title: PAF3

city: Rochester

first: Minsoo

last: Kim

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq version 2.19.1
Quality filtering and adapter removal are performed using FastP version 0.23.1 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y –r -j"
Processed/cleaned reads were then mapped to the GRCm39/gencode M27 or GRCm39/gencode M31 reference using STAR_2.7.9a with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM Unsorted – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
Genelevel read quantification was derived using the subread-2.0.1 package (featureCounts) with a GTF annotation file (GRCm39/gencode M31) and the following parameters for stranded RNA libraries "-s 2 -t exon -g gene_name" OR "-s 0 -t exon -g gene_name" for un stranded libraries
Differential expression analysis was performed using DESeq2-1.34.0 with a P-value threshold of 0.05 within R version 3.5.1 (https://www.R-project.org/)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw count values for each Sample
Supplementary files format and content: tab delimited deSeq2 counts files

source_name: Bone marrow

extract_protocol:
Total RNA from neutrophils were isolated using RNeasy plus mini kit (Qiagen). Total RNA was preamplified with SMARTer Ultra Low Input kit v4 per manufacturer’s protocol (Clontech). CDNA quality and quantity were measured using Qubit fluorometer (Life Technologies) and Agilent Bioanalyzer 2100. CDNA was used to generate Illumina-compatible sequencing libraries using NexteraXT library preparation kit (Illumina).
Clontech low input/Illumina mRNA

value: Bone marrow

value: Primary

value: Neutrophil

value: PAF


title: Control siRNA D0 replicate 2

status: Public on Sep 13 2024

type: SRA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

description: Cells were transfected with Control siRNA, and cultured in growth medium for 24 h - replicate 2

library_source: transcriptomic

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to mouse genome mm10, Ensembl v89 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to generate gene counts
Differential expression analysis of gene counts was performed using the DESeq2
Assembly: mm10
Supplementary files format and content: text files containing counts

molecule: total RNA

organism: Mus musculus

extract_protocol:
RNA was extracted with TriPure™ Isolation Reagent (Sigma-Aldrich) using Direct-zol RNA MiniPrep kit (ZYMO RESEARCH) following the manufacturer’s instructions.
Libraries were constructing using the TruSeq Stranded Total RNA protocol (Illumina) according to manufacturer's instructions.

tag: cell line

tag: cell type

value: mouse myoblasts

tag: genotype

value: WT

tag: treatment

value: Control siRNA transfection for 24 h in growth medium


title: MV411 DMSO 24h H3K79me2 soni rep3

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Bigwig is generated with Deeptools (v3.5.2).
Assembly: hg38
Supplementary files format and content: bigwig file, ChIP density profiles for genome browser.

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

growth_protocol: Human leukaemia cell lines MV4;11, was  maintained in RPMI (Corning, 10-040-CV) 10% Fetal Bovine Serum (Sigma, F4135) supplemented with 2 mM l-glutamine and 100 U ml−1 penicillin/streptomycin (Corning, 30-009-CI).

extract_protocol:
Eluted DNA were decrosslinked and extracted by QIAquick PCR Purification Kit (QIAGEN, Cat. 28106).
Libraries were constructed using Illumina standard protocols.

treatment_protocol: Human leukaemia cell lines are treated with DMSO, 100 nM MS41for 6h or 24h. Then cells are collected for Chip assay.

tag: tissue

value: cell line

value: human leukemia cell

value: DMSO


title: PAF2

molecule: polyA RNA


title: MV411 DMSO 24h H3K79me2 soni rep2


title: PAF1


title: Control siRNA D0 replicate 1

description: Cells were transfected with Control siRNA, and cultured in growth medium for 24 h - replicate 1


title: Cont3

value: Culture med.


title: MV411 DMSO 24h H3K79me2 soni rep1


title: 126_MDAMB231_docDPT1

city: LOS ANGELES

first: Michaek

middle: James

last: Schmidt

state: CA

address: 1002 Childs Way

department: Cancer Biology and Genomics

institute: University of Southern California

data_processing:
copy number profiling for segmented means
Assembly: hg19
Supplementary files format and content: csv file containing segmented means
Library strategy: scDNA-seq

source_name: Breast

extract_protocol:
WGA4
NEB NEXT ultra FS II

treatment_protocol: treat with chemotherapy for 72 hours and then allowed to recover for 1 or 10 days in regular medium.

value: Breast

value: epithelial cell line


title: 125_MDAMB231_docDPT1


title: BAT RetSat ko 5

city: Berlin

first: Michael

last: Schupp

address: Hessische Str. 3-4

department: Institute of Pharmacology

country: Germany

institute: Charite Universitätsmedizin Berlin

data_processing:
Sequence reads were trimmed with the trimmomatic tool and default parameters
Trimmed sequences were mapped to GRCm39/mm39 using the STAR method (v2.7.6)
read count extraction was performed using featureCounts v2.0.1
Assembly: mm39
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: brown adipose tissue (BAT)

growth_protocol: standard mouse colony

extract_protocol:
RNA was harvested using the RNeasy kit from Qiagen, following the manufacturer`s protocol
samples were further treated with the DNase I Set from Zymo Research,following the manufacturer`s protocol
Library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit and Module (New England Biolabs, USA) following manufacturer`s protocol

treatment_protocol: fed normal chow, mice euthanized at an age of 12-14 weeks

value: brown adipose tissue (BAT)

tag: strain

value: RetSat flox/flox Ucp1-Cre (+)

value: normal chow feeding


title: 127_MDAMB231_docDPT1


title: Cont2


title: BAT RetSat ko 4


title: BAT RetSat ko 3


title: Cont1


title: MV411 DMSO 24h DOT1L MNase rep2


title: spleen_tumor_d7_R3,GEX

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

institute: Leibniz Institute for Immunotherapy

description:
Reads contain mRNA sequences
p113_Tumor_pos_SPARE3_d7_library_run_1_barcodes.tsv.gz
p113_Tumor_pos_SPARE3_d7_library_run_1_features.tsv.gz
p113_Tumor_pos_SPARE3_d7_library_run_1_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
Sequencing with NextSeq2000 on a Flow cell P3 100 cycles: Y28:I10:I10:Y90
Dragon 3.8.4: Bclconvert for demultiplexing of Illumina UD library barcodes
Cellranger 7.0.0 was used for mapping and filtering of empty droplets
R and Seurat 4 were used for qc, demultiplexing of hashed libraries
Demultiplexing of treatments using HTOs with Seurat (version 4.0.5), identification of doublets via Cell Hashing and scDblFinder (version 1.8.0)
Normalization, scaling, finding variable features and PCA with Seurat, integration of batches with Harmony (version 0.1.0)
Clustering with Seurat
Annotation with SingleR (version 1.8.1)
Assembly: refdata-gex-mm10-2020-A:ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz, ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/gencode.vM23.primary_assembly.annotation.gtf.gz
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for each library, mRNA and HTO combined

source_name: spleen/tumor

growth_protocol: We co-cultured activated CD8+ T cells from 3 donor mice with BMSCs in which mitochondria are stably labeled with dsRed.

extract_protocol:
Sorted T cells were either processed for immediate scRNA-Seq ("d0") or transferred into B16KVP tumor-bearing B6 mice and re-isolated by flow cytometry on d7.
For multiplexing of d0 samples, biological replicates were marked using hashtags 1-3 and 4-6 for MitoPositive and MitoNegative cells, respectively.
Transferred T cells were isolated from spleen (#1 and #2) and tumor (#3 and #4 for MitoPositive and MitoNegative T cells, respectively) and pooled by donor after mulitplexing.
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1
Droplet sequencing with beads containing polydT capture sequences

treatment_protocol: After co-culture, we sorted dsRed+ (MitoPositive) T cells that had taken up mitochondria from BMSCs and dsRed-negative (MitoNegative) T cells.

value: spleen/tumor

value: CD8 Tcells

value: reisolation after transplantation

tag: library-type

value: mRNA


title: 123_PC3_cisDPT10

source_name: Prostate

value: Prostate


title: 124_PC3_cisDPT10


title: spleen_tumor_d7_R2,GEX

description:
Reads contain mRNA sequences
p113_Tumor_pos_D2_d7_library_run_1_barcodes.tsv.gz
p113_Tumor_pos_D2_d7_library_run_1_features.tsv.gz
p113_Tumor_pos_D2_d7_library_run_1_matrix.mtx.gz


title: MV411 DMSO 24h DOT1L MNase rep3


title: KO64A

type: RNA

city: Barcelona

first: Cristina

last: Lopez-Rodriguez

address: Carrer Dr. Aiguader, 88

department: Medicine and Life Sciences

country: Spain

institute: Universitat Pompeu Fabra

description: Nfat5 fl/fl Vav-Cre mice have been described in Huerga Encabo et al., 2020, J Exp Med, 2020. doi: 10.1084/jem.20190449

hyb_protocol: Sample was hybridized to Affymetrix Clariom S Human array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

label: Biotin

source_name: Total RNA from bone marrow hematopoietic multipotent progenitors (MPP), NFAT5-deficient

label_protocol: 300pg of total RNA from each sample was processed and labelled according to manual NuGEN Ovation® One-Direct System (M01312 v2), Encore™ Biotin Module (M01111 v8) (NuGEN, San Carlos, CA, USA)

growth_protocol: FACS-sorted CD45.2+ HSC (CD48-CD150+ within LSK) and CD45.2+ MPP (LSK CD48+CD150- within LSK) populations of Nfat5 +/+ Vav-Cre (wild-type) and Nfat5 fl/fl Vav-Cre (NFAT5-deficient) from bone marrow-transplated CD45.1+ wild-type mice 13 weeks after transplantation

extract_protocol: Total RNA was extracted following Qiagen protocol

treatment_protocol: Bone marrow was isolated from the respective mouse genotypes (CD45.2 background) and transplanted into irradiated wild-type CD45.1 recipient mice

value: KO

tag: mouse

value: A

tag: population

value: A (hematopoietic multipotent progenitor, MPP)


title: BAT control 5

value: RetSat flox/flox Ucp1-Cre (-)


title: BAT RetSat ko 1


title: MV411 DMSO 24h DOT1L MNase rep1

value: cell line

value: human leukemia cell

value: WT


title: 122_PC3_cisDPT10


title: 120_PC3_cisDPT10


title: spleen_tumor_d7_R3,HTO

description:
Reads contain HTO sequences
p113_Tumor_pos_SPARE3_d7_library_run_1_barcodes.tsv.gz
p113_Tumor_pos_SPARE3_d7_library_run_1_features.tsv.gz
p113_Tumor_pos_SPARE3_d7_library_run_1_matrix.mtx.gz

library_source: other

molecule: protein

value: HTO

tag: hto

value: TotalSeq-B 0301, TotalSeq-B 0302, TotalSeq-B 0303,TotalSeq-B 0304


title: BAT RetSat ko 2

value: brown adipose tissue (BAT)


title: Spleen_invitro,GEX

description:
Reads contain mRNA sequences
p113_invitro_d0_library_run_1_barcodes.tsv.gz
p113_invitro_d0_library_run_1_features.tsv.gz
p113_invitro_d0_library_run_1_matrix.mtx.gz

source_name: spleen

value: spleen


title: 121_PC3_cisDPT10

value: epithelial cell line


title: BAT control 3

value: normal chow feeding


title: spleen_tumor_d7_R2,HTO

description:
Reads contain HTO sequences
p113_Tumor_pos_D2_d7_library_run_1_barcodes.tsv.gz
p113_Tumor_pos_D2_d7_library_run_1_features.tsv.gz
p113_Tumor_pos_D2_d7_library_run_1_matrix.mtx.gz

value: spleen/tumor

value: CD8 Tcells


title: BAT control 4


title: 11_MDAMB231_cisDPT10

value: Breast


title: BAT control 1


title: spleen_tumor_d7_R1,HTO

description:
Reads contain HTO sequences
p113_Tumor_pos_D1_d7_library_run_1_barcodes.tsv.gz
p113_Tumor_pos_D1_d7_library_run_1_features.tsv.gz
p113_Tumor_pos_D1_d7_library_run_1_matrix.mtx.gz

value: reisolation after transplantation


title: Spleen_invitro,HTO

description:
Reads contain HTO sequences
p113_invitro_d0_library_run_1_barcodes.tsv.gz
p113_invitro_d0_library_run_1_features.tsv.gz
p113_invitro_d0_library_run_1_matrix.mtx.gz

value: TotalSeq-B 0301, TotalSeq-B 0302, TotalSeq-B 0303,TotalSeq-B 0304, TotalSeq-B 0305, TotalSeq-B 0306


title: 117_PC3_cisDPT10

value: Prostate


title: 118_PC3_cisDPT10


title: spleen_tumor_d7_R1,GEX

description:
Reads contain mRNA sequences
p113_Tumor_pos_D1_d7_library_run_1_barcodes.tsv.gz
p113_Tumor_pos_D1_d7_library_run_1_features.tsv.gz
p113_Tumor_pos_D1_d7_library_run_1_matrix.mtx.gz

value: mRNA


title: NBM08

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

data_processing:
Demultiplexing of bcl files into .fastq files was performed using cellranger 3.0.1 mkfastq software (10x Genomics) and alignments to the human (GRCh38) genome reference sequences were performed using cellranger count. The reference included all protein coding genes as well as mitochondrial genes for downstream analysis.
Assembly: GRCh38/hg38
Supplementary files format and content: count matrix incsv

molecule: nuclear RNA

source_name: Neuroblastoma

extract_protocol:
We used the Tween with salts and TRIS (TST) tissue lysis buffer combined with the dounce and iodixanol density gradient medium. For nucleus extraction, Snap-frozen tumor tissue pieces were placed in a glass dounce homogenizer containing TST lysis buffer.
After careful mechanical dissociation with the dounce pestle, followed by 5 minutes of incubation on ice in a total of 5 mL lysis buffer, the reaction was quenched by adding 5 mL wash buffer. The wash buffer consisted of 15 mL 10% bovine serum albumin (BSA, Sigma-Aldrich, cat. no. 05482-25G) dissolved in sterile nuclease-free water (Invitrogen, cat. no. 10977049); 70 μL of 100% glycerol (Sigma-Aldrich, cat. no. G5516), 30 μL Protector RNase inhibitor at 40 units/μL (Millipore Sigma, cat. no. 3335402001), and 15 mL sterile PBS (Gibco). The lysed suspension was passed through a 30 μm filter and centrifuged at 500g, 4°C, for 5 minutes, after which the pellet was resuspended in wash buffer, filtered, and centrifuged again. Next, the pellet was resuspended in 1 mL wash buffer, mixed with 1 mL 50% Optiprep solution (Iodixanol density gradient medium, Millipore Sigma, cat. no. D1556- 250). Optiprep was diluted in a buffer containing 20 mM tricine-KOH buffer at pH 7.8, 150 mM KCl, 5 mM MgCl2, and nuclease-free water. This 25% Optiprep/nucleus mix was layered on top of 2 mL 29% Optiprep and centrifuged at 10000g for 30 minutes at 4°C. The pellet was resuspended in a final nucleus suspension with 300 μL wash buffer and filtered through a 40 μm pipette tip filter.
10X Genomics Single cell 3' gene expression V2

value: Neuroblastoma

tag: age

value: 17 months

tag: risk group

value: High

tag: tumor type

value: Primary adrenal tumor

value: Surgical specimen


title: cell-1_igg

city: Shanghai

first: Yikui

last: Liu

address: No. 197 Ruijin 2nd Road, Huangpu District, Shanghai

country: China

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
library strategy: CUT&Tag
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
CUT&Tag reads were aligned to the mm10_M25_gencode using BWA . Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for IgG sample)

source_name: Cortex and hippocampus

extract_protocol:
CUT&Tag assay was performed as described previously with modifications(Hatice et al., 2019 ). Briefly，100000 cells were washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail).
To amplify libraries, 21μL DNA was mixed with 2μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. libraried clean-up was performed XP beads (Beckman Counter).

value: Cortex and hippocampus

value: primarily neurons

tag: chip antibody

value: IgG (Millipore,12-370)


title: Low-input nephrocyte, control, replicate 3

first: Hangnoh

middle: Joseph

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

description: Low-input nephrocyte 3

data_processing:
Nova-seq based sequencing was done by Psomagen (Rockville, MD)
We used STAR aligner 2.7.5c (PMID: 23104886) for the mapping of short reads onto the Drosophila genome.
We quantified RNA-Seq reads using RSEM 1.3.3 (PMID: 21816040)
For the quantification of RNA-Sequencing reads, we used Drosophila gene annotation 6.28 from FlyBase.
Assembly: Berkeley Drosophila Genome Project (BDGP) Release 6
Supplementary files format and content: Text file (compressed with gzip) containing gene expression profiles in transcripts per million reads (TPM).

organism: Drosophila melanogaster

source_name: Nephrocytes

growth_protocol: Flies were crossed, reared, and kept on standard food at 25°C.

extract_protocol:
RNA was harvested using SuperScript™ IV Single Cell/Low‑Input cDNA PreAmp Kit (Thermo Fisher Scientific) from flowcytometry-isolated adult fly nephrocytes.
cDNA libraries for RNA-seq were prepared using SuperScript™ IV Single Cell/Low‑Input cDNA PreAmp Kit (Thermo Fisher Scientific).

treatment_protocol: normal diet, contains 6% sucrose

value: Nephrocytes

value: Hand-GFP; Klf15-Gal4, UAS-RFP/CyO

value: normal diet, contains 6% sucrose


title: 114_PC3_cisDPT10

value: epithelial cell line


title: Sh_c3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited excel files include FPKM values for each Sample .
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Primarily neurons were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ALDH1L2 knockdown

tag: time

value: Day 5


title: 115_PC3_cisDPT10


title: Low-input nephrocyte, control, replicate 1

description: Low-input nephrocyte 1


title: Sh_c2


title: Sh_c1


title: BAT control 2

value: brown adipose tissue (BAT)

value: RetSat flox/flox Ucp1-Cre (-)

value: normal chow feeding


title: 113_PC3_cisDPT10

value: Prostate


title: cell


title: Sh_c4


title: 112_PC3_cisDPT10


title: pdx1 morpholino + 20mM STS 4

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
CPM estimates, generated with cpm function from edgeR version 3.17
Assembly: GRCz11
Supplementary files format and content: raw counts with kallisto quant version 0.4.6.
Supplementary files format and content: CPM estimates, generated with cpm function from edgeR version 3.17

organism: Danio rerio

source_name: larvae

extract_protocol:
RNA was isolated from whole-body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN (Hilden, 173 Germany).
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

value: larvae

tag: dose

tag: agent

value: STS


title: 119_PC3_cisDPT10

tag: cell line


title: 116_PC3_cisDPT10

tag: cell type


title: Low-input nephrocyte, control, replicate 2

description: Low-input nephrocyte 2

tag: genotype


title: 111_PC3_cisDPT10

tag: treatment


title: 110_PC3_cisDPT10

tag: tissue


title: pdx1 morpholino + 20mM STS 3

tag: strain


title: 10_PC3_docDPT1


title: pdx1 morpholino + 20mM STS 2


title: Sh_b1

value: MTHFD2 knockdown


title: pdx1 morpholino + 20mM STS 5


title: pdx1 morpholino + 15mM STS 5


title: Sh_b2


title: 109_PC3_cisDPT10


title: pdx1 morpholino + 20mM STS 1


title: 108_PC3_ctrl

value: ctrl


title: Sh_a4

value: Cortex and hippocampus

value: SHMT2 knockdown


title: pdx1 morpholino + 15mM STS 4


title: Sh_a3

value: primarily neurons


title: pdx1 morpholino + 15mM STS 3


title: Sh_b4


title: Sh_b3


title: 106_PC3_ctrl


title: pdx1 morpholino + 15mM STS 2


title: 105_PC3_ctrl


title: NC4

value: wild type


title: 103_PC3_ctrl


title: pdx1 morpholino + 0mM STS 5


title: pdx1 morpholino + 15mM STS 1


title: 104_PC3_ctrl


title: 102_PC3_ctrl


title: pdx1 morpholino + 0mM STS 4


title: NC3


title: 107_PC3_ctrl


title: 101_PC3_ctrl


title: NC2


title: Sh_a2


title: NC1


title: 100_PC3_docDPT10


title: E6

value: hemin-treated


title: pdx1 morpholino + 0mM STS 3


title: pdx1 morpholino + 0mM STS 1


title: pdx1 morpholino + 0mM STS 2


title: E5


title: Sh_a1


title: E4


title: iPSCs derived neurons, week 12, rep1

city: South San Francisco

first: Ai

last: Zhang

state: California

address: 1 DNA way

department: Neuroscience

institute: Genentech

data_processing:
Bulk RNAseq FASTQ data were aligned to the human reference genome (GRCh38) using the GSNAP aligner and HTSeqGenie pipeline
Assembly: human reference genome (GRCh38)
Supplementary files format and content: csv file of raw counts

source_name: neuronal differentiation

growth_protocol: neural induction was performed via a 3D based dual smad inhibition protocol, NPC were obtaind via manual rosette picking

extract_protocol:
RNA was extracted via the RNAeasy mini plus kit (Qiagen).
the Truseq Stranded mRNA kit (Illumina) was used with an input of 100-1000 nanograms of total RNA

value: neuronal differentiation

value: iPScs derived neurons

value: WT

value: week 12


title: E3

value: Day 5


title: Control morpholino + 20mM STS 4


title: iPSCs derived neurons, week 12, rep2


title: E2


title: iPSCs derived neurons, week 8, rep3

value: week 8


title: Control morpholino + 20mM STS 3


title: E1


title: Control morpholino + 20mM STS 2


title: iPSCs derived neurons, week 8, rep2


title: Control morpholino + 20mM STS 1


title: iPSCs derived neurons, week 8, rep1


title: iPSCs derived neurons, week 12, rep3


title: Control morpholino + 20mM STS 5


title: S6

value: sham


title: Control morpholino + 15mM STS 5


title: iPSCs derived neurons, week 4, rep3

value: week 4


title: S5


title: Control morpholino + 15mM STS 3

value: larvae


title: iPSCs derived neurons, week 4, rep2


title: S4


title: Control morpholino + 15mM STS 4

value: STS


title: Control morpholino + 15mM STS 2


title: S2


title: iPSCs derived neural precursors, rep2

value: iPSCs derived neural precursors


title: Control morpholino + 0mM STS 5

value: ctrl


title: iPSCs derived neural precursors, rep1


title: Lung_Sample24 [L101]

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Samples were analyzed using the nf-core rnaseq pipeline version 3.10.1 [https://nf-co.re/rnaseq/1.4.2] with nextflow version v22.10.4.
The intial fastq reads of all the samples were processed by Trimmgalore to trim/filter Illumina adapter sequences if any before processing further.
Reads aligned by STAR and gene expression values of each sample generated by Salmon program.
Assembly: GCF_016772045.1_ARS-UI_Ramb_v2.0_genomic
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Ovis aries

source_name: Lung

growth_protocol: As described in experimentla design above:Date-mated Merino ewes with singleton fetuses underwent treatment allocation as described below and then 48 hours post treatment lambs were surgically delivered with placement of a 4.5 mm endotracheal tube  secured by tracheostomy for ventilation. Following delivery lambs underwent a 30minute ventilation via endotracheal tube before necropsy and tissue collection.  Tissue for RNA sequencing was snap frozen on liquid nitrogen and stored at -80 degrees celcius prior to extraction.

extract_protocol:
RNA was extracted from snap-frozen hippocampal and lung tissue using RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions. The concentration of extracted RNA and RNA Integrity Number (RIN) was determined using Agilent Technologies RNA Nano Chip as per manufacturer’s instructions. All RNA extracts were diluted in nuclease-free water to yield a final RNA concentration of 30 ng/μl. Hippocampal and lung tissue bulk RNA sequencing was performed by Novogene Singapore.
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (Cat No. 7420)

treatment_protocol: Animals were then allocated to one of four groups (Figure 6), with first treatment given at 122 ± 2 dGA (term = 150 dGA). First injections occurring at 08:00 to control for circadian effects:    i) Saline Control Group, ewes received 4 x 2 ml sterile normal saline maternal IM injections at 12 h intervals (n=11);  ii) Dex High Group, ewes received 2 x 12 mg Dex-PO4 (DBL Dexamethasone sodium phosphate 4mg/ml, Hospira NZ, New Zealand) maternal IM injections at 12 h intervals followed by 2 x 2ml IM sterile saline injections at 12 h intervals (n=12); iii) Dex Low Group, ewes received 4 x 1.5 mg Dex-PO4 (DBL Dexamethasone sodium phosphate 4mg/ml, Hospira NZ, New Zealand) maternal IM injections 12 h intervals (n=12); or  iv) Beta Acetate Group, ewes received 1 x 0.125mg/kg Betamethasone Acetate maternal IM injection followed by 3 x 2 ml IM sterile normal saline injections at 12 h intervals (n=16).

value: Lung

value: B-Acetate 48hr

tag: response

value: Non-responder


title: Control morpholino + 15mM STS 1


title: Control morpholino + 0mM STS 4


title: WAT, 814, veh [NW814]

city: Oulu

first: Terhi

last: Piltonen

address: Aapistie 5A

country: Finland

institute: University of Oulu

description:
NW814
WAT_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
WAT_PCOS+vehicle_vs_control+vehicle.xlsx

data_processing:
Base calling software: Illumina Casava 1.8
The following data filtering steps were applied to the raw reads: 1. Remove reads with adapter contamination. 2. Remove reads when uncertain nucleotides constitute more than 10 percent of either read. 3. Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Alignment of reads was performed with HISAT2 v2.0.5.
Differentially expressed genes were screened with DESeq2 R-package (1.20.0) software. Parameters: |log2(FoldChange)| > 1 and adjusted p-value (padj) < 0.05.
Assembly: mm39
Supplementary files format and content: Microsoft Excel worksheet  files contain details from differential gene expression analyses between experimental groups, one analysis per each file. Each analysis concerns one tissue, either liver, muscle, or white adipose tissue, and includes one experimental group being compared to one other group. Roxadustat-treated PCOS mice were compared to vehicle-treated PCOS mice, to elucidate the effects of roxadustat in the context of PCOS. Vehicle-treated PCOS mice were also compared to vehicle-treated control mice, to investigate the effects of PCOS itself. Details are included in these files for every identified gene in each analysis: gene-id, log2 fold change, p-values, both regular and corrected for multiple testing (padj), name, chromosome, strand, start- and endpoint, length, biotype, description, and fpkm-value for each sample included in that analysis.

source_name: White adipose tissue

extract_protocol:
RNA was harvested from muscle and liver tissue using Rneasy mini kit (Qiagen) and from WAT using E.Z.N.A. Total RNA Kit II (Omega Bio-Tek). 300 ng of total RNA was used as starting material for mRNA purification and library preparation.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

value: White adipose tissue

tag: strain background

value: PCOS+vehicle


title: WAT, 822, veh [NW822]

description:
NW822
WAT_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
WAT_PCOS+vehicle_vs_control+vehicle.xlsx


title: Lung_Sample23 [L100]


title: Control morpholino + 0mM STS 3


title: Control morpholino + 0mM STS 1


title: Lung_Sample22 [L099]

value: Responder


title: WAT, 802, ctrl [NW802]

description:
NW802
WAT_PCOS+vehicle_vs_control+vehicle.xlsx

value: Ctrl+vehicle


title: biol rep 3, Donor 3, PBMCs, Spike protein+IL-2

city: Changchun

first: Chao

last: Niu

state: Jilin

address: Xinmin Street #1

department: Cancer Center

institute: The First Hospital of Jilin University

description:
biol rep 3
Spike protein+IL-2
Sample 12

data_processing:
CLC Genomics Workbench v 11.0.1
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the hg38.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: blood

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were adjusted to 1×10E6 cells/mL RPMI-1640 medium, and the PBMCs were inoculated into 24-well plates at 400 μL per well.

extract_protocol:
RNA was harvested using Trizol. To ensure the quality of the library, the effective concentration of the library is higher than 2nM.
RNA libraries for RNA-seq were prepared using NEB method.

treatment_protocol: Then PBS, spike protein, IL-2 (100 IU/mL), and IL-2 (100 IU/mL) combined with spike protein (10 μM) were added to PBMCs. After 16 hrs of incubation, the supernatant was collected for cytokine detection.

value: blood

value: peripheral blood mononuclear cells

value: treated with Spike protein and IL-2

value: total RNA


title: S3

value: Cortex and hippocampus

value: primarily neurons

value: sham

value: Day 5


title: D2_C

value: Bone marrow

value: Primary

value: Neutrophil

value: KCKO sup


title: WAT, 796, veh [NW796]

description:
NW796
WAT_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
WAT_PCOS+vehicle_vs_control+vehicle.xlsx


title: WAT, 809, rox [NW809]

description:
NW809
WAT_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx

value: PCOS+Roxadustat


title: iPSCs derived neurons, week 4, rep1

value: neuronal differentiation

value: iPScs derived neurons

value: WT

value: week 4


title: Lung_Sample21 [L098]

value: Lung

value: B-Acetate 48hr

value: Non-responder


title: S1


title: biol rep 3, Donor 3, PBMCs, IL-2

description:
biol rep 3
IL-2
Sample 11

value: blood

value: peripheral blood mononuclear cells

value: treated with IL-2

value: total RNA


title: D2_B


title: biol rep 3, Donor 3, PBMCs, Spike protein

description:
biol rep 3
Spike protein
Sample 10

value: treated with Spike protein


title: Control morpholino + 0mM STS 2

value: larvae

value: ctrl

value: STS


title: Lung_Sample20 [L096]

value: Responder


title: Lung_Sample19 [L094]


title: WAT, 795, rox [NW795]

description:
NW795
WAT_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx

value: White adipose tissue

value: PCOS+Roxadustat


title: WAT, 789, ctrl [NW789]

description:
NW789
WAT_PCOS+vehicle_vs_control+vehicle.xlsx

value: Ctrl+vehicle


title: iPSCs derived neural precursors, rep3

value: neuronal differentiation

value: iPSCs derived neural precursors

value: WT


title: biol rep 3, Donor 3, PBMCs, Control

description:
biol rep 3
Control
Sample 9

value: treated with PBS


title: D2_A

value: Bone marrow

value: Primary

value: Neutrophil

value: KCKO sup


title: Lung_Sample18 [L085]

value: Lung

value: 1.5mg Dex


title: WAT, 785, veh [NW785]

description:
NW785
WAT_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
WAT_PCOS+vehicle_vs_control+vehicle.xlsx

value: PCOS+vehicle


title: Lung_Sample17 [L084]

value: Non-responder


title: biol rep 2, Donor 2, PBMCs, Spike protein+IL-2

description:
biol rep 2
Spike protein+IL-2
Sample 8

value: blood

value: peripheral blood mononuclear cells

value: treated with Spike protein and IL-2

value: total RNA


title: D1_C


title: WAT, 782, rox [NW782]

description:
NW782
WAT_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx

value: White adipose tissue

value: PCOS+Roxadustat


title: WAT, 779, ctrl [NW779]

description:
NW779
WAT_PCOS+vehicle_vs_control+vehicle.xlsx

value: Ctrl+vehicle


title: Lung_Sample16 [L083]

value: Responder


title: biol rep 2, Donor 2, PBMCs, Spike protein

description:
biol rep 2
Spike protein
Sample 6

value: treated with Spike protein


title: D1_B

value: Bone marrow


title: KPC tumor from a WT mouse treated with PBS

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

description:
10x Genomics
Joe2

data_processing:
The Cell Ranger™ Single Cell Software Suite v.7.0.0 was used and The reads were aligned to the human transcriptome reference (cellranger mm10-2020-A) with STAR 2.6
Assembly: mm10-2020-A
Supplementary files format and content: standard output of cellranger with gzipped barcode, features (gene), and Unique Molecular Identifier (UMI)

source_name: Primary cells (mixed)

extract_protocol:
PVN ncueli was obtained from compiling 5 micorpunched PVNs together and then carrying out nuceli isolation using a sucrose gradient. The nuceli morpholohy and quantity were checked under the microscope by staining
Single cell Gene Expression Library was prepared according toChromium Next GEM Single Cell 3' Reagent Kits v3(10x Genomics). In Brief, single nuclei suspension, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification.

value: Primary cells (mixed)

value: Tumor

value: 7 months


title: WAT, 778, ctrl [NW778]

description:
NW778
WAT_PCOS+vehicle_vs_control+vehicle.xlsx


title: biol rep 2, Donor 2, PBMCs, Control

description:
biol rep 2
Control
Sample 5

value: treated with PBS


title: WAT, 773, veh [NW773]

description:
NW773
WAT_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
WAT_PCOS+vehicle_vs_control+vehicle.xlsx


title: Lung_Sample15 [L081]

value: Lung

value: Saline

value: Untreated


title: Lung_Sample13 [L077]

value: 12mg Dex

value: Non-responder


title: Lung_Sample14 [L080]


title: WAT, 770, veh [NW770]

description:
NW770
WAT_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
WAT_PCOS+vehicle_vs_control+vehicle.xlsx

value: PCOS+vehicle


title: biol rep 1, Donor 1, PBMCs, Spike protein+IL-2

description:
biol rep 1
Spike protein+IL-2
Sample 4

value: blood

value: peripheral blood mononuclear cells

value: treated with Spike protein and IL-2

value: total RNA


title: Lung_Sample12 [L076]


title: WAT, 767, rox [NW767]

description:
NW767
WAT_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx

value: White adipose tissue

value: PCOS+Roxadustat


title: KPC tumor from a Pdgfrb-TK mouse treated with GCV

description:
10x Genomics
Joe376

value: C57BL/6; Pdgfrb-TK


title: KPC tumor from a Pdgfrb-TK mouse treated with PBS

description:
10x Genomics
Joe221

value: Primary cells (mixed)


title: biol rep 1, Donor 1, PBMCs, IL-2

description:
biol rep 1
IL-2
Sample 3

value: treated with IL-2


title: KPC tumor from a WT mouse treated with D-CAN

description:
10x Genomics
Joe1

value: Tumor

value: 7 months


title: WAT, 764, rox [NW764]

description:
NW764
WAT_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx


title: biol rep 1, Donor 1, PBMCs, Spike protein

description:
biol rep 1
Spike protein
Sample 2

value: treated with Spike protein


title: Lung_Sample11 [L075]

value: Lung


title: WT-3, scRNAseq

city: New Haven

first: Romina

last: Fiorotto

state: CT

department: Internal Medicine

institute: Yale School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 .
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Briefly, livers from WT, CFTR-KO and CFTR-KO-GC mice were perfused with Hanks' A and then Hanks' B medium containing 0.05% collagenase (Roche Applied Science, Indianapolis, IN) and 0.8 units of trypsin inhibitor (Sigma-Aldrich, Saint Louis, MO) per unit of tryptic activity. The livers were excised and transferred into cold HBSS buffer on ice, the gallbladder was surgically removed, and the liver capsule was disrupted. Gentle mechanical agitation was applied to release most of the hepatocyte fraction, that was discarded. The hilum portion was removed, and the remaining tissue was subjected to a three-steps digestion with Collagenase Type IV (150 U/mL) for 30 mins at 37°C, Accutase (EMD Millipore) for 30 mins at 37°C and Trypsin (0.25%) for 20 minutes at 37°C. After each step, cells were collected and filtered with a 100 mm cell strainer, washed, and re-suspended in ice-cold resuspension buffer containing 2% FBS. After the last step, the single cell fractions were combined and cells were recovered by centrifugation (1200 rpm, 4 minutes). Cells were resuspended in resuspension buffer, filtered through a 35 µm filter (Corning), counted and checked for viability using Countess II automatic cell counter (Thermo Fisher Scientific). Cells (1000/ml) were resuspended in PBS-0.04% BSA and submitted to the Yale Center for Genome Analysis for processing.
For 10X Genomics, single cell RNA sequencing 10,000 cells were loaded onto 10X Genomics Single Cell 3' Chips along with maaster mix as per manufacturer's instructions. Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The resulting libraries were sequenced on a NovaSeq6000.

value: Biliary tract

value: Liver

value: 8 weeks old


title: biol rep 1, Donor 1, PBMCs, Control

description:
biol rep 1
Control
Sample 1

value: treated with PBS


title: Muscle, 814, veh [NM814]

description:
NM814
Muscle_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
Muscle_PCOS+vehicle_vs_control+vehicle.xlsx

source_name: Skeletal muscle

value: Skeletal muscle

value: PCOS+vehicle


title: Lung_Sample10 [L072]

value: Saline

value: Untreated


title: biol rep 2, Donor 2, PBMCs, IL-2

description:
biol rep 2
IL-2
Sample 7

value: blood

value: peripheral blood mononuclear cells

value: total RNA


title: WT-2, scRNAseq

description: 10x Genomics


title: D1_A

first: Minsoo

last: Kim

institute: University of Rochester

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq version 2.19.1
Quality filtering and adapter removal are performed using FastP version 0.23.1 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y –r -j"
Processed/cleaned reads were then mapped to the GRCm39/gencode M27 or GRCm39/gencode M31 reference using STAR_2.7.9a with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM Unsorted – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
Genelevel read quantification was derived using the subread-2.0.1 package (featureCounts) with a GTF annotation file (GRCm39/gencode M31) and the following parameters for stranded RNA libraries "-s 2 -t exon -g gene_name" OR "-s 0 -t exon -g gene_name" for un stranded libraries
Differential expression analysis was performed using DESeq2-1.34.0 with a P-value threshold of 0.05 within R version 3.5.1 (https://www.R-project.org/)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw count values for each Sample
Supplementary files format and content: tab delimited deSeq2 counts files

source_name: Bone marrow

extract_protocol:
Total RNA from neutrophils were isolated using RNeasy plus mini kit (Qiagen). Total RNA was preamplified with SMARTer Ultra Low Input kit v4 per manufacturer’s protocol (Clontech). CDNA quality and quantity were measured using Qubit fluorometer (Life Technologies) and Agilent Bioanalyzer 2100. CDNA was used to generate Illumina-compatible sequencing libraries using NexteraXT library preparation kit (Illumina).
Clontech low input/Illumina mRNA

value: Bone marrow

value: Primary

value: Neutrophil

value: KCKO sup


title: 19L1, d10

first: Alfonso

last: Saera-Vila

address: Dr. Trueta 179

institute: Sequientia Biotech

description: 61709_ID1885_22-19L1d10-A001-F03_S92_L004_R1_001

data_processing:
RNA-seq read quality control (QC) analyses and filtering of high-quality reads were executed using FastQC and BBDuk (Bushnell et al. 2017) by setting a minimum read length of 35 bp and a minimum Phred-quality score of 25. After trimming quality control, high quality reads were aligned to the mouse genome reference (GrCm38p6/mm10) with STAR 2.7.3a (Dobin et al. 2012), while FeatureCounts 1.6.3 package (Liao et al. 2014) was used to assign reads to genes.
Genes with low, constant levels of raw counts across one or more experimental conditions were filtered to eliminate the “uninformative” genes using HTSFilter 1.30.1 (Rau et al. 2013). Filtered gene data was further processed with the EdgeR package (Robinson et al. 2009) to normalize the raw counts.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with fpkm normalized gene counts for every gene and every sample

source_name: bone (femoral head)

growth_protocol: Human MSC isolated from femoral head were incubated in DMEM (PAN Biotech, Germany, Cat. No. P04-03550) supplemented with 1% (v/v) 100× Penicillin-Streptomycin Solution (Biowest, France, Cat. No. L0022), 10% (v/v) FCS (Biowest, France, Cat. No. S181S), 1% (v/v) 200mM L-Glutamine solution (Sigma, USA, Cat. No. G7513), 5ng/ml FGF-2 (Sigma, USA, Cat. No. F0291) and 10ng/ml FGF-4 (Sigma, USA, Cat. No. F8424) in a humidified atmosphere containing 5% CO2. To induce osteogenic differentiation, MSC were seeded on Nunc™ 24-well plates (Thermo Fisher, USA, Cat. No. 142475) or 48-well plates (Thermo Fisher, USA, Cat. No. 150687) at a density of 1.5 × 104 cells/cm2. After 24 h, differentiation was induced using StemPro® Osteogenesis Kit (Gibco/Life Technologies, USA, Cat. No. A10072-01). The medium was exchanged every 3 days.

extract_protocol:
Cells were harvested and resuspended in 1ml of QIAzol Lysis reagent (Qiagen, Cat. No.79306). Total RNA was then purified with RNeasy Plus Mini kit (Qiagen, cat. No. 74134) with minimal modifications to manufacturer’s instructions. DNase treatment (RNase free DNase set, Qiagen, Cat. No. 79254) was performed to remove any residual DNA. RNA quality and concentration were checked using a NanodropTM 2000 spectrophotometer (ThermoFisher).
Total RNA-seq library was prepared with CORALL Total RNA library prep with RiboCop rRNA for Human/Mouse/Rat depletion kit (Lexogen GmbH, Vienna, Austria) following manufacturer’s instructions (library type: fr-secondstrand) by IGA Technology service (Italy). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA).

treatment_protocol: Synthetic L1 RNA was transfected in MSC differentiating to osteoblasts at day 5 using LipofectamineTM MessengerMAXTM (Invitrogen, USA, Cat. No. LMRNA003) with a modified protocol for low RNA amount. RFP mRNA (System Bioscience, USA, Cat. No. MR800A-1) was used as negative control

tag: individual

tag: disease state

value: osteoporosis

value: bone (femoral head)

value: human mesenchymal stem cells (hMSC)

value: Transfected with L1 RNA


title: Lung_Sample9 [L071]

value: Lung


title: Muscle, 808, rox [NM808]

description:
NM808
Muscle_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx

value: PCOS+Roxadustat


title: Lung_Sample8 [L067]

value: 1.5mg Dex

value: Non-responder


title: 19RFP, d10

description: 61708_ID1885_21-19RFPd10-A001-E03_S91_L004_R1_001

value: Transfected with RFP mRNA


title: 16L1, d10

description: 61707_ID1885_20-16L1d10-A001-D03_S90_L004_R1_001


title: CFTR-KOGC-3 scRNAseq

description: 10x Genomics

value: Biliary tract

value: Liver

value: litter mates of B6.Cftrtm1Unc

tag: age

value: 8 weeks old


title: Muscle, 804, ctrl [NM804]

description:
NM804
Muscle_PCOS+vehicle_vs_control+vehicle.xlsx

value: Skeletal muscle

value: Ctrl+vehicle


title: Lung_Sample7 [L066]

value: Responder


title: 16RFP, d10

description: 61706_ID1885_19-16RFPd10-A001-C03_S89_L004_R1_001


title: Muscle, 801, ctrl [NM801]

description:
NM801
Muscle_PCOS+vehicle_vs_control+vehicle.xlsx


title: Muscle, 802, ctrl [NM802]

description:
NM802
Muscle_PCOS+vehicle_vs_control+vehicle.xlsx


title: 12L1, d10

description: 61705_ID1885_18-12L1d10-A001-B03_S88_L004_R1_001


title: Muscle, 795, rox [NM795]

description:
NM795
Muscle_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx


title: CFTR-KO-2, scRNAseq

description: 10x Genomics


title: CFTR-KOGC-2 scRNAseq

description: 10x Genomics


title: Lung_Sample6 [L065]

value: 12mg Dex


title: CFTR-KO-3, scRNAseq

description: 10x Genomics


title: Lung_Sample4 [L060]

value: Saline

value: Untreated


title: 12RFP, d10

description: 61704_ID1885_17-12RFPd10-A001-A03_S87_L004_R1_001

value: osteoporosis

value: bone (femoral head)

value: human mesenchymal stem cells (hMSC)


title: CFTR-KOGC, scRNAseq

description: 10x Genomics

tag: group

value: CFTR-KO-GC


title: WT, scRNAseq

description: 10x Genomics

value: WT


title: Muscle, 789, ctrl [NM789]

description:
NM789
Muscle_PCOS+vehicle_vs_control+vehicle.xlsx


title: Muscle, 785, veh [NM785]

description:
NM785
Muscle_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
Muscle_PCOS+vehicle_vs_control+vehicle.xlsx

value: PCOS+vehicle


title: Lung_Sample3 [L059]

value: Lung


title: 9L1, d10

description: 61703_ID1885_16-9L1d10-A001-H02_S86_L004_R1_001

value: Transfected with L1 RNA


title: CFTR-KO, scRNAseq

description: 10x Genomics

value: Biliary tract

value: Liver

value: CFTR-KO


title: 9RFP, d10

description: 61702_ID1885_15-9RFPd10-A001-G02_S85_L004_R1_001

value: Transfected with RFP mRNA


title: Lung_Sample2 [L055]

value: 1.5mg Dex

value: Non-responder


title: N3 4T1 orthtopic tumor RNA

city: Gary

first: Dipika

last: Gupta

state: IN

address: 3400 Broadway

department: School of Medicine

institute: Indiana University

data_processing:
Reads were adapter trimmed and quality filtered using Trimmomatic ver. 0.33 (http://www.usadellab.org/cms/?page=trimmomatic), with the cutoff threshold for average base quality score set at 20 over a window of 3 bases.
Reads shorter than 20 bases post-trimming were excluded.
Cleaned reads were mapped to mouse reference genome GRCm38 (gencode M16), using TopHat2 ver. 2.1.1 (https://doi.org/10.1186/gb-2013-14-4-r36).
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Differential expression with statistical analysis was calculated using the software DESeq2
Assembly: GRCm38

source_name: Breast tumor

extract_protocol:
RNA was isolated from the liver using TRIZOL and purified on RNeasy spin columns. The purity was checked with Agilent Tapestation.
Libraries were prepared according to Illumina's TruSeq Stranded mRNA library preparation kit protocol.

treatment_protocol: Mice were injected with 4T1 carcinoma cells into the mammary fat pad and 6 days later tumors were extracted

value: Breast tumor

value: Tumor

value: BALB/c

value: Injected with 4T1 carcinoma cells


title: 19L1, d6

description: 61698_ID1885_11-19L1d6-A001-C02_S81_L004_R1_001

value: osteoporosis

value: bone (femoral head)


title: Lung_Sample1 [L050]

value: 12mg Dex


title: N2 4T1 orthtopic tumor RNA


title: 19RFP, d6

description: 61697_ID1885_10-19RFPd6-A001-B02_S80_L004_R1_001

value: human mesenchymal stem cells (hMSC)


title: Lung_Sample5 [L064]


title: Muscle, 773, veh [NM773]

description:
NM773
Muscle_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
Muscle_PCOS+vehicle_vs_control+vehicle.xlsx

value: Skeletal muscle

value: PCOS+vehicle


title: N1 4T1 orthtopic tumor RNA


title: Muscle, 770, veh [NM770]

description:
NM770
Muscle_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
Muscle_PCOS+vehicle_vs_control+vehicle.xlsx


title: 16RFP, d6

description: 61695_ID1885_8-16RFPd6-A001-H01_S78_L004_R1_001


title: W3 4T1 orthtopic tumor RNA

value: WT


title: Hippocampal_Sample22 [H099]

source_name: Hippocampal

value: Hippocampal

value: B-Acetate 48hr

value: Responder


title: Muscle, 767, rox [NM767]

description:
NM767
Muscle_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx

value: PCOS+Roxadustat


title: Hippocampal_Sample23 [H100]


title: Hippocampal_Sample24 [H101]


title: Liver, 814, veh [NL814]

description:
NL814
Liver_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
Liver_PCOS+vehicle_vs_control+vehicle.xlsx

value: Liver


title: 12L1, d6

description: 61694_ID1885_7-12L1d6-A001-G01_S77_L004_R1_001

value: Transfected with L1 RNA


title: Hippocampal_Sample21 [H098]

value: Non-responder


title: Liver, 808, rox [NL808]

description:
NL808
Liver_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx


title: Muscle, 782, rox [NM782]

description:
NM782
Muscle_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx


title: W1 4T1 orthtopic tumor RNA

value: Breast tumor

value: Tumor


title: W2 4T1 orthtopic tumor RNA

value: BALB/c

value: Injected with 4T1 carcinoma cells


title: Hippocampal_Sample20 [H096]


title: 12RFP, d6

description: 61693_ID1885_6-12RFPd6-A001-F01_S76_L004_R1_001

value: osteoporosis

value: bone (femoral head)

value: Transfected with RFP mRNA


title: Liver, 804, ctrl [NL804]

description:
NL804
Liver_PCOS+vehicle_vs_control+vehicle.xlsx

value: Ctrl+vehicle


title: Multi-potent progenitor and LSK cells

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
The FastQ files were processed using scPipe v1.6.0 and Rsubread v1.32.4 software packages for alignment, de-multiplexing and gene count summarization. Note that the transcript is contained in the R2 file and the cell index and UMI in the R1 file.
ERCC spike in sequences were added to the samples. The data was therefore aligned to the mouse genome with ERCC sequences added using Rsubread.
Mouse genes were identified using Ensembl annotation vGRCm38.88
Barcode sequences are contained in the supplementary file 'Barcodes.txt'
Assembly: mm10 (NCBI build 38.1)
Supplementary files format and content: Processed data files are tab-delimited txt files. Columns represent Ensembl gene ID and total counts mapping to that gene for every cell in that cell type

source_name: e14 embryo

extract_protocol:
Fetal livers were isolated from E14 embryos and underwent mechanical pipetting into a single cell solution. Cells were stained with CKIT-APC and enriched using ANTI-APC microbeads/magnet separation (MACS columns). Cells were stained again with their respective cell surface markers and underwent single cell sorting onto 384 well plates. Two litters were used and all embryos within these litters were processed and pooled (including both sexes: males/females) All plates were sorted on the same day.
Libraries were prepared with a CELSeq2 protocol

value: mixed sample (non-demultiplexed)


title: 9L1, d6

description: 61692_ID1885_5-9L1d6-A001-E01_S75_L004_R1_001

value: human mesenchymal stem cells (hMSC)


title: Liver, 802, ctrl [NL802]

description:
NL802
Liver_PCOS+vehicle_vs_control+vehicle.xlsx


title: Hippocampal_Sample19 [H094]

value: Hippocampal


title: THA020.R

data_processing:
*library strategy: DNTR-seq
Paired-end raw RNA-seq reads were aligned using STAR  against iGenomes hg38 and RefSeq gene annotations with ERCC spike-ins added. PCR duplicates were removed using Picard and uniquely mapping fragments counted using featureCounts Quality of cells was then assessed based on number of total counts per cell (library size), requiring at least 800 reads per cell. https://github.com/EngeLab/DNTRseq
Assembly: hg38
Supplementary files format and content: mRNA read counts summarized over genes; DNA read counts summarized over genomic bins

source_name: neuroblastoma

growth_protocol: Fresh tumor samples (THA004, THA016) were processed at the day of surgery or cryo- preserved (THA018, THA019, THA020) viable single-cell solutions were used after gently thawing the sample. Tissue was mechanically and enzymatically dissociated as described under “Dissociaton”.

extract_protocol:
total RNA or DNA
Adrenergic cells were defined as CD45-/CD24+, SCP-like cells were selected as CD45-/ERBB3+. After FACS, plates containing sorted single cells were stored at -80°C to ensure efficient lysis of the cell membrane while keeping the cell nucleus intact. After splitting each cell, separate mRNA- (*R suffix) and DNA-libraries (*D suffix) were constructed. As comparison, a set of cells had mRNA libraries prepared with Smart-Seq2 (no suffix). Barcoded libraries were sequenced paired-end (37bp x 2) on an Illumina NextSeq.

treatment_protocol: Cells were untreated.

value: neuroblastoma

tag: age (month)

tag: risk group

value: High

tag: tumor type

value: Primary

tag: tissue type

value: Surgical specimen


title: 16L1, d6

description: 61696_ID1885_9-16L1d6-A001-A02_S79_L004_R1_001

value: Transfected with L1 RNA

tag: time


title: THA020.D


title: 9RFP, d6

description: 61691_ID1885_4-9RFPd6-A001-D01_S74_L004_R1_001


title: Liver, 801, ctrl [NL801]

description:
NL801
Liver_PCOS+vehicle_vs_control+vehicle.xlsx

value: Liver


title: Liver, 795, rox [NL795]

description:
NL795
Liver_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx

value: PCOS+Roxadustat


title: THA019.R


title: Hippocampal_Sample17 [H084]

value: 1.5mg Dex

value: Non-responder


title: patient_o_epidermis_progression_018

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

data_processing:
The generated FASTQ files were converted to output DCC files using the GeoMx NGS Pipeline v2.5.1.
Assembly: Hs_R_NGS_WTA_v1.0.pkc (Nanostring provided probe conversion file)
Supplementary files format and content: probe count files (.dcc). Files include the read count for each of the probes, corresponding to a unique gene.
Library strategy: Spatial Transcriptomics

source_name: epidermis

growth_protocol: Samples are biopsies

extract_protocol:
Tissue sections were incubated with DNA, PanCK and CD4 morphology markers and 68 areas of illumination consisting of areas enriched in CD4-positive cells and neighboring cells in the dermis, epidermis, and in Pautriers micro abscesses were profiled.
Library preparation was carried out according to the manufacturer's protocol (Nanostring Technologies).

treatment_protocol: Formalin-fixed, paraffin-embedded skin biopsies at time of diagnosis from 15 patients with MF were analyzed using the GeoMx to capture spatially resolved high-plex RNA gene expression data.

value: epidermis

value: progression


title: Hippocampal_Sample16 [H083]

value: Responder


title: THA019.D


title: patient_o_cd4cells_dermis_micro_progression_016


title: Liver, 789, ctrl [NL789]

description:
NL789
Liver_PCOS+vehicle_vs_control+vehicle.xlsx


title: patient_o_basal_layer_progression_017


title: THA018.R

value: Biopsy


title: Liver, 785, veh [NL785]

description:
NL785
Liver_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
Liver_PCOS+vehicle_vs_control+vehicle.xlsx

value: PCOS+vehicle


title: Hippocampal_Sample15 [H081]

value: Saline

value: Untreated


title: THA018.D


title: Hippocampal_Sample14 [H080]

value: Hippocampal


title: patient_n_epidermis_progression_015


title: Hippocampal_Sample13 [H077]

value: 12mg Dex


title: patient_o_cd4cells_dermis_progression_016


title: patient_n_basal_layer_progression_014


title: Liver, 773, veh [NL773]

description:
NL773
Liver_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
Liver_PCOS+vehicle_vs_control+vehicle.xlsx


title: THA017.R

value: neuroblastoma

value: Low


title: Liver, 770, veh [NL770]

description:
NL770
Liver_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx
Liver_PCOS+vehicle_vs_control+vehicle.xlsx


title: Hippocampal_Sample18 [H085]


title: Hippocampal_Sample12 [H076]


title: THA017.D

value: Primary

value: Surgical specimen


title: Liver, 767, rox [NL767]

description:
NL767
Liver_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx

value: Liver


title: THA016.R

value: High


title: patient_n_cd4cells_microabscess_progression_012


title: THA016.D


title: KO

city: 武汉

first: ZHEN

last: TANG

state: 湖北

address: 医学研究院

institute: 武汉大学

data_processing:
Raw reads were first processed with CeleScope to remove low-quality reads with Cutadapt v1.17 to trim poly-A tail and adapter sequences. Cell barcodes and UMI were extracted.
STAR v2.6.1a was used to map reads to the reference genome GRCm38 (ensembl version 92 annotation). UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 software, and used to generate expression matrix files for subsequent analysis.
We set the following thresholds to remove poor-quality cells: cells with few genes per cell (<500) and cells with a percentage of mitochondrial genes over 5%.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

growth_protocol: Neutrophils were sorted from lung tumors of KP and KPIL8 mice that were intranasally injected with Ad-Cre (2x106 pfu per mouse)

extract_protocol:
Neutrophils were loaded into a microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification.
The amplified cDNA is then fragmented and ligated with sequencing adapters. ScRNA-seq was performed using the GEXSCOPER Single-Cell RNA Library Kit (Singleron) following the Singleron GEXSCOPER protocol. The amplified cDNA is then fragmented and ligated with sequencing adapters. ScRNA-seq was performed using the GEXSCOPER Single-Cell RNA Library Kit (Singleron) following the Singleron GEXSCOPER protocol. The concentrations of neutrophils were adjusted to target a recovery of 6,000–10,000 cells per sample. Libraries of each sample were diluted to 4 nM, pooled, and sequenced on NovaSeq 6000 System with 150 bp paired-end reads (Illumina).

value: lung

value: Neutrophils

value: 10 weeks after intranasal injection of Ad-Cre


title: THA004.R


title: Liver, 782, rox [NL782]

description:
NL782
Liver_PCOS+Roxadustat_vs_PCOS+vehicle.xlsx

value: PCOS+Roxadustat


title: Hippocampal_Sample9 [H071]


title: Hippocampal_Sample11 [H075]

value: Non-responder


title: Hippocampal_Sample10 [H072]


title: Hippocampal_Sample7 [H066]

value: 1.5mg Dex

value: Responder


title: patient_m_basal_layer_nonprogression_009

value: nonprogression


title: allantoises,Isl1,WT2,cuttag

city: 上海市

first: 泽悦

last: 朱

address: 四平路1239号

institute: 同济大学

data_processing:
Basecalls were performed using bel2fastq v2. 17 for Novaseq output.
CUT&Tag reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0 33, discarding reads left with < 20 bp.
CUT&Tag reads were aligned to the UCSC hg38 genome using Bowtie version 1.1 2. Only uniquely mapping reads with at most two mismatches were retained.
To create CUT&Tag coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2. 1.0 with the significance cut-off a-value <=0.01.
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&Tag

source_name: allantoises

extract_protocol:
Fresh embryo tissue sample was separated and liquid nitrogen quick freezing. Nucleus were extracted using nuclear extraction kit (Solarbio).
CUT&Tag libraries were prepared using the hyperactive universal CUT&Tag assay kit for illumina pro TD904 (Vazyme) following manufacturer¡¯s protocols.

value: allantoises

tag: cuttag antibody

value: Islet1 (abcam, ab20670)

value: WT


title: DRG, naive vehicle treated, sample 5

city: Chicago

first: Rachel

middle: E

last: Miller

address: 1735 W Harrison St

institute: Rush University Medical Center

data_processing:
Cutadapt [1] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases
HISAT2 was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-107/fasta/mus_musculus/dna/
mapped reads of each sample were assembled using StringTie
StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts
Assembly: GRCm39
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: tab delimited text file includes FPKM values for each sample

source_name: L3-L5 dorsal root ganglia

extract_protocol: Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

value: L3-L5 dorsal root ganglia

value: macrophage Fas-Induced apoptosis (MaFIA) homozygous

value: naive, vehicle


title: patient_m_cd4cells_dermis_micro_nonprogression_008

tag: cell type


title: patient_n_cd4cells_dermis_micro_progression_013

value: progression


title: Hippocampal_Sample5 [H064]

value: Hippocampal

value: 12mg Dex


title: Hippocampal_Sample6 [H065]


title: patient_m_cd4cells_dermis_nonprogression_008


title: DRG, naive vehicle treated, sample 3

tag: genotype


title: THA004.D

first: Shenglin

last: Mei

institute: Harvard medical school (DMBI)

value: neuroblastoma

value: Low

value: Primary

value: Surgical specimen


title: TumorOrg.P25.Rep2

city: Tokyo

first: Taku

last: Sato

address: 1-5-45 Yushima Bunkyo-ku

department: Department of Biodefense Research

country: Japan

institute: Medical Research Institute, Tokyo Medical and Dental University (TMDU)

data_processing:
CAGE libraries were sequenced using single end reads of 75nt on a NextSeq 500 instrument (Illumina). Obtained reads (CAGE tags) were mapped to the human GRCh38 genome using BWA (version 0.7.17). Unmapped reads were then mapped by HISAT2 (version 2.0.5). CAGE tag clustering, detection of differential expressed genes and motif discovery were performed by pipeline RECLU (Ohmiya et al., BMC Genetics 2014, 15:269). Tag count data were clustered using the modified Paraclu program. Clusters with count per million (CPM) < 0.1 were discarded. Regions that have 90% overlap between replicates were extracted by BEDtools (version 2.12.0). The clusters with irreproducible discovery rate (IDR) ≥ 0.1 and clusters longer than 200 bp were discarded.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include CPM values for each sample.

source_name: Tongue

growth_protocol: Organoids were grown in basic organoid culture medium containig Noggin, EGF, RspoI, and Y27632.

extract_protocol:
Organoids were flash frozen by liquid nitrogen, and RNA was extracted using QIAGEN Rneasy mini kit.
The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed.

value: Tongue

value: Tumor cells


title: TumorOrg.P32.Rep2


title: NormalOrg.P32.Rep2

value: Normal tongue epithelial cells


title: patient_n_cd4cells_dermis_progression_013

tag: treatment


title: DRG, naive vehicle treated, sample 2

tag: tissue


title: TumorOrg.P18.Rep2


title: TumorOrg.P21.Rep2


title: Hippocampal_Sample8 [H067]

value: 1.5mg Dex

value: Non-responder


title: TumorOrg.P32


title: patient_l_epidermis_nonprogression_006

value: epidermis

value: nonprogression


title: patient_l_cd4cells_microabscess_nonprogression_004


title: DRG, naive AP20187 treated, sample 3

value: L3-L5 dorsal root ganglia

value: naive, AP20187


title: Hippocampal_Sample2 [H055]


title: Hippocampal_Sample4 [H060]

value: Saline

value: Untreated


title: patient_k_cd4cells_dermis_micro_nonprogression_003


title: Hippocampal_Sample3 [H059]

value: Hippocampal


title: patient_m_epidermis_nonprogression_011


title: TumorOrg.P03.Rep2


title: DRG, naive vehicle treated, sample 1

value: macrophage Fas-Induced apoptosis (MaFIA) homozygous

value: naive, vehicle


title: patient_l_basal_layer_nonprogression_005


title: patient_l_cd4cells_dermis_nonprogression_007


title: DRG, naive AP20187 treated, sample 4


title: WT

value: lung

value: Neutrophils

value: 10 weeks after intranasal injection of Ad-Cre


title: Sorted Fibroblasts, EMPA_IR_3

city: Lamia

first: Artemis

middle: Georgia

last: Hatzigeorgiou

state: Galaneika

address: Papasiopoulou 2-4

department: Computer Science and Biomedical Informatics

country: Greece

institute: University of Thessaly

data_processing:
Adapter content of RNA-seq samples was estimated by employing Minion v.15-065 from the EBI Kraken tools
Quality control of raw and pre-processed sequencing files was conducted using the FastQC Suite (www.bioinformatics.babraham.ac.uk/projects/fastqc/), followed by removal of low-quality reads (i.e. -q 20) using cutadapt (v2.8) and curation of the resulting length distribution of reads.
RNA alignment and quantification was performed by utilizing Salmon against GRCm39 genome assembly and Ensembl v106 genomic annotation.
Normalization of counts was performed using the Trimmed Mean of M-values (TMM) method
Prior to differential expression analysis, lowly-expressed genes were filtered out using the R (v4.0.3) package edgeR::filterByExpr (v3.32.1) function with default parameters
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Heart

growth_protocol: Mice were housed in a maximum of 6 per cage, in a specific pathogen-free facility at a temperature- controlled environment (20-25 °C), under 12-h light/dark cycle and received regular laboratory animal diet and water ad libitum.

extract_protocol:
Samples were sorted into sterilized and RNAase-free polypropylene tubes, each one containing 2 mL of the RL-Lysis buffer (provided within the Norgen single-cell RNA isolation kit), and then inserted into the cell collection chamber. Cells were sorted immediately into RL-Buffer and then vortexed.
QuantSeq 3‘ mRNA-Seq Library Prep Kit for Illumina (FWD) (Lexogen) was used, according to manufacturer’s instructions.

treatment_protocol:
Group 1- Sham: Mice were subjected to a daily oral administration of vehicle (5% DMSO in sterile normal saline) for 6 weeks and sham open chest operation.
Group 2- Control/Ischemia-Reperfusion (Control IR): Mice were subjected to a daily oral administration of vehicle for 6 weeks and subjected to 30 minutes of ischemia and 2 hours reperfusion.
Group 3- EMPA/Ischemia-Reperfusion (EMPA IR): Mice were subjected to a daily oral administration of EMPA (10mg/kg/day, diluted in vehicle) for 6 weeks and subjected to 30 minutes of ischemia and 2 hours reperfusion.
Ischemia was induced by left anterior descending artery (LAD) ligation.

value: Heart

value: Sorted Fibroblasts

value: Empagliflozin/Ischemia-Reperfusion


title: DRG, naive vehicle treated, sample 4


title: patient_l_cd4cells_dermis_micro_nonprogression_007


title: Hippocampal_Sample1 [H050]

value: 12mg Dex


title: Sorted Fibroblasts, EMPA_IR_4


title: Sorted Fibroblasts, EMPA_IR_2


title: DRG, naive AP20187 treated, sample 1


title: TumorOrg.P08.Rep2

value: Tongue

value: Tumor cells


title: patient_k_cd4cells_dermis_nonprogression_003

value: nonprogression


title: DRG, naive AP20187 treated, sample 5

value: L3-L5 dorsal root ganglia


title: DRG, DMM vehicle treated, sample 64

value: DMM surgery, vehicle


title: TumorOrg.P15


title: Sorted Fibroblasts, EMPA_IR_1


title: DRG, DMM vehicle treated, sample 63


title: patient_k_epidermis_nonprogression_002

value: epidermis


title: patient_j_cd4cells_dermis_micro_progression_021

value: progression


title: Sorted Fibroblasts, Control_IR_3

value: Control/Ischemia-Reperfusion


title: DRG, DMM vehicle treated, sample 33

value: macrophage Fas-Induced apoptosis (MaFIA) homozygous


title: DRG, DMM vehicle treated, sample 34


title: Sorted Fibroblasts, Control_IR_1


title: patient_j_cd4cells_dermis_progression_021


title: DRG, DMM vehicle treated, sample 32


title: DRG, DMM AP20187 treated, sample 61

value: DMM surgery, AP20187


title: Sorted Fibroblasts, Control_IR_2


title: Sorted Fibroblasts, SHAM_4

value: Sham


title: patient_j_epidermis_progression_019


title: patient_i_basal_layer_progression_018


title: DRG, DMM AP20187 treated, sample 60


title: Sorted Fibroblasts, SHAM_3


title: DRG, DMM AP20187 treated, sample 59


title: Sorted Fibroblasts, SHAM_2


title: patient_i_cd4cells_dermis_micro_progression_016


title: patient_i_epidermis_progression_017


title: Sorted Fibroblasts, SHAM_1


title: patient_j_basal_layer_progression_020


title: DRG, DMM AP20187 treated, sample 58


title: patient_i_cd4cells_dermis_progression_016


title: Sorted Fibroblasts, Control_IR_4


title: patient_k_basal_layer_nonprogression_001


title: D_monoculture 0hr [SL427844]

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

institute: Leibniz Institute for Immunotherapy

description:
Annotation.tsv
Filteredcounts.tsv
Rawcounts.tsv
RPKM_2023-04-11.xlsx
SL427844

data_processing:
bcl to fastq conversion using bcl2fastq controlled by longranger
trimming with cutadapt, mapping with STAR(2.7), feature assignment with featureCounts
DE gene analysis with DESeq2
Assembly: GRCm38.primary_assembly
Assembly: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/GRCm38.primary_assembly.genome.fa.gz
Supplementary files format and content: Raw count files, feature counts output

source_name: spleen

growth_protocol: CD8+ T cells in co-culture were maintained in RPMI media supplemented with 10% fetal bovine serum (FBS), Glutamax, Sodium Pyruvate, b-mercaptoethanol and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA HyperPrep kit (KAPA Biosystems) following manufacturer's protocols.
Total RNA Seq with ribo depletion

treatment_protocol: CD8+ T cells were co-cultured with DM5 (an immortalized BL6-derived bone marrow mesenchyme stromal cells) with DsRed labelled mitochondria for 36hrs, and then sorted using CD8+ BD Influx™ into MitoPositive cells (DsRed+) and MitoNegative (DsRed-).

value: spleen

tag: cell line

value: CD8+ T cells

value: T-cell CD8+

value: Pmel Ly5.1 mice [Jax-lD 005023 crossed with Jax-lD 002014]

value: control, no co-culture


title: Endothelial Cells, EMPA_IR_5

value: Heart

value: Endothelial Cells

value: Empagliflozin/Ischemia-Reperfusion


title: patient_h_cd4cells_dermis_micro_nonprogression_015

value: nonprogression


title: D_MitoNegative co-culture 0hr [SL427843]

description:
Annotation.tsv
Filteredcounts.tsv
Rawcounts.tsv
RPKM_2023-04-11.xlsx
SL427843

value: Co-culture with murine MSC with DsRed labelled mitochondria, FACS sorted DsRed negative


title: Endothelial Cells, EMPA_IR_4


title: Endothelial Cells, EMPA_IR_3


title: D_MitoPositive co-culture 0hr [SL427842]

description:
Annotation.tsv
Filteredcounts.tsv
Rawcounts.tsv
RPKM_2023-04-11.xlsx
SL427842

value: Co-culture with murine MSC with DsRed labelled mitochondria, FACS sorted DsRed positive


title: DRG, DMM AP20187 treated, sample 62

value: L3-L5 dorsal root ganglia


title: patient_h_epidermis_nonprogression_014

value: epidermis


title: patient_h_cd4cells_dermis_nonprogression_015


title: Endothelial Cells, EMPA_IR_2


title: patient_h_basal_layer_nonprogression_013


title: Endothelial Cells, EMPA_IR_1


title: C_MitoPositive co-culture 0hr [SL427836]

description:
Annotation.tsv
Filteredcounts.tsv
Rawcounts.tsv
RPKM_2023-04-11.xlsx
SL427836


title: C_MitoNegative co-culture 0hr [SL427837]

description:
Annotation.tsv
Filteredcounts.tsv
Rawcounts.tsv
RPKM_2023-04-11.xlsx
SL427837


title: C_monoculture 0hr [SL427838]

description:
Annotation.tsv
Filteredcounts.tsv
Rawcounts.tsv
RPKM_2023-04-11.xlsx
SL427838


title: B_monoculture 0hr [SL427832]

description:
Annotation.tsv
Filteredcounts.tsv
Rawcounts.tsv
RPKM_2023-04-11.xlsx
SL427832


title: Endothelial Cells, Control_IR_3

value: Control/Ischemia-Reperfusion


title: patient_g_cd4cells_dermis_nonprogression_012


title: B_MitoNegative co-culture 0hr [SL427831]

description:
Annotation.tsv
Filteredcounts.tsv
Rawcounts.tsv
RPKM_2023-04-11.xlsx
SL427831


title: Endothelial Cells, Control_IR_2


title: patient_g_basal_layer_nonprogression_011


title: Endothelial Cells, Control_IR_1


title: B_MitoPositive co-culture 0hr [SL427830]

description:
Annotation.tsv
Filteredcounts.tsv
Rawcounts.tsv
RPKM_2023-04-11.xlsx
SL427830


title: patient_f_cd4cells_dermis_micro_nonprogression_009


title: Endothelial Cells, SHAM_3


title: Endothelial Cells, SHAM_4


title: patient_f_cd4cells_dermis_nonprogression_009


title: ASF_KO

city: Jining

first: Xue

last: You

institute: Jining Medical University

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline (version 5.0.0) of 10×Genomics was applied to demultiplex cellular barcodes, employ the STAR aligner to map sequencing reads to the genome and transcriptome, generate a matrix of gene counts versus cells after down-sample reads as required to produce normalized aggregate data across samples, and analyze the unique molecular identifier (UMI) count matrix by the R package Seurat[1] (version 3.1.1).
To eliminate low-quality cells and likely multiplet captures, which is a major concern in microdroplet-based experiments, a set of criteria were conducted: Cells were filtered by (1) UMI/gene numbers out of the limit of mean value +/- 2 fold of standard deviations, assuming that each cell's UMI/gene numbers have a Gaussian distribution, (2) percentage of mitochondrial RNA UMIs (proportion of UMIs mapped to mitochondrialgenes > 10%).
we applied DoubletFinder package[2] (version 2.0.2) to identify potential doublet.
To obtain the normalized count, library size normalization was processed using NormalizeData function in Seurat
the gene expression measurements per cell were normalized by “LogNormalize” to total expression，the global-scaling normalization method, multiplied by a default scaling factor (10,000), and the results were log-transformed.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: pancreas

extract_protocol:
collagenase P was perfused along the common bile duct of the mice to fill the pancreas after mice were dissected, followed by digestion in a 37 ℃ water bath, and Hank's Balanced Salt Solution containing 10% FBS was added to terminate the digestion. Then the islet cells were picked under a stereomicroscope. In order to obtain single cell suspension, the selected islets were digested with trypsin and passed through a 40um single-cell sieve, and the single cells were finally used for single-cell sequencing.
RNA libraries were prepared with Chromium Single cell 3' Reagent v3 Kits according to the manufacturer's protocol.

value: pancreas

value: mouse islet cells

value: single cell

value: ASF-KO

value: 9 month


title: SC_35_KO

description: 10x Genomics


title: WT

description: 10x Genomics

value: wide type


title: Endothelial Cells, SHAM_2

value: Sham


title: Endothelial Cells, SHAM_1


title: patient_f_basal_layer_nonprogression_007


title: patient_f_epidermis_nonprogression_008


title: patient_g_cd4cells_dermis_micro_nonprogression_012


title: Endothelial Cells, Control_IR_4


title: RH6-3 epididymal fat

city: Shijiazhuang

first: Linlin

last: Yang

state: Hebei

address: 348, Heping west road

institute: Hebei General Hospital

description:
lncRNA_expression_matrix_with_annotation.xls
mRNA_expression_matrix_with_annotation.xls

data_processing:
fastp software was used for sequence filtering.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.91 whole genome using Hisat2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38.91
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: white adipose tissue

growth_protocol: 6 weeks old clean-grade C57BL/6J male mice weighing around 22g were purchased from Beijing Viton Lihua Experimental Center and sustained on a standard 12h light-dark cycles, with temperature (20-25℃) and humidity (40-60%). HFD mice were developed by feeding with a diet containing D12492J feed (20% protein, 20% carbohydrate, 60% fat) for 8 weeks.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Novaseq protocols

treatment_protocol: Eight weeks after C57BL / 6J mice fed a high-fat diet (HFD), the degree of insulin resistance was assessed by intraperitoneal glucose tolerance test (IPGTT) and the insulin resistance model was successfully established. Mice were then treated with resveratrol and metformin for 6 weeks and skeletal muscle was collected.

value: HFD + reveratrol

tag: strain


title: RH3-3 epididymal fat


title: patient_g_epidermis_nonprogression_010


title: RH1-4 epididymal fat


title: patient_g_cd4cells_microabscess_nonprogression_002


title: RH1-2 epididymal fat


title: patient_d_cd4cells_microabscess_progression_018

value: progression


title: Cardiomyocytes, EMPA_IR_2

value: Heart

value: Cardiomyocytes


title: Cardiomyocytes, Control_IR_5


title: patient_f_cd4cells_microabscess_nonprogression_001

value: nonprogression


title: Cardiomyocytes, EMPA_IR_1

value: Empagliflozin/Ischemia-Reperfusion


title: MH8-4 epididymal fat

value: HFD + metformin


title: patient_a_epidermis_nonprogression_016


title: MH8-2 epididymal fat


title: patient_c_epidermis_nonprogression_017


title: MH6-5 epididymal fat


title: patient_a_cd4cells_dermis_micro_nonprogression_015


title: patient_i_cd4cells_microabscess_progression_005


title: Cardiomyocytes, EMPA_IR_4


title: Neuroblastoma cell line, chick embryo during development, seqWell, E0, rep2

city: Lyon

first: Celine

last: Delloye-Bourgeois

address: 28 Rue Laennec

country: France

institute: Centre de Recherche en Cancerologie de Lyon

description: seqWell

data_processing:
Cells were multiplexed via dual index-strategy.
Bcl2fastq (v2.17.1.14) was used to generate one FASTQ file
Trimming process to remove the step of low-quality nucleotides and adapter sequences was carried out with the CutApapt software (v1.9.1)
Detection of cDNA contaminants was done with the FastQ Screen (v0.5.2)
Assembly: Sequenced libraries were mapped on pre-indexed GRCh38 human genome with ENSEMBL annotation (v93) through STAR software (v2.7) and 2-pass option
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol: Harvested tissue were kept on ice in F12 medium throughout the manipulation, then dissociated with type IV Collagenase (1.25 mg/ml, Sigma-Aldrich) and DNAse I (0.1 mg/mL, Sigma-Aldrich) for 10 min at 37°C followed by trypsin (2.9 mg/mL, Sigma-Aldrich) dissociation for 5 min at 37°C. The reaction was stopped with DMEM GlutaMAXTM (Life Technologies) supplemented with 10% Fetal Bovine Serum (FBS). Dissociated samples were frozen in DMEM containing 20% FBS and 10% DMSO.


title: MH4-3 epididymal fat


title: Cardiomyocytes, Control_IR_3


title: Neuroblastoma cell line, chick embryo during development, Smart-Seq2, E0, rep2


title: patient_a_cd4cells_dermis_nonprogression_015


title: H7-5 epididymal fat

value: HFD


title: Cardiomyocytes, EMPA_IR_3


title: patient_b_cd4cells_dermis_micro_nonprogression_014


title: Neuroblastoma cell line, chick embryo during development, Smart-Seq2, SG, rep1


title: H7-4 epididymal fat


title: Cardiomyocytes, Control_IR_1


title: patient_b_cd4cells_dermis_nonprogression_014


title: Cardiomyocytes, SHAM_4


title: H7-3 epididymal fat


title: Cardiomyocytes, SHAM_3


title: patient_b_epidermis_nonprogression_013

value: epidermis


title: H7-2 epididymal fat


title: Cardiomyocytes, Control_IR_4

value: Control/Ischemia-Reperfusion


title: patient_d_epidermis_progression_012


title: Cardiomyocytes, SHAM_2


title: TumorOrg.P25

description: Sase_processed_data_Gene_expression_cpm.txt

data_processing:
Real Time Analysis (RTA) software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using BWA (version 0.5.9) without changing any parameters from the default setting.
Unmapped reads were then mapped by HISAT2 (version 2.0.5) without changing any parameters from the default setting..
ReClu was used for peak-calling and calcutaion of Counts per million (CPM).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample.

source_name: Tongue tumor tissue

growth_protocol: Cell/Matrigel mixture was seeded and solidified, then tongue organoid medium was added to each well. Cells were cultured at 37°C with 5% CO2 and medium was changed every 3–4 days.

extract_protocol:
RNA was isolated from normal tissue, cncer tissue, normal tongue organoids, and cancer organoids using an RNeasy mini kit (Qiagen).
CAGE library preparation was performed by DNAFORM (Yokohama, Kanagawa, Japan). The first-strand cDNA was transcribed to the 5ʹ end of capped RNAs, attached to CAGE “bar code” tags.

treatment_protocol: Forty-eight hours after plating, 11 μM  cisplatin was added and cultured for 7 days.

tag: sample type

value: Organoid

tag: drug treatment


title: TumorTissue.P08

value: Primary tissue


title: TumorTissue.P13


title: patient_e_epidermis_progression_011


title: C2-2 epididymal fat

value: normal diet


title: TumorOrg.P21


title: Cardiomyocytes, Control_IR_2


title: C1-5 epididymal fat


title: 72 hr 3

city: Gainesville

first: Ley

middle: Cody

last: Smith

state: FL

address: 2187 Mowry Rd

institute: University of Florida

data_processing:
cDNA libraries were sequenced (75 bp single-ended, ~35-44M reads per sample) on an Illumina NextSeq instrument.
Raw reads in FastQ files were trimmed using Trimmomatic-0.39 and quality control of trimmed files performed using FastQC.
Salmon was used to align reads in mapping-based mode with selective alignment against a decoy-aware transcriptome generated from mouse transcriptome GENCODE Release M23 (GRCm38.p6).
Estimated counts per transcript were generated using the gcBias flag
Transcript level quantitation data was aggregated to the gene-level using tximport
Differential gene expression analysis was performed with air exposed mice as controls using DESeq2
Assembly: mouse transcriptome GENCODE Release M23 (GRCm38.p6)
Supplementary files format and content: CSV (comma-separated values) files that includes raw counts for each sample
Supplementary files format and content: .tar.gz files are Salmon output directories that contain individual quant.sf quantification files and associated meta data about processing

source_name: Lung

extract_protocol:
Cells were centrifuged and cell pellets resuspended in 1 mL Red Blood Cell Lysing Buffer Hybri-MaxTM (Product No R7767, Sigma-Aldrich, St. Louis, MO 63103) and incubated for 5 min at room temperature, then washed with HBSS supplemented with 2% FBS. Viable cells were enumerated using a hemocytometer with trypan blue dye exclusion. Total RNA was extracted from cells by phenol-chloroform extraction method using TRIzol RNA Isolation Reagent (Product No 15596026, ThermoFisher Scientific). Purified RNA was resuspended in 15 uL RNAsecureTM RNase Inactivation Reagent (Thermo Fisher Scientific) and stored at -80 °C.
RNA integrity numbers (RINs) were confirmed to be ≥ 8.8 using a 2100 Bioanalyzer Instrument (Agilent, Santa Clara, CA). cDNA libraries were prepared using mouse TruSeq® Stranded Total RNA Library Prep kit (illumina, San Diego, CA) and quantified using a KAPA Library Quantification kit (Roche, Pleasanton, CA).

value: Lung

value: Lung Macrophages

value: Wild type

value: Ozone


title: patient_e_cd4cells_dermis_micro_progression_010


title: C1-4 epididymal fat


title: TumorOrg.P18


title: patient_e_cd4cells_dermis_progression_010


title: Cardiomyocytes, SHAM_1

value: Sham


title: TumorOrg.P13


title: 72 hr 2


title: C1-1 epididymal fat


title: 72 hr 1


title: TumorOrg.P08


title: 24 hr 3


title: patient_d_basal_layer_progression_009

value: progression


title: patient_d_cd4cells_dermis_micro_progression_008


title: patient_d_cd4cells_dermis_progression_008


title: StsR_phototrophic_72h_rep3

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

description: Biologoical replicate 3

data_processing:
The software Curare v0.6 Blumenkamp et al., 2024)  was used for the differential gene expression analysis. The raw sequencing data was adapter trimmed and quality filtered (phred score < 20 filtered out) with fastp v0.23.4 (Chen et al., 2018 ). Afterward, the reads were aligned to the reference genome of R. sphaeroides (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2 and NC_009008.1) using bowtie2 v2.5.2 (Langmead and Salzberg)  and saved as binary alignment maps (BAM) with Samtools v1.18 (Danecek et al., 2021 ).
The differential gene expression analysis used subreads featureCounts v2.0.6 (Yang et al., 2014)  for counting and DESeq2 v1.40.2 (Love et al., 2014)  for the statistical analyses. Counting was done in featureCounts with "-s 1 -M --fraction" options on the "gene" level, and the NCBI GFF file for assembly GCF_000012905.2 was used as an annotation.
The alignments were summarized as bedgraph files using deeptools' v3.5.4 bamCoverage function [Ramirez et  al., 2016). The coverage data (bedgraph files) was normalized by dividing each data point/base position by the total read number in each sample. For the screenshots, the replicates of each condition were averaged by the arithmetic mean.
Assembly: Genome_build: GCF_000012905.2 ASM1290v2
Supplementary files format and content: count tabl/gene expression matrixe created with featureCounts in tab-separated format

organism: Cereibacter sphaeroides 2.4.1

source_name: chromosomal deletion of StsR encoding gene

growth_protocol: Independent biological triplicates of each strain were grown in malate minimal medium under microaerobic (~25 µM dissolved oxygen) or phototrophic (anaerobic and illuminated with 60 W per square meter) growth conditions to exponential or late stationary growth phase (72 hours).

extract_protocol:
Total RNA was isolated as published (Grützner et al., 2021, Nucelic Acids Res. 49(6), doi: 10.1093/nar/gkab146)
RNA was processed as published (Grützner et al., 2021, Nucleic Acids Res. 49(6), doi: 10.1093/nar/gkab146); NEBnext Multiplex Small RNA Library Prep Set

treatment_protocol: Cells were grown under microaerobic or phototrophic conditions and harvested during exponential or late stationary growth phase.

value: phototrophic growth to late stationary phase


title: TumorOrg.P08.CDDPResistant_Rep1

value: CDDP, 11 uM


title: TumorOrg.P03


title: 24 hr 2


title: StsR_phototrophic_72h_rep1

description: Biologoical replicate 1

value: chromosomal deletion of StsR encoding gene


title: StsR_microaerobic_72h_rep3

description: Biologoical replicate 3

value: microaerobic growth to late stationary phase


title: NormalTissue.P08

source_name: Normal tongue tissue


title: StsR_microaerobic_72h_rep2

description: Biologoical replicate 2


title: 24 hr 1


title: NormalTissue.P13


title: Air 3

value: Air


title: patient_c_basal_layer_nonprogression_003

value: nonprogression


title: TumorOrg.P08.CDDPResistant_Rep2


title: patient_a_cd4cells_microabscess_nonprogression_005


title: StsR_phototrophic_exp_rep2

description: Biologoical replicate 2

value: phototrophic growth to exponential phase


title: Air 2


title: Air 1


title: patient_c_cd4cells_dermis_micro_nonprogression_002


title: StsR_phototrophic_exp_rep3

description: Biologoical replicate 3


title: StsR_microaerobic_72h_rep1

description: Biologoical replicate 1


title: NormalOrg.P25


title: StsR_phototrophic_exp_rep1

description: Biologoical replicate 1


title: patient_e_basal_layer_progression_004


title: patient_c_cd4cells_dermis_nonprogression_002


title: patient_a_basal_layer_nonprogression_006


title: patient_d_cd4cells_microabscess_progression_007


title: Dopamine Treated Choroidal explant Sample 1

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

institute: Institut de la Vision

data_processing:
Fastq files obtained from the sequencing facility were trimmed using Trimmomatic v0.39 using the NexteraPE-PE adapter file. The paired reads were then aligned using STAR (v2.7.9a) against the mouse reference genome from Ensembl v106 (generated 2022/06/21), with option “--quantMode GeneCounts” to extract the raw counts for each gene, then all count files were concatenated into a single file.
A sample file was created with the sample data including the conditions (CTL, DOPA) and the replicate numbers. The count file and the sample file were loaded in our in-house R Shiny application EYE DV seq.
We added 1 to all counts in the count file to avoid any 0 read count errors. We then removed the genes having a total count < 10 across all samples. Finally the DESeq2 (v1.40.2) analysis was performed comparing the groups defined in the ‘condition’ column, with ‘CTL’ as control group and ‘DOPA’ as condition.
The results were then filtered for significant genes using the p-values (< 0,05). An enrichment analysis was performed to study the implicated pathways, using the Reactome database (using the Bioconductor package ‘ReactomePA’ (v1.44.0) and the GO database (using the Bioconductor packages ‘org.Mm.eg.db’ (3,10,0) and ‘clusterProfiler’ (v 4.8.1)).
Assembly: GRCm38 Ensembl release 106
Supplementary files format and content: Comma-separated file including raw counts for all Samples
Supplementary files format and content: Comma-separated file containing all Samples metadata

source_name: Choroidal explants

growth_protocol: Choroidal explants dissected from 2 week-old mice were embeded in matrigel and kept in culture in supplemented EGM2  (CC-3156 & CC-4176) for 3 days to allow vascular sprounting.

extract_protocol:
On day 4, choroidal explants were dissociated with collagenase, and CD31+CD11b- cells were sorted on a BD FACS melody cell sorter. Cells were immediatly flash frozen in in 96 well plates until library construction
Libraries were made from 500  sorted endothelial cells using smartseq V4 (Takara)

treatment_protocol: On day 3, choroidal explants were stimulated with 1 µM Dopamine

value: Choroidal explants

value: wt

value: Dopamine


title: Dopamine Treated Choroidal explant Sample 2


title: Control Choroidal explant Sample 3

value: Control


title: Dopamine Treated Choroidal explant Sample 3


title: NormalOrg.P21

value: Organoid


title: StsR_phototrophic_72h_rep2

description: Biologoical replicate 2


title: WT_D4_rep4

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

data_processing:
Sequenced reads were mapped to the Synechococcus elongates PCC7942 reference genome sequences using Rockhopper
The normalization and differentially expressed genes test were implemented by DESeq2.
Assembly: GCF_000012525.1_ASM1252v1
Supplementary files format and content: Excel file with all normalized counts for each sample

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: bacterial cell

extract_protocol:
Total RNA was extracted as previously described Simkovsky, R., et al. Front Microbiol, 2022. 13: p. 899150.
rRNA-depleted RNA (1 µg) was used for library construction using KAPA mRNA HYPER-PREP (KK8581) according to manufacturer's protocol, with a 7 cycles PCR (Kapa, Roche).

value: bacterial cell

value: wild-type


title: NormalOrg.P13


title: NormalOrg.P08


title: 158027 WT 24M H3K27me3

city: Hobart

first: Phillippa

middle: Claire

last: Taberlay

state: Tasmania

address: 17 Liverpool St

department: College of Health and Medicine

institute: University of Tasmania

data_processing:
Sequenced using HiSeq 2500 - mean read depth 13.9M H3K4me3, 16.2M H3K27ac.
Removed library tags.
Pseudoreplicates generated.
Mapped to MM10 using bowtie2.
bigwigs generated.
Assembly: MM10
Supplementary files format and content: Bigwigs

source_name: brain

extract_protocol:
Mice aged and samples collected at 3, 12, 24m, purified neurons extracted with FACS
Nugen Ovation Ultralow V2 library preparation - amplification for 17 cycles (H3K27ac), or 18 cycles (H3K4me3) 0347 V2 1-96/0344 V2 1-16.

value: brain

value: neurons

value: WT


title: WT_D1_rep4


title: patient_b_basal_layer_nonprogression_001


title: StsR_microaerobic_exp_rep3

description: Biologoical replicate 3

value: microaerobic growth to exponential phase


title: StsR_microaerobic_exp_rep2

description: Biologoical replicate 2


title: 158028 WT 24M H3K27me3


title: 158029 WT 24M H3K27me3


title: rne_phototrophic_72h_rep1

description: Biologoical replicate 1

source_name: rne(ts) strain (substitution of native rne gene with thermosensitive rne gene from E. coli)

value: phototrophic growth to late stationary phase


title: 157306 WT 12M H3K27me3


title: WT_D4_rep3


title: WT_D1_rep2