title: IMQ/Troglitazone, Day 6, rep3

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

institute: Pusan National University

data_processing:
Quality check and adapter trimming of RNA-seq data were conducted using FastQC and TrimGalore (https://www.bioinformatics.babraham.ac.uk/), respectively.
The cleaned reads were mapped to mouse genome assembly GRCm38 via the STAR aligner (v2.7.3a).
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) with mouse gene annotation GRCm38.86.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample

source_name: ear skin

extract_protocol:
RNA was extracted from tissue using mirVana™ miRNA Isolation Kit according to the manufacturer's recommended procedures. After total RNA purification, the sample was treated with DNase using DNA-Free kit to eliminate potential DNA contamination that could have interfered with the result interpretation.
mRNA sequencing libraries were prepared according to the manufacturer’s instructions (Illumina Truseq stranded mRNA library prep kit)

treatment_protocol: C57BL/6 mice within ages of 8 - 12 weeks were challenged topically with 20.8 mg of Aldara cream (containing 5 % imiquimod, w/w) on dorsal sides of their ears daily. One day after the last challenge, mice were euthanized. 20mg/kg of GW3965 or 150 mg/kg of troglitazone was intraperitoneally injected once daily from day 3. DMSO was injected as vehicle for GW3965 and troglitazone. Skin tissues were collected for RNA-seq analysis.

value: ear skin

value: IMQ+Troglitazone


title: CD11b+ myeloid cells, mtD2neg_1

status: Public on Apr 08 2024

type: SRA

city: Shanghai

first: Peng

last: Ding

address: No.600, Yishan Road

department: Orthopaedics

country: China

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

library_source: transcriptomic

data_processing:
After sequencing, generated reads were filtered and mapped to the reference genome using HISAT2 (v2.0.4)and assembled using StringTie (v1.3.4d) with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (v0.9.8) and the expression levels of all transcripts were calculated by Stringtie and ballgown.
Differential gene analysis was performed by DESeq2 software and then subjected to enrichment analysis of GO functions.
Assembly: Mus_musclus.GRCm38 V99
Supplementary files format and content: Excel file includes count and FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

growth_protocol: MtD2pos and mtD2neg CD11b+ myeloid cells were separated from Prx1creMitodendra+/+  mouse bone marrow

extract_protocol:
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent,CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
Following purification, mRNA library was constructed, fragmented, amplified and loaded into the nanoarray and sequencing was performed on Illumina Novaseq™ 6000 platform following the vendor’s recommender protocol.

treatment_protocol: Using flow cytometry to sort targeted CD11b+ myeloid cells  by green fluorescence.

tag: tissue

value: bone marrow

tag: cell type

value: CD11b+ myeloid cells

tag: genotype

tag: cell status


title: CD11b+ myeloid cells, mtD2neg_2


title: S10 slice 1

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

data_processing:
Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 (GRCz11) using STAR v2.7.1a, and the aligned reads were assigned to each gene using featureCounts v1.6.0.
For each embryo, gene counts of each slice were merged into a count matrix, and the genes that received more than 0.5 counts per million reads (CPM) in at least 3 slices were retained.
The count matrixes with slice position information were constructed into DGEList objects using edgeR, which were saved in rds format.
Assembly: GRCz11
Supplementary files format and content: rds  files include count matrixes and slice position information after running the processing steps.

organism: Danio rerio

source_name: embryonic cells

growth_protocol: Zebrafish embryos were raised in 0.3x Danieau buffer, and were then embedded in OCT at the required developmental stages of 10 hpf, 12hpf and 16 hpf.

extract_protocol:
RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol.
Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.

treatment_protocol: Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.

value: embryonic cells

tag: strain

value: AB

tag: age

value: 10 hpf


title: IMQ/Troglitazone, Day 6, rep2

country: South Korea

tag: treatment


title: HiC RPE/choroid, replicate 1

city: Sevilla

first: Pedro Manuel

last: Martínez-García

state: Sevilla

address: Ctra. de Utrera, km. 1, 41013 Montequinto, Sevilla

country: Spain

institute: CSIC

library_source: genomic

data_processing:
Paired-end reads were processed into multiresolution .hic files using Juicer (v1.6) with BWA-MEM mapping (v0.7.17).
Paired contacts from individual replicates were merged using Juicer "mega" to create combined .hic files for each tissue.
Assembly: Homo sapiens (hg38/GRCh38)
Supplementary files format and content: multiresolution hic files

molecule: genomic DNA

organism: Homo sapiens

source_name: RPE/choroid

extract_protocol:
Post-mortem human neural retina and RPE/choroid mixtures were obtained through the Tissue Bank of Ghent University Hospital and Antwerp University Hospital under ethical approval of the Ethics Committee of Ghent University (2018/1072, B670201837286). Eye globes were provided with a description of time and cause of death, post-mortem circulation time, age and sex. None of the 6 donors had a prior known ophthalmological condition.  The eye globes were dissected on ice, followed by extraction of the neural retina and the retinal pigment epithelium/choroid. The resulting tissues were resuspended in 1XPBS supplemented with 10% Fetal Bovine Serum. The samples were processed according to Matelot & Noordermeer (2016) and cross-linking of nuclei was performed using 2% formaldehyde. Finally, the obtained nuclei were aliquoted per 10 million and snap frozen after supernatant removal. Samples were stored at -80°C.
Crosslinked nuclei from four neural retina and four RPE/choroid samples were used to construct Hi-C libraries, following the in situ Hi-C protocol adopted by the 4D Nucleome consortium with a few adaptations. Briefly, for each replicate ~5 million pre-lysed, crosslinked nuclei were digested overnight using 250 U DpnII restriction enzyme (New England Biolabs, R0543L). DNA ends were marked by incorporating biotin-14-dATP (Life Technologies, 19524-016) and ligated for 4 hours using 2000 U T4 DNA ligase (New England Biolabs, M0202L). Subsequently, crosslinks were reversed overnight using proteinase K (Qiagen, 19131) and Hi-C template DNA was purified using 1x AMPure XP beads (Beckman Coulter, A63881) and stored at 4°C until library preparation. Hi-C template DNA was sheared to a size of 300-500 bp using microTUBE snap-caps (Covaris, 520045) in a Covaris M220 sonicator and MyOne Streptavidin T1 beads (Life Technologies, 65601) were used to pull down biotinylated ligation junctions. Next, samples were split into 5 µg aliquots for sequencing library preparation using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645L) and NEBNext Multiplex Oligos (New England Biolabs, E7335L). Amplified libraries were purified and size selected using 0.55x and 1.2x AMPure XP beads (Beckman Coulter, A63881). Pooled libraries were sequenced on an Illumina NovaSeq 6000 using 100 bp paired-end reads to a depth of ~500 million reads per sample.
in situ Hi-C

value: RPE/choroid

tag: developmental stage

value: Adult

value: wild-type

value: untreated


title: S10 slice 2


title: HiC neural retina, replicate 1

source_name: Neural retina

value: Neural retina


title: DDAC, 0.2500-4

city: Jeongeup

first: Yoon

last: Cho

state: Jeollabuk-do

address: 30, Baekhak 1-gil

institute: Korea Institute of Toxiology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastp), then mapped to mRatBN7.2 (NCBI) whole genome using STAR.
Read count extraction using HTSeq-count.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Rattus norvegicus

source_name: Lung

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: SD rats were administered to a single intratracheal instillation (ITI) of each QACs at varying concentrations.

value: Lung

value: WT


title: HiC RPE/choroid, replicate 2


title: LM33_rep1 (RNAseq)

city: Melbourne

first: Ian

last: Parish

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description: rawcounts.csv

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were trimed using bbduk (v38.90) to remove adapter sequences and poor quality ends.
trimmed reads were aligned using STAR (v2.7.5b) to the mouse reference genome (mm10)
Aligned reads were counted using featurecounts (v2.0.1)
Assembly: mm10
Supplementary files format and content: csv file include raw count (non-normalized) values for each sample

source_name: OT-I CD8+ T cell

extract_protocol:
RNA was harvested using the Qiagen MinElute RNAeasy kit. All isolated RNA was then used for library construction.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep with PolyA Selection following manufacturer's protocols.

treatment_protocol:
CTV labelled CD45.1+ OT-I cells were injected i.v. into RIP-OVAhi mice that were untreated B6 mice (Tolerance), injected i.p. with OVA protein (OVAp), LM-33 infected i.p. (LM-33) or LM-OVA infected i.p. (LM-OVA)
60h after transfer, divided CD45.1+ OT-I cells were sorted from pooled sacral and pancreatic LNs. As a control for naïve OT-I cells, naïve (CD44loCD62Lhi) CD8+ cells were sorted from CD45.1+ OT-I mice.

value: OT-I CD8+ T cell

value: CD45.1+ OT-I TCR transgenic

value: 2x10^6 CTV labelled CD45.1+ OT-I cells were injected i.v. into RIP-OVAhi transgenic B6 mice that were simultaneously infected i.p. with 2x10^6 cfu LM-33

tag: time


title: CD11b+ myeloid cells, mtD2pos_2


title: HiC RPE/choroid, replicate 3


title: LM33_rep3 (RNAseq)

description: rawcounts.csv


title: IMQ/Troglitazone, Day 6, rep1

value: ear skin


title: transduced MYCT1 knockdown, scRNAseq

city: Los Angeles

first: Júlia

last: Aguadé-Gorgorió

state: California

address: 615 Charles E Young Drive South

department: Molecular, Cell and Developmental Biology

country: USA

institute: University of California Los Angeles

description:
CB_KD
10x Genomics
aggregatedAll_barcodes.tsv.gz
aggregatedAll_features.tsv.gz
aggregatedAll_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 system.
Sequence data was mapped to the human reference genome (refdata-cellranger-GRCh38-1.2.0) using cellranger count.
Assembly: GRCh38
Supplementary files format and content: Annotated sequence data that contain cell barcodes (tsv), features (tsv) and gene expression matrix (mtx). Processed data files for the aggregated data of all samples is also provided (“aggregatedAll_”).

source_name: cord blood

growth_protocol: Human HSPCs were cultured in serum-free conditions with StemSpan SFEM II (StemCell Technologies, 9655) supplemented with 1% Pen/Strep, 1% L-glutamine, human FLT3-L (100 ng/mL, human TPO (50 ng/mL), human SCF (100 ng/mL) (Thermofisher Scientific15140122, 25030081 PHC9411, PHC9513, and PHC2113), human low-density lipoprotein (10 μg/mL), SR1 (500 nM) and UM171 (35 nM) (StemCell Technologies 2698, 72352, and 72914). Cells were cultured at 37 °C and 5% CO2, re-plated as necessary to maintain a cell density of ≤ 1x10^6/mL, and half media changes were performed every other day.

extract_protocol:
CB HSPCs were sorted after thawing (7AAD- CD34+ CD38- CD90+) and sequenced (uncultured) or transduced with control (empty vector, EV), MYCT1 OE, or MYCT1 KD and sorted again (7AAD- CD34+ CD38- CD90+ GFP+) 72 hours after transduction. Cells were sorted into PBS 0.04% Ultrapure BSA (Thermofisher Scientific AM2616) using a BD FACS Aria cell sorter.
A Chromium single cell instrument (10x genomics) was used for the generation of single-cell gel beads in emulsion. In brief, single-cell suspension of cells in 0.4% BSA-PBS were added to each channel on the 10X chip. Cells were partitioned with Gel Beads into emulsion in the Chromium instrument where cell lysis and barcoded reverse transcription of RNA occurred following amplification. scRNA-seq libraries were prepared by using the Chromium single-cell 3′ library and gel bead kit v3 (10x Genomics).

value: cord blood

value: HSPC

value: transduced MYCT1 knockdown


title: DDAC, 0.2500-3


title: LM33_rep2 (RNAseq)

description: rawcounts.csv


title: Tol_rep3 (RNAseq)

description: rawcounts.csv

value: 2x10^6 CTV labelled CD45.1+ OT-I cells were injected i.v. into RIP-OVAhi transgenic B6 mice


title: DDAC, 0.1250-4


title: DDAC, 0.2500-2


title: OVAp_rep1 (RNAseq)

description: rawcounts.csv

value: 2x10^6 CTV labelled CD45.1+ OT-I cells were injected i.v. into RIP-OVAhi transgenic B6 mice that were simultaneously injected i.p. with 2mg purified OVA protein


title: IMQ/GW3965, Day 6, rep3


title: DDAC, 0.2500-1


title: IMQ/GW3965, Day 6, rep2


title: transduced MYCT1 overexpression, scRNAseq

description:
CB_OE
10x Genomics
aggregatedAll_barcodes.tsv.gz
aggregatedAll_features.tsv.gz
aggregatedAll_matrix.mtx.gz

value: transduced MYCT1 overexpression


title: transduced control, scRNAseq

description:
CB_Ctrl
10x Genomics
aggregatedAll_barcodes.tsv.gz
aggregatedAll_features.tsv.gz
aggregatedAll_matrix.mtx.gz

value: transduced control


title: uncultured, scRNAseq

description:
CB_d0
10x Genomics
aggregatedAll_barcodes.tsv.gz
aggregatedAll_features.tsv.gz
aggregatedAll_matrix.mtx.gz

value: uncultured


title: DDAC, 0.1250-2


title: Naive_rep2 (RNAseq)

description: rawcounts.csv

value: Naïve OT-I cells were sorted from CD45.1+ OT-I mice


title: DDAC, 0.1250-3


title: IMQ/GW3965, Day 6, rep1


title: Naive_rep1 (RNAseq)

description: rawcounts.csv


title: 293_12h_mRNA-seq_Rep1

city: Shenzhen

first: Zhenzhen

last: Wang

address: 97 Buxin Road

institute: Chinese Academy of Agricultural Sciences

data_processing:
Sequence reads are mapped to h38 using HISTAT2(version 2.2.1) with default parameters
Raw counts for the feature of genes were extracted by featureCounts (version 2.0.3).
BigWig files were generated by using deepTools (version 3.5.1)
Assembly: GRCh38

extract_protocol:
Nucleic acid was extracted by SDS
gDNA library, mRNA library and mRNA&gDNA library were constructed by extracting whole nucleic acid from cells. RNase A enzyme is used to remove RNA from gDNA library. Genome DNA was removed by digested with DNase I in mRNA library while retained in mRNA&gDNA library as internal reference. mRNA was reverse-transcribed with oligo(dT) as the primer to synthesis the first strand of the complementary DNA (cDNA). To reduce bias and simplify our pipeline, fragmented cDNA without second strand synthesis and gDNA were denatured by heat following library preparation using a high-efficient ssDNA ligation technique, Adaptase from Accel-NGS 1S Plus DNA Library Kit (Swift Accel-NGS).

tag: cell line

tag: molecule

value: mRNA

value: Actinomycin D


title: Tol_rep1 (RNAseq)

description: rawcounts.csv


title: Naive_rep3 (RNAseq)

description: rawcounts.csv


title: IMQ/Veh, Day 6, rep2

value: IMQ+Veh


title: Tol_rep2 (RNAseq)

description: rawcounts.csv


title: 293_12h_mRNA-seq_Rep2


title: DDAC, 0.1250-1

value: Lung

value: WT


title: IMQ/Veh, Day 6, rep3


title: IMQ/Veh, Day 6, rep1


title: 293_12h_mRNA_gDNA-seq_Rep1

library_source: other

molecule: other

value: mRNA  gDNA


title: RAA 2, VDJ,TCR

city: London

first: Vishal

last: Vyas

address: Charterhouse Square

country: United Kingdom

institute: William Harvey Research Institute, Queen Mary University of London

data_processing:
CellRanger v6.0.1 count was used to quantify  gene expression reads following alignment to the human reference genome GRCh38.
VDJ reads were aligned to the GRCh38 VDJ reference dataset using cellranger vdj (v.6.01). 10x feature barcoding was performed using the antibodies outlined above, the reads for which were counted using cellranger count
Assembly: human reference genome GRCh38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix_h5 containing both the GEX and FB matrices. Additional metrics summaries in .csv format for FB.
Supplementary files format and content: CellRanger output files for VDJ reads summarised in the filtered_contig_annotations.csv files
Library strategy: CITE-seq

source_name: Human right atrial appendage tissue

extract_protocol:
Two paired human epicardial adipose tissue and right atrial appendage tissue specimens were obtained during open chest cardiac surgery. The tissue specimens were enzymatically digested to isolate the stromal vascular fraction. The CD45+ immune fraction was then isolated through PE bead enrichment using Nanobeads.  Cells were stained with CITE-Seq antibodies (antibody-derived tags) and further CD45+ enrichment was performed using fluorescence-activated cell sorting (FACS). The samples were maintained at a concentration of ~1000 cells/μL. Single cells were encapsulated in Gel Beds-in emulsion (GEMs) using the 10x Genomics Controller with a Chromium Single Cell 5' GEM Library and Gel Bead Kit.
The CITE-seq protocol described in the 10x Genomics document CG000330 - Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) User Guide with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping was followed to generate, a 5' gene expression library, cell surface protein library (antibody-derived tags) and VDJ libraries for TCR sequencing.

value: Human right atrial appendage tissue


title: RAA 2, RNA, GEX

molecule: polyA RNA


title: RAA 2, FB, ADT

molecule: protein


title: 293_12h_mRNA_gDNA-seq_Rep2


title: DDAC, 0.0625-2


title: UTX/Veh, Day 6, rep3

value: ear skin

value: UTX+Veh


title: DDAC, 0.0625-3


title: UTX/Veh, Day 6, rep2


title: EAT 2,VDJ, TCR

source_name: Human Epicardial Adipose Tissue

value: Human Epicardial Adipose Tissue


title: UTX/Veh, Day 6, rep1


title: DDAC, 0.0625-1


title: 293_0h_mRNA-seq_Rep1

value: untreatment


title: 293_0h_mRNA-seq_Rep2


title: mOCs_Mito_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: FPKM, counts

source_name: mature osteoclasts(mOCs)

growth_protocol: Primary BMMs was extracted from mouse femurs. The osteoclast precusors(OCPs) was differentiated from bone marrow-derived macrophage(BMMs) by cytokine M-CSF(100ng/ml) and RANKL(100ng/ml) for 3 days. The mature osteoclasts(mOCs) was differentiated from bone marrow-derived macrophage(BMMs) by cytokine M-CSF(100ng/ml) and RANKL(100ng/ml) for 5 days.Cells were maintained in α-MEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Bone marrow-derived macrophages(BMMs),osteoclast precusors(OCPs) and mature osteoclasts(mOCs) were transplanted by mitochondria for 1 day

value: mature osteoclasts(mOCs)

value: mT/mG

value: mature osteoclasts was induced with M-CSF (100ng/mL) and RANKL (100ng/mL) for three days from OCPs and mitochondria extracted from osteoblasts were transplanted at the third day of mOCs stage.


title: mOCs_Mito_2


title: DDAC, 0.0625-4


title: 293_0h_mRNA_gDNA-seq_Rep1


title: 293_0h_mRNA_gDNA-seq_Rep2


title: mOCs_Mito_1


title: BKC, 1.0000-2


title: BKC, 1.0000-3


title: 116_mRNA-seq_Rep2


title: BKC, 1.0000-1


title: mOCs_3

value: mature osteoclasts was induced with M-CSF (100ng/mL) and RANKL (100ng/mL) for three days from OCPs


title: 116_mRNA-seq_Rep1


title: RAA 1, FB, ADT


title: mOCs_2


title: RAA 1, RNA, GEX


title: EAT 1, VDJ,TCR


title: mOCs_1


title: BKC, 0.5000-4


title: 116_mRNA_gDNA-seq_Rep2


title: 116_mRNA_gDNA-seq_Rep1


title: BKC, 0.5000-3


title: EAT 2,FB, ADT


title: EAT 1, FB, ADT


title: EAT 2,RNA, GEX


title: 116_gDNA-seq_Rep2

value: gDNA


title: EAT 1, RNA, GEX


title: OCPs_Mito_3

source_name: Osteoclast Precusors(OCPs)

value: Osteoclast Precusors(OCPs)

value: Osteoclastogenesis was induced with M-CSF (100ng/mL) and RANKL (100ng/mL) for three days and mitochondria extracted from osteoblasts were transplanted at the third day of OCPs stage.


title: BKC, 1.0000-4


title: OCPs_Mito_1


title: 80_mRNA-seq_Rep2

value: mRNA


title: 116_gDNA-seq_Rep1


title: RAA1, VDJ,TCR


title: Human_islets_18hr_NMMA_3

city: Charleston

first: Jennifer

middle: S

last: Stancill

state: South Carolina

address: 173 Ashley Avenue, CR513

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

data_processing:
CellRanger (10x Genomics) function “mkfastq” was used to process raw BCL files into FastQ files
Assembly: hg38
Supplementary files format and content: CellRanger (10x Genomics) function “count” was used to generate gene-barcode matrices from FastQ files

source_name: Pancreatic islet

extract_protocol:
Following cytokine treatment, islets were dissociated into single cells and loaded on the Chromium Controller (10x Genomics).
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v3 Reagent Kit (10x Genomics) for replicate 1 and the Chromium Next GEM Single Cell 3′ v3.1 Reagent Kit (10x Genomics) for replicates 2 and 3 according to the manufacturer’s protocol. Libraries were sequenced using the NextSeq 500/550 High Output Kit v2.5 flow cell (150 cycles, Illumina) according to the 10x Genomics protocol. Samples were sequenced to a depth that returned approximately 30,000 reads per cell on average

treatment_protocol: Human pancreatic islets from cadaveric donors were obtained from Prodo Labs, Inc. They were exposed to cytokines ex vivo for either 6 or 18 hr.

value: Pancreatic islet


title: OCPs_3

value: Osteoclastogenesis was induced with M-CSF (100ng/mL) and RANKL (100ng/mL) for three days from BMMs.


title: Human_islets_18hr_IL-1b+IFN-g+NMMA_3


title: Human_islets_18hr_IL-1b+IFN-g_3


title: 80_mRNA-seq_Rep1


title: OCPs_2


title: BKC, 0.2500-3

value: Lung

value: WT


title: BKC, 0.2500-4


title: 80_mRNA_gDNA-seq_Rep2

value: mRNA  gDNA


title: OCPs_1


title: Human_islets_18hr_IL-1b_3


title: ADEB18, 0.5000-4


title: 80_mRNA_gDNA-seq_Rep1


title: BMMs_Mito_3

source_name: Bone marrow-derived macrophages(BMMs)

value: Bone marrow-derived macrophages(BMMs)

value: Bone marrow-derived macrophages(BMMs) was induced with M-CSF (20ng/mL) for three days from bone marrow derived mononuclear cell(BMMNC) and mitochondria extracted from osteoblasts were transplanted at the third day of bmms stage.


title: 80_gDNA-seq_Rep2


title: BKC, 0.5000-2


title: OCPs_Mito_2


title: BKC, 0.5000-1


title: Human_islets_6hr_IFN-g_3


title: BMMs_Mito_2


title: Human_islets_6hr_IL-1b_3


title: ADEB18, 0.5000-2


title: BMMs_Mito_1


title: Human_islets_untreated_3

value: Untreated


title: 80_gDNA-seq_Rep1

value: untreatment


title: 293_mRNA-seq_Rep2


title: ADEB18, 0.5000-1


title: Human_islets_18hr_NMMA_2


title: BKC, 0.2500-2


title: BKC, 0.2500-1


title: BMMs_2

value: Bone marrow-derived macrophages(BMMs) was induced with M-CSF (20ng/mL) for three days from bone marrow derived mononuclear cell(BMMNC)


title: BMMs_3

value: mT/mG


title: ADEB18, 0.2500-4


title: Human_islets_18hr_IL-1b+IFN-g+NMMA_2


title: 293_mRNA_gDNA-seq_Rep1


title: ADEB18, 0.2500-3


title: mtD2pos_3

data_processing:
After sequencing, generated reads were filtered and mapped to the reference genome using HISAT2 (v2.0.4)and assembled using StringTie (v1.3.4d) with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (v0.9.8) and the expression levels of all transcripts were calculated by Stringtie and ballgown.
Differential gene analysis was performed by DESeq2 software and then subjected to enrichment analysis of GO functions.
Assembly: Mus_musclus.GRCm38 V99
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: osteoclast progenitor (OCP)

growth_protocol: The osteoclast progenitors (OCPs)  were differentiated from bone marrow-derived macrophage(BMMs) for 2 days by cytokine MCSF(100ng/ml) and RANKL(100ng/ml), maintained in α-MEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

treatment_protocol:
OCPs were co-cultured with osteoblast cells (Prrx1creMitoDendra) for 1 day, maintained in α-MEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.
Using flow cytometry to sort targeted OCPs with red and green fluorescence.

value: osteoclast progenitor (OCP)

value: Co-cultured with osteoblastic cells (Prrx1creMitoDendra) for 1 day, then using flow cytometry to sort targeted OCPs with mitochondria transferred (with both red and green fluorescence)


title: BMMs_1


title: ADEB18, 0.2500-2


title: 293_gDNA-seq_Rep2

value: gDNA


title: ADEB18, 0.5000-3


title: Human_islets_18hr_IL-1b+IFN-g_2


title: mtD2pos_1


title: mtD2pos_2


title: 293_mRNA-seq_Rep1


title: Human_islets_18hr_IL-1b_2


title: ADEB18, 0.2500-1


title: ADEB18, 0.1250-4


title: 293_gDNA-seq_Rep1


title: 293_mRNA_gDNA-seq_Rep2


title: Human_islets_6hr_IFN-g_2


title: ADEB18, 0.1250-3


title: Human_islets_6hr_IL-1b_2


title: Human_islets_6hr_IL-1b+IFN-g_2


title: Human_islets_untreated_2


title: mtD2neg_1

value: Co-cultured with osteoblastic cells (Prrx1creMitoDendra) for 1 day, then using flow cytometry to sort targeted OCPs without mitochondria transferred (with red fluorescence but without green fluorescence)


title: ADEB18, 0.1250-1


title: e4-iN-1: APOE e4 neuron

city: Cambridge

first: Robin

last: Kleiman

state: MA

address: 225 Binney Street

institute: Biogen

description: APOE e4 neuron

data_processing:
Sequencing reads were mapped to GRCh38 (GENCODE annotation v35) using STAR (version 2.7.7a), and fragments that were uniquely mapped to the correct strand of the genes were counted using the featureCounts function from the Subread package1,2 (version 1.6.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: pair-end read counts

source_name: iPSC-derived neuron

extract_protocol:
Total RNA from the cells were prepared using the RNeasy Plus Mini Kit (Qiagen).
100ng RNA was used to generate stranded RNA-Seq library using the KAPA mRNA HyperPrep Kit

tag: apoe genotype

value: neuron

tag: replicate number


title: e4-iN-3: APOE e4 neuron

description: APOE e4 neuron


title: mtD2neg_3


title: ADEB18, 0.1250-2


title: e4-iN-2: APOE e4 neuron

description: APOE e4 neuron


title: e4-iN-4: APOE e4 neuron

description: APOE e4 neuron


title: Human_islets_18hr_NMMA_1


title: Ctrl3

value: untreated


title: Ctrl2


title: Human_islets_18hr_IL-1b+IFN-g+NMMA_1

value: Pancreatic islet


title: ABD, 0.5000-2


title: e4-iPSC-4: APOE e4 iPSC

description: APOE e4 iPSC

source_name: iPSC

value: iPSC


title: ABD, 0.5000-4

value: Lung


title: ABD, 0.5000-3

value: WT


title: Human_islets_18hr_IL-1b+IFN-g_1


title: Human_islets_6hr_IL-1b+IFN-g_1


title: e4-iPSC-1: APOE e4 iPSC

description: APOE e4 iPSC


title: immature Confined DCs, KO confined at 3µm, rep3

city: Paris

first: Wail

last: Zeitouni

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Raw reads were aligned to mm39 whole genome using STAR 2.7.5a.
Read count extraction was performed using FeatureCounts 1.5.0.
Read counts normalization and differential gene expression analysis were performed using DESeq2 and R 3.5.3.
Assembly: mm39 (GRCm39)
Supplementary files format and content: Normalized_counts_deseq2_Fastdb2021_2_annotation.txt: Tab-delimited text file of DESeq2 normalized counts with Fastdb 2021_2 annotation.

source_name: Bone marrow derived dendritic cells

growth_protocol: Cells are maintained in culture during 10 days in medium supplemented with fetal calf serum and granulocyte-macrophage colony stimulating factor-containing supernatant obtained from transfected J558 cells, as previously described by (Faure-Andre 2008). This medium supplemented with 1% of a penicillin/streptomycin cocktail to avoid bacterial contamination.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). RNA sequencing libraries were prepared from 300ng to 1µg of total RNA.
TruSeq Stranded mRNA Library preparation kit and the Illumina Stranded mRNA Prep Ligation kit which allow to perform a strand specific RNA sequencing.
A first step of polyA selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing and then ligated to the TruSeq indexed adapters (for the TruSeq kit) or RNA Index Anchors (for the mRNA Ligation kit). PCR amplification was finally achieved to create the final indexed cDNA libraries (with 13 cycles).

treatment_protocol: Cells were stimulated with 100 ng/ml of lipopolysaccharide (LPS) for 30 minutes then LPS was washed and cells left in incubator until the next day.

value: Bone marrow derived dendritic cells

value: KO of cPLA2

value: confinement at 3um height

value: 4 hours after confinement


title: mtD2neg_2


title: e4-iPSC-3: APOE e4 iPSC

description: APOE e4 iPSC


title: e4-iPSC-2: APOE e4 iPSC

description: APOE e4 iPSC


title: ABD, 0.5000-1


title: Ctrl1


title: e4-iCo-4: APOE e4 co-culture

description: APOE e4 co-culture

source_name: iPSC-derived astrocyte and neuron co-culture

value: co-culture


title: immature Confined DCs, KO confined at 3µm, rep2


title: Human_islets_6hr_IFN-g_1


title: ABD, 0.2500-3


title: immature Confined DCs, WT confined at 3µm, rep3

value: WT of cPLA2


title: e4-iCo-3: APOE e4 co-culture

description: APOE e4 co-culture


title: Human_islets_untreated_1

value: Untreated


title: e4-iCo-2: APOE e4 co-culture

description: APOE e4 co-culture


title: hTERT rep2

city: Chuo-ku

first: Mitsuhiro

last: Machitani

state: Tokyo

address: 5-1-1 Tsukiji

country: Japan

institute: National Cancer Center Research Institute

data_processing:
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.6.4_dev), Trimmomatic (version 0.39), and cutadapt (version 2.10) software.
Trimmed reads were then mapped to the human GRCh38 genome using STAR (version 2.7.9a).
Reads on annotated genes were counted using featureCounts (version 2.0.1).
FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HeLa

growth_protocol: The cells were cultured in DMEM with 10% heat-inactivated fetal bovine serum.

extract_protocol:
To separate cells into cytoplasmic fraction and nuclear pellet, 80~90% confluent cells in 150 mm dishes were lysed with HLB/NP40 buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 0.5% NP40, and 2.5 mM MgCl2) and incubated for 5 min on ice. After the incubation, HLB/NP40 buffer containing 10% sucrose was added under the lysate layer, followed isolation of nuclear pellet by centrifugation. Nuclear fraction was treated with MNase digestion to separate proteins associated with chromatins and treated with NaCl to remove nucleoplasmic proteins.  The final pellet was subjected to sonication and centrifugation, and the supernatant was collected as a nuclear speckle (NS)-enriched fraction. We then isolated hTERT complex by immunoprecipitation with an anti-hTERT mAb from the NS-enriched fraction and conducted RIP-seq analysis for RNAs associated with hTERT in nuclear speckles.
Sequencing cDNA libraries (RIP-seq libraries) were prepared using SMARTer stranded Total RNA Sample Prep Kit-HI Mammalian (Takara Bio) according to the manufacturer’s instruction.

value: HeLa

value: cervical carcinoma cell

value: purification of nuclear speckles


title: ABD, 0.2500-1


title: e4-iCo-1: APOE e4 co-culture

description: APOE e4 co-culture


title: immature Confined DCs, WT confined at 3µm, rep1


title: hTERT rep1


title: ABD, 0.2500-4


title: e4-iA-4: APOE e4 astrocyte

description: APOE e4 astrocyte

source_name: iPSC-derived astrocyte

value: astrocyte


title: mouse IgG rep2


title: ABD, 0.1250-4


title: LPS-activated non-confined DCs, KO, rep3

value: activation by LPS

value: 30 minutes with LPS then wash, recover the next day


title: LPS-activated non-confined DCs, KO, rep2


title: ABD, 0.1250-3


title: Human_islets_6hr_IL-1b_1

value: Pancreatic islet


title: ABD, 0.1250-1


title: LPS-activated non-confined DCs, KO, rep1


title: e4-iA-3: APOE e4 astrocyte

description: APOE e4 astrocyte


title: ABD, 0.1250-2


title: clone2 rep1

source_name: hTERT-CRISPR clone#2

growth_protocol: The cells were cultured in DMEM/F-12 with 5% heat-inactivated fetal bovine serum.

extract_protocol:
TRIzol extraction of total RNA was performed according to the manufacturer's instructions.
Sequencing cDNA libraries (RNA-seq libraries) were prepared using SMARTer stranded Total RNA Sample Prep Kit-HI Mammalian (Takara Bio) according to the manufacturer’s instruction.

treatment_protocol: We established two U2OS cell clones with heterozygous mutations in the hTERT gene locus by CRISPR-Cas9 system.

value: hTERT-CRISPR clone#2

value: osteosarcoma cell

value: hTERT +/-


title: e4-iA-1: APOE e4 astrocyte

description: APOE e4 astrocyte


title: e4-iA-2: APOE e4 astrocyte

description: APOE e4 astrocyte


title: mouse IgG rep1


title: clone2 rep2


title: ABD, 0.2500-2

source_name: Lung

value: Lung

value: WT


title: immature Confined DCs, KO confined at 3µm, rep1

value: Bone marrow derived dendritic cells

value: KO of cPLA2

value: confinement at 3um height


title: LPS-activated non-confined DCs, WT, rep3

value: WT of cPLA2


title: Control-3

value: ITI, DW


title: immature Confined DCs, WT confined at 3µm, rep2

value: 4 hours after confinement


title: LPS-activated non-confined DCs, WT, rep2


title: KO-iPSC-4: APOE KO iPSC

description: APOE KO iPSC

value: KO

value: iPSC


title: clone1 rep2

source_name: hTERT-CRISPR clone#1

value: hTERT-CRISPR clone#1


title: KO-iPSC-3: APOE KO iPSC

description: APOE KO iPSC


title: Control-2


title: KO-iPSC-2: APOE KO iPSC

description: APOE KO iPSC


title: clone1 rep1


title: LPS-activated non-confined DCs, WT, rep1

value: activation by LPS


title: Control-1


title: immature non-confined DCs, KO control, rep3

value: directly at end of culture


title: KO-iPSC-1: APOE KO iPSC

description: APOE KO iPSC


title: propionate 4 mM treated LS 174T''

city: seoul

first: seongho

last: ma

address: Anamro 145

institute: Korea university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2.
Read count extraction and normalization were performed using edgeR.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include read count values for each Sample.

source_name: LS 174T goblet cell

growth_protocol: LS 174T goblet cells were seeded at the concentration of 2.5 × 10e5 cells/ml on 6-well plate and incubated in RPMI 1640 media containing 10% fetal bovine serum and 1% penicillin and streptomycin at 37 ℃ with the atmosphere of 5% CO2 for overnight.

extract_protocol:
RNA was harvested using RiboEx reagent (Geneall, Seoul, Korea). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Propionate was treated at the final concentration of 4 mM for 4 h.

value: LS 174T

value: Colorectal adenocarcinoma cell line

tag: passage

value: Propionate


title: immature non-confined DCs, KO control, rep2


title: KO-iN-4: APOE KO neuron

description: APOE KO neuron

value: neuron


title: Control-4

value: Lung


title: immature non-confined DCs, KO control, rep1


title: KO-iN-3: APOE KO neuron

description: APOE KO neuron


title: immature non-confined DCs, WT control, rep3


title: immature non-confined DCs, WT control, rep2


title: P2 ovary, biol rep 1

city: Goettingen

first: Sarah Mae

last: Penir

address: Am Fassberg 11

department: Department of Meiosis

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciences

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation was performed using the Cell Ranger software 3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Whole ovary

extract_protocol:
Ovaries were isolated from postnatal day 2 mice. Single-cell suspensions were generated using a combination of ColIV and AccuMax treatments. After several rounds of filtration, cells were resuspended in PBS without Mg2+ and Ca2+ with 0.04% BSA.
Libraries were constructed according to the Chromium Single Cell 3' Reagent Kits (v2 Chemistry).

value: Whole ovary

value: CD1 strain background

tag: Sex

value: Female


title: KO-iN-2: APOE KO neuron

description: APOE KO neuron


title: CKD 3

city: Aurora

first: Makoto

last: Miyazaki

state: CO

address: 12700 E 22nd PL Denver CO

institute: University of Colorado

data_processing:
The sequencing strategy was PE150
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BasecallLite version 1.4.0.257
Trimmed sequence reads were mapped to GRCm38.p6_GCF_000001635.26(https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26/) using SOAPnuke Version v1.5.2  Parameters -l 15 -q 0.2 -n 0.05  Official Websitehttps://github.com/BGI-flexlab/SOAPnuke [1]Cock P., et al.(2010). The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research, 38(6): 1767-1771.
The steps of data QC and filter was   1) Removed the reads containing the adaptor(adaptor pollution);  2) Removed reads whose N content is greater than 5%;  3) Removed low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  4) The filtered "Clean Reads" are saved in FASTQ format.
We used Bowtie2[1] to map the clean reads to the reference gene sequence (transcriptome), and then used RSEM[2] to calculate the gene expression level of each sample.       Software Information:  Bowtie2:  Version：v2.2.5  Parameters：-q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200  Official Website：http://bowtie-bio.sourceforge.net/bowtie2/index.shtml  References：[1] Langmead, B. et al. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).    RSEM:  Version：v1.2.8  Parameters：-p 8 --forward-prob 0 --paired-end  Official Website：http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html  References：  [2] Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).
Assembly: GRCm38.p6_GCF_000001635.26(https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26/)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Aorta

growth_protocol: 8-week-old male SMMHC-GFP mice on DBA/2J backgroud were subjected to sham-operation or 5/6 nephrectomy.

extract_protocol:
Total RNAs were isolated using Direct-zol RNA isolation kit.
From this step, BGI  (www.BGI.com) performed all procedrures. RNA libraries for RNA-seq were prepared using 13462ES96#Hieff NGS™ Ultima Dual-mode mRNA Library Prep Kitfollowing manufacturer's protocols.

treatment_protocol: After 12 weeks of the surgeries, SMMHC-GFP-positive VSMC were isolated from enture aorta of sham-operated or 5/6 nephrectomized mice using a cell sorter.

value: Aorta

value: Male

tag: disease state

value: chronic kidney disease

value: VSMC

value: SMMHC-GFP

value: 5/6 nephrectomy


title: WT rep1

value: osteosarcoma cell

value: hTERT +/+


title: propionate 4 mM treated LS 174T'


title: KO-iN-1: APOE KO neuron

description: APOE KO neuron

value: KO


title: CKD 2


title: NC'

value: LS 174T


title: WT rep2


title: CKD 1


title: NC''

value: Colorectal adenocarcinoma cell line


title: immature non-confined DCs, WT control, rep1

value: Bone marrow derived dendritic cells

value: WT of cPLA2

value: directly at end of culture


title: propionate 4 mM treated LS 174T

value: Propionate


title: KO-iCo-3: APOE KO co-culture

description: APOE KO co-culture

value: co-culture


title: Ram_cko3

city: Glasgow

first: Alison

last: Galloway

address: Garscube Estate, Switchback Road

institute: Beatson CRUK

description: rRNA-depleted

data_processing:
Reads were aligned to mm10 with gencode vM25 annotation, and read counts for each gene calculated using STAR version 2.5.2b.
Gene expression was compared between controls and Rnmt/Ram cKO in R using EdgeR (Robinson et al., 2010).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Each reads per gene file contains a tab-delimited table of reads per gene counted during alignment in STAR. The first column indicates the Ensembl gene id, the second column shows all alignments, the third shows forwards alignments, and the fourth shows reverse alignments (reverse aligned reads are the reads counts to use for this library strategy).

source_name: 20 hour activated CD4 T cells

growth_protocol: CD4 T cells were sorted from lymph nodes using a MACS mouse CD4 T cell isolation kit (Miltenyi).

extract_protocol:
RNA was prepared using Trizol.
Libraries were constructed by Genewiz for Illumina, strand-specific RNA-seq with rRNA depletion. Libraries underwent 2x150 bp sequencing on an Illumina NovaSeq.

treatment_protocol: CD4 T cells were cultured for 20 hours in T cell culture medium (RPMI + 10% heat inactivated FCS + pen/strep + 50µM 2ME) on anti-CD3/CD28 coated plates prepared by incubating the plates with PBS with 5ug/ml anti-CD3 and 1ug/ml anti-CD28 at 37C for three hours.

value: Ram fl/fl CD4cre +

value: Female

value: Activated CD4 T cells


title: P2 ovary, biol rep 2

value: Whole ovary

value: CD1 strain background


title: NC


title: Ram_cko2

description: rRNA-depleted


title: NKD_sham 2

value: Aorta

value: Male

value: normal kidney

value: VSMC

value: SMMHC-GFP

value: sham operaton


title: NKD_sham 3


title: KO-iCo-2: APOE KO co-culture

description: APOE KO co-culture

value: KO


title: Ram_cko1

description: rRNA-depleted


title: NKD_sham 1


title: P45_AK

city: Stanford

first: Carolyn

last: Lee

state: CA

address: 269 Campus Drive

institute: Stanford University School of Medicine

data_processing:
Sampleswerepseudoalignedandquantifiedtothehg38referencegenomeusingSalmon(version1.5.1)togeneratecountmatrices
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing transcript by sample count matrix

source_name: Skin

extract_protocol:
TotalRNAwasthenisolatedfromhumantissuesusingQIAshredder(Qiagen)andTrizol(ThermoFisher)followedbyDNAremovalwiththeTURBODNA-freekit(Ambion)accordingtothemanufacturer’sinstructions.
RNA-Seq libraries were prepared with the mRNA Seq Sample Prep Kit (Illumina, Inc.) as recommended by the manufacturer.

value: Skin

value: Actinic Keratosis


title: KO-iCo-1: APOE KO co-culture

description: APOE KO co-culture


title: KO-iA-4: APOE KO astrocyte

description: APOE KO astrocyte

value: astrocyte


title: P34_AK


title: Ram_con3

description: rRNA-depleted

value: Ram fl/fl CD4cre -


title: P44_AK


title: 387-3 DLP, MYC, HFD

city: Montreal

first: David

middle: P

last: Labbé

state: QC

address: 1001 Decarie Boulevard

department: Urology

country: Canada

institute: Research Institute of McGill University Center

data_processing:
A count matrix was estimated through pseudo alignment with salmon (1) using mm39 ensembl 104 transcripts annotations, which where posteriorly summarized at gene level with the tximport R/Bioconductor package. Low count genes (< 5 CPM) were filtered and the remaining genes were normalized with the trimmed mean of M-Values method (2). A generalized linear model approach coupled with empirical Bayes moderation of standard errors and voom precision weights (3,4) was used to detect differentially expressed genes. between the selected contrasts
1. Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nature methods. 2017 Apr;14(4):417-9.
2. Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11(3):R25.
3. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article3.
4. Law CW, Chen Y, Shi W, Smyth GK. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014;15(2):R297.
Assembly: mm39 ensembl 104
Supplementary files format and content: Excel file include TPM values for each sample

organism: Mus

source_name: Prostate-dorsolateral lobe (DLP)

extract_protocol:
Frozen dorsolateral prostate lobes (DLP) were pulverized using a Cryoprep Pulverizer (Covaris). Total RNA was extracted with the Rneasy Plus MiniKit (Qiagen, #73404).
RNA-seq libraries were prepared from 50 ng of total purified RNA using the KAPA Biosystems RNA HyperPrep Kit with RiboErase (Roche, #08098140702). Prior to library preparation, RNA quality was checked with the Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 5 were fragmented at 94°C for 8 min according to manufacturer recommendation. Those with RIN < 5 were fragmented at 85 °C for 2 min. dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit (Roche, #07960298001), according to manufacturer protocols.
Uniquely indexed libraries were pooled in equimolar ratio and sequenced on an Illumina NovaSeq 6000 with paired end 50 bp reads at the Dana-Farber Cancer Institute Molecular Biology Core Facility.

treatment_protocol: Dorsolateral prostate lobels (DLP) were collected from MYC-transgenic and wild-type FVB mice fed high-fat diet or control diet for 21 weeks.

value: Prostate-dorsolateral lobe (DLP)

value: MYC-transgenic (MYC)

value: high-fat diet (HFD) for 21 weeks


title: KO-iA-2: APOE KO astrocyte

description: APOE KO astrocyte


title: 351-5 DLP, MYC, HFD


title: P32_AK


title: P33_AK


title: KO-iCo-4: APOE KO co-culture

description: APOE KO co-culture

value: co-culture


title: Ram_con2

description: rRNA-depleted

value: Female

value: Activated CD4 T cells


title: Ram_con1

description: rRNA-depleted


title: KO-iA-1: APOE KO astrocyte

description: APOE KO astrocyte


title: 351-1 DLP, MYC, HFD


title: P29_AK


title: Rnmt_cko3

description: rRNA-depleted

value: Rnmt fl/fl CD4cre +


title: 346-3 DLP, MYC, HFD


title: 351-4 DLP, MYC, HFD


title: e3-iPSC-4: APOE e3 iPSC

description: APOE e3 iPSC

value: iPSC


title: e3-iPSC-3: APOE e3 iPSC

description: APOE e3 iPSC


title: Rnmt_cko1

description: rRNA-depleted


title: Rnmt_cko2

description: rRNA-depleted


title: P24_AK


title: P16_AK


title: 364-3 DLP, MYC, CTD

value: control diet (CTD) for 21 weeks


title: e3-iPSC-2: APOE e3 iPSC

description: APOE e3 iPSC


title: Rnmt_con3

description: rRNA-depleted

value: Rnmt fl/fl CD4cre -


title: Rnmt_con2

description: rRNA-depleted


title: e3-iN-4: APOE e3 neuron

description: APOE e3 neuron

value: neuron


title: e3-iPSC-1: APOE e3 iPSC

description: APOE e3 iPSC


title: TGNF3

city: Dallas

first: Srinivasa R.

last: Sripathi

state: Texas

address: 9600 N Central Expressway Suite 200

institute: Retina Foundation of the Southwest

data_processing:
Reads were aligned to the human (NCBI build 37.2) reference genomes using TopHat with default setttings. Gene expression levels were quantified using Cuffquant with default settings. Gene expression levels were normalized across all samples using Cuffnorm with default settings
Assembly: NCBI build 37.2
Supplementary files format and content: CSV file containing FPKM for all samples

source_name: hiPS derived RPE monolayers

growth_protocol: hiPSC and hES lines were maintained on Matrigel basement membrane matrix coated tissue culture plates with mTeSR1 medium in 5% O2 and 10% CO2 conditions and amplified by clonal propagation using the ROCK pathway inhibitor blebbistatin. For hRPE differentiation, stem cells were plated at a higher density (25,000 cells per cm2) and maintained in mTeSR1 to form a monolayer. The culture medium was replaced with a differentiation medium (DM) for 7 weeks. Differentiating cells were enzymatically dissociated to make single-cell suspension using 0.25% (wt/vol) collagenase IV and resuspended in AccuMAX. Cells were re-plated on to Matrigel basement membrane matrix coated plates and maintained in an RPE medium [70% DMEM, 30% Ham’s F12 nutrient mix, 2% B27-serum-free supplement, 1% antibiotic-antimycotic solution (Invitrogen, Waltham, MA, USA)] for ~3 months to form mature RPE monolayers.

extract_protocol:
First-strand cDNA synthesis was performed with 200 ng total RNA using anchored oligo-dT and SuperScript III First-Strand Synthesis with SuperMix. Second-strand cDNA synthesis was performed using RNase H, DNA Polymerase I, and Invitrogen Second Strand Buffer. Double-stranded cDNA was purified using DNA Clean & Concentrator-5.
Library preparation was performed using the Nextera XT DNA Library Preparation Kit. Libraries were cleaned using Agencourt AMPure XP beads according to manufacturer’s instructions. Libraries were evaluated by the High Sensitivity DNA Kit on a 2100 Bioanalyzer. They were then multiplexed and sequenced on an Illumina HiSeq with 50 bp paired-end reads. Reads were aligned to NCBI build 37.2 using Tophat (v2.1.0). Cuffquant and Cuffnorm (Cufflinks v2.2.1) were used to quantify expression levels and calculate normalized FPKM values.

treatment_protocol: The small molecule kinase inhibitors BAY651942 and BMS345541 were reconstituted in DMSO (10 mM and 200 µM stocks), loaded into Echo qualified 384-well polypropylene microplates, and dispensed precisely in multiples of 2.5 nL droplets at the desired concentrations in triplicate using an ECHO 550 acoustic liquid handling system.

value: Stem cell-derived Retinal Pigment Epithelial Cells

value: hiPSC EP1

value: hiPS derived RPE monolayers

value: Retinal Pigment Epithelial Cells

value: TGF-beta/TNF-alpha


title: 363-2 DLP, MYC, CTD


title: Rnmt_con1

description: rRNA-depleted


title: TGNF2


title: TGNF1


title: 350-4 DLP, MYC, CTD


title: e3-iN-3: APOE e3 neuron

description: APOE e3 neuron


title: Human_islets_6hr_IL-1b+IFN-g_3

source_name: Pancreatic islet

value: Pancreatic islet


title: e3-iN-2: APOE e3 neuron

description: APOE e3 neuron

source_name: iPSC-derived neuron


title: 361-5 DLP, MYC, CTD

value: Prostate-dorsolateral lobe (DLP)


title: MLR3

value: UNTREATED


title: e3-iN-1: APOE e3 neuron

description: APOE e3 neuron


title: MLR2


title: L1_3

city: Hangzhou

first: Chenjia

last: Shen

state: Zhejiang

address: No.58,Haishu Rd, Cangqian, Yuhang District

department: College of Life and Environmental Sciences

institute: Hangzhou Normal University

data_processing:
Raw reads in fastq format were processed using the fastp program, and the low quality reads were deleted to produce clean reads.
The clean reads were mapped onto the T. mairei genome using HIST2 software.
The read counts of each gene were calculated by HTSeq-count software.
PCA was performed using R (ver. 3.2.0) to evaluate the sample supplication.
Hierarchical cluster analysis of DEGs was performed using R (ver. 3.2.0).
Assembly: Taxus mairei genome
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Taxus mairei

source_name: twig

extract_protocol:
Total RNAs were extracted using an Qiagen RNeasy Mini Kit (Hilden, Germany).
The purified and fragmented mRNAs were used to construct cDNA libraries using a VAHTS Universal V6 RNA-seq Library Prep Kit.

value: twig

value: Endophytic fungal infection

value: WT

value: fungal elicitors, L01 (Guignardia)


title: 351-3 DLP, WT, HFD

value: wild-type (WT)

value: high-fat diet (HFD) for 21 weeks


title: e3-iCo-4: APOE e3 co-culture

description: APOE e3 co-culture

value: co-culture


title: MLR1


title: 364-4 DLP, MYC, CTD

value: MYC-transgenic (MYC)

value: control diet (CTD) for 21 weeks


title: J2_3

value: fungal elicitors,  J02 (Diaporthe)


title: e3-iCo-3: APOE e3 co-culture

description: APOE e3 co-culture


title: 351-2 DLP, WT, HFD


title: DMSO3

value: Stem cell-derived Retinal Pigment Epithelial Cells

value: hiPSC EP1

value: DMSO


title: J2_2


title: 346-5 DLP, WT, HFD


title: J2_1


title: e3-iCo-2: APOE e3 co-culture

description: APOE e3 co-culture


title: e3-iCo-1: APOE e3 co-culture

description: APOE e3 co-culture


title: DMSO2

value: hiPS derived RPE monolayers

value: Retinal Pigment Epithelial Cells


title: CT_3

value: control


title: 363-1 DLP, WT, CTD

value: Prostate-dorsolateral lobe (DLP)


title: e3-iA-4: APOE e3 astrocyte

description: APOE e3 astrocyte

value: astrocyte


title: DMSO1


title: 353-2 DLP, WT, HFD


title: CT_2

value: twig

value: Endophytic fungal infection


title: e3-iA-3: APOE e3 astrocyte

description: APOE e3 astrocyte


title: BAY65_32uM2


title: L1_2

value: WT

value: fungal elicitors, L01 (Guignardia)


title: L1_1


title: e3-iA-2: APOE e3 astrocyte

description: APOE e3 astrocyte


title: CT_1


title: 361-3 DLP, WT, CTD

value: wild-type (WT)


title: 361-2 DLP, WT, CTD


title: BAY65_32uM1


title: 350-3 DLP, WT, CTD


title: e3-iA-1: APOE e3 astrocyte

description: APOE e3 astrocyte


title: BAY65_16uM2


title: Gastrocnemius muscle Cry2flox

status: Public on Apr 07 2024

city: Suzhou

first: Ting

last: Xue

state: Jiangsu

address: 199 Ren Ai Road, Suzhou 215123, China

department: Hematology Center, Cyrus Tang Medical Institute

institute: Soochow University

data_processing:
Illumina Casava  bcl2fastqv2.19 software used for basecalling.
Filter the Raw Reads obtained by sequencing to obtain clean Reads that can be used for data analysis, and apply Seqtk to filter. The main steps are as follows: 1. Remove the linker sequence contained in the reads; 2. Remove the 3'end quality Q less than 20 Bases, that is, the base error rate is less than 0.01, where Q=-10logerror_ratio; 3. Removal of reads less than 25 in length; 4. Removal of ribosome RNA reads of the species.
Use Hisat2 (version: 2.0.4) split mapping algorithm to perform Genome mapping on the preprocessed reads. This algorithm allows the splitting of reads that cannot be matched to the full length to be mapped, and is more suitable for eukaryotic (with intron inter-regions). ) Transcriptome sequencing data; default parameters are used.
In transcriptome sequencing, we can estimate the level of gene expression by mapping the number of reads to the gene region, but the number of reads is not only proportional to the level of gene expression, but also related to the length of the gene itself and the amount of sequencing data. In order to make the gene expression levels of different genes and different samples comparable, the reads were converted into FPKM (Fragments Per Kilobase of exon model per Million mapped reads) to standardize the gene expression levels.
We first use Stringtie (version: 1.3.0) to count the number of Fragments of each gene after Hisat2 comparison, then use the TMM (trimmed mean of M values) method to normalize, and finally use the perl script to calculate each gene FPKM value.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Gastrocnemius muscle

extract_protocol:
Gastrocnemius muscle was isolated from CRY2scko mice and CRY2flox/flox mice. Total RNA was extracted using the RNAsimple total RNA Kit per manufacturer’s instructions. The quality of the total RNA was inspected by Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA). Qualified total RNA was further purified by RNAClean XP Kit (Cat# A63987, Beckman Coulter, Inc, Brea, CA). The cDNA library was generated using a VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Cat# NR604-02, Vazyme, Nanjing, China) and sequenced on an Illumina system (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gastrocnemius muscle


title: Gastrocnemius muscle Cry2scko


title: BAY65_16uM1


title: 346-4 DLP, WT, HFD

value: high-fat diet (HFD) for 21 weeks


title: GV_5mc_300_cells_Input

city: Shanghai

first: Xiaodong

last: Zhao

address: 800 Dongchuan RD

institute: Shanghai Jiao Tong University

data_processing:
Raw reads were trimmed using Trimmomatic (version 0.38)
Bowtie (version 1.2.2) was used to align the clean reads to the reference genome (hg19 for human and mm10 for mouse).
The uniquely mapped reads after the removal of duplicates were used for the downstream analysis
Peaks were obtained using MACS (version 2.1.1) with corresponding input samples.
Genome_build: hg19  or mm10
Supplementary_files_format_and_content: The bigwig files were generated with the function bamCoverage from DeepTools27 using with the following parameters (--binSize 200 and --smoothLength 1,000), and binSize 1,000 was used when processing MeDIP data

source_name: GV

growth_protocol: GV oocytes were collected from the ovaries of a 6-week-old C57BL/6 female mouse 46-48 h after the injection of 8-10 U pregnant mare serum gonadotropin (PMSG)

extract_protocol:
gDNA was harvested using AllPrep DNA/RNA Mini Kit (Qiagen) and sonicated with a sonicator.
Libraries were prepared as super cChIP-seq or super cMeDIP-seq protocol described.

tag: sample type

value: GV oocytes


title: Pseudomonas aeruginosa, treated, rep 3

city: Münster

first: Verena

last: Spiegler

address: Corrensstraße 48

institute: University of Münster

data_processing:
Samples were demultiplexed to fastq data using bcl convert 3.8.4 and quality controlled in FastQ. Trimmomatic was used for adapter trimming and read filtering.
Trimmed reads were aligned to the reference genome of P. aeruginosa ATCC 27853 using Hisat2.
Aligned reads were sorted using samtools and counted using htsec-count.
Tests for differential expression were performed using the R-package DESeq2
Assembly: GCF_001687285.1
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample
Supplementary files format and content: tab-delimited text file contains results of differential expression analysis, including annotations

organism: Pseudomonas aeruginosa

growth_protocol: P. aeruginosa were maintained on LB agar. Prior to treatment, single colonies were grown for approx. 18 h in Vogel-Bonner minimal medium.

extract_protocol:
RNA was harvested using NucleoSpin® RNA II kit (Macherey-Nagel)
Library preparation of the total RNA was achieved using the NEBNext Ultra II RNA directional Kit according to the manufacturer's protocol.

treatment_protocol: Overnight cultures were diluted to 4 x 10^6 CFU/mL, supplemented with methylrhodomelol (75 µM; treated) or DMSO (0.1 %; untreated) and grown in VB-MM to mid-log phase at 37°C in an orbital shaker.

value: 75 microM methylrhodomelol


title: Pseudomonas aeruginosa, treated, rep 2


title: Pseudomonas aeruginosa, treated, rep 1


title: IMPRINT7_S439

city: Wuerzburg

first: Chase

last: Beisel

address: Josef-Schneider-Str. 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Paired-end reads were merged using BBMerge (version 38.69) with parameters “qtrim2=t, ecco, trimq=20, -Xmx1g”
Sequences with perfect matches of flanking sequences were extracted as potential RBS regions using a Python script
After filtering by 10 count per million in minimal 2 samples, differential abundance (log2FC) of potential RBS region sequences between time points was calculated using the quasi-likelihood F test after fitting in a generalized linear model.
Supplementary files format and content: TSV, counts of each RBS sequence in different samples
Supplementary files format and content: CSV, normalized differential abundance of each RBS sequence in different samples
Library strategy: DNA-seq

organism: Bifidobacterium breve

source_name: bacteria

growth_protocol: Escherichia coli was grown in LB media supplemented with 100 µg/mL ampicillin; Bifidobacterium breve was grown on reinforced clostridial agar with 20 ug/mL tetracycline or in MRS liquid broth (BD CN# 288130) supplemented with 0.03% L-cysteine and 20 ug/mL tetracycline.

extract_protocol:
Zyppy Plasmid Miniprep Kit
A plasmid library containing a stretch of nine randomized nucleotides was used. For NGS library preparation, adapters and unique dual indices based on Illumina TruSeq were added in a two-step amplification process using the KAPA HiFi HotStart Library Amplification Kit (KAPA Biosystems, KK2611), according to manufacturer's protocols. The samples were purified with Agencourt AMPure XP (Beckman Coulter, A63881).

treatment_protocol: Bifidobacterium breve was resuspend in 250uL of 30mg/mL lysozyme and incubate at 37°C for 30 minutes at 250 rpm, then removed lysozyme mix to harvest cells.

value: bacteria

value: Amplified on agar plates

tag: biological replicate

value: agar biol rep3


title: Pseudomonas aeruginosa, untreated, rep 3

value: 0.1 percent DMSO


title: KG1 cells

city: Los Angeles

first: Júlia

last: Aguadé-Gorgorió

address: 615 Charles E Young Drive South

institute: University of California Los Angeles

data_processing:
Sequencing was performed on Illumina HiSeq 3000 for SE 1x50 run.
Data quality check was done on Illumina SAV.
Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
Alignment to the human genome (hg38) was performed using STAR (Dobin et al. 2013). The hg38 - Ensembl Transcripts release 101 gtf was used for gene feature annotation.
For normalization, 1.0E-4 was added followed by RPKM normalization.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample.

growth_protocol: Immortalized human umbilical vein endothelial cells (E4EC) (Butler et al. 2012) were cultured on gelatin-coated flasks with Medium 199 containing (GE Life Sciences sh30253.01) 20% FBS (FB-01 Omega scientific), 1% penicillin–streptomycin, 1% L-Glutamine, 10mM HEPES (Thermofisher Scientific 15140-122, 2503-081, and 15630080), human FGF (20 ng/mL) (R&D systems 233-FB), human EGF (10 ng/mL), human IGF-I (10 ng/mL) (Peprotech AF-100-15 and 100-11), and heparin (50 μg/mL) (Sigma-Aldrich H3149-50KU). KG1 cells were cultured in RPMI with 10% FBS, 1% penicillin–streptomycin and 1% L-Glutamine.

extract_protocol:
Total RNA was extracted from KG1 and E4EC cell lines using the RNeasy Mini kit (Qiagen 74104).
Library was constructed using KAPA Stranded RNA-Seq Kit with RiboErase Kit. Different adapters were used for multiplexing samples in one lane.

tag: cell type

value: acute myeloid leukemia cell line


title: IMPRINT4_S436

value: Amplified in liquid culture

value: liquid biol rep3


title: IMPRINT6_S438

value: agar biol rep2


title: IMPRINT2_S434

value: liquid biol rep1


title: IMPRINT3_S435

value: liquid biol rep2


title: IMPRINT5_S437

value: agar biol rep1


title: 345-2 DLP, WT, CTD

tag: tissue

value: Prostate-dorsolateral lobe (DLP)

tag: genotype

value: control diet (CTD) for 21 weeks


title: Pseudomonas aeruginosa, untreated, rep 1

value: WT


title: FGSC_5mc_10K_cells_Input

source_name: FGSC

growth_protocol: FGSCs cultured on gelatinized plates with minimum essential medium (MEM)-α containing 10 % fetal bovine serum and several growth factors as in our previous report [Zhang et al. Genome Biology 2016]

value: FGSCs


title: GV_5mc_300_cells_super_cMeDIP-seq_Rep2

extract_protocol:
gDNA was harvested using AllPrep DNA/RNA Mini Kit (Qiagen) and sonicated with a sonicator and MeDIP DNA was isolated with antibody.
Libraries were prepared as super cChIP-seq or super cMeDIP-seq protocol described.

value: GV oocytes


title: FGSC_5mc_50_cells_super_cMeDIP-seq_Rep2


title: GV_5mc_300_cells_super_cMeDIP-seq_Rep1


title: FGSC_5mc_50_cells_super_cMeDIP-seq_Rep1


title: Kelly transfected piR-1254 5

city: Regensburg

first: Tilman

last: Heise

address: Franz Josef Strauss Allee 11

institute: Uniklinik Regensburg

description: S513 10

data_processing:
Quality filtering of reads using cutadapt with parameters --minimum-length 25 --cut 5 -q 20
Read mapping to the human reference genome (Gencode, GRCh38, v43) using STAR with default parameters
Using featureCounts to gather final read counts per gene
Assembly: GRCh38, Gencode v43
Supplementary files format and content: count table of each sample

source_name: Kelly

growth_protocol: Kelly cells were maintained in RPMI1640 supplemented with 10% fetal calf serum (FCS), 1% L-Glutamine and 1% Penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested 48 h after transfection with the Rneasy mini kit (Qiagen). 250 ng of total RNA was used for the construction of sequencing libraries.
Library preparation and RNAseq were carried out as described in the Illumina “Stranded mRNA Prep Ligation” Reference Guide, the Illumina NextSeq 2000 Sequencing System Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit - Illumina/ABI Prism (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA).

treatment_protocol: Kelly cells were reverse transient transfected with the lipofectamine RNAiMAX (Thermo Fisher) with piR-1254 or piR-Ctrl as control on a 6-well plate with 1.0 million cells per well and a final RNA concentration of 25 nM.

value: Kelly

value: Neuroblastoma

value: transient transfection sncRNA7SL


title: Kelly transfected piR-1254 4

description: S513 9


title: Pseudomonas aeruginosa, untreated, rep 2


title: E4EC cells

value: E4-immortalized HUVEC cell line


title: FGSC_5mc_200_cells_super_cMeDIP-seq_Rep2


title: Kelly transfected piR-1254 3

description: S513 8


title: FGSC_5mc_200_cells_super_cMeDIP-seq_Rep1


title: Kelly transfected piR-1254 2

description: S513 7


title: FGSC_5mc_200K_cells_Input


title: FGSC_5mc_1K_cells_super_cMeDIP-seq_Rep1


title: S3-E2st20

city: Freiburg

first: Peter

last: Walentek

state: BW

address: Breisacherstr. 113

department: Internal Medicine IV & IMITATE

institute: University Freiburg Medical Center

data_processing:
Quality control was done using FastQC v0.11.5
paired-end reads were mapped to Xenopus laevis genome assembly v9.2 using RNA STAR v2.6.0b-1
featureCounts v1.6.3 was used to count uniquely mapped reads per gene
statistical analysis of differential gene expression was conducted in DEseq2 v1.22.1
Assembly: X. laevis v9.2 genome assembly
Supplementary files format and content: tabular results files derived from DESeq2
Supplementary files format and content: DESeq2_result_st20vsst14.tabular file ( with GeneID, Base mean, log2(FC), StdErr, Wald-Stats, P-value, P-adj columns)

organism: Xenopus laevis

source_name: epidermis, animal cap explant, st20

growth_protocol: Explants were cut from the animal portion of stage 8 Xenopus laevis embryos in 1x Modified Barth's Saline (MBS), then they were maintained in the medium for at least 1 hour to heal. After healing of explants, they were transferred to 0.5x MBS containing 0.1% of Gentamycin and cultured in that medium until they reached the indicated stage.

extract_protocol:
Total RNA was extracted using the standard Trizol protocol.
500 ng total RNA per sample was used, poly-A selection and RNA-sequencing library preparation was done using non strand massively-parallel cDNA sequencing (mRNA-Seq) protocol from Illumina, the TruSeq RNA Library Preparation Kit v2, Set A (Illumina #RS-122-2301) according to manufacturer’s recommendation. Quality and integrity of RNA was assessed with the Fragment Analyzer from Advanced Analytical by using the standard sensitivity RNA Analysis Kit (Advanced Analytical #DNF-471). All samples selected for sequencing exhibited an RNA integrity number over 8. For accurate quantitation of cDNA libraries, the QuantiFluor™dsDNA System from Promega was used. The size of final cDNA libraries was determined using the dsDNA 905 Reagent Kit (Advanced Bioanalytical #DNF-905) exhibiting a sizing of 300 bp on average. Libraries were pooled and paired-end 100bp sequencing on a HiSeq4000 was conducted at the Vincent J. Coates Genomics Sequencing Lab, University of California at Berkeley.

treatment_protocol: Control embryos remained untreated.

value: epidermis, animal cap explant

tag: Stage

value: wt

value: control


title: FGSC_5mc_1K_cells_super_cMeDIP-seq_Rep2


title: Kelly transfected piR-Ctrl 5

description: S513 5

value: transient transfection sncRNACtrl


title: Kelly transfected piR-Ctrl 4

description: S513 4


title: S3-E2st14

source_name: epidermis, animal cap explant, st14


title: S3-E2st16

source_name: epidermis, animal cap explant, st16


title: Kelly transfected piR-Ctrl 3

description: S513 3


title: Ellagic acid-2

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

data_processing:
SOAPnuke (version: v1.5.2) was used for filter reads, parameters: -1 15 -q 0.5 -n 0.1.
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
HISAT (version: v2.0.4) was used to align clean reads to the mouse genome, parameters: -p 8 --phred64 --sensitive -I 1 -X 10000.
RSEM (version: v1.2.12) was used for abundance measurement, parameters: default.
FPKM method was used in calculated expression level.
Genome_build: hg 38
Supplementary_files_format_and_content: tab-delimited text files ChIPseeker

source_name: Human breast cancer cell line

growth_protocol: MDA-MB-231 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 mg/ml streptomycin.

extract_protocol:
Total RNA was extracted from the MDA-MB-231 cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard CapitalBio Technology protocols

treatment_protocol: Ellagic acid or control was added into MDA-MB-231 cells (n=3 per group) for 24 hours.

value: Ellagic acid


title: S3-E1st14


title: FGSC_5mc_200K_cells_super_cMeDIP-seq_Rep2


title: FGSC_5mc_200K_cells_super_cMeDIP-seq_Rep1


title: Ellagic acid-3


title: Kelly transfected piR-Ctrl 2

description: S513 2


title: S3-E1st16


title: FGSC_5mc_10K_cells_super_cMeDIP-seq_Rep2


title: lge1

city: shanghai

first: xujiao

last: zhou

address: fenyang road 83

institute: Eye & ENT Hospital, Fudan University

data_processing:
RNA Sequencing and Differentially Expressed Genes Analysis The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About 20.71G raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads. Then about xxxxxx clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT22. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq25. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar . Based on the hypergeometric distribution, GO6, KEGG7 pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Assembly: Gene Set Enrichment Analysis (GSEA) was performed using GSEA software8-9. The analysis was www.oebiotech.com used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: cornea

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.
The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: cornea

value: lacrimal gland excision


title: Ellagic acid-1


title: CO_02

city: Jinan

first: Xudong

last: Zhou

address: 4655 University Road, University Science and Technology Park, Changqing District, Jinan City, Shandong Province, China

department: First Clinical College

institute: Shandong University of Traditional Chinese Medicine

description: 10x Genomics

data_processing:
The raw data was mapped to the Rnor_6.0 rat reference genome using CellRanger (10x Genomics).
Assembly: Rnor_6.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cerebral hemisphere

extract_protocol:
Under sterile conditions, fresh rat brain tissue is first placed in pre-cooled phosphate-buffered saline (PBS) and transferred to a sterile workbench for processing. Then, the tissue is digested with PBS containing 0.25% trypsin and 0.1% DNAse I, gently shaking in a 37°C water bath for 15-30 minutes, with the time adjusted based on the actual digestion results. To terminate digestion, an equal volume of DMEM culture medium containing 10% fetal bovine serum (FBS) is added, and the mixture is filtered through a 40-70μm cell strainer to remove undigested tissue and cell clumps. Subsequently, the cells are centrifuged at 1300 rpm at 4°C for 5 minutes and resuspended in pre-cooled PBS, repeating the washing until the supernatant is clear. Cell density is measured using a cell counting plate or an automatic cell counter, and cell viability is assessed using a 0.4% trypan blue exclusion test, ensuring a viability rate of over 90%. This series of meticulous operations aims to obtain high-quality single-cell suspensions from rat brain tissue, laying the foundation for subsequent single-cell transcriptome analysis.
The key technology of the 10x Genomics Chromium™ system leverages millions of unique Barcodes to tag different samples (long DNA molecules/single cells). Initially, Gel beads containing Barcode sequences are mixed with a mixture of samples and enzymes, then combined with an oil surfactant to form GEMs (Gel Bead-In-Emulsions, meaning oil droplets encapsulating Gel beads, samples, and enzyme mixture). The GEMs are collected and flow into a reservoir, where Gel beads dissolve to release Barcode sequences, starting the sample tagging process. The products containing Barcode information from each droplet are mixed together to construct a standard sequencing library.

value: Cerebral hemisphere

value: Carbon monoxide poisoning


title: CO_03

description: 10x Genomics


title: K562_H3K27ac_1K_cells_Input

growth_protocol: K562 cells were cultured in RPMI-1640 medium supplemented with 10% fetal calf serum (FCS) and Penicillin-Streptomycin

extract_protocol:
Chromatin DNA was sonicated and followed by library construction
Libraries were prepared as super cChIP-seq or super cMeDIP-seq protocol described.

value: K562 cells


title: Control-2

value: Control


title: FGSC_5mc_10K_cells_super_cMeDIP-seq_Rep1

value: FGSCs


title: pnu1

value: PNU-282987 eyedrops 3 times a day


title: Control-1


title: Kelly transfected piR-1254 1

description: S513 6

value: Kelly


title: K562_H3K27ac_10_cells_super_cChIP-seq_Rep2

extract_protocol:
Chromatin DNA was sonicated and  ChIP DNA  was enriched with antibody.
Libraries were prepared as super cChIP-seq or super cMeDIP-seq protocol described.


title: S3-E1st20


title: CO_01

description: 10x Genomics


title: K562_H3K27ac_50_cells_super_cChIP-seq_Rep2


title: K562_H3K27ac_100_cells_super_cChIP-seq_Rep2


title: NC_03

description: 10x Genomics

value: Negative control


title: BMDMs, treated with supernatant from alive (+ LeTox) C57BL/6 cells, rep4

city: Ghent

first: Parul

last: Mehrotra

address: Zwijnaarde Technology Lab

department: Center for Inflammation Research

country: Belgium

institute: VIB - UGhent

data_processing:
Low quality reads (N > 10 or base quality < 20) and reads containing adaptors were removed (Performed by Novogene), levaing  above 90% of reads in all samples
HISAT2 was used to align reads to Mouse genome GRCm38/mm10 with an alignment rate above 93% in all samples (Performed by Novogene)
Aligned files' features were counted using featureCounts from the Rsubread (v.2.10.3) package
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file containing raw counts for all samples

source_name: cell culture

growth_protocol: Mouse  bone  marrow  cells were cultured in  Gibco  RPMI  1640,  supplemented  with  50ng/ml  of  murine MCSF,   10%   fetal   bovine   serum   (FBS),   and   1% penicillin-streptomycin   for   6 days   in   a humidified atmosphere containing 5% CO2 at 37°C

extract_protocol:
RNA was extracted using the Quiagen® RNAeasy kit and protocols. 1ug per sample was used to construct the sequencing libraries
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA), and index codes were added to attribute sequences to each sample (Performed by Novogene)

treatment_protocol:
Cells were treated with supernatants coming from media with Apoptotic (Casp), Pyroptotic (Nalp) or Alive cells (WT):
Apoptotic supernatants were obtained by treating C57BL/6 Nlrp1bTg+/-/Casp1/11KO  Mouse derived BMDMs with LeTox for 180 mins (Casp180). Controls (Casp0) had the same genotype but were not treated with LeTox.
Pyroptotic supernatants were obtained by treating C57BL/6 Nlrp1bTg+/- mouse derived BMDMs with LeTox for 120 mins (Nalp120). Controls (Nalp0) had the same genotype but were not treated with LeTox.
Alive cells supernatants were obtained by treating C57BL/6 cells with LeTox for 180 mins (WT180). Controls (WT0) had the same genotype but were not treated with LeTox.

value: cell culture

value: Primary Mouse bone marrow derived macrophages(BMDMs)

value: M0 Macrophages

value: 4 hrs with supernatants from alive (+ LeTox) C57BL/6 cells


title: K562_H3K27ac_50_cells_super_cChIP-seq_Rep1


title: Control-3


title: BMDMs, treated with supernatant from alive (+ LeTox) C57BL/6 cells, rep3


title: NC_02

description: 10x Genomics


title: K562_H3K27ac_1K_cells_super_cChIP-seq_Rep2


title: K562_H3K27ac_10_cells_super_cChIP-seq_Rep1


title: K562_H3K4me3_1K_cells_Input


title: K562_H3K27ac_1K_cells_super_cChIP-seq_Rep1


title: BMDMs, treated with supernatant from alive (+ LeTox) C57BL/6 cells, rep2


title: NC_01

description: 10x Genomics


title: BMDMs, treated with supernatants from alive (No LeTox) C57BL/6 cells, rep4

value: 4 hrs with supernatants from alive (No LeTox) C57BL/6 cells


title: BMDMs, treated with supernatant from alive (+ LeTox) C57BL/6 cells, rep1


title: isw1Δ chd1Δ isw2Δ mat alpha

city: Paris

first: Ashish

middle: Kumar

last: Singh

state: Ile-de-France

address: 25-28 Rue du Dr Roux

department: Development and Stem Cell Biology

institute: Institute Pasteur

data_processing:
Fastq files were demiltiplexed using Je demultiplex suite (Girardot et al., 2016).
Paired-end reads were mapped to sacCer3 R64-1-1 genome using Bowtie2 ((Langmead and Salzberg, 2012) with default setting except -X 500, --no-discordant, --no-mixed options.
Bam files were generated using samtools (Li et al., 2009).
Nucleosome dyad coverage and bigWig files were generated using 140-160 bp reads and resizing to 50 bp at the dyad center for MNase-Seq.
Assembly: R64-1-1 (sacCer3)
Supplementary files format and content: Signal intensity in bigWig file format

organism: Saccharomyces cerevisiae

source_name: isw1Δ chd1Δ isw2Δ

growth_protocol: Yeast strains were grown in YPAD media to OD 1.0-2.0.

extract_protocol:
Yeast nuclei was prepared according to (Almer and Horz, 1986). Cells were harvested  and incubated in 2 volume of preincubation solution (0.7 M ß-mercaptoethanol, 28 mM EDTA) for 25-30 mins. After washing with 1M sorbitol, cell wall was digested with Zymolyase. Spheroplasts were washed with 1M sorbitol and lysed with Ficoll buffer (18 % Ficoll, 20 mM KH2PO4 pH 6.8, 1 mM MgCl2, 0.25 mM EGTA, 0.25 mM EDTA). Nuclei was centrifuged and stored at -80 ̊C before use. For MNase digestion, nuclei was washed and dissolved in MNase digestion buffer (15 mM Tris-Cl pH 7.5, 50 mM NaCl, 1.4 mM CaCl2, 0.2 mM EGTA, 0.2 mM EDTA, 5 mM ß-mercaptoethanol). Equal volume of nuclei was digested with increasing amount of MNase for 20 mins at 37 ̊C. Reaction was stopped with 10 mM EDTA, 1% SDS and 50 mM Tris-Cl pH 8.5, followed by Proteinase K incubation for 30 mins at 37 ̊C. DNA was isolated by Phenol:Chloroform extraction and precipitation with 100% ethanol. Pellet was dissolved in TE buffer and RNA was removed with RNAse A incubation at 37 ̊C for 60 mins. DNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 50 μl TE. 25 μl DNA was loaded on 1.7% agarose gel and resolved for 4 hours at 2 V/cm. Appopriately digested sample with 70% mono-, 20% di- and 10% tri-nucleosome bands were used for library preparation without cutting mononucleosome band.
Libraries were prepared from whole MNase digested DNA. DNA fragments longer than 500 bp were removed using ampure size selection. 50 ng of size-selected DNA was used for library preparation with NEBNext Ultra II DNA Library Prep Kit, according to the manufacturer’s protocol. For PCR amplification step, 3 or 4 cycles were performed. Quality control on final libraries was performed using DNA 1000 Bioanalyzer and fragment length of ~270-280 bp was consistently observed, corresponding to ~150-160 bp insert length.

treatment_protocol: No treatment.

tag: strain background


title: K562_H3K4me3_50_cells_super_cChIP-seq_Rep1


title: K562_H3K4me3_50_cells_super_cChIP-seq_Rep2


title: K562_H3K4me3_100_cells_super_cChIP-seq_Rep2


title: K562_H3K4me3_10_cells_super_cChIP-seq_Rep1


title: isw1Δ chd1Δ isw2Δ mat a


title: sham1

tag: treatment

value: sham mice, an incision was made in the same zone without touching the glands.


title: K562_H3K4me3_100_cells_super_cChIP-seq_Rep1


title: BMDMs, treated with supernatants from alive (No LeTox) C57BL/6 cells, rep3


title: isw1Δ chd1Δ mat alpha

source_name: isw1Δ chd1Δ


title: K562_H3K4me3_1K_cells_super_cChIP-seq_Rep2


title: isw1Δ chd1Δ mat a


title: K562_H3K4me3_1K_cells_super_cChIP-seq_Rep1


title: K562_H3K27ac_100_cells_super_cChIP-seq_Rep1


title: PHT/MPP+ treatment biol rep 3

city: Onna-son

first: Marius

middle: Wilhelm

last: Baeken

address: 1919-1 Tancha

institute: Okinawa Institute of Science and Technology Graduate University

data_processing:
Sample demultiplexing and FastQ file generation was performed using Illumina bcl2fastq v2.19.1 and overall sequence quality was assessed with FastQC v.0.11.5.
Sequence reads were aligned to the human reference genome GRCh38 with annotation from Gencode release 25 using STAR v.2.5.2b with parameters "--outFilterMismatchNmax 2 --outFilterMultimapNmax 10", secondary alignments were removed with SAMtools v.1.5, and data quality was examined using RSeQC v2.6.4 and dupRadar v.1.8.0.
Read summarisation on the gene level was performed using Subread featureCounts v.1.5.1 with stranded option "-s 2". Pairwise differential expression comparisons between sample groups were performed using the Bioconductor package DESeq2 v.1.18.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with summarised read counts per gene from featureCounts

source_name: Mesencephalon

extract_protocol:
Total RNA extracted from cells using TRI Reagent following standard protocol. Subsequent digestion with recombinant Dnase I for 1h at 37°C. RNA extracted via ethanol precipitation.
NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illumina’s standard protocol (Part # 15031047 Rev. E). Libraries were prepared with a starting amount of 1000 ng and amplified in 10 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life Technologies). All samples were pooled in equimolar ratio and sequenced on a NextSeq 500 Flowcell, SR for 84 cycles plus 7 cycles for the index read.

value: Mesencephalon

value: LUHMES

value: Neuronal

value: WT

value: PHT/MPP+


title: isw2Δ itc1ΔN mat a

source_name: isw2Δ itc1ΔN


title: BMDMs, treated with supernatants from alive (No LeTox) C57BL/6 cells, rep1


title: BMDMs, treated with supernatants from alive (No LeTox) C57BL/6 cells, rep2


title: PHT/MPP+ treatment biol rep 2


title: PHT/MPP+ treatment biol rep 1


title: BMDMs, treated with supernatants from pyroptotic (+ LeTox) C57BL/6 Nlrp1bTg+/-, rep4

value: 4 hrs with supernatants from pyroptotic (+ LeTox) C57BL/6 Nlrp1bTg+/- cells


title: MPP+ treatment biol rep 1

value: MPP+


title: itc1Δ mat alpha rep1


title: MPP+ treatment biol rep 3


title: MPP+ treatment biol rep 2


title: Control biol rep 3

value: Control


title: itc1Δ mat a rep2


title: BMDMs, treated with supernatants from pyroptotic (+ LeTox) C57BL/6 Nlrp1bTg+/-, rep3


title: itc1Δ mat a rep1


title: BMDMs, treated with supernatants from pyroptotic (+ LeTox) C57BL/6 Nlrp1bTg+/- , rep1


title: Hep3B cells, si-CPSF6 #2

city: Seoul

first: Deok Yong

last: Sim

address: 26 Kyungheedae-ro

institute: Kyunghee university

data_processing:
QuantSeq 3' mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012). Bowtie2 indices were either generated from genome assembly sequence or the representative transcript sequences for aligning to the genome and transcriptome. The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes.
Differentially expressed gene were determined based on counts from unique and multiple

source_name: Liver

growth_protocol: Hep3B HCC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 1% CO2 at 37C

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Process 40uM of si-RNA for 2 days (BIONEER, Korea)

value: Liver

value: hepatocellular carcinoma cells

value: si-CPSF6 #2

value: Day 2


title: isw2Δ mat alpha rep1


title: BMDMs, treated with supernatants from alive (No LeTox) C57BL/6 Nlrp1bTg+/- cells, rep4

value: cell culture

value: Primary Mouse bone marrow derived macrophages(BMDMs)

value: 4 hrs with supernatants from alive (No LeTox) C57BL/6 Nlrp1bTg+/- cells


title: DD042G_distal_RNA

type: RNA

city: Chapel Hill

first: Scott

middle: H.

last: Randell

state: North Carolina

address: CB 7248, Room 1117 Marsico Hall, 125 Mason Farm Rd.

institute: UNC Chapel Hill

hyb_protocol: Microarrays were hybridized in an Robbins Scientific hybridization oven with 850ng of labeled Cy3 Reference and 850ng of Cy5 experimental samples using the Agilent hybridization kit as described by the manufacturer. The arrays were incubated overnight and then washed once for 10 minutes in 2X SSC and 0.0005% Triton X-102, twice for 5 minutes in 0.1XSSC, and then immersed into Agilent Stabilization and Drying solution for 20 seconds.

scan_protocol: Microarrays were scanned with Agilent Scanner and intensity was recorded using Agilent Feature Extraction Software.

data_processing:
Agilent feature extraction output was processed by normexp background correction and loess normalization using Bioconductor library limma.
Normalized_normalLung.txt file includes normalized log2 ratios (normal/reference).

source_name: Normal lung

label_protocol: The total RNA labeling and hybridization protocol used is described in the Agilent low RNA input linear amplification kit (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=10003), with the following two changes: 1) a Qiagen PCR purification kit was used to clean up the cRNA instead of the LiCl precipitation, and 2) all reagents volumes were reduced by one half.

extract_protocol: Total RNA was extracted using RNeasy kit from Qiagen following manufacturer's instructions. These total RNA samples were run on an Agilent Bioanalyzer 2100 (Agilent Technologies, Inc) to ensure RNA quality.

value: Normal lung

tag: airway size

value: small

source_name: Stratagene Human Universal Reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: Control biol rep 1

value: Mesencephalon

value: LUHMES


title: Control biol rep 2

value: Neuronal

value: WT


title: Hep3B cells, si-CPSF6 #1

value: si-CPSF6 #1

tag: time


title: isw2Δ mat a rep2


title: Primary human macrophages, siALOX15B, rep5

city: Frankfurt

first: Yvonne

last: Benatzy

address: Theodor-Stern-Kai 7, building 74

department: Institute of Biochemistry I

institute: Goethe-University Frankfurt

data_processing:
Processing of sequencing data was performed within the Lexogen QuantSeq 3´ mRNA-Seq integrated data analysis pipeline on the BlueBee on-line platform (BlueBee Holding BV, Rijswijk, The Netherlands).
FASTQ reads were trimmed (bbduk v35.92), mapped to the hg38 human genome assembly (STAR Aligner v2.5.2a with modified ENCODE settings), and gene-specific read counts were determined (HTSeq-count v0.6.0).
Differential gene expression analysis of read counts was conducted by DESeq2.
Assembly: hg38
Supplementary files format and content: counts file, siC vs siALOX15B_DE analysis

source_name: primary macrophages

extract_protocol:
Total RNA of control and ALOX15B-silenced macrophages was isolated using RNeasy Mini Kit (Qiagen, cat. no. 74104) and RNA was purified by precipitation. RNA quality was determined using an Agilent High Sensitivity RNA ScreenTape (cat. no. 5067-5579) with an Agilent TapeStation 4150 (Agilent Technologies, Waldbronn, Germany) and RNA concentration was quantified using a Qubit HS RNA Assay Kit (cat. no. Q32852) and Qubit 3 fluorometer (Thermo Fisher Scientific).
Library preparation of 500 ng RNA was performed using the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH, Vienna, Austria, cat. no. 015.24). Library quality and quantity was controlled by Qubit 3 fluorometer and Agilent D1000 DNA ScreenTape (cat. no. 5067-5582).
High Output Kit v2.5 (cat. no. 20024906)

treatment_protocol: Human monocytes derived from five individual donors were differentiated into naïve macrophages with RPMI 1640 medium containing 5% AB-positive human serum for 7 days. Subsequently, macrophages were transfected with non-targeting or ALOX15B-specific siRNA and after 5 days total RNA was isolated for next-generation sequencing.

tag: individual

value: primary macrophages

value: ALOX15B siRNA

value: ALOX15B silenced


title: BMDMs, treated with supernatants from alive (No LeTox) C57BL/6 Nlrp1bTg+/- cells, rep3

tag: cell line

value: M0 Macrophages


title: itc1ΔN mat a


title: DD042G_proximal_RNA

value: large


title: isw2Δ mat a rep1


title: DD042G_middle_RNA

value: medium


title: Primary human macrophages, siControl, rep5

value: control siRNA

value: control


title: BMDMs, treated with supernatants from alive (No LeTox) C57BL/6 Nlrp1bTg+/- cells, rep2

value: cell culture

value: Primary Mouse bone marrow derived macrophages(BMDMs)

value: 4 hrs with supernatants from alive (No LeTox) C57BL/6 Nlrp1bTg+/- cells


title: BMDMs, treated with supernatants from pyroptotic (+ LeTox) C57BL/6 Nlrp1bTg+/- , rep2

value: 4 hrs with supernatants from pyroptotic (+ LeTox) C57BL/6 Nlrp1bTg+/- cells


title: WT BY4742 rep1

source_name: WT


title: BMDMs, treated with supernatants from alive (No LeTox) C57BL/6 Nlrp1bTg+/- cells, rep1


title: Primary human macrophages, siControl, rep4


title: DD037G_proximal_RNA

value: Normal lung

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: Primary human macrophages, siALOX15B, rep4


title: DD037G_middle_RNA


title: WT BY4741 rep1


title: Hep3B cells, si-Control

value: Liver

value: hepatocellular carcinoma cells

value: si-Control

value: Day 2


title: Primary human macrophages, siALOX15B, rep3

value: primary macrophages

value: ALOX15B siRNA