title: KO2

city: Shenzhen, Guangdong

first: Wenjing

last: Chen

address: XueYuan Road

institute: SUSTech

data_processing:
The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix.
The purified double_x0002_stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA_x0002_tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor_x0002_ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered
Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing.
The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).
Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Genome_build: mm9
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: bone marrow

extract_protocol:
Cells were sorted by FACS from bone marrow and RNA was harvested using Trizol reagent.    1 μg total RNA with RIN value above 6.5 was used for following library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Fr.C+C' B cells

value: 8-12 weeks

tag: geneotype

value: ADAR1 KO


title: gan1162

status: Public on Dec 31 2023

type: SRA

city: Chengdu

first: Linhao

last: Zhang

state: Sichuan

address: No. 37 Guoxue Lane

department: Gastroenterology

country: China

institute: West China Hospital, Sichuan University

description: 10X Genomics Chromium Controller

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: Mice were provided ad libitum access to normal diet with a 12-hour light/dark cycle at room temperature with constant humidity.

extract_protocol:
Freshly collected liver cells from mice were washed with DPBS, diced and then extracted using Liver Dissociation Kit (mouse) with gentleMACS Dissociator from Miltenyi Biotec according to the manufacturer's instructions. Then the resuspended samples were sequentially applied to 70μm and 30μm strainer. The red blood cells were lysed with Red Blood Cell Lysis Solution. Then, after washing, the isolated liver cells were centrifuged with 50g for 30 seconds to remove most of hepatocytes. Next, cells in supernatant were washed and re-suspended in DPBS. A small portion of the cells were used for checking viability by staining with a Viability Dye. Finally, cells were washed in DPBS, centrifuged and resuspended in RPMI1640 medium with 5% BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

treatment_protocol: A mouse model of liver fibrosis was established by intraperitoneal injection of thioacetamide (TAA) for 12 weeks, and 7.5 mg/kg celecoxib (C7.5) or 30 mg/kg celecoxib (C30) treatment was given orally by gavage started from 5th week of TAA injection to fibrotic mice.  Mice were allocated to the control group, TAA group, TAA+C7.5 and  TAA+C30 group with 1 in each according to the treatment. Hepatic nonparenchymal cells were isolated from one mouse for each group (control, TAA, TAA+C7.5, and TAA+C30 groups) and subjected to scRNA-seq.

tag: tissue

value: Liver

tag: strain

tag: age

value: 18-20 weeks old

tag: genotype

value: Wild type

tag: treatment

value: Thioacetamide+Celecoxib 30mg/kg


title: 966868-300_lib31086

city: Seattle

first: Naresh

last: Doni Jayavelu

state: WA

address: 1201 9th AVE

department: Systems Immunology/Bioinformatics

country: USA

institute: Benaroya Research Institute at Virginia Mason

library_source: transcriptomic

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Reads were aligned by STAR v2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2), and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: raw_counts_ITN_GRASS_nasal_samples.csv is a csv file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

organism: Homo sapiens

source_name: Nasal Brush

extract_protocol:
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.

value: Nasal Brush

tag: Sex

value: Female

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

tag: visit number

value: Placebo


title: gan1134

description: 10X Genomics Chromium Controller

value: Control (normal saline)


title: KO1


title: WT2

value: wild type


title: 958447-300_lib31084


title: 963018-300_lib31085


title: 970416-300_lib31083

value: SLIT


title: SetxKO testis, 16dpp, rep3

city: Bunkyo-ku

first: Yasuhiro

last: Fujiwara

address: 1-1-1 Yayoi

department: IQB

country: Japan

institute: The University of Tokyo

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic.
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR
Read count extraction and normalization were performed using RSEM
Assembly: mm10
Supplementary files format and content: text files include TPM values for each sample

source_name: testis

extract_protocol:
Testicular cell samples were resuspended in QIAzol Lysis Reagent according to the manufacturer's instructions, and total RNAs were purified from homogenized cells using Qiagen RNeasy Mini Kit.
The mRNA sequencing libraries were prepared using the Illumina TruSeq methodology. mRNAs were purified from total RNA using biotin tagged poly dT oligonucleo- tides and streptavidin coated magnetic beads. The mRNAs were then fragmented and double stranded cDNA was generated by random priming.

value: testis

tag: cell type

value: testicular cells

value: SetxKO


title: Liver 1384-L F

city: Bar Harbor

first: Kristen

last: O'Connell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

library_source: genomic

data_processing:
Mouse raw-reads from the 386 samples described above were quality and adapter trimmed with cutadapt v2.3 . Filtered trimmed reads were mapped with Bowtie2 v2.3.5 [PMID: 22388286]. For C57BL/6J samples, reads were mapped to GRCm38 release 98 (ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz). For all other DO founder strains (A/J, 129S1/SvlmJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ), reads were mapped to strain-specific pseudo-references. Pseudo-references for each strain were constructed with g2gtools v0.1.31 (http://churchill-lab.github.io/g2gtools) by patching GRCm38 release 98 with strain-specific SNPs and Indels from the Mouse Genome Project [PMID: 21921910] REL-1807 (ftp://ftp-mouse.sanger.ac.uk/REL-1807-SNPs_Indels/). Mapped reads were filtered to remove PCR duplicates, mtDNA, and the following classes of reads: unmapped, mate unmapped, and non-primary alignment. DeepTools alignmentSieve v3.3.2 [PMID: 27079975] was used to offset all reads aligning to the positive strand by +4bp, and all reads aligning to the negative strand by -5bp to account for Tn5 transposase activity [PMID: 24097267 , PMID: 21143862]. Alignments from non-C57BL/6J samples were then lifted to GRCm38 coordinates with g2gtools. Peak calling was conducted on all pooled alignment files with Macs2 v2.2.7.1 [PMID: 22936215].
Assembly: mm10
Supplementary files format and content: narrowPeak : called peaks of signal enrichment, bed : peaks count matrix, bigwig : read coverage track

molecule: genomic DNA

source_name: liver

extract_protocol:
Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit (28204).
Adipose, liver, and muscle ATAC libraries were constructed as previously described  [PMID: 27526324] with a few exceptions. Briefly the protocol entails pelleting and washing cells in cold PBS, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) with the addition of 0.01% digitonin (2x TDE for adipose), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche). Islet ATAC libraries were constructed as previously described [PMID: 34491912] with a few exceptions. Briefly the protocol entails pelleting and washing approximately islets in cold PBS, incubating in ATAC lysis buffer, trituration with 25-gauge needle, centrifugation to generate crude nuclei pellet, washing in ATAC lysis buffer, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche).
All libraries were sequenced 100 bp paired end on an Illumina NovaSeq 6000.

treatment_protocol: Male and female mice of each CC founder strain were fed high fat high sugar 45% kcal fat plus 1360% kcal sucrose (Research Diets D19070208) or isocaloric control 10% kcal fat plus 0% kcal sucrose (Research Diets D19072203) diets for 9 weeks prior to tissue harvest and processing for ATAC-seq.

value: liver

value: NOD/ShiLtJ

value: Liver - liver left lobe

value: female


title: Liver 1387-L M

value: male


title: Liver 1388-L M


title: WT1

value: Fr.C+C' B cells

value: 8-12 weeks


title: Liver 1382-L M


title: Liver 1385-L F


title: Liver 1381-L M


title: VDR_NVDIP

city: Marseille

first: michel

last: PUCEAT

address: 27 bd Jean moulin

department: University aix marseille

country: France

institute: INSERM

data_processing:
Fastq files were aligned to the mouse (mm10) reference genome, PCR duplicates were removed using Samtools and normalized genome coverage tracks were generated from uniquely mapping reads (mapq > 30) using deepTools2.
Single-end reads, unmated reads, mate reads that map too far apart (> 4x fragment length) were extended by 200bp. Biological replicates were pooled and coverage was then calculated as average reads per million of mapped reads (RPM) in 10bp bins. To determine the peaks for ChIPs with narrow binding profiles, datasets were uniformly processed using the MACS2 with default parameters.
Genome_build: mouse mm10
Supplementary_files_format_and_content: txt include the narrow peaks

source_name: embryonic heart

extract_protocol: none provided by the submitter

value: left ventricle  from mother with Vitamin D deficient diet

tag: developmental stage

value: E16.5 embryo


title: Liver 1386-L F


title: SetxKO testis, 14dpp, rep4


title: SetxKO testis, 16dpp, rep1


title: SetxKO testis, 16dpp, rep2


title: SetxKO testis, 14dpp, rep3


title: SetxKO testis, 14dpp, rep2


title: 962946-300_lib31081

value: Nasal Brush

value: Female


title: SetxKO testis, 14dpp, rep1


title: 966798-300_lib31082


title: Liver 1380-L M


title: 958480-300_lib31080


title: SetxKO testis, 12dpp, rep3


title: SetxKO testis, 12dpp, rep4


title: 966874-300_lib31079

value: Male

value: Placebo


title: SetxKO testis, 12dpp, rep2


title: Liver 1378-L F


title: Liver 1379-L F


title: 958666-300_lib31077


title: Liver 1377-L F


title: 962978-300_lib31078


title: VDRIP

value: left ventricle  from mother with normal diet


title: SetxKO testis, 12dpp, rep1

value: testis


title: Liver 1375-L M

value: NZO/HlLtJ


title: 970479-300_lib31076

value: SCIT


title: SetxKO testis, 10dpp, rep2

value: testicular cells

value: SetxKO


title: MEKi_1w_rep1

city: Milano

first: Pietro

last: Delfino

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

description:
sample name:
s21

data_processing:
Sequence pairs were mapped to mouse genome GRCm38, using the STAR 2.5.3a software and the annotations retrieved from gencode vM16. Raw counts were normalized using DESeq2 v1.18.1 rlog function. The first principal component of the mean-adjusted gene expression matrix was strongly associated with acini contamination. The contamination was confirmed by reviewing cryostat sections of the corresponding specimens; therefore, this component was removed using SVD factorization and recomposition.
Genome_build: GRCm38
Supplementary_files_format_and_content: A single file containing vst normalized counts from each sample with gene symbols in row.

source_name: pancreas tumor_MEKi

extract_protocol:
RNA was extracted from freshly isolated tissues (isografts) using TRIzol (Invitrogen), followed by column-based purification with the PureLink RNA Mini Kit (Ambion)
The quality of purified RNA samples was determined using a Bioanalyzer 2100 (Agilent) with an RNA 6000 Nano Kit. RNAs with RNA Integrity Number (RIN) values greater than 7.5 were used to generate sequencing libraries using the TruSeq Stranded Total RNA Kit (Illumina) per manufacturer’s instructions. Sequencing libraries were run at Eurofinsgenomics using an Illumina HiSeq2000.

value: pancreas tumor


title: Ctrl_rep4

description:
sample name:
s20

source_name: pancreas tumor_control


title: 970461-300_lib31074


title: Ctrl_rep2

description:
sample name:
s18


title: MEKi_1w_rep4

description:
sample name:
s24


title: MEKi_1w_rep2

description:
sample name:
s22


title: Liver 1374-L M

value: liver

value: Liver - liver left lobe


title: Liver 1373-L M

value: male


title: Ctrl_rep1

description:
sample name:
s17


title: Liver 1202-L M


title: MEKi_1w_rep3

description:
sample name:
s23


title: 966840-300_lib31073


title: SetxKO testis, 10dpp, rep4


title: Liver 1201-L M


title: Ctrl_rep3

description:
sample name:
s19


title: WT-Col-0, Cesium (Cs), 0.5 mM KCl +0.3mLCsCl bio rep 3

city: Yokohama

first: Wen Dee

last: Ong

state: Kanagawa

address: 1-7-22 Suehiro-cho

institute: CSRS RIKEN

data_processing:
Low-quality reads were filtered using Bowtie 2 version 2.3.4.1.
Clean reads were subsequently mapped to the Arabidopsis TAIR10 genome using STAR_2.5.0c with default parameters.
FPKM values of protein-coding genes were calculated using Cufflinks v2.2.1
Assembly: Arabidopsis TAIR10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Plants were placed in a growth cabinet with a constant temperature (22°C) and a light intensity of 70–90 mmol m–2s –1. A 16 h light/8 h dark photoperiod was applied throughout all experimentation.

extract_protocol:
Total RNA was isolated using the Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
cDNA libraries were prepared using strand-specific transcriptome library construction following manufacturer's protocols.

treatment_protocol: Seed were sown on medium containing 2 mM Ca(NO3)2, 0.5 mM phosphoric acid, 0.75 mM MgSO4, 50 mM H3BO3, 10 mM MnCl2, 2 mM ZnSO4, 1.5 mM CuSO4, 0.075 mM NH4Mo7O24 and 74 mM Fe-EDTA was adjusted to pH 5.8 with Ca(OH)2 prior to the addition of 1% (w/v) sucrose and 1% (w/v) of SeaKem agarose (Lonza). For the low potassium stress experiment, medium was supplemented with 0.025 mM KCl, whereas 0.5mM KCl was supplemented for the control medium.

value: root

value: WT

value: 0.5 mM KCl +0.3mLCsCl


title: wt testis, 18dpp, rep4


title: Liver 1197-L F

value: female


title: 958479-300_lib31071

value: Nasal Brush


title: 958653-300_lib31075

value: Male


title: SetxKO testis, 10dpp, rep3


title: WT-Col-0, Cesium (Cs), 0.5 mM KCl +0.3mLCsCl bio rep 2


title: Liver 1185-L M

value: PWK/PhJ


title: wt testis, 18dpp, rep2


title: SetxKO testis, 10dpp, rep1


title: wt testis, 18dpp, rep3


title: WT-Col-0, Cesium (Cs), 0.5 mM KCl +0.3mLCsCl bio rep 1


title: wt testis, 18dpp, rep1


title: WT-Col-0, low K (K) 0.025 mM KCl bio rep 2

value: 0.025 mM KCl


title: 970449-300_lib31070

value: Female

value: SLIT


title: 970473-300_lib31068

value: Placebo


title: WT-Col-0, low K (K) 0.025 mM KCl bio rep 3


title: Liver 1164-L M

value: WSB/EiJ


title: WT-Col-0, low K (K) 0.025 mM KCl bio rep 1


title: 966850-300_lib31069


title: 963022-300_lib31067


title: wt testis, 16dpp, rep3

value: testis

value: testicular cells


title: 963007-300_lib31072

value: SCIT


title: Liver 1163-L M

value: liver

value: Liver - liver left lobe


title: wt testis, 16dpp, rep4


title: Liver 1160-L F


title: WT-Col-0, control (C), 0.5 mM KCl bio rep 3

value: root

value: 0.5 mM KCl


title: wt testis, 16dpp, rep2

value: WT


title: 958672-300_lib31066


title: Liver 1159-L M

value: CAST/EiJ

value: male


title: wt testis, 16dpp, rep1


title: WT-Col-0, control (C), 0.5 mM KCl bio rep 2


title: WT-Col-0, control (C), 0.5 mM KCl bio rep 1


title: Liver 1158-L M


title: 970431-300_lib31065

value: Nasal Brush


title: wt testis, 14dpp, rep4


title: 966878-300_lib31064


title: wt testis, 14dpp, rep3


title: Liver 1157-L M


title: wt testis, 14dpp, rep2


title: Liver 1154-L M

value: A/J


title: Liver 1162-L M


title: 970467-300_lib31061

value: Male


title: 959034-300_lib31062

value: Female


title: Liver 1153-L M


title: 962992-300_lib31063


title: Liver 1147-L M


title: wt testis, 14dpp, rep1


title: wt testis, 12dpp, rep4


title: Liver 1144-L F

value: female


title: 966873-300_lib31060


title: 962987-300_lib31059


title: Liver 1143-L M

value: NZO/HlLtJ


title: wt testis, 12dpp, rep3


title: wt testis, 12dpp, rep2


title: wt testis, 12dpp, rep1


title: Liver 1142-L M


title: MLS_1765-92_3D_4

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

data_processing:
Alignment was performed using STAR version 2.6 using the ENSEMBL GRCh38 assembly reference genome
Gene expression was quantified using HTseq python framework version 0.9.1
MLS_2645-94_2D_3.1 and MLS_2645-94_2D_3.2 were sequenced from the same sample and were collapsed as technical replicates after read count, before downstream analysis. The collapsed sample is referred to as MLS_2645-94_2D_3_collapsed in the read count file.
Assembly: ENSEMBL GRCh38
Supplementary files format and content: Excel file containing matrix of unnormalized reads mapped to each transcript as a result from HTseq analysis.

source_name: Myxoid liposarcoma cell line

growth_protocol:
For monolayer culture, RPMI Glutamax cell culture media was supplemented with 5% or 10% fetal bovine serum, 100U/ml penicillin and 100 mg/ml streptomycin. Stable expression of EGFP constructs were maintained by addition of 500µg/ml Geneticin.
For scaffold culture, tumor pieces retrieved from a myxoid liposarcoma patient-derived xenograft model were decellularized using detergent wash. The scaffolds were cut into small pieces and added to 48-well culture plates. 3x105 cells were added onto the scaffold in 0.5ml complete media and cultured for 21 days before harvesting for downstream analysis. Scaffold pieces were transferred to new wells with fresh media if cells were growing outside the scaffold area.

extract_protocol:
Scaffold samples were lysed in RLT lysis buffer and homogenized in a Qiagen TissueLyzer II using stainless steel beads. 2D samples were lysed in RLT lysis buffer or QIAzol lysis buffer. RNA was extracted from all samples using Qiagen RNeasy micro kit or miRNeasy micro kit, including DNase treatment.
The library was generated using the Smart-seq2 protocol (Picelli, Faridani et al. 2014) with some modifications.

tag: cell line

tag: transfected gene

tag: culture method

value: Scaffold culture


title: 958668-300_lib31058

tag: tissue


title: 970406-300_lib31057


title: wt testis, 10dpp, rep4

value: testis


title: 966854-300_lib31056


title: Liver 1141-L F

tag: strain


title: MLS_1765-92_3D_3


title: 957229-300_lib31054

tag: age


title: MLS_1765-92_3D_2


title: wt testis, 10dpp, rep2

value: testicular cells

tag: genotype


title: wt testis, 10dpp, rep3


title: MLS_1765-92_3D_1


title: Liver 1140-L F

tag: treatment


title: Liver 1138-L F

tag: Sex


title: Endothelial cells_52KO

type: RNA

city: Oslo

first: Monika

last: Szymanska

address: Songsvannsveien 20

department: Pathology

country: Norway

institute: Oslo University Hospital

description: Gene expression data from IL-33 knock-out rat

hyb_protocol: 2.3 ug of final target were hybridized for 16 hr at 45∘C to Clariom S rat Array in Gene Chip Hybridization Oven 645. The arrays  were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G

data_processing: The data were processed with Affymetrix Expression Console SST-RMA

label: biotin

organism: Rattus norvegicus

source_name: Endothelial cells isolated from dermal blood vessels

label_protocol: Fragmented and biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (WT Plus labeling protocol Affymetrix).

growth_protocol: Rat abdominal skin from three IL-33 knock-out and three wildtype animals was exercised (weight 2-2.5g)

extract_protocol: Isolation of total RNA was performed using Qiagen RNeasy Plus Micro kit according to the manufacturer's instructions.

treatment_protocol: Skin pieces were subjected to mechanical and enzymatic digestion protocol (2hrs incubations with Collagenase I and DNAseI at 37∘C with rotation). To isolate blood vessel endothelial cells, single cell suspensions were subjected to magnetic-activated cell sorting, sequentially depleting non-endothelial CD45+ cells and Lyve-1+ lymphatic endothelial cells. Finally, cells expressing CD31 (an endothelial cell marker) were positively selected and subjected to RNA isolation.

value: endothelial cells

value: Dermal blood vessels

value: IL-33 knock-out

value: Sprague-Dawley


title: Endothelial cells_37WT

description: Gene expression data from wild type rat

value: wildtype


title: Endothelial cells_45WT

description: Gene expression data from wild type rat


title: Endothelial cells_28KO


title: MLS_2645-94_3D_4


title: wt testis, 10dpp, rep1

value: WT


title: Endothelial cells_27KO


title: Liver 1137-L F

value: liver

value: Liver - liver left lobe


title: Endothelial cells_34WT

description: Gene expression data from wild type rat


title: C57BL/6  NRK-2 KO

city: Sharjah

first: Hezlin

last: Marzook

state: Sharjah

address: University city

department: Sharjah Institute of Medical Research

country: United Arab Emirates

institute: University of Sharjah

data_processing:
Bowtie2 splice-aware aligner
Sequence reads were trimmed for adaptor sequence/low-quality sequence, aligned to UCSC mm10 reference genome with HISAT2
Assembly: mm10
Supplementary files format and content: txt file with FPKM values for each Sample

source_name: Remote LV tissues

extract_protocol:
Total RNA was isolated from remote LV tissues after exclusion of the fibrotic scar and border area using RNeasy kit (Qiagen)
TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E

treatment_protocol: NRK-2 KO and littermate control male mice were subjected to permanent ligation of proximal left anterior descending (LAD) coronary artery

value: male

value: Remote LV tissues

value: NRK-2 KO

value: Permanent ligation of proximal LAD coronary artery

tag: time

value: 7 days


title: 970444-300_lib31053

value: Nasal Brush

value: Male

tag: fastq total_reads

tag: percent aligned

value: SLIT


title: MLS_2645-94_3D_3

value: Scaffold culture


title: 966849-300_lib31052

tag: aligned counts_in_millions

tag: median cv_coverage


title: C57BL/6  Control

value: Control


title: 962982-300_lib31051

tag: participant id

tag: visit number


title: Liver 1139-L F

value: NZO/HlLtJ

tag: cell type

value: female


title: Liver 1054-L M


title: MLS_2645-94_3D_1

tag: cell line


title: Liver 1043-L M

value: A/J


title: hypothalamus_T1_T3

city: Seoul

first: Yanuar

middle: Alan

last: Sulistio

address: Wangsimni-ro 222

department: Biomedical Science

country: South Korea

institute: Hanyang University

data_processing:
Cellranger v5.0.1 used to performs alignment,  filtering, barcode counting, and UMI counting.
Assembly: GRCh38
Supplementary files format and content: CellRanger output file of count matrix

molecule: nuclear RNA

source_name: whole hypothalamus

extract_protocol:
Frozen mouse whole hypothalamus from aging mice dissociated with EZ nucleus isolation kit
Chromium Next GEM Single Cell 3p RNA library v3.1

value: whole hypothalamus

value: Transplanted


title: 958474-300_lib31049

value: Placebo


title: 959035-300_lib31050


title: Liver 1041-L F

value: liver

value: Liver - liver left lobe


title: HT1080_FUS-DDIT3-EGFP_2D_3

description: Also included in GEO series GSE125941 with sample accession GSM3585521

source_name: Fibrosarcoma cell line

tag: transfected gene

value: Adherent 2D culture


title: HT1080_FUS-DDIT3-EGFP_2D_2

description: Also included in GEO series GSE125941 with sample accession GSM3585520

tag: culture method


title: HT1080_FUS-DDIT3-EGFP_2D_1

description: Also included in GEO series GSE125941 with sample accession GSM3585519


title: 970453-300_lib31048

tag: tissue

value: Female

value: SCIT


title: ATAC ApcDHep rep 12

city: Paris

first: Angelique

last: Gougelet

address: 15 rue de l'école de médecine

institute: INSERM U1138

data_processing:
Illumina RTA 1.18.64 (Hiseq2500)  and bcl2fastq Conversion Software v2.20 was used for basecalling and demultiplexing.
ATAC-seq reads were aligned to the mm9 genome assembly using bowtie2 the -X  2000 parameter
Bam were reordered and PCR duplicates removed using samtools
BigWig were generated using bamCoverage command from deepTools with the following parameters : --binSize 10 --normalizeUsing RPKM --extendReads
Assembly: Mus_musculus mm9
Supplementary files format and content: BigWig

source_name: mouse ApcDHep hepatocytes

extract_protocol: Transposition was performed on 50,000 hepatocytes with 4,5 L Tn5 and digitonin 0.1%

treatment_protocol: ATAC-seq profiles from hepatocytes isolated from  ApcDHep livers by perfusion with collagenase in three-month old mice injected  with tamoxifen for 7 days

tag: cell types

value: mouse  hepatocytes

tag: strain

value: tamoxifen 2mg 7 days


title: HT1080_EGFP_2D_4

description: Also included in GEO series GSE125941 with sample accession GSM3585518

value: EGFP


title: 966841-300_lib31047

value: Nasal Brush

tag: age


title: 963012-300_lib31046

tag: treatment


title: Liver 1136-L F

tag: Sex


title: Liver 1037-L F

value: PWK/PhJ


title: HT1080_EGFP_2D_3

description: Also included in GEO series GSE125941 with sample accession GSM3585517


title: Liver 1034-L M

value: male


title: ATAC ApcDHep rep 1


title: MLS_2645-94_3D_2

value: Scaffold culture


title: 958488-300_lib31045


title: ATAC wt rep 2

source_name: mouse wt hepatocytes


title: HT1080_EGFP_2D_2

description: Also included in GEO series GSE125941 with sample accession GSM3585516


title: Liver 1033-L M


title: hypothalamus_T4


title: ATAC wt rep 1


title: Liver 1029-L M

value: CAST/EiJ


title: hypothalamus_C1_C2

value: Control


title: Liver 1035-L F

value: female


title: hypothalamus_C4

value: whole hypothalamus


title: 962957-300_lib31042

value: Placebo


title: HT1080_WT_2D_4

description: Also included in GEO series GSE125941 with sample accession GSM3585514


title: Liver 1030-L M

value: liver


title: 966824-300_lib31043


title: 970481-300_lib31044


title: 958445-300_lib31041


title: HT1080_WT_2D_3

description: Also included in GEO series GSE125941 with sample accession GSM3585513


title: G370_11

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

description:
G370_11
controls  replicate2

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.20.0) allowing no mismatches in the index read. For mRNA-seq, BBDuk was used to trim/filter low-quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the mouse reference genome (mouse Ensembl release 67 (GRCm37 / NCBIM37 / mm9)) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (release 67: "Mus_musculus.Ensembl.NCBIM37.67.gtf"). For microRNA-seq, sequencing reads were subjected to quality filtering, quality trimming and adapter trimming by FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit), conducted by fastq_quality_filter function, fastq_quality_trimmer function, and fastq_clipper function, respectively, 4 bases were trimmed from both 5’ and 3’ ends of the sequencing reads by fastq_trimmer function. Oasis 2.0 suite (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2047-z) was used to align and count raw reads of all expressed small RNAs.
Assembly: mouse Ensembl release 67 (GRCm37 / NCBIM37 / mm9)
Supplementary files format and content: csv file containing raw read counts for each sample ("EG_merged.HTSeq.out.csv" for mRNA-seq, "EGmicro.out.csv" for microRNA-seq)

source_name: 120 hour_cont_2

growth_protocol: Mice were purchased from Jackson laboratory and housed in a room with an ambient temperature of 25 C, 30–70% humidity, a 12-h light–dark cycle, and ad libitum access to rodent chow

extract_protocol:
Animal was sacrificed, decapitated and brain was removed from skull. Hippocampus isolation was done  in PBS, right and left halves of hippocampus were flash frozen.Total RNA isolation waswere carried out from the leftfrom left hippocampus with Trizol reagent (15596018, Ambion, Carlsbad, CA, USA) as described in the vendor’s manual. The quality of RNA was assessed on an Agilent Bioanalyzer and confirmed fof their samples with RNA integrity numbers were between greater than 7.9.
For mRNA-seq, the libraries were prepared using the Illumina® Stranded mRNA Prep, Ligation kit (Illumina) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique dual index sequences (IDT® for Illumina® RNA UD Indexes Set A, Ligation, Illumina) were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). For microRNA-seq, the libraries were prepared using the NEXTflexTM Small RNA Library Prep Kit v3 (BioO Scientific) as per the manufacturer's instructions. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
The denatured libraries were loaded onto an S1 flow cell on a NovaSeq 6000 or a Rapid flow cell on a HiSeq2500 (Illumina) and run for 2X53 cycles (for mRNA-seq) or for 1X49-65 cycles (for microRNA-seq) according to the manufacturer's instructions.

treatment_protocol: C57BL/6j male and female mice 6-7weeks old   injected intraperitoneal  with pilocarpine (350 mg/kg) or vehicle (0.9% bacteriostatic sodium chloride)

value: adult 6-7 weeks

value: hippocampus

tag: molecule subtype

value: micro-RNA

tag: time

tag: batch


title: G370_9

description:
G370_9
pilocarpine seizure replicate 1

source_name: 120 hour seizure_1

value: Pilocarpine


title: HT1080_WT_2D_2

description: Also included in GEO series GSE125941 with sample accession GSM3585512

value: Adherent 2D culture


title: 970458-300_lib31040

value: Male

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

value: SLIT


title: Liver 1025-L F

value: Liver - liver left lobe


title: 966870-300_lib31039

value: Nasal Brush

tag: median cv_coverage

tag: participant id

tag: visit number


title: G370_7

description:
G370_7
pilocarpine seizure replicate 2

source_name: 24 hour seizure_2


title: HT1080_EGFP_2D_1

description: Also included in GEO series GSE125941 with sample accession GSM3585515

tag: cell line

tag: transfected gene

value: EGFP


title: 963020-300_lib31038

source_name: Nasal Brush

tag: tissue


title: Liver 1020-L F

tag: cell type


title: G370_12

description:
G370_12
pilocarpine seizure replicate 2

source_name: 129 hour seizure_2


title: 963017-300_lib31037

value: Female

value: SCIT


title: G370_8

description:
G370_8
controls  replicate2

source_name: 24 hour_cont_2


title: H99, DSF, B3

city: Nanjing

first: Min

last: Peng

state: Jiangsu

address: No. 305 Zhongshan East Road, Xuanwu District, Nanjing, Jiangsu Province, China 210002

institute: Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China

data_processing:
Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4 . PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 1.5 or foldchange < 0.67 was set as the threshold for significantly differential expression gene (DEGs).
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

organism: Cryptococcus neoformans

source_name: Cryptococcus neoformans

growth_protocol: The PBS-washed H99 solution was inoculated in fresh YPD at a final concentration of 1×106 CFU/mL for 4 h.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, US
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: Control and disulfiram (4 μg/mL) groups were prepared.

value: Cryptococcus neoformans

tag: genotype

value: VNI, serotype A

value: treated with 4 μg/mL of disulfiram  for 4h


title: H99, DSF, B1


title: G370_6

description:
G370_6
pilocarpine seizure replicate 1

source_name: 24 hour seizure_1

tag: age


title: Liver 1024-L F

source_name: liver

tag: strain

value: CAST/EiJ

value: female

tag: treatment


title: H99, DSF, B2


title: 959033-300_lib31036

tag: Sex


title: 970398-300_lib31035


title: H99, Control, A2

value: Control


title: Liver 1015-L M

value: liver

value: male


title: Liver 1016-L M


title: G370_10

description:
G370_10
controls  replicate1

source_name: 120 hour_cont_1

value: adult 6-7 weeks

value: hippocampus

tag: molecule subtype

value: micro-RNA

tag: time


title: 966847-300_lib31034

tag: fastq total_reads


title: H99, Control, A3


title: HT1080_WT_2D_1

description: Also included in GEO series GSE125941 with sample accession GSM3585511

tag: culture method

value: Adherent 2D culture


title: H99, Control, A1


title: Liver 1021-L F

value: Liver - liver left lobe


title: Liver 1019-L F


title: G370_2

description:
G370_2
pilocarpine seizure replicate 1

source_name: 1 hour seizure_1

value: Pilocarpine

tag: batch


title: G370_4

description:
G370_4
pilocarpine seizure replicate 2

source_name: 1 hour seizure_2


title: 962999-300_lib31033

value: Nasal Brush

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage


title: Liver 1014-L F


title: Liver 1013-L F


title: 958481-300_lib31032

value: Female

tag: participant id

tag: visit number


title: G370_3

description:
G370_3
controls  replicate2

source_name: 1 hour_cont_2

tag: tissue


title: 962929-300_lib31055

value: Male

value: SCIT


title: Liver 1018-L M

tag: cell type


title: RNAPII_ChIP_tfIIS_10min_rep2

city: Regensburg

first: Simon

last: Obermeyer

address: Universitätsstraße 31

country: Germany

institute: University Regensburg

data_processing:
Reads were aligned to the TAIR10 genome using Bowtie2 and coverage tracks were calculated with deeptools “bamCoverage”. Downstream analysis was mainly performed using the deepTools2 suite (version 3.5.0) and quality control was performed at several steps using FastQC. Genomic regions with aberrant coverage or low sequence complexity were filtered out, as previously described (Quadrana et al., 2016). After confirming high pairwise correlations, the biological replicates were merged and CPM normalised.
Macs3 callpeak was used to call peaks in tfiis-1 over Col-0 as control. The summits of the resulting peak files were converted to .bw tracks using deeptools bedGraphToBigWig.
Assembly: TAIR10
Supplementary files format and content: .bed files of MACS3 called summits of RNAPII ChIP-Seq in Col-0 with tfiis-1 as background and vice versa

source_name: seedlings

extract_protocol:
Arabidopsis plants (14 days after stratification, 14-DAS in vitro grown) were crosslinked with formaldehyde and used for isolation of nuclei, before chromatin was sheared using a Bioruptor pico device (Diagenode). Immunoprecipitation was performed using antibodies directed against S2P-modified (Ser2-phosphorylated heptapeptides of the carboxy-terminal domain of NRPB1) RNAPII (abcam, ab5095).
Sequencing libraries were made using the NEBnext UltraII library prep kit with 9 PCR cycles

value: seedlings

tag: genotype

value: 10’ heat shock


title: Liver 1012-L F


title: RNAPII_ChIP_tfIIS_10min_rep1


title: G370_1

description:
G370_1
controls  replicate1

source_name: 1 hour_cont_1

tag: age


title: G370_5

description:
G370_5
controls  replicate1

source_name: 24 hour_cont_1


title: 970462-300_lib31031

value: Placebo


title: Islet 967-I M

source_name: islet

value: islet

tag: strain

value: PWK/PhJ

value: Islet - islets of Langerhans


title: 966858-300_lib31030

tag: treatment


title: RNAPII_ChIP_Col0_10min_rep3


title: RNAPII_ChIP_tfIIs_10min_INPUT


title: Islet 966-I M

tag: Sex

value: male


title: Neural retina ChIP-seq_COUP-TFI

city: Shanghai

first: Ran

last: Wang

address: 320 Yue Yang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

description: ChIP-seq for COUP-TFI in neural retina cells.

data_processing:
The quality of the reads was evaluated using the FASTQC tool.
Raw reads were mapped to mm10 version of mouse genome using bowtie2 (version: 2.3.1) program.
Enriched peaks were identified using HOMER (version 4.2) program with default parameters.
The enrichment tags were visualized using Integrative Genomics Viewer (IGV, version 2.4).
Genome_build: mm10
Supplementary_files_format_and_content: 2 bedGraph files for visualization, 1 textfile includes all binding peaks.

source_name: Neural retina cells

growth_protocol: The wildtype neural retina was obtained from the E14.5 embryos and then transferred into a 15 ml tube which contained 10 ml DMEM: F12 medium with 10% FBS and 550 µl the 18.5% PFA.

extract_protocol:
The tissues were collected by centrifugation at the speed of 800 xg for 5 minutes at 4°C.
The ChIP assays were performed with an EZ ChIP Chromatin Immunoprecipitation Kit (Millipore) by following the manufactory’s protocol.

treatment_protocol: Samples were mixed and racked for 15 minutes at RT. Next, 1ml of 10× glycine was added into this tube, and racked for 15 minutes at RT. By low-speed centrifuge, the tissues were collected. After a rinse with 10 ml cold 1× PBS, the tissues were resuspended and then transferred into a 1.5 ml tube

tag: chip antibody

value: Anti-COUP-TFI


title: RNAPII_ChIP_Col0_10min_rep2


title: DC_rATB (rATB treatment)

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

country: Taiwan

institute: China Medical University

data_processing:
RNA-Seq libraries were prepared Illumina® TruSeq RNA Library Prep Kit v2 and were sequenced using Illumina® Hiseq2500 to obtain 150-bp paired-end reads.
The sequencing depth for each sample was >20 million reads. The reads were aligned with TopHat 2.0.13 to GRCh37 with default parameters and then were assembled by Cufflink 2.2.1,
using Ensembl v75 annotations. Transcript abundance was measured in fragments per kb of exon per million fragments mapped (FPKM).
Genome_build: GRCh37
Supplementary_files_format_and_content: txt

source_name: primary murine bone marrow-derived dendritic cells

growth_protocol: Bone marrow cells from mouse femurs and tibias were first depleted of red cells using lysis buffer. Cells were placed in 24-well plates, each having 1 mL of RPMI-1640 medium supplemented with 5 % fetal bovine serum, 500 U/mL recombinant murine granulocyte-macrophage colony-stimulating factor (GM-CSF) (Pepro Tech Inc., Rocky Hill, NJ, USA), 4 mM L-glutamine, 25 mM HEPES (pH 7.2), 50 μM 2-mercaptoethanol, 0.25 μg/mL amphotericin, 100 U/mL penicillin, and 100 μg/mL streptomycin. Contamination by macrophages was minimized by replacing the culture medium with fresh medium containing GM-CSF and transferring non-adherent cells to a new plate on each alternate day. On day 6 of culturing, BM-DCs, which were the non-adherent cells, were collected and treated with rATB fragments for 48 h. BM-DCs were then analyzed by flow cytometry to examine their surface marker expression and used for subsequent experiments.

extract_protocol:
Total RNA was extracted using TRIzol reagent.  RNA integrity was determined using the RNA6000 Nano kit on the Agilent 2100 Bioanalyzer .
RNA-seq libraries were prepared using Illumina® TruSeq RNA Library Prep Kit v2 and were sequenced using Illumina® Hiseq2500 to obtain 150-bp paired-end reads.

treatment_protocol: BM-DCs  were treated with or without 800ng/ml for 48 hr.

tag: cell line

value: primary

value: rATB

tag: dose


title: Islet 964-I F

value: A/J

value: female


title: Islet 963-I F


title: RNAPII_ChIP_tfIIS_10min_rep3


title: NC2 (Ctrl)

value: ctrl


title: RNAPII_ChIP_Col0_10min_rep1


title: 966876-300_lib31026

value: Nasal Brush

tag: fastq total_reads


title: b2 (buffer Ctrl)

value: buffer


title: 962967-300_lib31029

value: Female


title: RNAPII_ChIP_Col0_10min_INPUT


title: Islet 962-I F


title: Liver 1011-L F

value: liver

value: Liver - liver left lobe


title: 962928-300_lib31025

value: SCIT


title: 957249-300_lib31024


title: RNAPII_ChIP_tfIIS_3h_rep3

value: seedlings

value: 3h heat shock


title: Islet 960-I M

value: islet


title: RNAPII_ChIP_tfIIS_3h_rep2


title: 970440-300_lib31023

value: Male


title: 966832-300_lib31022


title: Islet 891-I M

value: WSB/EiJ

value: Islet - islets of Langerhans

value: male


title: Islet 892-I M


title: Islet 890-I M


title: RNAPII_ChIP_Col0_3h_rep2


title: 957227-300_lib31020


title: RNAPII_ChIP_tfIIs_3h_INPUT


title: RNAPII_ChIP_Col0_3h_rep1


title: Islet 889-I F


title: 958471-300_lib31019

value: SLIT


title: 962940-300_lib31021


title: Islet 887-I F


title: RNAPII_ChIP_Col0_3h_rep3


title: RNAPII_ChIP_tfIIS_3h_rep1


title: Islet 886-I F


title: 958434-300_lib31015


title: 958487-300_lib31028

value: Placebo


title: Islet 888-I F

value: female


title: Islet 885-I F


title: RNAPII_ChIP_tfIIS_30min_rep2

value: 30’ heat shock


title: RNAPII_ChIP_Col0_3h_INPUT


title: RNAPII_ChIP_tfIIS_30min_rep1


title: 963006-300_lib31016

value: Nasal Brush


title: 966834-300_lib31013


title: 966789-300_lib31017


title: Islet 878-I M


title: RNAPII_ChIP_Col0_30min_rep3


title: Islet 875-I M


title: Islet 877-I M


title: 958489-300_lib31011


title: Islet 871-I F


title: 962961-300_lib31012


title: 970469-300_lib31010


title: Islet 873-I F


title: RNAPII_ChIP_Col0_30min_rep1


title: Islet 806-I F

value: A/J


title: RNAPII_ChIP_tfIIS_0min_rep3


title: RRBS Control

first: ping

middle: Yan

last: Jia

state: Shanghai

address: 1239 siping road

department: School of Life Sciences and Technology

institute: Tongji University

description: RRBS Fzr1-OE-vs-Control.txt

data_processing:
For RNA-seq, clean data were aligned to the mm9 transcript genome using HISAT2 (V2.1.0) with the default parameter settings.
The summed FPKM (fragments per kilobase per million mapped reads) value for the transcripts sharing each gene ID was calculated and exported using Cufflinks (v2.2.1).
Differential expression analysis was performed using Cuffdiff 2, and the differentially expressed genes were defined by criteria of a q-value<=0.05 and a fold change>=2.
Gene Ontology analysis was performed using enrichGO in the R clusterProfiler package.
ChIP-seq data were first subjected to Trim_galore(version 0.6.4) for adaptor trimming and quality control with the default parameters. The trimmed paired-end reads were then aligned to mm9 reference genome by bowtie2 (version 2.3.5) using the parameters -p 30 --no-mixed --no-discordant. Genome coverage bigwig files were generated by deeptools (version 3.5.0) bamCoverage  with parameters --normalizeUsing RPKM -bs 50. The R package diffBind(version 2.12.0) were used to identify the differentially binding regions.  Fold change > 2 and FDR < 0.05 were used as cutoff for H3K9me3 up-regulated regions caused by overexpression Fzr1. Aggregation plot for H3K9me3 up-regulated regions was plotted by computeMatrix and plotProfile functions of Deeptools package. GREAT（Genomic Regions Enrichment of Annotations Tool ） was used to annotate the H3K9me3 up-regulated regions with the default settings
For RRBS sequencing analysis, the sequence obtained was compared with the reference genome using Bismark software with Bowtie 2. Determination of methylated C was performed with a sequencing depth >= 4× and a q-value after FDR correction of <= 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample,wig files,GO files

source_name: Subcutaneous fat

extract_protocol:
KAPA Hyper Prep Kit was used for cytoplasmic lysis of the indicated samples.
For RNA-seq, reverse transcription was performed directly with the cytoplasmic lysates of the indicated samples. A total cDNA library was then amplified over 18-20 cycles for library construction. The amplified cDNA was fragmented, and then a KAPA Hyper Prep Kit was used to generate sequence libraries. Paired-end 125 bp or 150 bp sequencing was further performed on a HiSeq 2500 system (Illumina) at Novogene.
For H3K9me3 ChIP-Seq, 500 cells were used per reaction, and two replicates were performed. All isolated cells were washed three times in 0.5% BSA in PBS solution (Sigma) to avoid possible contamination. The NChIP procedure was performed as previously described (Brind'Amour et al, 2015). Histone H3K9me3 Antibody (39161, Active Motif) was used for each immunoprecipitation reaction. The sequence libraries were generated using the KAPA Hyper Prep Kit for the Illumina platform (kk8504), following the manufacturer’s instructions. Paired-end 125-bp or 150-bp sequencing was performed on a HiSeq 2500 or X10 (Illumina) at Berry Genomics.
For RRBS, the subcutaneous adipose tissues of three 4-month-old mice in each group were collected, cryopreserved at -80°C. The whole-genomic DNA extracted from tissue was fragmented by ultrasound, A bases were added for end-repair, and methylated adaptor fragments were added. The obtained DNA was subjected to bisulfite treatment, and the final DNA library was obtained after PCR amplification. Paired-end 150 bp sequencing was further performed on a HiSeq 2500 system (Illumina) at Novogene.

value: Subcutaneous fat

value: Control


title: RNAPII_ChIP_tfIIS_0min_rep2


title: RNAPII_ChIP_tfIIs_30min_INPUT


title: Islet 876-I M


title: 966877-300_lib31009

first: Naresh

last: Doni Jayavelu

address: 1201 9th AVE

institute: Benaroya Research Institute at Virginia Mason

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Reads were aligned by STAR v2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2), and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: raw_counts_ITN_GRASS_nasal_samples.csv is a csv file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

source_name: Nasal Brush

extract_protocol:
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.


title: Islet 805-I F


title: RNAPII_ChIP_tfIIs_0min_INPUT


title: 970475-300_lib31006


title: RNAPII_ChIP_tfIIS_0min_rep1


title: Islet 803-I F


title: 963021-300_lib31008


title: 966865-300_lib31005


title: 959029-300_lib31007


title: Islet 801-I F


title: RRBS Fzr1-OE

description: RRBS Fzr1-OE-vs-Control.txt


title: Fat Control-rep1

description: Fat Fzr1-OE-vs-Control.txt

molecule: polyA RNA


title: Islet 800-I M

value: PWK/PhJ


title: Islet 802-I F


title: Fat Control-rep2

description: Fat Fzr1-OE-vs-Control.txt


title: RNAPII_ChIP_Col0_0min_rep1


title: Fat Fzr1-OE-rep3

description: Fat Fzr1-OE-vs-Control.txt


title: RNAPII_ChIP_Col0_0min_rep2


title: 958659-300_lib31003


title: Fat Control-rep3

description: Fat Fzr1-OE-vs-Control.txt


title: Islet 797-I M


title: RNAPII_ChIP_Col0_0min_rep3


title: RNAPII_ChIP_Col0_0min_INPUT


title: 970463-300_lib31002

value: Female


title: RNAPII_ChIP_tfIIS_30min_rep3

value: seedlings


title: 962974-300_lib31004


title: 962971-300_lib31001


title: Fat Fzr1-OE-rep1

description: Fat Fzr1-OE-vs-Control.txt


title: Islet 798-I M


title: Fat Fzr1-OE-rep2

description: Fat Fzr1-OE-vs-Control.txt


title: T2_ULO_SL_c

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

institute: University of Trento

data_processing:
RNASeq data were aligned on the Malus domestica genome using the new Tuxedo protocol. Alignment was carried out with HiSAT2, while read counting analysis was performed with StringTie. For the analysis fo the genes differentially expressed was used DEseq2.
Assembly: Malus domestica Genome available at NCBI
Supplementary files format and content: excell file with FPKM values for each Sample/Replicate

organism: Malus domestica

source_name: peel

extract_protocol:
RNA extraction was performed, for each of the three biological replicates with the Spectrum Plant total RNA kit (Sigma-Aldrich Co., St. Luis, MO, USA). RNA was quantified using a NanoDrop ND-8000 spectrophotometer (Thermo Scientific, Waltham, MA, USA), while its purity and integrity was assessed with a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
For each replicate/sample, 3 mg of RNA was used for the construction of a non-directional Illumina RNA-seq library, using TrySeq RNA sample preparation kits, v2 (Illumina, San Diego, CA, USA). Libraries were quantified using quantitative PCR and quality control was performed with the DNA 1000 series II chip bioanalyzer (Agilent, Santa Clara, CA, USA). Sequencing of libraries was performed with an Illumina HiSeq 1000 Sequencer using TruSeq SBS v3-HS kit (100 cycles) and TruSeq SR Cluster v3-cBot-HS kits (Illumina, San Diego, CA, USA) generating 100-bp reads.

treatment_protocol: DCA and ULO means storage in low oxygen condition (ULO:1%; DCA:<1%)

value: peel

value: Granny Smith


title: Islet 796-I F

first: Kristen

last: O'Connell

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Mouse raw-reads from the 386 samples described above were quality and adapter trimmed with cutadapt v2.3 . Filtered trimmed reads were mapped with Bowtie2 v2.3.5 [PMID: 22388286]. For C57BL/6J samples, reads were mapped to GRCm38 release 98 (ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz). For all other DO founder strains (A/J, 129S1/SvlmJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ), reads were mapped to strain-specific pseudo-references. Pseudo-references for each strain were constructed with g2gtools v0.1.31 (http://churchill-lab.github.io/g2gtools) by patching GRCm38 release 98 with strain-specific SNPs and Indels from the Mouse Genome Project [PMID: 21921910] REL-1807 (ftp://ftp-mouse.sanger.ac.uk/REL-1807-SNPs_Indels/). Mapped reads were filtered to remove PCR duplicates, mtDNA, and the following classes of reads: unmapped, mate unmapped, and non-primary alignment. DeepTools alignmentSieve v3.3.2 [PMID: 27079975] was used to offset all reads aligning to the positive strand by +4bp, and all reads aligning to the negative strand by -5bp to account for Tn5 transposase activity [PMID: 24097267 , PMID: 21143862]. Alignments from non-C57BL/6J samples were then lifted to GRCm38 coordinates with g2gtools. Peak calling was conducted on all pooled alignment files with Macs2 v2.2.7.1 [PMID: 22936215].
Assembly: mm10
Supplementary files format and content: narrowPeak : called peaks of signal enrichment, bed : peaks count matrix, bigwig : read coverage track

extract_protocol:
Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit (28204).
Adipose, liver, and muscle ATAC libraries were constructed as previously described  [PMID: 27526324] with a few exceptions. Briefly the protocol entails pelleting and washing cells in cold PBS, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) with the addition of 0.01% digitonin (2x TDE for adipose), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche). Islet ATAC libraries were constructed as previously described [PMID: 34491912] with a few exceptions. Briefly the protocol entails pelleting and washing approximately islets in cold PBS, incubating in ATAC lysis buffer, trituration with 25-gauge needle, centrifugation to generate crude nuclei pellet, washing in ATAC lysis buffer, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche).
All libraries were sequenced 100 bp paired end on an Illumina NovaSeq 6000.

value: islet


title: RNAPII_ChIP_Col0_30min_INPUT


title: H3K9me3 Control-input DNA

source_name: Blastocyst

value: embryo

value: Embryonic day 4.0


title: Islet 795-I F

value: Islet - islets of Langerhans


title: 958654-300_lib31000

city: Seattle

value: Male

value: SLIT


title: Islet 794-I F

value: female


title: H3K9me3 Control-rep2

value: H3K9me3(Active Motif, lot 39161)


title: T2_ULO_SL_a


title: Neural retina ChIP-seq_Input

description: Neural retina cells


title: Islet 793-I F


title: T2_ULO_SL_b


title: T2_ULO_c


title: 966831-300_lib30997

value: Nasal Brush

value: Placebo


title: H3K9me3 Control-rep1


title: T2_ULO_b


title: T2_ULO_a


title: H3K9me3 Fzr1-OE-input DNA


title: H3K9me3 Fzr1-OE-rep2


title: Islet 804-I F


title: Islet 2974-I M

value: WSB/EiJ

value: male


title: 966862-300_lib30995


title: 970399-300_lib30998


title: Islet 2292-I M

value: CAST/EiJ


title: T2_DCA_CF_SL_c


title: Islet 2155-I F


title: Islet 1601-I M

value: NZO/HlLtJ


title: 970437-300_lib30993


title: 959030-300_lib30994

value: Female


title: T2_DCA_CF_c

value: peel


title: 966785-300_lib30992


title: T2_DCA_CF_SL_a

value: Granny Smith


title: T2_DCA_CF_SL_b


title: Fzr1-OE-rep3


title: Control-rep2

value: Control


title: H3K9me3 Fzr1-OE-rep1

value: embryo


title: T2_DCA_CF_b


title: 963008-300_lib30996


title: Islet 2553-I M

value: islet

value: A/J


title: 970430-300_lib30999

value: Male

value: SCIT


title: 962996-300_lib30991


title: Islet 1389-I M

value: NOD/ShiLtJ

value: Islet - islets of Langerhans


title: Islet 1387-I M


title: T2_DCA_CF_a


title: Islet 1386-I F

value: female


title: 958440-300_lib30990

value: Nasal Brush

value: Placebo


title: Islet 1388-I M

value: male


title: Fzr1-OE-rep2

value: Embryonic day 4.0


title: Control-rep1


title: 962980-300_lib30988


title: 2cell IVF rep1

source_name: 2-cell embryo

value: IVF

value: Embryonic day 1.5


title: 2cell IVF rep2


title: T2_RA_SL_b

value: peel


title: T2_RA_SL_c

value: Granny Smith


title: 2cell sIVF rep2

value: sIVF


title: Fzr1-OE-rep1

value: embryo


title: Islet 1384-I F

value: islet


title: 966836-300_lib30985


title: 966823-300_lib30989


title: Islet 1382-I M


title: Islet 1385-I F


title: 970432-300_lib30986


title: Islet 1381-I M


title: 963005-300_lib30984


title: T2_RA_b


title: T2_RA_a


title: T2_RA_c


title: 958431-300_lib30983


title: Islet 1380-I M


title: 958485-300_lib30987


title: 2cell sIVF rep1


title: T2_RA_SL_a


title: 2cell WT rep2

value: WT


title: 2cell WT rep1


title: T1_ULO_SL_c


title: Islet 1378-I F


title: 970448-300_lib30982

value: Male

value: SLIT


title: WT4_ICZ_F5 (biological replicate 3)

city: State College

first: Gary

middle: H.

last: Perdew

address: 309A Life Sciences Building

institute: The Pennsylvania State University

data_processing:
Sequence quality per base was checked by FastQC (v0.11.2).
The adapters and a quality below Q10 were trimmed on the right end by using the BBDuk.
The filtered reads were aligned to the GRCm38.p6 (mm10) from EMBL-EBI with Burrows-Wheeler Aligner (BWA, v 0.7.17-r1188).
The large nucleotide sequence alignments were sorted and indexed, and the alignment reports were generated by using SAMtools (v1.10).
The raw count matrix for genes was obtained from HTSeq (v0.11.2).
Genome_build: GRCm38.p6 (mm10)
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: female C57B6/J small intestine epithelium

growth_protocol: Mice weaned and maintained on standard rodent chow then transferred to semi-purified diet (devoid of dietary AHR agonists) for 1 week prior to treatment

extract_protocol:
Total RNA from fractionated epithelial cells isolated with Trireagent.  Total RNA cleaned using Qiagen Rneasy columns.  RNA quantification and quality assessed through Qubit analysis.
RNA-Seq was processed for each sample by using QuantSeq 3’ mRNA-Seq Library Prep Kit.

treatment_protocol: 8-10 week old female C57B6/J mice were transferred to a semi-purified diet (AIN93G) for 1 week.  Mice were gavaged with vehicle or 10 ug ICZ in corn oil. 12 h later, small intestine removed and the epithelial crypt-villi cells fractionated through sequential EDTA dissociation

value: small intestine epithelia

value: 10 ug ICZ 12 h exposure

tag: gender


title: WT4_ICZ_F4 (biological replicate 3)

value: female


title: 970472-300_lib31014

value: Nasal Brush

tag: percent aligned


title: 966875-300_lib30981

tag: aligned counts_in_millions


title: Islet 1379-I F

city: Bar Harbor

value: NOD/ShiLtJ

value: Islet - islets of Langerhans


title: 970484-300_lib31018

tag: median cv_coverage

value: SCIT


title: Islet 1377-I F


title: T1_ULO_SL_a


title: WT4_ICZ_F3 (biological replicate 3)


title: T1_ULO_SL_b


title: 962968-300_lib30980

tag: participant id


title: 958661-300_lib30979

tag: visit number


title: WT4_ICZ_F2 (biological replicate 3)

tag: tissue


title: Islet 1375-I M

value: NZO/HlLtJ

tag: cell type

value: male


title: WT3_ICZ_F5 (biological replicate 2)


title: T1_ULO_c

value: peel

tag: genotype


title: T1_ULO_b

value: Granny Smith


title: 970454-300_lib30978

tag: age


title: T1_ULO_a


title: Islet 1374-I M

tag: strain


title: Islet 1373-I M

tag: treatment


title: 966812-300_lib30977

tag: Sex


title: Islet 1202-I M


title: WT3_ICZ_F3 (biological replicate 2)


title: 958656-300_lib30975


title: T1_DCA_CF_SL_c


title: Islet 1201-I M


title: 970489-300_lib30974


title: T1_DCA_CF_SL_b


title: T1_DCA_CF_SL_a


title: WT3_ICZ_F2 (biological replicate 2)


title: 966805-300_lib30973


title: T1_DCA_CF_c


title: 962963-300_lib30972


title: Islet 1185-I M

value: PWK/PhJ


title: WT3_ICZ_F4 (biological replicate 2)


title: Islet 1163-I M

value: WSB/EiJ


title: 970423-300_lib31027

value: Female


title: 958429-300_lib30971


title: T1_DCA_CF_a


title: WT2_ICZ_F4 (biological replicate 1)


title: WT3_ICZ_F1 (biological replicate 2)


title: WT2_ICZ_F3 (biological replicate 1)


title: WT2_ICZ_F5 (biological replicate 1)


title: Islet 1162-I M

value: islet


title: 970480-300_lib30970


title: WT2_ICZ_F2 (biological replicate 1)


title: 966860-300_lib30969


title: WT2_ICZ_F1 (biological replicate 1)


title: T1_RA_SL_c


title: Islet 1197-I F


title: Islet 1159-I M

value: CAST/EiJ


title: 958444-300_lib30968

value: Male

value: SLIT


title: Islet 1158-I M


title: WT4_Veh_F5 (biological replicate 3)

value: small intestine epithelia

value: vehicle 12 h exposure


title: T1_RA_SL_a


title: WT4_Veh_F4 (biological replicate 3)

value: female


title: 970425-300_lib30966

value: Nasal Brush


title: T1_DCA_CF_b


title: T1_RA_b


title: WT4_Veh_F3 (biological replicate 3)


title: 963016-300_lib30964


title: Islet 1154-I M

value: A/J

value: Islet - islets of Langerhans


title: Islet 1153-I M


title: T1_RA_a


title: WT4_Veh_F2 (biological replicate 3)


title: WT3_Veh_F5 (biological replicate 2)


title: 970476-300_lib30962

value: SCIT


title: 963002-300_lib30967


title: Islet 1147-I M

value: male


title: T1_RA_SL_b

value: peel


title: WT4_Veh_F1 (biological replicate 3)


title: Islet 1157-I M


title: Islet 1144-I F


title: 958448-300_lib30961

value: Placebo


title: T1_RA_c

value: Granny Smith


title: WT3_Veh_F4 (biological replicate 2)


title: Islet 1142-I M

value: NZO/HlLtJ


title: 35L11_DOX_d2

city: Worcester

first: Hong

last: Zhang

state: MA

address: 55 Lake Avenue North

department: Pediatrics

institute: University of Massachusetts Chan Medical School

data_processing:
Sequence reads were aligned using STAR v2.7.10b and samtools v1.15.1 to acquire bam files
Read counts were obtained using FeatureCounts in Subread v2.0.3
Normalized counts were genereated by log2-transforming read counts
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes read counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized log2-transformed read count values for each sample

growth_protocol: Human iPSCs were maintained in TeSR-E8 media in humidied atmosphere with 5% CO2 at 37°C. Cells were passaged every 4 days at 1:4 ratio.

extract_protocol:
Total RNA was extracted with TRI reagent (Millipore Sigma) and treated with DNase I (Qiagen) using a RNeasy MinElute Cleanup Kit (Qiagen). RNA integrity was determined using Agilent 4200 TapeStation.
Library preparation was performed with 1 µg of total RNA. Ribosomal RNA was removed by an RNase-H method using the RiboErase kit (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94°C for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III reverse transcriptase enzyme and random hexamers (Life Technologies) per manufacturer’s instructions. A second strand reaction was performed to yield double stranded cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases targeting 30M clusters.

treatment_protocol: The day before treatment, iPSC colonies were dissociated with TrypLE and seeded with TeSR-E8 supplemented with 10 µM Y-27632. On the day of treatment, cells were fed with fresh media with or without 0.3 µg/mL doxycycline (DOX).

value: Induced pluripotent stem cells

value: Healthy

value: DOX-treated for 2 days


title: 35L11_DOX_d4

value: DOX-treated for 4 days


title: AG25367_DOX_d2

value: AD


title: WT3_Veh_F3 (biological replicate 2)

value: small intestine epithelia


title: 962958-300_lib30960

value: Male


title: AG25367_DOX_d4


title: Islet 1160-I F

value: islet

value: WSB/EiJ

value: female


title: 966813-300_lib30959

value: Nasal Brush

value: SLIT


title: Islet 1140-I F

value: Islet - islets of Langerhans


title: WT3_Veh_F1 (biological replicate 2)

value: vehicle 12 h exposure


title: Islet 1143-I M

value: male


title: WT3_Veh_F2 (biological replicate 2)


title: WT1_Veh_F5 (biological replicate 1)


title: Islet 1139-I F


title: 35L11_CTL_d4

value: Untreated for 4 days


title: 958435-300_lib30957


title: Islet 1138-I F

value: NZO/HlLtJ


title: 35L11_CTL_d2

value: Induced pluripotent stem cells

value: Untreated for 2 days


title: WT1_Veh_F4 (biological replicate 1)


title: 962966-300_lib30958


title: Islet 1137-I F


title: 970450-300_lib30956

value: SCIT


title: BI_H3K27AC_Rep2

first: Bin

last: Li

address: Jinzun Road

institute: Shanghai jiaotong University

data_processing:
CUT&Tag-Seq 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.
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.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag-Seq

source_name: cardiomyocytes

extract_protocol:
Briefly, 1×105 cells were treated with ConA beads, then incubated with primary antibody overnight at 4℃. Cells were reacted with secondary antibody for 1 h after being washed for three times.
CUT&Tag assay was performed using Hyperactive® Universal CUT&Tag Assay Kit for Illumina (Vazyme) as indicated. Samples were incubated with pAG-Tn5 for 1 h. DNA tagmentation was performed at 37 °C for 1h and followed by DNA extraction. PCR was applied to amplify the libraries followed by product purification. Sequencing and data analysis were performed by Novogene Co. Ltd using Novaseq-PE150 (Illumina).

value: cardiomyocytes

value: HiPSC-derived cardiomyocytes

tag: antibody

tag: group

value: BI


title: 966871-300_lib30955

value: Male


title: WT1_Veh_F3 (biological replicate 1)

value: small intestine epithelia


title: WT1_Veh_F2 (biological replicate 1)


title: Islet 1136-I F

value: islet


title: Islet 1141-I F

value: female


title: 962939-300_lib30954

value: Nasal Brush


title: BI_H3K27AC_Rep1

tag: cell line


title: AG25367_CTL_d4

value: AD


title: Islet 1054-I M

value: Islet - islets of Langerhans


title: WT1_Veh_F1 (biological replicate 1)

value: vehicle 12 h exposure


title: RNAPII_ChIP_Col0_30min_rep2

value: seedlings

value: 30’ heat shock


title: BI_H3K27ME3_Rep2


title: BI_H3K27ME3_Rep1


title: Islet 1043-I M

value: A/J

value: male


title: Undetermined

source_name: undetermined

value: Unknown


title: AG25367_CTL_d2

value: Induced pluripotent stem cells

value: Untreated for 2 days


title: B6.Sst1S BMDM TNF Replica 2

city: Dublin

first: Vadim

last: Zhernovkov

address: Belfield

country: Ireland

institute: University College Dublin

data_processing:
cDNA libraries were sequenced using an Illumina HiSeq 2500 platform.
Raw sequencing reads were aligned to the mouse genome (mm10) using Spliced Transcripts Alignment to a Reference (STAR) (Dobin et al., 2013), and gene expression levels were measured by featureCounts (Liao et al, 2013).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Bone marrow

growth_protocol: Bone marrow cells were grown for 10 days in 10% L929-containing medium and differentiation in macrophages in 6 well plates.

extract_protocol:
Qiagen RNAeasy Kit
Poly A RNA libraries were prepared for sequencing using NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: BMDMs were stimulated with murine TNF at 10 ng/ml for 12 hours

tag: mouse strain

value: sst1-susceptible congenic mice

value: bone marrow-derived macrophages

value: TNF 10 ng/ml

tag: treatment duration

value: 12 hour stimulation


title: B6.Sst1S BMDM TNF Replica 3


title: Islet 1041-I F

value: islet


title: 958658-300_lib30965

value: Male

tag: fastq total_reads

tag: percent aligned

value: SCIT


title: Islet 1037-I F

value: PWK/PhJ

value: female


title: WT_H3K27AC_Rep2

value: cardiomyocytes

value: HiPSC-derived cardiomyocytes

value: WT


title: B6.Sst1S BMDM TNF Replica 1


title: 970491-300_lib30952

value: Nasal Brush

tag: aligned counts_in_millions

tag: median cv_coverage

value: Placebo


title: Islet 1035-I F

value: Islet - islets of Langerhans


title: 966845-300_lib30951

tag: participant id

tag: visit number


title: 970455-300_lib30950

tag: tissue


title: Islet 1034-I M

value: A/J

tag: cell type

value: male


title: 966856-300_lib30949

tag: age


title: B6 BMDM TNF Replica 3

tag: genotype

value: wild type


title: WT_H3K27ME3_Rep2


title: WT_H3K27ME3_Rep1


title: 963019-300_lib30948

tag: treatment


title: Islet 1033-I M

tag: strain

tag: Sex


title: 957250-300_lib30953


title: 958667-300_lib30947


title: B6 BMDM TNF Replica 1

value: bone marrow-derived macrophages


title: Islet 1030-I M

value: CAST/EiJ


title: B6 BMDM TNF Replica 2

value: TNF 10 ng/ml

value: 12 hour stimulation


title: WT_H3K27AC_Rep1

tag: antibody

tag: group


title: shNC 2

city: Dalian

first: Wenzhe

last: Duan

address: Shahekou Zone, Zhongshan Road 467

institute: Second hospital of Dalian Medical University

data_processing:
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 N base and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
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.
Assembly: Hisat2 v2.0.5
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lung cancer

growth_protocol: All cells were routinely cultured in Roswell Park Memorial Institute medium-1640 (RPMI1640) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin and streptomycin (all these reagents were obtained from Gibco, Invitrogen, Inc, California, USA) and maintained in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Trizol (Transgen, China) and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: lung cancer

tag: cell line

value: lung cancer cell line

value: routine culture


title: shNC 3


title: 962994-300_lib30944

value: Female

value: SLIT


title: Islet 1029-I M

value: islet


title: 959047-300_lib30943


title: 966863-300_lib30945


title: shNC 1

value: WT


title: shCD146 6

value: CD146 knockdown


title: 970447-300_lib30942

value: Nasal Brush

value: Male


title: Islet 1025-I F

value: Islet - islets of Langerhans

value: female


title: Islet 1021-I F


title: 958657-300_lib30941


title: Islet 1024-I F


title: Islet 1020-I F


title: shCD146 5


title: EGFL7-3

city: Kunming

first: Weipeng

last: Liu

state: Yunnan

address: Jiao ling road

department: Institute of Medical Biology

institute: Chinese Academy of Medical Sciences

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp  (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4  and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts  for each Sample

source_name: cervical tissue

growth_protocol: Cells were nurtured in Dulbecco's Modified Eagle medium (DMEM, Gibco), which was enriched with 10% fetal bovine serum (FBS, Gibco). All cell lines were maintained in an incubator set at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: cervical tissue

value: HeLa

value: cervical cancer cell

value: EGFL7 overexpression


title: Glis3-eGFP kidney, PND7, input for GLIS3 ChIP

city: Research Triangle Park

first: Hong Soon

last: Kang

state: NC

address: 111 T.W. Alexander Dr.

department: IIDL

institute: NIH/NIEHS

data_processing:
Reads were filtered to remove any  with mean base quality score < 20.
Adapters were removed by Cutadapt v1.12 and filtered to retain only those with length at least 30nt.
Filtered and trimmed reads were mapped via Bowtie v1.2 with parameter "-m 1".
Alignment files were combined via MergeSamFiles.jar (Picard tools v1.110) for samples with multiple sequencing runs.
Duplicate mapped reads were removed via MarkDuplicates.jar (Picard tools v1.110) with flag "REMOVE_DUPLICATES=TRUE".
Peak calls were made by HOMER (v4.10.3) with parameters “-style factor” then re-sized to 300bp centered on the called peak midpoints.
For visualization purposes, uniquely-mapped non-duplicate reads were extended to the 200bp estimated fragment size via BEDTools v2.29.2 "slop -s -r 125 -l 0", converted to bedGraph via BEDTools v2.29.2 "genomecov -bg", scaled to 10 million fragments per sample, then converted to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: peak calls (BED)
Supplementary files format and content: normalized depth tracks (bigWig)

source_name: kidney

extract_protocol:
Immunoprecipitated chromatin was washed and ChIPed-DNA was eluted, reverse cross-linked, and DNA fragments purified using PCR purification kit form Qiagen.
NEXTflex DNA-Seq kit from PerkinElmer was used.

value: kidney

tag: chip antibody


title: 970459-300_lib30940

tag: fastq total_reads


title: Glis3-eGFP kidney, PND7, GLIS3 ChIP

value: GFP (Abcam #290)


title: EGFL7-2


title: 966853-300_lib30939

tag: percent aligned


title: Islet 1019-I F

value: CAST/EiJ


title: Islet 1018-I M

value: male


title: Oxi-LA_13

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

data_processing:
For all sequencing data, the raw reads were subject to quality check using FastQC.
The sequencing data was further trimmed and analyzed by QIIME software qiime2-2020.11.
Sequences were then clustered into operational taxonomic unites (OTUs) using a public dataset (SILVA release 132) with 99% similarity threshold.
QIIME2 output were imported to R to build a phyloseq project.
Differential  abundance analysis in the polysome fraction was determine using AVONA.
Supplementary files format and content: tab-delimited text files include differential  abundance analysis results
Library strategy: 16S rRNA-seq

source_name: colon

growth_protocol: C57BL/6 male mice were fed with the diet containing un-oxidized or oxidized corn oil for 3 weeks.

extract_protocol:
Total fecal DNA was extracted using QIAamp DNA Stool Mini Kit (Qiagen) following the manufacturer’s instruction with the addition of bead-beating step.
PCR was performed to amplify the bacteria community with primers  that bound the V3-4 regions of the16S rRNA gene,which also incorporates the Illumina overhang adaptor.PCRs were performed in a 96-well format on a Veriti thermal cycler (Life Technology) with 2 × KAPA HiFi Hotstart ReadyMix (KAPA Biosystem). After purification with AMPure XP beads (Beckman Coulter), a limited cycle PCR was performed using the Nextera XT Index Kit (Illumina) to attach dual indices and Illumina sequencing adapters, followed by an additional purification with AMPure XP bead. The quantity of the purified PCR products was measured by Qubit dsDNA BR Assay kit (Life Technology) and the amplicon quality was estimated by ScreenTape Assay on Tape Station 2200 (Agilent). After quantification and qualification, samples were pooled in equimolar amount and pair-end 2×300 bp sequencing was performed on Illumina MiSeq platform and MiSeq reagent kit V3 (8% PhiX) (Illumina).

treatment_protocol: The fecal samples were collected from un-oxidized or oxidized corn oil-treated mice.

value: colon

value: Oxi-LA

tag: molecule

value: 16S rRNA


title: 962990-300_lib30938

tag: aligned counts_in_millions

tag: median cv_coverage

value: SLIT


title: EGFL7-1


title: Islet 1016-I M

value: islet


title: Oxi-LA_12


title: Oxi-LA_11


title: Control-3

value: Negative control


title: Islet 1015-I M


title: 958665-300_lib30937

value: Nasal Brush

value: Male

tag: participant id

tag: visit number


title: Control-2

tag: tissue

tag: cell type


title: 970408-300_lib30936

tag: age


title: Control-1

tag: genotype

tag: treatment


title: 966826-300_lib30935

tag: Sex


title: Islet 1013-I F

tag: strain

value: Islet - islets of Langerhans

value: female


title: shCD146 4

value: lung cancer

value: lung cancer cell line

value: CD146 knockdown

value: routine culture


title: Islet 1014-I F


title: Oxi-LA_10


title: Islet 1012-I F


title: Islet 1011-I F


title: Oxi-LA_7


title: 962938-300_lib30934


title: A549 cells, RSL3 and Fer-1, 24h, rep3

city: Beijing

first: Fumin

last: Tai

state: Beijing

address: 27 Taiping Road

institute: Beijing Institute of Radiation Medicine

data_processing:
A cDNA library constructed by technology from the pooled RNA from A549 cells was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo_sapiens.GRCh38（Ensemb v101）
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: A549 cells were maintained in DMEM suppplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 cells treated with DMSO,  RSL3 (2μM) alone, or co-treated with Fer-1 (5μM) for 24h.

value: RSL3+Fer-1, 24h


title: A549 cells, RSL3 and Fer-1, 24h, rep2


title: 957253-300_lib30933


title: 963014-300_lib30932

value: SCIT


title: Adipose 967-A M

source_name: adipose

value: adipose

value: PWK/PhJ

value: Adipose - gonadal fat pad

value: male


title: Oxi-LA_6

value: colon

value: Oxi-LA

value: 16S rRNA


title: A549 cells, RSL3, 24h, rep3

value: RSL3, 24h


title: 958482-300_lib30931

value: Nasal Brush

value: Male


title: Adipose 966-A M


title: A549 cells, RSL3, 24h, rep2


title: Oxi-LA_5


title: Oxi-LA_9


title: 970414-300_lib30930

value: SLIT


title: Adipose 964-A F

value: A/J

value: female


title: 966808-300_lib30929


title: Oxi-LA_8


title: Adipose 962-A F


title: Oxi-LA_3


title: 962988-300_lib30928


title: Oxi-LA_2


title: Oxi-LA_4


title: A549 cells, DMSO, 24h, rep2

value: DMSO, 24h


title: A549 cells, DMSO, 24h, rep3


title: A549 cells, RSL3, 24h, rep1


title: A549 cells, RSL3 and Fer-1, 24h, rep1


title: Oxi-LA_1


title: 957228-300_lib30927


title: A549 cells, DMSO, 24h, rep1


title: Adipose 892-A M

value: WSB/EiJ


title: Adipose 960-A M


title: 970468-300_lib30926


title: Ctrl_13

value: Ctrl


title: Ctrl_14


title: Combo-3

city: Guangzhou

first: Kexiu

last: Huang

address: 613W Huangpu Rd

institute: jinan university

data_processing:
HISAT2 was used to make clean reads align with the human GRCh38 genome.
Normalization of genes expression and differential expression genes (DEGs) analysis were performed by DESeq2.
Assembly: hg38
Supplementary files format and content: gene_expression_fpkm.csv
Supplementary files format and content: count and fpkm

growth_protocol: MV4-11 cell line was cultured in RPMI 1640 medium supplementied with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were maintained in a 37 °C humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA of each sample was extracted with TRlzol Reagent (Life Technologies).
1 ug of total RNA was used for the construction of sequencing library. Sequencing library were prepared with Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology)

treatment_protocol: MV4-11 cells were treated in triplicate with DMSO, 0.1 µM venetoclax, 10 µM HA, or combo (0.1 µM Venetocalx plus 10 µM HA) for 48 h.

value: acute myeloid leukemia

value: WT

value: VEN+HA


title: Adipose 891-A M

value: adipose

value: Adipose - gonadal fat pad


title: Combo-2


title: 966852-300_lib30925


title: 963013-300_lib30924


title: Adipose 890-A M

value: male


title: 966784-300_lib30923

value: Placebo


title: Adipose 889-A F


title: Ctrl_12

value: colon

value: 16S rRNA


title: HA-3

value: HA


title: Adipose 963-A F


title: Ctrl_11


title: 962991-300_lib30922

value: Nasal Brush

value: Male


title: Adipose 888-A F


title: HA-2


title: Ctrl_10


title: Adipose 887-A F


title: 958442-300_lib30921


title: HA-1


title: 970426-300_lib30920

value: SLIT


title: 966817-300_lib30919


title: Adipose 886-A F

value: female


title: VEN-3

value: VEN


title: Adipose 885-A F

value: WSB/EiJ


title: VEN-2


title: Ctrl_7

value: Ctrl


title: VEN-1

value: acute myeloid leukemia


title: Ctrl_6


title: 966838-300_lib30963

value: SCIT


title: 962950-300_lib30918


title: Adipose 878-A M


title: Combo-1

value: WT

value: VEN+HA


title: 957244-300_lib30917


title: Adipose 877-A M

value: adipose

value: Adipose - gonadal fat pad


title: Ctrl_5


title: 970429-300_lib30916


title: DMSO-3

value: DMSO


title: Ctrl_9

value: colon


title: Ctrl_4

value: 16S rRNA


title: Adipose 876-A M

value: male


title: Adipose 875-A M


title: DMSO-1


title: DMSO-2


title: Ctrl_3


title: 970477-300_lib30914

value: Nasal Brush

value: Placebo


title: Ctrl_2


title: Ctrl_8


title: Adipose 873-A F


title: 958476-300_lib30913

value: Female


title: Untreated sample used as control donor 3 replicate 2

city: Freiburg

first: Kay

middle: Ole

last: Chmielewski

address: Breisacherstr. 115

department: Institute for transfusion medicine and gene therapy

institute: University clininics Freiburg

data_processing:
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the CAST-Seq and D-CAST-Seq pipelines with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: hg38
Supplementary files format and content: matrix table of translocation sites detected with CAST-Seq and D-CAST pipelines. It includes the genomic coordinates of translocated sites, read coverage, alignment score against gRNA, translocation event classification and nearest genes annotation.
Library strategy: CAST-Seq

source_name: HSPCs

growth_protocol: All CD34+ HSPCs were cultured in GMP SCGM medium (Cellgenix) supplemented with SCF (100ngml-1), TPO (100ngml-1), Flt3 ligand (100ngml-1), IL-6 (100 ngml-1), and StemRegenin1 (0.75mM). Cells were cultured at 37C, 5% CO2, and 5% O2.

extract_protocol:
Between 2 and 4 days post targeting, gene edited cells were harvested and QuickExtract DNA extraction solution (Epicentre) was used to collect gDNA.
CAST-Seq was performed as previously described (Turchiano et al, 2021) with minor modifications. Briefly, genomic DNA was fragmented by enzymatic digestion (NEBNext® Ultra™ II FS DNA Library Prep Cat.# E7805S) to obtain average fragment lengths of 350-500 bp. After linker ligation (NEBNext®Ultra™ II FS DNA Library Prep Cat.# E7805S) and DNA purification, two rounds of PCR utilizing Q5 polymerase (NEB, Cat.# M0493S) were performed with the following conditions: 20 cycles at 95°C for 15 s, 61°/63°C (g1 or g1+2/g2, first reaction) or 68°C (second reaction) for 20 seconds, 72°C for 20 seconds.
A third PCR introduced the barcoded Illumina adapter for sequencing (NEB, NEBNext Multiplex Oligos for Illumina, Cat.# E7335, E7500, E7710, E7730). Libraries were sequenced by Azenta Life Sciences using the Illumina NovaSeq platform with a 2 x 150 bp configuration.

treatment_protocol: RNPs were complexed at a Cas9/sgRNA molar ratio of 1:2.5 at 25 °C for 10 min before electroporation. CD34+ cells were resuspended in P3 buffer (Lonza) with complexed RNPs. I53 peptide is added directly to the RNP and cell mixture immediately before electroporation. Electroporation was carried out using the Lonza 4D Nucleofector (program DZ-100 for HSPCs).

value: HSPCs

value: No treatment


title: CAST-seq on samples treated with RNP  in donor 3 replicate 2

value: RNP


title: Adipose 806-A F

treatment_protocol: Male and female mice of each CC founder strain were fed high fat high sugar 45% kcal fat plus 1360% kcal sucrose (Research Diets D19070208) or isocaloric control 10% kcal fat plus 0% kcal sucrose (Research Diets D19072203) diets for 9 weeks prior to tissue harvest and processing for ATAC-seq.

value: A/J

value: female


title: CAST-seq on samples treated with RNP + i53 peptide in donor 3 replicate 2

value: RNP + i53 peptide


title: Untreated sample used as control donor 3 replicate 1

description: used as untreated control


title: 970485-300_lib30910


title: Adipose 805-A F


title: 966842-300_lib30915

value: Male

value: SCIT


title: 966837-300_lib30911


title: tumor, KS100

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

institute: Penn State University

data_processing:
De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.20.0.422, Illumina), allowing no mismatches in the index read. After the quality and polyA trimming by BBDuk and alignment by HISAT2 (version 2.1.0), read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCm38.78).
Assembly: GRCm38.78
Supplementary files format and content: raw read counts are provided in a csv ifle

source_name: tumor

growth_protocol: Eight-week-old C57BL/6J (The Jackson Laboratory) were subcutaneously injected with mouse melanoma, B16F10 cells. When tumors were well-vascularized, mice were administered anti-PD-1, AZD5363+MK1775, AZD5363+MK1775+anti-PD-1, KS100, KS100+anti-PD-1 daily until control tumors reached 2000 mm3.  Control mice were treated with DMSO+ control IgG. Mice were sacrificed and tumors were collected for RNAanalysis.

extract_protocol:
30-60 mg tumor tissues were used for RNA extraction. A mass of stainless-steel beads (Next Advance, cat# SSB14B) equal to the mass of the tissue was added to the tube. Two volumes of TRI Reagent® (Zymo Research) were added to the tube, and samples were immediately mixed in the Bullet Blender (Next Advance) for 1 minute at a speed of ten. Samples were visually inspected to confirm desired homogenization and then incubated at 37 °C for 5 minutes. The TRI Reagent® was added up to 0.6 mL, and samples were mixed in the Bullet Blender for 1 minute. Total RNA was extracted using Direct-zol™ RNA Miniprep Kit (Zymo Research). Optical density values of extracted RNA were measured using a NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RNA integration number (RIN) was measured using BioAnalyzer (Agilent Technologies) RNA 6000 Nano Kit.
The cDNA libraries were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) as per the manufacturer’s instructions. Briefly, total RNA was reverse transcribed using oligo (dT) primers. The second cDNA strand was synthesized by random priming, in a manner that DNA polymerase is efficiently stopped when reaching the next hybridized random primer, so only the fragment close to the 3’ end gets captured for later indexed adapter ligation and PCR amplification. The processed libraries were assessed for their size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
The denatured libraries were loaded onto an MiSeq v3 flow cell on an Illumina MiSeq and run for 151 cycles using a single-read recipe according to the manufacturer's instructions.

treatment_protocol: Each mouse was then housed in polycarbonate cages and had ad lib access to irradiated rodent chow and water. The animal facility was programmed with a 12:12-h light: dark cycle. All experiments were conducted in accordance with institutional guidelines, the Guide for the Care and Use of Laboratory Animals, and approved by the Penn State College of Medicine Institutional Animal Care and Use Committee.

value: tumor

tag: mouse individuals

value: m5 (pooled)

tag: protocol

value: KS100 + control IgG

value: F


title: Adipose 804-A F

value: adipose

value: Adipose - gonadal fat pad


title: tumor, KS100+PD-1

value: m6 (pooled)

value: subcutaneously injected with mouse melanoma, B16F10 cells

value: KS100 + anti-PD-1


title: tumor, AZD+MK+PD-1

value: m4 (pooled)


title: CAST-seq on samples treated with RNP  in donor 3 replicate 1

value: HSPCs


title: CAST-seq on samples treated with RNP + i53 peptide in donor 3 replicate 1


title: Adipose 803-A F


title: Untreated sample used as control donor 1 replicate 2

description: used as untreated control

value: No treatment


title: tumor, control

value: m1 (pooled)

value: DMSO + control IgG


title: 962964-300_lib30908

value: Nasal Brush

value: Female


title: tumor, AZD+MK

value: m3 (pooled)

value: AZD5363 + MK1775 + control IgG


title: Adipose 871-A F

value: female


title: 970488-300_lib30907

value: SCIT


title: tumor, PD-1

value: tumor

value: m2 (pooled)

value: DMSO + anti-PD-1

value: F


title: Ctrl_1

value: colon

value: Ctrl

value: 16S rRNA


title: CAST-seq on samples treated with RNP  in donor 1 replicate 2

value: HSPCs

value: RNP


title: Adipose 802-A F

value: adipose

value: Adipose - gonadal fat pad


title: 963009-300_lib30912

value: Nasal Brush

value: Placebo


title: Adipose 800-A M

value: PWK/PhJ

value: male


title: 957242-300_lib30906

value: Male

value: SLIT


title: 962951-300_lib30905


title: Adipose 798-A M