title: kidney, 24 months, rep3

city: Hannover

first: Julius

last: Sinning

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

data_processing:
250ng of RNA pere sample were used for mRNA enrichment procedure with 'NEBNext® Poly(A) mRNA Magnetic Isolation Module' followed by straned cDNA library generation.
Steps were performed following manualE7760 except that all reactions were donscaled to 2/3 of initial volumes. One additional purification step was introduced at the end of the standard procedure.
cDNA libaries were barcoded by dual indexing approach using 'NEBNext Multiplex Oligos for Illumina'.
All cDNA libraries were amplified with 8 cycles of final PCR
Fragment length of distribution of individual libraries was monitored using 'Bioanalyzer High Sensitivity DNA Assay'
Assembly: Mus musculus, GRCm38; release M18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney

growth_protocol: PTEC: C57BL/6Rj mice were digested in 0125% Collagenase Type I at 37°C for 45 minutes. Tubular fragments were sedimented, sieved through 40µm cell strainers and cultured in REGM2 medium; Whole Kidney: After euthanization, one half of the right kidney was snap frozen for RNA extraction.

extract_protocol:
RNA extraction from murine kidneys and PTEC was performed using NucleoSpin RNA Plus (Machery-Nagel). 250ng of RNA per sample were used for RNAseq experiments
RNA libraries were generated using 'NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina'

treatment_protocol: Confluent PTEC were expoesed to γ-irradiation (10 Gray)

value: kidney

value: whole kidney

value: WT

tag: age

value: 24 months


title: Skin, control, day03, rep2, pair1

status: Public on Sep 11 2023

type: SRA

city: Worcester

first: Jing

last: Wang

state: MA

address: 100 Research Drive

country: USA

institute: AbbVie

description:
count data column name: YC04-16-D3A
cao_mouse_skin_genesymbol_count

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the mouse genome (GRCm39) with STAR
Assembly: GRCm39
Supplementary files format and content: .txt file containing raw counts for all samples

molecule: total RNA

organism: Mus musculus

source_name: skin

growth_protocol: HTNFki/kiLeprdb/db mice (8~12 weeks) were placed in a chamber and anesthetized with 5% isoflurane to prepare the animals. The fur on the dorsal skin was removed with an electric shaver, followed by the application of NairTM hair removal cream for no more than 1 min. The dorsal skin was cleaned and sterilized with iodine solution. After depilation, four 6-mm diameter full-thickness skin punches extending through the panniculus carnosus were made on the dorsa of mice with skin biopsy punches, and dressed by TegadermTM transparent film. Mice were administrated with tramadol (5 mg/kg, single dose) and indicated TNF inhibitors or vehicle control (twice a week by subcutaneous injection). Wounds were measured by caliper and photographed every other day and visually monitored for possible signs of infection. The wound area was quantified by tracing wound margins and calculated as a percent of the original wound size, with scaling normalized to the original wound. Secondary 8-mm full-thickness skin punches overlaying the original wounds were harvested on indicated days for RNA sequencing.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit according to the manufacturer’s instructions.
RNA library preparation from total RNA was conducted following the manufacturer’s protocol for the SMARTer Stranded Total RNA-Seq Kit V2-Pico
Final libraries were assessed using the Agilent Tapestation and Qubit assay methods, then sequenced on an Illumina NextSeq500 sequencer using 1x50bp read length for a depth of 50M reads

treatment_protocol: Wounded mice were administrated with either vehicle control (PBS) or adalimumab (20mg/kg, twice a week on days 0, 3, 7, and 10 by subcutaneous injection).

tag: tissue

value: skin

tag: biological replicate

tag: time

value: Day 3

tag: treatment

value: control


title: M-W-SF-1

city: Changsha

first: Yanxia

last: Guo

address: 100 Fubuhe Street, Yuelu District

country: China

institute: Hunan University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated
Raw reads of fastq format were processed using fastp 1 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-count
Assembly: StringTie2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: tumor tissue

extract_protocol:
RNA was harvested using  TRIzol reagent (Invitrogen, CA, USA)
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: tumor tissue

tag: cell line

tag: cell type

value: colon cancer cells

tag: genotype

value: WT C57BL/6 mice

value: Salmonella i.v. injection post 1 day


title: M-W-PM-2

value: PBS i.v. injection post 1 day


title: Skin, control, day00, rep2, pair1

description:
count data column name: YC04-16BLA
cao_mouse_skin_genesymbol_count

value: Day 0


title: kidney, 24 months, rep2

country: Germany


title: kidney, 24 months, rep1


title: M-W-PM-1


title: WT human gastric antral organoids-2

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

description: human-TNFa-con.csv

data_processing:
RNA-seq reads were aligned to the human, pig, rat or mouse genome available in Ensembl (release 95) with HISAT2 (v2.1.0)
StringTie (v1.3.3b) for transcript assembly
The quantitative gene expression (FPKM) was obtained with Ballgown
Assembly: Human: hg38, Pig: Sscrofa11.1, Rat: Rnor_6.0, Mouse: mm10
Supplementary files format and content: csv

organism: Homo sapiens

source_name: Gastric antral organoids

growth_protocol: Organoids were embedded in Matrigel and seeded on 48- or 24- well plate. After Matrigel polymerization, the CM medium (Advanced DMEM/F12 supplemented with Penicillin/Streptomycin, GlutaMAX, N2, B27, and N-acetylcysteine containing 50 ng/mL EGF, 100 ng/mL Noggin, 500 ng/mL R-spondin1, 5 μM CHIR, 10 nM Gastrin, 10 μM SB431542, 100 ng/mL FGF10 and 10 μM Y27632) was added and refreshed every 2 days.

extract_protocol:
Organoids were digested with Tryple and alive cells were sorted by flow cytometry. Total RNA was extracted with RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.
The library were prepared for sequecing using NEBNext Ultra RNA library Prep Kit for Illumina.

treatment_protocol: Organoids derived from antral glands of 4 kinds of species were treated with Tnfa 10 ng/ml for 2 days.

tag: strategy

value: RNA-Seq

value: Sleeve gastric surgery

value: Untreated


title: Skin, control, day03, rep1, pair1

description:
count data column name: YC04-15-D3A
cao_mouse_skin_genesymbol_count


title: kidney, 12 months, rep3

value: 12 months


title: M-W-PF-1


title: Skin, control, day00, rep1, pair1

description:
count data column name: YC04-15BLA
cao_mouse_skin_genesymbol_count


title: WT human gastric antral organoids-1

description: human-TNFa-con.csv


title: kidney, 12 months, rep2

value: kidney


title: pig antrum scRNA-seq

library_source: transcriptomic single cell

data_processing:
Raw reads were aligned to the different species genome (Human: GRCh38/hg38, Pig: Sscrofa11.1, Rat: Rnor_6.0, Mouse: GRCm38/mm10), and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers (UMIs).
Raw aligned features were loaded and processed using the Seurat package (v4.0.2)
Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes
Assembly: Human: hg38, Pig: Sscrofa11.1, Rat: Rnor_6.0, Mouse: mm10
Supplementary files format and content: text files

source_name: antral epithelium and stromal cells

extract_protocol:
Gastric glands were isolated and digested with EDTA and Tryple, alive cells were sorted by flow cytometry. Single cell suspensions were captured using the 10X Genomics Chromium
ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000.

value: antral epithelium and stromal cells

tag: strain

value: scRNA-seq

value: Wild type


title: Skin, Adalimumab, day10, rep1, pair1

description:
count data column name: Day10-1A
cao_mouse_skin_genesymbol_count

value: skin

value: Day 10

value: Adalimumab


title: bulk RNA-seq of human gastric antral organoids


title: kidney, 12 months, rep1

value: whole kidney

value: WT


title: TNFa treated mouse gastric antral organoids-2

description: mouse-TNFa-con.csv

value: Treated with TNFa 2 days


title: Skin, control, day10, rep1, pair1

description:
count data column name: 9-Day10A
cao_mouse_skin_genesymbol_count

value: control


title: ACLYi-2

city: shanghai

first: Ranran

last: Li

state: shanghai

address: ruijin hospital

institute: ruijin hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HUVEC

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: HUVEC

value: ACLYi+LPS


title: ACLYi-1


title: kidney, 3 months, rep3

value: 3 months


title: WT mouse gastric antral organoids-2

description: mouse-TNFa-con.csv

value: RNA-Seq


title: Skin, Adalimumab, day07, rep3, pair1

description:
count data column name: 5-Day7A
cao_mouse_skin_genesymbol_count

value: Day 7


title: TNFa treated human gastric antral organoids-1

description: human-TNFa-con.csv

value: Sleeve gastric surgery


title: kidney, 3 months, rep2

value: kidney


title: Skin, Adalimumab, day07, rep2, pair1

description:
count data column name: 4-Day7A
cao_mouse_skin_genesymbol_count


title: WT mouse gastric antral organoids-1

description: mouse-TNFa-con.csv

value: Untreated


title: Skin, Adalimumab, day07, rep1, pair1

description:
count data column name: 3-Day7A
cao_mouse_skin_genesymbol_count


title: kidney, 3 months, rep1


title: bulk RNA-seq of mouse gastric antral organoids


title: LPS1

value: LPS


title: LPS2


title: PB-Cre4/PTENfl/fl/ERG/Snd1fl/fl mouse prostate gland ventral lobe 245 #2

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
genome build: mm10
Sequencing reads were mapped using STAR.v2.7.3a.
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

extract_protocol:
Total RNA was extracted with QIAzol (QIAGEN) followed by RNase-free DNAase treatment (QIAGEN) and purification using RNeasy kit (QIAGEN).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

treatment_protocol: All procedures involving mice and experimental protocols were approved by the IACUC of Fred Hutchinson Cancer Center (FHCC) and followed NIH guidelines for animal welfare. Mice with a conditional Snd1 allele containing exon 3 flanked by LoxP sequences were generated using conventional embryonic stem cell gene targeting technology. PCR with oligos Snd1-F (5′-GGAACTGTTGCTGTGTTCGT -3′) and Snd1-R (5′-GCTAAAGAGTCCCTAGAAAG -3′) was used for genotyping (wild-type allele, 236 base pairs [bp]; floxed allele, 364 bp). PB-Cre4/Snd1fl/fl mice were generated by crossing PB-Cre438 with Snd1fl/fl mice. PB-Cre4/PTENfl/fl/ERG mice were generated by crossing PB-Cre4/PTENfl/fl mice49 with Tg(Pbsn-ERG)1Vv mice45. PB-Cre4/PTENfl/fl/ERG/Snd1fl/fl were made by crossing PB-Cre4/PTENfl/fl/ERG mice with Snd1fl/fl mice. All mice were maintained on a mixed 129S1/SvlmJ / C57BL/6J/ genetic background.

tag: Sex

value: male

value: mouse prostate gland ventral lobe


title: Skin, control, day07, rep3, pair1

description:
count data column name: 14-Day7A
cao_mouse_skin_genesymbol_count

value: skin


title: TNFa treated mouse gastric antral organoids-1

description: mouse-TNFa-con.csv

value: Wild type


title: PTEC, day 16_irradiated, rep2

value: proximal tubular cells

value: irradiation 10 Gy

value: day 16


title: PB-Cre4/PTENfl/fl/ERG/Snd1fl/fl mouse prostate gland ventral lobe 245 #1


title: PTEC, day 16_irradiated, rep1

value: WT


title: Skin, control, day07, rep2, pair1

description:
count data column name: 13-Day7A
cao_mouse_skin_genesymbol_count

value: control


title: VCaP siSND1 oligo 2 #3

data_processing:
genome build: hg38
Sequencing reads were mapped using STAR.v2.7.3a.
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: VCaP siSND1 oligo 2

growth_protocol: VCaP cells were cultured in DMEM media (Thermo Fisher, 11965-092) with 10% fetal bovine serum (Hyclone), sodium pyruvate (Thermo Fisher, 11360-070), non-essential amino acids (Thermo Fisher, 11140-050) and primocin (InvivoGen, ant-pm-2).

treatment_protocol: Transient transfection with siRNA oligos was performed using Lipofectamine RNAiMAX according to manufacturer protocols (Thermo Fisher, 13778-075). All siRNA oligos were purchased from Qiagen. siRNA oligos targeting human SND1: #2 custom with target sequence 5’-CAGCGTAGTTCGGGATATCCA-3’.

value: prostate cancer

value: VCaP (ATCC CRL-2876)


title: Skin, control, day07, rep1, pair1

description:
count data column name: 12-Day7A
cao_mouse_skin_genesymbol_count


title: PB-Cre4/PTENfl/fl/ERG/Snd1fl/fl mouse prostate gland ventral lobe 238 #2


title: VCaP siSND1 oligo 2 #2


title: PTEC, day 6, rep4

value: day 6


title: Skin, control, day10, rep3, pair1

description:
count data column name: 11-Day10A
cao_mouse_skin_genesymbol_count

value: Day 10


title: Skin, control, day10, rep2, pair1

description:
count data column name: 10-Day10A
cao_mouse_skin_genesymbol_count


title: PTEC, day 6, rep3


title: PB-Cre4/PTENfl/fl/ERG mouse prostate gland ventral lobe 354 #2


title: CT2

value: HUVEC

value: CT


title: PTEC, day 16_irradiated, rep3

value: kidney


title: PTEC, day 6, rep2


title: Skin, Adalimumab, day10, rep2, pair1

description:
count data column name: 2-Day10A
cao_mouse_skin_genesymbol_count

value: Adalimumab


title: VCaP siSND1 oligo 1 #3

source_name: VCaP siSND1 oligo 1

treatment_protocol: Transient transfection with siRNA oligos was performed using Lipofectamine RNAiMAX according to manufacturer protocols (Thermo Fisher, 13778-075). All siRNA oligos were purchased from Qiagen. siRNA oligos targeting human SND1: #1 custom with target sequence 5’-CAGGCTGAACCTGTGGCGCTA-3’.

value: male


title: VCaP siSND1 oligo 1 #2


title: anti-PD1_Rep3

city: La Jolla

first: Ze'ev

middle: A.

last: Ronai

state: CA

address: 10901 North Torrey Pines Road

department: Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Illumina Truseq adapters and polyA/polyT sequences were trimmed from raw reads using Cutadapt version 2.3.
Trimmed reads were aligned to mouse genome version mm10 and Ensembl gene annotations version 84 using STAR version 2.7.0d_0221 adopting alignment parameters from ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline).
RSEM version 1.3.1 was used to obtain gene level estimated counts and transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes TPM (Transcripts Per Million) values for each sample.

growth_protocol: RNA samples were prepared from bulk tumors, MACS-sorted tumor cells, and cultured cells for gene expression analysis. To purify tumor cells from bulk tumor tissue, collected B16F10 tumors were minced, chopped, and incubated in Collagenase D solution [0.1 % (w/v) Collagenase D, 0.5 % (w/v) BSA, 100 g/ml DNase in PBS] for 1 h at 30 °C. A single-cell suspension was obtained using a cell strainer (70m, Falcon). Tumor cells were purified by depletion of stromal cells using a Tumor Cell Isolation kit (Miltenyi Biotech). The purity of isolated tumor cells was validated by FACS using a CD45 antibody.

extract_protocol:
RNA from bulk tumors, MACS-sorted tumor cells, and cultured cells were purified using a GenElute total RNA purification kit (Sigma-Aldrich).
PolyA RNA was isolated using NEBNext® Poly(A) mRNA Magnetic Isolation Module, and bar-coded libraries were constructed using the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA). Libraries were pooled and sequenced from a single-end (1X75) on an Illumina NextSeq 500 system using the High output V2 kit (Illumina Inc., San Diego, CA) at a sequencing depth of 23-31 million reads.

tag: group


title: PTEC, day 6, rep1


title: PTEC, day 16_irradiated, rep4


title: PB-Cre4/PTENfl/fl/ERG mouse prostate gland ventral lobe 354 #1

value: mouse prostate gland ventral lobe


title: PB-Cre4/PTENfl/fl/ERG mouse prostate gland ventral lobe 4 #2


title: VCaP siSND1 oligo 1 #1


title: PB-Cre4/PTENfl/fl/ERG mouse prostate gland ventral lobe 4 #1


title: Brown adiose tissue, Thermoneutrality (TN), Spatial

city: Philadelphia

first: Patrick

last: Lundgren

state: PA

address: 302 Johnson Pavilion, 3610 Hamilton Walk

institute: University of Pennsylvania

data_processing:
Spaceranger v1.3
Supplementary files format and content: mm10
Supplementary files format and content: h5
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

source_name: Brown adipose tissue (BAT)

extract_protocol:
Brown adipose tissue was collected from mouse at thermoneutrality and mouse that had undergone transient acute cold exposure 4 days previously.
Sample preparation, sectioning, staining, imaging, library preparation, and sequencing was performed following the Visium protocol (10X Genomics).

value: Brown adipose tissue (BAT)

value: mice housed at thermoneutrality (TN)


title: anti-PD1_Rep2


title: VCaP siERG oligo 3 #3

source_name: VCaP siERG oligo 3

treatment_protocol: Transient transfection with siRNA oligos was performed using Lipofectamine RNAiMAX according to manufacturer protocols (Thermo Fisher, 13778-075). All siRNA oligos were purchased from Qiagen. siRNA oligos targeting human ERG: #3 custom with target sequence 5’-GATGATGTTGATAAAGCCTTA-3’.


title: IgG_Control_Rep2


title: PB-Cre4/PTENfl/fl/ERG/Snd1fl/fl mouse prostate gland ventral lobe 238 #1


title: anti-PD1_Rep1


title: PB-Cre4/PTENfl/fl/ERG mouse prostate gland ventral lobe 3 #2


title: PB-Cre4/PTENfl/fl/ERG mouse prostate gland ventral lobe 3 #1


title: IgG_Control_Rep1


title: VCaP siSND1 oligo 2 #1


title: VCaP siERG oligo 3 #1


title: Brown adipose tissue, Thermoneutrality (TN), snRNAseq

data_processing:
Cellranger v3
Supplementary files format and content: mm10
Supplementary files format and content: matrix, barcodes, and gene files

extract_protocol:
Nuclei were isolated as described in manuscript, sorted based on DAPI positivity, and loaded into 10X Genomics platform
10X Genomics according to manufacturers protocol
snRNAseq


title: VCaP siERG oligo 1 #3

source_name: VCaP siERG oligo 1

treatment_protocol: Transient transfection with siRNA oligos was performed using Lipofectamine RNAiMAX according to manufacturer protocols (Thermo Fisher, 13778-075). All siRNA oligos were purchased from Qiagen. siRNA oligos targeting human ERG: #1 custom with target sequence 5’-AACGACATCCTTCTCTCACAT-3’.


title: PB-Cre4/PTENfl/fl mouse prostate gland ventral lobe 456 #1


title: single cell RNA-seq 1

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

data_processing:
Base-calling was performed with Illumina RTA v2 and fastq files were generated in Illumina NextSeq 550.
The gene expression count matrix was generated using BD Rhapsody Analysis pipelines (v1.9.1) on the Seven Bridges Genomics platform with the default setting.
Assembly: mm10

source_name: Mesenchymal chondrosarcoma

growth_protocol: Mouse sarcoma was transplanted into the subcutaneous part of a nude mouse

extract_protocol:
A total of 200 mg of tumor tissue was dissected into small pieces and digested using a Tumor Dissociation Kit and GentleMACS Dissociator (Miltenyi Biotec). The digested tumor tissue was filtered through a 70 μm MACS SmartStrainer (Miltenyi Biotec), and the mass remaining on the filter was dissociated using Accutase (Nacalai Tesque) to obtain a single-cell suspension.
The scRNA-seq library was prepared using BD Rhapsody™ Single-Cell Analysis system (BD) following the manufacturer's instruction. Briefly, 20,000 cells were loaded onto the BD Rhapsody microwell cartridge, and cDNAs were synthesized using a BD Rhapsody™ Whole Transcriptome Analysis Amplification Kit.

treatment_protocol: HEY1-NCOA2 was introduced by retrovirus-mediated gene transfer

value: HEY1-NCOA2-expressing murine mesenchymal chondrosarcoma

value: Balb/c


title: Sorted_Tumor_Cell_sg495_Rep1

value: MACS-sorted tumor cells

value: NR2F6 KO


title: Sorted_Tumor_Cell_sg495_Rep2


title: VCaP siERG oligo 1 #2


title: VCaP siERG oligo 1 #1


title: PB-Cre4/PTENfl/fl mouse prostate gland ventral lobe 444 #2


title: macrophage, infected, 24h, rep3

type: RNA

city: Ribeirão Preto

first: Juliane

middle: Cristina Ribeiro

last: Fernandes

address: Av. Bandeirantes, 3900

country: Brazil

institute: University of São Paulo

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/us/analyze
the fold_change.txt reports test/control (i.e., infected/non-infected macrophages) ratios.
the average_normalized.txt has averaged normalized value per group.

label: SYBR Green

source_name: THP-1-derived macrophages

label_protocol: The reverse transcription of mature miRNAs was performed using the “miScript II RT Kit” (Qiagen) from 2 µg of total RNA following the manufacturer’s instructions. PCR assays were performed using the Qiagen Human Inflammatory Response & Autoimmunity, RT-PCR Array

growth_protocol: THP-1 cells were plated and differentiated in 6-well plates and maintained in a incubator at 34oC and 5% CO2. Leishmania promastigotes were cultivated at 25oC.

extract_protocol: Macrophages were lysed using QIAZOL reagent. Total RNA was extracted with RNeasy Mini Kit.

treatment_protocol: Leishmania amazonensis promastigotes at stationary growth phase were used to infect THP-1 at MOI 5 for 4 hours.

value: Macrophage

tag: treatment group

value: 24 hours

tag: molecule subtype

value: miRNA


title: Sorted_Tumor_Cell_sg492_Rep2


title: PB-Cre4/PTENfl/fl mouse prostate gland ventral lobe 444 #1


title: Brown adipose tissue, 4 days after primary cold challenge (1cyc), Spatial

value: mice that had undergone transient acute cold exposure 4 days previously (1cyc)


title: VCaP siERG oligo 3 #2

value: prostate cancer

value: VCaP (ATCC CRL-2876)


title: CT1

value: HUVEC

value: CT


title: VCaP siControl #3

source_name: VCaP siControl

treatment_protocol: Transient transfection with siRNA oligos was performed using Lipofectamine RNAiMAX according to manufacturer protocols (Thermo Fisher, 13778-075). All siRNA oligos were purchased from Qiagen. AllStars Negative Control siRNA (Qiagen, Cat# 1027281) was used as control.


title: PB-Cre4/PTENfl/fl mouse prostate gland ventral lobe 286 #2


title: Sorted_Tumor_Cell_Control_Rep2

value: WT


title: PB-Cre4/PTENfl/fl mouse prostate gland ventral lobe 286 #1

value: male


title: PB-Cre4/PTENfl/fl mouse prostate gland ventral lobe 456 #2

value: mouse prostate gland ventral lobe


title: VCaP siControl #2


title: macrophage, infected, 24h, rep1


title: Sorted_Tumor_Cell_Control_Rep1


title: macrophage, infected, 24h, rep2


title: PB-Cre4/PTENfl/fl mouse prostate gland ventral lobe 282 #2


title: VCaP siControl #1


title: macrophage, infected, 24h, rep4


title: Cultured_Cell_sg495_Rep2

value: cultured cells


title: macrophage, non-infected, 24h, rep3

value: Non-infected macrophages


title: Human-PC-CD45+

city: Shang Hai

first: Ping

middle: Ping

last: Nie

address: Songhu Road 2005

institute: Fudan University

data_processing:
Sequencing depth was normalized by using CellRanger (version v3.1.0).
We used Seurat package (version 3.0)  in R (version 3.5.3) to perform data filtering (both gene and cell), normalization, PCA and t-SNE.
Cells defined as neutrophils, macrophage, monocyte, dendritic cells, natural killer cells, T cells and B cells.
We constructed single-cell trajectory of neutrophils  by using reversed graph embedding method implemented in R Monocle package (version 2.6.3)
Genome_build: mm10;hsa
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Human gastric cancer

extract_protocol:
All murine tissues in this study were prepared from mice sacrificed by cervical dislocation at the same time. For the isolation of bone marrow cells, leg bones from murine femur were flushed using a 21-gauge needle in RPMI1640 medium containing 1% FBS. For the isolation of spleen cells, the whole spleen was dissected and homogenized into single-cell suspensions using a 1 ml syringe plunger with a 21-gauge needle. For the isolation of peripheral blood immune cells, 600~800 ml blood was collected by retro-orbital bleeding. For the isolation of gastric cancer infiltrated immune cells from xenograft tumor tissues (300~1,000mm3) and gastric cancer patient, tumor tissues were dissected into 1~2 mm pieces with scissors in PBS buffer and digested in RPMI 1640 Medium with 1 mg/ml Collagenase II and 100 mg/ml DNase I at 37 °C for 30 min. Subsequently, BM, SP, PB and GC cells were filtered with a 70 mm cell strainer. After a 5 min centrifugation at 500 g, cells were resuspended with red blood cell lysis buffer to deplete red blood cells. Subsequently, cells were washed 2~3 times and stained with fluorophore-conjugated anti-mouse antibodies against Live/dead, CD45, CD11b and Ly6G for 30 min at 4°C. After exclusion of cell doublets and dead cells with, single cells were purified by fluorescence-activated cell sorting (FACS) using a FACS AriaIII cell sorter and Diva software (both BD Biosciences) to achieve > 98% purity.
Libraries were constructed using the Single Cell 3’ Library Kit V2 (10× Genomics).

treatment_protocol: WT or KO mice were injected with 3 × 106 MFC cells/per mouse to   induce tumor formation for 3d or 10d.

value: CD45+ immune cells


title: Cultured_Cell_sg495_Rep1


title: macrophage, non-infected, 24h, rep2


title: Human-Blood-CD45+


title: macrophage, non-infected, 24h, rep1


title: KO-Tumor-CD45+

source_name: Tumor

value: KO

value: 10 days after MFC subcutaneously injection


title: Cultured_Cell_sg492_Rep2

value: NR2F6 KO


title: Sorted_Tumor_Cell_sg492_Rep1

value: MACS-sorted tumor cells


title: Hob2, Dox off, Flag

city: Copenhagen

first: William

middle: Winston

last: Agace

address: Blegdamsvej 3B

department: Skin Immunology Research Center

country: Denmark

institute: Copenhagen University

library_source: genomic

data_processing:
Adapter sequences were removed from reads with cutadapt v3.5
CUT&RUN-seq reads were aligned to Hg19 using bowtie2 v2.4.2
Alignments were filtered and sorted using samtools v1.2, and converted to bed and subsequently bedgraphs using bedtools v2.30.0
Peaks were called uing SEACR v1.3
bigWig files were generated using bamcoverage from deeptools v3.5.1
Differential peaks were detected using DiffBind v3.4.3
Assembly: hg19
Supplementary files format and content: bigWig, bed
Library strategy: CUT&RIN

molecule: genomic DNA

source_name: Jurkat

growth_protocol: RPMI 10% FCS.

extract_protocol:
Epicypher CUT&RUN protocol
CUT&RUN libraries  were prepared following the protocol NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

treatment_protocol: grown with or without 1 ug/uL of doxycycline

value: Jurkat

tag: antibody

value: Dox off, Flag


title: WT-Tumor-CD45+

value: wild type


title: macrophage, infected, 4h, rep4

value: Macrophage

value: 4 hours

value: miRNA


title: Cultured_Cell_sg492_Rep1


title: macrophage, non-infected, 24h, rep4

value: 24 hours


title: macrophage, infected, 4h, rep3


title: Hob1, Dox off, Flag


title: Cultured_Cell_Control_Rep2

value: WT


title: D10-TAN

value: neutrophils


title: macrophage, infected, 4h, rep2


title: Hob2, Flag

value: Flag


title: Bulk_Tumor_sg495_Rep2

value: bulk tumors


title: Blood Neus

source_name: Blood


title: Hob2, IgG, Isotype

value: IgG, Isotype


title: Bulk_Tumor_sg495_Rep1


title: PB-Cre4/PTENfl/fl mouse prostate gland ventral lobe 282 #1

value: male

value: mouse prostate gland ventral lobe


title: SP Neus

source_name: Spleen

value: 10 days after MFC subcutaneously injection


title: Hob2, H3K4me3, His

value: H3K4me3, His


title: BM Neus

source_name: Bone marrow


title: macrophage, non-infected, 4h, rep4

value: Non-infected macrophages


title: Human-Tumor-CD45+

value: CD45+ immune cells


title: macrophage, non-infected, 4h, rep3


title: Hob1, Flag

value: Jurkat


title: Bulk_Tumor_sg492_Rep2

value: NR2F6 KO


title: Bulk_Tumor_sg492_Rep1


title: macrophage, non-infected, 4h, rep2

value: Macrophage


title: PLAC-seq E13.5 BG 10k resolution

city: Davis

first: Alex

middle: S.

last: Nord

address: 1544 Newton Court

department: Center for Neuroscience

institute: University of California Davis

data_processing:
We applied the MAPS pipeline to detect statistically significant H3K4me3-centric long-range chromatin interactions from PLAC-seq data. We only analyzed intra-chromosomal interactions for autosomal chromosomes, and identified chromatin interactions at 10-kb bin resolution between 20 kb and 1 Mb. We first mapped the raw paired-end reads (i.e. FASTQ file) to the mm10 reference genome using BWA mem. Next, we applied filtering steps to remove PCR duplicates, low-quality reads (MAPQ <= 30) and chimeric reads. We then split the remaining mapped reads into short-range (distance between pair ends within 1 kb) and long-range reads (distance between pair ends between 1 kb and 1 Mb). We used the short-range and long-range reads to measure protein immunoprecipitation (IP) efficiency and detect long-range chromatin interactions, respectively.
For ChIP-seq, quality-controlled FASTQ files containing the reads were further cleaned-up from the remaining adapter sequences using Trim Galore version 0.4.5. The resulting reads were aligned to the mouse (mm10) genome using BWA version 0.7.9a, and duplicates removed with Samtools version 1.8. Peaks of enriched binding regions against both negative binding and input DNA control were called using MACS version 2.1 with p-value cutoffs of 10E-4.
Assembly: mm10
Supplementary files format and content: PLAC-seq: interaction bed files
Supplementary files format and content: ChIP-seq: narrow peaks

source_name: brain

extract_protocol:
ChIP was performed using antibodies against SP9, ARX, ASCL1, GSX2, and NR2F1. Basal ganglia were dissected in cold PBS from CD1 embryos (2 L/Ab for NR2F1; 3 L/Ab for ARX, ASCL1, and GSX2). The basal ganglia consisted of the LGE, MGE and CGE progenitor and mantle zones. The dissected basal ganglia were either fixed in 1% formaldehyde at RT for 10 min (SP9, ASCL1, GSX2, NR2F1) or fixed in 1.5% formaldehyde at RT for 20 min (ARX), neutralized with glycine, and washed gently in PBS. The fixed cells were lysed with a hypotonic buffer (50 mM Tris pH 7.5 / 0.5% NP40 / 0.25% sodium deoxycholate / 0.1% SDS / 150 mM NaCl) to obtain the nuclei; these were then lysed in 1% SDS buffer and the chromatin was sheared into 300-1000 bp fragments by sonicating for 40 cycles (30 sec on and 45 sec off) using a bioruptor (Diagenode). Immunoprecipitation (IP) reactions were performed with the sheared chromatin diluted 1/10 times with “dilution buffer” (0.01% SDS, 1.1% Triton X- 100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167mM NaCl, usually in 6 ml. Antibody was then added to either 5 µg (ARX, SP9, NR2F1) or 8 µg (ACSL1, GSX2) specific antibodies. Negative control ChIP reactions used either IgG (5µg) or blocking peptide (ARX, 400x molar excess). Antibody/chromatin complexes were purified using Dynabeads (Invitrogen) and washed extensively in “wash buffer” (low salt, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl; high salt, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 500 mM NaCl; LiCl, 0.25 M LiCl, 1% IGEPAL CA630, 1% deoxycholic acid (sodium salt), 1mM EDTA, 10mM Tris, pH 8.1 and TE). Complexes were eluted with 1% SDS, 10 mM sodium bicarbonate buffer at 65 ºC for 10 min. Eluted chromatin was reverse-crosslinked overnight at 65 ºC in the presence of 500 mM NaCl, then subsequently treated with RNase (10 µg/200 µL reaction, 15 min at 37 ºC) and Proteinase K (10 µg/200 µL reaction, 60 min at 55 ºC) and cleaned using a ChIP DNA Clean & Concentrator kit (Zymo Research). The chromatin was quality-controlled (QC) using qPCR to check for enrichment of genomic DNA fragments that were expected, and not expected, to have the different TF binding.
For ChIP-seq, libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size- selected in the range of 300 bp on a chip from BluePippin (Sage Science) and lastly QC tested on a Bioanalyzer (Agilent). The libraries were sequenced as single-end 50-bp reads on a HiSeq 4000 (Illumina) at the Center for Advanced Technology (UCSF). PLAC-seq libraries for E13.5 basal ganglia were prepared similar to a previously published protocol61. 3 to 7 million cells were used for each library. If the cells appeared aggregated, they were dissociated with gentle MACS dissociator or Dounce homogenizer. Each PLAC-seq library was prepared using DpnII as the restriction enzyme and Dynabeads M-280 sheep anti-rabbit IgG (Invitrogen #11203D) mixed with 5 µg of H3K4me3 (04-745, Millipore) for the chromatin immunoprecipitation step. Finally, libraries were prepared with the Illumina TruSeq adaptors and the final libraries were sent for paired-end sequencing on the HiSeq X Ten (150-bp reads) equipment.
ChIP-seq, PLAC-seq

value: brain

value: basal ganglia

value: wild-type

tag: chip antibody

value: Millipore cat# 04-745 (H3K4me3)


title: Hob1, IgG, Isotype


title: Bulk_Tumor_Control_Rep2

value: WT


title: D3-TAN

value: neutrophils

value: wild type

value: 3 days after MFC subcutaneously injection


title: Cultured_Cell_Control_Rep1

value: cultured cells


title: MM1+CO D1525

city: Busan

first: LEE

middle: SEONG

last: HYUK

address: Haeyang-ro

department: Department of Marine Biotechnology

country: South Korea

institute: Korea Institute of Ocean Science and Technology

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic 0.32 as default parameter, then mapped to mm8 whole genome using bowtie v 2.2.4 with parameters -t --very-sensitive
Differential expression profiles indicated by FPKM and TPM value.
Genome_build: PRJNA59043 (2013-06-10)
Supplementary_files_format_and_content: Excel file includes differential expression profiles and locus tags for genes of T. onnurineus NA1

organism: Thermococcus onnurineus NA1

source_name: RNA from Archaeal cells

extract_protocol:
After cell harvest, RNA samples were prepared using TRIzol reagent. Genomic DNA was eliminated by DNaseI treatment.
To remove rRNA in total RNA, Ribo-Zero rRNA Removal Kits (Human/Mouse/Rat) (MRZH-11124, Epicentre, USA) was used. Illumina Stranded TruSeq Total RNA Sample Prep Kit (Cat#FC-122-2201) was used with 1 ug of rRNA depleted RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: medium

tag: growth phase

value: exponential phase


title: macrophage, infected, 4h, rep1

value: 4 hours

value: miRNA


title: macrophage, non-infected, 4h, rep1

value: Non-infected macrophages


title: MM1+CO WT


title: Bulk_Tumor_Control_Rep1

value: bulk tumors


title: Hob1, H3K4me3, His

value: Jurkat

value: H3K4me3, His


title: IP_2h1_TRB1-GFP_rep2

status: Public on Sep 10 2023

city: Paris

first: Fredy

last: BARNECHE

address: Rue d'Ulm

department: IBENS

country: France

institute: CNRS

description: ChIP-DNA

data_processing:
Reads were trimmed using Trimmomatic 0.38 with the following command "java -jar trimmomatic-0.38.jar PE -phred33 -validatePairs ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:20"
Trimmed read were aligned to Arabidopsis thaliana genome assembly (TAIR10) using bowtie2 v2.4.2 and the setting "--very-sensitive".
Unmapped reads were removed, together with supplementary alignments, not primary alignments, duplicated reads and read mapping on regions with low mappability defined as in Quadrana L, et al., The Arabidopsis thaliana mobilome and its impact at the species level. Elife (2016) 3;5:e15716. doi: 10.7554/eLife.15716.
Read coverage was computed from the filtered bam files with Deeptools 3.5.1 bamCoverage, with the parameters "-bs 10 effectiveGenomeSize 119000000 --normalizeUsing RPGC" to normalize the sequencing depth.
Assembly: TAIR10
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: 8-day-old Arabidopsis seedlings

growth_protocol: Arabidopsis seeds were surface-sterilized, plated on half strength Murashige and Skoog (MS) medium 0.9% agar, 0.5% sucrose and cultivated under long-day (16h/8h) light/dark and 23/19°C periods

extract_protocol:
anti-GFP ChIP were performed as follow: Chromatin was extracted and resuspended in 300 µL Nuclei Lysis Buffer, the samples were flash frozen in liquid nitrogen to help breaking the nuclei. Chromatin was sheared using a Diageode Bioruptor to obtain fragments between 75 and 300 bp.
ChIP-Seq NEBNEXT Ultra II kit

treatment_protocol: WT Col-0 or the TRB1-GFP (Prochazkova Schrumpfova et al., 2016 doi:10.1007/s11103-015-0409-8) 8-day-old seedlings freshly crosslinked twice for 7 min with 1% formaldehyde.

value: anti-GFP (Thermo Fisher #A11122)

tag: tissue

value: entire seedlings


title: IP_Wtcoseg_TRB1-GFP_rep2

description: ChIP-DNA


title: Input_Wtcoseg_TRB1-GFP

description: input

value: input


title: IP_2h1_TRB1-GFP

description: ChIP-DNA


title: IP_Wtcoseg_TRB1-GFP

description: ChIP-DNA


title: IP_H1.2-GFP_rep3

description: ChIP-DNA

data_processing:
Reads were trimmed using Trimmomatic 0.36 with the following command "java -jar trimmomatic-0.36.jar SE -phred33 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:20"
Trimmed read were aligned to Arabidopsis thaliana genome assembly (TAIR10) using bowtie2 v2.3.3 and the setting "--very-sensitive".
Duplicated mapped reads were removed with sambamba 0.7.1 markdup and reads with mapping quality lower than MAPQ 10 discarded with sambamba 0.7.1 and the command [view -F "mapping_quality >= 10"].
Bigwig files with the
Read coverage was computed from the filtered bam files with Deeptools 3.4.0 bamCoverage, using the parameters "effectiveGenomeSize 119000000 --normalizeUsing RPGC" to normalize the sequencing depth.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

source_name: 5-day-old Arabidopsis seedlings

growth_protocol: Arabidopsis seeds were surface-sterilized, plated on half strength Murashige and Skoog (MS) medium 0.9% agar and cultivated under long-day (16h/8h) light/dark and 23/19°C periods

extract_protocol:
anti-GFP and anti-H3 ChIP were performed as follow: crosslinked dissected cotyledons were frozen in liquid nitrogen and ground in Eppendorf tubes using a Tissue Lyser (Qiagen) for 90 seconds at 30 Hz. Chromatin was extracted and resuspended in 100 µL Nuclei Lysis Buffer, the samples were flash frozen in liquid nitrogen to help breaking the nuclei. Chromatin was sheared using a S220 Focused-ultrasonicator (Covaris) for 17 min at 105 W of power to obtain fragments between 75 and 300 bp.
ChIP-Seq TruSeq kit

treatment_protocol: Fresh cotyledons of the WT Col-0 or the pH1.2::H1.2-GFP line were manually dissected from 200 5-day-old seedlings freshly crosslinked for 15 min with 1% formaldehyde.

tag: plant line

value: cotyledons


title: IP_H1.2-GFP_rep2

description: ChIP-DNA


title: IP_H1.2-GFP_rep1

description: ChIP-DNA


title: IP_H3

description: ChIP-DNA

value: anti-H3 (Abcam #Ab1791)


title: input_H1.2-GFP_rep1

description: ChIP-DNA


title: input_H1.2-GFP_rep2

description: ChIP-DNA


title: IP_K27_WT_rep2

description: ChIP-DNA

data_processing:
Reads were trimmed using Trimmomatic 0.36 with the following command "java -jar trimmomatic-0.36.jar SE -phred33 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:20"
Trimmed read were aligned  against a genome that combines the Arabidopsis thaliana (TAIR10) and Drosophila melanogaster (dm6) genomes using bowtie2 v2.3.3 and the setting "--very-sensitive". The reads mapping to Drosophila genome were first normalized according to the number of input reads and then used to obtain a normalization factor for each sample.
Duplicated mapped reads were removed with sambamba 0.7.1 markdup and reads with mapping quality lower than MAPQ 10 discarded with sambamba 0.7.1 and the command [view -F "mapping_quality >= 10"].
Read coverage was computed from the filtered bam files with Deeptools 3.4.0 bamCoverage. The sequencing depth was normalized using the scaling factor calculated as described above.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

extract_protocol:
ChIP experiments were performed as in Nassrallah et al., eLife (2018; doi: 10.7554/eLife.37892).
ChIP-Seq TruSeq kit was used, SE 50bp reads were produced

treatment_protocol: Fresh seedlings of the WT Col-0 or the 2h1 mutant line were crosslinked for 15 min using 1% formaldehyde.

value: WT


title: Input_h1.1h1.2_rep2

description: ChIP-DNA


title: IP_K27_WT_rep1

description: ChIP-DNA


title: Input_h1.1h1.2_rep1

description: ChIP-DNA


title: IP_K27_h1.1h1.2_rep2

description: ChIP-DNA


title: IP_K27_h1.1h1.2_rep1

description: ChIP-DNA


title: Input_WT_rep1

description: ChIP-DNA


title: Input_2h1_TRB1-GFP

description: input


title: Mock_WT

description: mock IP

value: mock


title: 22RV1 cells treated with Canagliflozin (10uM) + Radiation (5Gy) (RT(5Gy)+10Cana-A) 24Hr

city: Hamilton

first: Amr

middle: Mohamed Ahmed

last: Ali

state: ON

address: 699 concession street-4-212

department: Oncology

country: Canada

institute: Mcmaster University

description: 10-22RV1-RT(5Gy)+10Cana-A 24Hr

data_processing:
The trimmomatic tool Cutadapt was employed to enhance sequence quality by trimming and filtering low-quality reads. The trimming process involved setting a Minimum length and Quality cut-off of "20", a Minimum overlap length of "3", and using the 5' adapter sequence "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA".
Next, the last group of reads undergoes alignment to the human gene (hg38) using the HISAT2 tool, with the specified strand information set to "reverse (R)"
The DESeq2 tool was utilized to identify features that displayed differential expression based on count tables and subsequently normalized the data.
The human gene annotation reference file was acquired from Ensembl gene using the annotateMyIDs tool.
The adjusted p-value (FDR; false discovery rate) was filtered using a tool with a threshold set to "<= 0.05", resulting in the generation of the r-log normalized list.he adjusted p-value (FDR; false discovery rate) was filtered using a tool with a threshold set to "<= 0.05", resulting in the generation of the r-log normalized list.
Assembly: human gene (hg38)
Supplementary files format and content: PC3 cells: an excel sheet inclueded normalized feature count
Supplementary files format and content: 22RV1 cells: an excel sheet inclueded rlog normalized feature count

source_name: 22RV1 cells

growth_protocol: PC3 and 22RV1 cells: RPMI media with 10%FBS and 1%antibiotic-anti-mycotic.

extract_protocol:
RNA extraction was carried out using chloroform, centrifugation, and isopropanol precipitation. The obtained RNA was used to prepare cDNA using the ReverAid™ First Strand cDNA Synthesis Kit and stored at -20°C.
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: DMSO, 10uM canagliflozin, 5Gy radiation or combination of Canagliflozin and radiation theapies

tag: disease state

value: Prostate cancer

value: 22RV1 cells

value: CRPC

value: Canagliflozin 10uM + Radiation (5Gy)


title: 22RV1 cells treated with Canagliflozin (10uM) + Radiation (5Gy) (RT(5Gy)+10Cana-B) 24Hr

description: 11-22RV1-RT(5Gy)+10Cana-B 24Hr

tag: treatment


title: 22RV1 cells treated with Radiation (5GY) (RT(5Gy B) 24Hr

description: 8-22RV1-RT(5GY)-B 24Hr

tag: cell line

value: Radiation (5Gy)


title: 22RV1 cells treated with Canagliflozin (10uM) + Radiation (5Gy) (RT(5Gy)+10Cana-C) 24Hr

description: 12-22RV1-RT(5Gy)+10Cana-C 24Hr

tag: cell type


title: 22RV1 cells treated with Canagliflozin (10uM) (10CANA C) 24Hr

description: 6-22RV1-10-CANA-C 24Hr

value: Canagliflozin 10uM


title: 22RV1 cells treated with DMSO (Control C) 24Hr

description: 3-22RV1-CONTROL-C 24Hr

value: DMSO


title: 22RV1 cells treated with DMSO (Control A) 24Hr

description: 1-22RV1-CONTROL-A 24Hr


title: PC3 cells treated with Canagliflozin (10uM) (10CANA C) 24Hr

description: 6- PC3 10CANA C 24Hr

source_name: PC3 cells

value: PC3 cells

value: mCRPC


title: 22RV1 cells treated with Radiation (5GY) (RT(5Gy C) 24Hr

description: 9-22RV1-RT(5GY)-C 24Hr


title: PC3 cells treated with Canagliflozin (10uM) (10CANA B) 24Hr

description: 5- PC3 10CANA B 24Hr


title: 22RV1 cells treated with Radiation (5GY) (RT(5Gy A) 24Hr

description: 7-22RV1-RT(5GY)-A 24Hr


title: 22RV1 cells treated with DMSO (Control B) 24Hr

description: 2-22RV1-CONTROL-B 24Hr


title: Input_WT_rep2

description: ChIP-DNA


title: PC3 cells treated with DMSO (Control B) 24Hr

description: 2- PC3 Control B 24Hr


title: PC3 cells treated with DMSO (Control C) 24Hr

description: 3- PC3 Control C 24Hr


title: PC3 cells treated with Canagliflozin (10uM) (10CANA A) 24Hr

description: 4- PC3 10CANA A 24Hr


title: PC3 cells treated with DMSO (Control A) 24Hr

description: 1- PC3 Control A 24Hr


title: ATAC_2h1_rep2

description: ATAC-seq

data_processing:
Fastq files were processed with the software ASAP v2.1 (available at https://github.com/akramdi/ASAP) using default settings for mapping and post-mapping processing.
Read coverage was computed from the bam files using Deeptools 3.4.0 bamCoverage, using the parameters "effectiveGenomeSize 119000000 --normalizeUsing RPGC" to normalize the sequencing depth.
Assembly: TAIR10
Supplementary files format and content: bigwig files contaning normalized read coverage (Reads per 1x genomic content)

growth_protocol: Arabidopsis seeds were surface-sterilized, plated on half strength Murashige and Skoog (MS) medium 0.9% agar and cultivated 5 daysunder long-day (16h/8h) light/dark and 23/19°C periods

extract_protocol:
200 cotyledons were dissected and 20.000 4C nuclei were isolated upon centrifugation over a Percoll gradient and fluorescence activated nuclear sorting (FANS) before flash freezing in liquid nitrogen. Tagmentation and following steps of ATAC-seq were performed on intact nuclei using a Nextera DNA Library Preparation kit (FC-121-1030) following the instructions of the manufacturer.
Nextera DNA library prep Kit Illumina Cat #FC-121-1030

tag: genotype

tag: enzyme


title: 22RV1 cells treated with Canagliflozin (10uM) (10CANA B) 24Hr

description: 5-22RV1-10-CANA-B 24Hr


title: 22RV1 cells treated with Canagliflozin (10uM) (10CANA A) 24Hr

description: 4-22RV1-10-CANA-A 24Hr


title: ATAC_WT_rep2

description: ATAC-seq


title: ATAC_2h1

description: ATAC-seq


title: ATAC_WT

description: ATAC-seq


title: 3trb.BR1.input

description: ChIP-DNA

data_processing:
Reads were aligned  against a genome that combines the Arabidopsis thaliana (TAIR10) and Drosophila melanogaster (dm6) genomes using bowtie2 v2.4.2 and the setting "--very-sensitive". The reads mapping to Drosophila genome were first normalized according to the number of input reads and then used to obtain a normalization factor for each sample.
Reads mapping to Drosophila genome were removed, together with unmapped reads, not primary alignments, supplementary alignments, duplicated reads and read mapping on regions with low mappability defined as in Quadrana L, et al., The Arabidopsis thaliana mobilome and its impact at the species level. Elife (2016) 3;5:e15716. doi: 10.7554/eLife.15716.
Read coverage was computed from the filtered bam files with Deeptools 3.5.1 bamCoverage, with the parameters "-bs 10 --scaleFactor". The sequencing depth was normalized using the scaling factor calculated as described above.
Assembly: TAIR10
Supplementary files format and content: bigwig files contaning normalized read coverage

source_name: Arabidopsis seedlings

extract_protocol:
ChIP experiments were performed as in Nassrallah et al., eLife (2018; doi: 10.7554/eLife.37892).
Nextera DNA library prep Kit Illumina Cat #FC-121-1030

treatment_protocol: Fresh seedlings of WT and mutant lines were crosslinked for 15 min using 1% formaldehyde.

tag: developmental stage

value: 8 dpi (WT phenotypes) or 12 dpi (tiny phenotypes)


title: 2h1wt3_coseg.BR1.input

description: ChIP-DNA

value: h1.2h1.2 segregant from the cross


title: 2h1wt3_coseg.BR2.IP

description: ChIP-DNA

value: anti-H3K27me3 (Diagenode #C15410069)

value: entire seedlings


title: 3trb.BR1.IP

description: ChIP-DNA


title: 2h1wt3_coseg.BR2.input

description: ChIP-DNA

value: input


title: 3trb.BR2.input

description: ChIP-DNA


title: 3trb.BR2.IP

description: ChIP-DNA


title: 2h1wt3_coseg.BR1.IP

description: ChIP-DNA


title: HM5_2h1trb123.BR1.input

description: ChIP-DNA


title: Mutant 3

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

data_processing:
Base calling was performed using bcl2fastq version 2.17.1.14.
Transcript abundance was estimated without aligning reads using Salmon against an index of coding sequences from the Ensembl GRCm38 assembly.
Transcript-level abundance was imported and count and offset matrices generated using the tximport R/Bioconductor package.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file including FPKM values for each sample.

source_name: Foxd1-Cre; Ntn1c/c mouse kidneys

extract_protocol:
Dissected kidneys stored in RNA later solution (Invitrogen, Cat. AM7020). RNA was extracted with the QIAGEN's RNeasy Micro Kit (QIAGEN Cat. 74004).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Foxd1-Cre; Ntn1/cc


title: HM5_2h1trb123.BR1.IP

description: ChIP-DNA


title: Mutant 1


title: Cre control replicate 3

source_name: Foxd1-Cre mouse kidneys


title: Mutant 2


title: HM5_2h1trb123.BR2.input

description: ChIP-DNA


title: HM5_2h1trb123.BR2.IP

description: ChIP-DNA


title: ora59-SEP3OX_17hpi_rep4

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

description: Gene expression of leaves of ora59-SEP3OX plant at 17 h post inoculation of Colletotrichum tropicale

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarray 4x44K (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: The images were analyzed using Feature Extraction Software (Ver. 10.7.3.1; Agilent Technologies). These data were analyzed further with GeneSpring GX12.1 software (Agilent Technologies). Normalization was performed as follows: 1, intensity-dependent Lowess normalization; 2, data transformation, with measurements less than 0.01 set to 0.01; 3, per-chip normalization, in which the 75th percentile method was used to normalize each array

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

growth_protocol: Arabidopsis seeds were sown on rockwool (Grodan, http://www.grodan.com) and kept at 4˚C in the dark for 2 days, later grown at 25˚C with a 16h/8h (light/dark) in Hoagland medium.

extract_protocol: After sampling at 17 hours post-inoculation (hpi), total RNA was extracted by using Plant RNA Isolation Mini Kit (Agilent Technologies., CA, USA). 200 ng of total RNAs were used to prepare Cy3-labeled cRNA, using a Low Input Quick Amp Labeling Kit (Agilent Technologies).

treatment_protocol: Colletotrichum tropicale conidial suspension (5x10^5 conidia/ml) were spray-inoculated with 0.1% glucose onto 4-5 weeks old pen2 and ora59-SEP3OX plants, and kept at 100% of relative humidity for 17 hours.

value: mature rosette leaves

tag: time

value: 17 h post-inoculation

value: inoculated leaves with Alternaria brassicicola


title: ora59-SEP3OX_17hpi_rep3


title: ora59-SEP3OX_17hpi_rep1


title: pen2_17hpi_rep2

description: Gene expression of leaves of pen2 mutant at 17 h post inoculation of Colletotrichum tropicale


title: Cre control replicate 2


title: pen2_17hpi_rep4


title: ora59-SEP3OX_17hpi_rep2


title: wt5_coseg.BR1.input

description: ChIP-DNA

value: WT


title: pen2_17hpi_rep3


title: pen2_17hpi_rep1


title: Cre control replicate 1


title: wt5_coseg.BR1.IP

description: ChIP-DNA


title: Wild type 4

source_name: Wild-type mouse kidneys

value: Wild type


title: wt5_coseg.BR2.IP

description: ChIP-DNA


title: Wild type 2


title: wt5_coseg.BR2.input

description: ChIP-DNA


title: c587ts;hopTum-l-STAT-Dam

first: Ruiyan

last: Kong

address: 105 Xi San Huan Bei Lu, Haidian District, Beijing

institute: Capital Normal University

data_processing:
Library strategy: DamID-Seq
The reads had a quality score > 30, using Trimmomatic v0.38.0, discarding reads left with < 20 bp
Reads were aligned using Bowtie (version 1.1.2) to build version BDGP6 of the D. melanogaster genome.
MACS (version 1.4.1) was used to identify regions of ChIP-seq enrichment.
The density of reads in each region was normalized to reads per million(rpm).
BigWig files were generated for visualization using the Homer package.
Assembly: BDGP6
Supplementary files format and content: bigWig

organism: Drosophila melanogaster

source_name: testis

growth_protocol: The crosses were raised at 18°C and the desired adult flies were picked up and transferred to new vials with fresh food two days at 29°C and dissected the testes.

extract_protocol:
Testes from Stat92E-Dam and UAS-Dam (control) were dissected in cold 1XPBS and immediately preserved on dry ice and kept at -80°C. Genomic DNA was then isolated.
Genomic DNA was treated by DpnII and alkaline phosphatase.The treated samples were digested with DpnI and ligated with adaptor for ligation-mediated polymerase chain reaction (LM-PCR). Following PCR, the amplified DNAs were treated with T7 exonuclease and purified for sequencing following fragmentation.

value: testis

value: 2 days at 29℃


title: Wild type 1


title: Hi-C_2h1 BR3

description:
S_2h1_L_DNB-16
In situ Hi-C

data_processing:
Fastq files were processed with HiC-Pro with default parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: .validPairs from HiC-Pro.
Supplementary_files_format_and_content: .hic files for visualization with Juicebox.

growth_protocol: Arabidopsis seeds were surface-sterilized, plated on half strength Murashige and Skoog (MS) medium 0.9% agar and cultivated under long-day (16h/8h) light/dark and 23/19°C periods.

extract_protocol:
For each sample, 1000 cotyledons were processed for In situ Hi-C as described in Grob et al. (2014; doi: 10.1016/j.molcel.2014.07.009) upon downscaling to accommodate for low input material.
Hi-C custom protocol, using KAPA HiFi host start Roche.

treatment_protocol: 5-day-old seedlings were fixed in 4% (v/v) formaldehyde before manual dissection of cotyledons.

value: DpnII

value: cotyledons

tag: age

value: 5 days


title: c587ts;hopTum-l-UAS-Dam


title: Hi-C_2h1 BR2

description:
S_2h1_L_DNB-15
In situ Hi-C


title: Hi-C_WT BR1

description:
S_WT_L_DNB-9
In situ Hi-C


title: Hi-C_2h1 BR1

description:
S_2h1_L_DNB-13
In situ Hi-C


title: Hi-C_WT BR2

description:
S_WT_L_DNB-11
In situ Hi-C


title: A549 cells, control-2

city: Hefei

first: YiXuan

address: 81 Meishan Road

institute: Anhui Medical University

data_processing:
1. Base-Calling and Quality Assessment: Software: Bcl2fastq Version: v2.17.1.14 Description: Converts raw image data into base calls, performs an initial quality assessment, and generates FASTQ files containing the sequence and quality information. 2. Quality Control of Sequencing Data: Software: FastQC Version: v0.10.1 Description: Evaluates sequencing data quality by analyzing the base quality score distribution and average sequence quality. 3. Sequence Data Filtering: Software: Cutadapt - Version: 1.9.1 Description: Processes sequencing data by removing adapter sequences, trimming low-quality bases from the 5’ and 3’ ends, and discarding short reads (less than 75bp). 4. Genome Alignment: Software: Hisat2 -Version: v2.0.1 Description: Aligns the cleaned sequence reads to a reference genome. The distribution of the aligned reads was found to be 93.57% in exons, 1.34% in intergenic regions, and 5.09% in introns. 5. Transcript Assembly and Novel Transcript Prediction: Software: StringTie, Cuffcompare - Versions: StringTie(v1.3.3b), Cuffcompare(V2.2.1) Description: Assembles transcripts and compares them to known gene models to predict new transcripts, novel exonic regions, and refine gene start and end positions. 6. Gene Expression Quantification: Software: Htseq - Version: V 0.6.1 - Description: Computes gene expression levels using the FPKM method. The expression of individual genes is presented, and general thresholds (e.g., FPKM > 0.1 or 1) are applied to determine active gene expression. 7. Differential Gene Expression Analysis: Software: edgeR - Version: V3.4.6 Description: Utilizes read count data to determine differentially expressed genes between conditions. Genes with more than 2-fold expression change and a q-value (FDR or padj) ≤ 0.05 are considered significantly differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: human lung adenocarcinoma

extract_protocol:
Nucleic Acid (RNA) Extraction Protocol from A549 Cells 1. Cell Washing: After 48 hours of post-transfection incubation, A549 cells in 6-well plates are washed twice with cold phosphate-buffered saline (PBS) to remove any residual media and non-adherent cells. 2. Reagent Preparation: TRIzol reagent (Invitrogen) is brought to room temperature before use. 3. RNA Isolation: Approximately 1 mL of TRIzol reagent is added directly to each well, and cells are lysed by pipetting up and down. The lysate is collected and transferred to a microcentrifuge tube. 4. Phase Separation: The cell lysate is incubated at room temperature for 5 minutes to permit the complete dissociation of nucleoprotein complexes. Then, it is centrifuged with chloroform for phase separation. 5. RNA Precipitation: The aqueous phase containing RNA is transferred to a new tube. RNA is precipitated by adding isopropanol, followed by a brief incubation and centrifugation. 6. RNA Washing: The RNA pellet is washed with 75% ethanol to remove impurities, followed by a centrifugation step. 7. RNA Resuspension: The RNA pellet is air-dried and then resuspended in a suitable volume of RNase-free water. 8. RNA Quantification: The quantity and quality of the extracted RNA are assessed using a NanoDrop One Microvolume UV-Vis Spectrophotometer to ensure adequate yield and purity for downstream applications.
RNA Library Construction Protocol for RNA-Seq 1. Quality Control: Prior to library construction, ensure that the isolated RNA has high purity and integrity, usually assessed via NanoDrop and possibly an RNA Integrity Number (RIN). 2. RNA Quantification: Measure 500 ng of high-quality total RNA as the starting material for the library preparation. 3. Kit Preparation: Use the TruSeq RNA Sample Preparation Kit (Illumina) and prepare the reagents as per the manufacturer’s guidelines. 4. RNA Fragmentation: The RNA is first fragmented into smaller pieces, either enzymatically or thermally, depending on the kit's protocol. 5. First-Strand cDNA Synthesis: Use reverse transcriptase to synthesize the first strand of cDNA from the fragmented RNA, using random primers. 6. Second-Strand cDNA Synthesis: A second cDNA strand is synthesized to form a stable double-stranded cDNA fragment. 7. End Repair: The double-stranded cDNA fragments undergo end-repair to create blunt ends, facilitating adapter ligation. 8. Adapter Ligation: Adapters containing the sequences necessary for downstream sequencing are ligated to the repaired cDNA ends. 9. PCR Amplification: The adapter-ligated cDNA is amplified using PCR to produce sufficient material for sequencing. This step also incorporates index sequences that allow for multiplexing. 10. Library Validation: Confirm the quality and size distribution of the prepared library, often using a Bioanalyzer or TapeStation. 11. Library Quantification: Quantify the final library concentration to ensure it meets the requirements for sequencing, typically using qPCR or fluorometric methods like Qubit. 12. Sequencing: Load the validated and quantified library into the Illumina HiSeq 4000 sequencing instrument for downstream high-throughput sequencing.

value: human lung adenocarcinoma

value: epithelial cell

value: control


title: RNA-seq_2h1-rep1

description: RNA-seq

data_processing:
Trimming (trim_galore --paired --length 35)
Mapping (STAR --alignIntronMin 20 --alignIntronMax 100000 --outFilterMultimapNmax 20 --outMultimapperOrder Random --outFilterMismatchNmax 8 --outSAMmultNmax 1 --alignMatesGapMax 100000)
Filtering (samtools view -bh -f 3 $i | samtools view -b -F 2308)
Bigwig files (bamCoverage --binSize 10 --normalizeUsing RPKM)
Remove multimapper Tag (samtools view -h $f | sed -E 's/\tNH:i:[[:digit:]]+//g' | samtools view -hb)
Read count (htseq-count -s reverse --nonunique all -f bam -i ID -r pos -t locus -a 0)
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files with read density coverage
Supplementary_files_format_and_content: table with raw read counts

source_name: 5-day-old  seedlings

extract_protocol:
Total RNA was extracted using the microRNeasy kit (Qiagen) following manufactureer instruction.
Illumina truseq stranded library after polyA enrichment of mRNA, DNBseq Stranded mRNA Library(B05) PE 100bp

treatment_protocol: 5-day-old seedlings were fixed in acetone and 200 cotyledons were manually dissected.


title: A549 cells, control-3


title: A549 cells, siGSE1-3


title: A549 cells, control-1


title: A549 cells, siGSE1-2


title: RNA-seq_WT-rep2

description: RNA-seq


title: A549 cells, siGSE1-1


title: RNA-seq_WT-rep1

description: RNA-seq


title: R124-14

city: Shenzhen

first: Epigenomics

last: Gao

address: Dapeng district

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

data_processing:
Quality control of the raw data was performed using FastQC software (v0.11.9). Sequencing data were filtered for adapter contamination by cutadapt (v2.10), parsed through quality filtration using the Trimmomatic program (v0.39) (Phred ≥ 35).
Mapping was performed using hisat2 (v2.2.0)  with the default parameters. Reference genome annotation files were downloaded from NCBI (GRCh37.p5). A human genome reference was constructed from UCSC (GRCh38) chromosomes 1–22, X, and Y and mitochondrial DNA.
The gene expression levels were quantified using featureCounts (v2.0.3) with raw counts. Gene expression levels were calculated using the transcripts per kilobase million (TPM) method that was used for further data processing.
Differential gene expression was assessed with DESeq2 (v1.32.0) using the raw count tables generated by featureCounts.
Assembly: GRCh38
Supplementary files format and content: excel file includes raw counts for each Sample.

source_name: colon

extract_protocol:
Total RNA of each sample was extracted by using RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. The amount of total RNA was measured by Nanodrop 1000 (ThermoFisher Scientific, USA), and the integrity of RNA was checked by 2100 Bioanalyzer System (Agilent, USA).
The transcriptome libraries were constructed by using NEBNext® Ultra RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations as described previously.

value: colon

value: human colon cancer cell


title: R112-14


title: Wild type 3


title: R10024-14


title: TLS12, scRNA-seq

city: Seoul

first: Taehee

last: Kim

address: 211 Eonjuro, Gangnam-gu

department: Department of Dermatology and Cutaneous Biology Research Institute

institute: Gangnam Severance Hospital, Yonsei University College of Medicine

description: Single cell RNA seq

data_processing:
All downstream analyses were performed using Cell Ranger 7.0.
Assembly: hg38
Supplementary files format and content: Tap-separated values files and matrix files.

source_name: Skin tertiary lymphoid structure

extract_protocol:
Skin tissue samples were obtained by 6-mm punch biopsy. After removal of subcutaneous fat, the tissues were chopped and digested with 50 mg/ml Collagenase 1A (Sigma-Aldrich, St. Louis, MO) using a gentleMACSTM dissociator (Miltenyi Biotec) for 2 hours. After incubation, 1 mg/ml DNase I (Sigma-Aldrich) was added. Dead cells were excluded using the Live/Dead Fixable Near-IR Cell Stain kit (Invitrogen) and single cells were stained with BV421-conjugated anti-CD45 (HI30) and PE-conjugated anti-EpCAM (9C4) (both from BioLegend). Live CD45+EpCAM‒ cells were sorted using a FACS Aria III cell sorter (BD Bioscience).
Single-cell RNA-seq and TCR-seq libraries were generated using the Chromium single-cell 5′ Library kit V1.1, Chromium 5′ Gel Bead Kit V1.1, and Chromium V(D)J Human T-cell Enrichment Kit (10X Genomics) following the manufacturer’s instructions. Libraries were constructed and sequenced at a depth of 20,000 reads per cell for RNA or 5,000 reads per cell for TCR using the HiSeq 4000 platform (Illumina).

value: Skin tertiary lymphoid structure

tag: condition

value: pemphigus

tag: individual


title: TLS11, scRNA-seq

description: Single cell RNA seq


title: TLS10, TCR, scRNA-seq

description: Single cell TCR seq

data_processing:
All downstream analyses were performed using Cell Ranger 7.0.
Assembly: hg38
Supplementary files format and content: Tap-separated values files and matrix files.
Library strategy: scTCR-seq


title: Hi-C_WT BR3

description:
S_WT_L_DNB-14
In situ Hi-C


title: R012-14


title: TLS11, TCR, scRNA-seq

description: Single cell TCR seq


title: TLS10, scRNA-seq

description: Single cell RNA seq


title: R10012-14


title: G124-14


title: TLS12, TCR, scRNA-seq

description: Single cell TCR seq


title: R024-14


title: TLS9, scRNA-seq

description: Single cell RNA seq


title: G112-14


title: RNA-seq_2h1-rep2

description: RNA-seq


title: G10024-14


title: TLS9, TCR, scRNA-seq

description: Single cell TCR seq


title: G10012-14


title: G024-14


title: C124-14


title: G012-14


title: C124-11


title: C124-10


title: C112-14


title: C112-10


title: C10024-11


title: C10024-10


title: old mice, anterior and posterior meninges

city: Rensselaer

first: Farhad

last: Farjood

state: NY

address: 1 Discovery Drive

institute: Neural Stem Cell Institute

description:
SMART-Seq ICELL8 Application Kit
126191

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cogent software v1.0 (https://www.takarabio.com/products/next-generation-sequencing/bioinformatics-tools/cogent-ngs-analysis-pipeline)
Seurat package was used to make and integrate seurat objects for downstream analysis. Code available at Github (https://github.com/neural-stem-cell-institute/RPESC_TREX/tree/main/R).
Assembly: mm10
Supplementary files format and content: rds, includes Seurat objects containing read counts and clustering results

source_name: leptomeninges

extract_protocol:
Tissue lysis and nuclei isolation were performed according to the 10x genomics nuclei isolation for single cell RNA sequencing protocol
Single cell library preparation was performed using the SMART-Seq ICELL8 Application Kit

value: meninges

value: leptomeninges

value: 18 months


title: young mice, anterior meninges

description:
SMART-Seq ICELL8 Application Kit
126254

value: 3 months


title: young mice, posterior meninges

description:
SMART-Seq ICELL8 Application Kit
126275


title: C10012-11


title: C10012-10


title: C024-14


title: ESCC_rep3 [lncRNAs and mRNAs]

city: Anyang

first: Yaowen

last: Zhang

state: Henan

address: No. 1 Huanbin North Road, Beiguan District

department: Radiotherapy

institute: Anyang Cancer Hospital

description: Gene expression of esophageal squamous cell carcinoma tissue

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: ESCC tissues and normal adjacent tissues  from 5 samples

tag: gender

value: male


title: ESCC_rep2 [lncRNAs and mRNAs]

source_name: esophageal squamous cell carcinoma tissue


title: ESCC_rep5 [lncRNAs and mRNAs]


title: Normal_rep3 [lncRNAs and mRNAs]

description: Gene expression of esophageal adjacent normal tissues

source_name: esophageal adjacent normal tissues


title: Normal_rep6 [miRNA]

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: ESCC tissues and normal adjacent tissues  from 6 samples

value: female


title: Normal_rep2 [lncRNAs and mRNAs]


title: C10024-14


title: ESCC_rep1 [lncRNAs and mRNAs]


title: C112-11


title: T2KO_old_LSK_Smart_RNAseq_2

city: Shanghai

first: Shengli

last: Li

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The raw single cell RNA sequencing reads were first trimmed by cutadapt (v1.8.1) with parameters: -m 20 --trim-n --max-n 0.7 –q20; trimmed reads were then mapped to reference mouse genome (GRCm38) by using STAR (v2.5.2b) and assigned to GENCODE genes (Release M25) by featureCounts
The raw SMART RNA sequencig reads were first trimmed to filter low-quality bases/reads by Trimommatic (version 0.38); the trimmed reads were then aligned to reference human genome (GRCm38) by HISAT2; mapped reads were subject to Stringtie (version 1.35) to quantify gene-level expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: expression matrix in cvs/txt format

growth_protocol: 6-8 weeks WT mice were used as WT-young; 12-24 months WT mice were used as WT-old;  6-8 weeks Tet2KO mice were used as Tet2KO-young; 12-24 months Tet2KO mice were used as Tet2KO-old;

extract_protocol:
RNA was purified using Qiagen AllPrep DNA/RNA micro kitt. Single-cell RNA-seq libraries were generated using the Chromium Single-Cell 3′ Reagent V2 Kit (10× Genomics).
1. Single-cell RNA-seq libraries were generated using the Chromium Single-Cell 3′ Reagent V2 Kit (10× Genomics); 2. Low amount RNA seq libraries were generated using Takara SMART-Seq Single Cell Kit

treatment_protocol: We used Lin- cells from young and aged WT/ Tet2KO mice (CD45.2) as donor and 1:10 mixed them with total bone marrow from WT young mice (CD45.1) before injected into WT young recipient mice (CD45.1). After 10 weeks reconstitution, CD45.2_Lin-cKit+Sca1+ cells were isolated for SMART-RNA seq and CMSIP libraries generation

tag: genotype/variation

value: TET2 knockout

tag: recipient mouse

value: 01142020BMT mice_10 weeks


title: Normal_rep4 [lncRNAs and mRNAs]


title: T2KO_Young_LSK_Smart_RNAseq_2


title: Normal_rep1 [lncRNAs and mRNAs]


title: C024-11

tag: tissue


title: ESCC_rep4 [lncRNAs and mRNAs]


title: Normal_rep5 [lncRNAs and mRNAs]


title: C10012-14


title: T2KO_old_LSK_Smart_RNAseq_1


title: WT_old_LSK_Smart_RNAseq_2

value: wild-type


title: T2KO_Young_LSK_Smart_RNAseq_1


title: C024-10


title: C012-14


title: ESCC_rep6 [miRNA]


title: WT_old_LSK_Smart_RNAseq_1


title: C012-10


title: C012-11


title: Normal_rep5 [miRNA]


title: ESCC_rep5 [miRNA]


title: WT_Young_LSK_Smart_RNAseq_1


title: 0H-P11


title: WT_Young_LSK_Smart_RNAseq_2


title: 0H-P14


title: scRNA_Lin-_T2KO-Old_Batch02

value: Lin-


title: Normal_rep4 [miRNA]


title: Normal_rep3 [miRNA]


title: ESCC_rep4 [miRNA]


title: Normal_rep6 [circRNA]


title: Normal_rep2 [miRNA]


title: ESCC_rep3 [miRNA]


title: 0H-P10


title: Normal_rep5 [circRNA]


title: ESCC_rep6 [circRNA]


title: scRNA_Lin-_WT-Old_Batch02


title: scRNA_Lin-_WT-Young_Batch02


title: scRNA_Lin-_CD45,2_T2KO-Old


title: ESCC_rep2 [miRNA]


title: Treg single-positive Foxp3+, Biol rep 2

city: Rehovot

first: Stav

last: Miller

address: Herzl

country: Israel

institute: Weizmann Institute of Science

data_processing:
Editing R1 Sequence header to contain UMI
Trim first 3 bases, adapter and poly A/T bases using cutadapt
Map the edited fastq using STAR
Modify BAM file - move UMI from read name to FLAG
Sort and index the resulting bam using 'samtools sort' and 'samtools index'
Run HTSeq on modified GTF file to produce raw counts
Add feature tag to bams (gene)
Mark duplicate Reads
Run HTSeq to produce deDuplicated counts
Correct deDuplicated counts
Assembly: MM10
Supplementary files format and content: xlsx format, gene counts per sample

source_name: Excised spleens

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen) from 150x10^5 cells. 10ng of total RNA was used for the construction of sequencing libraries.
MARS-seq according to Jaitin, D.A, et al, Science, 2014.

value: Excised spleens

value: T cells

tag: cell subset

value: Treg single-positive Foxp3+

tag: Sex

value: Male

value: TGFβ & IL2 for 3 days


title: Normal_rep1 [miRNA]


title: scRNA_Lin-_CD45.2_WT-Old


title: Treg single-positive Foxp3+, Biol rep 1

tag: treatment


title: ESCC_rep1 [miRNA]


title: ESCC_rep4 [circRNA]


title: ESCC_rep5 [circRNA]


title: Normal_rep4 [circRNA]


title: scRNA_Lin-_CD45.2_T2KO-Young


title: CRS skin 2

city: NANJING

first: zan

last: peng

state: JIANGSU

address: 2F, Building 3, South District, Life Science and Technology Town, No. 18, Zhilan Road, Jiangning District

institute: CHINA PHARMCUTICAL UNIVERSITY

data_processing:
HISAT2 software used for mapping
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: skin

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

value: chronic restraint stress


title: ESCC_rep2 [circRNA]


title: Normal_rep3 [circRNA]


title: ESCC_rep3 [circRNA]


title: Normal_rep2 [circRNA]


title: Th17 double-positive RORƴt+ Foxp3+, Biol rep 2

value: Th17 double-positive RORƴt+ Foxp3+

value: TGFβ & IL6 for 3 days


title: CRS skin 3


title: scRNA_Lin-_CD45.2_WT-Young


title: CRS skin 1


title: Th17 double-positive RORƴt+ Foxp3+, Biol rep 3


title: Th17 double-positive RORƴt+ Foxp3+, Biol rep 1


title: scRNA_Lin-_T2KO-Old_Batch01


title: ESCC_rep1 [circRNA]


title: CON skin 3

value: control


title: CON skin 2


title: Th17 single-positive RORƴt+, Biol rep 3

value: Th17 single-positive RORƴt+


title: Th17 single-positive RORƴt+, Biol rep 2


title: CON skin 1


title: scRNA_Lin-_WT-Old_Batch01


title: scRNA_Lin-_T2KO-Young_Batch01


title: Th17 single-positive RORƴt+, Biol rep 1


title: scRNA_Lin-_WT-Young_Batch01


title: Normal_rep1 [circRNA]


title: preoperative_CSF_delirium_matched pair#18

status: Public on Sep 09 2023

type: protein

city: Boston

first: Simon

middle: T

last: Dillon

state: Massachusetts

address: 99 Brookline Ave, Research North Bldg, Room 107

department: IMBIO

institute: BIDMC RESEARCH

hyb_protocol: Hybridized overnight (19 hours) at 55 C as recommended by SomaLogic

scan_protocol: SOMAmer matching probes printed onto Agilent slides.  After overnight hybridization slides were scanned on an Agilent Microarray SureScan Scanner model D.

data_processing: Standard data processing method as per SomaLogic recommended methods.  Normalized and calibrated using kit control samples

label: Cy3 labelled SOMAmer

molecule: protein

source_name: CSF, before surgery, delirium

label_protocol: Samples run in the manual version of the 1.3k SomaScan assay protocol

extract_protocol: CSF was collected via dropwise collection into collection tubes. To minimize potential blood contamination of the CSF, samples were centrifuged at 1000xg for 10 minutes prior to subaliquoting and storage at -80oC.

treatment_protocol: All HiPOR study participants underwent spinal anesthesia for surgery. During induction of spinal anesthesia, 1 ml of CSF was obtained from a spinal needle prior to the administration of local anesthetic.

tag: sample type

value: CSF taken before surgery, no postoperative delirium


title: preoperative_CSF_delirium_matched pair#19


title: preoperative_CSF_delirium_matched pair#20


title: preoperative_CSF_delirium_matched pair#17


title: preoperative_CSF_delirium_matched pair#21


title: preoperative_CSF_delirium_matched pair#22


title: preoperative_CSF_delirium_matched pair#23


title: preoperative_CSF_delirium_matched pair#16


title: preoperative_CSF_delirium_matched pair#24


title: preoperative_CSF_delirium_matched pair#15


title: preoperative_CSF_delirium_matched pair#14


title: Treg single-positive Foxp3+, Biol rep 3

tag: cell type


title: scRNA_Lin-_T2KO-Young_Batch02


title: preoperative_CSF_delirium_matched pair#11


title: preoperative_CSF_delirium_matched pair#10


title: preoperative_CSF_delirium_matched pair#8


title: preoperative_CSF_delirium_matched pair#9


title: preoperative_CSF_delirium_matched pair#13


title: preoperative_CSF_delirium_matched pair#3


title: preoperative_CSF_delirium_matched pair#4


title: preoperative_CSF_delirium_matched pair#12


title: preoperative_CSF_delirium_matched pair#6


title: preoperative_CSF_delirium_matched pair#5


title: preoperative_CSF_control_matched pair#23

source_name: CSF, before surgery, no delirium


title: preoperative_CSF_control_matched pair#22


title: preoperative_CSF_control_matched pair#24


title: preoperative_CSF_delirium_matched pair#2


title: preoperative_CSF_delirium_matched pair#1


title: preoperative_CSF_control_matched pair#21


title: preoperative_CSF_control_matched pair#20


title: preoperative_CSF_control_matched pair#17


title: preoperative_CSF_control_matched pair#16


title: preoperative_CSF_control_matched pair#15


title: preoperative_CSF_control_matched pair#14


title: preoperative_CSF_control_matched pair#19


title: preoperative_CSF_control_matched pair#18


title: preoperative_CSF_control_matched pair#11


title: preoperative_CSF_control_matched pair#9


title: preoperative_CSF_control_matched pair#8


title: preoperative_CSF_control_matched pair#10


title: preoperative_CSF_control_matched pair#12


title: preoperative_CSF_control_matched pair#5


title: preoperative_CSF_control_matched pair#3


title: preoperative_CSF_control_matched pair#6


title: preoperative_CSF_control_matched pair#4


title: preoperative_CSF_control_matched pair#13


title: Sweet orange leaves, infection,  day14, rep3

city: kunming

first: xiuyao

last: yang

state: yunnan

address: Southwest Forestry University, 300 Bailong Road, Qingyun Street, Panlong District, Kunming, Yunnan Province, China

institute: Southwest Forestry University

data_processing:
Sequencing data quality control includes filtering sequences, assessing the quality of sequencing data and calculating sequence length distributions.
Data alignment analysis is performed on sequences that have been aligned to the genome, and sequentially classified and characterised according to the different genome annotation information.
The corresponding expressions are calculated.
Differential expression analysis is then performed.
Among the conventional transcriptome analyses are also Variable splicing analysis, de novo transcript prediction and deep analysis of variant analysis and other personalised analyses are also performed.
Assembly: The assembled sweet orange genome data (Citrus sinensis v3.0 ) was downloaded from the Sweet Orange Database CPBD (http://citrus.hzau.edu.cn/index.php) for read comparison.
Supplementary files format and content: Tab-delimited text includes the FPKM values for each sample (The gene ID of the sweet orange protein sequence file (SWO.v3.0.protein.fa) downloaded from the Sweet Orange Database CPBD (http://citrus.hzau.edu.cn/index.php) matches the ID in the text file. As the same gene can be cut in many different ways, different cuts will result in different transcripts, e.g. Cs_ont_5g000040.3. However, it is generally only accurate to the gene level, so Cs_ont_5g000040.3 and Cs_ont_5g000040 are the same gene.)

organism: Citrus sinensis

source_name: Leaf tissue

growth_protocol: 30 μl of Lecanicillium psalliotae was injected into sweet orange leaves and infested for 14 days. The physiological state of the leaves was observed during this process

extract_protocol: Transcriptome sequencing by Wuhan Baiyi Huineng Biotechnology Co.

value: Leaf tissue

value: mesenchymal stem cell

value: infested with Lecanicillium psalliotae


title: Sweet orange leaves, infection,  day14, rep2


title: Sweet orange leaves, infection,  day14, rep1


title: preoperative_CSF_control_matched pair#2


title: Sweet orange leaves, Control,  day14, rep3


title: preoperative_CSF_control_matched pair#7


title: preoperative_CSF_control_matched pair#1


title: Sweet orange leaves, Control,  day14, rep1


title: Sweet orange leaves, Control,  day14, rep2


title: ExpA52

city: Shen Zhen

first: Shaohua

last: Ma

state: Guangdong Province

address: nanshan street

institute: Tsinghua University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) .
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: GRCh38.p13
Supplementary files format and content: gene_exp_txw.xlsx contains read counts and TPM of gene expression

source_name: Human  embryonic stem cell(H5)  induced cerebral organoids

extract_protocol:
1. Transfer appropriate sample to corresponding grinding tube, then add 1.5 mL TRIzol lysis buffer, transfer to the grinding machine, grind 30 s, stay at 5 min. Dispense 1.5 mL of TRIzol lysis buffer to a 2 mL tube, and take appropriate amount of tissue samples, grind the tissue samples into powder with liquid nitrogen and transfer into the lysis buffer.  Stand flat for 5 min for the fully lysis of tissue cells. 2. Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃. Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking；Centrifuge at 12000×g for 8 min in 4℃; Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, Gently invert and mix, place in -20℃ refrigerator for more than 2 h. Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting. Centrifuge at 17500×g for 3 min in 4℃;Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min.Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
1 Sample QC; 2 mRNA is enriched by oligo (dT) -attached magnetic beads; 3 mRNA Fragmentation; 4 cDNA Synthesis; 5 End Repair, Add A and Adaptor Ligation; 6 PCR; 7 Library QC; 8 Circularization and make DNB; 9 Sequencing on DNBSEQ platform

value: development with Cerebral Organnoid Kit + calcium alginate encapsulation


title: Con10

source_name: Human  embryonic stem cell(H2)  induced cerebral organoids

value: development with Cerebral Organnoid Kit


title: ExpA16

source_name: Human  embryonic stem cell(H3)  induced cerebral organoids


title: ExpA31

source_name: Human  embryonic stem cell(H4)  induced cerebral organoids


title: Normal_rep4 [DNA methylation]

type: genomic

description:
esophageal adjacent normal tissues
con-942

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v1.8

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: male


title: Con1

source_name: Human  embryonic stem cell(H1)  induced cerebral organoids


title: preoperative_CSF_delirium_matched pair#7


title: Normal_rep5 [DNA methylation]

description:
esophageal adjacent normal tissues
con-933


title: Liver_C3H_SL_ZT18_3

city: Copenhagen

first: Lewin

last: Small

address: Blegdamsvej 3B

department: CBMR

institute: University of Copenhagen

data_processing:
Fastq files were generated using bcl2fastq2 v. 2.20.0
Reads were aligned to the GRCm38 release 99 primary assembly using STAR v. 2.7.2b with the flags “--outReadsUnmapped Fastx --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated” against a reference built using the ENSEMBL release 99 gene model.
Aligned reads were counted against the same gene model using featureCounts v. 1.6.2 with the flags “-p -B -C -t exon -g gene_id”
Assembly: mm10 GRC 38
Supplementary files format and content: counts.csv: unfiltered count matrix
Supplementary files format and content: processed.data.csv: log transformed counts per million (logCPM)

source_name: Liver

extract_protocol:
Trizol+ Qiagen Rneasy according to manufacturers instructions
Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA protocol (Illumina). Poly-A containing mRNAs were purified by poly-T attached magnetic beads, fragmented, and cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was adenylated to prime for adapter ligation and after a clean-up using AMPure beads (Beckman coulter), DNA fragments were amplified using PCR followed by a final clean-up.

value: Liver

tag: zt

tag: photoperiod

value: SL

tag: diet

value: HFD


title: Liver_C3H_SL_ZT0_4

tag: strain


title: Liver_C3H_SL_ZT0_3


title: Liver_C3H_LL_ZT18_4

value: LL


title: ESCC_rep4 [DNA methylation]

description:
esophageal squamous cell carcinoma tissue
ca-942


title: ESCC_rep5 [DNA methylation]

description:
esophageal squamous cell carcinoma tissue
ca-933


title: Liver_C3H_SL_ZT12_4


title: Liver_C3H_SL_ZT18_2


title: Liver_C3H_SL_ZT6_4


title: Liver_C3H_LL_ZT6_4


title: Liver_C3H_LL_ZT0_4


title: Liver_C3H_SL_ZT18_1


title: Liver_C3H_LL_ZT0_3


title: ESCC_rep3 [DNA methylation]

description:
esophageal squamous cell carcinoma tissue
ca-944


title: Liver_C3H_LL_ZT12_3


title: Liver_C3H_LL_ZT12_4


title: Liver_C3H_SL_ZT6_3


title: Liver_C3H_LL_ZT18_3


title: Liver_C3H_LL_ZT12_2


title: Liver_C3H_LL_ZT6_3


title: Liver_C3H_LL_ZT6_2


title: Liver_C3H_SL_ZT0_2


title: Liver_C3H_LL_ZT6_1


title: ESCC_rep1 [DNA methylation]

description:
esophageal squamous cell carcinoma tissue
ca-973

value: female


title: Liver_C3H_LL_ZT12_1


title: Liver_C3H_SL_ZT18_4


title: Liver_C3H_LL_ZT0_2


title: Liver_C3H_LL_ZT18_2


title: Liver_C3H_LL_ZT0_1


title: Liver_C3H_SL_ZT6_2


title: Normal_rep2 [DNA methylation]

description:
esophageal adjacent normal tissues
con-962


title: Liver_C3H_SL_ZT12_2


title: ESCC_rep2 [DNA methylation]

description:
esophageal squamous cell carcinoma tissue
ca-962


title: Liver_C3H_SL_ZT12_1


title: Liver_C3H_SL_ZT0_1


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT0 [0101_99]

data_processing:
Data were aligned to mm10_GRCm38_release99 using star/2.7.2b, counted using subread/1.6.2.
Star setting were: STAR --runThreadN 40 --outReadsUnmapped Fastx --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated  --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat
featureCounts settings were: featureCounts -p -B -C -T $threads -t exon -g gene_id
Assembly: mm10 GRC 38

extract_protocol:
Trizol+ Qiagen Rneasy according to manufacturers instructions
Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA protocol (Illumina). Poly-A containing mRNAs were purified by poly-T attached magnetic beads, fragmented, and cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was adenylated to prime for adapter ligation and after a clean-up using AMPure beads (Beckman coulter), DNA fragments were amplified using PCR followed by a final clean-up.
Libraries were quality-controlled using a Bioanalyzer instrument (Agilent Technologies) and subjected to 52-bp paired-end sequencing on a NovaSeq6000 (Illumina).

tag: timepoint

value: Equal light


title: Liver_C3H_SL_ZT6_1


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT16 [0101_97]

value: LFD


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT4 [0101_98]

value: Long light


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT16 [0101_96]

value: Short light


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT0 [0101_95]


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT0 [0101_94]


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT4 [0101_93]


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT12 [0101_91]


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT12 [0101_92]


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT12 [0101_90]


title: Normal_rep1 [DNA methylation]

description:
esophageal adjacent normal tissues
con-973

tag: age


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT4 [0101_89]


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT12 [0101_9]


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT16 [0101_88]


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT20 [0101_87]


title: Normal_rep3 [DNA methylation]

description:
esophageal adjacent normal tissues
con-944


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT0 [0101_86]


title: Liver_C3H_LL_ZT18_1


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT0 [0101_85]


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT20 [0101_82]


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT0 [0101_81]


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT0 [0101_83]


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT8 [0101_8]


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT16 [0101_80]


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT16 [0101_84]


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT20 [0101_78]


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT12 [0101_75]


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT8 [0101_76]


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT12 [0101_74]


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT4 [0101_73]


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT12 [0101_72]


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT16 [0101_71]


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT16 [0101_70]


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT8 [0101_77]


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT12 [0101_68]


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT20 [0101_7]


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT4 [0101_69]


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT8 [0101_65]


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT8 [0101_66]


title: Liver_C3H_SL_ZT12_3


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT0 [0101_63]


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT20 [0101_67]


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT16 [0101_62]


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT20 [0101_60]


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT4 [0101_6]