC4ACXX-3-GCTCAT


title: MX1303-C5JC4ACXX-3-CGGCCT


title: Micorwell-seq datasets of Xenopus_bladder_COL121

value: wild-type

value: one year elder

value: bladder


title: MX1302-C5JC4ACXX-2-ATCAGT


title: DSRCT-PDX1_AR_ASO AR_ChIPseq

city: Houston

first: Mahinur

last: Mattohti

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

data_processing:
ChIPseq reads were aligned to hg19 genome using bowtie1 with max 1 mismatch, duplicated reads were removed
peaks were called using MACS14  using pvalue cutoff of 1e-5, and was further filtered for downstream analysis using a more stringent cutoff of 1e-9 for H3K27Ac, 1e-7 for AR
bigwig files were generated by deeptools bamCoverage normalized by RPKM
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contains the ChIPseq signal normalized by RPKM. Bed files contain the peaks called by MACS14

growth_protocol: Cells were maintained in 10% FBS DMEM, high glucose and 1% antibiotic-antimycotic. Male NOD (SCID)-IL-2Rgnull mice (The Jackson Laboratory; Farmington, CT) were subcutaneously injected with JN-DSRCT cells (5X106 cells/animal) or received PDX explants (2 mm) to generate DSRCT xenograft and PDX mouse models.

extract_protocol:
Crosslinked treated or untreated JN-DSRCT samples were thawed on ice and resuspended in RIPA lysis buffer supplemented with protease inhibitor, lysed the cells on ice then sheared the chromatin by sonication. After centrifuge, the clean sonicated cell lysate mixed with protein G magnetic dynabeads (Invitrogen) coupled to antibodies described above and incubated over night at 4 degrees. Samples was washed 5 times with cold RIPA, twice with high salt RIPA, twice with LiCl buffer, twice with TE, and then eluted in elution buffer. The eluate was reverse crosslinked at 65C. Solid-phase reversible immobilization (SPRI) cleanup steps were performed. Beads were washed twice on the magnet with 70% ethanol and then air-dried. The DNA was eluted in EB buffer.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.

treatment_protocol: JN-DSRCT cells cultivated for 24 hours to let them adhere, before adding serially diluted concentrations of dihydrotestosterone (DHT, 0.0064-2000nM; Selleckchem), treated with control-ASO or AR-ASO. For mouse tumors, once their tumors reached a volume of 150 mm3, 5 mice per group received AR ASOs (25 mg/kg subcutaneously daily, 5 times per week), or control ASOs (50 mg/kg subcutaneously daily, 5 times per week).

value: DSRCT

tag: chip antibody

tag: treatment

value: AR-ASO


title: DSRCT-PDX1_AR_ASO H3K27ac_ChIPseq


title: DSRCT-PDX1_AR_ASO Input DNA


title: NA01178

source_name: Skin Fibroblast

value: M

value: Skin Fibroblast

value: 20 yr

value: HGPS


title: 12 week Con group liver, biological replicate 2

description: Transcriptomics Array in  mice liver under chow diet, replicate 2


title: JN-DSRCT_AR H3K27ac_ChIPseq


title: DSRCT-PDX1_Control_ASO H3K27ac_ChIPseq

value: control-ASO


title: JN-DSRCT_AR AR_ChIPseq


title: JN-DSRCT_Control-ASO Input DNA


title: DHT AR ASO Input DNA

description: Input DNA

source_name: DHT AR ASO

growth_protocol: Cells were maintained in 10% FBS DMEM, high glucose and 1% antibiotic-antimycotic.

treatment_protocol: JN-DSRCT cells cultivated for 24 hours to let them adhere, before adding serially diluted concentrations of dihydrotestosterone (DHT, 0.0064-2000nM; Selleckchem), treated with control-ASO or AR-ASO


title: DSRCT-PDX1_Control_ASO Input DNA


title: JN-DSRCT_Control-ASO H3K27ac_ChIPseq


title: DHT AR ASO H3K27ac_ChIPseq


title: JN-DSRCT_Control-ASO AR_ChIPseq


title: DHT AR ASO AR_ChIPseq


title: AR ASO Input DNA

description: Input DNA

source_name: AR ASO


title: AR ASO AR_ChIPseq


title: DHT Control ASO Input DNA

description: Input DNA

source_name: DHT Control ASO


title: AR ASO H3K27ac_ChIPseq


title: DHT Control ASO H3K27ac_ChIPseq


title: DHT Control ASO AR_ChIPseq


title: Control ASO Input DNA

description: Input DNA

source_name: Control ASO


title: Control ASO AR_ChIPseq


title: Cardiomimetic matrix maturation (Replicate 2)

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

description:
CMM.2
D2_TAATGCGC_L001

data_processing:
Reads were aligned using HISAT2
Aligned reads were counted using HTSeq
Genome_build: GRCh38
Supplementary_files_format_and_content: Read counts for each gene from HTSeq

extract_protocol:
Cardiac cells were harvested in Qiagen RNAProtect (Cat# 76526), and RNA isolated using Qiagen RNeasy Plus Micro Kit (Cat#74034). About 1 ug of total RNA was used for the construction of the sequencing libraries.
RNA libraries were prepared using standard Illumina protocols.

value: hiPSC-CM

tag: maturation

value: CMM


title: Cardiomimetic matrix maturation (Replicate 1)

description:
CMM.1
D1_CTGAAGCT_L001


title: 60 days maturation (Replicate 3)

description:
d60.3
B3_CGCTCATT_L002


title: Cardiomimetic matrix maturation (Replicate 3)

description:
CMM.3
D3_CGGCTATG_L001


title: 60 days maturation (Replicate 1)

description:
d60.1
B1_ATTACTCG_L002


title: DSRCT-PDX1_Control_ASO AR_ChIPseq


title: 30 days maturation (Replicate 2)

description:
d30.2
A2_TCCGGAGA_L001


title: 60 days maturation (Replicate 2)

description:
d60.2
B2_TCCGGAGA_L002


title: 30 days maturation (Replicate 1)

description:
d30.1
A1_ATTACTCG_L001


title: JN-DSRCT_AR Input DNA


title: Control ASO H3K27ac_ChIPseq


title: PBMC, 750 nM 25(OH)D2, 24 h, rep3

city: Kuopio

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
750 nM 25(OH)D2 for 24 h
25D2_750nM_24h_R3

data_processing:
Read alignment and quantification via nf-core/rnaseq STAR-Salmon pipeline 3.0 (http://doi.org/10.5281/zenodo.4323183).
Filtering for protein coding genes, read counts normalization via EdgeR 3.36.0 (TMM-normalized CPM).
Assembly: hg38, Aligned to Ensembl annotation version 103, final annotation (via Biomart) to Ensembl version 104.
Supplementary files format and content: normalized_counts.xlsx: Excel table of TMM-normalized read counts (CPM; EdgeR pipeline).

source_name: PBMC

growth_protocol: RPMI 1640 medium supplemented with 10% charcoal-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and were at 37 °C in a humidified 95% air/5% CO2 incubator.

extract_protocol:
Extraction of total RNA using High Pure RNA Isolation kit (Roche).
rRNA-deplete cDNA library following NEB protocols.

value: peripheral blood mononuclear cells

value: male

value: 25-hydroxyvitamin D2 (750 nM)

tag: time point


title: PBMC, 500 nM 25(OH)D2, 24 h, rep2

description:
500 nM 25(OH)D2 for 24 h
25D2_500nM_24h_R2

value: 25-hydroxyvitamin D2 (500 nM)


title: PBMC, 750 nM 25(OH)D2, 24 h, rep2

description:
750 nM 25(OH)D2 for 24 h
25D2_750nM_24h_R2


title: PBMC, 1000 nM 25(OH)D2, 24 h, rep1

description:
1000 nM 25(OH)D2 for 24 h
25D2_1000nM_24h_R1

value: 25-hydroxyvitamin D2 (1000 nM)


title: PBMC, 1000 nM 25(OH)D2, 24 h, rep2

description:
1000 nM 25(OH)D2 for 24 h
25D2_1000nM_24h_R2


title: PBMC, 1000 nM 25(OH)D2, 24 h, rep3

description:
1000 nM 25(OH)D2 for 24 h
25D2_1000nM_24h_R3


title: PBMC, 100 nM 25(OH)D2, 24 h, rep2

description:
100 nM 25(OH)D2 for 24 h
25D2_100nM_24h_R2

value: 25-hydroxyvitamin D2 (100 nM)


title: PBMC, 250 nM 25(OH)D2, 24 h, rep1

description:
250 nM 25(OH)D2 for 24 h
25D2_250nM_24h_R1

value: 25-hydroxyvitamin D2 (250 nM)


title: PBMC, 500 nM 25(OH)D2, 24 h, rep1

description:
500 nM 25(OH)D2 for 24 h
25D2_500nM_24h_R1


title: PBMC, 750 nM 25(OH)D2, 24 h, rep1

description:
750 nM 25(OH)D2 for 24 h
25D2_750nM_24h_R1


title: PBMC, 100 nM 25(OH)D2, 24 h, rep1

description:
100 nM 25(OH)D2 for 24 h
25D2_100nM_24h_R1


title: PBMC, 250 nM 25(OH)D2, 24 h, rep2

description:
250 nM 25(OH)D2 for 24 h
25D2_250nM_24h_R2


title: 30 days maturation (Replicate 3)

description:
d30.3
A3_CGCTCATT_L001


title: PBMC, 750 nM 25(OH)D3, 24 h, rep3

description:
750 nM 25(OH)D3 for 24 h
25D3_750nM_24h_R3

value: 25-hydroxyvitamin D3 (750 nM)


title: PBMC, 750 nM 25(OH)D3, 24 h, rep2

description:
750 nM 25(OH)D3 for 24 h
25D3_750nM_24h_R2


title: PBMC, 500 nM 25(OH)D3, 24 h, rep3

description:
500 nM 25(OH)D3 for 24 h
25D3_500nM_24h_R3

value: 25-hydroxyvitamin D3 (500 nM)


title: PBMC, 750 nM 25(OH)D3, 24 h, rep1

description:
750 nM 25(OH)D3 for 24 h
25D3_750nM_24h_R1


title: PBMC, 1000 nM 25(OH)D3, 24 h, rep1

description:
1000 nM 25(OH)D3 for 24 h
25D3_1000nM_24h_R1

value: 25-hydroxyvitamin D3 (1000 nM)


title: PBMC, 500 nM 25(OH)D3, 24 h, rep2

description:
500 nM 25(OH)D3 for 24 h
25D3_500nM_24h_R2


title: PBMC, 1000 nM 25(OH)D3, 24 h, rep2

description:
1000 nM 25(OH)D3 for 24 h
25D3_1000nM_24h_R2


title: PBMC, 500 nM 25(OH)D3, 24 h, rep1

description:
500 nM 25(OH)D3 for 24 h
25D3_500nM_24h_R1


title: PBMC, 500 nM 25(OH)D2, 24 h, rep3

description:
500 nM 25(OH)D2 for 24 h
25D2_500nM_24h_R3


title: PBMC, 250 nM 25(OH)D3, 24 h, rep2

description:
250 nM 25(OH)D3 for 24 h
25D3_250nM_24h_R2

value: 25-hydroxyvitamin D3 (250 nM)


title: PBMC, 250 nM 25(OH)D3, 24 h, rep1

description:
250 nM 25(OH)D3 for 24 h
25D3_250nM_24h_R1


title: PBMC, 250 nM 25(OH)D2, 24 h, rep3

description:
250 nM 25(OH)D2 for 24 h
25D2_250nM_24h_R3


title: PBMC, 250 nM 25(OH)D3, 24 h, rep3

description:
250 nM 25(OH)D3 for 24 h
25D3_250nM_24h_R3


title: PBMC, 100 nM 25(OH)D3, 24 h, rep3

description:
100 nM 25(OH)D3 for 24 h
25D3_100nM_24h_R3

value: 25-hydroxyvitamin D3 (100 nM)


title: PBMC, 100 nM 25(OH)D2, 24 h, rep3

description:
100 nM 25(OH)D2 for 24 h
25D2_100nM_24h_R3


title: PBMC, 10 nM 1,25(OH)2D3, 24 h, rep2

description:
10 nM 1,25(OH)2D3 for 24 h
125D3_10nM_24h_R2

value: 1alpha,25-dihydroxyvitamin D3 (10 nM)


title: PBMC, 10 nM 1,25(OH)2D3, 24 h, rep1

description:
10 nM 1,25(OH)2D3 for 24 h
125D3_10nM_24h_R1


title: PBMC, 1 nM 1,25(OH)2D3, 24 h, rep3

description:
1 nM 1,25(OH)2D3 for 24 h
125D3_1nM_24h_R3

value: 1alpha,25-dihydroxyvitamin D3 (1 nM)


title: PBMC, 100 nM 25(OH)D3, 24 h, rep1

description:
100 nM 25(OH)D3 for 24 h
25D3_100nM_24h_R1


title: PBMC, 1000 nM 25(OH)D3, 24 h, rep3

description:
1000 nM 25(OH)D3 for 24 h
25D3_1000nM_24h_R3


title: ⍺FITC-Gas6 (E)_3

city: Daejeon

first: Hyuncheol

last: Jung

address: Daehakro 291

country: South Korea

institute: KAIST

description: 1-hour incubation with FITC-labelled Beads (5.7μm)  and ⍺FITC-Gas6 (E)

data_processing:
cDNA libraries were sequenced using a DNBSEQ-G400
Sequenced reads were aligned to the human genome (hg38) using STAR (v2.6.1d)
Raw read counts was quantificated using by featureCounts (v1.24.2)
Differential gene expression analysis was performed using DESeq2 (v1.32.0)
Genome_build: hg38
Supplementary_files_format_and_content: matrix of raw read counts per gene for each sample.

source_name: THP-1, Human monocytic cell line

growth_protocol: THP-1 cells were purchased from Korean Cell Line Bank and cultured in RPMI1640 supplemented with 10% FBS, 1%, 1X HEPES, 1X Beta-mercaptoethanol, 1% penicillin, and streptomycin

extract_protocol:
Total RNA was extracted using by NucleoSpin RNA XS (Macherey-Nagel)
Library was prepared from extracted RNA using by TruSeq® Stranded mRNA Library Prep according to the manufacturer’s instructions. Then, prepared library was converted to MGI sequencing platform by using MGIEasy Universal Library Conversion Kit (App-A ).

treatment_protocol: Axl overexpressed THP-1 cells were harvested after 2h incubation with 5.7-size FITC labeled beads and E2 or aFITC-Gas6 (E).

value: Monocytic cell line derived from an acute monocytic leukemia patient

tag: protocol

value: 1-hour incubation with FITC-labelled Beads (5.7microm)  and alphaFITC-Gas6 (E)


title: PBMC, 10 nM 1,25(OH)2D3, 24 h, rep3

description:
10 nM 1,25(OH)2D3 for 24 h
125D3_10nM_24h_R3


title: PBMC, 1 nM 1,25(OH)2D3, 24 h, rep1

description:
1 nM 1,25(OH)2D3 for 24 h
125D3_1nM_24h_R1


title: ⍺FITC-Gas6 (E)_1


title: E2_3

description: 1-hour incubation with FITC-labelled Beads (5.7μm)  and E2 antibody

value: 1-hour incubation with FITC-labelled Beads (5.7microm)  and E2 antibody


title: ⍺FITC-Gas6 (E)_2


title: PBMC, 1 nM 1,25(OH)2D3, 24 h, rep2

description:
1 nM 1,25(OH)2D3 for 24 h
125D3_1nM_24h_R2

value: peripheral blood mononuclear cells


title: E2_2


title: PBMC, 0.1 nM 1,25(OH)2D3, 24 h, rep2

description:
0.1 nM 1,25(OH)2D3 for 24 h
125D3_0.1nM_24h_R2

value: male

value: 1alpha,25-dihydroxyvitamin D3 (0.1 nM)


title: Beads_3

description: 1-hour incubation with FITC-labelled Beads (5.7μm)

value: 1-hour incubation with FITC-labelled Beads (5.7microm)


title: E2_1


title: PBMC, 1000 nM 25(OH)D2, 08 h, rep3

description:
1000 nM 25(OH)D2 for 8 h
25D2_1000nM_08h_R3

value: 25-hydroxyvitamin D2 (1000 nM)

value: 8 h


title: PBMC, 100 nM 25(OH)D3, 24 h, rep2

description:
100 nM 25(OH)D3 for 24 h
25D3_100nM_24h_R2


title: PBMC, 1000 nM 25(OH)D2, 08 h, rep1

description:
1000 nM 25(OH)D2 for 8 h
25D2_1000nM_08h_R1


title: Beads_1


title: PBMC, 0.1 nM 1,25(OH)2D3, 24 h, rep1

description:
0.1 nM 1,25(OH)2D3 for 24 h
125D3_0.1nM_24h_R1


title: PBMC, 0.1 nM 1,25(OH)2D3, 24 h, rep3

description:
0.1 nM 1,25(OH)2D3 for 24 h
125D3_0.1nM_24h_R3


title: PBMC, 1000 nM 25(OH)D2, 04 h, rep3

description:
1000 nM 25(OH)D2 for 4 h
25D2_1000nM_04h_R3

value: 4 h


title: PBMC, 1000 nM 25(OH)D2, 08 h, rep2

description:
1000 nM 25(OH)D2 for 8 h
25D2_1000nM_08h_R2


title: C3H/HeN, radiation [s4]

city: Beijing

first: Gangqiao

last: Zhou

address: 27 Taiping Road, Haidian District, Beijing

institute: Beijing Institute of Radiation Medicine

description: 10x Genomics

data_processing:
Cell Ranger (version 2.2.0)’s mkfastq function was used to demultiplex raw base call files from the sequencer, into sample-specific FASTQ files. Afterward, FASTQ files for each sample were processed with CellRanger’s count function, which was used to align reads to the reference mouse genome (mm10, NCBI Build 38) and quantify gene expression levels in single cells.
Assembly: mm10
Supplementary files format and content: RILI_scRNAseq_UMIcount.txt.gz: tab-delimited text file including single cell gene expression measured in raw UMI counts
Supplementary files format and content: RILI_scRNAseq_normalized.txt.gz: tab-delimited text file including normalized and log-transformed single cell gene expression

source_name: Lung

extract_protocol:
Single-cell suspensions were obtained by first removing whole lung tissues from healthy mice and day 1 post irradiation mice. The tissues were cleaned with cold phosphate-buffered saline, cut into small pieces with lengths of approximately 2 mm, and separated according to the manufacturer’s instructions using the Lung Dissociation Kit (mouse) and GentleMACS Dissociator (Miltenyi Biotec, Germany). Next, the lung tissue mixtures were filtered through a 40-µm cell sieve on ice, centrifuged at 4 °C, and washed twice with regular medium to remove incompletely digested fragments and tissues.
Single-cell suspensions were converted to barcoded scRNA-seq libraries by using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics), aiming for an estimated 5,000 cells per library and following the manufacturer’s instructions. The generated scRNA-seq libraries were sequenced on an Illumina HiSeq 3000 sequencer.

tag: tissue

value: Lung

tag: strain

value: 6-8 weeks old

value: Radiation


title: C57BL/6N, radiation [s2]

description: 10x Genomics

tag: age


title: C3H/HeN, control [s3]

description: 10x Genomics

value: Control


title: PBMC, 1000 nM 25(OH)D2, 04 h, rep1

description:
1000 nM 25(OH)D2 for 4 h
25D2_1000nM_04h_R1


title: PBMC, 1000 nM 25(OH)D2, 04 h, rep2

description:
1000 nM 25(OH)D2 for 4 h
25D2_1000nM_04h_R2


title: C57BL/6N, control [sfei2]

description: 10x Genomics


title: PBMC, 1000 nM 25(OH)D3, 04 h, rep3

description:
1000 nM 25(OH)D3 for 4 h
25D3_1000nM_04h_R3

value: 25-hydroxyvitamin D3 (1000 nM)


title: Beads_2


title: PBMC, 1000 nM 25(OH)D3, 04 h, rep2

description:
1000 nM 25(OH)D3 for 4 h
25D3_1000nM_04h_R2


title: PBMC, 1000 nM 25(OH)D3, 08 h, rep1

description:
1000 nM 25(OH)D3 for 8 h
25D3_1000nM_08h_R1


title: PBMC, 1000 nM 25(OH)D3, 04 h, rep1

description:
1000 nM 25(OH)D3 for 4 h
25D3_1000nM_04h_R1


title: PBMC, 10 nM 1,25(OH)2D3, 08 h, rep3

description:
10 nM 1,25(OH)2D3 for 8 h
125D3_10nM_08h_R3

value: 1alpha,25-dihydroxyvitamin D3 (10 nM)


title: PBMC, 10 nM 1,25(OH)2D3, 04 h, rep2

description:
10 nM 1,25(OH)2D3 for 4 h
125D3_10nM_04h_R2


title: PBMC, 10 nM 1,25(OH)2D3, 08 h, rep1

description:
10 nM 1,25(OH)2D3 for 8 h
125D3_10nM_08h_R1


title: PBMC, 10 nM 1,25(OH)2D3, 04 h, rep3

description:
10 nM 1,25(OH)2D3 for 4 h
125D3_10nM_04h_R3


title: PBMC, 1000 nM 25(OH)D3, 08 h, rep2

description:
1000 nM 25(OH)D3 for 8 h
25D3_1000nM_08h_R2


title: PBMC, 10 nM 1,25(OH)2D3, 04 h, rep1

description:
10 nM 1,25(OH)2D3 for 4 h
125D3_10nM_04h_R1


title: donor B_IgG treated

city: Glasgow

first: Carl

last: Goodyear

address: 120 University Place

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

hyb_protocol: hybridized to Illumina HumanHT-12 V4.0 expression beadchip by Whole-Genome Gene Expression Direct Hybridization Assay

scan_protocol: Illumina BeadArray reader

data_processing: Illumina GenomeStudio (V2011.1), data were quantile normalized (with no background correction)

label: Biotin

source_name: monocytes treated with m-CSF/RANKL and IgG

label_protocol: amplified and labeled with biotin using Illumina TotalPrep RNA Kit using the standard protocol

growth_protocol: primary human monocytes were isolated from peripheral blood (buffy coats of three independent blood donors: A, B or C) using Stemcell CD14 magnetic cell seperation and incubated over night with 10ng/ml M-CSF and then differentiated with 100ng/ml RANKL and 10ng?ml RANKL for 24hrs

extract_protocol: total RNA was extracted using Qiagen miRNeasy Kit according to the manufacturer's instruction

treatment_protocol: Cells have been treated for the 24hr differentiation period either in the absence (Control) or prescence of 25 mg/ml SIC (immunecomplexes consisting of SpA and IgG) or the appropriate concentration of IgG or SpA alone.

tag: donor id

value: B

value: peripheral blood

value: primary peripheral CD14+ monocytes

value: m-CSF/RANKL and IgG


title: PBMC, 10 nM 1,25(OH)2D3, 08 h, rep2

description:
10 nM 1,25(OH)2D3 for 8 h
125D3_10nM_08h_R2

value: peripheral blood mononuclear cells


title: PBMC, 0.1% EtOH, 24 h, rep2

description:
0.1% ethanol for 24 h
EtOH_24h_R2

value: male

value: Ethanol


title: PBMC, 0.1% EtOH, 24 h, rep1

description:
0.1% ethanol for 24 h
EtOH_24h_R1


title: PBMC, 0.1% EtOH, 24 h, rep3

description:
0.1% ethanol for 24 h
EtOH_24h_R3


title: PBMC, 1000 nM 25(OH)D3, 08 h, rep3

description:
1000 nM 25(OH)D3 for 8 h
25D3_1000nM_08h_R3


title: donor A_Control

source_name: monocytes treated with m-CSF/RANKL

value: A

value: m-CSF/RANKL


title: donor C_Control

value: C


title: PBMC, 0.1% EtOH, 08 h, rep3

description:
0.1% ethanol for 8 h
EtOH_08h_R3

value: 8 h


title: donor C_SpA treated

source_name: monocytes treated with m-CSF/RANKL and SpA

value: m-CSF/RANKL and SpA


title: Lens epithelium

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

description: E12.5 Lens epithelium

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using rank invariant normalisation method  in R

label: biotin

source_name: Lens

label_protocol: Standard protocol for Illumina arrays

extract_protocol: Standard total RNA isolation protocol by RNeasy mini kit (Qiagen)


title: PBMC, 0.1% EtOH, 08 h, rep1

description:
0.1% ethanol for 8 h
EtOH_08h_R1


title: PBMC, 0.1% EtOH, 04 h, rep3

description:
0.1% ethanol for 4 h
EtOH_04h_R3

value: 4 h


title: PBMC, 0.1% EtOH, 04 h, rep2

description:
0.1% ethanol for 4 h
EtOH_04h_R2


title: PBMC, 0.1% EtOH, 04 h, rep1

description:
0.1% ethanol for 4 h
EtOH_04h_R1


title: donor C_SIC treated

source_name: monocytes treated with m-CSF/RANKL and SIC

value: m-CSF/RANKL and SIC


title: Rnd1 siRNA replicate-2

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

country: India

institute: IISER Bhopal

data_processing:
Raw data files were quality checked using FastQC and bad quality bases were removed using Trimmomatic.
Cleaned fastqc files were mapped to human reference genome using HISAT2 on usegalaxy.org
Cufflinks  was used to calculate abundance, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: A549 cells

growth_protocol: Cells were seeded at a cell density of 5x1o^5 per well of a 6 well plate and were maintained in DMEM suplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen)
Libraries were prepared according to instructions accompanying the Illumina library preparation kit.

treatment_protocol: Cells were transfected either with control siRNA (siCtrl) or  siRNA targeting Rnd1 (siRnd1) using lipofectamine 3000 in Opti-MEM media. The following day, cells were infected with H1N1 high pathogenicity influenza virus. Cells were harvested for RNA extraction 24 hours after infection.

value: Rnd1 knock down


title: Rnd1 siRNA replicate-1


title: donor A_SpA treated


title: donor A_SIC treated


title: donor B_Control


title: FTSEC-5

city: San Antonio

first: Kate

last: Lawrenson

address: 7703 Floyd Curl Dr.

institute: Cedars Sinai Medical Center

data_processing:
STAR
featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: txt file

source_name: Primary Fallopian Tube Secretory Epithelium

extract_protocol:
TRIzol LS
NEBNext Ultra Directional RNA Library Prep Kit
paired-end 75 bp reads on NextSeq 500 platform

tag: sample type

value: Primary


title: control siRNA replicate-2

value: control


title: control siRNA replicate-1


title: donor C_IgG treated


title: LV-Aducanumab 2

data_processing:
Single cell gene expression data was analysed using Cell Ranger v5.0.0
Raw BCL files from Illumina HiSeq were demultiplexed to generate FASTQ files using ‘cellranger mkfastq’
Raw FASTQ files were analyzed using ‘cellranger count’ which includes mapping to the Mouse reference genome (mm10-2020-A) and measuring gene expression with unique molecular identifier (UMI) and cell barcode
Raw counts data analysis was done by Seurat package.
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: raw counts

source_name: Hippocampus

extract_protocol:
Isolated cells were counted by LUNA-FLTM Automated Fluorescence Cell Counter (logos biosystems) and processed following the manufacturer’s instruction; 10x Genomics Single Cell Protocols Cell Preparation Guide and the Guidelines for Optimal Sample Preparation flowchart (Documents CG00053 and CG000126, respectively). Briefly, the cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 3’ v3.1 Gel Beads and Partitioning Oil into a chromium Next GEM chip G. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.
Libraries were prepared using the Chromium controller according to the 10x chromium Next GEM Single Cell 3’ v3.1 protocol (CG000204)

treatment_protocol: We collected 8m-old 5xFAD mouse hippocampus 3 weeks after LV-control stereotaxic injection

value: Hippocampus

value: 8 month

tag: genotype

value: Sacrifice 3 weeks after LV-Aducanumab stereotaxic injection


title: FTSEC-4


title: LV-Aducanumab 1


title: donor B_SIC treated

value: B

value: peripheral blood

value: primary peripheral CD14+ monocytes


title: donor A_IgG treated

value: m-CSF/RANKL and IgG


title: FTSEC-3


title: LV-⍺Aβ-Gas6 1

value: Sacrifice 3 weeks after LV-⍺Aβ-Gas6 stereotaxic injection


title: donor B_SpA treated


title: LV-⍺Aβ-Gas6 2


title: LV-Control 2

value: Sacrifice 3 weeks after LV-control stereotaxic injection


title: POF_model_rep2

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

description: replicate 2

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio

source_name: premature ovarian failure models

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPre RNA Amplification kit(IL1791) for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit according to the prescribed protocol provided with the kit. Quality control was performed with nanodrop-1000 and electrophoresis.

value: ovaries

value: premature ovarian failure


title: LV-Control 1


title: FTSEC-2


title: SSCTR_recipient_rep2

description: replicate 2

source_name: cell transplanted recipients

value: spermatogonial stem cells transplanted recipients


title: input_2747_140616_SN583_0116_AH7PJVADXX

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

data_processing:
reads were aligned to the human reference genome build hg19 with bowtie for single-end runs and bowtie2 for paired-end runs, and bigwig files were generated for visualization with bedtools genomecov and UCSC bedGraphToBigWig. Peaks were determined using the MACS2 program with default parameters. The tracks were normalized per million reads and visualized as genome browser profiles using the Fluff package.
Peak Callind under MACS3(band width 300, model fold = [5, 50], q=0.01), narrowPeak files were then analysed in CHIPSeeker and Deeptools
Assembly: hg19

source_name: acute myeloid leukemia patient, bone marrow

growth_protocol: The MOLM-1 and HNT-34 cell lines were cultured in RPMI with 10% FCS. The MUTZ3 cell lines were cultured in αMEM with 20% FCS and 20% conditioned 5637 medium. Patient 2747 samples were not cultured

extract_protocol:
Nuclear lysates were sonicated and pulled down with antibody.
ChIP samples were processed according   to the Illumina TruSeq ChIP Sample Preparation Protocol (Illumina)   or Diagenode Library V3 preparation protocol (Diagenode) and   either sequenced single-end (1 × 50 bp) on the HiSeq 2500 platform   (Illumina) or paired-end (2 × 100 bp) on the Novaseq 6000 platform   (Illumina)

tag: rearrangement of chromosome 3q

tag: sf3b1 mutations

value: Yes, K700E


title: SSCTR_recipient_rep3

description: replicate 3


title: POF_model_rep3

description: replicate 3


title: Lens fibers

description: E12.5 Lens fibers


title: EVI1_2747_140519_SN583_0115_AH7CFPADXX

value: Anti-EVI1 (Cell Signaling, 2593)


title: SSCTR_recipient_rep1

description: replicate 1


title: POF_model_rep1

description: replicate 1


title: FTSEC-1


title: WT_control_rep2

description: replicate 2

source_name: wild-type samples

value: wild type control


title: WT_control_rep3

description: replicate 3


title: EVI1_MUTZ3_141211_SN583_0132_AC66ATACXX

source_name: acute myelomonocytic leukemia cell line

value: Yes, K666N


title: 4178-cells

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

country: Germany

institute: German Diabetes Center

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse MTA arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression Console v4.0 using default analysis settings for combined RNA analyses dabg .CHP files.

source_name: RNA from primary hepatocytes

label_protocol: 150 ng total RNAwas amplified using the Ambion WT Expression Kit and the WT Terminal Labeling Kit (Affymetrix, Freiburg, Germany).

growth_protocol: Primary hepatocytes were isolated and cultured 24 h before harvesting.

extract_protocol: RNA extraction was made with RNeasy mini kit (Exo-easy kit, miRNA extraction kit, Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: C57Bl6 (C57Bl6) and B6-TgN(alb-HA-SREBP-1cNT) (alb-SREBP-1c) [18] mice were bred and maintained under standard conditions (12h light/dark cycle; 22°C ± 1°C, 50% ± 5% humidity). At 6 weeks of age, male littermates of each genotype were kept under standardized conditions with free access to water and regular laboratory chow (13.7 mJ/kg: 53% carbohydrate, 36% protein, 11% fat (Ssniff, Soest, Germany)). Mice were sacrificed by CO2 asphyxiation (7:00 am) at 24 weeks of age. Blood samples were collected by left ventricular puncture, and liver were removed. The Animal Care Committee of the University Duesseldorf approved animal care and procedure (Approval#84-02.04.2015.A424; 02. April 2015). Primary hepatocytes were isolated as described (Fahlbusch et al., Int J Mol Sci. 2020 Jun 10;21(11):4144. doi: 10.3390/ijms21114144.).

value: C57Bl6-TgN alb-HA-hSREBP-1c-NT (alb-SREBP-1c)[Knebel et al. PLoS One. 2012;7(2):e31812. doi:10.1371/journal.pone.0031812]

value: male

value: primary hepatocytes


title: WAT: miR-203 Inhibitor 2

city: Singapore

first: Lei

last: Sun

address: 8 College Road

country: Singapore

institute: Duke-NUS

data_processing:
Reads were aligned to mm10, using Tophat (version tophat-2.0.11) and genes were quantified using Cufflinks (Version 2.1.1)
Genome_build: mm10

source_name: Subcutaneous WAT

extract_protocol:
Adipose tissues were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: white adipose tissue (WAT)


title: 4177-cells


title: WAT: negative control 1 (NC1)


title: 4169-cells


title: EVI1_input_MUTZ3_141211_SN583_0132_AC66ATACXX


title: AP_day8_rep2

city: Kyoto

first: Masatoshi

last: Ohgushi

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Instutute for Frontier Life and Medical Sciences

institute: Kyoto University

data_processing:
BaseSpace Onsite (Illumina) were used for basecalling and generation of fastq files
Sequence reads were aligned against GRCh38 genome assembly using STAR (version 2.6.1d).
Read counts and TPM (transcripts per million) values of each gene were quantified and calculated using RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with TPMs for every gene and every sample

source_name: ESC derivatives

growth_protocol: Human ESCs were cultured on feeder layers of mouse embryonic fibroblasts in DMEM/F12/KSR medium (D-MEM/F12 supplemented with 20% KSR additive, 2 mM glutamine, 0.1 mM non-essential amino acids, 0.1 mM 2-mercaptoethanol and 5 ng/ml basic FGF). TSLCs were cultured in TSC medium (DMEM/F12 supplemented with 0.1mM 2-mercaptoethanol, 0.2% FBS, 0.3% BSA, 1% ITS-X supplement, 1.5 mg/ml L-ascorbic acid, 50 ng/ml EGF, 2 µM CHIR99021, 0.5 µM A83-01, 1 µM SB431542, 0.8 µM VPA and 5 µM Y27632)

extract_protocol:
Total RNAs were extracted using RNeasy micro kit (QUIAGEN) following the manufacturer's protocol
Sequencing libraries were prepared from 1 μg total RNAs using the TruSeq Standard mRNA LT Sample Preparation Kit (Illumina)

treatment_protocol: Undifferentiated human ESCs were transferred onto matrigel-coated dishs, and on the following day culture media was switched to a fresh one containing A83-01 (1µM) and PD173074 (0.1µM). To BMP signal inhibition, BMP bloker NOGGIN and LDN-011999 were added to culture media.

tag: cell line

value: ESC derivatives

value: AP-treated


title: WT_control_rep1

description: replicate 1


title: WAT: miR-203 Inhibitor 1


title: WAT: negative control 2 (NC2)


title: EVI1_HNT34_141211_SN583_0132_AC66ATACXX

source_name: acute myeloid leukemia cell line


title: 4168-cells


title: AP_day8_rep1


title: AP_day4_rep2


title: 4167-cells


title: EVI1_input_HNT34_141211_SN583_0132_AC66ATACXX


title: 3959-cells


title: 3958-cells


title: EVI1_Molm1_140415_SN583_0110_AC3UTLACXX

source_name: chronic myeloid leukemia cell line

value: No


title: 3749-cells


title: AP_day2_rep1


title: 3748-cells


title: 3946-cells


title: AP_day2_rep2


title: AP_day4_rep1


title: input_Molm1_140616_SN583_0116_AH7PJVADXX


title: AP_day1_rep2


title: AP_day1_rep1


title: HepG2_xenograft_DKD_4

city: Badalona

first: Roberto

last: Malinverni

state: Barcelona

address: Josep Carreras Building, Ctra de Can Ruti,

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Illumina Casava 1.7 software was used for basecalling.
To quantify the transcript expression we used Salmon version 0.14.0 (Patro et al., 2017), using libtype A and the “validateMappigs” option active. The raw reads were “quasi-aligned” to the human Ensembl genome annotation GRCh38.12.
Satatistical analysis preformed using DESeq2 (Love et al., 2014)
Genome_build: hg38
Supplementary_files_format_and_content: Comma separated table with raw or normalized counts for all samples (one column per sample)

growth_protocol: Four weeks old NOD.CB17-PRKDCSCID immunosuppressed mice were purchased from Charles Rivers Laboratories (strain code 394). The animals were kept in specific pathogen free (SPF) conditions for the duration of the experiment. The animals were kept in the stall for two weeks before the experimental procedure. CTL and DKD HepG2 cells were resuspended in a Matrigel (Corning) and PBS mix 1:1. The animals were anesthesiated with isofluorane and two subcutaneous injections were performed in each lower flank of the animal consisting of 100 µL Matrigel:PBS 1:1 containing 5 million cells. A total of 5 mice (three males, two females) per condition was used, effectively resulting in 10 injections for each cell line. The weight and overall condition of the mice were regularly monitored. 21 days after the injection, tumors were resected with the mice under anesthesia and all animals were sacrificed. Tumors were cleaned with PBS and cut in half. One half was fixed in formalin and embedded in paraffin for histological analysis, while the other half was immediately frozen in liquid nitrogen and later subject to RNA extraction and expression analysis. RNA extracted from 5 different tumors derived from each cell line was submitted for sequencing. The animal experimentation procedure used for the xenograft experiment has been approved by the Animal Experimentation Comission of the Catalan Goverment (Comissó d’Experimentació Animal de la Generalitat de Catalunya) with project reference 9500.

extract_protocol:
Total RNA from xenograft samples was isolated using the TRIzol™ Reagent (ThermoFisher Scientific).
RNA-Seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The double knock-down of macroH2A1 and macroH2A2 transcripts in HepG2 was achieved by stable integration of shRNA expression cassettes through retroviral transduction of pRetroSUPER vectors, as described in Douet et al., 2017.

tag: cell line source

value: double knock-down (DKD)

tag: host strain

value: HepG2-xenograft tumor


title: HepG2_xenograft_DKD_5


title: 293T cells expressing 3xHA

data_processing:
bcl2fastq
MACS 2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: peak filles

source_name: human embryonic kidney cells

growth_protocol: 293T cells were cultured with DMEM, supplemented with 10% fetal bovine serum, 100 u/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
Chromatin fractions from HEK293T cells were prepared using the fanChIP method, as described previously (doi.org/10.1016/j.xpro.2021.100404). Cells were suspended in CSK buffer (100 mM NaCl, 10 mM PIPES [pH 6.8], 3 mM MgCl2, 1 mM EGTA, 0.3 M sucrose, 0.5% Triton X-100, 5 mM sodium butyrate, 0.5 mM DTT, and protease inhibitor cocktail) and centrifuged (400× g for 5 min, at 4°C) to remove the soluble fraction. The pellet was resuspended in MNase buffer (50 mM Tris-HCl [pH 7.5], 4 mM MgCl2, 1 mM CaCl2, 0.3 M sucrose, 5 mM sodium butyrate, 0.5 mM DTT, and protease inhibitor cocktail) and treated with MNase at 37°C for 3–6 min to obtain oligonucleosomes. MNase reaction was then stopped by adding EDTA (pH 8.0) to a final concentration of 20 mM. An equal amount of lysis buffer (250 mM NaCl, 20 mM sodium phosphate [pH 7.0], 30 mM sodium pyrophosphate, 5 mM EDTA, 10 mM NaF, 0.1% NP-40, 10% glycerol, 1 mM DTT, and EDTA-free protease inhibitor cocktail) was added to increase solubility. The chromatin fraction was cleared by centrifugation (15,000 rpm for 5 min, 4°C) and subjected to immunoprecipitation with anti-HA antibody (3F10, Roche) and Protein-G magnetic microbeads (Invitrogen). Immunoprecipitates were then washed five times with washing buffer (1:1 mixture of lysis buffer and MNase buffer with 20 mM EDTA) and eluted in elution buffer (1% SDS and 50 mM NaHCO3). The eluted DNA material was fragmented by DNA shearing system (M220 Covaris).
TruSeq ChIP Sample Prep Kit (illumina)

tag: treatment (transfection)

tag: transfection type

value: transient

value: anti-HA (Roche, 3F10)


title: 293T cells expressing Empty vector

tag: chip antibody


title: 293T cells expressing 3xHA_EVI1-WT


title: HepG2_xenograft_DKD_3


title: AP_day0_rep1

source_name: ESCs

tag: cell type

value: ESCs

tag: treatment

value: untreated


title: AP_day0_rep2


title: HepG2_xenograft_DKD_2


title: HepG2_xenograft_DKD_1


title: FEDKO4

city: Lausanne

first: Nadia

last: Bresciani

address: Route Cantonale

department: SV

country: Switzerland

institute: EPFL

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Mus musculus.GRCm38.92 genome using STAR (v. 2.5.3a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.92 gene annotation.
Genome_build: Mus musculus.GRCm38.92
Supplementary_files_format_and_content: raw gene counts for every gene in every sample

source_name: Liver

extract_protocol:
Lver was removed, flash frozen on liquid Nitrogen. RNA was isolated using Trizol reagent; RNA quality and integrity was assesed by fragment analyzer.
RNA-seq libraries were prepared using 500 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA)

value: Liver

value: C57BL/6 Slc25a47tm1c(EUCOMM)Hmgu

value: 9 weeks old

value: Fed state (Chow diet)

tag: Sex


title: Injury_PVAT_Replicate_2

city: Tokyo

first: Yusuke

last: Adachi

state: Outside US/Canada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

institute: The University of Tokyo

data_processing:
150bp paired-end sequencing reads were obtained using Illumina HiSeq 2500 platform.
The Fastq sequences were initially checked for quality through the FastQC program v0.11.8.
Adaptor sequences were removed by Cutadapt v1.18. Sequencing reads from RNA-seq libraries were then trimmed using Trimmomatic v0.39, where reads with alignment quality < Q33 were discarded, and aligned to the mouse reference genome (mm9) using STAR aligner v2.6.0a
RSubread-2.0.1-FeatureCounts software for quantification and DESeq2 v.1.28.0 software for differential analysis were used on R v.3.6.0.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Perivascular adipose tissue (PVAT) from ovariectomized female mouse

extract_protocol:
Outer tissues surrounding the femoral arteries 48 h after injury or sham operation  were collected.
Total RNA (480 ng) from each sample was used to generate RNA-seq libraries using TruSeq Stranded mRNA Library Prep kit (llumina).

treatment_protocol: Endovascular injury of femoral arteries with wire insertion was performed using a straight spring wire (0.38 mm in diameter, COOK).

tag: tissue

value: outer tissues surrounding the femoral artery

value: injury

value: wild type

value: female


title: Sham_PVAT_Replicate_2

value: sham

tag: strain


title: Sham_PVAT_Replicate_1

tag: age


title: HepG2_xenograft_CTL_5

value: control (CTL)


title: FEDKO3

value: male


title: 293T cells expressing 3xHA_EVI1+18


title: FEDKO2


title: HepG2_xenograft_CTL_4


title: Injury_PVAT_Replicate_1


title: HepG2_xenograft_CTL_2


title: BT549/control for shIRF1, rep2

city: Boston

first: Nami

last: Yamashita

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
BT549 shIRF1_Gene_TPM.csv
BT549_shIRF1vControl.deseq.csv

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: GRCh38.74
Supplementary files format and content: Gene_TPM, log2FoldChange

growth_protocol: MDAMB436 cells were cultured in RPMI 1640 medium (Corning, Corning, NY, USA) supplemented with 10% FBS. BT549cells were cultured in RPMI 1640 medium (Corning, Corning, NY, USA) supplemented with 10% FBS and 10ug/ml Insulin.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline for inducible model.

tag: disease state

value: Breast Cancer

tag: resistance

value: puromycin resistance

tag: phenotype

value: TNBC

tag: shRNA

value: control shRNA (stable)


title: BT549/control for shIRF1, rep3


title: BT549/shIRF1, rep2

value: shIRF1 (stable)


title: BT549/shIRF1, rep3


title: FEDKO1

tag: genotype


title: BT549/control for shIRF1, rep1

tag: cell line


title: FEDWT4


title: HepG2_xenograft_CTL_1

tag: cell line source

value: HepG2-xenograft tumor


title: BT549/shPBRM1, rep2

description:
BT549 shPBRM1_Gene_TPM.csv
BT549_shPBRM1_v_Control.deseq.csv

value: shPBRM1 (stable)


title: BT549/shPBRM1, rep3


title: BT549/shPBRM1, rep1


title: FEDWT3

value: Liver

value: C57BL/6 Slc25a47tm1c(EUCOMM)Hmgu


title: FEDWT2

value: 9 weeks old

value: Fed state (Chow diet)


title: HepG2_DKD_TNFa_3

growth_protocol: HepG2 cells (ATCC, HB-8065) were routinely cultured in Dulbecco's modified Eagle medium (DMEM) containing 4.5 g/L glucose (Gibco) supplemented with 10% v/v fetal bovine serum (FBS) (Gibco), 2 mM L-glutamine (Gibco), 50 U/ml penicillin (Gibco) and 50 mg/ml streptomycin (Gibco) at 37°C in 5% CO2.

extract_protocol:
Total RNA was isolated using the Maxwell® RSC simplyRNA Cells Kit (Promega) together with the Maxwell® RSC Instrument (Promega) according to the manufacturer’s instructions.
RNA-Seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The double knock-down of macroH2A1 and macroH2A2 transcripts in HepG2 was achieved by stable integration of shRNA expression cassettes through retroviral transduction of pRetroSUPER vectors, as described in Douet et al., 2017. The following procedure was followed to treat the cells with TNFα: 500 thousand  HepG2 cells were seeded in six-well plates and incubated overnight in standard conditions. Then, the cells were subject to an overnight serum starvation by reducing the FBS concentration to 0.5%. After that, TNFα (PeproTech, resuspended in PBS 0.1% BSA) was added to the media to a final concentration of 20 ng/mL. An equal volume of PBS 0.1% BSA was added as the untreated control condition. The cells were treated for 24h, then collected and subject to RNA expression analysis.

value: double knock-down (DKD)

value: TNFα


title: BT549/control for shPBRM1, rep3


title: HepG2_DKD_TNFa_2


title: BT549/control for shPBRM1, rep2


title: FEDWT1


title: HepG2_DKD_TNFa_1


title: MDAMB436/tet-MUC1shRNA, DOX+, rep3

description:
MDAMB436-t8_Gene_TPM.csv
MDAMB436_Dox_v_noDox.deseq_star.csv

value: DOX+


title: HepG2_xenograft_CTL_3

tag: host strain


title: BT549/control for shPBRM1, rep1


title: FASTKO4

value: Overnight fasting


title: MDAMB436/tet-MUC1shRNA, DOX+, rep2


title: HepG2_CTL_TNFa_3

value: control (CTL)


title: MDAMB436/tet-MUC1shRNA, DOX+, rep1


title: MDAMB436/tet-MUC1shRNA, DOX-, rep2

value: DOX-


title: FASTKO3

value: male


title: PSC monocyte-derived macrophages, line 1414

city: Gainesville

first: Clayton

middle: E

last: Mathews

state: FL

address: 1275 Center Drive

department: Pathology

institute: University of Florida

description:
column name in processed data file: F1414iMDM
iMDMvspMDM.DEG.txt

data_processing:
Data processing was performed by Novogene.
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulated data.
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCh38.p12 (hg38)
Supplementary files format and content: iMonovspMono.DEG.txt - Tab delimmited file including read count, fpkm, and differential expression analysis
Supplementary files format and content: imoDCvspmoDC.DEG.txt - Tab delimmited file including read count, fpkm, and differential expression analysis
Supplementary files format and content: iMDMvspMDM.DEG.txt - Tab delimmited file including read count, fpkm, and differential expression analysis

source_name: PSC monocyte-derived macrophages

extract_protocol:
RNA was purified using the QIAGEN Rneasy mini plus kit
1μg of total RNA/sample was used for input and libraries were constructed using NEBNext® Ultra TM RNA Library Prep Kit for Illumina®

value: PSC monocyte-derived macrophages

tag: cell source

value: iPSC line 1414

value: M-CSF


title: MDAMB436/tet-MUC1shRNA, DOX-, rep3

value: Breast Cancer

value: puromycin resistance

value: TNBC


title: PSC monocyte-derived macrophages, line 2395

description:
column name in processed data file: F2395iMDM
iMDMvspMDM.DEG.txt

value: iPSC line 2395


title: HepG2_CTL_TNFa_2


title: HepG2_CTL_TNFa_1


title: primary monocyte-derived macrophages, leukopak 355

description:
column name in processed data file: E355pMDM
iMDMvspMDM.DEG.txt

source_name: primary monocyte-derived macrophages

value: primary monocyte-derived macrophages

value: primary cells


title: primary monocyte-derived macrophages, leukopak 353

description:
column name in processed data file: E353pMDM
iMDMvspMDM.DEG.txt


title: FASTWT4

value: Liver

value: C57BL/6 Slc25a47tm1c(EUCOMM)Hmgu

value: 9 weeks old


title: PSC monocyte-derived macrophages, line 1064

description:
column name in processed data file: F1064iMDM
iMDMvspMDM.DEG.txt

value: iPSC line 1064


title: FASTKO2

value: Overnight fasting


title: BT549/shIRF1, rep1

value: shIRF1 (stable)


title: HepG2_DKD_untreated_3

value: double knock-down (DKD)

value: untreated


title: primary monocyte-derived macrophages, leukopak 341

description:
column name in processed data file: E341pMDM
iMDMvspMDM.DEG.txt


title: FASTWT3

value: male


title: FASTKO1


title: HepG2_DKD_untreated_2


title: PSC monocyte-derived dendritic cells, line 2395

description:
column name in processed data file: D2395imoD
imoDCvspmoDC.DEG.txt

source_name: PSC monocyte-derived dendritic cells

value: PSC monocyte-derived dendritic cells

value: IL-4 and GM-CSF


title: HepG2_CTL_untreated_3

value: control (CTL)


title: PSC monocyte-derived dendritic cells, line 1064

description:
column name in processed data file: D1064imoD
imoDCvspmoDC.DEG.txt


title: PSC monocyte-derived dendritic cells, line 1414

description:
column name in processed data file: D1414imoD
imoDCvspmoDC.DEG.txt

value: iPSC line 1414


title: FASTWT2


title: primary monocyte-derived dendritic cells, leukopak 358

description:
column name in processed data file: C358pmoD
imoDCvspmoDC.DEG.txt


title: primary monocyte-derived dendritic cells, leukopak 355

description:
column name in processed data file: C355pmoD
imoDCvspmoDC.DEG.txt


title: MDAMB436/tet-MUC1shRNA, DOX-, rep1

value: Breast Cancer

value: puromycin resistance

value: TNBC

value: DOX-


title: PBMC, 0.1% EtOH, 08 h, rep2

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

institute: University of Eastern Finland

description:
0.1% ethanol for 8 h
EtOH_08h_R2

data_processing:
Read alignment and quantification via nf-core/rnaseq STAR-Salmon pipeline 3.0 (http://doi.org/10.5281/zenodo.4323183).
Filtering for protein coding genes, read counts normalization via EdgeR 3.36.0 (TMM-normalized CPM).
Assembly: hg38, Aligned to Ensembl annotation version 103, final annotation (via Biomart) to Ensembl version 104.
Supplementary files format and content: normalized_counts.xlsx: Excel table of TMM-normalized read counts (CPM; EdgeR pipeline).

source_name: PBMC

extract_protocol:
Extraction of total RNA using High Pure RNA Isolation kit (Roche).
rRNA-deplete cDNA library following NEB protocols.

value: peripheral blood mononuclear cells

value: Ethanol

tag: time point

value: 8 h


title: HepG2_CTL_untreated_2


title: KOP5

city: Bethesda

first: Shioko

last: Kimura

state: MD

address: 9000 Rockville Pike

department: CCR

institute: NIH

data_processing:
RNA samples sequenced on HiSeq2500 using Illumina TruSeq v4 chemistry
FasgtQC, trimming and alignment with STAR were conducted. Heseq were used for rawcounts calling. Deseq2 were used for downstream analysis and normalized raw counts with gene symbol name were created
Genome_build: mm10

source_name: Lung

extract_protocol:
RNA from lung tissue was prepared using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Knock out

value: Lung


title: primary monocyte-derived dendritic cells, leukopak 353

description:
column name in processed data file: C353pmoD
imoDCvspmoDC.DEG.txt

value: primary cells


title: PSC-derived monocytes, line 2395

description:
column name in processed data file: B2395imon
iMonovspMono.DEG.txt

source_name: PSC monocytes

value: PSC monocytes

value: iPSC line 2395


title: HepG2_DKD_untreated_1

value: double knock-down (DKD)

value: untreated


title: KOP3


title: KOP4


title: PSC-derived monocytes, line 1414

description:
column name in processed data file: B1414imon
iMonovspMono.DEG.txt


title: PSC-derived monocytes, line 1064

description:
column name in processed data file: B1064imon
iMonovspMono.DEG.txt

value: iPSC line 1064


title: primary monocytes, leukopak 353

description:
column name in processed data file: A353pmon
iMonovspMono.DEG.txt

source_name: primary monocytes

value: primary monocytes


title: primary monocytes, leukopak 356

description:
column name in processed data file: A356pmon
iMonovspMono.DEG.txt


title: WTP6

value: Wild type


title: WTP4


title: blood, P-6

city: shijiazhuang

first: Yanpeng

last: He

state: hebei

address: No.215 Heping West Road

department: The First Department of Pulmonary and Critical Care Medicine

institute: The Second Hospital of Hebei Medical University

data_processing:
Quality control: The quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data.
Genomic alignment and quantification: Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters. HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz. The CIRCexplorer program (v2.3.8) was used to identify both the circularizing junction and the spliced sequence of circRNAs. All circRNA candidates with junction reads less than 2 were discarded. The remaining circRNA candidates were considered bonafide circRNAs.
DESeq2 (v2) was applied for the detection of differentially expressed mRNAs between tumor and non-tumor samples, the limma R package (3.40.6) was used for differentially expressed circRNAs.
Assembly: GRCh38
Supplementary files format and content: File includes Count and  FPKM/TPM values for each sample

source_name: blood

extract_protocol:
Samples were collected using EDTA anticoagulated blood collection vessels. Take a 15 ml tube, add 6 ml trizol and 2 ml fresh blood (trizol: blood =3:1), and blow several times with a pipette to help split the cells in the sample. The sample oscillates violently and mixes 1-2 min until all the flocs were dissolved.Incubate at room temperature for 5 min to completely decompose the ribosomes. The samples were stored in the refrigerator at -80℃ for long-term storage for high-throughput sequencing.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: blood

value: patient with benign tracheal stenosis


title: blood, P-4


title: FASTWT1

value: Liver

value: C57BL/6 Slc25a47tm1c(EUCOMM)Hmgu

value: 9 weeks old

value: Overnight fasting

value: male


title: blood, P-3


title: blood, P-2


title: blood, P-5


title: WTP3


title: DKD, rep3, EREG

data_processing:
UMI-4C analysis was performed using the UMI4Cats R package (Ramos-Rodríguez et al., 2021).
Assembly: hg19
Supplementary files format and content: The processed files are tab-delimited tables with headers: chromosome of the bait (chr_bait), start coordinate of the bait (start_bait), end coordinate of the bait (end_bait), chromosome of the contact (chr_contact), start coordinate of the contact (start_contact), end coordinate of the contact (end_contact), detected UMIs (UMIs)
Library strategy: UMI-4C

extract_protocol: UMI-4C was performed essentially following a described protocol (Schwartzman et al., 2016). More specifically, 2.5 million HepG2 cells were seeded in 6-well plates. The day after, the cells were fixed by addition of PBS 1% FA and incubation for 10 min at RT. The reaction was stopped by adding glycine to a final concentration of 0.125M and incubation for 5 min on ice. The cells were then collected by scraping, washed with PBS and resuspended in 500 µL of lysis buffer (10 mM TRIS pH 8, 10 mM NaCl, 0.2% NP-40) and incubated for 30 min on ice. Nuclei were isolated by centrifugation for 5 min at 760 g and resuspended in 500 µL of DpnII buffer (NEB). 15 µL of SDS 10% were added to the tube and incubated for 60min at 37ºC shaking at 900rpm. Then, 150 µL of 10% Triton X-100 were added and the sample was incubated for 60 min at 37ºC. Afterwards, digestion of the nuclei was achieved by addition of 400U DpnII (NEB) and o/n incubation at 37ºC. The next morning, 200U DpnII were added again and the sample was incubated for 4 more hours at 37ºC, afterwards DpnII was inactivated for 20min at 65ºC. Digested nuclei were pelleted by centrifugation for 5 min at 600 g and resuspended in 5.7mL milli-Q H2O. Then, 700 µL T4 ligation buffer (Promega) and 20 µL T4 ligase (Promega, 3 U/µL) were added. The samples were incubated overnight at 16ºC. The samples were then digested with 5 µL RNAse A (10 mg/µL) and 10 µL proteinase K (10 mg/mL) for 30min at 37ºC and decrosslinked o/n at 65ºC. DNA was purified by phenol-chloroform extraction and ethanol precipitation and quantified with the Qubit™ dsDNA HS Assay Kit (Thermo Fisher). A total of 5 µg of DNA were sonicated with a Covaris S2 instrument with the following parameters: duty cycle 10%, intensity 4, cycles per burst 200 and time 60 s. Sequencing libraries were prepared as described (Schwartzman et al., 2016). The procedure is based in a nested PCR using oligonucleotides aligned to a specific region functioning as “bait” or “point of view” for capturing contacts.

treatment_protocol: No additional treatment was performed

tag: gene where the umi-4c bait is positioned

value: EREG


title: DKD, rep1, EREG, L2


title: CTL, rep3, EREG, L2

value: control (CTL)


title: CTL, rep1, EREG, L2


title: DKD, rep2, EREG, L2


title: CTL, rep2, EREG, L2


title: blood, P-1


title: HepG2_CTL_untreated_1


title: DKD, rep2, EREG, L1


title: primary monocytes, leukopak 355

description:
column name in processed data file: A355pmon
iMonovspMono.DEG.txt

tag: cell type

value: primary cells


title: DKD, rep1, EREG, L1


title: CTL, rep3, EREG, L1


title: peritoneal cells from wild type mice (KO3) intraperitoneal injection with LPS

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

description: Expression data for peritoneal cells isolated fromlactoferrin knockout mice intraperitoneal injection with LPS

data_processing:
Raw data (raw reads) were processed using NGS QC Toolkit. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference human genome using Tophat.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq functions estimate Size Factors and nbinomTest. P value < 0.05 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: mouse genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each samples

source_name: mouse  peritoneal lavage fluid

growth_protocol: Mice were maintained in Central Sourth University Animal Facility according to the Institutional Animal Care Guidelines. All animals were housed in plastic cages (5 mice/cage) with free access to distilled water and a standard diet under specific-pathogen free (SPF) conditions of humidity (50±10%), lightning (12-h light/dark cycle) and temperature (24±0.5℃).

extract_protocol:
mirVana miRNA ISOlation Kit (Ambion#1561) extraction of RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Solexa protocols.

treatment_protocol: No special treatment in this protocol

tag: agent

value: lactoferrin knockout

value: LPS


title: peritoneal cells from wild type mice (KO2) intraperitoneal injection with LPS


title: blood, N-4

value: normal


title: osrdr2-3-pa Bs-seq

city: Nanjing

first: Lili

last: Wang

address: Weigang No.1

institute: Nanjing Agricultural University

description:
des1-3 Bs-seq
des1-3_methy.txt.gz

data_processing:
Low-quality sequences(q<20) and adapters were trimmed using trimmomatic.
Reads were mapped to MSU7.0 using MSMAP 2.87 with parameters -g 1
methratio.py pathon script of BSMAP was used to extrac methylation ratios from BSMAP results with parameters -z and -r
Genome_build: MSU 7.0
Supplementary_files_format_and_content: tdf, methy.txt.gz

organism: Oryza sativa

source_name: young panicle

growth_protocol: RIce plants grown in soil in Hannan province

extract_protocol:
genomic DNA was extrated using CTAB method.
Genomic DNA was sonicated and then end-repaired with End repair Enzyme Mix. The blunt-ended DNA were treated with Klenow fragment and dATP to yield a proruding3-"A" and cytosine-methylated adaptors from Illumina were ligated according to manufacture's instructions.

tag: cultivar

value: japonica

value: panicle

value: DES1 mutant


title: WTP2

value: Wild type

tag: tissue

value: Lung


title: osrdr2-3-pa sRNA-seq

data_processing:
Adapter sequences were trimed and clean reads with sizes ranging from 18 to 35 were mapped to TRAI10 using Bowtie with parameter -v 0 -k 10.
Annotated structure RNAs were excluded.
Read counts were normalized to RPTM.
Supplementary_files_format_and_content: tdf, map.txt

extract_protocol:
RNA was extrated using TRIzol method.
18-35nt small RNA was cut from PAGE gel.


title: peritoneal cells from wild type mice (KO1) intraperitoneal injection with LPS

tag: strain


title: blood, N-3

value: blood


title: CTL, rep1, EREG, L1


title: peritoneal cells from wild type mice (KO3) intraperitoneal injection with PBS

description: Expression data for peritoneal cells isolated fromlactoferrin knockout mice intraperitoneal injection with PBS

value: PBS


title: peritoneal cells from wild type mice (KO2) intraperitoneal injection with PBS


title: blood, N-2


title: DKD, rep4, MBL2

value: double knock-down (DKD)


title: blood, N-1


title: AGED_DAY_9_rep3

city: Providence

first: Gerard

middle: J

last: Nau

state: RI

address: 593 Eddy St.

department: Medicine

institute: Alpert School of Medicine at Brown University

hyb_protocol: Labeled cRNA (1.65 µg) was hybridized to Whole Mouse Genome 4x44K microarrays (Agilent) following the manufacturer’s recommendations.  Array chambers were placed in a rotating hybridization oven (10 rpm, 65°C) for 17 hours. After hybridization, arrays were washed using pre-warmed (37°C) gene expression wash buffer 2 (Agilent) and scanned immediately in an Agilent G2565 microarray scanner

scan_protocol: Arrays were washed using pre-warmed (37°C) gene expression wash buffer 2 (Agilent) and scanned immediately in an Agilent G2565 microarray scanner.

data_processing: Summary expression files of each microarray scan were generated using limma: (a)  (backgroundCorrect(dat, method="normexp", offset=1)), then (b) normalized using  (normalizeBetweenArrays(dat$E, method="quantile")), then (c) the probe with the highest intensity (for a given gene) was selected as the representative of that gene.

source_name: Lung, AGED, DAY, 9, rep3

label_protocol: Five hundred ng of total lung RNA was reverse transcribed to cDNA and processed to cyanine-3 labeled cRNA using the one-color Quick Amp Labeling Kit (Agilent) according to the product handbook.  Labeled cRNA samples were purified using the RNeasy mini kit (QIAGEN).  Cy-3 integration and cRNA amplification were assessed using spectrophotometry, and samples with approximately 10 pmole Cy3/ug cRNA integration and greater than 5 µg total cRNA yield were hybridized to arrays.

extract_protocol: Whole mouse lungs were homogenized in 2 ml MagNA lyser Green Bead tubes (Roche Applied Science) with 1 mL TRI-reagent (Molecular Research Center, Inc.) at 6000 rpm for 1 min.  Homogenates were transferred to 1.5 mL RNase-free safe-lock tubes (Eppendorf) containing 1 mL of TRI-Reagent (Molecular Research Center).  For RNA isolation with TRI-Reagent, the manufacturer’s protocol for phase separation and RNA precipitation were followed except that samples were placed at -80°C overnight after adding isopropanol. To complete the isolation, tubes were thawed on ice, RNA was pelleted by centrifugation (12,000 rpm, 45 min, 4°C), and pellets were washed twice with cold 75% RNase-free ethanol (1 mL, 12,000 rpm, 10 min, 4°C).  After removing the ethanol wash, RNA pellets were dried for 3-5 minutes on the bench top, and then resuspended in 50 µL RNase-free water.  RNA was stored at -80°C until microarray labeling.  RNA integrity was evaluated using the Agilent RNA 6000 Nano Kit and 2100 BioAnalyzer according to the product handbooks.  RNA quantity was measured using a DU 800 UV/Vis Spectrophotometer (Beckman Coulter).

treatment_protocol: Mice were anesthetized (ketamine and xylazine mix) and intranasally instilled with 50 μl of PBS containing 50-100 pfu of PR8.

value: BALB/c

value: left lung

tag: Sex

value: Female

tag: age group

value: AGED

tag: timepoint

value: DAY 9


title: Nip-pa-R1 sRNA-seq

value: control


title: peritoneal cells from wild type mice (KO1) intraperitoneal injection with PBS

value: lactoferrin knockout


title: AGED_DAY_9_rep2

source_name: Lung, AGED, DAY, 9, rep2


title: AGED_DAY_9_rep1

source_name: Lung, AGED, DAY, 9, rep1


title: DKD, rep2, MBL2


title: peritoneal cells from wild type mice (WT2) intraperitoneal injection with LPS

description: Expression data for peritoneal cells isolated from wild type mice intraperitoneal injection with LPS

value: wild type

value: LPS


title: DKD, rep1, MBL2


title: ADULT_DAY_9_rep3

source_name: Lung, ADULT, DAY, 9, rep3

value: ADULT


title: blood, N-5

tag: disease state

value: normal


title: peritoneal cells from wild type mice (WT1) intraperitoneal injection with LPS


title: ADULT_DAY_9_rep2

source_name: Lung, ADULT, DAY, 9, rep2


title: Nip-pa-R1 Bs-seq

description:
ck Bs-seq
ck_methy.txt.gz

value: japonica

value: panicle


title: CTL, rep4, MBL2

value: control (CTL)


title: ADULT_DAY_9_rep1

source_name: Lung, ADULT, DAY, 9, rep1


title: CTL, rep2, EREG, L1

value: EREG


title: peritoneal cells from wild type mice (WT3) intraperitoneal injection with PBS

description: Expression data for peritoneal cells isolated from wild type mice intraperitoneal injection with PBS

value: PBS


title: DKD, rep3, MBL2

value: double knock-down (DKD)


title: peritoneal cells from wild type mice (WT2) intraperitoneal injection with PBS


title: CTL, rep2, MBL2


title: peritoneal cells from wild type mice (WT1) intraperitoneal injection with PBS


title: peritoneal cells from wild type mice (WT3) intraperitoneal injection with LPS


title: CTL, rep1, MBL2


title: AGED_DAY_7_rep2

source_name: Lung, AGED, DAY, 7, rep2

value: BALB/c

value: DAY 7


title: AGED_DAY_7_rep1

source_name: Lung, AGED, DAY, 7, rep1

value: left lung

value: Female


title: cDC2 flox rep2 (ATAC-seq)

city: Lund

first: Jonas

last: Ungerback

address: Klinikgatan 26

department: Division of Molecular Hematology

country: Sweden

institute: Lund University

description: cDC2_flox_out_ppr.IDR0.1.filt.no_chrY.narrowPeak

data_processing:
RNA-seq: RNA-sequence pre-processing  RNA-sequenced reads were trimmed Trimmomatiic (v0.38) for removal of adapter –and low quality sequences. Resulting reads were then mapped onto the mouse genome build mm10 with STAR (v2.6.0) (Dobin et al, 2013)  and post-processed with RSEM (v. 1.2.30) (http://deweylab.github.io/RSEM/) (Li et al, 2011) according to the settings in the ENCODE long-rna-seq-pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh) with the minor modifications that settings “--output-genome-bam --sampling-for-bam” was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build mm10 together with the Ensembl gene model file Mus_musculus.NCBIM37.66.gtf. The resulting bam-files were used to create HOMER tag directories (makeTagDirectory with –keepAll setting). For analysis of statistical significance among differentially expressed genes the raw gene counts were derived from each tag directory with analyzeRepeats.pl with the –noadj -condenseGenes options and tested for differential gene expression using the DESeq2 package ( https://www.bioconductor.org/packages/devel/bioc/html/DESeq2.html) (Love et al, 2014 #38) via HOMER getDifferentialExpression.pl.  t.
ATAC-seq: Reads were trimmed using Trimmomatic and mapped to mm10 (Gencode build GRCm38.p5) with Bowtie2 (v. 2.3.4) (Langmead et al, 2012). PCR duplicates were removed with Picard MarkDuplicates (v. 2.15.0) and files were further filtered for mapq score of 10 using Samtools (v. 1.7). Peak calling from the mapq10 filtered bam files (duplicates) was performed using the Kundaje lab ATAC-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL792NWO/) with MACS2 and IDR (irreproducible discovery rate) threshhold set to 0.05 and 0.1, respectively. Samtools was used to remove mitochondrial reads prior to peak calling. From each processed duplicate, the Optimal peak set was used for downstream analysis.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: RNA-seq: Raw count matrix derived with HOMER tools analyzeRepeats.pl rna mm10 -condenseGenes -count exons -raw -d {path-to-tagdirs}    ATAC-seq: IDR-processed MACS2 peak file. Filtered bam-files were processed with Kundaje lab ATAC-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL792NWO/) with MACS2 and IDR (irreproducible discovery rate) threshhold set to 0.05 and 0.1, respectively.

source_name: conventional dendritic cell

extract_protocol:
RNA-seq: Cells were FACS sorted based on the following surface parameters. Common pre-gate to all samples: Live, Singlets, CD11c+ Lin- (CD19, TCRb, B220, NK1.1). cDC1_migratory_XCR1Cre+_IRF4_flox (MHC-II high GFP+ XCR1+ CD11b-); cDC1_migratory_XCR1Cre-_IRF4_flox (MHC-II high XCR1+ CD11b-); cDC1_resident_XCR1Cre+_IRF4_flox (MHC-II low GFP+ XCR1+ CD11b-); cDC1_resident_XCR1Cre-_IRF4_flox (MHC-II low XCR1+ CD11b-); cDC1_wt (MHC-II hi YFP+); cDC2_wt (MHC-II hi YFP- CD11b+); ex_cDC1 (MHC-II hi YFP+); cDC2_flox (MHC-II hi YFP- CD11b+); DKO ( MHC-II hi YFP+); RNeasy Micro Kit  according to manufacturers protocol (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer with the RNA 6000 nano kit (Agilent).   ATAC-seq: Briefly, sorted cells (same populations as in RNA-seq: cDC1, cDC2_wt, ex_cDC1 and cDC2_flox) were rinsed with resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2 in sterile water), lysed and immediately after added tagmentation reaction mix from the Nextera DNA library preparation kit (Illumina). After 30  min incubation at 37C, samples were cleaned up using MinElute PCR purification kit (Qiagen). The libraries were constructed and barcoded using a Nextera library preparation kit (Illumina). The final amplified libraries were purified and size-selected (x1.2 bead-to-DNA ratio for ~100-150bp cutoff DNA size) using SPRI select (Beckman-Coulter). Each biological sample was run in triplicates. Libraries were sequenced paired-end on HiSeq2500 (Illumina) using 50 cycles paired-end mode (Illumina).
RNA-seq: RNA was extracted with RNeasy Micro kit (Qiagen). Revere transcription and amplification was performed using Ovation RNA-Seq System V2 kit (NuGEN). Amplified cDNA was purified using the MinElute Reaction Cleanup kit (Qiagen). Final librariers were constructed and indexed with the Ovation Ultralow system V2 kit (NuGEN) and quantified by Agilent 2100 Bioanalyzer (High sensitivity DNA kit).    ATAC-seq:  ATAC-seq library preparation was done as described in (Corces et al. 2017) using Transposomes from Nextera DNA library preparation kit (Illumina) and custom primers. Libraries were run paired-end on the Illumina HiSeq2500.

value: XCR1-cre.Irf8fl/fl. R26R.EYFP

value: mesenteric lymph nodes

tag: age

value: 12 weeks


title: cDC2 flox rep3 (ATAC-seq)


title: ADULT_DAY_7_rep3

source_name: Lung, ADULT, DAY, 7, rep3


title: HBEC3 cells, succinat treatment,5 days, rep1

city: Grand Rapids

first: Gerd

last: Pfeifer

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Research Institute

data_processing:
Paired-end reads were trimmed using TrimGalore(version 0.5.0) with the following parameters : --length 50, --clip_R1 10, --clip_R2 18, --three_prime_clip_R1 10, and --three_prime_clip_R2 10.
Trimmed reads were aligned to the hg19 using Bismark version 0.19.0
Duplication were  removed using the deduplicate_bismark script provided with Bismark
CpG methylation values were called  by the bismark_methylation_extractor script provided with Bismark and the following parameters: --no_overlap, --comprehensive, --merge_non_CpG, and --cytosine_report.
Assembly: hg19
Supplementary files format and content: Bismark Coverage report in a GZIP compressed format

growth_protocol: keratinocyte SFM medium , Cells were cultured at 37C at 5% CO2.

extract_protocol:
Genomic DNA was extracted using a Quick-DNA Miniprep Plus kit (Zymo Research, D4070).
The Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, 30024) was used according to the manufacturer’s instructions to perform bisulfite conversion and library preparation.

treatment_protocol: The cells were exposed to 10 mM of cell-permeable dimethyl-succinate for 5 days, the culture media with the same concentrations of succinate were replenished every 24 hours.

value: Human Bronchial cells

tag: genotype

value: WT

tag: treatment

value: succinate 10mM


title: WS_Rep2

city: La Jolla

first: Yunjiang

last: Qiu

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Illumina Casava1.8 software was used for basecalling.
Reads were aligned to the hg19 reference genome using STAR 2.4.2a with default parameters.
Only uniquely mapped reads were kept for further analysis.
FPKM values for each gene were computed using cufflinks v2.2.1 with default parameters according to Gencode human annotation release 24.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

source_name: U87-MG cells

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Total RNAs were extracted by TRIzol (Thermo Fisher Scientific) from U87-MG cells with or without SEMA3s treatment.
The resulting RNA was then used to prepare libraries using Illumina TruSeq Stranded mRNA Library Prep Kit Set A (Illumina, RS- 122-2101) or Set B (Illumina, RS-122-2102).

treatment_protocol: Cells were treated with 500 ng/ml recombinant SEMA3A proteins for 6 hours.


title: WS_Rep3


title: HBEC3 cells ,WT, rep2

tag: cell line

value: non treatment


title: HBEC3 cells,succinat treatment, 5 days, rep2


title: WS_Rep1


title: HBEC3 cells, WT, rep1


title: ex cDC1 rep3 (ATAC-seq)

description: ex_cDC1_out_ppr.IDR0.1.filt.no_chrY.narrowPeak


title: WC_Rep3


title: CTL, rep3, MBL2


title: AGED_DAY_7_rep3

source_name: Lung, AGED, DAY, 7, rep3

value: AGED


title: ex cDC1 rep2 (ATAC-seq)


title: ex cDC1 rep1 (ATAC-seq)


title: AGED_DAY_5_rep2

source_name: Lung, AGED, DAY, 5, rep2

value: DAY 5


title: WC_Rep2


title: AGED_DAY_5_rep3

source_name: Lung, AGED, DAY, 5, rep3


title: ADULT_DAY_7_rep2

source_name: Lung, ADULT, DAY, 7, rep2

value: ADULT


title: AP_day4

data_processing: Sequence reads were aligned against GRCh38 genome assembly and a count matrix of unique molecular identifiers (UMIs) was generated using using Cell Ranger (version 4.0.0)

source_name: ESC derivatives

growth_protocol: Human ESCs were cultured on feeder layers of mouse embryonic fibroblasts in DMEM/F12/KSR medium (D-MEM/F12 supplemented with 20% KSR additive, 2 mM glutamine, 0.1 mM non-essential amino acids, 0.1 mM 2-mercaptoethanol and 5 ng/ml basic FGF). ESC-derived TSLCs were culture on collagen-VI-coated plates in TS basal medium (DMEM/F12 supplemented with 0.1mM 2-mercaptoethanol, 0.2% FBS, 0.3% BSA, 1% ITS-X supplement, 1.5 mg/ml L-ascorbic acid) containing 50 ng/ml EGF, 2 µM CHIR-99021, 0.5 µM A83-01, 1 µM SB431542, 0.8 µM VPA and 5 µM Y27632.

extract_protocol:
Total RNAs were extracted using A Chromium Single Cell 3’ Library & Gel Beads Kit v3.1 (10x Genomics) following the manufacturer's protocol
Sequencing libraries were extracted using A Chromium Single Cell 3’ Library & Gel Beads Kit v3.1 (10x Genomics) following the manufacturer's protocol

treatment_protocol: Undifferentiated human ESCs were transferred onto matrigel-coated dishs, and on the following day culture media was switched to a fresh one containing A83-01 (1µM) and PD173074 (0.1µM).

tag: source

value: ESC derivatives

value: AP-treated


title: cDC2 flox rep1 (ATAC-seq)


title: AGED_DAY_5_rep1

source_name: Lung, AGED, DAY, 5, rep1


title: DC2 wt rep2 (ATAC-seq)

description: DC2_wt_out_ppr.IDR0.1.filt.no_chrY.narrowPeak

value: XCR1-cre. R26R.EYFP


title: ADULT_DAY_5_rep3

source_name: Lung, ADULT, DAY, 5, rep3

value: BALB/c


title: DC2 wt rep1 (ATAC-seq)


title: WC_Rep1


title: AP_day2


title: AP_day3


title: Kp-EV

city: Suita

first: Masaki

last: Nomura

address: 2-2, Yamadaoka

institute: Graduate School of Medicine, The University of Osaka

data_processing:
bcl2fastq
nf-core/rnaseq 3.0
Genome_build: hg19
Supplementary_files_format_and_content: gene expression (counts, TPMs, FPKMs)

source_name: hematopoietic cells (K562 cells)

growth_protocol: K562 cells were cultured with RPMI-1640 supplemented with 10% fetal bovine serum, 100 u/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen) following the manufacturer’s protocol
TruSeq RNA Library Kit v2

value: chronic myelogeneous leukemia cell

tag: treatment (transfection)

value: pMYs-IG_empty vector

tag: expression type

value: stably expressed

tag: expression level

value: retroviral overexpression


title: Kp-H18

tag: cell type


title: ADULT_DAY_5_rep2

source_name: Lung, ADULT, DAY, 5, rep2

value: left lung

value: Female


title: ADULT_DAY_7_rep1

source_name: Lung, ADULT, DAY, 7, rep1

value: DAY 7


title: KC_Rep2

value: KO


title: KS_Rep1


title: DC1 wt rep1 (ATAC-seq)

description: DC1_wt_out_ppr.IDR0.1.filt.no_chrY.narrowPeak

value: mesenteric lymph nodes

value: 12 weeks


title: Kp-HW


title: AGED_DAY_3_rep2

source_name: Lung, AGED, DAY, 3, rep2

value: AGED

value: DAY 3


title: KC_Rep3


title: ADULT_DAY_5_rep1

source_name: Lung, ADULT, DAY, 5, rep1

value: ADULT

value: DAY 5


title: ex_cDC1_IRF4_IRF8.DKO.rep3 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
ex_cDC1_IRF4_IRF8.DKO.rep3

value: 8-16 weeks


title: ex_cDC1_IRF4_IRF8.DKO.rep2 (RNA-seq)

description:
analyzeRepeats_immuno_samples.raw_exon_counts.txt
ex_cDC1_IRF4_IRF8.DKO.rep2